wip work at beamline

# Conflicts:
#   docs/user/ptychography/omny.md

.gitlab-ci.yml

@@ -6,3 +6,15 @@ include:
       target: "csaxs_bec"
       branch: $CHILD_PIPELINE_BRANCH
 
+pages:
+  stage: Deploy
+  needs: []
+  variables:
+    TARGET_BRANCH: $CI_COMMIT_REF_NAME
+  rules:
+    - if: "$CI_COMMIT_TAG != null"
+      variables:
+        TARGET_BRANCH: $CI_COMMIT_TAG
+    - if: '$CI_COMMIT_REF_NAME == "main" && $CI_PROJECT_PATH == "bec/csaxs_bec"'
+  script:
+    - curl -X POST -d "branches=$CI_COMMIT_REF_NAME" -d "token=$RTD_TOKEN" https://readthedocs.org/api/v2/webhook/sls-csaxs/270162/

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+  jobs:
+    pre_install:
+      - pip install .
+
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt
+

LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -280,14 +280,22 @@ class LamNIOpticsMixin:
         umv(dev.losaz, losaz_out)
         umv(dev.losay, losay_out)
 
-    def lfzp_info(self):
+    def lfzp_info(self, mokev_val=-1):
+
+        if mokev_val == -1:
+            try:
+                mokev_val = dev.mokev.readback.get()
+            except:
+                print(
+                    "Device mokev does not exist. You can specify the energy in keV as an argument instead."
+                )
+                return
         loptz_val = dev.loptz.read()["loptz"]["value"]
         distance = -loptz_val + 85.6 + 52
         print(f"The sample is in a distance of {distance:.1f} mm from the FZP.")
 
         diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
 
-        mokev_val = dev.mokev.read()["mokev"]["value"]
         console = Console()
         table = Table(
             title=f"At the current energy of {mokev_val:.4f} keV we have following options:",

csaxs_bec/bec_ipython_client/plugins/flomni/correction_flomni_20210300_360deg.txt

@@ -0,0 +1,351 @@
+corr_elements = 175 
+corr_angle[0] = 0.100000 
+corr_angle[1] = 1.001000 
+corr_angle[2] = 1.902000 
+corr_angle[3] = 2.798000 
+corr_angle[4] = 7.305000 
+corr_angle[5] = 8.204000 
+corr_angle[6] = 9.104000 
+corr_angle[7] = 10.005000 
+corr_angle[8] = 14.504000 
+corr_angle[9] = 15.404000 
+corr_angle[10] = 16.304000 
+corr_angle[11] = 17.204000 
+corr_angle[12] = 21.704000 
+corr_angle[13] = 22.604000 
+corr_angle[14] = 23.504000 
+corr_angle[15] = 24.404000 
+corr_angle[16] = 28.904000 
+corr_angle[17] = 29.804000 
+corr_angle[18] = 30.704000 
+corr_angle[19] = 31.604000 
+corr_angle[20] = 36.104000 
+corr_angle[21] = 37.004000 
+corr_angle[22] = 37.904000 
+corr_angle[23] = 38.804000 
+corr_angle[24] = 43.305000 
+corr_angle[25] = 44.205000 
+corr_angle[26] = 45.104000 
+corr_angle[27] = 46.005000 
+corr_angle[28] = 50.504000 
+corr_angle[29] = 51.404000 
+corr_angle[30] = 52.305000 
+corr_angle[31] = 53.205000 
+corr_angle[32] = 57.705000 
+corr_angle[33] = 58.605000 
+corr_angle[34] = 59.505000 
+corr_angle[35] = 60.405000 
+corr_angle[36] = 64.904000 
+corr_angle[37] = 65.804000 
+corr_angle[38] = 66.704000 
+corr_angle[39] = 67.604000 
+corr_angle[40] = 72.104000 
+corr_angle[41] = 73.004000 
+corr_angle[42] = 73.904000 
+corr_angle[43] = 74.804000 
+corr_angle[44] = 79.304000 
+corr_angle[45] = 80.204000 
+corr_angle[46] = 81.104000 
+corr_angle[47] = 82.005000 
+corr_angle[48] = 86.505000 
+corr_angle[49] = 87.404000 
+corr_angle[50] = 88.304000 
+corr_angle[51] = 89.205000 
+corr_angle[52] = 93.704000 
+corr_angle[53] = 94.604000 
+corr_angle[54] = 95.505000 
+corr_angle[55] = 96.404000 
+corr_angle[56] = 100.904000 
+corr_angle[57] = 101.804000 
+corr_angle[58] = 102.704000 
+corr_angle[59] = 103.604000 
+corr_angle[60] = 108.104000 
+corr_angle[61] = 109.004000 
+corr_angle[62] = 109.904000 
+corr_angle[63] = 110.804000 
+corr_angle[64] = 115.304000 
+corr_angle[65] = 116.204000 
+corr_angle[66] = 117.104000 
+corr_angle[67] = 118.004000 
+corr_angle[68] = 122.504000 
+corr_angle[69] = 123.404000 
+corr_angle[70] = 124.304000 
+corr_angle[71] = 125.204000 
+corr_angle[72] = 129.704000 
+corr_angle[73] = 130.604000 
+corr_angle[74] = 131.504000 
+corr_angle[75] = 132.404000 
+corr_angle[76] = 136.904000 
+corr_angle[77] = 137.804000 
+corr_angle[78] = 138.701000 
+corr_angle[79] = 139.604000 
+corr_angle[80] = 144.104000 
+corr_angle[81] = 145.004000 
+corr_angle[82] = 145.904000 
+corr_angle[83] = 146.804000 
+corr_angle[84] = 151.304000 
+corr_angle[85] = 152.204000 
+corr_angle[86] = 153.104000 
+corr_angle[87] = 154.004000 
+corr_angle[88] = 158.504000 
+corr_angle[89] = 159.404000 
+corr_angle[90] = 160.304000 
+corr_angle[91] = 161.204000 
+corr_angle[92] = 165.704000 
+corr_angle[93] = 166.604000 
+corr_angle[94] = 167.504000 
+corr_angle[95] = 168.404000 
+corr_angle[96] = 172.904000 
+corr_angle[97] = 173.805000 
+corr_angle[98] = 174.704000 
+corr_angle[99] = 180.104000 
+corr_angle[100] = 183.704000 
+corr_angle[101] = 184.603000 
+corr_angle[102] = 185.504000 
+corr_angle[103] = 190.904000 
+corr_angle[104] = 191.805000 
+corr_angle[105] = 192.704000 
+corr_angle[106] = 198.104000 
+corr_angle[107] = 199.004000 
+corr_angle[108] = 199.904000 
+corr_angle[109] = 205.304000 
+corr_angle[110] = 206.204000 
+corr_angle[111] = 207.104000 
+corr_angle[112] = 212.504000 
+corr_angle[113] = 213.404000 
+corr_angle[114] = 214.304000 
+corr_angle[115] = 219.704000 
+corr_angle[116] = 220.604000 
+corr_angle[117] = 221.504000 
+corr_angle[118] = 226.904000 
+corr_angle[119] = 227.804000 
+corr_angle[120] = 228.704000 
+corr_angle[121] = 234.104000 
+corr_angle[122] = 235.004000 
+corr_angle[123] = 235.904000 
+corr_angle[124] = 241.304000 
+corr_angle[125] = 242.204000 
+corr_angle[126] = 243.104000 
+corr_angle[127] = 248.504000 
+corr_angle[128] = 249.404000 
+corr_angle[129] = 250.304000 
+corr_angle[130] = 255.704000 
+corr_angle[131] = 256.604000 
+corr_angle[132] = 257.504000 
+corr_angle[133] = 262.904000 
+corr_angle[134] = 263.804000 
+corr_angle[135] = 264.704000 
+corr_angle[136] = 270.104000 
+corr_angle[137] = 271.004000 
+corr_angle[138] = 271.904000 
+corr_angle[139] = 277.304000 
+corr_angle[140] = 278.205000 
+corr_angle[141] = 279.104000 
+corr_angle[142] = 284.504000 
+corr_angle[143] = 285.405000 
+corr_angle[144] = 286.304000 
+corr_angle[145] = 291.703000 
+corr_angle[146] = 292.604000 
+corr_angle[147] = 293.504000 
+corr_angle[148] = 298.904000 
+corr_angle[149] = 299.804000 
+corr_angle[150] = 300.704000 
+corr_angle[151] = 306.104000 
+corr_angle[152] = 307.004000 
+corr_angle[153] = 307.904000 
+corr_angle[154] = 313.304000 
+corr_angle[155] = 314.204000 
+corr_angle[156] = 315.104000 
+corr_angle[157] = 320.504000 
+corr_angle[158] = 321.404000 
+corr_angle[159] = 322.304000 
+corr_angle[160] = 327.704000 
+corr_angle[161] = 328.605000 
+corr_angle[162] = 329.504000 
+corr_angle[163] = 334.904000 
+corr_angle[164] = 335.804000 
+corr_angle[165] = 336.705000 
+corr_angle[166] = 342.104000 
+corr_angle[167] = 343.004000 
+corr_angle[168] = 343.904000 
+corr_angle[169] = 349.304000 
+corr_angle[170] = 350.204000 
+corr_angle[171] = 351.104000 
+corr_angle[172] = 356.504000 
+corr_angle[173] = 357.404000 
+corr_angle[174] = 358.304000 
+corr_pos[0] = 0.012330 
+corr_pos[1] = 0.024870 
+corr_pos[2] = 0.037262 
+corr_pos[3] = 0.049438 
+corr_pos[4] = 0.108462 
+corr_pos[5] = 0.119791 
+corr_pos[6] = 0.130986 
+corr_pos[7] = 0.142044 
+corr_pos[8] = 0.195045 
+corr_pos[9] = 0.205834 
+corr_pos[10] = 0.216589 
+corr_pos[11] = 0.226402 
+corr_pos[12] = 0.271931 
+corr_pos[13] = 0.281684 
+corr_pos[14] = 0.290769 
+corr_pos[15] = 0.299392 
+corr_pos[16] = 0.337986 
+corr_pos[17] = 0.345178 
+corr_pos[18] = 0.352253 
+corr_pos[19] = 0.358528 
+corr_pos[20] = 0.379520 
+corr_pos[21] = 0.382947 
+corr_pos[22] = 0.386110 
+corr_pos[23] = 0.388887 
+corr_pos[24] = 0.395645 
+corr_pos[25] = 0.396154 
+corr_pos[26] = 0.396679 
+corr_pos[27] = 0.396367 
+corr_pos[28] = 0.392400 
+corr_pos[29] = 0.392530 
+corr_pos[30] = 0.391826 
+corr_pos[31] = 0.391325 
+corr_pos[32] = 0.379188 
+corr_pos[33] = 0.376449 
+corr_pos[34] = 0.373195 
+corr_pos[35] = 0.369588 
+corr_pos[36] = 0.343021 
+corr_pos[37] = 0.336754 
+corr_pos[38] = 0.330310 
+corr_pos[39] = 0.323447 
+corr_pos[40] = 0.281171 
+corr_pos[41] = 0.272735 
+corr_pos[42] = 0.263888 
+corr_pos[43] = 0.254469 
+corr_pos[44] = 0.203024 
+corr_pos[45] = 0.192980 
+corr_pos[46] = 0.182359 
+corr_pos[47] = 0.170780 
+corr_pos[48] = 0.111580 
+corr_pos[49] = 0.101222 
+corr_pos[50] = 0.090051 
+corr_pos[51] = 0.077918 
+corr_pos[52] = 0.015225 
+corr_pos[53] = 0.003876 
+corr_pos[54] = -0.007756 
+corr_pos[55] = -0.020383 
+corr_pos[56] = -0.084910 
+corr_pos[57] = -0.096848 
+corr_pos[58] = -0.108732 
+corr_pos[59] = -0.121432 
+corr_pos[60] = -0.184349 
+corr_pos[61] = -0.195904 
+corr_pos[62] = -0.207113 
+corr_pos[63] = -0.219319 
+corr_pos[64] = -0.274799 
+corr_pos[65] = -0.284942 
+corr_pos[66] = -0.294809 
+corr_pos[67] = -0.305437 
+corr_pos[68] = -0.352114 
+corr_pos[69] = -0.359689 
+corr_pos[70] = -0.367451 
+corr_pos[71] = -0.375629 
+corr_pos[72] = -0.404347 
+corr_pos[73] = -0.407683 
+corr_pos[74] = -0.410857 
+corr_pos[75] = -0.414904 
+corr_pos[76] = -0.424625 
+corr_pos[77] = -0.424357 
+corr_pos[78] = -0.424411 
+corr_pos[79] = -0.424615 
+corr_pos[80] = -0.421392 
+corr_pos[81] = -0.419977 
+corr_pos[82] = -0.417860 
+corr_pos[83] = -0.416400 
+corr_pos[84] = -0.398108 
+corr_pos[85] = -0.392613 
+corr_pos[86] = -0.386455 
+corr_pos[87] = -0.380338 
+corr_pos[88] = -0.341288 
+corr_pos[89] = -0.332298 
+corr_pos[90] = -0.322767 
+corr_pos[91] = -0.311630 
+corr_pos[92] = -0.256798 
+corr_pos[93] = -0.244808 
+corr_pos[94] = -0.232932 
+corr_pos[95] = -0.219785 
+corr_pos[96] = -0.158685 
+corr_pos[97] = -0.146198 
+corr_pos[98] = -0.130743 
+corr_pos[99] = -0.054066 
+corr_pos[100] = -0.001498 
+corr_pos[101] = 0.012010 
+corr_pos[102] = 0.025195 
+corr_pos[103] = 0.094982 
+corr_pos[104] = 0.109235 
+corr_pos[105] = 0.120813 
+corr_pos[106] = 0.179893 
+corr_pos[107] = 0.192147 
+corr_pos[108] = 0.201902 
+corr_pos[109] = 0.245092 
+corr_pos[110] = 0.250501 
+corr_pos[111] = 0.255536 
+corr_pos[112] = 0.280598 
+corr_pos[113] = 0.280673 
+corr_pos[114] = 0.282529 
+corr_pos[115] = 0.293286 
+corr_pos[116] = 0.292713 
+corr_pos[117] = 0.291123 
+corr_pos[118] = 0.288721 
+corr_pos[119] = 0.288260 
+corr_pos[120] = 0.286480 
+corr_pos[121] = 0.271630 
+corr_pos[122] = 0.268004 
+corr_pos[123] = 0.265418 
+corr_pos[124] = 0.239187 
+corr_pos[125] = 0.233224 
+corr_pos[126] = 0.226652 
+corr_pos[127] = 0.189034 
+corr_pos[128] = 0.180302 
+corr_pos[129] = 0.170931 
+corr_pos[130] = 0.125760 
+corr_pos[131] = 0.116433 
+corr_pos[132] = 0.106845 
+corr_pos[133] = 0.057551 
+corr_pos[134] = 0.048531 
+corr_pos[135] = 0.038276 
+corr_pos[136] = -0.012292 
+corr_pos[137] = -0.021223 
+corr_pos[138] = -0.030046 
+corr_pos[139] = -0.077647 
+corr_pos[140] = -0.085863 
+corr_pos[141] = -0.093816 
+corr_pos[142] = -0.138532 
+corr_pos[143] = -0.145584 
+corr_pos[144] = -0.152699 
+corr_pos[145] = -0.192594 
+corr_pos[146] = -0.200980 
+corr_pos[147] = -0.208816 
+corr_pos[148] = -0.241983 
+corr_pos[149] = -0.248319 
+corr_pos[150] = -0.253789 
+corr_pos[151] = -0.276869 
+corr_pos[152] = -0.279240 
+corr_pos[153] = -0.281538 
+corr_pos[154] = -0.294317 
+corr_pos[155] = -0.295586 
+corr_pos[156] = -0.296029 
+corr_pos[157] = -0.297443 
+corr_pos[158] = -0.297185 
+corr_pos[159] = -0.295946 
+corr_pos[160] = -0.284463 
+corr_pos[161] = -0.282598 
+corr_pos[162] = -0.281260 
+corr_pos[163] = -0.256509 
+corr_pos[164] = -0.250326 
+corr_pos[165] = -0.244372 
+corr_pos[166] = -0.204043 
+corr_pos[167] = -0.196147 
+corr_pos[168] = -0.187928 
+corr_pos[169] = -0.131831 
+corr_pos[170] = -0.121351 
+corr_pos[171] = -0.110548 
+corr_pos[172] = -0.038951 
+corr_pos[173] = -0.025887 
+corr_pos[174] = -0.012501 

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -424,18 +424,18 @@ class FlomniSampleTransferMixin:
     def show_signal_strength_interferometer(self):
         dev.rtx.controller.show_signal_strength_interferometer()
 
-    def rt_feedback_disable(self):
+    def feedback_disable(self):
         self.device_manager.devices.rtx.controller.feedback_disable()
 
-    def rt_feedback_enable_with_reset(self):
+    def feedback_enable_with_reset(self):
         self.device_manager.devices.rtx.controller.feedback_enable_with_reset()
         self.rt_feedback_status()
 
-    def rt_feedback_enable_without_reset(self):
+    def feedback_enable_without_reset(self):
         self.device_manager.devices.rtx.controller.feedback_enable_without_reset()
         self.rt_feedback_status()
 
-    def rt_feedback_status(self):
+    def feedback_status(self):
         feedback_status = self.device_manager.devices.rtx.controller.feedback_is_running()
         if feedback_status == True:
             print("The rt feedback is \x1b[92mrunning\x1b[0m.")
@@ -455,7 +455,7 @@ class FlomniSampleTransferMixin:
 
         umv(dev.fsamroy, 0)
 
-        self.rt_feedback_disable()
+        self.feedback_disable()
 
         self.ensure_fheater_up()
 
@@ -1051,7 +1051,7 @@ class FlomniAlignmentMixin:
                 value = line.split(" ")[2]
                 name = line.split(" ")[0].split("[")[0]
                 if name == "corr_pos":
-                    corr_pos.append(float(value) / 1000)
+                    corr_pos.append(float(value))
                 elif name == "corr_angle":
                     corr_angle.append(float(value))
         print(
@@ -1142,7 +1142,7 @@ class Flomni(
                 fsamx_in = self._get_user_param_safe(dev.fsamx, "in")
                 if np.isclose(fsamx_in, dev.fsamx.readback.get(), 0.5):
                     print("Stopping alignment. Returning to fsamx in position.")
-                    self.rt_feedback_disable()
+                    self.feedback_disable()
                     umv(dev.fsamx, fsamx_in)
                 raise exc
 
@@ -1521,7 +1521,7 @@ class Flomni(
             angles = np.flip(angles)
         for angle in angles:
             self.progress["subtomo"] = subtomo_number
-            self.progress["subtomo_projection"] = angles.index(angle)
+            self.progress["subtomo_projection"] = np.where(angles == angle)[0][0]
             self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
             self.progress["projection"] = (subtomo_number - 1) * self.progress[
                 "subtomo_total_projections"
@@ -1701,7 +1701,7 @@ class Flomni(
     def _print_progress(self):
         print("\x1b[95mProgress report:")
         print(f"Tomo type: ....................... {self.progress['tomo_type']}")
-        print(f"Projection: ...................... {self.progress['projection']}")
+        print(f"Projection: ...................... {self.progress['projection']:.0f}")
         print(f"Total projections expected ....... {self.progress['total_projections']}")
         print(f"Angle: ........................... {self.progress['angle']}")
         print(f"Current subtomo: ................. {self.progress['subtomo']}")

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -100,7 +100,7 @@ class XrayEyeAlign:
 
         self.flomni.laser_tracker_on()
 
-        self.flomni.rt_feedback_enable_with_reset()
+        self.flomni.feedback_enable_with_reset()
 
         # disable movement buttons
         self.movement_buttons_enabled = False
@@ -109,7 +109,7 @@ class XrayEyeAlign:
         epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", sample_name)
 
         # this makes sure we are in a defined state
-        self.flomni.rt_feedback_disable()
+        self.flomni.feedback_disable()
 
         epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
 
@@ -143,13 +143,13 @@ class XrayEyeAlign:
                     self.movement_buttons_enabled = False
                     epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
 
-                    self.flomni.rt_feedback_disable()
+                    self.flomni.feedback_disable()
                     fsamx_in = self.flomni._get_user_param_safe("fsamx", "in")
                     umv(dev.fsamx, fsamx_in)
 
                     self.flomni.foptics_out()
 
-                    self.flomni.rt_feedback_disable()
+                    self.flomni.feedback_disable()
                     umv(dev.fsamx, fsamx_in - 0.25)
 
                     self.update_frame()
@@ -160,7 +160,7 @@ class XrayEyeAlign:
 
                     umv(dev.fsamx, fsamx_in)
                     time.sleep(0.5)
-                    self.flomni.rt_feedback_enable_with_reset()
+                    self.flomni.feedback_enable_with_reset()
 
                     self.update_frame()
                     self.send_message("Adjust sample height and submit center")
@@ -205,11 +205,11 @@ class XrayEyeAlign:
                 # allow movements, store movements to calculate center
                 _xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
                 if _xrayeyalignmvy != 0:
-                    self.flomni.rt_feedback_disable()
+                    self.flomni.feedback_disable()
                     umvr(dev.fsamy, _xrayeyalignmvy / 1000)
                     time.sleep(2)
                     epics_put("XOMNYI-XEYE-MVY:0", 0)
-                    self.flomni.rt_feedback_enable_with_reset()
+                    self.flomni.feedback_enable_with_reset()
                     self.update_frame()
             time.sleep(0.2)
 

csaxs_bec/bec_ipython_client/plugins/omny/__init__.py

@@ -0,0 +1 @@
+from .omny import OMNY

csaxs_bec/bec_ipython_client/plugins/omny/correction_omny_202204.txt

@@ -0,0 +1,715 @@
+corr_elements = 357 
+corr_angle[0] = 0.097400 
+corr_angle[1] = 0.603500 
+corr_angle[2] = 1.134200 
+corr_angle[3] = 1.625000 
+corr_angle[4] = 2.162200 
+corr_angle[5] = 2.700100 
+corr_angle[6] = 3.191600 
+corr_angle[7] = 3.714300 
+corr_angle[8] = 4.223200 
+corr_angle[9] = 4.730900 
+corr_angle[10] = 5.253300 
+corr_angle[11] = 5.743300 
+corr_angle[12] = 6.279200 
+corr_angle[13] = 6.782900 
+corr_angle[14] = 7.301200 
+corr_angle[15] = 7.808100 
+corr_angle[16] = 8.325300 
+corr_angle[17] = 8.859400 
+corr_angle[18] = 9.359400 
+corr_angle[19] = 9.887900 
+corr_angle[20] = 10.395400 
+corr_angle[21] = 10.930700 
+corr_angle[22] = 11.415400 
+corr_angle[23] = 11.928900 
+corr_angle[24] = 12.456900 
+corr_angle[25] = 12.955900 
+corr_angle[26] = 13.479000 
+corr_angle[27] = 13.982700 
+corr_angle[28] = 14.500900 
+corr_angle[29] = 15.016200 
+corr_angle[30] = 15.528000 
+corr_angle[31] = 16.053800 
+corr_angle[32] = 16.562800 
+corr_angle[33] = 17.076600 
+corr_angle[34] = 17.592400 
+corr_angle[35] = 18.094100 
+corr_angle[36] = 18.623800 
+corr_angle[37] = 19.118400 
+corr_angle[38] = 19.655000 
+corr_angle[39] = 20.143900 
+corr_angle[40] = 20.672200 
+corr_angle[41] = 21.171500 
+corr_angle[42] = 21.696300 
+corr_angle[43] = 22.215900 
+corr_angle[44] = 22.728900 
+corr_angle[45] = 23.233100 
+corr_angle[46] = 23.760000 
+corr_angle[47] = 24.267700 
+corr_angle[48] = 24.792100 
+corr_angle[49] = 25.287900 
+corr_angle[50] = 25.824600 
+corr_angle[51] = 26.321900 
+corr_angle[52] = 26.842600 
+corr_angle[53] = 27.337200 
+corr_angle[54] = 27.873500 
+corr_angle[55] = 28.373900 
+corr_angle[56] = 28.895900 
+corr_angle[57] = 29.404900 
+corr_angle[58] = 29.926700 
+corr_angle[59] = 30.439300 
+corr_angle[60] = 30.963700 
+corr_angle[61] = 31.460000 
+corr_angle[62] = 31.989500 
+corr_angle[63] = 32.489700 
+corr_angle[64] = 33.026400 
+corr_angle[65] = 33.516500 
+corr_angle[66] = 34.044000 
+corr_angle[67] = 34.547700 
+corr_angle[68] = 35.070800 
+corr_angle[69] = 35.578400 
+corr_angle[70] = 36.103200 
+corr_angle[71] = 36.603200 
+corr_angle[72] = 37.128200 
+corr_angle[73] = 37.645200 
+corr_angle[74] = 38.164300 
+corr_angle[75] = 38.662100 
+corr_angle[76] = 39.191000 
+corr_angle[77] = 39.693400 
+corr_angle[78] = 40.222500 
+corr_angle[79] = 40.719500 
+corr_angle[80] = 41.247000 
+corr_angle[81] = 41.755700 
+corr_angle[82] = 42.271300 
+corr_angle[83] = 42.767600 
+corr_angle[84] = 43.302200 
+corr_angle[85] = 43.818700 
+corr_angle[86] = 44.330000 
+corr_angle[87] = 44.835300 
+corr_angle[88] = 45.359800 
+corr_angle[89] = 45.867200 
+corr_angle[90] = 46.396200 
+corr_angle[91] = 46.895000 
+corr_angle[92] = 47.411500 
+corr_angle[93] = 47.915200 
+corr_angle[94] = 48.436600 
+corr_angle[95] = 48.946100 
+corr_angle[96] = 49.472300 
+corr_angle[97] = 49.979800 
+corr_angle[98] = 50.503300 
+corr_angle[99] = 51.008700 
+corr_angle[100] = 51.535000 
+corr_angle[101] = 52.036700 
+corr_angle[102] = 52.563700 
+corr_angle[103] = 53.063600 
+corr_angle[104] = 53.591700 
+corr_angle[105] = 54.091200 
+corr_angle[106] = 54.618900 
+corr_angle[107] = 55.116900 
+corr_angle[108] = 55.636100 
+corr_angle[109] = 56.143100 
+corr_angle[110] = 56.672200 
+corr_angle[111] = 57.172900 
+corr_angle[112] = 57.704600 
+corr_angle[113] = 58.204800 
+corr_angle[114] = 58.728600 
+corr_angle[115] = 59.239500 
+corr_angle[116] = 59.768400 
+corr_angle[117] = 60.268300 
+corr_angle[118] = 60.788800 
+corr_angle[119] = 61.289300 
+corr_angle[120] = 61.813300 
+corr_angle[121] = 62.310800 
+corr_angle[122] = 62.836700 
+corr_angle[123] = 63.353700 
+corr_angle[124] = 63.866600 
+corr_angle[125] = 64.377200 
+corr_angle[126] = 64.906600 
+corr_angle[127] = 65.414000 
+corr_angle[128] = 65.937100 
+corr_angle[129] = 66.429400 
+corr_angle[130] = 66.970000 
+corr_angle[131] = 67.459200 
+corr_angle[132] = 67.996400 
+corr_angle[133] = 68.499800 
+corr_angle[134] = 69.014500 
+corr_angle[135] = 69.509500 
+corr_angle[136] = 70.044000 
+corr_angle[137] = 70.543200 
+corr_angle[138] = 71.079400 
+corr_angle[139] = 71.579300 
+corr_angle[140] = 72.103500 
+corr_angle[141] = 72.607000 
+corr_angle[142] = 73.137100 
+corr_angle[143] = 73.633000 
+corr_angle[144] = 74.164500 
+corr_angle[145] = 74.660200 
+corr_angle[146] = 75.180600 
+corr_angle[147] = 75.674200 
+corr_angle[148] = 76.215400 
+corr_angle[149] = 76.718900 
+corr_angle[150] = 77.242300 
+corr_angle[151] = 77.752000 
+corr_angle[152] = 78.279300 
+corr_angle[153] = 78.780500 
+corr_angle[154] = 79.314900 
+corr_angle[155] = 79.424500 
+corr_angle[156] = 79.807000 
+corr_angle[157] = 80.336500 
+corr_angle[158] = 80.338700 
+corr_angle[159] = 80.835300 
+corr_angle[160] = 81.367100 
+corr_angle[161] = 81.376100 
+corr_angle[162] = 81.859000 
+corr_angle[163] = 82.382300 
+corr_angle[164] = 82.384000 
+corr_angle[165] = 82.881100 
+corr_angle[166] = 83.415000 
+corr_angle[167] = 83.421600 
+corr_angle[168] = 83.917100 
+corr_angle[169] = 84.439200 
+corr_angle[170] = 84.439300 
+corr_angle[171] = 84.947400 
+corr_angle[172] = 85.472700 
+corr_angle[173] = 85.987700 
+corr_angle[174] = 86.512400 
+corr_angle[175] = 87.009500 
+corr_angle[176] = 87.536500 
+corr_angle[177] = 88.035600 
+corr_angle[178] = 88.560100 
+corr_angle[179] = 89.057600 
+corr_angle[180] = 89.583200 
+corr_angle[181] = 90.090500 
+corr_angle[182] = 90.614600 
+corr_angle[183] = 91.119900 
+corr_angle[184] = 91.638300 
+corr_angle[185] = 92.153300 
+corr_angle[186] = 92.681600 
+corr_angle[187] = 93.181800 
+corr_angle[188] = 93.710900 
+corr_angle[189] = 94.206100 
+corr_angle[190] = 94.732700 
+corr_angle[191] = 95.226600 
+corr_angle[192] = 95.766400 
+corr_angle[193] = 96.259000 
+corr_angle[194] = 96.783400 
+corr_angle[195] = 97.283100 
+corr_angle[196] = 97.811500 
+corr_angle[197] = 98.323600 
+corr_angle[198] = 98.839400 
+corr_angle[199] = 99.350700 
+corr_angle[200] = 99.880200 
+corr_angle[201] = 100.378100 
+corr_angle[202] = 100.913300 
+corr_angle[203] = 101.405000 
+corr_angle[204] = 101.935700 
+corr_angle[205] = 102.426300 
+corr_angle[206] = 102.957300 
+corr_angle[207] = 103.456500 
+corr_angle[208] = 103.985100 
+corr_angle[209] = 104.490300 
+corr_angle[210] = 105.015100 
+corr_angle[211] = 105.518400 
+corr_angle[212] = 106.047400 
+corr_angle[213] = 106.551100 
+corr_angle[214] = 107.077100 
+corr_angle[215] = 107.575800 
+corr_angle[216] = 108.115200 
+corr_angle[217] = 108.598800 
+corr_angle[218] = 109.129100 
+corr_angle[219] = 109.626200 
+corr_angle[220] = 110.158400 
+corr_angle[221] = 110.661700 
+corr_angle[222] = 111.188600 
+corr_angle[223] = 111.695000 
+corr_angle[224] = 112.216400 
+corr_angle[225] = 112.720000 
+corr_angle[226] = 113.246200 
+corr_angle[227] = 113.757100 
+corr_angle[228] = 114.281900 
+corr_angle[229] = 114.780000 
+corr_angle[230] = 115.306800 
+corr_angle[231] = 115.799800 
+corr_angle[232] = 116.328400 
+corr_angle[233] = 116.829900 
+corr_angle[234] = 117.355400 
+corr_angle[235] = 117.858200 
+corr_angle[236] = 118.380600 
+corr_angle[237] = 118.893200 
+corr_angle[238] = 119.418200 
+corr_angle[239] = 119.921000 
+corr_angle[240] = 120.446100 
+corr_angle[241] = 120.953800 
+corr_angle[242] = 121.480300 
+corr_angle[243] = 121.977600 
+corr_angle[244] = 122.507100 
+corr_angle[245] = 122.996200 
+corr_angle[246] = 123.529600 
+corr_angle[247] = 124.032200 
+corr_angle[248] = 124.554800 
+corr_angle[249] = 125.057800 
+corr_angle[250] = 125.580800 
+corr_angle[251] = 126.090000 
+corr_angle[252] = 126.611600 
+corr_angle[253] = 127.127000 
+corr_angle[254] = 127.650900 
+corr_angle[255] = 128.153700 
+corr_angle[256] = 128.677200 
+corr_angle[257] = 129.170800 
+corr_angle[258] = 129.703000 
+corr_angle[259] = 130.194900 
+corr_angle[260] = 130.733600 
+corr_angle[261] = 131.228300 
+corr_angle[262] = 131.756900 
+corr_angle[263] = 132.263200 
+corr_angle[264] = 132.784700 
+corr_angle[265] = 133.296300 
+corr_angle[266] = 133.818800 
+corr_angle[267] = 134.318900 
+corr_angle[268] = 134.846800 
+corr_angle[269] = 135.344800 
+corr_angle[270] = 135.876000 
+corr_angle[271] = 136.372600 
+corr_angle[272] = 136.902700 
+corr_angle[273] = 137.397800 
+corr_angle[274] = 137.926800 
+corr_angle[275] = 138.428000 
+corr_angle[276] = 138.953700 
+corr_angle[277] = 139.461300 
+corr_angle[278] = 139.987800 
+corr_angle[279] = 140.492600 
+corr_angle[280] = 141.017900 
+corr_angle[281] = 141.524000 
+corr_angle[282] = 142.061200 
+corr_angle[283] = 142.545400 
+corr_angle[284] = 143.069900 
+corr_angle[285] = 143.568700 
+corr_angle[286] = 144.102200 
+corr_angle[287] = 144.596200 
+corr_angle[288] = 145.126400 
+corr_angle[289] = 145.626900 
+corr_angle[290] = 146.158700 
+corr_angle[291] = 146.662200 
+corr_angle[292] = 147.184700 
+corr_angle[293] = 147.692300 
+corr_angle[294] = 148.225900 
+corr_angle[295] = 148.716000 
+corr_angle[296] = 149.243400 
+corr_angle[297] = 149.739400 
+corr_angle[298] = 150.272400 
+corr_angle[299] = 150.762100 
+corr_angle[300] = 151.301800 
+corr_angle[301] = 151.796300 
+corr_angle[302] = 152.333500 
+corr_angle[303] = 152.833100 
+corr_angle[304] = 153.363600 
+corr_angle[305] = 153.862900 
+corr_angle[306] = 154.396100 
+corr_angle[307] = 154.895400 
+corr_angle[308] = 155.417700 
+corr_angle[309] = 155.916900 
+corr_angle[310] = 156.451600 
+corr_angle[311] = 156.942700 
+corr_angle[312] = 157.467600 
+corr_angle[313] = 157.970900 
+corr_angle[314] = 158.501100 
+corr_angle[315] = 158.999600 
+corr_angle[316] = 159.526100 
+corr_angle[317] = 160.028100 
+corr_angle[318] = 160.555800 
+corr_angle[319] = 161.067700 
+corr_angle[320] = 161.597300 
+corr_angle[321] = 162.091300 
+corr_angle[322] = 162.616600 
+corr_angle[323] = 163.107400 
+corr_angle[324] = 163.639100 
+corr_angle[325] = 164.139700 
+corr_angle[326] = 164.672500 
+corr_angle[327] = 165.176800 
+corr_angle[328] = 165.698600 
+corr_angle[329] = 166.205400 
+corr_angle[330] = 166.727300 
+corr_angle[331] = 167.238600 
+corr_angle[332] = 167.771500 
+corr_angle[333] = 168.265000 
+corr_angle[334] = 168.794800 
+corr_angle[335] = 169.293800 
+corr_angle[336] = 169.813300 
+corr_angle[337] = 170.320200 
+corr_angle[338] = 170.845100 
+corr_angle[339] = 171.344000 
+corr_angle[340] = 171.866200 
+corr_angle[341] = 172.375300 
+corr_angle[342] = 172.899400 
+corr_angle[343] = 173.404400 
+corr_angle[344] = 173.928500 
+corr_angle[345] = 174.430800 
+corr_angle[346] = 174.827800 
+corr_angle[347] = 175.460400 
+corr_angle[348] = 175.993100 
+corr_angle[349] = 176.492100 
+corr_angle[350] = 177.014200 
+corr_angle[351] = 177.512100 
+corr_angle[352] = 178.044200 
+corr_angle[353] = 178.643800 
+corr_angle[354] = 179.067200 
+corr_angle[355] = 179.571600 
+corr_angle[356] = 180.093700 
+corr_pos[0] = -0.814519 
+corr_pos[1] = -0.810675 
+corr_pos[2] = -0.806338 
+corr_pos[3] = -0.802047 
+corr_pos[4] = -0.797044 
+corr_pos[5] = -0.791712 
+corr_pos[6] = -0.786558 
+corr_pos[7] = -0.780781 
+corr_pos[8] = -0.774864 
+corr_pos[9] = -0.768674 
+corr_pos[10] = -0.762005 
+corr_pos[11] = -0.755474 
+corr_pos[12] = -0.748024 
+corr_pos[13] = -0.740730 
+corr_pos[14] = -0.732929 
+corr_pos[15] = -0.725011 
+corr_pos[16] = -0.716637 
+corr_pos[17] = -0.707676 
+corr_pos[18] = -0.698861 
+corr_pos[19] = -0.686245 
+corr_pos[20] = -0.676596 
+corr_pos[21] = -0.663643 
+corr_pos[22] = -0.655664 
+corr_pos[23] = -0.642249 
+corr_pos[24] = -0.633516 
+corr_pos[25] = -0.621402 
+corr_pos[26] = -0.612846 
+corr_pos[27] = -0.599978 
+corr_pos[28] = -0.592135 
+corr_pos[29] = -0.577949 
+corr_pos[30] = -0.570695 
+corr_pos[31] = -0.555560 
+corr_pos[32] = -0.549015 
+corr_pos[33] = -0.532162 
+corr_pos[34] = -0.524479 
+corr_pos[35] = -0.507848 
+corr_pos[36] = -0.500301 
+corr_pos[37] = -0.484361 
+corr_pos[38] = -0.477365 
+corr_pos[39] = -0.461751 
+corr_pos[40] = -0.455963 
+corr_pos[41] = -0.439438 
+corr_pos[42] = -0.436103 
+corr_pos[43] = -0.420587 
+corr_pos[44] = -0.417361 
+corr_pos[45] = -0.402270 
+corr_pos[46] = -0.400459 
+corr_pos[47] = -0.384745 
+corr_pos[48] = -0.385280 
+corr_pos[49] = -0.371217 
+corr_pos[50] = -0.373612 
+corr_pos[51] = -0.361838 
+corr_pos[52] = -0.365771 
+corr_pos[53] = -0.354641 
+corr_pos[54] = -0.360647 
+corr_pos[55] = -0.351446 
+corr_pos[56] = -0.359147 
+corr_pos[57] = -0.348696 
+corr_pos[58] = -0.359348 
+corr_pos[59] = -0.349962 
+corr_pos[60] = -0.360782 
+corr_pos[61] = -0.355040 
+corr_pos[62] = -0.367441 
+corr_pos[63] = -0.360511 
+corr_pos[64] = -0.372617 
+corr_pos[65] = -0.366120 
+corr_pos[66] = -0.377568 
+corr_pos[67] = -0.370362 
+corr_pos[68] = -0.380918 
+corr_pos[69] = -0.372553 
+corr_pos[70] = -0.381460 
+corr_pos[71] = -0.371828 
+corr_pos[72] = -0.379428 
+corr_pos[73] = -0.368465 
+corr_pos[74] = -0.374297 
+corr_pos[75] = -0.360340 
+corr_pos[76] = -0.365429 
+corr_pos[77] = -0.349168 
+corr_pos[78] = -0.351544 
+corr_pos[79] = -0.332514 
+corr_pos[80] = -0.333505 
+corr_pos[81] = -0.313316 
+corr_pos[82] = -0.313014 
+corr_pos[83] = -0.291107 
+corr_pos[84] = -0.287807 
+corr_pos[85] = -0.264483 
+corr_pos[86] = -0.260891 
+corr_pos[87] = -0.236646 
+corr_pos[88] = -0.231362 
+corr_pos[89] = -0.205833 
+corr_pos[90] = -0.200663 
+corr_pos[91] = -0.174834 
+corr_pos[92] = -0.171662 
+corr_pos[93] = -0.146200 
+corr_pos[94] = -0.142890 
+corr_pos[95] = -0.118389 
+corr_pos[96] = -0.112895 
+corr_pos[97] = -0.088879 
+corr_pos[98] = -0.084146 
+corr_pos[99] = -0.061625 
+corr_pos[100] = -0.054742 
+corr_pos[101] = -0.032741 
+corr_pos[102] = -0.026725 
+corr_pos[103] = -0.004827 
+corr_pos[104] = 0.002678 
+corr_pos[105] = 0.024418 
+corr_pos[106] = 0.031105 
+corr_pos[107] = 0.052334 
+corr_pos[108] = 0.060072 
+corr_pos[109] = 0.081470 
+corr_pos[110] = 0.088550 
+corr_pos[111] = 0.109685 
+corr_pos[112] = 0.116675 
+corr_pos[113] = 0.136298 
+corr_pos[114] = 0.142152 
+corr_pos[115] = 0.161986 
+corr_pos[116] = 0.166996 
+corr_pos[117] = 0.186466 
+corr_pos[118] = 0.190874 
+corr_pos[119] = 0.208729 
+corr_pos[120] = 0.212714 
+corr_pos[121] = 0.229992 
+corr_pos[122] = 0.232685 
+corr_pos[123] = 0.248748 
+corr_pos[124] = 0.249688 
+corr_pos[125] = 0.264768 
+corr_pos[126] = 0.264432 
+corr_pos[127] = 0.278801 
+corr_pos[128] = 0.278424 
+corr_pos[129] = 0.289656 
+corr_pos[130] = 0.289612 
+corr_pos[131] = 0.299899 
+corr_pos[132] = 0.299782 
+corr_pos[133] = 0.307473 
+corr_pos[134] = 0.309489 
+corr_pos[135] = 0.315999 
+corr_pos[136] = 0.317413 
+corr_pos[137] = 0.325060 
+corr_pos[138] = 0.325931 
+corr_pos[139] = 0.332544 
+corr_pos[140] = 0.332095 
+corr_pos[141] = 0.338738 
+corr_pos[142] = 0.337864 
+corr_pos[143] = 0.343909 
+corr_pos[144] = 0.342973 
+corr_pos[145] = 0.348449 
+corr_pos[146] = 0.346060 
+corr_pos[147] = 0.351949 
+corr_pos[148] = 0.349873 
+corr_pos[149] = 0.354969 
+corr_pos[150] = 0.352375 
+corr_pos[151] = 0.358388 
+corr_pos[152] = 0.354736 
+corr_pos[153] = 0.359539 
+corr_pos[154] = 0.354369 
+corr_pos[155] = 0.358549 
+corr_pos[156] = 0.353217 
+corr_pos[157] = 0.355795 
+corr_pos[158] = 0.351299 
+corr_pos[159] = 0.352922 
+corr_pos[160] = 0.346933 
+corr_pos[161] = 0.350201 
+corr_pos[162] = 0.343937 
+corr_pos[163] = 0.349304 
+corr_pos[164] = 0.344857 
+corr_pos[165] = 0.347471 
+corr_pos[166] = 0.335793 
+corr_pos[167] = 0.341109 
+corr_pos[168] = 0.330453 
+corr_pos[169] = 0.326576 
+corr_pos[170] = 0.320299 
+corr_pos[171] = 0.315348 
+corr_pos[172] = 0.300744 
+corr_pos[173] = 0.294366 
+corr_pos[174] = 0.280438 
+corr_pos[175] = 0.273618 
+corr_pos[176] = 0.259335 
+corr_pos[177] = 0.251464 
+corr_pos[178] = 0.237247 
+corr_pos[179] = 0.229092 
+corr_pos[180] = 0.214882 
+corr_pos[181] = 0.207363 
+corr_pos[182] = 0.193246 
+corr_pos[183] = 0.185868 
+corr_pos[184] = 0.173256 
+corr_pos[185] = 0.165378 
+corr_pos[186] = 0.153853 
+corr_pos[187] = 0.147031 
+corr_pos[188] = 0.135535 
+corr_pos[189] = 0.129435 
+corr_pos[190] = 0.119843 
+corr_pos[191] = 0.115062 
+corr_pos[192] = 0.107115 
+corr_pos[193] = 0.105182 
+corr_pos[194] = 0.099647 
+corr_pos[195] = 0.098162 
+corr_pos[196] = 0.094628 
+corr_pos[197] = 0.095257 
+corr_pos[198] = 0.084490 
+corr_pos[199] = 0.085389 
+corr_pos[200] = 0.074302 
+corr_pos[201] = 0.075265 
+corr_pos[202] = 0.063623 
+corr_pos[203] = 0.064487 
+corr_pos[204] = 0.052841 
+corr_pos[205] = 0.053559 
+corr_pos[206] = 0.042022 
+corr_pos[207] = 0.043321 
+corr_pos[208] = 0.032826 
+corr_pos[209] = 0.032277 
+corr_pos[210] = 0.022169 
+corr_pos[211] = 0.020740 
+corr_pos[212] = 0.010378 
+corr_pos[213] = 0.008668 
+corr_pos[214] = -0.001930 
+corr_pos[215] = -0.003882 
+corr_pos[216] = -0.014694 
+corr_pos[217] = -0.016629 
+corr_pos[218] = -0.026380 
+corr_pos[219] = -0.028069 
+corr_pos[220] = -0.037125 
+corr_pos[221] = -0.039429 
+corr_pos[222] = -0.047773 
+corr_pos[223] = -0.049261 
+corr_pos[224] = -0.056872 
+corr_pos[225] = -0.058756 
+corr_pos[226] = -0.065279 
+corr_pos[227] = -0.066859 
+corr_pos[228] = -0.073027 
+corr_pos[229] = -0.074253 
+corr_pos[230] = -0.079062 
+corr_pos[231] = -0.079800 
+corr_pos[232] = -0.084350 
+corr_pos[233] = -0.084805 
+corr_pos[234] = -0.088621 
+corr_pos[235] = -0.088437 
+corr_pos[236] = -0.092166 
+corr_pos[237] = -0.090769 
+corr_pos[238] = -0.093820 
+corr_pos[239] = -0.091724 
+corr_pos[240] = -0.094152 
+corr_pos[241] = -0.090866 
+corr_pos[242] = -0.092575 
+corr_pos[243] = -0.089239 
+corr_pos[244] = -0.089666 
+corr_pos[245] = -0.086864 
+corr_pos[246] = -0.087183 
+corr_pos[247] = -0.083974 
+corr_pos[248] = -0.083709 
+corr_pos[249] = -0.079848 
+corr_pos[250] = -0.078494 
+corr_pos[251] = -0.072782 
+corr_pos[252] = -0.069638 
+corr_pos[253] = -0.063004 
+corr_pos[254] = -0.058599 
+corr_pos[255] = -0.051737 
+corr_pos[256] = -0.046451 
+corr_pos[257] = -0.040238 
+corr_pos[258] = -0.034071 
+corr_pos[259] = -0.028578 
+corr_pos[260] = -0.021481 
+corr_pos[261] = -0.016346 
+corr_pos[262] = -0.009475 
+corr_pos[263] = -0.004141 
+corr_pos[264] = 0.002780 
+corr_pos[265] = 0.008455 
+corr_pos[266] = 0.015507 
+corr_pos[267] = 0.021672 
+corr_pos[268] = 0.029704 
+corr_pos[269] = 0.036662 
+corr_pos[270] = 0.044794 
+corr_pos[271] = 0.052031 
+corr_pos[272] = 0.061478 
+corr_pos[273] = 0.069150 
+corr_pos[274] = 0.078715 
+corr_pos[275] = 0.087785 
+corr_pos[276] = 0.098593 
+corr_pos[277] = 0.107863 
+corr_pos[278] = 0.118256 
+corr_pos[279] = 0.127631 
+corr_pos[280] = 0.139011 
+corr_pos[281] = 0.150077 
+corr_pos[282] = 0.162154 
+corr_pos[283] = 0.173758 
+corr_pos[284] = 0.186998 
+corr_pos[285] = 0.200111 
+corr_pos[286] = 0.214116 
+corr_pos[287] = 0.227291 
+corr_pos[288] = 0.240662 
+corr_pos[289] = 0.252955 
+corr_pos[290] = 0.265359 
+corr_pos[291] = 0.275995 
+corr_pos[292] = 0.287613 
+corr_pos[293] = 0.295789 
+corr_pos[294] = 0.306424 
+corr_pos[295] = 0.313027 
+corr_pos[296] = 0.322181 
+corr_pos[297] = 0.329313 
+corr_pos[298] = 0.338191 
+corr_pos[299] = 0.345243 
+corr_pos[300] = 0.353316 
+corr_pos[301] = 0.360491 
+corr_pos[302] = 0.367891 
+corr_pos[303] = 0.375027 
+corr_pos[304] = 0.380865 
+corr_pos[305] = 0.388354 
+corr_pos[306] = 0.395257 
+corr_pos[307] = 0.401478 
+corr_pos[308] = 0.408087 
+corr_pos[309] = 0.414083 
+corr_pos[310] = 0.420361 
+corr_pos[311] = 0.424284 
+corr_pos[312] = 0.429614 
+corr_pos[313] = 0.433888 
+corr_pos[314] = 0.438529 
+corr_pos[315] = 0.442302 
+corr_pos[316] = 0.445899 
+corr_pos[317] = 0.449014 
+corr_pos[318] = 0.451693 
+corr_pos[319] = 0.453795 
+corr_pos[320] = 0.455132 
+corr_pos[321] = 0.455438 
+corr_pos[322] = 0.455334 
+corr_pos[323] = 0.454055 
+corr_pos[324] = 0.451146 
+corr_pos[325] = 0.447259 
+corr_pos[326] = 0.442478 
+corr_pos[327] = 0.437520 
+corr_pos[328] = 0.432297 
+corr_pos[329] = 0.426442 
+corr_pos[330] = 0.418918 
+corr_pos[331] = 0.411040 
+corr_pos[332] = 0.402610 
+corr_pos[333] = 0.394491 
+corr_pos[334] = 0.383925 
+corr_pos[335] = 0.374590 
+corr_pos[336] = 0.363650 
+corr_pos[337] = 0.353143 
+corr_pos[338] = 0.339756 
+corr_pos[339] = 0.328074 
+corr_pos[340] = 0.315463 
+corr_pos[341] = 0.302641 
+corr_pos[342] = 0.288898 
+corr_pos[343] = 0.275134 
+corr_pos[344] = 0.260308 
+corr_pos[345] = 0.245582 
+corr_pos[346] = 0.233584 
+corr_pos[347] = 0.213812 
+corr_pos[348] = 0.196540 
+corr_pos[349] = 0.179844 
+corr_pos[350] = 0.161839 
+corr_pos[351] = 0.144160 
+corr_pos[352] = 0.124715 
+corr_pos[353] = 0.102123 
+corr_pos[354] = 0.085736 
+corr_pos[355] = 0.065743 
+corr_pos[356] = 0.044511 

csaxs_bec/bec_ipython_client/plugins/omny/gui_tools.py

@@ -0,0 +1,171 @@
+import builtins
+
+from bec_widgets.cli.client import BECDockArea
+
+# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
+
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
+
+
+class OMNYGuiToolsError(Exception):
+    pass
+
+
+class OMNYGuiTools:
+
+    def __init__(self, client):
+        self.gui = getattr(client, "gui", None)
+        self.gui_window = self.gui.windows['main'].widget
+        self.fig200 = None
+        self.fig201 = None
+        self.fig202 = None
+        self.fig203 = None
+        self.progressbar = None
+        self.text_box = None
+        self.idle_text_box = None
+
+    def omnygui_show_gui(self):
+        self.gui_window.show()
+
+    def omnygui_stop_gui(self):
+        self.gui_window.hide()
+
+    def _omnycam_parking(self):
+        self.omnygui_show_omnycam_parking()
+
+    def omnygui_show_omnycam_parking(self):
+        self.omnygui_show_gui()
+        if self.fig200 is None:
+            self._omnycam_clear()
+            self.fig200 = self.gui_window.add_dock(name="omnycam200").add_widget("BECImageWidget")
+            if self._omnycam_check_device_exists(dev.cam200):
+                fig = self.fig200.image("cam200")
+                fig.set_rotation(deg_90=3)
+                self.fig200.lock_aspect_ratio(True)
+            else:
+                print("Cannot open cam200. Device does not exist.")
+            self.fig203 = self.gui_window.add_dock(name="omnycam203").add_widget("BECImageWidget")
+            if self._omnycam_check_device_exists(dev.cam203):
+                fig = self.fig203.image("cam203")
+                fig.set_rotation(deg_90=3)
+                self.fig203.lock_aspect_ratio(True)
+            else:
+                print("Cannot open cam203. Device does not exist.")
+            try:
+                self.gui_window.remove_dock(name="default_figure")
+            except:
+                pass
+
+    def omnygui_remove_all_docks(self):
+        self.gui_window.clear_all()
+        self.fig200 = None
+        self.fig201 = None
+        self.fig202 = None
+        self.fig203 = None
+        self.progressbar = None
+        self.text_box = None
+        self.idle_text_box = None
+
+    def omnygui_idle(self):
+        self.omnygui_show_gui()
+        if self.idle_text_box is None:
+            self.omnygui_remove_all_docks()
+            self.idle_text_box = self.gui_window.add_dock(name="idle_text").add_widget("TextBox")
+            try:
+                self.gui_window.remove_dock(name="default_figure")
+            except:
+                pass
+        text = (
+            "<pre>"
+            + "    ,o888888o.           ,8.       ,8.          b.             8 `8.`8888.      ,8' \n"
+            + " . 8888     `88.        ,888.     ,888.         888o.          8  `8.`8888.    ,8'  \n"
+            + ",8 8888       `8b      .`8888.   .`8888.        Y88888o.       8   `8.`8888.  ,8'   \n"
+            + "88 8888        `8b    ,8.`8888. ,8.`8888.       .`Y888888o.    8    `8.`8888.,8'    \n"
+            + "88 8888         88   ,8'8.`8888,8^8.`8888.      8o. `Y888888o. 8     `8.`88888'     \n"
+            + "88 8888         88  ,8' `8.`8888' `8.`8888.     8`Y8o. `Y88888o8      `8. 8888      \n"
+            + "88 8888        ,8P ,8'   `8.`88'   `8.`8888.    8   `Y8o. `Y8888       `8 8888      \n"
+            + "`8 8888       ,8P ,8'     `8.`'     `8.`8888.   8      `Y8o. `Y8        8 8888      \n"
+            + " ` 8888     ,88' ,8'       `8        `8.`8888.  8         `Y8o.`        8 8888      \n"
+            + "    `8888888P'  ,8'         `         `8.`8888. 8            `Yo        8 8888      \n"
+            + "</pre>"
+        )
+        self.idle_text_box.set_html_text(text)
+
+    def _omnycam_clear(self):
+        self.omnygui_remove_all_docks()
+
+    def _omnycam_check_device_exists(self, device):
+        try:
+            device
+        except:
+            return False
+        else:
+            return True
+
+    def _omnycam_samplestage(self):
+        self.omnygui_show_omnycam_samplestage()
+
+    def omnygui_show_omnycam_samplestage(self):
+        self.omnygui_show_gui()
+        if self.fig201 is None:
+            self.omnygui_remove_all_docks()
+            self.fig201 = self.gui_window.add_dock(name="omnycam201").add_widget("BECImageWidget")
+            if self._omnycam_check_device_exists(dev.cam201):
+                fig = self.fig201.image("cam201")
+                fig.set_rotation(deg_90=3)
+                self.fig201.lock_aspect_ratio(True)
+            else:
+                print("Cannot open cam201. Device does not exist.")
+            self.fig202 = self.gui_window.add_dock(name="omnycam202").add_widget("BECImageWidget")
+            if self._omnycam_check_device_exists(dev.cam202):
+                fig = self.fig202.image("cam202")
+                fig.set_rotation(deg_90=3)
+                self.fig202.lock_aspect_ratio(True)
+            else:
+                print("Cannot open cam202. Device does not exist.")
+            try:
+                self.gui_window.remove_dock(name="default_figure")
+            except:
+                pass
+
+    def omnygui_show_progress(self):
+        self.omnygui_show_gui()
+        if self.progressbar is None:
+            self.omnygui_remove_all_docks()
+            # Add a new dock with a RingProgressBar widget
+            self.progressbar = self.gui_window.add_dock(name="progress").add_widget("RingProgressBar")
+            # Customize the size of the progress ring
+            self.progressbar.set_line_widths(20)
+            # Disable automatic updates and manually set the self.progressbar value
+            self.progressbar.enable_auto_updates(False)
+            # Set precision for the self.progressbar display
+            self.progressbar.set_precision(1)  # Display self.progressbar with one decimal places
+            # Setting multiple rigns with different values
+            self.progressbar.set_number_of_bars(3)
+            self.progressbar.rings[2].set_update("scan")
+            # Set the values of the rings to 50, 75, and 25 from outer to inner ring
+            # self.progressbar.set_value([50, 75])
+            # Add a new dock with a TextBox widget
+            self.text_box = self.gui_window.add_dock(name="progress_text").add_widget("TextBox")
+            try:
+                self.gui_window.remove_dock(name="default_figure")
+            except:
+                pass
+        self._omnygui_update_progress()
+
+    def _omnygui_update_progress(self):
+        if self.progressbar is not None:
+            progress = self.progress["projection"] / self.progress["total_projections"] * 100
+            subotmo_progress = (
+                self.progress["subtomo_projection"]
+                / self.progress["subtomo_total_projections"]
+                * 100
+            )
+            self.progressbar.set_value([progress, subotmo_progress])
+
+            text = f"Progress report:\n Tomo type: ....................... {self.progress['tomo_type']}\n Projection: ...................... {self.progress['projection']:.0f}\n Total projections expected ....... {self.progress['total_projections']}\n Angle: ........................... {self.progress['angle']}\n Current subtomo: ................. {self.progress['subtomo']}\n Current projection within subtomo: {self.progress['subtomo_projection']}\n Total projections per subtomo: ... {self.progress['subtomo_total_projections']}"
+            self.text_box.set_plain_text(text)

csaxs_bec/bec_ipython_client/plugins/omny/omny_alignment_mixin.py

@@ -0,0 +1,246 @@
+import time
+import numpy as np
+import os
+
+from rich import box
+from rich.console import Console
+from rich.table import Table
+
+from typeguard import typechecked
+from bec_lib import bec_logger
+
+logger = bec_logger.logger
+
+
+class OMNYAlignmentError(Exception):
+    pass
+
+
+class OMNYAlignmentMixin:
+    default_correction_file = "correction_omny_202204.txt"
+    default_correction_file_x = "correction_omny_202204_x.txt"
+
+    def reset_correction(self, use_default_correction=True):
+        """
+        Reset the correction to the default values.
+        If use_default_correction is False, the correction will be set to empty values.
+        Otherwise the default values will be loaded.
+
+        Args:
+            use_default_correction (bool, optional): If set to true, a call reset the correction to the default values. Defaults to True.
+        """
+        self.corr_pos_x = []
+        self.corr_angle_x = []
+        self.corr_pos_y = []
+        self.corr_angle_y = []
+        self.corr_pos_y_2 = []
+        self.corr_angle_y_2 = []
+
+        if use_default_correction:
+            try:
+                self.read_additional_correction_x(self.default_correction_file_x)
+                logger.info(f"Applying default x correction from {self.default_correction_file_x}")
+            except FileNotFoundError:
+                logger.warning(
+                    f"Could not find default correction file {self.default_correction_file_x}."
+                )
+                logger.warning("Not applying any correction.")
+            try:
+                self.read_additional_correction_y(self.default_correction_file)
+                logger.info(f"Applying default y correction from {self.default_correction_file}")
+            except FileNotFoundError:
+                logger.warning(
+                    f"Could not find default correction file {self.default_correction_file}."
+                )
+                logger.warning("Not applying any correction.")
+
+    def reset_tomo_alignment_fit(self):
+        self.client.delete_global_var("tomo_alignment_fit")
+
+    def read_alignment_offset(
+        self,
+        dir_path=os.path.expanduser("~/Data10/specES1/internal/"),
+        setup="omny",
+        use_vertical_default_values=True,
+    ):
+        """
+        Read the alignment offset from the given directory and set the global parameter
+        tomo_alignment_fit.
+
+        Args:
+            dir_path (str, optional): The directory to read the alignment offset from. Defaults to os.path.expanduser("~/Data10/specES1/internal/").
+        """
+        tomo_alignment_fit = np.zeros((2, 5))
+        with open(os.path.join(dir_path, "ptychotomoalign_Ax.txt"), "r") as file:
+            tomo_alignment_fit[0][0] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Bx.txt"), "r") as file:
+            tomo_alignment_fit[0][1] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Cx.txt"), "r") as file:
+            tomo_alignment_fit[0][2] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Ay.txt"), "r") as file:
+            tomo_alignment_fit[1][0] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_By.txt"), "r") as file:
+            tomo_alignment_fit[1][1] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Cy.txt"), "r") as file:
+            tomo_alignment_fit[1][2] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Ay3.txt"), "r") as file:
+            tomo_alignment_fit[1][3] = file.readline()
+
+        with open(os.path.join(dir_path, "ptychotomoalign_Cy3.txt"), "r") as file:
+            tomo_alignment_fit[1][4] = file.readline()
+
+        print("New alignment parameters loaded:")
+        print(
+            f"X Amplitude {tomo_alignment_fit[0][0]}, "
+            f"X Phase {tomo_alignment_fit[0][1]}, "
+            f"X Offset {tomo_alignment_fit[0][2]}, "
+            f"Y Amplitude {tomo_alignment_fit[1][0]}, "
+            f"Y Phase {tomo_alignment_fit[1][1]}, "
+            f"Y Offset {tomo_alignment_fit[1][2]}, "
+            f"Y 3rd Order Amplitude {tomo_alignment_fit[1][3]}, "
+            f"Y 3rd Order Phase {tomo_alignment_fit[1][4]} ."
+        )
+
+        if use_vertical_default_values:
+            print(
+                f"Using default values for vertical alignment for setup {setup}. Optional: use_vertical_default_values=False"
+            )
+            if setup == "flomni":
+                tomo_alignment_fit[1][0] = 0
+                tomo_alignment_fit[1][1] = 0
+                tomo_alignment_fit[1][2] = 0
+                tomo_alignment_fit[1][3] = 0
+                tomo_alignment_fit[1][4] = 0
+            elif setup == "omny":
+                tomo_alignment_fit[1][0] = 2.588628
+                tomo_alignment_fit[1][1] = -2.385422
+                tomo_alignment_fit[1][2] = 0
+                tomo_alignment_fit[1][3] = 1.010583
+                tomo_alignment_fit[1][4] = -1.359157
+
+            print("Follwing parameters will be used:")
+            print(
+                f"X Amplitude {tomo_alignment_fit[0][0]}, "
+                f"X Phase {tomo_alignment_fit[0][1]}, "
+                f"X Offset {tomo_alignment_fit[0][2]}, "
+                f"Y Amplitude {tomo_alignment_fit[1][0]}, "
+                f"Y Phase {tomo_alignment_fit[1][1]}, "
+                f"Y Offset {tomo_alignment_fit[1][2]}, "
+                f"Y 3rd Order Amplitude {tomo_alignment_fit[1][3]}, "
+                f"Y 3rd Order Phase {tomo_alignment_fit[1][4]} ."
+            )
+
+        self.client.set_global_var("tomo_alignment_fit", tomo_alignment_fit.tolist())
+        # x amp, phase, offset, y amp, phase, offset, 3rd order amp, 3rd order phase
+        #  0 0    0 1    0 2     1 0    1 1    1 2       1 3           1 4
+
+    def get_alignment_offset(self, angle: float):
+        """
+        Compute the alignment offset for the given angle.
+
+        Args:
+            angle (float): The angle to compute the alignment offset for.
+
+        Returns:
+            tuple: The alignment offset in x, y and z direction.
+        """
+        tomo_alignment_fit = self.client.get_global_var("tomo_alignment_fit")
+        if tomo_alignment_fit is None:
+            print("Not applying any alignment offsets. No tomo alignment fit data available.\n")
+            return (0, 0, 0)
+
+        # x amp, phase, offset, y amp, phase, offset
+        #  0 0    0 1    0 2     1 0    1 1    1 2
+        correction_x = (
+            tomo_alignment_fit[0][0] * np.sin(np.radians(angle) + tomo_alignment_fit[0][1])
+            + tomo_alignment_fit[0][2]
+        )
+        correction_y = (
+            tomo_alignment_fit[1][0] * np.sin(np.radians(angle) + tomo_alignment_fit[1][1])
+            + tomo_alignment_fit[1][2]
+            + tomo_alignment_fit[1][3] * np.sin(3 * np.radians(angle) + tomo_alignment_fit[1][4])
+        )
+        correction_z = tomo_alignment_fit[0][0] * np.sin(
+            np.radians(angle + 90) + tomo_alignment_fit[0][1]
+        )
+
+        print(
+            f"Alignment offset x {correction_x}, y {correction_y}, z {correction_z} for angle"
+            f" {angle}\n"
+        )
+        return (correction_x, correction_y, correction_z)
+
+    def _read_correction_file(self, correction_file: str):
+        with open(correction_file, "r") as f:
+            num_elements = f.readline()
+            int_num_elements = int(num_elements.split(" ")[2])
+            corr_pos = []
+            corr_angle = []
+            for j in range(int_num_elements * 2):
+                line = f.readline()
+                value = line.split(" ")[2]
+                name = line.split(" ")[0].split("[")[0]
+                if name == "corr_pos":
+                    corr_pos.append(float(value))
+                elif name == "corr_angle":
+                    corr_angle.append(float(value))
+        print(
+            f"Loading default mirror correction from file {correction_file} containing {int_num_elements} elements."
+        )
+        # print(corr_pos)
+        return corr_pos, corr_angle
+
+    def read_additional_correction_x(self, correction_file: str):
+        self.corr_pos_x, self.corr_angle_x = self._read_correction_file(correction_file)
+
+    def read_additional_correction_y(self, correction_file: str):
+        self.corr_pos_y, self.corr_angle_y = self._read_correction_file(correction_file)
+
+    def read_additional_correction_y_2(self, correction_file: str):
+        self.corr_pos_y_2, self.corr_angle_y_2 = self._read_correction_file(correction_file)
+
+    def compute_additional_correction_x(self, angle):
+        return self._compute_additional_correction(angle, iteration="x1")
+
+    def compute_additional_correction_y(self, angle):
+        return self._compute_additional_correction(angle, iteration="y1")
+
+    def compute_additional_correction_y_2(self, angle):
+        return self._compute_additional_correction(angle, iteration="y2")
+
+    def _compute_additional_correction(self, angle, iteration="y1"):
+        if iteration == "x1":
+            corr_pos = self.corr_pos_x
+            corr_angle = self.corr_angle_x
+        elif iteration == "y1":
+            corr_pos = self.corr_pos_y
+            corr_angle = self.corr_angle_y
+        elif iteration == "y2":
+            corr_pos = self.corr_pos_y_2
+            corr_angle = self.corr_angle_y_2
+        if not corr_pos:
+            print(f"Not applying any additional correction {iteration}. No data available.\n")
+            return 0
+
+        # find index of closest angle
+        for j, _ in enumerate(corr_pos):
+            newangledelta = np.fabs(corr_angle[j] - angle)
+            if j == 0:
+                angledelta = newangledelta
+                additional_correction_shift = corr_pos[j]
+                continue
+
+            if newangledelta < angledelta:
+                additional_correction_shift = corr_pos[j]
+                angledelta = newangledelta
+
+        if additional_correction_shift == 0 and angle > corr_angle[-1]:
+            additional_correction_shift = corr_pos[-1]
+        print(f"Additional correction shift {iteration}: {additional_correction_shift}")
+        return additional_correction_shift

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -0,0 +1,153 @@
+import time
+import numpy as np
+import sys
+import termios
+import tty
+import fcntl
+import os
+import builtins
+
+from rich import box
+from rich.console import Console
+from rich.table import Table
+
+# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
+
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
+
+
+class OMNYToolsError(Exception):
+    pass
+
+
+class OMNYTools:
+
+    HEADER = "\033[95m"
+    OKBLUE = "\033[94m"
+    OKCYAN = "\033[96m"
+    OKGREEN = "\033[92m"
+    WARNING = "\033[93m"
+    FAIL = "\033[91m"
+    ENDC = "\033[0m"
+    BOLD = "\033[1m"
+    UNDERLINE = "\033[4m"
+
+    def __init__(self, client) -> None:
+        self.client = client
+
+    @staticmethod
+    def _get_user_param_safe(device, var):
+        param = dev[device].user_parameter
+        if not param or param.get(var) is None:
+            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
+        return param.get(var)
+
+    def printgreen(self, string: str):
+        print(self.OKGREEN + string + self.ENDC)
+
+    def printgreenbold(self, string: str):
+        print(self.BOLD + self.OKGREEN + string + self.ENDC)
+
+    def yesno(self, message: str, default="none", autoconfirm=0) -> bool:
+        if autoconfirm and default == "y":
+            self.printgreen(message + " Automatically confirming default: yes")
+            return True
+        elif autoconfirm and default == "n":
+            self.printgreen(message + " Automatically confirming default: no")
+            return False
+        if default == "y":
+            message_ending = " [Y]/n? "
+        elif default == "n":
+            message_ending = " y/[N]? "
+        else:
+            message_ending = " y/n? "
+        while True:
+            user_input = input(self.OKBLUE + message + message_ending + self.ENDC)
+            if (
+                user_input == "Y" or user_input == "y" or user_input == "yes" or user_input == "Yes"
+            ) or (default == "y" and user_input == ""):
+                return True
+            if (
+                user_input == "N" or user_input == "n" or user_input == "no" or user_input == "No"
+            ) or (default == "n" and user_input == ""):
+                return False
+            else:
+                print("Please expicitely confirm y or n.")
+
+    def tweak_cursor(
+        self, dev1, step1: float, dev2="none", step2: float = "0", special_command="none"
+    ):
+        if dev1 not in dev.enabled_devices:
+            print(f"Device 1 {dev} is not in enabled devices.")
+            return
+        if dev2 not in dev.enabled_devices and dev2 != "none":
+            print(f"Device 2 {dev} is not in enabled devices.")
+            return
+        # Save the current terminal settings
+        fd = sys.stdin.fileno()
+        old_term = termios.tcgetattr(fd)
+        try:
+            # Set the terminal to raw mode to capture single key presses
+            tty.setraw(fd)
+            # Set stdin to non-blocking mode
+            old_flags = fcntl.fcntl(fd, fcntl.F_GETFL)
+            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags | os.O_NONBLOCK)
+            print("Tweak Cursor." + self.BOLD + self.OKBLUE + "Press (q) to quit!\r" + self.ENDC)
+            while True:
+                try:
+                    # Read single character input
+                    key = sys.stdin.read(1)
+                    if key == "q":
+                        print("\n\rExiting tweak mode\r")
+                        break
+                    elif key == "\x1b":  # Escape sequences for arrow keys
+                        next1, next2 = sys.stdin.read(2)
+                        if next1 == "[":
+                            if next2 == "A":
+                                # print("up")
+                                if dev2 != "none":
+                                    umvr(dev2, step2)
+                                    if special_command != "none":
+                                        special_command()
+                            elif next2 == "B":
+                                # print(" down")
+                                if dev2 != "none":
+                                    umvr(dev2, -step2)
+                                    if special_command != "none":
+                                        special_command()
+                            elif next2 == "C":
+                                # print("right")
+                                umvr(dev1, step1)
+                                if special_command != "none":
+                                    special_command()
+                            elif next2 == "D":
+                                # print("left")
+                                umvr(dev1, -step1)
+                                if special_command != "none":
+                                    special_command()
+
+                    elif key == "+":
+                        step1 = step1 * 2
+                        if dev2 != "none":
+                            step2 = step2 * 2
+                        print(f"\rDouble step size. New step size: {step1}, {step2}\r")
+                    elif key == "-":
+                        step1 = step1 / 2
+                        if dev2 != "none":
+                            step2 = step2 / 2
+                        print(f"\rHalf step size. New step size: {step1}, {step2}\r")
+                except IOError:
+                    # No input available, keep looping
+                    pass
+
+                # Sleep for a short period to avoid high CPU usage
+                time.sleep(0.02)
+
+        finally:
+            # Restore the terminal to its original state
+            termios.tcsetattr(fd, termios.TCSADRAIN, old_term)
+            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags)

csaxs_bec/bec_ipython_client/plugins/omny/omny_optics_mixin.py

@@ -0,0 +1,384 @@
+import time
+import numpy as np
+
+from rich import box
+from rich.console import Console
+from rich.table import Table
+
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
+
+
+class OMNYError(Exception):
+    pass
+
+
+class OMNYOpticsMixin:
+    @staticmethod
+    def _get_user_param_safe(device, var):
+        param = dev[device].user_parameter
+        if not param or param.get(var) is None:
+            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
+        return param.get(var)
+
+    def ooptics_in(self):
+        self.ofzp_in()
+        # ocs_in
+        self.oosa_in()
+
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_enable()
+
+        self.align.update_frame()
+
+        user_input = input(
+            "Is the direct beam gone on the xray eye? Do you see the cone of the FZP?"
+        )
+        if user_input == "y":
+            printf("Next oeye_out...\n")
+        else:
+            raise OMNYError("Failed to properly move in the Xray optics")
+
+    def _oeyey_mv(self, position):
+        # direction dependent speeds
+        if dev.oeyez.get().readback < position:
+            dev.oeyez.controller.socket_put_confirmed("axspeed[7]=15000")
+        else:
+            dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
+        umv(dev.oeyey, position)
+        dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
+
+    def oeye_out(self):
+        fshclose()
+        if self.OMNYTools.yesno("Did you move in the optics?"):
+            umv(dev.oeyez, -2)
+            self._oeyey_mv(-60.3)
+            # free camera
+            epics_put("XOMNYI-XEYE-ACQ:0", 2)
+        else:
+            raise OMNYError("The optics were not moved in. Please do so prior to eyey_out")
+        self.OMNYTools.printgreen("Oeye is out.")
+
+    def oeye_cam_in(self):
+        if dev.oeyez.get().readback < -80:
+            umv(dev.oeyez, -50)
+
+        if np.fabs(dev.oeyey.get().readback + 4.8) > 0.1:
+            self._oeyey_mv(-4.8)
+
+        if np.fabs(dev.oeyez.get().readback + 2) > 0.1 or np.fabs(dev.oeyex.get().readback) > 0.1:
+            umv(dev.oeyez, -2, dev.oeyex, 0)
+        # if still too close in z -- safety check
+        if np.fabs(dev.oeyez.get().readback + 2) > 0.1:
+            raise OMNYError("The oeye is too close in z for transfer. ERROR! Aborting.")
+        self.OMNYTools.printgreen("Oeye is at cam position.")
+
+    def _oeye_xray_is_in(self) -> bool:
+        omny_oeye_xray_inx = self._get_user_param_safe("oeyex", "xray_in")
+        omny_oeye_xray_iny = self._get_user_param_safe("oeyey", "xray_in")
+        omny_oeye_currentx = dev.oeyex.get().readback
+        omny_oeye_currenty = dev.oeyey.get().readback
+
+        if (
+            np.fabs(omny_oeye_currentx - omny_oeye_xray_inx) < 0.1
+            and np.fabs(omny_oeye_currenty - omny_oeye_xray_iny) < 0.1
+        ):
+            return True
+        else:
+            return False
+
+    def oeye_xray_in(self):
+        if self._oeye_xray_is_in():
+            pass
+        else:
+            # todo
+            #            self._otransfer_gripper_safe_xray_in_operation()
+            # if(!_oshield_is_ST_closed())
+            # {
+            #  printf("The shield of the sample stage is not closed. Aborting.\n")
+            #  exit
+            # }
+            omny_oeye_xray_inx = self._get_user_param_safe("oeyex", "xray_in")
+            omny_oeye_xray_iny = self._get_user_param_safe("oeyey", "xray_in")
+            omny_oeye_xray_inz = self._get_user_param_safe("oeyez", "xray_in")
+
+            self._oeyey_mv(omny_oeye_xray_iny)
+            omny_oeye_currenty = dev.oeyey.get().readback
+            if np.fabs(omny_oeye_currenty - omny_oeye_xray_iny) > 0.1:
+                raise OMNYError("The oeye did not move up.\n")
+            umv(dev.oeyex, omny_oeye_xray_inx, dev.oeyez, omny_oeye_xray_inz)
+            self.OMNYTools.printgreen("Oeye is at X-ray position.")
+
+            # some notes for the vis microscope:
+            # initial position for the vis light microscope
+            # do not open the shield when the microscope is at the vis mic position
+            # found eoeyx -45.13, z -84.9, y 0.64
+            # for a samy position of 2.8 with delta off
+            # the osa position should be in z around 7.4. in x it seems better
+            # around -0.6, where potentially xrays dont pass anymore
+            #
+
+    def _oosa_check_y(self):
+        omny_oosa_currenty = dev.oosay.get().readback
+        if np.fabs(omny_oosa_currenty - 0.9) > 0.05:
+            umv(dev.oosay, 0.9)
+        omny_oosa_currenty = dev.oosay.get().readback
+        if np.fabs(omny_oosa_currenty - 0.9) > 0.05:
+            raise OMNYError("oosay is not around 0.9. Aborting.")
+
+    def _oosa_to_move_corridor(self):
+        self._oosa_check_y()
+        dev.oosax.limits = [-3, 3.7]  # risk collision with shield
+        umv(dev.oosax, -2)
+        dev.oosax.read(cached=False)
+        omny_oosa_currentx = dev.oosax.get().readback
+        if np.fabs(omny_oosa_currentx + 2) > 0.1:
+            raise OMNYError("oosax did not reach target position. Not moving in z.\n")
+
+    def oosa_in(self):
+        self._oosa_check_y()
+        dev.oshield.read(cached=False)
+        omny_oshield_current = dev.oshield.get().readback
+        if omny_oshield_current < 15:
+            self._oshield_ST_close()
+        if self.near_field == False:
+            x_in_pos = self._get_user_param_safe("oosax", "far_field_in")
+            y_in_pos = self._get_user_param_safe("oosay", "far_field_in")
+            z_in_pos = self._get_user_param_safe("oosaz", "far_field_in")
+            print("OSA movement in far-field mode.")
+            dev.oosaz.read(cached=False)
+            omny_oosa_currentz = dev.oosaz.get().readback
+            if omny_oosa_currentz < 6.4:
+                self._oosa_to_move_corridor()
+            dev.oosaz.limits = [6.4, 6.6]
+            umv(dev.oosaz, z_in_pos)
+            umv(dev.oosax, x_in_pos)
+            umv(dev.oosay, y_in_pos)
+            #### For the 30 nm FZP 220 um we use this part
+            #  umv oosaz 6.5
+            #  umv oosax 3.2453
+            #  umv oosay 0.386015
+
+        if self.near_field == True:
+            x_in_pos = self._get_user_param_safe("oosax", "near_field_in")
+            y_in_pos = self._get_user_param_safe("oosay", "near_field_in")
+            z_in_pos = self._get_user_param_safe("oosaz", "near_field_in")
+            print("OSA movement in near-field mode.")
+            dev.oosaz.read(cached=False)
+            omny_oosa_currentz = dev.oosaz.get().readback
+            if omny_oosa_currentz > 0:
+                self._oosa_to_move_corridor()
+            dev.oosaz.limits = [-0.4, -0.6]
+            umv(dev.oosaz, z_in_pos)
+            umv(dev.oosax, x_in_pos)
+            omny_osamy_current = dev.osamy.get().readback
+            if omny_osamy_current < 3.25:
+                umv(dev.oosay, y_in_pos)
+            else:
+                raise OMNYError("Failed to move oosa in. osamy position is too large.")
+
+        self.OMNYTools.printgreen("OSA is in.")
+
+        # todo
+        # _omny_interferometer_align_tracking
+        # rt_feedback_enable
+
+    def oosa_out(self):
+        self._oosa_check_y()
+        dev.oshield.read(cached=False)
+        omny_oshield_current = dev.oshield.get().readback
+        if omny_oshield_current < 15:
+            self._oshield_ST_close()
+        omny_oosaz_current = dev.oosaz.get().readback
+        if self.near_field == False:
+            print("OSA movement in far-field mode.")
+            if omny_oosaz_current < 6.4:
+                self._oosa_to_move_corridor()
+            dev.oosaz.limits = [6.4, 6.6]
+            umv(dev.oosaz, 6.5)
+            umv(dev.oosax, -2)
+        if self.near_field == True:
+            print("OSA movement in near-field mode.")
+            if omny_oosaz_current > 0:
+                self._oosa_to_move_corridor()
+            dev.oosaz.limits = [-0.4, -0.6]
+            umv(dev.oosaz, -0.45)
+            umv(dev.oosax, -2)
+        # todo _omny_interferometer_align_tracking
+
+        self.OMNYTools.printgreen("OSA is out.")
+
+    def oosa_move_out_of_shield(self):
+        # todo: _omnycam_samplestage
+        self._oosa_check_y()
+        self._oosa_to_move_corridor()
+        omny_osamx_current = dev.osamx.get().readback
+        if np.fabs(omny_osamx_current) > 0.2:
+            umv(dev.osamx, 0)
+        omny_oosaz_current = dev.oosaz.get().readback
+        if omny_oosaz_current > 0.1:
+            dev.oosaz.limits = [-0.1, 0.1]
+            umv(dev.oosaz, 0)
+
+        self.OMNYTools.printgreen("OSA is out of shield.")
+
+    def ofzp_out(self):
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_disable()
+        y_out_pos = self._get_user_param_safe("ofzpy", "out")
+        if np.fabs(dev.ofzpy.get().readback - y_out_pos) > 0.02:
+            umv(dev.ofzpy, y_out_pos)
+        self.OMNYTools.printgreen("FZP at out position")
+
+    def ofzp_in(self):
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_disable()
+        x_in_pos = self._get_user_param_safe("ofzpx", "in")
+        y_in_pos = self._get_user_param_safe("ofzpy", "in")
+        if np.fabs(dev.ofzpy.get().readback - y_in_pos) > 0.02:
+            umv(dev.ofzpy, y_in_pos)
+
+        if np.fabs(dev.ofzpx.get().readback - x_in_pos) > 0.02:
+            umv(dev.ofzpx, x_in_pos)
+        self.OMNYTools.printgreen("FZP at in position")
+        # 220 mu FZP at ofzpz 31.8025 for eiger probe (about 2.4 mm propagation after focus)
+        # umv(dev.ofzpy, 0.7944)
+        # if np.fabs(dev.ofzpx.get().readback+0.4317)>0.05:
+        #     umv(dev.ofzpx, -0.4317)
+        # note the 220 fzp also works for near field 6.2 kev by just moving back osa and fzp
+        # ofzpz 24.8 leads to a 9.5 mm propagation distance.
+        # With the 220 mu FZP this gives 100 nm pixel recons
+        # for the oosa macro set near_field=1
+        # 170 mu FZP at 6.2 kev for large beam at ofzpz 31.8025 of about 58 mu diameter
+        # 120 mu FZP at ofzpz 28.1991
+
+        # 250 mu FZP 60 nm at 5.65 keV
+        # ofzpz 29.7 for propagation distance 2.2
+        # umv ofzpx -0.4457
+        # umv ofzpy 0.193630
+
+        # 150 um fzp, 60 nm, ofzpz 33.8 at 8.9 kev for propagation of 1.7 mm after focus
+        # umv ofzpx -0.756678
+        # umv ofzpy 0.193515
+
+        # 250 um 30 nm FZP upper right
+        # small abberrations, seems to give good results in weak objects
+        # ofzpx -0.609240
+        # umv ofzpy 0.118265
+        # 250 um 30 nm FZP lower right very aberated
+        # ofzpx -0.881935
+        # umv ofzpy 0.537050
+
+        # ofzpz 28.4027
+        # 5.30 mm prop at 8.9 keV, 45 nm pixel in near field
+
+        # ofzpz 33.103
+        # 0.6 mm prop at 8.9 kev far field 7 m flight tube at foptz
+
+        # ofzpz 49.4 is reachable just without interferometer swap
+        # which at 6.2 keV and 250 um diam, 30 nm should gives a propagation of 0.8 after focus
+        # and a beam size of 6 microns diamter
+        ###coordinates 30 nm FZP for comparing them
+        # not sure if that is really correct
+        # FZP 1 - FZP 2
+        #   FZP 5
+        # FZP 4 - FZP 1
+
+        # FZP
+        ##upper right
+        # umv ofzpx -0.6154 ofzpy 0.1183
+        # umv ocsx -0.6070 ocsy 0.0540
+
+        # lower right
+        # umv ofzpx -0.8341 ofzpy 0.5683
+        # umv ocsx -0.3880 ocsy -0.3960
+
+        # lower left
+        # umv ofzpx -0.3876 ofzpy 0.7902
+        # umv ocsx -0.8380 ocsy -0.6180
+
+        # upper left
+        # umv ofzpx -0.1678 ofzpy 0.3403
+        # umv ocsx -1.0550 ocsy -0.1680
+
+    def ofzp_info(self, mokev_val=-1, ofzpz_val=-1):
+        print(f"{ofzpz_val}")
+
+        if mokev_val == -1:
+            try:
+                mokev_val = dev.mokev.readback.get()
+            except:
+                print(
+                    "Device mokev does not exist. You can specify the energy in keV as an argument instead."
+                )
+                return
+        if ofzpz_val == -1:
+            ofzpz_val = dev.ofzpz.readback.get()
+        distance = 66 + 2.4 + 31.8025 - ofzpz_val
+        print(
+            f"\nThe sample is in a distance of \033[1m{distance:.1f} mm\033[0m from the 60 nm FZP.\n"
+        )
+        print(f"At the current energy of {mokev_val:.4f} keV we have following options:\n")
+
+        diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
+
+        console = Console()
+        table = Table(title="Outermost zone width \033[1m60 nm\033[0m", box=box.SQUARE)
+        table.add_column("Diameter", justify="center")
+        table.add_column("Focal distance", justify="center")
+        table.add_column("Current beam size", justify="center")
+
+        wavelength = 1.2398e-9 / mokev_val
+
+        for diameter in diameters:
+            outermost_zonewidth = 60e-9
+            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
+            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
+            table.add_row(
+                f"{diameter*1e6:.2f} microns",
+                f"{focal_distance:.2f} mm",
+                f"{beam_size:.2f} microns",
+            )
+
+        console.print(table)
+
+        # 30 nm with additional spacer
+        distance = 53.84 + 0.6 + 33.1 - ofzpz_val
+        print(
+            f"\nThe sample is in a distance of \033[1m{distance:.1f} mm\033[0m from the 30 nm FZP.\n"
+        )
+
+        diameters = [150e-6, 250e-6]
+
+        console = Console()
+        table = Table(title="Outermost zone width \033[1m30 nm\033[0m", box=box.SQUARE)
+        table.add_column("Diameter", justify="center")
+        table.add_column("Focal distance", justify="center")
+        table.add_column("Current beam size", justify="center")
+
+        wavelength = 1.2398e-9 / mokev_val
+
+        for diameter in diameters:
+            outermost_zonewidth = 30e-9
+            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
+            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
+            table.add_row(
+                f"{diameter*1e6:.2f} microns",
+                f"{focal_distance:.2f} mm",
+                f"{beam_size:.2f} microns",
+            )
+
+        console.print(table)
+
+        print(
+            "This function can be called with explicit energy and ofzpz position.\n Example: omny.ffzp_info(mokev_val=6.2, ofzpz_val=33.2)"
+        )
+
+        # from flomni
+        # oosaz_val = dev.oosaz.readback.get()
+
+        # print("\nOSA Information:")
+        # print(f"  Current fosaz {fosaz_val:.1f}")
+        # print(
+        #     f"  The OSA will collide with a normal OMNY pin at fosaz \033[1m{(33-fosaz_val):.1f}\033[0m"
+        # )
+        # print(f"  Remaining space: \033[1m{-fosaz_val+(33-foptz_val):.1f}\033[0m")

csaxs_bec/bec_ipython_client/plugins/omny/omny_rt.py

@@ -0,0 +1,241 @@
+import time
+import numpy as np
+import sys
+import termios
+import tty
+import fcntl
+import os
+
+
+from rich import box
+from rich.console import Console
+from rich.table import Table
+
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
+
+
+class OMNY_rt_clientError(Exception):
+    pass
+
+
+class OMNY_rt_client:
+    def __init__(self):
+        self.mirror_channel = -1
+        self.mirror_amplitutde_increase = 0
+        self.mirror_parameters = {}
+        for j in range(1, 9):
+            self.mirror_parameters[j] = dev.rtx.controller.get_mirror_parameters(j)
+
+    @staticmethod
+    def _get_user_param_safe(device, var):
+        param = dev[device].user_parameter
+        if not param or param.get(var) is None:
+            raise OMNY_rt_clientError(
+                f"Device {device} has no user parameter definition for {var}."
+            )
+        return param.get(var)
+
+    def _omny_interferometer_openloop_steps(self, channel, steps, amplitude):
+        dev.rtx.controller._omny_interferometer_openloop_steps(channel, steps, amplitude)
+
+    def interferometer_tweaking(self):
+        self._tweak_interferometer()
+
+    def _tweak_interferometer(self):
+        self.mirror_channel = -1
+
+        # Save the current terminal settings
+        fd = sys.stdin.fileno()
+        old_term = termios.tcgetattr(fd)
+
+        print("Ready to tweak the interferometer. Press q to quit.")
+        print("The arrows adjust directions.")
+        print("Numbers select the mirror aligner.")
+
+        try:
+            # Set the terminal to raw mode to capture single key presses
+            tty.setraw(fd)
+            # Set stdin to non-blocking mode
+            old_flags = fcntl.fcntl(fd, fcntl.F_GETFL)
+            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags | os.O_NONBLOCK)
+            opt_mirrorname = "none"
+            max = 0
+            while True:
+                try:
+                    # Read single character input
+                    key = sys.stdin.read(1)
+
+                    if key == "q":
+                        self.mirror_amplitutde_increase = 0
+                        self.mirror_channel = -1
+                        print("\n\rExiting tweak mode\r")
+                        break
+                    elif key == "\x1b":  # Escape sequences for arrow keys
+                        next1, next2 = sys.stdin.read(2)
+
+                        if next1 == "[":
+                            printit = True
+                            if next2 == "A":
+                                # print("up")
+                                if self.mirror_channel != -1:
+                                    self._omny_interferometer_openloop_steps(
+                                        4,
+                                        -self.mirror_parameters[self.mirror_channel][
+                                            "opt_steps2_neg"
+                                        ],
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_amplitude2_neg"
+                                        ]
+                                        + self.mirror_amplitutde_increase,
+                                    )
+                            elif next2 == "B":
+                                # print(" down")
+                                if self.mirror_channel != -1:
+                                    self._omny_interferometer_openloop_steps(
+                                        4,
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_steps2_pos"
+                                        ],
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_amplitude2_pos"
+                                        ]
+                                        + self.mirror_amplitutde_increase,
+                                    )
+                            elif next2 == "C":
+                                # print("right")
+                                if self.mirror_channel != -1:
+                                    self._omny_interferometer_openloop_steps(
+                                        3,
+                                        -self.mirror_parameters[self.mirror_channel][
+                                            "opt_steps1_neg"
+                                        ],
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_amplitude1_neg"
+                                        ]
+                                        + self.mirror_amplitutde_increase,
+                                    )
+                            elif next2 == "D":
+                                # print("left")
+                                if self.mirror_channel != -1:
+                                    self._omny_interferometer_openloop_steps(
+                                        3,
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_steps1_pos"
+                                        ],
+                                        self.mirror_parameters[self.mirror_channel][
+                                            "opt_amplitude1_pos"
+                                        ]
+                                        + self.mirror_amplitutde_increase,
+                                    )
+                    elif key.isdigit() and 1 <= int(key) <= 8:
+                        self.mirror_channel = int(key)
+                        opt_mirrorname = self.mirror_parameters[self.mirror_channel][
+                            "opt_mirrorname"
+                        ]
+                        autostop = self.mirror_parameters[self.mirror_channel]["opt_signal_stop"]
+                        averaging_time = self.mirror_parameters[self.mirror_channel][
+                            "opt_averaging_time"
+                        ]
+                        print(
+                            f"\nSelected mirror channel {self.mirror_channel}: {opt_mirrorname}. Autostop {autostop}. Signal averaging time: {averaging_time}\r"
+                        )
+                        if int(key) == 6:
+                            dev.rtx.controller.laser_tracker_on()
+                        dev.rtx.controller._omny_interferometer_switch_channel(self.mirror_channel)
+                        max = 0
+                        printit = True
+                    elif key == "+":
+                        print("\nIncreasing voltage amplitudes by 100.\r")
+                        self.mirror_amplitutde_increase += 100
+                    elif key == "-":
+                        print("\nDecreasing voltage amplitudes by 100.\r")
+                        self.mirror_amplitutde_increase -= 100
+                    elif key == "a":
+                        if self.mirror_channel != -1:
+                            dev.rtx.controller._omny_interferometer_optimize(
+                                mirror_channel=self.mirror_channel, channel=3
+                            )
+                            dev.rtx.controller._omny_interferometer_optimize(
+                                mirror_channel=self.mirror_channel, channel=4
+                            )
+                            dev.rtx.controller._omny_interferometer_optimize(
+                                mirror_channel=self.mirror_channel, channel=3
+                            )
+                            dev.rtx.controller._omny_interferometer_optimize(
+                                mirror_channel=self.mirror_channel, channel=4
+                            )
+                    if self.mirror_channel != -1 and printit:
+                        printit = False
+                        signal = dev.rtx.controller._omny_interferometer_get_signalsample(
+                            self.mirror_parameters[self.mirror_channel]["opt_signalchannel"],
+                            self.mirror_parameters[self.mirror_channel]["opt_averaging_time"],
+                        )
+                        if signal > max:
+                            max = signal
+                        info_str = f"Channel {self.mirror_channel}, {opt_mirrorname}, Current signal: {signal:.0f}"
+                        filling = " " * (50 - len(info_str))
+                        # Calculate the number of filled and unfilled segments
+                        length = 30
+                        percentage = signal / max
+                        filled_length = int(length * percentage)
+                        unfilled_length = length - filled_length
+                        bar = "#" * filled_length + "-" * unfilled_length
+                        print(info_str + filling + "0 " + bar + f" {max:.0f}      (q)uit\r", end="")
+
+                except IOError:
+                    # No input available, keep looping
+                    pass
+
+                # Sleep for a short period to avoid high CPU usage
+                time.sleep(0.02)
+
+        finally:
+            # Restore the terminal to its original state
+            termios.tcsetattr(fd, termios.TCSADRAIN, old_term)
+            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags)
+            dev.rtx.controller._omny_interferometer_switch_alloff()
+            self.mirror_channel = -1
+            self.mirror_amplitutde_increase = 0
+            dev.rtx.controller.show_signal_strength_interferometer()
+
+    def show_signal_strength_interferometer(self):
+        dev.rtx.controller.show_signal_strength_interferometer()
+
+    def omny_interferometer_align_incoupling_angle(self):
+        dev.rtx.controller.omny_interferometer_align_incoupling_angle()
+
+    def interferometer_tweak_otrack(self):
+        self.OMNYTools.tweak_cursor(
+            dev.otrackz,
+            0.1,
+            dev.otracky,
+            0.1,
+            special_command=dev.rtx.controller.laser_tracker_print_intensity_for_otrack_tweaking,
+        )
+
+    def feedback_enable_with_reset(self):
+        dev.rtx.controller.feedback_enable_with_reset()
+
+    def feedback_disable(self):
+        dev.rtx.controller.feedback_disable()
+
+    def feedback_status(self):
+        if dev.rtx.controller.feedback_is_running():
+            print("Feedback is running.")
+        else:
+            print("Feedback is NOT running.")
+
+    def laser_tracker_on(self):
+        dev.rtx.controller.laser_tracker_on()
+
+    def laser_tracker_off(self):
+        dev.rtx.controller.laser_tracker_off()
+
+    def laser_tracker_show_all(self):
+        dev.rtx.controller.laser_tracker_show_all()
+
+    def omny_interferometer_align_tracking(self):
+        dev.rtx.controller.omny_interferometer_align_tracking()
+
+    def laser_tracker_check_and_wait_for_signalstrength(self):
+        dev.rtx.controller.laser_tracker_check_and_wait_for_signalstrength()

csaxs_bec/bec_ipython_client/plugins/omny/x_ray_eye_align.py

@@ -0,0 +1,235 @@
+from __future__ import annotations
+
+import builtins
+import os
+import time
+from typing import TYPE_CHECKING
+
+from bec_lib import bec_logger
+
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen
+
+logger = bec_logger.logger
+# import builtins to avoid linter errors
+bec = builtins.__dict__.get("bec")
+dev = builtins.__dict__.get("dev")
+umv = builtins.__dict__.get("umv")
+umvr = builtins.__dict__.get("umvr")
+
+if TYPE_CHECKING:
+    from bec_ipython_client.plugins.omny import OMNY
+
+
+class XrayEyeAlign:
+    # pixel calibration, multiply to get mm
+    PIXEL_CALIBRATION = 0.2 / 218  # .2 with binning
+
+    def __init__(self, client, omny: OMNY) -> None:
+        self.client = client
+        self.omny = omny
+        self.device_manager = client.device_manager
+        self.scans = client.scans
+        self.alignment_values = {}
+        self.omny.reset_correction()
+        self.omny.reset_tomo_alignment_fit()
+
+    def _reset_init_values(self):
+        self.shift_xy = [0, 0]
+        self._xray_fov_xy = [0, 0]
+
+    def save_frame(self):
+        epics_put("XOMNYI-XEYE-SAVFRAME:0", 1)
+
+    def update_frame(self):
+        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
+        # start live
+        epics_put("XOMNYI-XEYE-ACQ:0", 1)
+        # wait for start live
+        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
+            time.sleep(0.5)
+            print("waiting for live view to start...")
+        fshopen()
+
+        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
+
+        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
+            print("waiting for new frame...")
+            time.sleep(0.5)
+
+        time.sleep(0.5)
+        # stop live view
+        epics_put("XOMNYI-XEYE-ACQ:0", 0)
+        time.sleep(1)
+        # fshclose
+        print("got new frame")
+
+    def tomo_rotate(self, val: float):
+        # pylint: disable=undefined-variable
+        umv(self.device_manager.devices.osamroy, val)
+
+    def get_tomo_angle(self):
+        return self.device_manager.devices.osamroy.readback.get()
+
+    def update_fov(self, k: int):
+        self._xray_fov_xy[0] = max(epics_get(f"XOMNYI-XEYE-XWIDTH_X:{k}"), self._xray_fov_xy[0])
+        self._xray_fov_xy[1] = max(0, self._xray_fov_xy[0])
+
+    @property
+    def movement_buttons_enabled(self):
+        return [epics_get("XOMNYI-XEYE-ENAMVX:0"), epics_get("XOMNYI-XEYE-ENAMVY:0")]
+
+    @movement_buttons_enabled.setter
+    def movement_buttons_enabled(self, enabled: bool):
+        enabled = int(enabled)
+        epics_put("XOMNYI-XEYE-ENAMVX:0", enabled)
+        epics_put("XOMNYI-XEYE-ENAMVY:0", enabled)
+
+    def send_message(self, msg: str):
+        epics_put("XOMNYI-XEYE-MESSAGE:0.DESC", msg)
+
+    def align(self):
+        # reset shift xy and fov params
+        self._reset_init_values()
+
+        self.tomo_rotate(0)
+        epics_put("XOMNYI-XEYE-ANGLE:0", 0)
+
+        self.omny.oeye_xray_in()
+
+        self.omny.feedback_enable_with_reset()
+
+        # disable movement buttons
+        self.movement_buttons_enabled = False
+
+        sample_name = dev.omny_samples.get_sample_name_in_samplestage()
+        epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", sample_name)
+
+        # this makes sure we are in a defined state
+        self.omny.feedback_disable()
+
+        epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
+
+        osamx_in = self.omny.OMNYTools._get_user_param_safe("osamx", "in")
+        umv(dev.osamx, osamx_in - 0.35)
+
+        self.omny.ofzp_in()
+        self.update_frame()
+
+        # enable submit buttons
+        self.movement_buttons_enabled = False
+        epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+        epics_put("XOMNYI-XEYE-STEP:0", 0)
+        self.send_message("Submit center value of FZP.")
+
+        k = 0
+        while True:
+            if epics_get("XOMNYI-XEYE-SUBMIT:0") == 1:
+                val_x = epics_get(f"XOMNYI-XEYE-XVAL_X:{k}") / 2 * self.PIXEL_CALIBRATION  # in mm
+                self.alignment_values[k] = val_x
+                print(f"Clicked position {k}: x {self.alignment_values[k]}")
+                rtx_position = dev.rtx.readback.get() / 1000
+                print(f"Current rtx position {rtx_position}")
+                self.alignment_values[k] -= rtx_position
+                print(f"Corrected position {k}: x {self.alignment_values[k]}")
+
+                if k == 0:  # received center value of FZP
+                    self.send_message("please wait ...")
+                    self.movement_buttons_enabled = False
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
+
+                    self.omny.feedback_disable()
+                    osamx_in = self.omny.OMNYTools._get_user_param_safe("osamx", "in")
+                    umv(dev.osamx, osamx_in)
+
+                    self.omny.ofzp_out()
+
+                    self.update_frame()
+                    epics_put("XOMNYI-XEYE-RECBG:0", 1)
+                    while epics_get("XOMNYI-XEYE-RECBG:0") == 1:
+                        time.sleep(0.5)
+                        print("waiting for background frame...")
+
+                    umv(dev.osamx, osamx_in)
+                    time.sleep(0.5)
+                    self.omny.feedback_enable_with_reset()
+
+                    self.update_frame()
+                    self.send_message("Adjust sample height and submit center")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+                    self.movement_buttons_enabled = True
+
+                elif 1 <= k < 5:  # received sample center value at samroy 0 ... 315
+                    self.send_message("please wait ...")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
+                    self.movement_buttons_enabled = False
+
+                    umv(dev.rtx, 0)
+                    self.tomo_rotate(k * 45)
+                    epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
+                    self.update_frame()
+                    self.send_message("Submit sample center")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+                    epics_put("XOMNYI-XEYE-ENAMVX:0", 1)
+                    self.update_fov(k)
+
+                elif k == 5:  # received sample center value at samroy 270 and done
+                    self.send_message("done...")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
+                    self.movement_buttons_enabled = False
+                    self.update_fov(k)
+                    break
+
+                k += 1
+                epics_put("XOMNYI-XEYE-STEP:0", k)
+
+            _xrayeyalignmvx = epics_get("XOMNYI-XEYE-MVX:0")
+            if _xrayeyalignmvx != 0:
+                umvr(dev.rtx, _xrayeyalignmvx)
+                print(f"Current rtx position {dev.rtx.readback.get() / 1000}")
+                epics_put("XOMNYI-XEYE-MVX:0", 0)
+                if k > 0:
+                    epics_put(f"XOMNYI-XEYE-STAGEPOSX:{k}", dev.rtx.readback.get() / 1000)
+                time.sleep(3)
+                self.update_frame()
+
+            if k < 2:
+                # allow movements, store movements to calculate center
+                _xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
+                if _xrayeyalignmvy != 0:
+                    self.omny.feedback_disable()
+                    umvr(dev.osamy, _xrayeyalignmvy / 1000)
+                    time.sleep(2)
+                    epics_put("XOMNYI-XEYE-MVY:0", 0)
+                    self.omny.feedback_enable_with_reset()
+                    self.update_frame()
+            time.sleep(0.2)
+
+        self.write_output()
+        fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
+        fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
+
+        self.tomo_rotate(0)
+
+        umv(dev.rtx, 0)
+
+        # free camera
+        epics_put("XOMNYI-XEYE-ACQ:0", 2)
+
+        print(
+            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns, fovy"
+            f" = {fovy:.0f} microns"
+        )
+        print("Use the matlab routine to FIT the current alignment...")
+
+        print("Then LOAD ALIGNMENT PARAMETERS by running omny.read_alignment_offset()\n")
+
+    def write_output(self):
+        file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")
+        if not os.path.exists(file):
+            os.makedirs(os.path.dirname(file), exist_ok=True)
+        with open(file, "w") as alignment_values_file:
+            alignment_values_file.write("angle\thorizontal\n")
+            for k in range(1, 6):
+                fovx_offset = self.alignment_values[0] - self.alignment_values[k]
+                print(f"Writing to file new alignment: number {k}, value x {fovx_offset}")
+                alignment_values_file.write(f"{(k-1)*45}\t{fovx_offset*1000}\n")

csaxs_bec/bec_ipython_client/startup/post_startup.py

@@ -62,7 +62,6 @@ bec._beamline_mixin._bl_info_register(OperatorInfo)
 bec._ip.prompts.username = _session_name
 bec._ip.prompts.status = 1
 
-
 # REGISTER BEAMLINE CHECKS
 from bec_lib.bl_conditions import (
     FastOrbitFeedbackCondition,

csaxs_bec/bec_ipython_client/startup/pre_startup.py

@@ -12,3 +12,10 @@ def extend_command_line_args(parser):
     parser.add_argument("--session", help="Session name", type=str, default="cSAXS")
 
     return parser
+
+
+# def get_config() -> ServiceConfig:
+#     """
+#     Create and return the service configuration.
+#     """
+#     return ServiceConfig(redis={"host": "localhost", "port": 6379})

csaxs_bec/deployment/device_server/startup.py

@@ -2,8 +2,8 @@ import os
 
 
 def setup_epics_ca():
-    os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
-    os.environ["EPICS_CA_ADDR_LIST"] = "129.129.122.255 sls-x12sa-cagw.psi.ch:5836"
+    #os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
+    #os.environ["EPICS_CA_ADDR_LIST"] = "129.129.122.255 sls-x12sa-cagw.psi.ch:5836"
     os.environ["PYTHONIOENCODING"] = "latin1"
 
 

csaxs_bec/device_configs/epics_devices_config.yaml

@@ -0,0 +1,50 @@
+ddg_detectors:
+  description: DelayGenerator for detector triggering
+  deviceClass: csaxs_bec.devices.epics.delay_generator_csaxs.DelayGeneratorcSAXS
+  deviceConfig:
+    prefix: 'X12SA-CPCL-DDG3:'
+    ddg_config:
+      delay_burst: 40.e-3
+      delta_width: 0
+      additional_triggers: 0
+      polarity:
+      - 1 # T0 -> DDG MCS
+      - 0 # eiger
+      - 1 # falcon
+      - 1 
+      - 1
+      amplitude: 4.5
+      offset: 0
+      thres_trig_level: 2.5
+      set_high_on_exposure: False
+      set_high_on_stage: False
+  deviceTags:
+  - cSAXS
+  - ddg_detectors
+  onFailure: buffer
+  enabled: true
+  readoutPriority: async
+  softwareTrigger: True
+bpm4i:
+  readoutPriority: monitored
+  deviceClass: ophyd_devices.SimMonitor
+  deviceConfig:
+  deviceTags:
+    - beamline
+  enabled: true
+  readOnly: false
+samx:
+  readoutPriority: baseline
+  deviceClass: ophyd_devices.SimPositioner
+  deviceConfig:
+    delay: 1
+    limits:
+      - -50
+      - 50
+    tolerance: 0.01
+    update_frequency: 400
+  deviceTags:
+    - user motors
+  enabled: true
+  readOnly: false
+  

csaxs_bec/device_configs/jungfrau_joch_test_config.yaml

@@ -0,0 +1,64 @@
+eiger9m:
+  description: Eiger9m HPC area detector 9M with JungfrauJoch backend
+  deviceClass: csaxs_bec.devices.jungfraujoch.eiger_jfj.Eiger9MCSAXS
+  deviceConfig:
+    host: "http://sls-jfjoch-001"
+    port: 8080
+  deviceTags:
+  - cSAXS
+  - eiger9m
+  onFailure: buffer
+  enabled: true
+  readoutPriority: async
+  softwareTrigger: false
+ddg_jfj:
+  description: DelayGenerator for triggering all detectors
+  deviceClass: csaxs_bec.devices.epics.delay_generator_csaxs.DelayGeneratorcSAXS
+  deviceConfig:
+    prefix: 'X12SA-CPCL-DDG3:'
+    # ddg_config:
+    #   delay_burst: 40.e-3
+    #   delta_width: 0
+    #   additional_triggers: 0
+    #   polarity:
+    #   - 1 # T0 -> DDG MCS
+    #   - 0 # eiger
+    #   - 1 # falcon
+    #   - 1 
+    #   - 1
+    #   amplitude: 4.5
+    #   offset: 0
+    #   thres_trig_level: 2.5
+    #   set_high_on_exposure: False
+    #   set_high_on_stage: False
+  deviceTags:
+  - cSAXS
+  - ddg_detectors
+  onFailure: buffer
+  enabled: true
+  readoutPriority: async
+  softwareTrigger: True
+
+# Two test devices from the simulation
+samx:
+  readoutPriority: baseline
+  deviceClass: ophyd_devices.SimPositioner
+  deviceConfig:
+    delay: 1
+    limits:
+      - -50
+      - 50
+    tolerance: 0.01
+    update_frequency: 400
+  deviceTags:
+    - user motors
+  enabled: true
+  readOnly: false
+bpm4i:
+  readoutPriority: monitored
+  deviceClass: ophyd_devices.SimMonitor
+  deviceConfig:
+  deviceTags:
+    - beamline
+  enabled: true
+  readOnly: false

csaxs_bec/device_configs/npoint_template.yaml

@@ -0,0 +1,38 @@
+############################################################
+#################### npoint motors #########################
+############################################################
+
+npx:
+  description: nPoint x axis on the big npoint controller
+  deviceClass: csaxs_bec.devices.npoint.npoint.NPointAxis
+  deviceConfig:
+    axis_Id: A
+    host: "nPoint000003.psi.ch"
+    limits:
+    - -50
+    - 50
+    port: 23
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  deviceTags:
+  - npoint
+npy:
+  description: nPoint y axis on the big npoint controller
+  deviceClass: csaxs_bec.devices.npoint.npoint.NPointAxis
+  deviceConfig:
+    axis_Id: B
+    host: "nPoint000003.psi.ch"
+    limits:
+    - -50
+    - 50
+    port: 23
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  deviceTags:
+  - npoint

csaxs_bec/device_configs/omny_config.yaml

@@ -1,3 +1,107 @@
+# ############################################################
+# #################### IDS Camera ######################
+# ############################################################
+cam200:
+  description: Camera200
+  deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
+  deviceConfig:
+    camera_ID: 200
+    bits_per_pixel: 24
+    channels: 3
+    m_n_colormode: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: async
+
+cam201:
+  description: Camera201
+  deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
+  deviceConfig:
+    camera_ID: 201
+    bits_per_pixel: 24
+    channels: 3
+    m_n_colormode: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: async
+
+cam202:
+  description: Camera202
+  deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
+  deviceConfig:
+    camera_ID: 202
+    bits_per_pixel: 24
+    channels: 3
+    m_n_colormode: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: async
+
+cam203:
+  description: Camera203
+  deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
+  deviceConfig:
+    camera_ID: 203
+    bits_per_pixel: 24
+    channels: 3
+    m_n_colormode: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: async
+
+############################################################
+#################### OMNY RT motors ########################
+############################################################
+  
+rtx:
+  description: OMNY rt
+  deviceClass: csaxs_bec.devices.omny.rt.rt_omny_ophyd.RtOMNYMotor
+  deviceConfig:
+    axis_Id: A
+    host: mpc3217.psi.ch
+    port: 3333
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: on_request
+  userParameter:
+    low_signal: 8500
+    min_signal: 8000
+rty:
+  description: OMNY rt
+  deviceClass: csaxs_bec.devices.omny.rt.rt_omny_ophyd.RtOMNYMotor
+  deviceConfig:
+    axis_Id: B
+    host: mpc3217.psi.ch
+    port: 3333
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: on_request
+  userParameter:
+    tomo_additional_offsety: 0
+rtz:
+  description: OMNY rt
+  deviceClass: csaxs_bec.devices.omny.rt.rt_omny_ophyd.RtOMNYMotor
+  deviceConfig:
+    axis_Id: C
+    host: mpc3217.psi.ch
+    port: 3333
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: on_request
+  
+# ############################################################
+# ##################### OMNY samples #########################
+# ############################################################
 omny_samples:
   description: OMNYSampleStorage
   deviceClass: csaxs_bec.devices.omny.omny_sample_storage.OMNYSampleStorage 
@@ -6,3 +110,501 @@ omny_samples:
   onFailure: buffer
   readOnly: false
   readoutPriority: baseline
+# ############################################################
+# ##################### OMNY vacuum ##########################
+# ############################################################
+# omny_vcs:
+#   description: OMNYVCS
+#   deviceClass: csaxs_bec.devices.omny.omny_vcs.OMNYVCS 
+#   deviceConfig: {}
+#   enabled: true
+#   onFailure: buffer
+#   readOnly: false
+#   readoutPriority: baseline
+# ############################################################
+# ##################### OMNY dewar ###########################
+# ############################################################
+omny_dewar:
+  description: OMNY Dewar Information
+  deviceClass: csaxs_bec.devices.omny.omny_dewar.OMNYDewar
+  deviceConfig: {}
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+
+# ############################################################
+# ##################### OMNY temperatures ####################
+# ############################################################
+omny_temperatures:
+  description: OMNY Temperatures and pressures
+  deviceClass: csaxs_bec.devices.omny.omny_temperatures.OMNYTemperatures
+  deviceConfig: {}
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+
+############################################################
+##################### OMNY Galil motors ####################
+############################################################
+ofzpx:
+  description: FZP X
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: A
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: -0.4317
+ofzpy:
+  description: FZP Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: B
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0.7944
+    out: 0.6377
+ofzpz:
+  description: FZP Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: C
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: -1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+otransx:
+  description: Transfer X
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: D
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+otransy:
+  description: Transfer Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: E
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    up_position: -1.2
+    gripper_sensorvoltagetarget: -2.30
+otransz:
+  description: Transfer Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: F
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8081
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+osamx:
+  description: Sample X
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: A
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: -0.1
+osamz:
+  description: Sample Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: B
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: false
+  onFailure: buffer
+  readOnly: true
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+oosay:
+  description: OSA Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: C
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    near_field_in: 0.531
+    far_field_in: 0.4122
+oosax:
+  description: OSA X
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: D
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: -1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    near_field_in: 3.2044
+    far_field_in: 3.022
+oosaz:
+  description: OSA Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: E
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: -1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    near_field_in: -0.4452
+    far_field_in: 6.5
+oparkz:
+  description: OSA Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: F
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+oshuttleopen:
+  description: Shuttle opener
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: G
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: true
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+oshuttlealign:
+  description: Shuttle aligner
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: H
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8082
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: true
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+osamy:
+  description: Sample Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: A
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+otracky:
+  description: Laser Tracker Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: B
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    start_pos: -4.3431
+osamroy:
+  description: Sample rotation
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: C
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    in: 0
+otrackz:
+  description: Laser Tracker Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: E
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: -1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    start_pos: -0.6948
+oeyex:
+  description: Xray eye X
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: F
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    xray_in: -45.7394
+oeyez:
+  description: Xray eye Z
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: G
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    xray_in: -2
+oeyey:
+  description: Xray eye Y
+  deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor
+  deviceConfig:
+    axis_Id: H
+    host: mpc3217.psi.ch
+    limits:
+      - 0
+      - 0
+    port: 8083
+    sign: 1
+  deviceTags:
+  - omny
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    xray_in: 0.0229
+
+############################################################
+#################### flOMNI Smaract motors #################
+############################################################
+
+ocsx:
+  description: Central Stop X
+  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+  deviceConfig:
+    axis_Id: B
+    host: mpc3217.psi.ch
+    limits:
+    - -2
+    - 2
+    port: 3334
+    sign: -1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    nothing: 0
+ocsy:
+  description: Central Stop Y
+  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+  deviceConfig:
+    axis_Id: A
+    host: mpc3217.psi.ch
+    limits:
+    - -2
+    - 2
+    port: 3334
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    nothing: 0
+oshield:
+  description: Thermal Shield Sample Stage
+  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+  deviceConfig:
+    axis_Id: C
+    host: mpc3217.psi.ch
+    limits:
+    - -14.5
+    - 15.8
+    port: 3334
+    sign: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: baseline
+  userParameter:
+    nothing: 0

csaxs_bec/devices/device_list.md

@@ -3,35 +3,42 @@
 ### csaxs_bec 
 | Device | Documentation | Module |
 | :----- | :------------- | :------ |
-| InsertionDevice | Python wrapper for the CSAXS insertion device control<br><br>    This wrapper provides a positioner interface for the ID control.<br>    is completely custom XBPM with templates directly in the<br>    VME repo. Thus it needs a custom ophyd template as well...<br><br>    WARN: The x and y are not updated by the IOC<br>     | [csaxs_bec.devices.epics.InsertionDevice](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/InsertionDevice.py) |
-| XbpmBase | Python wrapper for X-ray Beam Position Monitors<br><br>    XBPM's consist of a metal-coated diamond window that ejects<br>    photoelectrons from the incoming X-ray beam. These electons<br>    are collected and their current is measured. Effectively<br>    they act as four quadrant photodiodes and are used as BPMs<br>    at the undulator beamlines of SLS.<br><br>    Note: EPICS provided signals are read only, but the user can<br>    change the beam position offset.<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
-| XbpmCsaxsOp | Python wrapper for custom XBPMs in the cSAXS optics hutch<br><br>    This is  completely custom XBPM with templates directly in the<br>    VME repo. Thus it needs a custom ophyd template as well...<br><br>    WARN: The x and y are not updated by the IOC<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
-| XbpmSim | Python wrapper for simulated X-ray Beam Position Monitors<br><br>    XBPM's consist of a metal-coated diamond window that ejects<br>    photoelectrons from the incoming X-ray beam. These electons<br>    are collected and their current is measured. Effectively<br>    they act as four quadrant photodiodes and are used as BPMs<br>    at the undulator beamlines of SLS.<br><br>    Note: EPICS provided signals are read only, but the user can<br>       change the beam position offset.<br><br>    This simulation device extends the basic proxy with a script that<br>    fills signals with quasi-randomized values.<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
-| DelayGeneratorcSAXS | <br>    DG645 delay generator at cSAXS (multiple can be in use depending on the setup)<br><br>    Default values for setting up DDG.<br>    Note: checks of set calues are not (only partially) included, check manual for details on possible settings.<br>    https://www.thinksrs.com/downloads/pdfs/manuals/DG645m.pdf<br><br>    - delay_burst               : (float >=0) Delay between trigger and first pulse in burst mode<br>    - delta_width               : (float >= 0) Add width to fast shutter signal to make sure its open during acquisition<br>    - additional_triggers       : (int) add additional triggers to burst mode (mcs card needs +1 triggers per line)<br>    - polarity                  : (list of 0/1) polarity for different channels<br>    - amplitude                 : (float) amplitude voltage of TTLs<br>    - offset                    : (float) offset for ampltitude<br>    - thres_trig_level          : (float) threshold of trigger amplitude<br><br>    Custom signals for logic in different DDGs during scans (for custom_prepare.prepare_ddg):<br><br>    - set_high_on_exposure      : (bool): if True, then TTL signal should go high during the full acquisition time of a scan.<br>    # TODO trigger_width and fixed_ttl could be combined into single list.<br>    - fixed_ttl_width           : (list of either 1 or 0), one for each channel.<br>    - trigger_width             : (float) if fixed_ttl_width is True, then the width of the TTL pulse is set to this value.<br>    - set_trigger_source        : (TriggerSource) specifies the default trigger source for the DDG.<br>    - premove_trigger           : (bool) if True, then a trigger should be executed before the scan starts (to be implemented in on_pre_scan).<br>    - set_high_on_stage         : (bool) if True, then TTL signal should go high already on stage.<br>     | [csaxs_bec.devices.epics.delay_generator_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/delay_generator_csaxs.py) |
-| Eiger9McSAXS | <br>    Eiger9M detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (FalconSetup)        : Custom detector setup class for cSAXS,<br>                                                  inherits from CustomDetectorMixin<br>        PSIDetectorBase.set_min_readout (float) : Minimum readout time for the detector<br>        Various EpicsPVs for controlling the detector<br>     | [csaxs_bec.devices.epics.eiger9m_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/eiger9m_csaxs.py) |
-| SLSDetectorCam | SLS Detector Camera - Pilatus<br><br>    Base class to map EPICS PVs to ophyd signals.<br>     | [csaxs_bec.devices.epics.pilatus_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/pilatus_csaxs.py) |
-| EpicsDXPFalcon | <br>    DXP parameters for Falcon detector<br><br>    Base class to map EPICS PVs from DXP parameters to ophyd signals.<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
-| FalconHDF5Plugins | <br>    HDF5 parameters for Falcon detector<br><br>    Base class to map EPICS PVs from HDF5 Plugin to ophyd signals.<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
-| FalconcSAXS | <br>    Falcon Sitoro detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (FalconSetup)        : Custom detector setup class for cSAXS,<br>                                                  inherits from CustomDetectorMixin<br>        PSIDetectorBase.set_min_readout (float) : Minimum readout time for the detector<br>        dxp (EpicsDXPFalcon)                    : DXP parameters for Falcon detector<br>        mca (EpicsMCARecord)                    : MCA parameters for Falcon detector<br>        hdf5 (FalconHDF5Plugins)                : HDF5 parameters for Falcon detector<br>        MIN_READOUT (float)                     : Minimum readout time for the detector<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
-| MCScSAXS | MCS card for cSAXS for implementation at cSAXS beamline | [csaxs_bec.devices.epics.mcs_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/mcs_csaxs.py) |
-| SIS38XX | SIS38XX card for access to EPICs PVs at cSAXS beamline | [csaxs_bec.devices.epics.mcs_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/mcs_csaxs.py) |
-| PilatuscSAXS | Pilatus_2 300k detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (Eiger9MSetup)   : Custom detector setup class for cSAXS,<br>                                              inherits from CustomDetectorMixin<br>        cam (SLSDetectorCam)                : Detector camera<br>        MIN_READOUT (float)                 : Minimum readout time for the detector<br><br>     | [csaxs_bec.devices.epics.pilatus_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/pilatus_csaxs.py) |
 | Bpm4i |  | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
+| DelayGeneratorcSAXS | <br>    DG645 delay generator at cSAXS (multiple can be in use depending on the setup)<br><br>    Default values for setting up DDG.<br>    Note: checks of set calues are not (only partially) included, check manual for details on possible settings.<br>    https://www.thinksrs.com/downloads/pdfs/manuals/DG645m.pdf<br><br>    - delay_burst               : (float >=0) Delay between trigger and first pulse in burst mode<br>    - delta_width               : (float >= 0) Add width to fast shutter signal to make sure its open during acquisition<br>    - additional_triggers       : (int) add additional triggers to burst mode (mcs card needs +1 triggers per line)<br>    - polarity                  : (list of 0/1) polarity for different channels<br>    - amplitude                 : (float) amplitude voltage of TTLs<br>    - offset                    : (float) offset for ampltitude<br>    - thres_trig_level          : (float) threshold of trigger amplitude<br><br>    Custom signals for logic in different DDGs during scans (for custom_prepare.prepare_ddg):<br><br>    - set_high_on_exposure      : (bool): if True, then TTL signal should go high during the full acquisition time of a scan.<br>    # TODO trigger_width and fixed_ttl could be combined into single list.<br>    - fixed_ttl_width           : (list of either 1 or 0), one for each channel.<br>    - trigger_width             : (float) if fixed_ttl_width is True, then the width of the TTL pulse is set to this value.<br>    - set_trigger_source        : (TriggerSource) specifies the default trigger source for the DDG.<br>    - premove_trigger           : (bool) if True, then a trigger should be executed before the scan starts (to be implemented in on_pre_scan).<br>    - set_high_on_stage         : (bool) if True, then TTL signal should go high already on stage.<br>     | [csaxs_bec.devices.epics.delay_generator_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/delay_generator_csaxs.py) |
+| Eiger1p5MDetector |  | [csaxs_bec.devices.omny.eiger1p5m](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/eiger1p5m.py) |
+| Eiger9McSAXS | <br>    Eiger9M detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (FalconSetup)        : Custom detector setup class for cSAXS,<br>                                                  inherits from CustomDetectorMixin<br>        PSIDetectorBase.set_min_readout (float) : Minimum readout time for the detector<br>        Various EpicsPVs for controlling the detector<br>     | [csaxs_bec.devices.epics.eiger9m_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/eiger9m_csaxs.py) |
+| EpicsDXPFalcon | <br>    DXP parameters for Falcon detector<br><br>    Base class to map EPICS PVs from DXP parameters to ophyd signals.<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
+| FalconcSAXS | <br>    Falcon Sitoro detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (FalconSetup)        : Custom detector setup class for cSAXS,<br>                                                  inherits from CustomDetectorMixin<br>        PSIDetectorBase.set_min_readout (float) : Minimum readout time for the detector<br>        dxp (EpicsDXPFalcon)                    : DXP parameters for Falcon detector<br>        mca (EpicsMCARecord)                    : MCA parameters for Falcon detector<br>        hdf5 (FalconHDF5Plugins)                : HDF5 parameters for Falcon detector<br>        MIN_READOUT (float)                     : Minimum readout time for the detector<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
+| FalconHDF5Plugins | <br>    HDF5 parameters for Falcon detector<br><br>    Base class to map EPICS PVs from HDF5 Plugin to ophyd signals.<br>     | [csaxs_bec.devices.epics.falcon_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/falcon_csaxs.py) |
+| FlomniGalilMotor |  | [csaxs_bec.devices.omny.galil.fgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/fgalil_ophyd.py) |
+| FlomniSampleStorage |  | [csaxs_bec.devices.omny.flomni_sample_storage](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/flomni_sample_storage.py) |
+| FuprGalilMotor |  | [csaxs_bec.devices.omny.galil.fupr_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/fupr_ophyd.py) |
 | GirderMotorPITCH | Girder YAW pseudo motor | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
 | GirderMotorROLL | Girder ROLL pseudo motor | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
 | GirderMotorX1 | Girder X translation pseudo motor | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
 | GirderMotorY1 | Girder Y translation pseudo motor | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
 | GirderMotorYAW | Girder YAW pseudo motor | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
+| IDSCamera |  | [csaxs_bec.devices.ids_cameras.ids_camera](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/ids_cameras/ids_camera.py) |
+| InsertionDevice | Python wrapper for the CSAXS insertion device control<br><br>    This wrapper provides a positioner interface for the ID control.<br>    is completely custom XBPM with templates directly in the<br>    VME repo. Thus it needs a custom ophyd template as well...<br><br>    WARN: The x and y are not updated by the IOC<br>     | [csaxs_bec.devices.epics.InsertionDevice](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/InsertionDevice.py) |
+| LamniGalilMotor |  | [csaxs_bec.devices.omny.galil.lgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/lgalil_ophyd.py) |
+| MCScSAXS | MCS card for cSAXS for implementation at cSAXS beamline | [csaxs_bec.devices.epics.mcs_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/mcs_csaxs.py) |
+| NPointAxis | <br>    NPointAxis class, which inherits from Device and PositionerBase. This class<br>    represents an axis of an nPoint piezo stage and provides the necessary<br>    functionality to move the axis and read its current position.<br>     | [csaxs_bec.devices.npoint.npoint](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/npoint/npoint.py) |
+| OMNYDewar |  | [csaxs_bec.devices.omny.omny_dewar](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/omny_dewar.py) |
+| OMNYGalilMotor |  | [csaxs_bec.devices.omny.galil.ogalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/ogalil_ophyd.py) |
+| OMNYSampleStorage |  | [csaxs_bec.devices.omny.omny_sample_storage](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/omny_sample_storage.py) |
+| OMNYTemperatures |  | [csaxs_bec.devices.omny.omny_temperatures](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/omny_temperatures.py) |
+| OMNYVCS |  | [csaxs_bec.devices.omny.omny_vcs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/omny_vcs.py) |
+| PilatuscSAXS | Pilatus_2 300k detector for CSAXS<br><br>    Parent class: PSIDetectorBase<br><br>    class attributes:<br>        custom_prepare_cls (Eiger9MSetup)   : Custom detector setup class for cSAXS,<br>                                              inherits from CustomDetectorMixin<br>        cam (SLSDetectorCam)                : Detector camera<br>        MIN_READOUT (float)                 : Minimum readout time for the detector<br><br>     | [csaxs_bec.devices.epics.pilatus_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/pilatus_csaxs.py) |
 | PmDetectorRotation | Detector rotation pseudo motor<br><br>    Small wrapper to convert detector pusher position to rotation angle.<br>     | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
 | PmMonoBender | Monochromator bender<br><br>    Small wrapper to combine the four monochromator bender motors.<br>     | [csaxs_bec.devices.epics.specMotors](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/specMotors.py) |
-| Xeye |  | [csaxs_bec.devices.sls_devices.cSAXS.xeye](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/sls_devices/cSAXS/xeye.py) |
-| SmaractMotor |  | [csaxs_bec.devices.smaract.smaract_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/smaract/smaract_ophyd.py) |
-| Eiger1p5MDetector |  | [csaxs_bec.devices.omny.eiger1p5m](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/eiger1p5m.py) |
-| FlomniSampleStorage |  | [csaxs_bec.devices.omny.flomni_sample_storage](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/flomni_sample_storage.py) |
-| OMNYSampleStorage |  | [csaxs_bec.devices.omny.omny_sample_storage](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/omny_sample_storage.py) |
-| FlomniGalilMotor |  | [csaxs_bec.devices.omny.galil.fgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/fgalil_ophyd.py) |
-| FuprGalilMotor |  | [csaxs_bec.devices.omny.galil.fupr_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/fupr_ophyd.py) |
-| LamniGalilMotor |  | [csaxs_bec.devices.omny.galil.lgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/lgalil_ophyd.py) |
-| SGalilMotor |  "SGalil Motors at cSAXS have a<br>    DC motor (y axis - vertical) - implemented as C<br>    and a step motor (x-axis horizontal) - implemented as E<br>    that require different communication for control<br>     | [csaxs_bec.devices.omny.galil.sgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/sgalil_ophyd.py) |
 | RtFlomniMotor |  | [csaxs_bec.devices.omny.rt.rt_flomni_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py) |
 | RtLamniMotor |  | [csaxs_bec.devices.omny.rt.rt_lamni_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/rt/rt_lamni_ophyd.py) |
+| RtOMNYMotor |  | [csaxs_bec.devices.omny.rt.rt_omny_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/rt/rt_omny_ophyd.py) |
+| SGalilMotor |  "SGalil Motors at cSAXS have a<br>    DC motor (y axis - vertical) - implemented as C<br>    and a step motor (x-axis horizontal) - implemented as E<br>    that require different communication for control<br>     | [csaxs_bec.devices.omny.galil.sgalil_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/omny/galil/sgalil_ophyd.py) |
+| SIS38XX | SIS38XX card for access to EPICs PVs at cSAXS beamline | [csaxs_bec.devices.epics.mcs_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/mcs_csaxs.py) |
+| SLSDetectorCam | SLS Detector Camera - Pilatus<br><br>    Base class to map EPICS PVs to ophyd signals.<br>     | [csaxs_bec.devices.epics.pilatus_csaxs](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/pilatus_csaxs.py) |
+| SmaractMotor |  | [csaxs_bec.devices.smaract.smaract_ophyd](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/smaract/smaract_ophyd.py) |
+| XbpmBase | Python wrapper for X-ray Beam Position Monitors<br><br>    XBPM's consist of a metal-coated diamond window that ejects<br>    photoelectrons from the incoming X-ray beam. These electons<br>    are collected and their current is measured. Effectively<br>    they act as four quadrant photodiodes and are used as BPMs<br>    at the undulator beamlines of SLS.<br><br>    Note: EPICS provided signals are read only, but the user can<br>    change the beam position offset.<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
+| XbpmCsaxsOp | Python wrapper for custom XBPMs in the cSAXS optics hutch<br><br>    This is  completely custom XBPM with templates directly in the<br>    VME repo. Thus it needs a custom ophyd template as well...<br><br>    WARN: The x and y are not updated by the IOC<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
+| XbpmSim | Python wrapper for simulated X-ray Beam Position Monitors<br><br>    XBPM's consist of a metal-coated diamond window that ejects<br>    photoelectrons from the incoming X-ray beam. These electons<br>    are collected and their current is measured. Effectively<br>    they act as four quadrant photodiodes and are used as BPMs<br>    at the undulator beamlines of SLS.<br><br>    Note: EPICS provided signals are read only, but the user can<br>       change the beam position offset.<br><br>    This simulation device extends the basic proxy with a script that<br>    fills signals with quasi-randomized values.<br>     | [csaxs_bec.devices.epics.XbpmBase](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/epics/XbpmBase.py) |
+| Xeye |  | [csaxs_bec.devices.sls_devices.cSAXS.xeye](https://gitlab.psi.ch/bec/csaxs_bec/-/blob/main/csaxs_bec/devices/sls_devices/cSAXS/xeye.py) |

csaxs_bec/devices/epics/eiger9m_csaxs.py

@@ -5,8 +5,6 @@ import time
 from typing import Any
 
 import numpy as np
-from bec_lib import messages
-from bec_lib.endpoints import MessageEndpoints
 from bec_lib.logger import bec_logger
 from ophyd import ADComponent as ADCpt
 from ophyd import Device, EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
@@ -42,6 +40,17 @@ class Eiger9MSetup(CustomDetectorMixin):
         self.std_client = None
         self._lock = threading.RLock()
 
+    def on_init(self) -> None:
+        """Initialize the detector"""
+        self.initialize_default_parameter()
+        self.initialize_detector()
+        self.initialize_detector_backend()
+
+    def initialize_detector(self) -> None:
+        """Initialize detector"""
+        self.stop_detector()
+        self.parent.cam.trigger_mode.put(TriggerSource.GATING)
+
     def initialize_default_parameter(self) -> None:
         """Set default parameters for Eiger9M detector"""
         self.update_readout_time()
@@ -55,29 +64,19 @@ class Eiger9MSetup(CustomDetectorMixin):
         )
         self.parent.readout_time = max(readout_time, self.parent.MIN_READOUT)
 
-    def initialize_detector(self) -> None:
-        """Initialize detector"""
-        # Stops the detector
-        self.stop_detector()
-        # Sets the trigger source to GATING
-        self.parent.set_trigger(TriggerSource.GATING)
-
     def initialize_detector_backend(self) -> None:
         """Initialize detector backend"""
 
-        # Std client
         self.std_client = StdDaqClient(url_base=self.std_rest_server_url)
-
-        # Stop writer
         self.std_client.stop_writer()
-
-        # Change e-account
         eacc = self.parent.scaninfo.username
         self.update_std_cfg("writer_user_id", int(eacc.strip(" e")))
 
         signal_conditions = [(lambda: self.std_client.get_status()["state"], "READY")]
         if not self.wait_for_signals(
-            signal_conditions=signal_conditions, timeout=self.parent.timeout, all_signals=True
+            signal_conditions=signal_conditions,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS,
+            all_signals=True,
         ):
             raise EigerTimeoutError(
                 f"Std client not in READY state, returns: {self.std_client.get_status()}"
@@ -98,7 +97,6 @@ class Eiger9MSetup(CustomDetectorMixin):
 
         """
 
-        # Load config from client and check old value
         cfg = self.std_client.get_config()
         old_value = cfg.get(cfg_key)
         if old_value is None:
@@ -111,19 +109,112 @@ class Eiger9MSetup(CustomDetectorMixin):
                 f" {type(old_value)}:{old_value}"
             )
 
-        # Update config with new value and send back to client
         cfg.update({cfg_key: value})
         logger.debug(cfg)
         self.std_client.set_config(cfg)
         logger.debug(f"Updated std_daq config for key {cfg_key} from {old_value} to {value}")
 
+    def on_stage(self) -> None:
+        """Prepare the detector for scan"""
+        self.prepare_detector()
+        self.prepare_data_backend()
+        self.publish_file_location(done=False, successful=False)
+        self.arm_acquisition()
+
+    def prepare_detector(self) -> None:
+        """Prepare detector for scan"""
+        self.set_detector_threshold()
+        self.set_acquisition_params()
+        self.parent.cam.trigger_mode.put(TriggerSource.GATING)
+
+    def set_detector_threshold(self) -> None:
+        """
+        Set the detector threshold
+
+        The function sets the detector threshold automatically to 1/2 of the beam energy.
+        """
+        mokev = self.parent.device_manager.devices.mokev.obj.read()[
+            self.parent.device_manager.devices.mokev.name
+        ]["value"]
+        factor = 1
+        unit = getattr(self.parent.cam.threshold_energy, "units", None)
+
+        if unit is not None and unit == "eV":
+            factor = 1000
+        setpoint = int(mokev * factor)
+        energy = self.parent.cam.beam_energy.read()[self.parent.cam.beam_energy.name]["value"]
+
+        if setpoint != energy:
+            self.parent.cam.beam_energy.set(setpoint)
+
+        threshold = self.parent.cam.threshold_energy.read()[self.parent.cam.threshold_energy.name][
+            "value"
+        ]
+        if not np.isclose(setpoint / 2, threshold, rtol=0.05):
+            self.parent.cam.threshold_energy.set(setpoint / 2)
+
+    def set_acquisition_params(self) -> None:
+        """Set acquisition parameters for the detector"""
+        self.parent.cam.num_images.put(
+            int(self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger)
+        )
+        self.parent.cam.num_frames.put(1)
+        self.update_readout_time()
+
+    def prepare_data_backend(self) -> None:
+        """Prepare the data backend for the scan"""
+        self.parent.filepath.set(
+            self.parent.filewriter.compile_full_filename(f"{self.parent.name}.h5")
+        ).wait()
+        self.filepath_exists(self.parent.filepath.get())
+        self.stop_detector_backend()
+        try:
+            self.std_client.start_writer_async(
+                {
+                    "output_file": self.parent.filepath.get(),
+                    "n_images": int(
+                        self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger
+                    ),
+                }
+            )
+        except Exception as exc:
+            time.sleep(5)
+            if self.std_client.get_status()["state"] == "READY":
+                raise EigerTimeoutError(f"Timeout of start_writer_async with {exc}") from exc
+
+        signal_conditions = [
+            (lambda: self.std_client.get_status()["acquisition"]["state"], "WAITING_IMAGES")
+        ]
+        if not self.wait_for_signals(
+            signal_conditions=signal_conditions,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS,
+            check_stopped=False,
+            all_signals=True,
+        ):
+            raise EigerTimeoutError(
+                "Timeout of 5s reached for std_daq start_writer_async with std_daq client status"
+                f" {self.std_client.get_status()}"
+            )
+
+    def on_unstage(self) -> None:
+        """Unstage the detector"""
+        pass
+
+    def on_complete(self) -> None:
+        """Complete the detector"""
+        self.finished(timeout=self.parent.TIMEOUT_FOR_SIGNALS)
+        self.publish_file_location(done=True, successful=True)
+
+    def on_stop(self) -> None:
+        """Stop the detector"""
+        self.stop_detector()
+        self.stop_detector_backend()
+
     def stop_detector(self) -> None:
         """Stop the detector"""
 
         # Stop detector
         self.parent.cam.acquire.put(0)
-
-        # Check if detector returned in idle state
         signal_conditions = [
             (
                 lambda: self.parent.cam.detector_state.read()[self.parent.cam.detector_state.name][
@@ -135,7 +226,7 @@ class Eiger9MSetup(CustomDetectorMixin):
 
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout - self.parent.timeout // 2,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS - self.parent.TIMEOUT_FOR_SIGNALS // 2,
             check_stopped=True,
             all_signals=False,
         ):
@@ -143,7 +234,7 @@ class Eiger9MSetup(CustomDetectorMixin):
             self.parent.cam.acquire.put(0)
             if not self.wait_for_signals(
                 signal_conditions=signal_conditions,
-                timeout=self.parent.timeout - self.parent.timeout // 2,
+                timeout=self.parent.TIMEOUT_FOR_SIGNALS - self.parent.TIMEOUT_FOR_SIGNALS // 2,
                 check_stopped=True,
                 all_signals=False,
             ):
@@ -155,97 +246,12 @@ class Eiger9MSetup(CustomDetectorMixin):
         """Close file writer"""
         self.std_client.stop_writer()
 
-    def prepare_detector(self) -> None:
-        """Prepare detector for scan"""
-        self.set_detector_threshold()
-        self.set_acquisition_params()
-        self.parent.set_trigger(TriggerSource.GATING)
-
-    def set_detector_threshold(self) -> None:
-        """
-        Set the detector threshold
-
-        The function sets the detector threshold automatically to 1/2 of the beam energy.
-        """
-
-        # get current beam energy from device manageer
-        mokev = self.parent.device_manager.devices.mokev.obj.read()[
-            self.parent.device_manager.devices.mokev.name
-        ]["value"]
-        factor = 1
-
-        # Check if energies are eV or keV, assume keV as the default
-        unit = getattr(self.parent.cam.threshold_energy, "units", None)
-        if unit is not None and unit == "eV":
-            factor = 1000
-
-        # set energy on detector
-        setpoint = int(mokev * factor)
-        energy = self.parent.cam.beam_energy.read()[self.parent.cam.beam_energy.name]["value"]
-        if setpoint != energy:
-            self.parent.cam.beam_energy.set(setpoint)
-
-        # set threshold on detector
-        threshold = self.parent.cam.threshold_energy.read()[self.parent.cam.threshold_energy.name][
-            "value"
-        ]
-        if not np.isclose(setpoint / 2, threshold, rtol=0.05):
-            self.parent.cam.threshold_energy.set(setpoint / 2)
-
-    def set_acquisition_params(self) -> None:
-        """Set acquisition parameters for the detector"""
-
-        # Set number of images and frames (frames is for internal burst of detector)
-        self.parent.cam.num_images.put(
-            int(self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger)
-        )
-        self.parent.cam.num_frames.put(1)
-
-        # Update the readout time of the detector
-        self.update_readout_time()
-
-    def prepare_data_backend(self) -> None:
-        """Prepare the data backend for the scan"""
-        self.parent.filepath = self.parent.filewriter.compile_full_filename(
-            f"{self.parent.name}.h5"
-        )
-        self.filepath_exists(self.parent.filepath)
-        self.stop_detector_backend()
-        try:
-            self.std_client.start_writer_async(
-                {
-                    "output_file": self.parent.filepath,
-                    "n_images": int(
-                        self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger
-                    ),
-                }
-            )
-        except Exception as exc:
-            time.sleep(5)
-            if self.std_client.get_status()["state"] == "READY":
-                raise EigerTimeoutError(f"Timeout of start_writer_async with {exc}") from exc
-
-        # Check status of std_daq
-        signal_conditions = [
-            (lambda: self.std_client.get_status()["acquisition"]["state"], "WAITING_IMAGES")
-        ]
-        if not self.wait_for_signals(
-            signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
-            check_stopped=False,
-            all_signals=True,
-        ):
-            raise EigerTimeoutError(
-                "Timeout of 5s reached for std_daq start_writer_async with std_daq client status"
-                f" {self.std_client.get_status()}"
-            )
-
     def filepath_exists(self, filepath: str) -> None:
         """Check if filepath exists"""
         signal_conditions = [(lambda: os.path.exists(os.path.dirname(filepath)), True)]
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS,
             check_stopped=False,
             all_signals=True,
         ):
@@ -264,7 +270,7 @@ class Eiger9MSetup(CustomDetectorMixin):
         ]
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS,
             check_stopped=True,
             all_signals=False,
         ):
@@ -272,43 +278,7 @@ class Eiger9MSetup(CustomDetectorMixin):
                 f"Failed to arm the acquisition. Detector state {signal_conditions[0][0]}"
             )
 
-    def check_scan_id(self) -> None:
-        """Checks if scan_id has changed and stops the scan if it has"""
-        old_scan_id = self.parent.scaninfo.scan_id
-        self.parent.scaninfo.load_scan_metadata()
-        if self.parent.scaninfo.scan_id != old_scan_id:
-            self.parent.stopped = True
-
-    def publish_file_location(self, done: bool = False, successful: bool = None) -> None:
-        """
-        Publish the filepath to REDIS.
-
-        We publish two events here:
-        - file_event: event for the filewriter
-        - public_file: event for any secondary service (e.g. radial integ code)
-
-        Args:
-            done (bool): True if scan is finished
-            successful (bool): True if scan was successful
-        """
-        pipe = self.parent.connector.pipeline()
-        if successful is None:
-            msg = messages.FileMessage(file_path=self.parent.filepath, done=done)
-        else:
-            msg = messages.FileMessage(
-                file_path=self.parent.filepath, done=done, successful=successful
-            )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.public_file(self.parent.scaninfo.scan_id, self.parent.name),
-            msg,
-            pipe=pipe,
-        )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.file_event(self.parent.name), msg, pipe=pipe
-        )
-        pipe.execute()
-
-    def finished(self):
+    def finished(self, timeout: int = 5) -> None:
         """Check if acquisition is finished."""
         with self._lock:
             signal_conditions = [
@@ -326,7 +296,7 @@ class Eiger9MSetup(CustomDetectorMixin):
             ]
             if not self.wait_for_signals(
                 signal_conditions=signal_conditions,
-                timeout=self.parent.timeout,
+                timeout=timeout,
                 check_stopped=True,
                 all_signals=True,
             ):
@@ -357,7 +327,7 @@ class SLSDetectorCam(Device):
     detector_state = ADCpt(EpicsSignalRO, "DetectorState_RBV")
 
 
-class TriggerSource(enum.IntEnum):
+class TriggerSource(int, enum.Enum):
     """Trigger signals for Eiger9M detector"""
 
     AUTO = 0
@@ -366,7 +336,7 @@ class TriggerSource(enum.IntEnum):
     BURST_TRIGGER = 3
 
 
-class DetectorState(enum.IntEnum):
+class DetectorState(int, enum.Enum):
     """Detector states for Eiger9M detector"""
 
     IDLE = 0
@@ -396,37 +366,16 @@ class Eiger9McSAXS(PSIDetectorBase):
     """
 
     # Specify which functions are revealed to the user in BEC client
-    USER_ACCESS = ["describe"]
+    USER_ACCESS = []
 
     # specify Setup class
     custom_prepare_cls = Eiger9MSetup
-    # specify minimum readout time for detector
+    # specify minimum readout time for detector and timeout for checks after unstage
     MIN_READOUT = 3e-3
+    TIMEOUT_FOR_SIGNALS = 5
     # specify class attributes
     cam = ADCpt(SLSDetectorCam, "cam1:")
 
-    def set_trigger(self, trigger_source: TriggerSource) -> None:
-        """Set trigger source for the detector.
-        Check the TriggerSource enum for possible values
-
-        Args:
-            trigger_source (TriggerSource): Trigger source for the detector
-
-        """
-        value = trigger_source
-        self.cam.trigger_mode.put(value)
-
-    def stage(self) -> list[object]:
-        """
-        Add functionality to stage, and arm the detector
-
-        Additional call to:
-        - custom_prepare.arm_acquisition()
-        """
-        rtr = super().stage()
-        self.custom_prepare.arm_acquisition()
-        return rtr
-
 
 if __name__ == "__main__":
     eiger = Eiger9McSAXS(name="eiger", prefix="X12SA-ES-EIGER9M:", sim_mode=True)

csaxs_bec/devices/epics/falcon_csaxs.py

@@ -1,8 +1,7 @@
 import enum
 import os
+import threading
 
-from bec_lib import messages
-from bec_lib.endpoints import MessageEndpoints
 from bec_lib.logger import bec_logger
 from ophyd import Component as Cpt
 from ophyd import Device, EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
@@ -99,6 +98,16 @@ class FalconSetup(CustomDetectorMixin):
 
     """
 
+    def __init__(self, *args, parent: Device = None, **kwargs) -> None:
+        super().__init__(*args, parent=parent, **kwargs)
+        self._lock = threading.RLock()
+
+    def on_init(self) -> None:
+        """Initialize Falcon detector"""
+        self.initialize_default_parameter()
+        self.initialize_detector()
+        self.initialize_detector_backend()
+
     def initialize_default_parameter(self) -> None:
         """
         Set default parameters for Falcon
@@ -124,7 +133,7 @@ class FalconSetup(CustomDetectorMixin):
         """Initialize Falcon detector"""
         self.stop_detector()
         self.stop_detector_backend()
-        self.parent.set_trigger(
+        self.set_trigger(
             mapping_mode=MappingSource.MAPPING, trigger_source=TriggerSource.GATE, ignore_gate=0
         )
         # 1 Realtime
@@ -136,30 +145,6 @@ class FalconSetup(CustomDetectorMixin):
         # Sets the number of pixels/spectra in the buffer
         self.parent.pixels_per_buffer.put(self.parent.value_pixel_per_buffer)
 
-    def stop_detector(self) -> None:
-        """Stops detector"""
-
-        self.parent.stop_all.put(1)
-        self.parent.erase_all.put(1)
-
-        signal_conditions = [
-            (lambda: self.parent.state.read()[self.parent.state.name]["value"], DetectorState.DONE)
-        ]
-
-        if not self.wait_for_signals(
-            signal_conditions=signal_conditions,
-            timeout=self.parent.timeout - self.parent.timeout // 2,
-            all_signals=False,
-        ):
-            # Retry stop detector and wait for remaining time
-            raise FalconTimeoutError(
-                f"Failed to stop detector, timeout with state {signal_conditions[0][0]}"
-            )
-
-    def stop_detector_backend(self) -> None:
-        """Stop the detector backend"""
-        self.parent.hdf5.capture.put(0)
-
     def initialize_detector_backend(self) -> None:
         """Initialize the detector backend for Falcon."""
         self.parent.hdf5.enable.put(1)
@@ -173,9 +158,16 @@ class FalconSetup(CustomDetectorMixin):
         # Segmentation into Spectra within EPICS, 1 is activate, 0 is deactivate
         self.parent.nd_array_mode.put(1)
 
+    def on_stage(self) -> None:
+        """Prepare detector and backend for acquisition"""
+        self.prepare_detector()
+        self.prepare_data_backend()
+        self.publish_file_location(done=False, successful=False)
+        self.arm_acquisition()
+
     def prepare_detector(self) -> None:
         """Prepare detector for acquisition"""
-        self.parent.set_trigger(
+        self.set_trigger(
             mapping_mode=MappingSource.MAPPING, trigger_source=TriggerSource.GATE, ignore_gate=0
         )
         self.parent.preset_real.put(self.parent.scaninfo.exp_time)
@@ -185,10 +177,10 @@ class FalconSetup(CustomDetectorMixin):
 
     def prepare_data_backend(self) -> None:
         """Prepare data backend for acquisition"""
-        self.parent.filepath = self.parent.filewriter.compile_full_filename(
-            f"{self.parent.name}.h5"
-        )
-        file_path, file_name = os.path.split(self.parent.filepath)
+        self.parent.filepath.set(
+            self.parent.filewriter.compile_full_filename(f"{self.parent.name}.h5")
+        ).wait()
+        file_path, file_name = os.path.split(self.parent.filepath.get())
         self.parent.hdf5.file_path.put(file_path)
         self.parent.hdf5.file_name.put(file_name)
         self.parent.hdf5.file_template.put("%s%s")
@@ -212,7 +204,7 @@ class FalconSetup(CustomDetectorMixin):
         ]
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS,
             check_stopped=True,
             all_signals=False,
         ):
@@ -220,65 +212,86 @@ class FalconSetup(CustomDetectorMixin):
                 f"Failed to arm the acquisition. Detector state {signal_conditions[0][0]}"
             )
 
-    def check_scan_id(self) -> None:
-        """Checks if scan_id has changed and stops the scan if it has"""
-        old_scan_id = self.parent.scaninfo.scan_id
-        self.parent.scaninfo.load_scan_metadata()
-        if self.parent.scaninfo.scan_id != old_scan_id:
-            self.parent.stopped = True
+    def on_unstage(self) -> None:
+        """Unstage detector and backend"""
+        pass
 
-    def publish_file_location(self, done: bool = False, successful: bool = None) -> None:
-        """
-        Publish the filepath to REDIS.
+    def on_complete(self) -> None:
+        """Complete detector and backend"""
+        self.finished(timeout=self.parent.TIMEOUT_FOR_SIGNALS)
+        self.publish_file_location(done=True, successful=True)
 
-        We publish two events here:
-        - file_event: event for the filewriter
-        - public_file: event for any secondary service (e.g. radial integ code)
-
-        Args:
-            done (bool): True if scan is finished
-            successful (bool): True if scan was successful
-        """
-        pipe = self.parent.connector.pipeline()
-        if successful is None:
-            msg = messages.FileMessage(file_path=self.parent.filepath, done=done)
-        else:
-            msg = messages.FileMessage(
-                file_path=self.parent.filepath, done=done, successful=successful
-            )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.public_file(self.parent.scaninfo.scan_id, self.parent.name),
-            msg,
-            pipe=pipe,
-        )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.file_event(self.parent.name), msg, pipe=pipe
-        )
-        pipe.execute()
-
-    def finished(self) -> None:
-        """Check if scan finished succesfully"""
-        total_frames = int(
-            self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger
-        )
-        signal_conditions = [
-            (self.parent.dxp.current_pixel.get, total_frames),
-            (self.parent.hdf5.array_counter.get, total_frames),
-        ]
-        if not self.wait_for_signals(
-            signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
-            check_stopped=True,
-            all_signals=True,
-        ):
-            logger.debug(
-                f"Falcon missed a trigger: received trigger {self.parent.dxp.current_pixel.get()},"
-                f" send data {self.parent.hdf5.array_counter.get()} from total_frames"
-                f" {total_frames}"
-            )
+    def on_stop(self) -> None:
+        """Stop detector and backend"""
         self.stop_detector()
         self.stop_detector_backend()
 
+    def stop_detector(self) -> None:
+        """Stops detector"""
+
+        self.parent.stop_all.put(1)
+        self.parent.erase_all.put(1)
+
+        signal_conditions = [
+            (lambda: self.parent.state.read()[self.parent.state.name]["value"], DetectorState.DONE)
+        ]
+
+        if not self.wait_for_signals(
+            signal_conditions=signal_conditions,
+            timeout=self.parent.TIMEOUT_FOR_SIGNALS - self.parent.TIMEOUT_FOR_SIGNALS // 2,
+            all_signals=False,
+        ):
+            # Retry stop detector and wait for remaining time
+            raise FalconTimeoutError(
+                f"Failed to stop detector, timeout with state {signal_conditions[0][0]}"
+            )
+
+    def stop_detector_backend(self) -> None:
+        """Stop the detector backend"""
+        self.parent.hdf5.capture.put(0)
+
+    def finished(self, timeout: int = 5) -> None:
+        """Check if scan finished succesfully"""
+        with self._lock:
+            total_frames = int(
+                self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger
+            )
+            signal_conditions = [
+                (self.parent.dxp.current_pixel.get, total_frames),
+                (self.parent.hdf5.array_counter.get, total_frames),
+            ]
+            if not self.wait_for_signals(
+                signal_conditions=signal_conditions,
+                timeout=timeout,
+                check_stopped=True,
+                all_signals=True,
+            ):
+                logger.debug(
+                    f"Falcon missed a trigger: received trigger {self.parent.dxp.current_pixel.get()},"
+                    f" send data {self.parent.hdf5.array_counter.get()} from total_frames"
+                    f" {total_frames}"
+                )
+            self.stop_detector()
+            self.stop_detector_backend()
+
+    def set_trigger(
+        self, mapping_mode: MappingSource, trigger_source: TriggerSource, ignore_gate: int = 0
+    ) -> None:
+        """
+        Set triggering mode for detector
+
+        Args:
+            mapping_mode (MappingSource): Mapping mode for the detector
+            trigger_source (TriggerSource): Trigger source for the detector, pixel_advance_signal
+            ignore_gate (int): Ignore gate from TTL signal; defaults to 0
+
+        """
+        mapping = int(mapping_mode)
+        trigger = trigger_source
+        self.parent.collect_mode.put(mapping)
+        self.parent.pixel_advance_mode.put(trigger)
+        self.parent.ignore_gate.put(ignore_gate)
+
 
 class FalconcSAXS(PSIDetectorBase):
     """
@@ -303,6 +316,7 @@ class FalconcSAXS(PSIDetectorBase):
     custom_prepare_cls = FalconSetup
     # specify minimum readout time for detector
     MIN_READOUT = 3e-3
+    TIMEOUT_FOR_SIGNALS = 5
 
     # specify class attributes
     dxp = Cpt(EpicsDXPFalcon, "dxp1:")
@@ -330,30 +344,6 @@ class FalconcSAXS(PSIDetectorBase):
     pixels_per_run = Cpt(EpicsSignal, "PixelsPerRun")
     nd_array_mode = Cpt(EpicsSignal, "NDArrayMode")
 
-    def set_trigger(
-        self, mapping_mode: MappingSource, trigger_source: TriggerSource, ignore_gate: int = 0
-    ) -> None:
-        """
-        Set triggering mode for detector
-
-        Args:
-            mapping_mode (MappingSource): Mapping mode for the detector
-            trigger_source (TriggerSource): Trigger source for the detector, pixel_advance_signal
-            ignore_gate (int): Ignore gate from TTL signal; defaults to 0
-
-        """
-        mapping = int(mapping_mode)
-        trigger = trigger_source
-        self.collect_mode.put(mapping)
-        self.pixel_advance_mode.put(trigger)
-        self.ignore_gate.put(ignore_gate)
-
-    def stage(self) -> list[object]:
-        """Stage"""
-        rtr = super().stage()
-        self.custom_prepare.arm_acquisition()
-        return rtr
-
 
 if __name__ == "__main__":
     falcon = FalconcSAXS(name="falcon", prefix="X12SA-SITORO:", sim_mode=True)

csaxs_bec/devices/epics/mcs_csaxs.py

@@ -74,6 +74,11 @@ class MCSSetup(CustomDetectorMixin):
         ]
         self.mca_data = defaultdict(lambda: [])
 
+    def on_init(self) -> None:
+        """Init sequence for the detector"""
+        self.initialize_detector()
+        self.initialize_detector_backend()
+
     def initialize_detector(self) -> None:
         """Initialize detector"""
         # External trigger for pixel advance
@@ -84,7 +89,7 @@ class MCSSetup(CustomDetectorMixin):
         # Set number of channels to 5
         self.parent.mux_output.set(5)
         # Trigger Mode used for cSAXS
-        self.parent.set_trigger(TriggerSource.MODE3)
+        self.parent.input_mode.set(TriggerSource.MODE3)
         # specify polarity of trigger signals
         self.parent.input_polarity.set(0)
         self.parent.output_polarity.set(1)
@@ -142,10 +147,15 @@ class MCSSetup(CustomDetectorMixin):
             expire=self._stream_ttl,
         )
 
+    def on_stage(self) -> None:
+        """Stage detector"""
+        self.prepare_detector()
+        self.prepare_detector_backend()
+
     def prepare_detector(self) -> None:
         """Prepare detector for scan"""
         self.set_acquisition_params()
-        self.parent.set_trigger(TriggerSource.MODE3)
+        self.parent.input_mode.set(TriggerSource.MODE3)
 
     def set_acquisition_params(self) -> None:
         """Set acquisition parameters for scan"""
@@ -175,7 +185,15 @@ class MCSSetup(CustomDetectorMixin):
         self.counter = 0
         self.parent.erase_start.set(1)
 
-    def finished(self) -> None:
+    def on_unstage(self) -> None:
+        """Unstage detector"""
+        pass
+
+    def on_complete(self) -> None:
+        """Complete detector"""
+        self.finished(timeout=self.parent.TIMEOUT_FOR_SIGNALS)
+
+    def finished(self, timeout: int = 5) -> None:
         """Check if acquisition is finished, if not successful, rais MCSTimeoutError"""
         signal_conditions = [
             (lambda: self.acquisition_done, True),
@@ -183,7 +201,7 @@ class MCSSetup(CustomDetectorMixin):
         ]
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
+            timeout=timeout,
             check_stopped=True,
             all_signals=True,
         ):
@@ -195,12 +213,15 @@ class MCSSetup(CustomDetectorMixin):
                 f" {total_frames} frames arriving at the mcs card"
             )
 
+    def on_stop(self) -> None:
+        """Stop detector"""
+        self.stop_detector()
+        self.stop_detector_backend()
+
     def stop_detector(self) -> None:
         """Stop detector"""
         self.parent.stop_all.set(1)
 
-        return super().stop_detector()
-
     def stop_detector_backend(self) -> None:
         """Stop acquisition of data"""
         self.acquisition_done = True
@@ -213,7 +234,7 @@ class SIS38XX(Device):
 class MCScSAXS(PSIDetectorBase):
     """MCS card for cSAXS for implementation at cSAXS beamline"""
 
-    USER_ACCESS = ["describe", "_init_mcs"]
+    USER_ACCESS = []
     SUB_PROGRESS = "progress"
     SUB_VALUE = "value"
     _default_sub = SUB_VALUE
@@ -222,6 +243,7 @@ class MCScSAXS(PSIDetectorBase):
     custom_prepare_cls = MCSSetup
     # specify minimum readout time for detector
     MIN_READOUT = 0
+    TIMEOUT_FOR_SIGNALS = 5
 
     # PV access to SISS38XX card
     # Acquisition
@@ -272,11 +294,8 @@ class MCScSAXS(PSIDetectorBase):
         *,
         name,
         kind=None,
-        read_attrs=None,
-        configuration_attrs=None,
         parent=None,
         device_manager=None,
-        sim_mode=False,
         mcs_config=None,
         **kwargs,
     ):
@@ -289,25 +308,11 @@ class MCScSAXS(PSIDetectorBase):
             prefix=prefix,
             name=name,
             kind=kind,
-            read_attrs=read_attrs,
-            configuration_attrs=configuration_attrs,
             parent=parent,
             device_manager=device_manager,
-            sim_mode=sim_mode,
             **kwargs,
         )
 
-    def set_trigger(self, trigger_source: TriggerSource) -> None:
-        """Set trigger mode from TriggerSource"""
-        value = int(trigger_source)
-        self.input_mode.set(value)
-
-    def stage(self) -> list[object]:
-        """stage the detector for upcoming acquisition"""
-        rtr = super().stage()
-        self.custom_prepare.arm_acquisition()
-        return rtr
-
 
 # Automatically connect to test environmenr if directly invoked
 if __name__ == "__main__":

csaxs_bec/devices/epics/pilatus_csaxs.py

@@ -1,12 +1,12 @@
 import enum
 import json
 import os
+import threading
 import time
 
 import numpy as np
 import requests
-from bec_lib import bec_logger, messages
-from bec_lib.endpoints import MessageEndpoints
+from bec_lib import bec_logger
 from ophyd import ADComponent as ADCpt
 from ophyd import Device, EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV, Staged
 from ophyd_devices.interfaces.base_classes.psi_detector_base import (
@@ -16,8 +16,6 @@ from ophyd_devices.interfaces.base_classes.psi_detector_base import (
 
 logger = bec_logger.logger
 
-MIN_READOUT = 3e-3
-
 
 class PilatusError(Exception):
     """Base class for exceptions in this module."""
@@ -72,6 +70,15 @@ class PilatusSetup(CustomDetectorMixin):
 
     """
 
+    def __init__(self, *args, parent: Device = None, **kwargs) -> None:
+        super().__init__(*args, parent=parent, **kwargs)
+        self._lock = threading.RLock()
+
+    def on_init(self) -> None:
+        """Initialize the detector"""
+        self.initialize_default_parameter()
+        self.initialize_detector()
+
     def initialize_default_parameter(self) -> None:
         """Set default parameters for Eiger9M detector"""
         self.update_readout_time()
@@ -90,7 +97,15 @@ class PilatusSetup(CustomDetectorMixin):
         # Stops the detector
         self.stop_detector()
         # Sets the trigger source to GATING
-        self.parent.set_trigger(TriggerSource.EXT_ENABLE)
+        self.parent.cam.trigger_mode.put(TriggerSource.EXT_ENABLE)
+
+    def on_stage(self) -> None:
+        """Stage the detector for scan"""
+        self.prepare_detector()
+        self.prepare_data_backend()
+        self.publish_file_location(
+            done=False, successful=False, metadata={"input_path": self.parent.filepath_raw}
+        )
 
     def prepare_detector(self) -> None:
         """
@@ -101,84 +116,7 @@ class PilatusSetup(CustomDetectorMixin):
         """
         self.set_detector_threshold()
         self.set_acquisition_params()
-        self.parent.set_trigger(TriggerSource.EXT_ENABLE)
-
-    def set_detector_threshold(self) -> None:
-        """
-        Set correct detector threshold to 1/2 of current X-ray energy, allow 5% tolerance
-
-        Threshold might be in ev or keV
-        """
-
-        # get current beam energy from device manageer
-        mokev = self.parent.device_manager.devices.mokev.obj.read()[
-            self.parent.device_manager.devices.mokev.name
-        ]["value"]
-        factor = 1
-
-        # Check if energies are eV or keV, assume keV as the default
-        unit = getattr(self.parent.cam.threshold_energy, "units", None)
-        if unit is not None and unit == "eV":
-            factor = 1000
-
-        # set energy on detector
-        setpoint = int(mokev * factor)
-
-        # set threshold on detector
-        threshold = self.parent.cam.threshold_energy.read()[self.parent.cam.threshold_energy.name][
-            "value"
-        ]
-        if not np.isclose(setpoint / 2, threshold, rtol=0.05):
-            self.parent.cam.threshold_energy.set(setpoint / 2)
-
-    def set_acquisition_params(self) -> None:
-        """Set acquisition parameters for the detector"""
-
-        # Set number of images and frames (frames is for internal burst of detector)
-        self.parent.cam.num_images.put(
-            int(self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger)
-        )
-        self.parent.cam.num_frames.put(1)
-
-        # Update the readout time of the detector
-        self.update_readout_time()
-
-    def create_directory(self, filepath: str) -> None:
-        """Create directory if it does not exist"""
-        os.makedirs(filepath, exist_ok=True)
-
-    def stop_detector_backend(self) -> None:
-        """Stop the file writer zmq service for pilatus_2"""
-        self.close_file_writer()
-        time.sleep(0.1)
-        self.stop_file_writer()
-        time.sleep(0.1)
-
-    def close_file_writer(self) -> None:
-        """
-        Close the file writer for pilatus_2
-
-        Delete the data from x12sa-pd-2
-
-        """
-        url = "http://x12sa-pd-2:8080/stream/pilatus_2"
-        try:
-            res = self.send_requests_delete(url=url)
-            if not res.ok:
-                res.raise_for_status()
-        except Exception as exc:
-            logger.info(f"Pilatus2 close threw Exception: {exc}")
-
-    def stop_file_writer(self) -> None:
-        """
-        Stop the file writer for pilatus_2
-
-        Runs on xbl-daq-34
-        """
-        url = "http://xbl-daq-34:8091/pilatus_2/stop"
-        res = self.send_requests_put(url=url)
-        if not res.ok:
-            res.raise_for_status()
+        self.parent.cam.trigger_mode.put(TriggerSource.EXT_ENABLE)
 
     def prepare_data_backend(self) -> None:
         """
@@ -191,7 +129,9 @@ class PilatusSetup(CustomDetectorMixin):
 
         self.stop_detector_backend()
 
-        self.parent.filepath = self.parent.filewriter.compile_full_filename("pilatus_2.h5")
+        self.parent.filepath.set(
+            self.parent.filewriter.compile_full_filename("pilatus_2.h5")
+        ).wait()
         self.parent.cam.file_path.put("/dev/shm/zmq/")
         self.parent.cam.file_name.put(
             f"{self.parent.scaninfo.username}_2_{self.parent.scaninfo.scan_number:05d}"
@@ -275,6 +215,76 @@ class PilatusSetup(CustomDetectorMixin):
         except Exception as exc:
             logger.info(f"Pilatus2 wait threw Exception: {exc}")
 
+    def set_detector_threshold(self) -> None:
+        """
+        Set correct detector threshold to 1/2 of current X-ray energy, allow 5% tolerance
+
+        Threshold might be in ev or keV
+        """
+
+        # get current beam energy from device manageer
+        mokev = self.parent.device_manager.devices.mokev.obj.read()[
+            self.parent.device_manager.devices.mokev.name
+        ]["value"]
+        factor = 1
+
+        # Check if energies are eV or keV, assume keV as the default
+        unit = getattr(self.parent.cam.threshold_energy, "units", None)
+        if unit is not None and unit == "eV":
+            factor = 1000
+
+        # set energy on detector
+        setpoint = int(mokev * factor)
+
+        # set threshold on detector
+        threshold = self.parent.cam.threshold_energy.read()[self.parent.cam.threshold_energy.name][
+            "value"
+        ]
+        if not np.isclose(setpoint / 2, threshold, rtol=0.05):
+            self.parent.cam.threshold_energy.set(setpoint / 2)
+
+    def set_acquisition_params(self) -> None:
+        """Set acquisition parameters for the detector"""
+
+        # Set number of images and frames (frames is for internal burst of detector)
+        self.parent.cam.num_images.put(
+            int(self.parent.scaninfo.num_points * self.parent.scaninfo.frames_per_trigger)
+        )
+        self.parent.cam.num_frames.put(1)
+
+        # Update the readout time of the detector
+        self.update_readout_time()
+
+    def create_directory(self, filepath: str) -> None:
+        """Create directory if it does not exist"""
+        os.makedirs(filepath, exist_ok=True)
+
+    def close_file_writer(self) -> None:
+        """
+        Close the file writer for pilatus_2
+
+        Delete the data from x12sa-pd-2
+
+        """
+        url = "http://x12sa-pd-2:8080/stream/pilatus_2"
+        try:
+            res = self.send_requests_delete(url=url)
+            if not res.ok:
+                res.raise_for_status()
+        except Exception as exc:
+            logger.info(f"Pilatus2 close threw Exception: {exc}")
+
+    def stop_file_writer(self) -> None:
+        """
+        Stop the file writer for pilatus_2
+
+        Runs on xbl-daq-34
+        """
+        url = "http://xbl-daq-34:8091/pilatus_2/stop"
+        res = self.send_requests_put(url=url)
+        if not res.ok:
+            res.raise_for_status()
+
     def send_requests_put(self, url: str, data: list = None, headers: dict = None) -> object:
         """
         Send a put request to the given url
@@ -302,14 +312,8 @@ class PilatusSetup(CustomDetectorMixin):
         """
         return requests.delete(url=url, headers=headers, timeout=5)
 
-    def pre_scan(self) -> None:
-        """
-        Pre_scan function call
-
-        This function is called just before the scan core.
-        Here it is used to arm the detector for the acquisition
-
-        """
+    def on_pre_scan(self) -> None:
+        """Prepare detector for scan"""
         self.arm_acquisition()
 
     def arm_acquisition(self) -> None:
@@ -318,43 +322,18 @@ class PilatusSetup(CustomDetectorMixin):
         # TODO is this sleep needed? to be tested with detector and for how long
         time.sleep(0.5)
 
-    def publish_file_location(self, done: bool = False, successful: bool = None) -> None:
-        """
-        Publish the filepath to REDIS and publish the event for the h5_converter
+    def on_unstage(self) -> None:
+        """Unstage the detector"""
+        pass
 
-        We publish two events here:
-        - file_event: event for the filewriter
-        - public_file: event for any secondary service (e.g. radial integ code)
-
-        Args:
-            done (bool): True if scan is finished
-            successful (bool): True if scan was successful
-        """
-        pipe = self.parent.connector.pipeline()
-        if successful is None:
-            msg = messages.FileMessage(
-                file_path=self.parent.filepath,
-                done=done,
-                metadata={"input_path": self.parent.filepath_raw},
-            )
-        else:
-            msg = messages.FileMessage(
-                file_path=self.parent.filepath,
-                done=done,
-                successful=successful,
-                metadata={"input_path": self.parent.filepath_raw},
-            )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.public_file(self.parent.scaninfo.scan_id, self.parent.name),
-            msg,
-            pipe=pipe,
+    def on_complete(self) -> None:
+        """Complete the scan"""
+        self.finished(timeout=self.parent.TIMEOUT_FOR_SIGNALS)
+        self.publish_file_location(
+            done=True, successful=True, metadata={"input_path": self.parent.filepath_raw}
         )
-        self.parent.connector.set_and_publish(
-            MessageEndpoints.file_event(self.parent.name), msg, pipe=pipe
-        )
-        pipe.execute()
 
-    def finished(self) -> None:
+    def finished(self, timeout: int = 5) -> None:
         """Check if acquisition is finished."""
         # pylint: disable=protected-access
         # TODO: at the moment this relies on device.mcs.obj._staged attribute
@@ -363,7 +342,7 @@ class PilatusSetup(CustomDetectorMixin):
         ]
         if not self.wait_for_signals(
             signal_conditions=signal_conditions,
-            timeout=self.parent.timeout,
+            timeout=timeout,
             check_stopped=True,
             all_signals=True,
         ):
@@ -375,16 +354,21 @@ class PilatusSetup(CustomDetectorMixin):
         self.stop_detector()
         self.stop_detector_backend()
 
+    def on_stop(self) -> None:
+        """Stop detector"""
+        self.stop_detector()
+        self.stop_detector_backend()
+
     def stop_detector(self) -> None:
         """Stop detector"""
         self.parent.cam.acquire.put(0)
 
-    def check_scan_id(self) -> None:
-        """Checks if scan_id has changed and stops the scan if it has"""
-        old_scan_id = self.parent.scaninfo.scan_id
-        self.parent.scaninfo.load_scan_metadata()
-        if self.parent.scaninfo.scan_id != old_scan_id:
-            self.parent.stopped = True
+    def stop_detector_backend(self) -> None:
+        """Stop the file writer zmq service for pilatus_2"""
+        self.close_file_writer()
+        time.sleep(0.1)
+        self.stop_file_writer()
+        time.sleep(0.1)
 
 
 class PilatuscSAXS(PSIDetectorBase):
@@ -401,20 +385,16 @@ class PilatuscSAXS(PSIDetectorBase):
     """
 
     # Specify which functions are revealed to the user in BEC client
-    USER_ACCESS = ["describe"]
+    USER_ACCESS = []
 
     # specify Setup class
     custom_prepare_cls = PilatusSetup
     # specify minimum readout time for detector
     MIN_READOUT = 3e-3
+    TIMEOUT_FOR_SIGNALS = 5
     # specify class attributes
     cam = ADCpt(SLSDetectorCam, "cam1:")
 
-    def set_trigger(self, trigger_source: TriggerSource) -> None:
-        """Set trigger source for the detector"""
-        value = trigger_source
-        self.cam.trigger_mode.put(value)
-
 
 if __name__ == "__main__":
     pilatus_2 = PilatuscSAXS(name="pilatus_2", prefix="X12SA-ES-PILATUS300K:", sim_mode=True)

csaxs_bec/devices/ids_cameras/ids_camera.py

@@ -0,0 +1,479 @@
+import threading
+import time
+
+import numpy as np
+from ophyd import Component as Cpt
+from ophyd import Device, Kind
+from ophyd_devices.interfaces.base_classes.psi_detector_base import (
+    CustomDetectorMixin,
+    PSIDetectorBase,
+)
+from ophyd_devices.sim.sim_signals import SetableSignal
+
+try:
+    from pyueye import ueye
+except ImportError:
+    # The pyueye library is not installed or doesn't provide the necessary c libs
+    ueye = None
+
+
+class IDSCustomPrepare(CustomDetectorMixin):
+
+    USER_ACCESS = ["pyueye"]
+    pyueye = ueye
+
+    def __init__(self, *_args, parent: Device = None, **_kwargs) -> None:
+        super().__init__(*_args, parent=parent, **_kwargs)
+        self.ueye = ueye
+        self.h_cam = None
+        self.s_info = None
+        self.data_thread = None
+        self.thread_event = None
+
+    def on_connection_established(self):
+        self.hCam = self.ueye.HIDS(
+            self.parent.camera_ID
+        )  # 0: first available camera;  1-254: The camera with the specified camera ID
+        self.sInfo = self.ueye.SENSORINFO()
+        self.cInfo = self.ueye.CAMINFO()
+        self.pcImageMemory = self.ueye.c_mem_p()
+        self.MemID = self.ueye.int()
+        self.rectAOI = self.ueye.IS_RECT()
+        self.pitch = self.ueye.INT()
+        self.nBitsPerPixel = self.ueye.INT(
+            self.parent.bits_per_pixel
+        )  # 24: bits per pixel for color mode; take 8 bits per pixel for monochrome
+        self.channels = (
+            self.parent.channels
+        )  # 3: channels for color mode(RGB); take 1 channel for monochrome
+        self.m_nColorMode = self.ueye.INT(
+            self.parent.m_n_colormode
+        )  # Y8/RGB16/RGB24/REG32 (1 for our color cameras)
+        self.bytes_per_pixel = int(self.nBitsPerPixel / 8)
+
+        # Starts the driver and establishes the connection to the camera
+        nRet = self.ueye.is_InitCamera(self.hCam, None)
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_InitCamera ERROR")
+
+        # Reads out the data hard-coded in the non-volatile camera memory and writes it to the data structure that cInfo points to
+        nRet = self.ueye.is_GetCameraInfo(self.hCam, self.cInfo)
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_GetCameraInfo ERROR")
+
+        # You can query additional information about the sensor type used in the camera
+        nRet = self.ueye.is_GetSensorInfo(self.hCam, self.sInfo)
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_GetSensorInfo ERROR")
+
+        nRet = self.ueye.is_ResetToDefault(self.hCam)
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_ResetToDefault ERROR")
+
+        # Set display mode to DIB
+        nRet = self.ueye.is_SetDisplayMode(self.hCam, self.ueye.IS_SET_DM_DIB)
+
+        # Set the right color mode
+        if (
+            int.from_bytes(self.sInfo.nColorMode.value, byteorder="big")
+            == self.ueye.IS_COLORMODE_BAYER
+        ):
+            # setup the color depth to the current windows setting
+            self.ueye.is_GetColorDepth(self.hCam, self.nBitsPerPixel, self.m_nColorMode)
+            bytes_per_pixel = int(self.nBitsPerPixel / 8)
+            print("IS_COLORMODE_BAYER: ")
+            print("\tm_nColorMode: \t\t", self.m_nColorMode)
+            print("\tnBitsPerPixel: \t\t", self.nBitsPerPixel)
+            print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+            print()
+
+        elif (
+            int.from_bytes(self.sInfo.nColorMode.value, byteorder="big")
+            == self.ueye.IS_COLORMODE_CBYCRY
+        ):
+            # for color camera models use RGB32 mode
+            m_nColorMode = ueye.IS_CM_BGRA8_PACKED
+            nBitsPerPixel = ueye.INT(32)
+            bytes_per_pixel = int(self.nBitsPerPixel / 8)
+            print("IS_COLORMODE_CBYCRY: ")
+            print("\tm_nColorMode: \t\t", m_nColorMode)
+            print("\tnBitsPerPixel: \t\t", nBitsPerPixel)
+            print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+            print()
+
+        elif (
+            int.from_bytes(self.sInfo.nColorMode.value, byteorder="big")
+            == self.ueye.IS_COLORMODE_MONOCHROME
+        ):
+            # for color camera models use RGB32 mode
+            m_nColorMode = self.ueye.IS_CM_MONO8
+            nBitsPerPixel = self.ueye.INT(8)
+            bytes_per_pixel = int(nBitsPerPixel / 8)
+            print("IS_COLORMODE_MONOCHROME: ")
+            print("\tm_nColorMode: \t\t", m_nColorMode)
+            print("\tnBitsPerPixel: \t\t", nBitsPerPixel)
+            print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+            print()
+
+        else:
+            # for monochrome camera models use Y8 mode
+            m_nColorMode = self.ueye.IS_CM_MONO8
+            nBitsPerPixel = self.ueye.INT(8)
+            bytes_per_pixel = int(nBitsPerPixel / 8)
+            print("else")
+
+        # Can be used to set the size and position of an "area of interest"(AOI) within an image
+        nRet = self.ueye.is_AOI(
+            self.hCam, ueye.IS_AOI_IMAGE_GET_AOI, self.rectAOI, self.ueye.sizeof(self.rectAOI)
+        )
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_AOI ERROR")
+
+        self.width = self.rectAOI.s32Width
+        self.height = self.rectAOI.s32Height
+
+        # Prints out some information about the camera and the sensor
+        print("Camera model:\t\t", self.sInfo.strSensorName.decode("utf-8"))
+        print("Camera serial no.:\t", self.cInfo.SerNo.decode("utf-8"))
+        print("Maximum image width:\t", self.width)
+        print("Maximum image height:\t", self.height)
+        print()
+
+        # ---------------------------------------------------------------------------------------------------------------------------------------
+
+        # Allocates an image memory for an image having its dimensions defined by width and height and its color depth defined by nBitsPerPixel
+        nRet = self.ueye.is_AllocImageMem(
+            self.hCam, self.width, self.height, self.nBitsPerPixel, self.pcImageMemory, self.MemID
+        )
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_AllocImageMem ERROR")
+        else:
+            # Makes the specified image memory the active memory
+            nRet = self.ueye.is_SetImageMem(self.hCam, self.pcImageMemory, self.MemID)
+            if nRet != self.ueye.IS_SUCCESS:
+                print("is_SetImageMem ERROR")
+            else:
+                # Set the desired color mode
+                nRet = self.ueye.is_SetColorMode(self.hCam, self.m_nColorMode)
+
+        # Activates the camera's live video mode (free run mode)
+        nRet = self.ueye.is_CaptureVideo(self.hCam, self.ueye.IS_DONT_WAIT)
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_CaptureVideo ERROR")
+
+        # Enables the queue mode for existing image memory sequences
+        nRet = self.ueye.is_InquireImageMem(
+            self.hCam,
+            self.pcImageMemory,
+            self.MemID,
+            self.width,
+            self.height,
+            self.nBitsPerPixel,
+            self.pitch,
+        )
+        if nRet != self.ueye.IS_SUCCESS:
+            print("is_InquireImageMem ERROR")
+        else:
+            print("Press q to leave the programm")
+        startmeasureframerate = True
+        Gain = False
+
+        # Start live mode of camera immediately
+        self.parent.start_live_mode()
+
+    def _start_data_thread(self):
+        self.thread_event = threading.Event()
+        self.data_thread = threading.Thread(target=self._receive_data_from_camera, daemon=True)
+        self.data_thread.start()
+
+    def _receive_data_from_camera(self):
+        while not self.thread_event.is_set():
+
+            # In order to display the image in an OpenCV window we need to...
+            # ...extract the data of our image memory
+            array = ueye.get_data(
+                self.pcImageMemory,
+                self.width,
+                self.height,
+                self.nBitsPerPixel,
+                self.pitch,
+                copy=False,
+            )
+
+            # bytes_per_pixel = int(nBitsPerPixel / 8)
+
+            # ...reshape it in an numpy array...
+            frame = np.reshape(array, (self.height.value, self.width.value, self.bytes_per_pixel))
+            self.parent.image_data.put(frame)
+            self.parent._run_subs(sub_type=self.parent.SUB_MONITOR, value=frame)
+
+            time.sleep(0.1)
+
+    def on_trigger(self):
+        pass
+        # self.parent._run_subs(sub_type=self.parent.SUB_MONITOR, value=self.parent.image_data.get())
+
+
+class IDSCamera(PSIDetectorBase):
+    USER_ACCESS = ["start_live_mode", "stop_live_mode"]
+
+    custom_prepare_cls = IDSCustomPrepare
+
+    image_data = Cpt(SetableSignal, value=np.empty((100, 100)), kind=Kind.omitted)
+
+    SUB_MONITOR = "device_monitor_2d"
+    _default_sub = SUB_MONITOR
+
+    def __init__(
+        self,
+        prefix="",
+        *,
+        name: str,
+        camera_ID: int,
+        bits_per_pixel: int,
+        channels: int,
+        m_n_colormode: int,
+        kind=None,
+        parent=None,
+        device_manager=None,
+        **kwargs,
+    ):
+        super().__init__(
+            prefix, name=name, kind=kind, parent=parent, device_manager=device_manager, **kwargs
+        )
+        self.camera_ID = camera_ID
+        self.bits_per_pixel = bits_per_pixel
+        self.channels = channels
+        self.m_n_colormode = m_n_colormode
+        #TODO fix connected and wait_for_connection
+        self.custom_prepare.on_connection_established()
+
+    def wait_for_connection(self, all_signals=False, timeout=10):
+        if ueye is None:
+            raise ImportError(
+                "The pyueye library is not installed or doesn't provide the necessary c libs"
+            )
+        super().wait_for_connection(all_signals, timeout)
+        #self.custom_prepare.on_connection_established()
+
+    def destroy(self):
+        """Extend Ophyds destroy function to kill the data thread"""
+        self.stop_live_mode()
+        super().destroy()
+
+    def start_live_mode(self):
+        if self.custom_prepare.data_thread is not None:
+            self.stop_live_mode()
+        self.custom_prepare._start_data_thread()
+
+    def stop_live_mode(self):
+        """Stopping the camera live mode."""
+        if self.custom_prepare.thread_event is not None:
+            self.custom_prepare.thread_event.set()
+        if self.custom_prepare.data_thread is not None:
+            self.custom_prepare.data_thread.join()
+        self.custom_prepare.thread_event = None
+        self.custom_prepare.data_thread = None
+
+
+"""from pyueye import ueye
+import numpy as np
+import cv2
+import sys
+import time
+
+#---------------------------------------------------------------------------------------------------------------------------------------
+
+#Variables
+hCam = ueye.HIDS(202)             #0: first available camera;  1-254: The camera with the specified camera ID
+sInfo = ueye.SENSORINFO()
+cInfo = ueye.CAMINFO()
+pcImageMemory = ueye.c_mem_p()
+MemID = ueye.int()
+rectAOI = ueye.IS_RECT()
+pitch = ueye.INT()
+nBitsPerPixel = ueye.INT(24)    #24: bits per pixel for color mode; take 8 bits per pixel for monochrome
+channels = 3                    #3: channels for color mode(RGB); take 1 channel for monochrome
+m_nColorMode = ueye.INT(1)		# Y8/RGB16/RGB24/REG32 (1 for our color cameras)
+bytes_per_pixel = int(nBitsPerPixel / 8)
+
+ids_cam
+  ...
+  deviceConfig:
+    camera_ID: 202
+    bits_per_pixel: 24
+    channels: 3
+    m_n_colormode: 1  
+
+#---------------------------------------------------------------------------------------------------------------------------------------
+print("START")
+print()
+
+# Starts the driver and establishes the connection to the camera
+nRet = ueye.is_InitCamera(hCam, None)
+if nRet != ueye.IS_SUCCESS:
+    print("is_InitCamera ERROR")
+
+# Reads out the data hard-coded in the non-volatile camera memory and writes it to the data structure that cInfo points to
+nRet = ueye.is_GetCameraInfo(hCam, cInfo)
+if nRet != ueye.IS_SUCCESS:
+    print("is_GetCameraInfo ERROR")
+
+# You can query additional information about the sensor type used in the camera
+nRet = ueye.is_GetSensorInfo(hCam, sInfo)
+if nRet != ueye.IS_SUCCESS:
+    print("is_GetSensorInfo ERROR")
+
+nRet = ueye.is_ResetToDefault( hCam)
+if nRet != ueye.IS_SUCCESS:
+    print("is_ResetToDefault ERROR")
+
+# Set display mode to DIB
+nRet = ueye.is_SetDisplayMode(hCam, ueye.IS_SET_DM_DIB)
+
+
+
+# Set the right color mode
+if int.from_bytes(sInfo.nColorMode.value, byteorder='big') == ueye.IS_COLORMODE_BAYER:
+    # setup the color depth to the current windows setting
+    ueye.is_GetColorDepth(hCam, nBitsPerPixel, m_nColorMode)
+    bytes_per_pixel = int(nBitsPerPixel / 8)
+    print("IS_COLORMODE_BAYER: ", )
+    print("\tm_nColorMode: \t\t", m_nColorMode)
+    print("\tnBitsPerPixel: \t\t", nBitsPerPixel)
+    print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+    print()
+
+elif int.from_bytes(sInfo.nColorMode.value, byteorder='big') == ueye.IS_COLORMODE_CBYCRY:
+    # for color camera models use RGB32 mode
+    m_nColorMode = ueye.IS_CM_BGRA8_PACKED
+    nBitsPerPixel = ueye.INT(32)
+    bytes_per_pixel = int(nBitsPerPixel / 8)
+    print("IS_COLORMODE_CBYCRY: ", )
+    print("\tm_nColorMode: \t\t", m_nColorMode)
+    print("\tnBitsPerPixel: \t\t", nBitsPerPixel)
+    print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+    print()
+
+elif int.from_bytes(sInfo.nColorMode.value, byteorder='big') == ueye.IS_COLORMODE_MONOCHROME:
+    # for color camera models use RGB32 mode
+    m_nColorMode = ueye.IS_CM_MONO8
+    nBitsPerPixel = ueye.INT(8)
+    bytes_per_pixel = int(nBitsPerPixel / 8)
+    print("IS_COLORMODE_MONOCHROME: ", )
+    print("\tm_nColorMode: \t\t", m_nColorMode)
+    print("\tnBitsPerPixel: \t\t", nBitsPerPixel)
+    print("\tbytes_per_pixel: \t\t", bytes_per_pixel)
+    print()
+
+else:
+    # for monochrome camera models use Y8 mode
+    m_nColorMode = ueye.IS_CM_MONO8
+    nBitsPerPixel = ueye.INT(8)
+    bytes_per_pixel = int(nBitsPerPixel / 8)
+    print("else")
+
+# Can be used to set the size and position of an "area of interest"(AOI) within an image
+nRet = ueye.is_AOI(hCam, ueye.IS_AOI_IMAGE_GET_AOI, rectAOI, ueye.sizeof(rectAOI))
+if nRet != ueye.IS_SUCCESS:
+    print("is_AOI ERROR")
+
+width = rectAOI.s32Width
+height = rectAOI.s32Height
+
+# Prints out some information about the camera and the sensor
+print("Camera model:\t\t", sInfo.strSensorName.decode('utf-8'))
+print("Camera serial no.:\t", cInfo.SerNo.decode('utf-8'))
+print("Maximum image width:\t", width)
+print("Maximum image height:\t", height)
+print()
+
+#---------------------------------------------------------------------------------------------------------------------------------------
+
+# Allocates an image memory for an image having its dimensions defined by width and height and its color depth defined by nBitsPerPixel
+nRet = ueye.is_AllocImageMem(hCam, width, height, nBitsPerPixel, pcImageMemory, MemID)
+if nRet != ueye.IS_SUCCESS:
+    print("is_AllocImageMem ERROR")
+else:
+    # Makes the specified image memory the active memory
+    nRet = ueye.is_SetImageMem(hCam, pcImageMemory, MemID)
+    if nRet != ueye.IS_SUCCESS:
+        print("is_SetImageMem ERROR")
+    else:
+        # Set the desired color mode
+        nRet = ueye.is_SetColorMode(hCam, m_nColorMode)
+
+
+
+# Activates the camera's live video mode (free run mode)
+nRet = ueye.is_CaptureVideo(hCam, ueye.IS_DONT_WAIT)
+if nRet != ueye.IS_SUCCESS:
+    print("is_CaptureVideo ERROR")
+
+# Enables the queue mode for existing image memory sequences
+nRet = ueye.is_InquireImageMem(hCam, pcImageMemory, MemID, width, height, nBitsPerPixel, pitch)
+if nRet != ueye.IS_SUCCESS:
+    print("is_InquireImageMem ERROR")
+else:
+    print("Press q to leave the programm")
+startmeasureframerate=True
+Gain = False
+#---------------------------------------------------------------------------------------------------------------------------------------
+
+# Continuous image display
+while(nRet == ueye.IS_SUCCESS):
+
+    # In order to display the image in an OpenCV window we need to...
+    # ...extract the data of our image memory
+    array = ueye.get_data(pcImageMemory, width, height, nBitsPerPixel, pitch, copy=False)
+
+    # bytes_per_pixel = int(nBitsPerPixel / 8)
+
+    # ...reshape it in an numpy array...
+    frame = np.reshape(array,(height.value, width.value, bytes_per_pixel))
+
+    # ...resize the image by a half
+    frame = cv2.resize(frame,(0,0),fx=0.5, fy=0.5)
+    
+#---------------------------------------------------------------------------------------------------------------------------------------
+    #Include image data processing here
+
+#---------------------------------------------------------------------------------------------------------------------------------------
+
+    #...and finally display it
+    cv2.imshow("SimpleLive_Python_uEye_OpenCV", frame)
+    if startmeasureframerate:   
+        starttime = time.time()
+        startmeasureframerate=False
+        framenumber=0
+    if time.time() > starttime+5:
+        print(f"Caught {framenumber/5} frames per second")
+        startmeasureframerate=True
+        Gain = ~Gain
+        if Gain:
+            nRet = ueye.is_SetGainBoost(hCam, 1)
+        else:
+            nRet = ueye.is_SetGainBoost(hCam, 0)
+        print(f"Gain setting status {nRet}")
+    #...and finally display it
+    cv2.imshow("SimpleLive_Python_uEye_OpenCV", frame)
+    framenumber+=1
+    time.sleep(0.1)
+
+    # Press q if you want to end the loop
+    if (cv2.waitKey(1) & 0xFF) == ord('q'):
+        break
+#---------------------------------------------------------------------------------------------------------------------------------------
+
+# Releases an image memory that was allocated using is_AllocImageMem() and removes it from the driver management
+ueye.is_FreeImageMem(hCam, pcImageMemory, MemID)
+
+# Disables the hCam camera handle and releases the data structures and memory areas taken up by the uEye camera
+ueye.is_ExitCamera(hCam)
+
+# Destroys the OpenCv windows
+cv2.destroyAllWindows()
+
+print()
+print("END")
+"""

csaxs_bec/devices/ids_cameras/ids_ueye_signals.py

@@ -0,0 +1,83 @@
+import time
+
+import numpy as np
+from bec_lib import bec_logger
+from ophyd import Kind, Signal
+from ophyd.utils import ReadOnlyError
+
+from ophyd_devices.utils.bec_device_base import BECDeviceBase
+
+logger = bec_logger.logger
+
+# Readout precision for Setable/ReadOnlySignal signals
+PRECISION = 3
+
+
+class ReadOnlySignal(Signal):
+    """Setable signal for simulated devices.
+
+    The signal will store the value in sim_state of the SimulatedData class of the parent device.
+    It will also return the value from sim_state when get is called. Compared to the ReadOnlySignal,
+    this signal can be written to.
+    The setable signal inherits from the Signal class of ophyd, thus the class attribute needs to be
+    initiated as a Component (class from ophyd).
+
+    >>> signal = SetableSignal(name="signal", parent=parent, value=0)
+
+    Parameters
+    ----------
+
+    name  (string)           : Name of the signal
+    parent (object)          : Parent object of the signal, default none.
+    value (any)              : Initial value of the signal, default 0.
+    kind (int)               : Kind of the signal, default Kind.normal.
+    precision (float)        : Precision of the signal, default PRECISION.
+    """
+
+    def __init__(
+        self,
+        name: str,
+        *args,
+        fcn: callable,
+        kind: int = Kind.normal,
+        precision: float = PRECISION,
+        **kwargs,
+    ):
+        super().__init__(*args, name=name, value=value, kind=kind, **kwargs)
+        self._metadata.update(connected=True, write_access=False)
+        self._value = None
+        self.precision = precision
+        self.fcn = fcn
+
+    # pylint: disable=arguments-differ
+    def get(self):
+        """Get the current position of the simulated device.
+
+        Core function for signal.
+        """
+        self._value = self.fcn()
+        return self._value
+
+    # pylint: disable=arguments-differ
+    def put(self, value):
+        """Put the value to the simulated device.
+
+        Core function for signal.
+        """
+        self._update_sim_state(value)
+        self._value = value
+
+    def describe(self):
+        """Describe the readback signal.
+
+        Core function for signal.
+        """
+        res = super().describe()
+        if self.precision is not None:
+            res[self.name]["precision"] = self.precision
+        return res
+
+    @property
+    def timestamp(self):
+        """Timestamp of the readback value"""
+        return self._get_timestamp()

csaxs_bec/devices/jungfraujoch/eiger_jfj.py

@@ -0,0 +1,221 @@
+"""Eiger detector for cSAXS beamline at the Swiss Light Source.
+
+16bit mode supports 8e7 counts/s per pixel,
+you will never have more than 12bit subframes, which means 4000 counts per subframe.
+32bit mode supports 2e7 counts/s per pixel,
+you will never have more than 24bit subframe, which means 16.7 million counts per subframe.
+"""
+
+import enum
+from typing import TYPE_CHECKING
+
+from bec_lib.devicemanager import ScanInfo
+from bec_lib.logger import bec_logger
+from jfjoch_client.models.dataset_settings import DatasetSettings
+from jfjoch_client.models.detector_settings import DetectorSettings
+from jfjoch_client.models.detector_timing import DetectorTiming
+from ophyd import DeviceStatus
+from ophyd_devices.interfaces.base_classes.psi_device_base import PSIDeviceBase
+
+from csaxs_bec.devices.jungfraujoch.jungfrau_joch_client import JungfrauJochClient
+from csaxs_bec.devices.jungfraujoch.readout_constants import EIGER9M_READOUT_TIME_32BIT
+
+if TYPE_CHECKING:  # pragma no cover
+    from bec_lib.devicemanager import ScanInfo
+    from bec_server.device_server.device_server import DeviceManagerDS
+
+logger = bec_logger.logger
+
+
+class EigerCSAXSBitDepth(int, enum.Enum):
+    """Bit depth for EIGER detector at cSAXS beamline."""
+
+    BIT_DEPTH_16 = 16
+    BIT_DEPTH_32 = 32
+
+
+class Eiger9MCSAXS(PSIDeviceBase):
+    """
+    -----------
+    JungfrauJoch - one needs to connect to the jfj-server (sls-jfjoch-001)
+
+    Relevant commands for debugging:
+    sudo systemctl restart jfjoch_broker
+    sudo systemctl status jfjoch_broker
+
+    Some additional notes:
+    ------------
+    - If energy on JFJ is set via DetectorSettings, the one in DatasetSettings will be ignored.
+        - One can set this initially, and then set it to none in DetectorSettings such that any update in DatasetSettings will be considered.
+        - IMPORTANT: Any change in energy will be detector. It will be best to have a check ourselves with a certain tolerance of ~ % to not constantly update the energy.
+    - in 'gating' mode, frame_time_us and count_time_us are not used.
+    - The image_time_us of the DatasetSettings and the frame_time_us of the DetectorSettings need to be the same.
+    - The difference between frame_time_us and count_time_us is the readout time.
+    - 16bit and 32bit, when do we switch?
+        - If switching is desired, the readout time needs to be adapted as a function of internal exposure time, and bit depth.
+          This can be up to ~400us for 32bit, and long exposures. This needs to be discussed!
+    - 16bit mode supports 8e7 counts/s per pixel,
+    It needs to be se to None.
+
+    ------------
+    Eiger - if power cycling is needed. Use a combination of commands that connect to the chip, and the conda package.
+    The package is available via:
+    cd /sls/X12SA/data/gac-x12sa/erik/micromamba
+    source setup_9m.sh
+
+    ------------
+    Nice to set high voltage low first, from conda package (sls_detector_package)
+    p highvoltage 0 or 150 (operational)
+    g highvoltage
+    # Put high voltage to 0 before power cylcing it.
+    telnet bchip500
+    cd power_control_user/
+    ./on
+    ./off
+    """
+
+    ########################################
+    #  Beamline Specific Implementations   #
+    ########################################
+
+    USER_ACCESS = ["jfj_client"]
+
+    def __init__(
+        self,
+        name: str,
+        host: str = "http://sls-jfjoch-001",
+        port: int = 8080,
+        scan_info: ScanInfo = None,
+        device_manager=None,
+        **kwargs,
+    ):
+        """
+        Initialize the PSI Device Base class.
+
+        Args:
+            name (str) : Name of the device
+            scan_info (ScanInfo): The scan info to use.
+        """
+        super().__init__(name=name, scan_info=scan_info, **kwargs)
+        self._host = f"{host}:{port}"
+        self.jfj_client = JungfrauJochClient(host=self._host, parent=self)
+        self.device_manager = device_manager
+        if self.device_manager is not None:
+            self.device_manager: DeviceManagerDS
+        self._bit_depth = 16
+        self.frame_time = 500e-6  # 500us, will be ignored in DetectorTiming.Gated
+        self.count_time = 300e-6  # 480us, will be ignored in DetectorTiming.Gated
+        # If not gated, frame_time and count_time will be used and logic has to be adjusted
+        self._timing = DetectorTiming.GATED
+
+    def on_init(self) -> None:
+        """
+        Called when the device is initialized.
+
+        No siganls are connected at this point,
+        thus should not be set here but in on_connected instead.
+        """
+
+    def on_connected(self) -> None:
+        """
+        Called after the device is connected and its signals are connected.
+        Default values for signals should be set here.
+        """
+        # Stop first in case it was in an uncertain state (i.e. measuring)
+        logger.info(f"On connected for {self.name}")
+        self.jfj_client.stop()
+        # Try to connect, needs to be in Inactive or Error state
+        self.jfj_client.connect_and_initialise(timeout=5)
+
+        # Set energy threshold for EIGER detector
+        threshold_ke_v = 6.200  # Grab this from mono energy pseudo device
+        # Energy threshold provided in DetectorSettings, than it is ignored in DatasetSettings
+
+        # This sets the energy threshold for the EIGER detector
+        settings = DetectorSettings(
+            frame_time_us=int(self.frame_time * 1e6),
+            count_time_us=int(self.count_time * 1e6),
+            eiger_bit_depth=self._bit_depth,
+            eiger_threshold_ke_v=threshold_ke_v,
+            timing=self._timing,
+        )
+        self.jfj_client.set_detector_settings(settings)
+        # Second call is needed to ensure that eiger_threshold_ke_v is set to None
+        # if not, DatasetSettings for eiger_threshold_ke_v will be ignored
+        # settings = DetectorSettings(
+        #     frame_time_us=int(self.frame_time * 1e6),
+        #     count_time_us=int(self.count_time * 1e6),
+        #     eiger_bit_depth=self._bit_depth,
+        #     timing=self._timing,
+        # )
+        # self.jfj_client.set_detector_settings(settings)
+
+    def on_stage(self) -> DeviceStatus | None:
+        """
+        Called while staging the device.
+
+        Information about the upcoming scan can be accessed from the scan_info object.
+        """
+        # Delay generator ddg_jfj needs to be activate
+        ddg = self.device_manager.devices.get("ddg_jfj", None)
+        if ddg is None:
+            logger.warning("ddg_jfj not found in device manager")
+            raise ValueError("ddg_jfj not found in device manager")
+        ntrigger = ddg.compute_num_trigger()
+        if self.scan_info.msg.scan_type == "step":
+            # Energy threshold provided in DetectorSettings, than it is ignored in DatasetSettings
+            print()
+            data_settings = DatasetSettings(
+                image_time_us=int(self.frame_time * 1e6),  # this is frame_time
+                ntrigger=ntrigger,
+                beam_x_pxl=0,
+                beam_y_pxl=0,
+                detector_distance_mm=100,
+                incident_energy_ke_v=10.00,
+                # file_prefix = full_path_to_file,
+            )
+            # status = self.task_handler.submit_task(
+            #     self.jfj_client.start, task_args=(data_settings,), run=True
+            # )
+            # return status
+            self.jfj_client.start(settings=data_settings)
+
+    # This method computes trigger_pulse_width, ntriggers and bit_depth
+    # trigger_pulse_width -> image_time in s (image_time_us)
+    # ntriggers -> number of images per trigger
+    # bit_depth -> 16 or 32
+
+    def on_unstage(self) -> DeviceStatus | None:
+        """Called while unstaging the device."""
+
+    def on_pre_scan(self) -> DeviceStatus | None:
+        """Called right before the scan starts on all devices automatically."""
+
+    def on_trigger(self) -> DeviceStatus | None:
+        """Called when the device is triggered."""
+
+    def on_complete(self) -> DeviceStatus | None:
+        """Called to inquire if a device has completed a scans."""
+
+        def wait_for_complete():
+            timeout = 10
+            for _ in range(timeout):
+                try:
+                    self.jfj_client.wait_till_done(timeout=1)
+                except TimeoutError:
+                    continue
+                except Exception as e:
+                    raise ValueError(f"Error in complete for {self.name}, exception: {e}") from e
+                else:
+                    break
+
+        status = self.task_handler.submit_task(wait_for_complete, run=True)
+        return status
+
+    def on_kickoff(self) -> DeviceStatus | None:
+        """Called to kickoff a device for a fly scan. Has to be called explicitly."""
+
+    def on_stop(self) -> None:
+        """Called when the device is stopped."""
+        self.jfj_client.stop()
+        self.task_handler.shutdown()

csaxs_bec/devices/jungfraujoch/jungfrau_joch_client.py

@@ -0,0 +1,193 @@
+"""Module with client interface for the Jungfrau Joch detector API"""
+
+import enum
+import math
+import time
+
+from bec_lib.logger import bec_logger
+from jfjoch_client.api.default_api import DefaultApi
+from jfjoch_client.api_client import ApiClient
+from jfjoch_client.api_response import ApiResponse
+from jfjoch_client.configuration import Configuration
+from jfjoch_client.models.broker_status import BrokerStatus
+from jfjoch_client.models.dataset_settings import DatasetSettings
+from jfjoch_client.models.detector_settings import DetectorSettings
+from ophyd import Device
+
+logger = bec_logger.logger
+
+
+class JungfrauJochClientError(Exception):
+    """Base class for exceptions in this module."""
+
+
+class DetectorState(str, enum.Enum):
+    """Possible Detector states for Jungfrau Joch detector"""
+
+    INACTIVE = "Inactive"
+    IDLE = "Idle"
+    BUSY = "Busy"
+    MEASURING = "Measuring"
+    PEDESTAL = "Pedestal"
+    ERROR = "Error"
+
+
+class ResponseWaitDone(int, enum.Enum):
+    """Response state for Jungfrau Joch detector wait till done call"""
+
+    DETECTOR_IDLE = 200
+    TIMEOUT_PARAM_OUT_OF_BOUNDS = 400
+    JUNGFRAU_ERROR = 500
+    DETECTOR_INACTIVE = 502
+    TIMEOUT_REACHED = 504
+
+
+class ResponseCancelDone(int, enum.Enum):
+    """HTTP Response for cancel post"""
+
+    CANCEL_SENT_TO_FPGA = 200
+
+
+class JungfrauJochClient:
+    """Thin wrapper around the Jungfrau Joch API client.
+
+    sudo systemctl restart jfjoch_broker
+    sudo systemctl status jfjoch_broker
+
+    It looks as if the detector is not being stopped properly.
+    One module remains running, how can we restart the detector?
+    """
+
+    def __init__(
+        self, host: str = "http://sls-jfjoch-001:8080", parent: Device | None = None
+    ) -> None:
+        self._initialised = False
+        configuration = Configuration(host=host)
+        api_client = ApiClient(configuration)
+        self.api = DefaultApi(api_client)
+        self._parent_name = parent.name if parent else self.__class__.__name__
+
+    @property
+    def jjf_state(self) -> BrokerStatus:
+        """Get the status of JungfrauJoch"""
+        response = self.api.status_get()
+        return BrokerStatus(**response.to_dict())
+
+    @property
+    def initialised(self) -> bool:
+        """Check if jfj is connected and ready to receive commands"""
+        return self._initialised
+
+    @initialised.setter
+    def initialised(self, value: bool) -> None:
+        """Set the connected status"""
+        self._initialised = value
+
+    def get_detector_state(self) -> DetectorState:
+        """Get the status of JungfrauJoch"""
+        return DetectorState(self.jjf_state.state)
+
+    def connect_and_initialise(self, timeout: int = 5) -> None:
+        """Check if JungfrauJoch is connected and ready to receive commands"""
+        status = self.get_detector_state()
+        if status != DetectorState.IDLE:
+            self.api.initialize_post()
+            self.wait_till_done(timeout)  # Blocking call
+        self.initialised = True
+
+    def set_detector_settings(self, settings: dict | DetectorSettings) -> None:
+        """Set the detector settings. JungfrauJoch must be in IDLE, Error or Inactive state.
+        Note, the full settings have to be provided, otherwise the settings will be overwritten with default values.
+
+        Args:
+            settings (dict): dictionary of settings
+        """
+        state = self.api.status_get().state
+        if state not in [DetectorState.IDLE, DetectorState.ERROR, DetectorState.INACTIVE]:
+            time.sleep(1)  # This can be improved.... #TODO
+        state = self.api.status_get().state
+        if state not in [DetectorState.IDLE, DetectorState.ERROR, DetectorState.INACTIVE]:
+            raise JungfrauJochClientError(
+                f"Error in {self._parent_name}. Detector must be in IDLE, ERROR or INACTIVE state to set settings. Current state: {state}"
+            )
+
+        if isinstance(settings, dict):
+            settings = DetectorSettings(**settings)
+        self.api.config_detector_put(detector_settings=settings)
+        # Check with Filip if this call is blocking! also check if put_with_http is better
+
+    def start(self, settings: dict | DatasetSettings) -> None:
+        """Start the mesaurement. DatasetSettings must be provided, and JungfrauJoch must be in IDLE state.
+        The method call is blocking and JungfrauJoch will be ready to measure after the call resolves.
+
+        Args:
+            settings (dict): dictionary of settings
+
+        Please check the DataSettings class for the available settings. Minimum required settings are
+        beam_x_pxl, beam_y_pxl, detector_distance_mm, incident_energy_keV.
+
+        """
+        state = self.get_detector_state()
+        if state != DetectorState.IDLE:
+            raise JungfrauJochClientError(
+                f"Error in {self._parent_name}. Detector must be in IDLE state to set settings. Current state: {state}"
+            )
+
+        if isinstance(settings, dict):
+            settings = DatasetSettings(**settings)
+        try:
+            res: ApiResponse = self.api.start_post_with_http_info(dataset_settings=settings)
+            if res.status_code != 200:
+                response = f"Error in {self._parent_name}, while setting measurement settings {settings}, response: {res}"
+                raise JungfrauJochClientError(response)
+        except JungfrauJochClientError as e:
+            logger.error(e)
+            raise e
+        except Exception as e:
+            response = f"Error in {self._parent_name}, while setting measurement settings {settings}, exception: {e}"
+            logger.error(response)
+            raise JungfrauJochClientError(response) from e
+
+    def stop(self) -> None:
+        """Stop the acquisition"""
+        try:
+            res: ApiResponse = self.api.cancel_post_with_http_info()  # Should we use a timeout?
+            if res.status_code != ResponseCancelDone.CANCEL_SENT_TO_FPGA:
+                response = f"Error in device {self._parent_name} while stopping the measurement. API Response: {res}"
+                raise JungfrauJochClientError(response)
+        except JungfrauJochClientError as e:
+            raise e
+        except Exception as exc:
+            raise JungfrauJochClientError from exc
+
+    def wait_till_done(self, timeout: int = 5) -> None:
+        """Wait for JungfrauJoch to be in Idle state. Blocking call with timeout.
+
+        Args:
+            timeout (int): timeout in seconds
+        """
+        try:
+            response = self.api.wait_till_done_post_with_http_info(math.ceil(timeout / 2))
+            if response.status_code == ResponseWaitDone.DETECTOR_IDLE:
+                return
+            logger.info(
+                f"Waiting for device {self._parent_name}, jungfrau joch to become IDLE, "
+                f"status: {ResponseWaitDone(response.status_code)}; response msg {response}"
+            )
+            response = self.api.wait_till_done_post_with_http_info(math.floor(timeout / 2))
+            if response.status_code == ResponseWaitDone.DETECTOR_IDLE:
+                return
+        except Exception as e:
+            logger.error(
+                f"Error in device {self._parent_name} while waiting for JungfrauJoch to initialise: {e}"
+            )
+            raise JungfrauJochClientError(
+                f"Error in device {self._parent_name} while waiting for JungfrauJoch to initialise. Exception: {e}"
+            ) from e
+        # If the response is IDLE, this part is never reached. We will raise a TimeoutError.
+        msg = (
+            f"TimeoutError in device {self._parent_name}, failed to initialise JungfrauJoch with status:"
+            f"{response.status_code}; response msg {response}"
+        )
+        logger.error(msg)
+        raise TimeoutError(msg)

csaxs_bec/devices/jungfraujoch/readout_constants.py

@@ -0,0 +1,4 @@
+"""Readout constants for all relevant detectors at cSAXS beamline."""
+
+# -> should 20e-6, 20us : parallel vs nonparallel, exact values to be checked
+EIGER9M_READOUT_TIME_32BIT = 100e-6  # s

csaxs_bec/devices/npoint/npoint.py

@@ -1,12 +1,15 @@
 import functools
-import socket
 import threading
 import time
 
-from ophyd_devices.utils.controller import threadlocked
-from ophyd_devices.utils.socket import raise_if_disconnected
+import numpy as np
+from ophyd import Component as Cpt
+from ophyd import Device, PositionerBase, Signal, SignalRO
+from ophyd.status import wait as status_wait
+from ophyd.utils import LimitError, ReadOnlyError
+from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
 from prettytable import PrettyTable
-from typeguard import typechecked
 
 
 def channel_checked(fcn):
@@ -14,81 +17,32 @@ def channel_checked(fcn):
 
     @functools.wraps(fcn)
     def wrapper(self, *args, **kwargs):
+        # pylint: disable=protected-access
         self._check_channel(args[0])
         return fcn(self, *args, **kwargs)
 
     return wrapper
 
 
-class SocketIO:
-    """SocketIO helper class for TCP IP connections"""
-
-    def __init__(self, sock=None):
-        self.is_open = False
-        if sock is None:
-            self.open()
-        else:
-            self.sock = sock
-
-    def connect(self, host, port):
-        print(f"connecting to {host} port {port}")
-        # self.sock.create_connection((host, port))
-        self.sock.connect((host, port))
-
-    def _put(self, msg_bytes):
-        return self.sock.send(msg_bytes)
-
-    def _recv(self, buffer_length=1024):
-        return self.sock.recv(buffer_length)
-
-    def _initialize_socket(self):
-        self.sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-        self.sock.settimeout(5)
-
-    def put(self, msg):
-        return self._put(msg)
-
-    def receive(self, buffer_length=1024):
-        return self._recv(buffer_length=buffer_length)
-
-    def open(self):
-        self._initialize_socket()
-        self.is_open = True
-
-    def close(self):
-        self.sock.close()
-        self.sock = None
-        self.is_open = False
+class NpointError(Exception):
+    """
+    Base class for Npoint errors.
+    """
 
 
-class NPointController:
-    _controller_instance = None
+class NPointController(Controller):
+    """
+    Controller for nPoint piezo stages. This class inherits from the Controller class
+    and provides a singleton interface to the nPoint controller.
+    """
 
-    NUM_CHANNELS = 3
+    _axes_per_controller = 3
     _read_single_loc_bit = "A0"
     _write_single_loc_bit = "A2"
     _trailing_bit = "55"
     _range_offset = "78"
     _channel_base = ["11", "83"]
 
-    def __init__(
-        self, comm_socket: SocketIO, server_ip: str = "129.129.99.87", server_port: int = 23
-    ) -> None:
-        self._lock = threading.RLock()
-        super().__init__()
-        self._server_and_port_name = (server_ip, server_port)
-        self.socket = comm_socket
-        self.connected = False
-
-    def __new__(cls, *args, **kwargs):
-        if not NPointController._controller_instance:
-            NPointController._controller_instance = object.__new__(cls)
-        return NPointController._controller_instance
-
-    @classmethod
-    def create(cls):
-        return cls(SocketIO())
-
     def show_all(self) -> None:
         """Display current status of all channels
 
@@ -98,54 +52,13 @@ class NPointController:
         if not self.connected:
             print("npoint controller is currently disabled.")
             return
-        print(f"Connected to controller at {self._server_and_port_name}")
+        print(f"Connected to controller at {self._socket_host}:{self._socket_port}")
         t = PrettyTable()
         t.field_names = ["Channel", "Range", "Position", "Target"]
-        for ii in range(self.NUM_CHANNELS):
-            t.add_row(
-                [ii, self._get_range(ii), self._get_current_pos(ii), self._get_target_pos(ii)]
-            )
+        for ii in range(self._axes_per_controller):
+            t.add_row([ii, self._get_range(ii), self.get_current_pos(ii), self.get_target_pos(ii)])
         print(t)
 
-    @threadlocked
-    def on(self) -> None:
-        """Enable the NPoint controller and open a new socket.
-
-        Raises:
-            TimeoutError: Raised if the socket connection raises a timeout.
-
-        Returns:
-            None
-        """
-        if self.connected:
-            print("You are already connected to the NPoint controller.")
-            return
-        if not self.socket.is_open:
-            self.socket.open()
-        try:
-            self.socket.connect(self._server_and_port_name[0], self._server_and_port_name[1])
-        except socket.timeout:
-            raise TimeoutError(
-                f"Failed to connect to the specified server and port {self._server_and_port_name}."
-            )
-        except OSError:
-            print("ERROR while connecting. Let's try again")
-            self.socket.close()
-            time.sleep(0.5)
-            self.socket.open()
-            self.socket.connect(self._server_and_port_name[0], self._server_and_port_name[1])
-        self.connected = True
-
-    @threadlocked
-    def off(self) -> None:
-        """Disable the controller and close the socket.
-
-        Returns:
-            None
-        """
-        self.socket.close()
-        self.connected = False
-
     @channel_checked
     def _get_range(self, channel: int) -> int:
         """Get the range of the specified channel axis.
@@ -174,7 +87,7 @@ class NPointController:
         return device_range
 
     @channel_checked
-    def _get_current_pos(self, channel: int) -> float:
+    def get_current_pos(self, channel: int) -> float:
         # for first channel: 0x11 83 13 34
         addr = self._channel_base.copy()
         addr.extend([f"{19 + 16 * channel:x}", "34"])
@@ -187,7 +100,7 @@ class NPointController:
         return pos
 
     @channel_checked
-    def _set_target_pos(self, channel: int, pos: float) -> None:
+    def set_target_pos(self, channel: int, pos: float) -> None:
         # for first channel: 0x11 83 12 18 00 00 00 00
         addr = self._channel_base.copy()
         addr.extend([f"{18 + channel * 16:x}", "18"])
@@ -199,7 +112,7 @@ class NPointController:
         self._put(send_buffer)
 
     @channel_checked
-    def _get_target_pos(self, channel: int) -> float:
+    def get_target_pos(self, channel: int) -> float:
         # for first channel: 0x11 83 12 18
         addr = self._channel_base.copy()
         addr.extend([f"{18 + channel * 16:x}", "18"])
@@ -214,17 +127,17 @@ class NPointController:
     def _set_servo(self, channel: int, enable: bool) -> None:
         print("Not tested")
         return
-        # for first channel: 0x11 83 10 84 00 00 00 00
-        addr = self._channel_base.copy()
-        addr.extend([f"{16 + channel * 16:x}", "84"])
+        # # for first channel: 0x11 83 10 84 00 00 00 00
+        # addr = self._channel_base.copy()
+        # addr.extend([f"{16 + channel * 16:x}", "84"])
 
-        if enable:
-            data = ["00"] * 3 + ["01"]
-        else:
-            data = ["00"] * 4
-        send_buffer = self.__write_single_location_buffer(addr, data)
+        # if enable:
+        #     data = ["00"] * 3 + ["01"]
+        # else:
+        #     data = ["00"] * 4
+        # send_buffer = self.__write_single_location_buffer(addr, data)
 
-        self._put(send_buffer)
+        # self._put(send_buffer)
 
     @channel_checked
     def _get_servo(self, channel: int) -> int:
@@ -250,7 +163,7 @@ class NPointController:
         """
 
         buffer = b"".join([bytes.fromhex(m) for m in buffer])
-        self.socket.put(buffer)
+        self.sock.put(buffer)
 
     @threadlocked
     def _put_and_receive(self, msg_hex_list: list) -> list:
@@ -264,8 +177,8 @@ class NPointController:
         """
 
         buffer = b"".join([bytes.fromhex(m) for m in msg_hex_list])
-        self.socket.put(buffer)
-        recv_msg = self.socket.receive()
+        self.sock.put(buffer)
+        recv_msg = self.sock.receive()
         recv_hex_list = [hex(m) for m in recv_msg]
         self._verify_received_msg(msg_hex_list, recv_hex_list)
         return recv_hex_list
@@ -293,9 +206,9 @@ class NPointController:
             raise RuntimeError("Connection failure. Please restart the controller.")
 
     def _check_channel(self, channel: int) -> None:
-        if channel >= self.NUM_CHANNELS:
+        if channel >= self._axes_per_controller:
             raise ValueError(
-                f"Channel {channel+1} exceeds the available number of channels ({self.NUM_CHANNELS})"
+                f"Channel {channel+1} exceeds the available number of channels ({self._axes_per_controller})"
             )
 
     @staticmethod
@@ -391,155 +304,285 @@ class NPointController:
             self.off()
 
 
-class NPointAxis:
-    def __init__(self, controller: NPointController, channel: int, name: str) -> None:
-        super().__init__()
-        self._axis_range = 100
-        self.controller = controller
-        self.channel = channel
-        self.name = name
-        self.controller._check_channel(channel)
-        self._settling_time = 0.1
+class NpointSignalBase(SocketSignal):
+    """
+    Base class for nPoint signals.
+    """
 
-        if self.settling_time == 0:
-            self.settling_time = 0.1
-            print(f"Setting the npoint settling time to {self.settling_time:.2f} s.")
-            print(
-                "You can set the settling time depending on the stage tuning\nusing the settling_time property."
-            )
-            print("This is the waiting time before the counting is done.")
+    def __init__(self, signal_name, **kwargs):
+        self.signal_name = signal_name
+        super().__init__(**kwargs)
+        self.controller: NPointController = self.parent.controller
+        self.sock = self.parent.controller.sock
 
-    def show_all(self) -> None:
-        self.controller.show_all()
 
-    @raise_if_disconnected
-    def get(self) -> float:
-        """Get current position for this channel.
+class NpointSignalRO(NpointSignalBase):
+    """
+    Base class for read-only signals.
+    """
 
-        Raises:
-            RuntimeError: Raised if channel is not connected.
+    def __init__(self, signal_name, **kwargs):
+        super().__init__(signal_name, **kwargs)
+        self._metadata["write_access"] = False
 
-        Returns:
-            float: position
+    @threadlocked
+    def _socket_set(self, val):
+        raise ReadOnlyError("Read-only signals cannot be set")
+
+
+class NpointReadbackSignal(NpointSignalRO):
+    """
+    Signal to read the current position of an nPoint piezo stage.
+    """
+
+    @threadlocked
+    def _socket_get(self):
+
+        return self.controller.get_current_pos(self.parent.axis_Id_numeric) * self.parent.sign
+
+
+class NpointSetpointSignal(NpointSignalBase):
+    """
+    Signal to set the target position of an nPoint piezo stage.
+    """
+
+    setpoint = 0
+
+    @threadlocked
+    def _socket_get(self):
+        return self.controller.get_target_pos(self.parent.axis_Id_numeric) * self.parent.sign
+
+    @threadlocked
+    def _socket_set(self, val):
+        target_val = val * self.parent.sign
+        self.setpoint = target_val
+        return self.controller.set_target_pos(
+            self.parent.axis_Id_numeric, target_val * self.parent.sign
+        )
+
+
+class NpointMotorIsMoving(SignalRO):
+    """
+    Signal to indicate whether the motor is currently moving or not.
+    """
+
+    def set_motor_is_moving(self, value: int) -> None:
         """
-        return self.controller._get_current_pos(self.channel)
-
-    @raise_if_disconnected
-    def get_target_pos(self) -> float:
-        """Get target position for this channel.
-
-        Raises:
-            RuntimeError: Raised if channel is not connected.
-
-        Returns:
-            float: position
-        """
-        return self.controller._get_target_pos(self.channel)
-
-    @raise_if_disconnected
-    @typechecked
-    def set(self, pos: float) -> None:
-        """Set a new target position and wait until settled (settling_time).
+        Set the motor_is_moving signal to the specified value.
 
         Args:
-            pos (float): New target position
-
-        Raises:
-            RuntimeError: Raised if channel is not connected.
-
-        Returns:
-            None
+            value (int): 1 if the motor is moving, 0 otherwise.
         """
-        self.controller._set_target_pos(self.channel, pos)
-        time.sleep(self.settling_time)
+        self._readback = value
+
+
+class NPointAxis(Device, PositionerBase):
+    """
+    NPointAxis class, which inherits from Device and PositionerBase. This class
+    represents an axis of an nPoint piezo stage and provides the necessary
+    functionality to move the axis and read its current position.
+    """
+
+    USER_ACCESS = ["controller"]
+    readback = Cpt(NpointReadbackSignal, signal_name="readback", kind="hinted")
+    user_setpoint = Cpt(NpointSetpointSignal, signal_name="setpoint")
+
+    motor_is_moving = Cpt(NpointMotorIsMoving, value=0, kind="normal")
+    settling_time = Cpt(Signal, value=0.1, kind="config")
+    high_limit_travel = Cpt(Signal, value=0, kind="omitted")
+    low_limit_travel = Cpt(Signal, value=0, kind="omitted")
+
+    SUB_READBACK = "readback"
+    SUB_CONNECTION_CHANGE = "connection_change"
+    _default_sub = SUB_READBACK
+
+    def __init__(
+        self,
+        axis_Id,
+        prefix="",
+        *,
+        name,
+        kind=None,
+        read_attrs=None,
+        configuration_attrs=None,
+        parent=None,
+        host="mpc2680.psi.ch",
+        port=8085,
+        limits=None,
+        sign=1,
+        socket_cls=SocketIO,
+        tolerance: float = 0.05,
+        **kwargs,
+    ):
+        self.controller = NPointController(
+            socket_cls=socket_cls, socket_host=host, socket_port=port
+        )
+        self.axis_Id = axis_Id
+        self.sign = sign
+        self.controller.set_axis(axis=self, axis_nr=self.axis_Id_numeric)
+        self.tolerance = tolerance
+
+        super().__init__(
+            prefix,
+            name=name,
+            kind=kind,
+            read_attrs=read_attrs,
+            configuration_attrs=configuration_attrs,
+            parent=parent,
+            **kwargs,
+        )
+        self.readback.name = self.name
+        self.controller.subscribe(
+            self._update_connection_state, event_type=self.SUB_CONNECTION_CHANGE
+        )
+        self._update_connection_state()
+        if limits is not None:
+            assert len(limits) == 2
+            self.low_limit_travel.put(limits[0])
+            self.high_limit_travel.put(limits[1])
 
     @property
-    def connected(self) -> bool:
-        return self.controller.connected
+    def limits(self):
+        return (self.low_limit_travel.get(), self.high_limit_travel.get())
 
     @property
+    def low_limit(self):
+        return self.limits[0]
+
+    @property
+    def high_limit(self):
+        return self.limits[1]
+
+    def check_value(self, pos):
+        """Check that the position is within the soft limits"""
+        low_limit, high_limit = self.limits
+
+        if low_limit < high_limit and not (low_limit <= pos <= high_limit):
+            raise LimitError(f"position={pos} not within limits {self.limits}")
+
+    def _update_connection_state(self, **kwargs):
+        for walk in self.walk_signals():
+            walk.item._metadata["connected"] = self.controller.connected
+
     @raise_if_disconnected
-    def servo(self) -> int:
-        """Get servo status
+    def move(self, position, wait=True, **kwargs):
+        """Move to a specified position, optionally waiting for motion to
+        complete.
 
-        Raises:
-            RuntimeError: Raised if channel is not connected.
+        Parameters
+        ----------
+        position
+            Position to move to
+        moved_cb : callable
+            Call this callback when movement has finished. This callback must
+            accept one keyword argument: 'obj' which will be set to this
+            positioner instance.
+        timeout : float, optional
+            Maximum time to wait for the motion. If None, the default timeout
+            for this positioner is used.
 
-        Returns:
-            int: Servo status
+        Returns
+        -------
+        status : MoveStatus
+
+        Raises
+        ------
+        TimeoutError
+            When motion takes longer than `timeout`
+        ValueError
+            On invalid positions
+        RuntimeError
+            If motion fails other than timing out
         """
-        return self.controller._get_servo(self.channel)
+        self._started_moving = False
+        timeout = kwargs.pop("timeout", 10)
+        status = super().move(position, timeout=timeout, **kwargs)
+        self.user_setpoint.put(position, wait=False)
 
-    @servo.setter
-    @raise_if_disconnected
-    @typechecked
-    def servo(self, val: bool) -> None:
-        """Set servo status
+        def move_and_finish():
+            self.motor_is_moving.set_motor_is_moving(1)
+            val = self.readback.read()
+            self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+            time.sleep(self.settling_time.get())
+            self.motor_is_moving.set_motor_is_moving(0)
+            val = self.readback.read()
+            self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+            success = np.isclose(val[self.name]["value"], position, atol=self.tolerance)
+            self._done_moving(success=success)
+
+        threading.Thread(target=move_and_finish, daemon=True).start()
+        try:
+            if wait:
+                status_wait(status)
+        except KeyboardInterrupt:
+            self.stop()
+            raise
+
+        return status
+
+    @property
+    def axis_Id(self):
+        """
+        Return the axis_Id_alpha.
+        """
+        return self._axis_Id_alpha
+
+    @axis_Id.setter
+    def axis_Id(self, val: str):
+        """
+        Set the axis_Id_alpha and axis_Id_numeric based on the alpha value.
 
         Args:
-            val (bool): Servo status
-
-        Raises:
-            RuntimeError: Raised if channel is not connected.
-
-        Returns:
-            None
+            val (str): Single-character axis identifier.
         """
-        self.controller._set_servo(self.channel, val)
-
-    @property
-    def settling_time(self) -> float:
-        return self._settling_time
-
-    @settling_time.setter
-    @typechecked
-    def settling_time(self, val: float) -> None:
-        self._settling_time = val
-        print(f"Setting the npoint settling time to {val:.2f} s.")
-
-
-class NPointEpics(NPointAxis):
-    def __init__(self, controller: NPointController, channel: int, name: str) -> None:
-        super().__init__(controller, channel, name)
-        self.low_limit = -50
-        self.high_limit = 50
-        self._prefix = name
-
-    def get_pv(self) -> str:
-        return self.name
-
-    def get_position(self, readback=True) -> float:
-        if readback:
-            return self.get()
+        if isinstance(val, str):
+            if len(val) != 1:
+                raise ValueError("Only single-character axis_Ids are supported.")
+            self._axis_Id_alpha = val
+            self._axis_Id_numeric = ord(val.lower()) - 97
         else:
-            return self.get_target_pos()
+            raise TypeError(f"Expected value of type str but received {type(val)}")
 
-    def within_limits(self, pos: float) -> bool:
-        return pos > self.low_limit and pos < self.high_limit
+    @property
+    def axis_Id_numeric(self):
+        """
+        Return the numeric value of the axis_Id.
+        """
+        return self._axis_Id_numeric
 
-    def move(self, position: float, wait=True) -> None:
-        self.set(position)
+    @axis_Id_numeric.setter
+    def axis_Id_numeric(self, val: int):
+        """
+        Set the axis_Id_numeric and axis_Id_alpha based on the numeric value.
+
+        Args:
+            val (int): Numeric axis identifier.
+        """
+        if isinstance(val, int):
+            if val > 26:
+                raise ValueError("Numeric value exceeds supported range.")
+            self._axis_Id_alpha = val
+            self._axis_Id_numeric = (chr(val + 97)).capitalize()
+        else:
+            raise TypeError(f"Expected value of type int but received {type(val)}")
+
+    @property
+    def egu(self):
+        """The engineering units (EGU) for positions"""
+        return "um"
+
+    def stage(self) -> list[object]:
+        return super().stage()
+
+    def unstage(self) -> list[object]:
+        return super().unstage()
 
 
 if __name__ == "__main__":
-    ## EXAMPLES ##
-    #
-    # Create controller and socket instance explicitly:
-    #     controller = NPointController(SocketIO())
-    #     npointx = NPointAxis(controller, 0, "nx")
-    #     npointy = NPointAxis(controller, 1, "ny")
-
-    # Create controller instance explicitly
-    #     controller = NPointController.create()
-    #     npointx = NPointAxis(controller, 0, "nx")
-    #     npointy = NPointAxis(controller, 1, "ny")
-
-    # Single-line axis:
-    #     npointx = NPointAxis(NPointController.create(), 0, "nx")
-    #
-    # EPICS wrapper:
-    #     nx = NPointEpics(NPointController.create(), 0, "nx")
-
-    controller = NPointController.create()
-    npointx = NPointAxis(NPointController.create(), 0, "nx")
-    npointy = NPointAxis(NPointController.create(), 0, "ny")
+    npx = NPointAxis(axis_Id="A", name="npx", host="nPoint000003.psi.ch", port=23)
+    npy = NPointAxis(axis_Id="B", name="npy", host="nPoint000003.psi.ch", port=23)
+    npx.controller.on()
+    print("socket is open, axis is ready!")
+    npx.move(10)
+    print(npx.read())
+    npx.controller.off()

csaxs_bec/devices/omny/galil/fgalil_ophyd.py

@@ -141,7 +141,7 @@ class FlomniGalilAxesReferenced(GalilAxesReferenced):
 
 
 class FlomniGalilMotor(Device, PositionerBase):
-    USER_ACCESS = ["controller"]
+    USER_ACCESS = ["controller", "drive_axis_to_limit"]
     readback = Cpt(FlomniGalilReadbackSignal, signal_name="readback", kind="hinted")
     user_setpoint = Cpt(FlomniGalilSetpointSignal, signal_name="setpoint")
     motor_resolution = Cpt(FlomniGalilMotorResolution, signal_name="resolution", kind="config")
@@ -337,6 +337,18 @@ class FlomniGalilMotor(Device, PositionerBase):
     def unstage(self) -> list[object]:
         return super().unstage()
 
+    def drive_axis_to_limit(self, direction: str) -> None:
+        """
+        Drive an axis to the limit in a specified direction.
+
+        Args:
+            direction (str): Direction in which the axis should be driven to the limit. Either 'forward' or 'reverse'.        
+        """
+        self.controller.drive_axis_to_limit(self.axis_Id_numeric, direction)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
     def stop(self, *, success=False):
         self.controller.stop_all_axes()
         return super().stop(success=success)

csaxs_bec/devices/omny/galil/fupr_ophyd.py

@@ -17,8 +17,8 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilError,
     GalilMotorIsMoving,
     GalilMotorResolution,
-    GalilReadbackSignal,
     GalilSetpointSignal,
+    GalilSignalRO,
     retry_once,
 )
 
@@ -44,7 +44,7 @@ class FuprGalilController(GalilController):
         raise NotImplementedError("This function is not implemented for the FuprGalilController.")
 
 
-class FuprGalilReadbackSignal(GalilReadbackSignal):
+class FuprGalilReadbackSignal(GalilSignalRO):
     @retry_once
     @threadlocked
     def _socket_get(self) -> float:

csaxs_bec/devices/omny/galil/galil_ophyd.py

@@ -59,6 +59,13 @@ class GalilController(Controller):
         "all_axes_referenced",
     ]
 
+    OKBLUE = '\033[94m'
+    OKCYAN = '\033[96m'
+    OKGREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+
     @threadlocked
     def socket_put(self, val: str) -> None:
         self.sock.put(f"{val}\r".encode())
@@ -98,21 +105,64 @@ class GalilController(Controller):
         return True
 
     def stop_all_axes(self) -> str:
-        return self.socket_put_and_receive("XQ#STOP,1")
+        if not self.is_thread_active(1):
+            return self.socket_put_and_receive("XQ#STOP,1")
+        else:
+            return ":"
 
     def get_digital_input(self, channel):
         return bool(float(self.socket_put_and_receive(f"MG @IN[{channel}]").strip()))
 
     def axis_is_referenced(self, axis_Id_numeric) -> bool:
         return bool(float(self.socket_put_and_receive(f"MG axisref[{axis_Id_numeric}]").strip()))
+    
+    def folerr_status(self, axis_Id_numeric) -> bool:
+        return bool(float(self.socket_put_and_receive(f"MG folaxerr[{axis_Id_numeric}]").strip()))
+
+    def motor_temperature(self, axis_Id_numeric) -> float:
+        #this is only valid for omny. consider moving to ogalil
+        voltage = float(self.socket_put_and_receive(f"MG @AN[{axis_Id_numeric+1}]").strip())
+        voltage2 = float(self.socket_put_and_receive(f"MG @AN[{axis_Id_numeric+1}]").strip())
+        if voltage2 < voltage:
+            voltage = voltage2
+        # convert from [-10,10]V to [0,300]degC
+        temperature_degC = round((voltage+10.0) / 20.0 * 300.0, 1)
+
+        #the motors of the parking station have a different offset
+        #the range is reduced, so if at the limit, we show an extreme value
+        if self.sock.port == 8082:
+            #controller 2
+            if axis_Id_numeric == 6:
+                temperature_degC = round((voltage+10.0-11.4) / 20.0 * 300.0, 1)
+                if voltage > 9.9:
+                    temperature_degC = 300
+            if axis_Id_numeric == 7:
+                temperature_degC = round((voltage+.0-12) / 20.0 * 300.0, 1)
+                if voltage > 9.9:
+                    temperature_degC = 300
+        return temperature_degC
 
     def all_axes_referenced(self) -> bool:
         """
         Check if all axes are referenced.
         """
         return bool(float(self.socket_put_and_receive("MG allaxref").strip()))
+    
+    def _omny_get_microstep_position(self,axis_Id):
+        return float(self.socket_put_and_receive(f"MG _TD{axis_Id}").strip())
+    
+    
+    def _omny_get_reference_limit(self,axis_Id):
+        get_axis_no = float(self.socket_put_and_receive(f"MG frmmv").strip())
+        if(get_axis_no>0):
+            reference_is_before = float(self.socket_put_and_receive(f"MG _FL{axis_Id}").strip())
+        elif(get_axis_no<0):
+            reference_is_before = float(self.socket_put_and_receive(f"MG _BL{axis_Id}").strip())
+        else:
+            reference_is_before = 0
+        return reference_is_before
 
-    def drive_axis_to_limit(self, axis_Id_numeric: int, direction: str) -> None:
+    def drive_axis_to_limit(self, axis_Id_numeric: int, direction: str, verbose=0) -> None:
         """
         Drive an axis to the limit in a specified direction.
 
@@ -133,10 +183,13 @@ class GalilController(Controller):
         time.sleep(0.1)
         self.socket_put_confirmed("XQ#FES")
         time.sleep(0.1)
+        axis_Id = self.axis_Id_numeric_to_alpha(axis_Id_numeric)
         while self.is_axis_moving(None, axis_Id_numeric):
             time.sleep(0.01)
+            if verbose:
+                self.get_device_manager().connector.send_client_info(f"Current microstep position {self._omny_get_microstep_position(axis_Id):.0f}", scope="drive axis to limit", show_asap=True)
+                time.sleep(0.5)
 
-        axis_Id = self.axis_Id_numeric_to_alpha(axis_Id_numeric)
         # check if we actually hit the limit
         if direction == "forward":
             limit = self.get_motor_limit_switch(axis_Id)[1]
@@ -145,8 +198,16 @@ class GalilController(Controller):
 
         if not limit:
             raise GalilError(f"Failed to drive axis {axis_Id}/{axis_Id_numeric} to limit.")
+        else:
+            print("Limit reached.")
 
-    def find_reference(self, axis_Id_numeric: int) -> None:
+    def get_device_manager(self):
+        for axis in self._axis:
+            if hasattr(axis, "device_manager") and axis.device_manager:
+                return axis.device_manager
+        raise BECConfigError("Could not access the device_manager")
+
+    def find_reference(self, axis_Id_numeric: int, verbose=0, raise_error = 1) -> None:
         """
         Find the reference of an axis.
 
@@ -159,14 +220,23 @@ class GalilController(Controller):
         time.sleep(0.1)
         self.socket_put_confirmed("XQ#FRM")
         time.sleep(0.1)
+        axis_Id = self.axis_Id_numeric_to_alpha(axis_Id_numeric)
         while self.is_axis_moving(None, axis_Id_numeric):
             time.sleep(0.1)
+            if verbose:
+                self.get_device_manager().connector.send_client_info(f"Current microstep position {self._omny_get_microstep_position(axis_Id):.0f} reference is before {self._omny_get_reference_limit(axis_Id)}", scope="find axis reference", show_asap=True)
+                time.sleep(0.5)
 
         if not self.axis_is_referenced(axis_Id_numeric):
-            raise GalilError(f"Failed to find reference of axis {axis_Id_numeric}.")
-
-        logger.info(f"Successfully found reference of axis {axis_Id_numeric}.")
+            if raise_error:
+                raise GalilError(f"Failed to find reference of axis {axis_Id_numeric}.")
+            else:
+                print(f"Failed to find reference of axis {axis_Id_numeric}.")
+        else:
+            logger.info(f"Successfully found reference of axis {axis_Id_numeric}.")
+            print(f"Successfully found reference of axis {axis_Id_numeric}.")
 
+        
     def show_running_threads(self) -> None:
         t = PrettyTable()
         t.title = f"Threads on {self.sock.host}:{self.sock.port}"
@@ -181,7 +251,7 @@ class GalilController(Controller):
 
     def is_motor_on(self, axis_Id) -> bool:
         return not bool(float(self.socket_put_and_receive(f"MG _MO{axis_Id}").strip()))
-
+    
     def get_motor_limit_switch(self, axis_Id) -> list:
         """
         Get the status of the motor limit switches.
@@ -199,29 +269,60 @@ class GalilController(Controller):
     def describe(self) -> None:
         t = PrettyTable()
         t.title = f"{self.__class__.__name__} on {self.sock.host}:{self.sock.port}"
-        t.field_names = [
+        field_names = [
             "Axis",
             "Name",
-            "Connected",
             "Referenced",
             "Motor On",
             "Limits",
             "Position",
         ]
+        # in case of OMNY
+        if self.sock.host == "mpc3217.psi.ch":
+            field_names.append("Temperature")
+            field_names.append("FolErr")
+        t.field_names = field_names
         for ax in range(self._axes_per_controller):
             axis = self._axis[ax]
             if axis is not None:
-                t.add_row(
-                    [
-                        f"{axis.axis_Id_numeric}/{axis.axis_Id}",
-                        axis.name,
-                        axis.connected,
-                        self.axis_is_referenced(axis.axis_Id_numeric),
-                        self.is_motor_on(axis.axis_Id),
-                        self.get_motor_limit_switch(axis.axis_Id),
-                        axis.readback.read().get(axis.name).get("value"),
-                    ]
-                )
+                if self.sock.host == "mpc3217.psi.ch":
+                    #case of omny. possibly consider moving to ogalil
+                    motor_on = self.is_motor_on(axis.axis_Id)
+                    if motor_on == True:
+                        motor_on = self.WARNING + "ON" + self.ENDC
+                    else:
+                        motor_on = "OFF"
+
+                    folerr_status = self.folerr_status(axis.axis_Id_numeric)
+                    if folerr_status == True:
+                        folerr_status = self.WARNING + "True" + self.ENDC
+                    else:
+                        folerr_status = "False"
+                    position = axis.readback.read().get(axis.name).get("value")
+                    position = f'{position:.3f}'
+                    t.add_row(
+                        [
+                            f"{axis.axis_Id_numeric}/{axis.axis_Id}",
+                            axis.name,
+                            self.axis_is_referenced(axis.axis_Id_numeric),
+                            motor_on,
+                            self.get_motor_limit_switch(axis.axis_Id),
+                            position,
+                            self.motor_temperature(axis.axis_Id_numeric),
+                            self.folerr_status(axis.axis_Id_numeric),
+                        ]
+                    )
+                else:
+                    t.add_row(
+                        [
+                            f"{axis.axis_Id_numeric}/{axis.axis_Id}",
+                            axis.name,
+                            self.axis_is_referenced(axis.axis_Id_numeric),
+                            self.is_motor_on(axis.axis_Id),
+                            self.get_motor_limit_switch(axis.axis_Id),
+                            axis.readback.read().get(axis.name).get("value"),
+                        ]
+                    )
             else:
                 t.add_row([None for t in t.field_names])
         print(t)
@@ -229,6 +330,8 @@ class GalilController(Controller):
         self.show_running_threads()
         self.show_status_other()
 
+
+
     def show_status_other(self) -> None:
         """
         Show additional device-specific status information.
@@ -254,7 +357,6 @@ class GalilSignalBase(SocketSignal):
         self.signal_name = signal_name
         super().__init__(**kwargs)
         self.controller = self.parent.controller
-        self.sock = self.parent.controller.sock
 
 
 class GalilSignalRO(GalilSignalBase):
@@ -275,7 +377,6 @@ class GalilReadbackSignal(GalilSignalRO):
         Returns:
             float: Readback value after adjusting for sign and motor resolution.
         """
-
         current_pos = float(self.controller.socket_put_and_receive(f"TD{self.parent.axis_Id}"))
         current_pos *= self.parent.sign
         step_mm = self.parent.motor_resolution.get()
@@ -284,13 +385,6 @@ class GalilReadbackSignal(GalilSignalRO):
     def read(self):
         self._metadata["timestamp"] = time.time()
         val = super().read()
-        if self.parent.axis_Id_numeric == 2:
-            try:
-                rt = self.parent.device_manager.devices[self.parent.rt]
-                if rt.enabled:
-                    rt.obj.controller.set_rotation_angle(val[self.parent.name]["value"])
-            except KeyError:
-                logger.warning("Failed to set RT value during readback.")
         return val
 
 
@@ -326,7 +420,8 @@ class GalilSetpointSignal(GalilSignalBase):
             while self.controller.is_thread_active(0):
                 time.sleep(0.1)
 
-            if self.parent.axis_Id_numeric == 2:
+            #in the case of lamni, consider moving to lgalil
+            if self.parent.axis_Id_numeric == 2 and self.controller.sock.host == "mpc2680.psi.ch":
                 try:
                     rt = self.parent.device_manager.devices[self.parent.rt]
                     if rt.enabled:

csaxs_bec/devices/omny/galil/lgalil_ophyd.py

@@ -7,6 +7,7 @@ from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
+from ophyd_devices.utils.controller import threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
@@ -15,8 +16,9 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilController,
     GalilMotorIsMoving,
     GalilMotorResolution,
-    GalilReadbackSignal,
     GalilSetpointSignal,
+    GalilSignalRO,
+    retry_once,
 )
 
 logger = bec_logger.logger
@@ -71,10 +73,35 @@ class LamniGalilController(GalilController):
         air_off = bool(self.socket_put_and_receive("MG@OUT[13]"))
         return rt_not_blocked_by_galil and air_off
 
+class LamniGalilReadbackSignal(GalilSignalRO):
+    @retry_once
+    @threadlocked
+    def _socket_get(self) -> float:
+        """Get command for the readback signal
+
+        Returns:
+            float: Readback value after adjusting for sign and motor resolution.
+        """
+        current_pos = float(self.controller.socket_put_and_receive(f"TD{self.parent.axis_Id}"))
+        current_pos *= self.parent.sign
+        step_mm = self.parent.motor_resolution.get()
+        return current_pos / step_mm
+
+    def read(self):
+        self._metadata["timestamp"] = time.time()
+        val = super().read()
+        if self.parent.axis_Id_numeric == 2:
+            try:
+                rt = self.parent.device_manager.devices[self.parent.rtx]
+                if rt.enabled:
+                    rt.obj.controller.set_rotation_angle(val[self.parent.name]["value"])
+            except KeyError:
+                logger.warning("Failed to set RT value during readback.")
+        return val
 
 class LamniGalilMotor(Device, PositionerBase):
-    USER_ACCESS = ["controller"]
-    readback = Cpt(GalilReadbackSignal, signal_name="readback", kind="hinted")
+    USER_ACCESS = ["controller", "drive_axis_to_limit", "find_reference"]
+    readback = Cpt(LamniGalilReadbackSignal, signal_name="readback", kind="hinted")
     user_setpoint = Cpt(GalilSetpointSignal, signal_name="setpoint")
     motor_resolution = Cpt(GalilMotorResolution, signal_name="resolution", kind="config")
     motor_is_moving = Cpt(GalilMotorIsMoving, signal_name="motor_is_moving", kind="normal")
@@ -260,6 +287,27 @@ class LamniGalilMotor(Device, PositionerBase):
         """The engineering units (EGU) for positions"""
         return "mm"
 
+    def find_reference(self):
+        """
+        Find the reference of the axis.
+        """
+        self.controller.find_reference(self.axis_Id_numeric)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
+    def drive_axis_to_limit(self, direction: str) -> None:
+        """
+        Drive an axis to the limit in a specified direction.
+
+        Args:
+            direction (str): Direction in which the axis should be driven to the limit. Either 'forward' or 'reverse'.        
+        """
+        self.controller.drive_axis_to_limit(self.axis_Id_numeric, direction)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
     def stop(self, *, success=False):
         self.controller.stop_all_axes()
         return super().stop(success=success)

csaxs_bec/devices/omny/galil/ogalil_ophyd.py

@@ -0,0 +1,515 @@
+import functools
+import threading
+import time
+import urllib.request
+import xml.etree.ElementTree as ET
+
+import numpy as np
+from bec_lib.logger import bec_logger
+from ophyd import Component as Cpt
+from ophyd import Device, PositionerBase, Signal
+from ophyd.status import wait as status_wait
+from ophyd.utils import LimitError
+from ophyd_devices.utils.controller import threadlocked
+from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
+
+from csaxs_bec.devices.omny.galil.galil_ophyd import (
+    BECConfigError,
+    GalilAxesReferenced,
+    GalilCommunicationError,
+    GalilController,
+    GalilError,
+    GalilMotorIsMoving,
+    GalilSetpointSignal,
+    GalilSignalRO,
+)
+
+logger = bec_logger.logger
+
+
+def retry_once(fcn):
+    """Decorator to rerun a function in case a Galil communication error was raised. This may happen if the buffer was not empty."""
+
+    @functools.wraps(fcn)
+    def wrapper(self, *args, **kwargs):
+        try:
+            val = fcn(self, *args, **kwargs)
+        except (GalilCommunicationError, GalilError):
+            val = fcn(self, *args, **kwargs)
+        return val
+
+    return wrapper
+
+
+class GalilMotorResolution(GalilSignalRO):
+    @retry_once
+    @threadlocked
+    def _socket_get(self):
+        if self.controller.sock.port == 8083 and self.parent.axis_Id_numeric == 2:
+        # rotation stage
+            return 89565.8666667
+        else:
+            return 51200
+
+
+class OMNYGalilReadbackSignal(GalilSignalRO):
+
+    previous_rotation_angle = 0
+    ignore_glitch = True
+
+    @retry_once
+    @threadlocked
+    def _socket_get(self) -> float:
+        """Get command for the readback signal
+
+        Returns:
+            float: Readback value after adjusting for sign and motor resolution.
+        """
+
+        current_pos = float(self.controller.socket_put_and_receive(f"TP{self.parent.axis_Id}"))
+        current_pos *= self.parent.sign
+        step_mm = self.parent.motor_resolution.get()
+        #here we introduce an offset of 25 to the rotation axis
+        #when setting a position this is taken into account in the controller
+        #that way we just do tomography from 0 to 180 degrees
+        if self.parent.axis_Id_numeric == 2 and self.controller.sock.port == 8083:
+            return (current_pos / step_mm)+25
+        else:
+            return current_pos / step_mm
+
+    def read(self):
+        self._metadata["timestamp"] = time.time()
+        val = super().read()
+       
+        #if reading rotation stage angle
+        if self.parent.axis_Id_numeric == 2 and self.controller.sock.port == 8083:
+            current_readback_value = val[self.parent.name]["value"]
+            #print (f"previous rotation angle {self.previous_rotation_angle}, current readback {current_readback_value}.")
+
+            if np.fabs((self.previous_rotation_angle-current_readback_value)>10):
+                message = f"Glitch detected in rotation stage. Previous rotation angle {self.previous_rotation_angle}, current readback {current_readback_value}."
+                print(message)
+                self.parent.device_manager.connector.send_client_info(message, scope="glitch detector", show_asap=True)
+            
+            val = super().read()
+            current_readback_value = val[self.parent.name]["value"]
+
+            if np.fabs((self.previous_rotation_angle-current_readback_value)>10):
+                message = f"Glitch detected in rotation stage second read. Previous rotation angle {self.previous_rotation_angle}, current readback {current_readback_value}. Disabling the controller."
+                print(message)
+                self.parent.device_manager.connector.send_client_info(message, scope="glitch detector", show_asap=True)
+            
+                self.parent.device_manager.devices["osamroy"].obj.controller.socket_put_confirmed("allaxref=0")
+                self.parent.device_manager.devices["osamroy"].obj.enabled = False
+
+                return val
+
+            self.previous_rotation_angle = current_readback_value
+            try:
+                rt = self.parent.device_manager.devices["rtx"]
+                if rt.enabled:
+                    rt.obj.controller.set_rotation_angle(val[self.parent.name]["value"]-25+54)
+            except KeyError:
+                logger.warning("Failed to set RT value during ogalil readback.")        
+        return val
+
+
+
+class OMNYGalilController(GalilController):
+    USER_ACCESS = [
+        "describe",
+        "show_running_threads",
+        "galil_show_all",
+        "socket_put_and_receive",
+        "socket_put_confirmed",
+        "get_motor_limit_switch",
+        "is_motor_on",
+        "all_axes_referenced",
+        "_ogalil_switchsocket",
+        "_ogalil_switchsocket_switch_all_on",
+        "_ogalil_switchsocket_status",
+        "_ogalil_switchsocket_are_all_on",
+        "_ogalil_folerr_not_ignore",
+    ]
+
+    OKBLUE = '\033[94m'
+    OKCYAN = '\033[96m'
+    OKGREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    
+    def on(self) -> None:
+        """Open a new socket connection to the controller"""
+        self._ogalil_switchsocket_switch_all_on()
+        time.sleep(0.3)
+        super().on()
+
+    def _ogalil_switchsocket(self, number: int, switch: bool):
+        # number is socket number ranging from 1 to 4
+        # switch is either 0 or 1
+        if number not in range(1, 5):
+            raise Exception("Socket number ranges from 1 to 4")
+        else:
+            contents = urllib.request.urlopen(
+                f"http://mpc3217:8091/netio.cgi?pass=24A42C3929C5&output{number}={switch}"
+            ).read()
+            # print(contents)
+            if b"OK" in contents:
+                print(f"Controller number switchsocket {number} is now {switch}")
+                return 1
+            else:
+                print(f"Failed to switch controller number {number}")
+                return 0
+
+    def _ogalil_switchsocket_are_all_on(self):
+        if self._ogalil_switchsocket_status() == [1, 1, 1, 1]:
+            return 1
+        else:
+            return 0
+
+    def _ogalil_tempdisabledebug(self):
+        # sock_put(_ogalil_debugging_host_and_port_str[ogalil_no][],"WH\r\n") < 1) {
+        # ret_str = sock_get(_ogalil_debugging_host_and_port_str[ogalil_no][],_ogalil_prompt_str)
+        #        printf("%s   _ogalil_redirect_debug_output(%d): expected \"IHx\" received \"%s\"\n",\
+        # cmd_str = sprintf("CF %s\r\n",substr(ret_str,3,1))
+        # if (sock_put(_ogalil_debugging_host_and_port_str[ogalil_no][],cmd_str) < 1) {
+        # cmd_str = sprintf("CW 2\r\n")
+        # if (sock_put(_ogalil_debugging_host_and_port_str[ogalil_no][],cmd_str) < 1) {
+        print("not yet implemented")
+        return 0
+
+    def _ogalil_folerr_reset_and_ignore(self, axis_id_numeric: int) -> None:
+        self.socket_put_confirmed(f"folaxerr[{axis_id_numeric}]=0")
+        self.socket_put_confirmed("folerr=0")
+        self.socket_put_confirmed("IgNoFol=1")
+        self.socket_put_confirmed("XQ#STOP,1")
+
+
+    def _ogalil_set_axis_to_pos_wo_reference_search(self, axis_id_numeric, axis_id, pos_mm, motor_resolution, motor_sign):
+
+        self.socket_put_confirmed("IgNoFol=1")
+
+        # pos_mm = pos_encoder / motor_resolution
+        pos_encoder = pos_mm * motor_resolution * motor_sign
+        #print(motor_resolution)
+    
+        self.socket_put_confirmed(f"DE{axis_id}={pos_encoder:.0f}")
+        self.socket_put_confirmed(f"DP{axis_id}=_TP{axis_id}*ratio[{axis_id_numeric:.0f}]")
+
+        self.socket_put_confirmed(f"folaxerr[{axis_id_numeric}]=0")
+        self.socket_put_confirmed(f"axisref[{axis_id_numeric}]=1")
+        self.socket_put_confirmed("folerr=0")
+
+        self._ogalil_folerr_not_ignore()
+
+
+    def _ogalil_folerr_not_ignore(self):
+        self.socket_put_confirmed("IgNoFol=0")
+
+    def _ogalil_switchsocket_switch_all_on(self):
+        if not self._ogalil_switchsocket_are_all_on():
+            for j in range(1, 5):
+                self._ogalil_switchsocket(j, 1)
+                time.sleep(0.4)
+
+    def _ogalil_switchsocket_status(self):
+        contents = urllib.request.urlopen("http://mpc3217:8091/netio.xml").read()
+        root = ET.fromstring(contents)
+        returnvalue = []
+        for j in range(0, 4):
+            status = int(root[1][j][2].text)
+            returnvalue.append(int(root[1][j][2].text))
+            if status:
+                print(f"Controller {j+1} is ON")
+            else:
+                print(f"Controller {j+1} is OFF")
+        return returnvalue
+
+    def show_status_other(self):
+        swver = float(self.socket_put_and_receive("MGswver"))
+        allaxref = float(self.socket_put_and_receive("MGallaxref"))
+        tempab = float(self.socket_put_and_receive("MGtempab"))
+        timeab = float(self.socket_put_and_receive("MGtimeab"))
+        IgNoFol = float(self.socket_put_and_receive("MGIgNoFol"))
+        print(
+            f"OMNY galil firmware {swver:2.0f}, TempAbort: {tempab:1.0f}, Allaxref: {allaxref:1.0f}, TimeAbort: {timeab:1.0f}, Ignore Folerr: {IgNoFol:1.0f}\n"
+        )
+        if self.sock.port == 8083:
+            self._ogalil_switchsocket_status()
+
+
+class OMNYGalilMotor(Device, PositionerBase):
+    USER_ACCESS = ["controller", "find_reference", "omny_osamx_to_scan_center", "drive_axis_to_limit", "_ogalil_folerr_reset_and_ignore", "_ogalil_set_axis_to_pos_wo_reference_search", "get_motor_limit_switch", "axis_is_referenced", "get_motor_temperature", "folerr_status"]
+    readback = Cpt(OMNYGalilReadbackSignal, signal_name="readback", kind="hinted")
+    user_setpoint = Cpt(GalilSetpointSignal, signal_name="setpoint")
+    motor_resolution = Cpt(GalilMotorResolution, signal_name="resolution", kind="config")
+    motor_is_moving = Cpt(GalilMotorIsMoving, signal_name="motor_is_moving", kind="normal")
+    all_axes_referenced = Cpt(GalilAxesReferenced, signal_name="all_axes_referenced", kind="config")
+    high_limit_travel = Cpt(Signal, value=0, kind="omitted")
+    low_limit_travel = Cpt(Signal, value=0, kind="omitted")
+
+    SUB_READBACK = "readback"
+    SUB_CONNECTION_CHANGE = "connection_change"
+    _default_sub = SUB_READBACK
+
+    def __init__(
+        self,
+        axis_Id,
+        prefix="",
+        *,
+        name,
+        kind=None,
+        read_attrs=None,
+        configuration_attrs=None,
+        parent=None,
+        host="mpc3217.psi.ch",
+        port=8081,
+        limits=None,
+        sign=1,
+        socket_cls=SocketIO,
+        device_manager=None,
+        **kwargs,
+    ):
+        self.controller = OMNYGalilController(
+            socket_cls=socket_cls, socket_host=host, socket_port=port
+        )
+        self.axis_Id = axis_Id
+        self.controller.set_axis(axis=self, axis_nr=self.axis_Id_numeric)
+        self.sign = sign
+        self.tolerance = kwargs.pop("tolerance", 0.5)
+        self.device_mapping = kwargs.pop("device_mapping", {})
+        self.device_manager = device_manager
+
+        if len(self.device_mapping) > 0 and self.device_manager is None:
+            raise BECConfigError(
+                "device_mapping has been specified but the device_manager cannot be accessed."
+            )
+        self.rt = self.device_mapping.get("rt")
+
+        super().__init__(
+            prefix,
+            name=name,
+            kind=kind,
+            read_attrs=read_attrs,
+            configuration_attrs=configuration_attrs,
+            parent=parent,
+            **kwargs,
+        )
+        self.readback.name = self.name
+        self.controller.subscribe(
+            self._update_connection_state, event_type=self.SUB_CONNECTION_CHANGE
+        )
+        self._update_connection_state()
+        # self.readback.subscribe(self._forward_readback, event_type=self.readback.SUB_VALUE)
+
+        if limits is not None:
+            assert len(limits) == 2
+            self.low_limit_travel.put(limits[0])
+            self.high_limit_travel.put(limits[1])
+
+    @property
+    def limits(self):
+        return (self.low_limit_travel.get(), self.high_limit_travel.get())
+
+    @property
+    def low_limit(self):
+        return self.limits[0]
+
+    @property
+    def high_limit(self):
+        return self.limits[1]
+
+    def check_value(self, pos):
+        """Check that the position is within the soft limits"""
+        low_limit, high_limit = self.limits
+
+        if low_limit < high_limit and not (low_limit <= pos <= high_limit):
+            raise LimitError(f"position={pos} not within limits {self.limits}")
+
+    def _update_connection_state(self, **kwargs):
+        for walk in self.walk_signals():
+            walk.item._metadata["connected"] = self.controller.connected
+
+    def _forward_readback(self, **kwargs):
+        kwargs.pop("sub_type")
+        self._run_subs(sub_type="readback", **kwargs)
+
+    @raise_if_disconnected
+    def move(self, position, wait=True, **kwargs):
+        """Move to a specified position, optionally waiting for motion to
+        complete.
+
+        Parameters
+        ----------
+        position
+            Position to move to
+        moved_cb : callable
+            Call this callback when movement has finished. This callback must
+            accept one keyword argument: 'obj' which will be set to this
+            positioner instance.
+        timeout : float, optional
+            Maximum time to wait for the motion. If None, the default timeout
+            for this positioner is used.
+
+        Returns
+        -------
+        status : MoveStatus
+
+        Raises
+        ------
+        TimeoutError
+            When motion takes longer than `timeout`
+        ValueError
+            On invalid positions
+        RuntimeError
+            If motion fails other than timing out
+        """
+        self._started_moving = False
+        timeout = kwargs.pop("timeout", 100)
+        status = super().move(position, timeout=timeout, **kwargs)
+        self.user_setpoint.put(position, wait=False)
+
+        def move_and_finish():
+            while self.motor_is_moving.get():
+                logger.info("motor is moving")
+                val = self.readback.read()
+                self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+                time.sleep(0.1)
+            val = self.readback.read()
+            success = np.isclose(val[self.name]["value"], position, atol=self.tolerance)
+
+            if not success:
+                print(" stop")
+            self._done_moving(success=success)
+            logger.info("Move finished")
+
+        threading.Thread(target=move_and_finish, daemon=True).start()
+        try:
+            if wait:
+                status_wait(status)
+        except KeyboardInterrupt:
+            self.stop()
+            raise
+
+        return status
+
+    @property
+    def axis_Id(self):
+        return self._axis_Id_alpha
+
+    @axis_Id.setter
+    def axis_Id(self, val):
+        if isinstance(val, str):
+            if len(val) != 1:
+                raise ValueError("Only single-character axis_Ids are supported.")
+            self._axis_Id_alpha = val
+            self._axis_Id_numeric = self.controller.axis_Id_to_numeric(val)
+        else:
+            raise TypeError(f"Expected value of type str but received {type(val)}")
+
+    @property
+    def axis_Id_numeric(self):
+        return self._axis_Id_numeric
+
+    @axis_Id_numeric.setter
+    def axis_Id_numeric(self, val):
+        if isinstance(val, int):
+            if val > 26:
+                raise ValueError("Numeric value exceeds supported range.")
+            self._axis_Id_alpha = self.controller.axis_Id_numeric_to_alpha(val)
+            self._axis_Id_numeric = val
+        else:
+            raise TypeError(f"Expected value of type int but received {type(val)}")
+
+    @property
+    def egu(self):
+        """The engineering units (EGU) for positions"""
+        return "mm"
+
+    def _ogalil_folerr_reset_and_ignore(self):
+        # pylint: disable=protected-access
+        self.controller._ogalil_folerr_reset_and_ignore(self.axis_Id_numeric)
+
+    def _ogalil_set_axis_to_pos_wo_reference_search(self, pos_mm):
+        motor_resolution = self.motor_resolution.get()
+        self.controller._ogalil_set_axis_to_pos_wo_reference_search(self.axis_Id_numeric, self.axis_Id, pos_mm, motor_resolution, self.sign)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
+    def find_reference(self, raise_error=1):
+        """
+        Find the reference of the axis.
+        """
+        verbose=1
+        self.controller.find_reference(self.axis_Id_numeric, verbose, raise_error)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
+    def drive_axis_to_limit(self, direction: str) -> None:
+        """
+        Drive an axis to the limit in a specified direction.
+
+        Args:
+            direction (str): Direction in which the axis should be driven to the limit. Either 'forward' or 'reverse'.        
+        """
+        self.controller.drive_axis_to_limit(self.axis_Id_numeric, direction, verbose=1)
+        #now force position read to cache
+        val = self.readback.read()
+        self._run_subs(sub_type=self.SUB_READBACK, value=val, timestamp=time.time())
+
+    def get_motor_limit_switch(self) -> list:
+        """
+        Get status of the motor limit switches
+        """
+        return self.controller.get_motor_limit_switch(self.axis_Id)
+
+    def get_motor_temperature(self) -> float:
+        """
+        Get motor temperature
+        """
+        return self.controller.motor_temperature(self.axis_Id_numeric)
+
+    def axis_is_referenced(self) -> bool:
+        """
+        check if an axis is referenced
+        """
+        return self.controller.axis_is_referenced(self.axis_Id_numeric)
+
+    def _get_user_param_safe(self, device, var):
+        param = self.device_manager.devices[device].user_parameter
+        if not param or param.get(var) is None:
+            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
+        return param.get(var)
+
+    def omny_osamx_to_scan_center(self, cenx):
+        if self.controller.sock.port == 8082 and self.axis_Id_numeric == 0:
+            # get last setpoint
+                osamx = self.device_manager.devices["osamx"]
+                osamx_current_setpoint = osamx.obj.readback.get()
+                omny_samx_in = self._get_user_param_safe("osamx","in")
+                if np.fabs(osamx_current_setpoint-(omny_samx_in+cenx/1000)) > 0.025:
+                    message=f"Moving osamx to scan center. new osamx target {omny_samx_in+cenx/1000:.3f}."
+                    logger.info(message)
+
+                    osamx.read_only = False
+                    #osamx.controller.("osamx", "controller.socket_put_confirmed('axspeed[0]=1000')")
+                    osamx.set(omny_samx_in+cenx/1000)
+                    time.sleep(0.1)
+                    while(osamx.motor_is_moving.get()):
+                        time.sleep(0.05)
+                    osamx.read_only = True
+                    time.sleep(2)
+                    rt = self.device_manager.devices["rtx"]
+                    if rt.enabled:
+                        rt.obj.controller.laser_tracker_on()
+                        rt.obj.controller.laser_tracker_check_and_wait_for_signalstrength()
+
+    def folerr_status(self) -> bool:
+        return self.controller.folerr_status(self.axis_Id_numeric)
+    
+    def stop(self, *, success=False):
+        self.controller.stop_all_axes()
+        return super().stop(success=success)

csaxs_bec/devices/omny/omny_dewar.py

@@ -0,0 +1,111 @@
+import time
+import datetime
+
+from ophyd import Component as Cpt
+from ophyd import Device
+from ophyd import DynamicDeviceComponent as Dcpt
+from ophyd import EpicsSignal
+from prettytable import FRAME, PrettyTable
+import numpy as np
+
+class OMNYDewarError(Exception):
+    pass
+
+
+class OMNYDewar(Device):
+    USER_ACCESS = [
+        "show_all",
+        "is_flow_low",
+        "help",
+    ]
+    SUB_VALUE = "value"
+    _default_sub = SUB_VALUE
+
+
+
+    dewar_press_0 = Cpt(
+        EpicsSignal, name="dewar_press_0", read_pv="XOMNY-TEMP-DEWAR-PRESS0:GET"
+    )
+
+    dewar_refilling = Cpt(
+        EpicsSignal, name="dewar_refilling", read_pv="XOMNY-TEMP-DEWAR-Refilling:GET"
+    )
+
+    dewar_press_1 = Cpt(
+        EpicsSignal, name="dewar_press_1", read_pv="XOMNY-TEMP-DEWAR-PRESS1:GET"
+    )
+
+    dewar_press_2 = Cpt(
+        EpicsSignal, name="dewar_press_2", read_pv="XOMNY-TEMP-DEWAR-PRESS2:GET"
+    )
+
+    dewar_flow_0 = Cpt(
+        EpicsSignal, name="dewar_flow_0", read_pv="XOMNY-TEMP-DEWAR-FLOW0:GET"
+    )
+
+    dewar_valvepos = Cpt(
+        EpicsSignal, name="dewar_valvepos", read_pv="XOMNY-TEMP-DEWAR-ValvePos:GET"
+    )
+
+    dewar_supply_voltage = Cpt(
+        EpicsSignal, name="dewar_supply_voltage", read_pv="XOMNY-TEMP-DEWAR-SupplyVoltage:GET"
+    )
+
+    dewar_uptime_h = Cpt(
+        EpicsSignal, name="dewar_uptime_h", read_pv="XOMNY-TEMP-DEWAR-UpH:GET"
+    )
+    dewar_uptime_m = Cpt(
+        EpicsSignal, name="dewar_uptime_m", read_pv="XOMNY-TEMP-DEWAR-UpM:GET"
+    )
+    dewar_uptime_s = Cpt(
+        EpicsSignal, name="dewar_uptime_s", read_pv="XOMNY-TEMP-DEWAR-UpS:GET"
+    )
+
+    dewar_valve_movements_h = Cpt(
+        EpicsSignal, name="dewar_valve_movements_h", read_pv="XOMNY-TEMP-DEWAR-MovH:GET"
+    )
+    dewar_valve_movements_m = Cpt(
+        EpicsSignal, name="dewar_valve_movements_m", read_pv="XOMNY-TEMP-DEWAR-MovM:GET"
+    )
+    dewar_valve_movements_s = Cpt(
+        EpicsSignal, name="dewar_valve_movements_s", read_pv="XOMNY-TEMP-DEWAR-MovS:GET"
+    )
+
+    def __init__(self, prefix="", *, name, **kwargs):
+        super().__init__(prefix, name=name, **kwargs)
+        self.dewar_flow_0.subscribe(self._emit_value)
+
+    def _emit_value(self, **kwargs):
+        timestamp = kwargs.pop("timestamp", time.time())
+        self.wait_for_connection()
+        self._run_subs(sub_type=self.SUB_VALUE, timestamp=timestamp, obj=self)
+
+
+    def is_flow_low(self):
+        if(float(self.dewar_flow_0.get())<3.8):
+            return True
+        else:
+            return False
+        
+    def show_all(self):
+        red = "\x1b[91m"
+        white = "\x1b[0m"
+
+
+        print("OMNY Dewar Status")
+        print(f"  DewarPressure:           {float(self.dewar_press_0.get()):.0f} mbar")
+        print(f"  Dewar Refilling:         {float(self.dewar_refilling.get()):.0f}")
+        print(f"  LN2flow In Pressure:     {float(self.dewar_press_1.get()):.0f} mbar")
+        print(f"  LN2flow Out Pressure:    {float(self.dewar_press_2.get()):.0f} mbar")
+        print(f"  LN2flow In Flow Rate:    {float(self.dewar_flow_0.get()):.1f} l/s")
+        if self.is_flow_low():
+            print(red + "This flow rate is LOW. Increase the LN2flow In Pressure" + white)
+        print(f"  Valve Opening (0-1):     {float(self.dewar_valvepos.get()):.2f}")
+        print(f"  Valve Supply Voltage:    {float(self.dewar_supply_voltage.get()):.2f} V")
+        print(f"  Uptime of System:        {float(self.dewar_uptime_h.get()):2.0f}:{float(self.dewar_uptime_m.get()):2.0f}:{float(self.dewar_uptime_s.get()):2.0f}")
+        print(f"  Active Valve Movements:  {float(self.dewar_valve_movements_h.get()):2.0f}:{float(self.dewar_valve_movements_m.get()):2.0f}:{float(self.dewar_valve_movements_s.get()):2.0f}")
+  
+
+    def help(self):
+        print("Help for OMNY Dewar:")
+        print("This device shows an overview of the dewar status. Use show_all()")

csaxs_bec/devices/omny/omny_sample_storage.py

@@ -22,6 +22,7 @@ class OMNYSampleStorage(Device):
         "set_sample_in_samplestage",
         "unset_sample_in_samplestage",
         "get_sample_name_in_samplestage",
+        "get_sample_name_in_gripper",
         "get_sample_name",
         "is_sample_in_samplestage",
         "set_shuttle_slot",
@@ -30,6 +31,7 @@ class OMNYSampleStorage(Device):
         "is_shuttle_slot_used",
         "search_shuttle_in_slot",
         "show_all",
+        "help",
     ]
     SUB_VALUE = "value"
     _default_sub = SUB_VALUE
@@ -137,20 +139,28 @@ class OMNYSampleStorage(Device):
         elif container == "C":
             getattr(self.sample_shuttle_C_placed, f"sample{slot_nr}").set(1)
             getattr(self.sample_shuttle_C_names, f"sample{slot_nr}").set(name)
+        elif container == "O":
+            getattr(self.sample_placed, f"sample{slot_nr}").set(1)
+            getattr(self.sample_names, f"sample{slot_nr}").set(name)
 
-    def unset_sample_slot(self, shuttle: str, slot_nr: int) -> bool:
+
+    def unset_sample_slot(self, container: str, slot_nr: int) -> bool:
         if slot_nr > 20:
             raise OMNYSampleStorageError(f"Invalid slot number {slot_nr}.")
 
-        if shuttle == "A":
+        if container == "A":
             getattr(self.sample_shuttle_A_placed, f"sample{slot_nr}").set(0)
             getattr(self.sample_shuttle_A_names, f"sample{slot_nr}").set("-")
-        if shuttle == "B":
+        elif container == "B":
             getattr(self.sample_shuttle_B_placed, f"sample{slot_nr}").set(0)
             getattr(self.sample_shuttle_B_names, f"sample{slot_nr}").set("-")
-        if shuttle == "C":
+        elif container == "C":
             getattr(self.sample_shuttle_C_placed, f"sample{slot_nr}").set(0)
             getattr(self.sample_shuttle_C_names, f"sample{slot_nr}").set("-")
+        elif container == "O":
+            getattr(self.sample_placed, f"sample{slot_nr}").set(0)
+            getattr(self.sample_names, f"sample{slot_nr}").set("-")
+
 
     def set_shuttle_slot(self, container: str, slot_nr: int) -> bool:
         if slot_nr > 6:
@@ -275,8 +285,24 @@ class OMNYSampleStorage(Device):
             row = []
             row.extend([f"Position {i:3d}"])
             if self.is_sample_slot_used("O", i):
-                row.extend(self.get_sample_name("O", i))
+                name = self.get_sample_name("O", i)
+                row.extend([name])
             else:
                 row.extend(["free"])
             t.add_row(row)
         print(t)
+
+        print("Use dev.omny_samples.help() for assistance.")
+
+    def help(self):
+        print("Help for OMNY sample storage:")
+        print(" To get an overview use dev.omny_samples.show_all()")
+        print(" Modify a slot:")
+        print(" dev.omny_samples.unset_sample_slot('system',position)")
+        print(" dev.omny_samples.set_sample_slot('system',position,'name')")
+        print("   system can be A, B, C, O")
+        print(" dev.omny_samples.set_sample_in_gripper('name') / unset_sample_in_gripper()")
+        print(" dev.omny_samples.set_sample_in_samplestage('name'), unset_sample_in_samplestage()")
+        print(" dev.omny_samples.set_shuttle_slot(container, slot_nr) / unset_shuttle_slot(slot_nr)")
+        print(" dev.omny_samples.set_shuttle_slot('A',2)")
+        print(" omny.otransfer_help()")

csaxs_bec/devices/omny/omny_temperatures.py

@@ -0,0 +1,260 @@
+import time
+import datetime
+
+from ophyd import Component as Cpt
+from ophyd import Device
+from ophyd import DynamicDeviceComponent as Dcpt
+from ophyd import EpicsSignal
+from prettytable import FRAME, PrettyTable
+import numpy as np
+
+class OMNYTemperaturesError(Exception):
+    pass
+
+
+class OMNYTemperatures(Device):
+    USER_ACCESS = [
+        "temperature_controller_used_get_name_and_values",
+        "set_setpoint",
+        "show_all",
+        "help",
+        "_set_TEMP_default_setpoints",
+        "temperature_controller_TEMP_running",
+        "temperature_controller_CRYO_running",
+    ]
+    SUB_VALUE = "value"
+    _default_sub = SUB_VALUE
+
+    temperature = {
+        f"temperature{i}": (EpicsSignal, f"XOMNY-TEMP{i}:GET", {}) for i in range(1, 49)
+    }
+    temperature = Dcpt(temperature)
+
+    temperature_setpoint = {
+        f"temperature_setpoint{i}": (EpicsSignal, f"XOMNY-TEMP{i}:SET", {}) for i in range(1, 49)
+    }
+    temperature_setpoint = Dcpt(temperature_setpoint)
+
+    temperature_unit = {
+        f"temperature_unit{i}": (EpicsSignal, f"XOMNY-TEMP{i}:GET.EGU", {}) for i in range(1, 49)
+    }
+    temperature_unit = Dcpt(temperature_unit)
+
+    temperature_alarmstate = {
+        f"temperature_alarmstate{i}": (EpicsSignal, f"XOMNY-TEMP{i}:ALARM", {}) for i in range(1, 49)
+    }
+    temperature_alarmstate = Dcpt(temperature_alarmstate)
+
+    temperature_names = {
+        f"temperature_name{i}": (EpicsSignal, f"XOMNY-TEMP{i}:GET.DESC", {"string": True})
+        for i in range(1, 49)
+    }
+    temperature_names = Dcpt(temperature_names)
+
+    temperature_update_time = Cpt(
+        EpicsSignal, name="temperature_update_time", read_pv="XOMNY-TEMP:UPDATED.VAL"
+    )
+
+    cryo_temperature = {
+        f"cryo_temperature{i}": (EpicsSignal, f"XOMNY-TEMP-CRYO-{chr(i+ord('A')-1)}:GET.VAL", {}) for i in range(1,5)
+    }
+    cryo_temperature = Dcpt(cryo_temperature)
+
+    cryo_temperature_setpoint = {
+        f"cryo_temperature_setpoint{i}": (EpicsSignal, f"XOMNY-TEMP-CRYO-{chr(i+ord('A')-1)}:SET.VAL", {}) for i in range(1,5)
+    }
+    cryo_temperature_setpoint = Dcpt(cryo_temperature_setpoint)
+
+    cryo_temperature_name = {
+        f"cryo_temperature_name{i}": (EpicsSignal, f"XOMNY-TEMP-CRYO-{chr(i+ord('A')-1)}:GET.DESC", {}) for i in range(1,5)
+    }
+    cryo_temperature_name = Dcpt(cryo_temperature_name)
+
+    cryo_temperature_update_time = Cpt(
+        EpicsSignal, name="cryo_temperature_update_time", read_pv="XOMNY-TEMP-CRYO:UPDATED.VAL"
+    )
+
+    cryo_temperature_closed_loop = Cpt(
+        EpicsSignal, name="cryo_temperature_closed_loop", read_pv="XOMNY-TEMP-CRYO:CLOSEDLOOP.VAL"
+    )
+
+    def __init__(self, prefix="", *, name, **kwargs):
+        super().__init__(prefix, name=name, **kwargs)
+        self.temperature.temperature1.subscribe(self._emit_value)
+
+    def _emit_value(self, **kwargs):
+        timestamp = kwargs.pop("timestamp", time.time())
+        self.wait_for_connection()
+        self._run_subs(sub_type=self.SUB_VALUE, timestamp=timestamp, obj=self)
+
+    def set_setpoint(self, type: str, controller_nr: int, temperature: float):
+        if type == "TEMP":
+            getattr(self.temperature_setpoint, f"temperature_setpoint{controller_nr}").set(temperature)
+        elif type == "CRYO":
+            getattr(self.cryo_temperature_setpoint, f"cryo_temperature_setpoint{controller_nr}").set(temperature)
+        else:
+            raise OMNYTemperaturesError("invalid type")
+
+
+    def _set_TEMP_default_setpoints(self):
+        self.set_setpoint("TEMP",8,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",9,23)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",10,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",16,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",17,23)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",18,26)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",19,26)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",20,26)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",21,23)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",22,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",23,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",24,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",25,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",27,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",28,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",29,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",30,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",31,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",35,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",36,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",37,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",38,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",39,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",41,30)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",42,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",44,25)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",45,-199.9)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",46,73.2)
+        time.sleep(0.1)
+        self.set_setpoint("TEMP",47,73.2)
+        time.sleep(0.1)
+
+    def temperature_controller_TEMP_running(self):
+        time_diff = np.fabs(float(self.temperature_update_time.get()) - time.time())
+        if time_diff > 600:
+            return False
+        else:
+            return True
+
+    def temperature_controller_CRYO_running(self):
+        time_diff = np.fabs(float(self.cryo_temperature_update_time.get()) - time.time())
+        if time_diff > 600:
+            return False
+        else:
+            return True
+
+    def temperature_controller_used_get_name_and_values(self, type: str, controller_nr: int) -> bool:
+        if type == "TEMP":
+            controller_name = str(getattr(self.temperature_names, f"temperature_name{controller_nr}").get())
+            if controller_name == '-' or controller_name == 'NOT INITIALIZED':
+                return (False, "none", 0, 0, "none", False, False)
+            else:
+                temperature = float(getattr(self.temperature, f"temperature{controller_nr}").get())
+                setpoint = float(getattr(self.temperature_setpoint, f"temperature_setpoint{controller_nr}").get())
+                unit = str(getattr(self.temperature_unit, f"temperature_unit{controller_nr}").get())
+                alarmstate = bool(getattr(self.temperature_alarmstate, f"temperature_alarmstate{controller_nr}").get())
+                controller_running = self.temperature_controller_TEMP_running()
+                return (True, controller_name, temperature, setpoint, unit, alarmstate,controller_running)
+        elif type == "CRYO":
+            controller_name = str(getattr(self.cryo_temperature_name, f"cryo_temperature_name{controller_nr}").get())
+            temperature = float(getattr(self.cryo_temperature, f"cryo_temperature{controller_nr}").get())
+            setpoint = float(getattr(self.cryo_temperature_setpoint, f"cryo_temperature_setpoint{controller_nr}").get())
+            unit = 'K'
+            alarmstate = False
+            controller_running = self.temperature_controller_CRYO_running()
+            return (True, controller_name, temperature, setpoint, unit, alarmstate,controller_running)
+        else:
+            raise OMNYTemperaturesError("invalid type")
+
+
+
+    def show_all(self):
+        red = "\x1b[91m"
+        white = "\x1b[0m"
+        t = PrettyTable()
+        t.clear()
+        t.title = "OMNY Temperature Controllers"
+        t.field_names = ["Channel","Name","Temperature","Setpoint","Unit","AlarmState"]
+        for i in range (1,49):
+            controller_status = self.temperature_controller_used_get_name_and_values("TEMP", i)
+            if controller_status[0]:
+                row = []
+                row.extend([f"{i}"])
+                row.extend([controller_status[1]])
+                row.extend([f"{controller_status[2]:.2f}"])
+                if (controller_status[3] < -199 and controller_status[4] == "degC") or (np.fabs(controller_status[3]-73.25) < 0.1 and controller_status[4] == "K"):
+                    row.extend([" "])
+                else:
+                    row.extend([f"{controller_status[3]:.2f}"])
+                row.extend([f"{controller_status[4]}"])
+                if controller_status[5]:
+                    row.extend(["Alarm"])
+                else:
+                    row.extend([" "])
+                t.add_row(row)
+        t.header = True
+        t.vrules = FRAME
+        print(t)
+        if not self.temperature_controller_TEMP_running():
+            print (red + "Warning: the temperature controller communication is not running" + white)
+        print (f"The last update was {datetime.datetime.fromtimestamp(float(self.temperature_update_time.get())).strftime('%c')}\n")
+
+
+        t.clear()
+        t.title = "OMNY Cryo Temperature Controller"
+        t.field_names = ["Channel","Name","Temperature","Setpoint","Unit"]
+        for i in range (1,5):
+            controller_status = self.temperature_controller_used_get_name_and_values("CRYO", i)
+            if controller_status[0]:
+                row = []
+                row.extend([f"{i}"])
+                row.extend([controller_status[1]])
+                row.extend([f"{controller_status[2]:.2f}"])
+                row.extend([f"{controller_status[3]:.2f}"])
+                row.extend([f"{controller_status[4]}"])
+                t.add_row(row)
+        t.header = True
+        t.vrules = FRAME
+        print(t)
+
+        if bool(self.cryo_temperature_closed_loop.get()):
+            print ("Cryo controller is running in closed loop.")
+        else:
+            print ("Cryo controller is running in " + red + "open" + white + " loop.")
+
+        if not self.temperature_controller_CRYO_running():
+            print (red + "Warning: the temperature controller communication is not running" + white)
+
+        print (f"The last update was {datetime.datetime.fromtimestamp(float(self.cryo_temperature_update_time.get())).strftime('%c')}\n")
+
+    print("Use dev.omny_temperatures.help() for assistance.")
+
+    def help(self):
+        print("Help for OMNY temperatures:")

csaxs_bec/devices/omny/omny_vcs.py

@@ -0,0 +1,161 @@
+import time
+import datetime
+
+from ophyd import Component as Cpt
+from ophyd import Device
+from ophyd import DynamicDeviceComponent as Dcpt
+from ophyd import EpicsSignal
+from prettytable import FRAME, PrettyTable
+import numpy as np
+
+class OMNYVCSError(Exception):
+    pass
+
+
+class OMNYVCS(Device):
+    USER_ACCESS = [
+        "show_all",
+        "valves_in_measurement_position",
+        "help",
+    ]
+    SUB_VALUE = "value"
+    _default_sub = SUB_VALUE
+
+
+
+    XOMNY_ES1_EXPMP1_VOLTAGE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_EXPMP1_VOLTAGE", read_pv="XOMNY-ES1-EXPMP1:VOLTAGE"
+    )
+
+    XOMNY_ES1_EXPMP1_PRESSURE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_EXPMP1_PRESSURE", read_pv="XOMNY-ES1-EXPMP1:PRESSURE"
+    )
+
+    XOMNY_ES1_PU2MT1_VOLTAGE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_PU2MT1_VOLTAGE", read_pv="XOMNY-ES1-PU2MT1:VOLTAGE"
+    )
+
+    XOMNY_ES1_PU2MT1_PRESSURE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_PU2MT1_PRESSURE", read_pv="XOMNY-ES1-PU2MT1:PRESSURE"
+    )
+
+    XOMNY_ES1_PU1MF1_VOLTAGE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_PU1MF1_VOLTAGE", read_pv="XOMNY-ES1-PU1MF1:VOLTAGE"
+    )
+
+    XOMNY_ES1_PU1MF1_PRESSURE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_PU1MF1_PRESSURE", read_pv="XOMNY-ES1-PU1MF1:PRESSURE"
+    )
+
+    XOMNY_ES1_LL1MF1_VOLTAGE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1MF1_VOLTAGE", read_pv="XOMNY-ES1-LL1MF1:VOLTAGE"
+    )
+
+    XOMNY_ES1_LL1MF1_PRESSURE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1MF1_PRESSURE", read_pv="XOMNY-ES1-LL1MF1:PRESSURE"
+    )
+
+    XOMNY_ES1_VV1MT1_VOLTAGE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_VV1MT1_VOLTAGE", read_pv="XOMNY-ES1-VV1MT1:VOLTAGE"
+    )
+
+    XOMNY_ES1_VV1MT1_PRESSURE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_VV1MT1_PRESSURE", read_pv="XOMNY-ES1-VV1MT1:PRESSURE"
+    )
+
+    XOMNY_ES1_EXPVG1_POSITION = Cpt(
+        EpicsSignal, name="XOMNY_ES1_EXPVG1_POSITION", read_pv="XOMNY-ES1-EXPVG1:POSITION"
+    )
+
+    XOMNY_ES1_WI2VG1_POSITION = Cpt(
+        EpicsSignal, name="XOMNY_ES1_WI2VG1_POSITION", read_pv="XOMNY-ES1-WI2VG1:POSITION"
+    )
+
+    XOMNY_ES1_EXPVG2_POSITION = Cpt(
+        EpicsSignal, name="XOMNY_ES1_EXPVG2_POSITION", read_pv="XOMNY-ES1-EXPVG2:POSITION"
+    )
+
+    XOMNY_ES1_LL1VG1_CLOSE = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1VG1_CLOSE", read_pv="XOMNY-ES1-LL1VG1:CLOSE"
+    )
+
+    XOMNY_ES1_LL1DK_VG_CLOSED = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1DK_VG_CLOSED", read_pv="XOMNY-ES1-LL1DK:VG_CLOSED"
+    )
+
+    XOMNY_ES1_LL1SH_VG_CLOSED = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1SH_VG_CLOSED", read_pv="XOMNY-ES1-LL1SH:VG_CLOSED"
+    )
+
+    XOMNY_ES1_LL1SH_MAN_POS_OK = Cpt(
+        EpicsSignal, name="XOMNY_ES1_LL1SH_MAN_POS_OK", read_pv="XOMNY-ES1-LL1SH:MAN_POS_OK"
+    )
+
+
+    def __init__(self, prefix="", *, name, **kwargs):
+        super().__init__(prefix, name=name, **kwargs)
+        self.XOMNY_ES1_LL1SH_MAN_POS_OK.subscribe(self._emit_value)
+
+    def _emit_value(self, **kwargs):
+        timestamp = kwargs.pop("timestamp", time.time())
+        self.wait_for_connection()
+        self._run_subs(sub_type=self.SUB_VALUE, timestamp=timestamp, obj=self)
+
+        
+    def show_all(self):
+        red = "\x1b[91m"
+        white = "\x1b[0m"
+
+        print("OMNY Vaccum Status")
+        if float(self.XOMNY_ES1_EXPMP1_VOLTAGE.get()) < 0.5:
+            print(red + "  Main chamber:    Sensor failure" + white)
+        else:
+            print(f"  Main chamber:    {float(self.XOMNY_ES1_EXPMP1_PRESSURE.get()):.2e} mbar")
+  
+        if float(self.XOMNY_ES1_PU2MT1_VOLTAGE.get()) < 0.5:
+            print(red + "  Flight tube:     Sensor failure" + white)
+        else:
+            print(f"  Flight tube:     {float(self.XOMNY_ES1_PU2MT1_PRESSURE.get()):.2e} mbar")
+  
+        if float(self.XOMNY_ES1_PU1MF1_VOLTAGE.get()) < 0.5:
+            print(red+"  Beamline:        Sensor failure"+white)
+        else:
+            print(f"  Beamline:        {float(self.XOMNY_ES1_PU1MF1_PRESSURE.get()):.2e} mbar")
+
+        if float(self.XOMNY_ES1_LL1MF1_VOLTAGE.get()) < 0.5:
+            print(red+"  LoadLock:        Sensor failure"+white)
+        else:
+            print(f"  LoadLock:        {float(self.XOMNY_ES1_LL1MF1_PRESSURE.get()):.2e} mbar")
+
+        if float(self.XOMNY_ES1_VV1MT1_VOLTAGE.get()) < 0.5:
+            print(red+"  Pre-pump:        Sensor failure"+white)
+        else:
+            print(f"  Pre-pump:        {float(self.XOMNY_ES1_VV1MT1_PRESSURE.get()):.2e} mbar")
+
+        print("\nValve status")
+        print(f"  Upstream gate valve:        {str(self.XOMNY_ES1_EXPVG1_POSITION.get())}")
+#printf ("  Upstream window valve:      %s\n", _ovcs_upstream_window_valve)
+        print(f"  Downstream window bypass:   {str(self.XOMNY_ES1_WI2VG1_POSITION.get())}")
+        print(f"  Downstream gate valve:      {str(self.XOMNY_ES1_EXPVG2_POSITION.get())}")
+        if self.valves_in_measurement_position():
+            print("The OMNY valves are in the correct configuration to perform a measurement")
+        else:
+            print(red+"The valves of the OMNY vacuum system are not in the state for measurements."+white)
+
+
+        print("\nLoad Lock Status")
+        print(f"  Chamber:            {str(self.XOMNY_ES1_LL1VG1_CLOSE.get())}")
+        print(f"  Dock:               {str(self.XOMNY_ES1_LL1DK_VG_CLOSED.get())}")
+        print(f"  Shuttle:            {str(self.XOMNY_ES1_LL1SH_VG_CLOSED.get())}")
+        print(f"  Manipulator status: {str(self.XOMNY_ES1_LL1SH_MAN_POS_OK.get())}")
+
+    def valves_in_measurement_position(self):
+        if str(self.XOMNY_ES1_EXPVG1_POSITION.get()) == "OPEN" and str(self.XOMNY_ES1_WI2VG1_POSITION.get()) == "CLOSED" and str(self.XOMNY_ES1_EXPVG2_POSITION.get()) == "OPEN":
+            return True
+        else:
+            return False
+
+
+    def help(self):
+        print("Help for OMNY Vacuum System:")
+        print("This device shows an overview of the OMNY vacuum status. Use show_all()")

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -47,6 +47,7 @@ class RtFlomniController(Controller):
         "read_ssi_interferometer",
         "laser_tracker_check_signalstrength",
         "laser_tracker_check_enabled",
+        "is_axis_moving",
     ]
 
     def __init__(
@@ -538,8 +539,8 @@ class RtFlomniController(Controller):
 
         logger.info(
             "Flomni statistics: Average of all standard deviations: x"
-            f" {self.average_stdeviations_x_st_fzp/number_of_samples_to_read}, y"
-            f" {self.average_stdeviations_y_st_fzp/number_of_samples_to_read}."
+            f" {self.average_stdeviations_x_st_fzp/read_counter*1000:.1f}, y"
+            f" {self.average_stdeviations_y_st_fzp/read_counter*1000:.1f}"
         )
 
     def publish_device_data(self, signals, point_id):

csaxs_bec/devices/smaract/smaract_controller.py

@@ -80,6 +80,8 @@ class SmaractController(Controller):
         "describe",
         "axis_is_referenced",
         "all_axes_referenced",
+        "set_closed_loop_move_speed",
+        "is_axis_moving",
     ]
 
     def __init__(

csaxs_bec/devices/tests_utils/utils.py

@@ -0,0 +1,9 @@
+def patch_dual_pvs(device):
+    device.wait_for_connection(all_signals=True)
+    for walk in device.walk_signals():
+        if not hasattr(walk.item, "_read_pv"):
+            continue
+        if not hasattr(walk.item, "_write_pv"):
+            continue
+        if walk.item._read_pv.pvname.endswith("_RBV"):
+            walk.item._read_pv = walk.item._write_pv

csaxs_bec/scans/LamNIFermatScan.py

@@ -110,9 +110,8 @@ class LamNIMixin:
             logger.info(
                 f"Compensating {[val/1000 for val in lamni_to_stage_coordinates(x_drift,y_drift)]}"
             )
-            yield from self.stubs.set_and_wait(
-                device=["lsamx", "lsamy"], positions=[move_x, move_y]
-            )
+            yield from self.stubs.set(device="lsamx", value=move_x)
+            yield from self.stubs.set(device="lsamy", value=move_y)
 
         time.sleep(0.01)
         rtx_current = yield from self.stubs.send_rpc_and_wait("rtx", "readback.get")
@@ -148,9 +147,9 @@ class LamNIMixin:
                 + lamni_to_stage_coordinates(x_drift, y_drift)[1] / 1000
                 + lamni_to_stage_coordinates(x_drift2, y_drift2)[1] / 1000
             )
-            yield from self.stubs.set_and_wait(
-                device=["lsamx", "lsamy"], positions=[move_x, move_y]
-            )
+            yield from self.stubs.set(device="lsamx", value=move_x)
+            yield from self.stubs.set(device="lsamy", value=move_y)
+
             time.sleep(0.01)
             rtx_current = yield from self.stubs.send_rpc_and_wait("rtx", "readback.get")
             rty_current = yield from self.stubs.send_rpc_and_wait("rty", "readback.get")
@@ -444,7 +443,7 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
                     }
                 }
             )
-            yield from self.stubs.set_and_wait(device=["lsamrot"], positions=[angle])
+            yield from self.stubs.set(device="lsamrot", value=angle)
 
     def scan_core(self):
         if self.scan_type == "step":
@@ -457,7 +456,7 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
             # scan ID before sending the message to the device server
             yield from self.stubs.kickoff(device="rtx")
             while True:
-                yield from self.stubs.read_and_wait(group="primary", wait_group="readout_primary")
+                yield from self.stubs.read(group="monitored")
                 msg = self.device_manager.connector.get(MessageEndpoints.device_status("rt_scan"))
                 if msg:
                     status = msg

csaxs_bec/scans/__init__.py

@@ -1,4 +1,6 @@
 from .flomni_fermat_scan import FlomniFermatScan
+from .jungfrau_joch_scan import JungfrauJochTestScan
 from .LamNIFermatScan import LamNIFermatScan, LamNIMoveToScanCenter
+from .omny_fermat_scan import OMNYFermatScan
 from .owis_grid import OwisGrid
 from .sgalil_grid import SgalilGrid

csaxs_bec/scans/flomni_fermat_scan.py

@@ -35,7 +35,7 @@ class FlomniFermatScan(SyncFlyScanBase):
     scan_name = "flomni_fermat_scan"
     scan_report_hint = "table"
     scan_type = "fly"
-    required_kwargs = ["fov_size", "exp_time", "step", "angle"]
+    required_kwargs = ["fovx", "fovy", "exp_time", "step", "angle"]
     arg_input = {}
     arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
 
@@ -59,8 +59,8 @@ class FlomniFermatScan(SyncFlyScanBase):
         Args:
             fovx(float) [um]: Fov in the piezo plane (i.e. piezo range). Max 200 um
             fovy(float) [um]: Fov in the piezo plane (i.e. piezo range). Max 100 um
-            cenx(float) [mm]: center position in x.
-            ceny(float) [mm]: center position in y.
+            cenx(float) [um]: center position in x.
+            ceny(float) [um]: center position in y.
             exp_time(float) [s]: exposure time
             step(float) [um]: stepsize
             zshift(float) [um]: shift in z
@@ -95,6 +95,7 @@ class FlomniFermatScan(SyncFlyScanBase):
         if self.zshift < -100:
             logger.warning("The zshift is smaller than -100 um. It will be limited to -100 um.")
             self.zshift = -100
+        self.flomni_rotation_status = None
 
     def initialize(self):
         self.scan_motors = []
@@ -150,17 +151,17 @@ class FlomniFermatScan(SyncFlyScanBase):
         yield from self.stubs.send_rpc_and_wait("rty", "set", self.positions[0][1])
 
     def _prepare_setup_part2(self):
-        yield from self.stubs.wait(wait_type="move", device="fsamroy", wait_group="flomni_rotation")
-        yield from self.stubs.set(
-            device="rtx", value=self.positions[0][0], wait_group="prepare_setup_part2"
-        )
-        yield from self.stubs.set(
-            device="rtz", value=self.positions[0][2], wait_group="prepare_setup_part2"
-        )
+        if self.flomni_rotation_status:
+            self.flomni_rotation_status.wait()
+
+        rtx_status = yield from self.stubs.set(device="rtx", value=self.positions[0][0], wait=False)
+        rtz_status = yield from self.stubs.set(device="rtz", value=self.positions[0][2], wait=False)
+
         yield from self.stubs.send_rpc_and_wait("rtx", "controller.laser_tracker_on")
-        yield from self.stubs.wait(
-            wait_type="move", device=["rtx", "rtz"], wait_group="prepare_setup_part2"
-        )
+
+        rtx_status.wait()
+        rtz_status.wait()
+
         yield from self._transfer_positions_to_flomni()
         yield from self.stubs.send_rpc_and_wait(
             "rtx", "controller.move_samx_to_scan_region", self.fovx, self.cenx
@@ -200,7 +201,9 @@ class FlomniFermatScan(SyncFlyScanBase):
                     }
                 }
             )
-            yield from self.stubs.set(device="fsamroy", value=angle, wait_group="flomni_rotation")
+            self.flomni_rotation_status = yield from self.stubs.set(
+                device="fsamroy", value=angle, wait=False
+            )
 
     def _transfer_positions_to_flomni(self):
         yield from self.stubs.send_rpc_and_wait(
@@ -276,7 +279,7 @@ class FlomniFermatScan(SyncFlyScanBase):
         # scan ID before sending the message to the device server
         yield from self.stubs.kickoff(device="rtx")
         while True:
-            yield from self.stubs.read_and_wait(group="primary", wait_group="readout_primary")
+            yield from self.stubs.read(group="monitored")
             status = self.device_manager.producer.get(MessageEndpoints.device_status("rt_scan"))
             if status:
                 status_id = status.content.get("status", 1)
@@ -297,19 +300,7 @@ class FlomniFermatScan(SyncFlyScanBase):
         """return to the start position"""
         # in flomni, we need to move to the start position of the next scan
         if isinstance(self.positions, np.ndarray) and len(self.positions[-1]) == 3:
-            yield from self.stubs.set(
-                device="rtx", value=self.positions[-1][0], wait_group="scan_motor"
-            )
-            yield from self.stubs.set(
-                device="rty", value=self.positions[-1][1], wait_group="scan_motor"
-            )
-            yield from self.stubs.set(
-                device="rtz", value=self.positions[-1][2], wait_group="scan_motor"
-            )
-
-            yield from self.stubs.wait(
-                wait_type="move", device=["rtx", "rty", "rtz"], wait_group="scan_motor"
-            )
+            yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=self.positions[-1])
             return
 
         logger.warning("No positions found to return to start")

csaxs_bec/scans/jungfrau_joch_scan.py

@@ -0,0 +1,58 @@
+""" Module with JungfrauJochTestScan class. """
+
+from bec_lib import bec_logger
+from bec_server.scan_server.scans import AsyncFlyScanBase, ScanAbortion
+
+logger = bec_logger.logger
+
+
+class JungfrauJochTestScan(AsyncFlyScanBase):
+    """Owis-based grid scan."""
+
+    scan_name = "jjf_test"
+    # scan_report_hint = "device_progress"
+    required_kwargs = ["points", "exp_time", "readout_time"]
+    arg_input = {}
+    arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
+    gui_config = {
+        "Acquisition Parameters": ["num_points", "cycles"],
+        "Exposure Parameters": ["exp_time", "readout_time"],
+    }
+
+    def __init__(
+        self, num_points: int, exp_time: float, readout_time: float, cycles: int = 1, **kwargs
+    ):
+        """
+        JungfrauJoch Test scan.
+
+        Args:
+            device (DeviceBase) : The device to be triggered, currently only for delaygenerator csaxs
+            num_points (int) : Number of points per burst
+            exp_time (float) : exposure time.
+            readout_time (float): readout time of detector
+            cycles (int) : number of cycles, default is 1
+
+        Example:
+           scans.jjf_test(points = 100, exp_time= 1e-3, readout_time=1e-3, cycles = 2)
+        """
+        if readout_time <= 0:
+            raise ScanAbortion(f"Readout time must be larger than 0, provided value {readout_time}")
+        super().__init__(exp_time=exp_time, readout_time=readout_time, **kwargs)
+        self.device = "ddg"
+        self.num_points = num_points
+        self.cycles = cycles
+        self.primary_readout_cycle = 0.2
+
+    def scan_core(self):
+        logger.info(f"Starting with Scan Core")
+        total_exposure = self.num_points * (self.exp_time + self.readout_time)
+        for i in range(self.cycles):
+            logger.info(f"Beginning cycle {i} of {self.cycles}")
+
+            status = yield from self.stubs.trigger(min_wait=total_exposure, wait=False)
+            yield from self.stubs.read(group="monitored", point_id=self.point_id, wait=True)
+            self.point_id += 1
+            status.wait()
+            logger.info(f"Finished cycle {i} of {self.cycles}")
+        logger.info(f"Finished scan")
+        self.num_pos = self.point_id

csaxs_bec/scans/omny_fermat_scan.py

@@ -0,0 +1,305 @@
+"""
+SCAN PLUGINS
+
+All new scans should be derived from ScanBase. ScanBase provides various methods that can be customized and overriden
+but they are executed in a specific order:
+
+- self.initialize                        # initialize the class if needed
+- self.read_scan_motors                  # used to retrieve the start position (and the relative position shift if needed)
+- self.prepare_positions                 # prepare the positions for the scan. The preparation is split into multiple sub fuctions:
+    - self._calculate_positions          # calculate the positions
+    - self._set_positions_offset         # apply the previously retrieved scan position shift (if needed)
+    - self._check_limits                 # tests to ensure the limits won't be reached
+- self.open_scan                         # send an open_scan message including the scan name, the number of points and the scan motor names
+- self.stage                             # stage all devices for the upcoming acquisiton
+- self.run_baseline_readings             # read all devices to get a baseline for the upcoming scan
+- self.scan_core                         # run a loop over all position
+    - self._at_each_point(ind, pos)      # called at each position with the current index and the target positions as arguments
+- self.finalize                          # clean up the scan, e.g. move back to the start position; wait everything to finish
+- self.unstage                           # unstage all devices that have been staged before
+- self.cleanup                           # send a close scan message and perform additional cleanups if needed
+"""
+
+import time
+
+import numpy as np
+from bec_lib import bec_logger, messages
+from bec_lib.endpoints import MessageEndpoints
+from bec_server.scan_server.errors import ScanAbortion
+from bec_server.scan_server.scans import SyncFlyScanBase
+
+logger = bec_logger.logger
+
+
+class OMNYFermatScan(SyncFlyScanBase):
+    scan_name = "omny_fermat_scan"
+    scan_report_hint = "table"
+    scan_type = "fly"
+    required_kwargs = ["fovx", "fovy", "exp_time", "step", "angle"]
+    arg_input = {}
+    arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
+
+    def __init__(
+        self,
+        fovx: float,
+        fovy: float,
+        cenx: float,
+        ceny: float,
+        exp_time: float,
+        step: float,
+        zshift: float,
+        angle: float = None,
+        corridor_size: float = 3,
+        parameter: dict = None,
+        **kwargs,
+    ):
+        """
+        An OMNY scan following Fermat's spiral.
+
+        Args:
+            fovx(float) [um]: Fov in the piezo plane (i.e. piezo range). Max 200 um
+            fovy(float) [um]: Fov in the piezo plane (i.e. piezo range). Max 100 um
+            cenx(float) [um]: center position in x.
+            ceny(float) [um]: center position in y.
+            exp_time(float) [s]: exposure time
+            step(float) [um]: stepsize
+            zshift(float) [um]: shift in z
+            angle(float) [deg]: rotation angle (will rotate first)
+            corridor_size(float) [um]: corridor size for the corridor optimization. Default 3 um
+
+        Returns:
+
+        Examples:
+            >>> scans.omny_fermat_scan(fovx=20, fovy=25, cenx=10, ceny=0, zshift=0, angle=0, step=2, exp_time=0.01)
+        """
+
+        super().__init__(parameter=parameter, **kwargs)
+        self.axis = []
+        self.fovx = fovx
+        self.fovy = fovy
+        self.cenx = cenx
+        self.ceny = ceny
+        self.exp_time = exp_time
+        self.step = step
+        self.zshift = zshift
+        self.angle = angle
+        self.optim_trajectory = "corridor"
+        self.optim_trajectory_corridor = corridor_size
+        if self.fovy > 100:
+            raise ScanAbortion("The FOV in y must be smaller than 100 um.")
+        if self.fovx > 200:
+            raise ScanAbortion("The FOV in x must be smaller than 200 um.")
+        if self.zshift > 100:
+            logger.warning("The zshift is larger than 100 um. It will be limited to 100 um.")
+            self.zshift = 100
+        if self.zshift < -100:
+            logger.warning("The zshift is smaller than -100 um. It will be limited to -100 um.")
+            self.zshift = -100
+        self.omny_rotation_status = None
+
+    def initialize(self):
+        self.scan_motors = []
+        self.update_readout_priority()
+
+    def _optimize_trajectory(self):
+        self.positions = self.optimize_corridor(
+            self.positions, corridor_size=self.optim_trajectory_corridor
+        )
+
+    @property
+    def monitor_sync(self):
+        return "rt_omny"
+
+    def reverse_trajectory(self):
+        """
+        Reverse the trajectory. Every other scan should be reversed to
+        shorten the movement time. In order to keep the last state, even if the
+        server is restarted, the state is stored in a global variable in redis.
+        """
+        producer = self.device_manager.producer
+        msg = producer.get(MessageEndpoints.global_vars("reverse_omny_trajectory"))
+        if msg:
+            val = msg.content.get("value", False)
+        else:
+            val = False
+        producer.set(
+            MessageEndpoints.global_vars("reverse_omny_trajectory"),
+            messages.VariableMessage(value=(not val)),
+        )
+        return val
+
+    def prepare_positions(self):
+        self._calculate_positions()
+        self._optimize_trajectory()
+        flip_axes = self.reverse_trajectory()
+        if flip_axes:
+            self.positions = np.flipud(self.positions)
+
+        self.num_pos = len(self.positions)
+        self._check_min_positions()
+
+    def _check_min_positions(self):
+        if self.num_pos < 20:
+            raise ScanAbortion(
+                f"The number of positions must exceed 20. Currently: {self.num_pos}."
+            )
+
+    def _prepare_setup(self):
+        yield from self.stubs.send_rpc_and_wait("rtx", "controller.clear_trajectory_generator")
+        yield from self.omny_rotation(self.angle)
+
+        yield from self.stubs.send_rpc_and_wait("rty", "set", self.positions[0][1])
+
+    def _prepare_setup_part2(self):
+        if self.omny_rotation_status:
+            self.omny_rotation_status.wait()
+
+        rtx_status = yield from self.stubs.set(device="rtx", value=self.positions[0][0], wait=False)
+        rtz_status = yield from self.stubs.set(device="rtz", value=self.positions[0][2], wait=False)
+
+        yield from self.stubs.send_rpc_and_wait(
+            "rtx", "controller.laser_tracker_check_and_wait_for_signalstrength"
+        )
+
+        rtx_status.wait()
+        rtz_status.wait()
+
+        yield from self._transfer_positions_to_omny()
+        yield from self.stubs.send_rpc_and_wait("osamx", "omny_osamx_to_scan_center", self.cenx)
+
+    def omny_rotation(self, angle):
+        # get last setpoint (cannot be based on pos get because they will deviate slightly)
+        osamroy_current_setpoint = yield from self.stubs.send_rpc_and_wait(
+            "osamroy", "user_setpoint.get"
+        )
+        if angle == osamroy_current_setpoint:
+            logger.info("No rotation required")
+        else:
+            logger.info("Rotating to requested angle")
+            yield from self.stubs.scan_report_instruction(
+                {
+                    "readback": {
+                        "RID": self.metadata["RID"],
+                        "devices": ["osamroy"],
+                        "start": [osamroy_current_setpoint],
+                        "end": [angle],
+                    }
+                }
+            )
+            self.omny_rotation_status = yield from self.stubs.set(
+                device="osamroy", value=angle, wait=False
+            )
+
+    def _transfer_positions_to_omny(self):
+        yield from self.stubs.send_rpc_and_wait(
+            "rtx", "controller.add_pos_to_scan", self.positions.tolist()
+        )
+
+    def _calculate_positions(self):
+        self.positions = self.get_omny_fermat_spiral_pos(
+            -np.abs(self.fovx / 2),
+            np.abs(self.fovx / 2),
+            -np.abs(self.fovy / 2),
+            np.abs(self.fovy / 2),
+            step=self.step,
+            spiral_type=0,
+            center=False,
+        )
+
+    def get_omny_fermat_spiral_pos(
+        self, m1_start, m1_stop, m2_start, m2_stop, step=1, spiral_type=0, center=False
+    ):
+        """
+        Calculate positions for a Fermat spiral scan.
+
+        Args:
+            m1_start(float): start position in m1
+            m1_stop(float): stop position in m1
+            m2_start(float): start position in m2
+            m2_stop(float): stop position in m2
+            step(float): stepsize
+            spiral_type(int): 0 for traditional Fermat spiral
+            center(bool): whether to include the center position
+
+        Returns:
+            positions(array): positions
+        """
+        positions = []
+        phi = 2 * np.pi * ((1 + np.sqrt(5)) / 2.0) + spiral_type * np.pi
+
+        start = int(not center)
+
+        length_axis1 = np.abs(m1_stop - m1_start)
+        length_axis2 = np.abs(m2_stop - m2_start)
+        n_max = int(length_axis1 * length_axis2 * 3.2 / step / step)
+
+        z_pos = self.zshift
+
+        for ii in range(start, n_max):
+            radius = step * 0.57 * np.sqrt(ii)
+            # FOV is restructed below at check pos in range
+            if abs(radius * np.sin(ii * phi)) > length_axis1 / 2:
+                continue
+            if abs(radius * np.cos(ii * phi)) > length_axis2 / 2:
+                continue
+            x = radius * np.sin(ii * phi)
+            y = radius * np.cos(ii * phi)
+            positions.append([x + self.cenx, y + self.ceny, z_pos])
+        left_lower_corner = [
+            min(m1_start, m1_stop) + self.cenx,
+            min(m2_start, m2_stop) + self.ceny,
+            z_pos,
+        ]
+        right_upper_corner = [
+            max(m1_start, m1_stop) + self.cenx,
+            max(m2_start, m2_stop) + self.ceny,
+            z_pos,
+        ]
+        positions.append(left_lower_corner)
+        positions.append(right_upper_corner)
+        return np.array(positions)
+
+    def scan_core(self):
+        # use a device message to receive the scan number and
+        # scan ID before sending the message to the device server
+        yield from self.stubs.kickoff(device="rtx")
+        while True:
+            yield from self.stubs.read(group="monitored")
+            status = self.device_manager.producer.get(MessageEndpoints.device_status("rt_scan"))
+            if status:
+                status_id = status.content.get("status", 1)
+                request_id = status.metadata.get("RID")
+                if status_id == 0 and self.metadata.get("RID") == request_id:
+                    break
+                if status_id == 2 and self.metadata.get("RID") == request_id:
+                    raise ScanAbortion(
+                        "An error occured during the omny readout:"
+                        f" {status.metadata.get('error')}"
+                    )
+
+            time.sleep(1)
+            logger.debug("reading monitors")
+        # yield from self.device_rpc("rtx", "controller.kickoff")
+
+    def return_to_start(self):
+        """return to the start position"""
+        # in omny, we need to move to the start position of the next scan
+        if isinstance(self.positions, np.ndarray) and len(self.positions[-1]) == 3:
+            yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=self.positions[-1])
+            return
+
+        logger.warning("No positions found to return to start")
+
+    def run(self):
+        self.initialize()
+        yield from self.read_scan_motors()
+        self.prepare_positions()
+        yield from self._prepare_setup()
+        yield from self.open_scan()
+        yield from self.stage()
+        yield from self.run_baseline_reading()
+        yield from self._prepare_setup_part2()
+        yield from self.scan_core()
+        yield from self.finalize()
+        yield from self.unstage()
+        yield from self.cleanup()

csaxs_bec/scans/owis_grid.py

@@ -262,10 +262,8 @@ class OwisGrid(AsyncFlyScanBase):
             yield from self.stubs.send_rpc_and_wait("samy", "acceleration.put", self.acc_time)
 
             # Start motion and send triggers
-            yield from self.stubs.set(
-                device="samy",
-                value=(self.end_y + (self.sign * self.premove_distance)),
-                wait_group="flyer",
+            flyer_status = yield from self.stubs.set(
+                device="samy", value=(self.end_y + (self.sign * self.premove_distance)), wait=False
             )
             # Trigger fast shutter, open them right away
             yield from self.stubs.send_rpc_and_wait("ddg_fsh", "trigger")
@@ -275,32 +273,28 @@ class OwisGrid(AsyncFlyScanBase):
             # Trigger detectors
             yield from self.stubs.send_rpc_and_wait("ddg_detectors", "trigger")
 
-            # Readout primary devices, this waits and could lead to additional overheads
-            # if devices are slow to response. For optimizing performance, primary devices
+            # Readout monitored devices, this waits and could lead to additional overheads
+            # if devices are slow to response. For optimizing performance, monitored devices
             # could be read out only once at beginning and end
-            yield from self.stubs.read_and_wait(
-                group="primary", wait_group="readout_primary", point_id=self.point_id
-            )
+            yield from self.stubs.read(group="monitored", point_id=self.point_id)
             self.point_id += 1
 
             # Wait for motion to finish
-            yield from self.stubs.wait(device="samy", wait_group="flyer", wait_type="move")
+            flyer_status.wait()
 
             # Move second axis by a step
-            yield from self.stubs.set(
-                device="samx", value=(self.start_x - ii * self.stepping_x), wait_group="motion"
+            status_x = yield from self.stubs.set(
+                device="samx", value=(self.start_x - ii * self.stepping_x), wait=False
             )
             # Set acceleration and velocity to max
             yield from self.stubs.send_rpc_and_wait("samy", "velocity.put", self.high_velocity)
             yield from self.stubs.send_rpc_and_wait("samy", "acceleration.put", self.high_acc_time)
 
             # Move back to start
-            status_prepos = yield from self.stubs.send_rpc_and_wait(
-                "samy", "move", (self.start_y - self.premove_distance)
-            )
+            yield from self.stubs.set(device="samy", value=(self.start_y - self.premove_distance))
 
             # Wait for motion to finish
-            status_prepos.wait()
+            status_x.wait()
 
     # Set speed and acceleration to initial values
     def finalize(self):

csaxs_bec/scans/sgalil_grid.py

@@ -126,7 +126,7 @@ class SgalilGrid(AsyncFlyScanBase):
         """
 
         # set up the delay generators
-        status_ddg_detectors_burst = yield from self.stubs.send_rpc_and_wait(
+        yield from self.stubs.send_rpc_and_wait(
             "ddg_detectors",
             "burst_enable",
             count=self.interval_y,
@@ -134,7 +134,7 @@ class SgalilGrid(AsyncFlyScanBase):
             period=(self.exp_time + self.readout_time),
             config="first",
         )
-        status_ddg_mcs_burst = yield from self.stubs.send_rpc_and_wait(
+        yield from self.stubs.send_rpc_and_wait(
             "ddg_mcs",
             "burst_enable",
             count=self.interval_y,
@@ -143,9 +143,9 @@ class SgalilGrid(AsyncFlyScanBase):
             config="first",
         )
         # Disable burst mod on DDF for fsh and EN of MCS card
-        status_ddg_fsh_burst = yield from self.stubs.send_rpc_and_wait("ddg_fsh", "burst_disable")
+        yield from self.stubs.send_rpc_and_wait("ddg_fsh", "burst_disable")
         # Set width of FSH opening to 0
-        status_ddg_fsh_ttlwidth = yield from self.stubs.send_rpc_and_wait(
+        yield from self.stubs.send_rpc_and_wait(
             "ddg_fsh", "set_channels", "width", 0, channels=["channelCD"]
         )
 
@@ -166,19 +166,17 @@ class SgalilGrid(AsyncFlyScanBase):
         # status_ddg_mcs_ttlwidth = yield from self.stubs.send_rpc_and_wait(
         #     "ddg_mcs", "set_channels", "width", 3e-3
         # )
-        status_ddg_mcs_ttldelay = yield from self.stubs.send_rpc_and_wait(
-            "ddg_mcs", "set_channels", "delay", 0
-        )
+        yield from self.stubs.send_rpc_and_wait("ddg_mcs", "set_channels", "delay", 0)
 
         # wait for the delay generators to finish setting up
         status_ddg_detectors_source.wait()
         status_ddg_mcs_source.wait()
-        trigger_ddg_fsh = yield from self.stubs.send_rpc_and_wait("ddg_fsh", "trigger")
+        yield from self.stubs.send_rpc_and_wait("ddg_fsh", "trigger")
         # trigger_ddg_fsh.wait()
         # status_mcs_points_per_line.wait()
         # status_mcs_lines.wait()
 
-        yield from self.stubs.kickoff(
+        kickoff_status = yield from self.stubs.kickoff(
             device="samx",
             parameter={
                 "start_y": self.start_y,
@@ -190,19 +188,14 @@ class SgalilGrid(AsyncFlyScanBase):
                 "exp_time": self.exp_time,
                 "readout_time": self.readout_time,
             },
+            wait=False,
         )
-        target_diid = self.DIID - 1
-        while True:
-            # readout the primary device and wait for the fly scan to finish
-            yield from self.stubs.read_and_wait(
-                group="primary", wait_group="readout_primary", point_id=self.point_id
-            )
+
+        while not kickoff_status.done:
+            # readout the monitored device and wait for the fly scan to finish
+            yield from self.stubs.read(group="monitored", point_id=self.point_id)
             self.point_id += 1
-            status = self.stubs.get_req_status(
-                device="samx", RID=self.metadata["RID"], DIID=target_diid
-            )
-            if status:
-                break
+
             time.sleep(self.sleep_time)
             if self.scan_progress() > int(self.timeout_scan_abortion / self.sleep_time):
                 logger.info("would have raised a scan abortion here")

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/custom-class-template.rst

@@ -0,0 +1,34 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if not item.startswith('_') %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/_templates/custom-module-template.rst

@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/api_reference/api_reference.md

@@ -0,0 +1,12 @@
+(api_reference)=
+# API Reference
+
+```{eval-rst}
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   csaxs_bec
+
+```

docs/assets/biotech.svg

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docs/assets/index_contribute.svg

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docs/assets/index_user_guide.svg

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docs/conf.py

@@ -0,0 +1,67 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+
+project = "SLS cSAXS"
+copyright = "2024, Paul Scherrer Institute"
+author = "Paul Scherrer Institute"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    # "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx_toolbox.collapse",
+    "sphinx_copybutton",
+    "myst_parser",
+    "sphinx_design",
+    "sphinx_inline_tabs",
+]
+
+myst_enable_extensions = [
+    "amsmath",
+    "attrs_inline",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+add_module_names = False  # Remove namespaces from class/method signatures
+autodoc_inherit_docstrings = True  # If no docstring, inherit from base class
+set_type_checking_flag = True  # Enable 'expensive' imports for sphinx_autodoc_typehints
+autoclass_content = "both"  # Include both class docstring and __init__
+autodoc_mock_imports = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+language = "Python"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+html_css_files = ["custom.css"]
+# html_logo = "./assets/csaxs_icon.png"
+html_title = "SLS cSAXS"

docs/developer/developer.md

@@ -0,0 +1,3 @@
+(developer)=
+# Developer 
+

docs/index.md

@@ -0,0 +1,50 @@
+:html_theme.sidebar_secondary.remove:
+
+# cSAXS documentation
+
+Welcome to the cSAXS documentation. This documentation is divided into two main sections: the user guide and the developer guide. The user guide is intended for users of the cSAXS beamline, while the developer guide is intended for developers of the cSAXS beamline.
+
+<br><br>
+
+````{grid} 2
+:gutter: 5
+
+```{grid-item-card}
+:link: introduction
+:link-type: ref
+:img-top: /assets/index_user_guide.svg
+:text-align: center
+:class-item: index-card
+
+## User guide
+
+Information for users of the cSAXS beamline.
+```
+
+```{grid-item-card} 
+:link: developer
+:link-type: ref
+:img-top: /assets/index_contribute.svg
+:text-align: center
+:class-item: index-card
+
+## Developer guide
+
+Information for developers of the cSAXS beamline.
+```
+
+````
+
+
+```{toctree}
+---
+numbered: true
+maxdepth: 2
+hidden: true
+---
+
+introduction/introduction
+user/user
+developer/developer
+api_reference/api_reference
+```

docs/introduction/introduction.md

@@ -0,0 +1,16 @@
+(introduction)=
+# The cSAXS Beamline
+
+## Overview
+
+cSAXS is a beamline dedicated to small-angle X-ray scattering (SAXS) and coherent diffractive imaging, particularly ptychography, located at the Swiss Light Source at the Paul Scherrer Institut in Villigen, Switzerland. See the beamline's endstations website for information on experimental setups, geometries, and sample preparation details. We strongly encourage all prospective users to discuss their experimental plans with the beamline staff before submitting proposals.
+
+Access to cSAXS is granted through the biannual SLS call for proposals. Access to PSI data analysis center is described in Photon Science Data Analysis.
+
+## Experiment types
+
+Experiments performed at cSAXS include, inter alia,
+
+* Ptychographic nanotomography, see for example Dierolf et al., Nature 467, 436 (2010) or Holler et al., Nature Electronics 2, 464 (2019). Dedicated instrumentation, available to users, is described in Holler et al., Sci. Rep. 4, 3857 (2014), Holler et al., Rev. Sci. Instrum. 88, 113701 (2017), Holler et al., Rev. Sci. Instrum. 89, 043706 (2018), and Holler et al., J. Synchrotron Rad. 27, 730 (2020).
+* Optics characterization, see for example: Vila-Comamala et al. Opt Express 19, 21333 (2011)
+* Small-angle X-ray scattering (SAXS), e.g., Smeulders et al., Nature 478, 412 (2011), can be performed with spatial resolution as microscopy technique in 2D (Bunk et al. New J. Phys. 11, 123016 (2009)) and 3D (Liebi et al. Nature 527, 349 (2015)). SAXS is also available with time resolution in the millisecond range (Westenhoff et al., Nature Methods 7, 775 (2010)).

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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.add_custom_image:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.add_custom_image, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_autorange:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_autorange, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_autorange_mode:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_autorange_mode, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_color_map:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_color_map, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_fft:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_fft, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_grid:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_grid, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_image_properties:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_image_properties, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_log:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_log, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_monitor:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_monitor, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_processing:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_processing, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_rotation:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_rotation, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_title:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_title, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_transpose:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_transpose, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_vrange:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_vrange, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_x_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_x_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_x_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_x_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_x_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_x_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECImageShow.set_y_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECImageShow.set_y_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECImageShow, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMap.reset_history:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMap.reset_history, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMap, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMap.set_max_points:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMap.set_max_points, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMap, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMap.set_num_dim_points:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMap.set_num_dim_points, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMap, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMap.set_scatter_size:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMap.set_scatter_size, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMap, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMapWidget.get_data:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMapWidget.get_data, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMapWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMapWidget.set_background_value:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMapWidget.set_background_value, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMapWidget, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMapWidget.set_max_points:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMapWidget.set_max_points, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMapWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECMotorMapWidget.set_scatter_size:1: WARNING: duplicate object description of bec_widgets.cli.client.BECMotorMapWidget.set_scatter_size, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECMotorMapWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.export:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.export, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.lock_aspect_ratio:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.lock_aspect_ratio, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.remove:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.remove, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_grid:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_grid, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_legend_label_size:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_legend_label_size, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_title:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_title, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_x_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_x_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_x_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_x_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_x_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_x_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_y_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_y_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_y_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_y_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECPlotBase.set_y_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECPlotBase.set_y_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECPlotBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECQueue:1: WARNING: duplicate object description of bec_widgets.cli.client.BECQueue, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECQueue, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.BECQueue.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECQueue, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECStatusBox:1: WARNING: duplicate object description of bec_widgets.cli.client.BECStatusBox, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECStatusBox, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.BECStatusBox.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECStatusBox, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.add_dap:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.add_dap, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.clear_all:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.clear_all, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.curves:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.curves, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.export:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.export, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.get_all_data:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.get_all_data, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.get_curve:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.get_curve, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.get_dap_params:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.get_dap_params, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.lock_aspect_ratio:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.lock_aspect_ratio, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.plot:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.plot, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.remove:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.remove, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.remove_curve:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.remove_curve, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.scan_history:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.scan_history, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_colormap:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_colormap, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_grid:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_grid, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_legend_label_size:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_legend_label_size, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_title:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_title, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_x:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_x, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_x_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_x_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_x_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_x_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_x_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_x_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_y_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_y_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_y_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_y_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveform.set_y_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveform.set_y_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveform, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveformWidget:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveformWidget, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveformWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveformWidget.set_x:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveformWidget.set_x, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveformWidget, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveformWidget.set_x_label:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveformWidget.set_x_label, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveformWidget, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveformWidget.set_x_lim:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveformWidget.set_x_lim, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveformWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECWaveformWidget.set_y_scale:1: WARNING: duplicate object description of bec_widgets.cli.client.BECWaveformWidget.set_y_scale, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECWaveformWidget, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceBox.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceBox, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.DeviceComboBox:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceComboBox, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceComboBox, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceComboBox.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceComboBox, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.DeviceInputBase:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceInputBase, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceInputBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceInputBase.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceInputBase, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.DeviceLineEdit:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceLineEdit, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceLineEdit, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.DeviceLineEdit.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.DeviceLineEdit, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.reset_connection:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.reset_connection, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_background:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_background, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_color:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_color, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_line_width:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_line_width, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_min_max_values:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_min_max_values, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_start_angle:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_start_angle, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_update:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_update, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.Ring.set_value:1: WARNING: duplicate object description of bec_widgets.cli.client.Ring.set_value, other instance in api_reference/_autosummary/bec_widgets.cli.client.Ring, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.add_ring:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.add_ring, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.enable_auto_updates:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.enable_auto_updates, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.remove_ring:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.remove_ring, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.reset_diameter:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.reset_diameter, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.rings:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.rings, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_colors_directly:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_colors_directly, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_colors_from_map:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_colors_from_map, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_diameter:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_diameter, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_gap:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_gap, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_line_widths:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_line_widths, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_min_max_values:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_min_max_values, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_number_of_bars:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_number_of_bars, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_precision:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_precision, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.set_value:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.set_value, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.RingProgressBar.update_config:1: WARNING: duplicate object description of bec_widgets.cli.client.RingProgressBar.update_config, other instance in api_reference/_autosummary/bec_widgets.cli.client.RingProgressBar, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.ScanControl.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.ScanControl, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.StopButton.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.StopButton, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client_utils.RPCBase.gui_is_alive:1: WARNING: duplicate object description of bec_widgets.cli.client.TextBox.gui_is_alive, other instance in api_reference/_autosummary/bec_widgets.cli.client.TextBox, use :no-index: for one of them
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+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECDockArea.panels:1: WARNING: duplicate object description of bec_widgets.cli.client.BECDockArea.panels, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECDockArea, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECDockArea.remove_dock:1: WARNING: duplicate object description of bec_widgets.cli.client.BECDockArea.remove_dock, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECDockArea, use :no-index: for one of them
+/Users/wakonig_k/.pyenv/versions/bec_widgets_docs/lib/python3.10/site-packages/bec_widgets/cli/client.py:docstring of bec_widgets.cli.client.BECDockArea.restore_state:1: WARNING: duplicate object description of bec_widgets.cli.client.BECDockArea.restore_state, other instance in api_reference/_autosummary/bec_widgets.cli.client.BECDockArea, use :no-index: for one of them
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docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,10 @@
+sphinx
+sphinx_copybutton
+recommonmark
+sphinx-toolbox
+pydata-sphinx-theme
+sphinx-copybutton
+sphinx-inline-tabs
+myst-parser
+sphinx-design
+tomli

docs/user/before_you_arrive/before_you_arrive.md

@@ -0,0 +1,5 @@
+(user.before_you_arrive)=
+# Before you arrive
+
+
+## Before you arrive

docs/user/ptychography/flomni.md

@@ -0,0 +1,292 @@
+(user.ptychography.flomni)=
+# flOMNI
+
+flOMNI is an instrument for tomographic measurements via X-ray ptychography. The sample environment is at atmospheric pressure and room temperature (or higher).
+An early version of the setup is described [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:12560). Nano positioning is based on closed loop control to a position signal obtained from dedicated [laser interferometry](https://www.dora.lib4ri.ch/psi/islandora/object/psi:7524). For fast scanning a combined motion of the sample (slow axis) and beam defining fresnel zone plate (fast axis) is used. The method is described [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:21021). The setup is equipped with a [heater](https://www.dora.lib4ri.ch/psi/islandora/object/psi:45302), that can be used to apply hot gas streams to the sample.
+Samples are to be mounted on [OMNY pins](https://www.dora.lib4ri.ch/psi/islandora/object/psi:4528).
+
+## How to flOMNI 
+
+… a step-by-step guide for users
+
+(user.ptychography.flomni.transfer)=
+### Sample storage and transfer
+
+Print the current usage of the sample storage  
+`flomni.ftransfer_show_all()`
+
+flOMNI has to know about the loaded positions and sample names. To modify use  
+`flomni.ftransfer_modify_storage(<position>, 0 (=free) / 1 (=used))`  
+positions `<1> .. <20>` are available slots in the tray.
+Special position: `0 = sample stage`, `100 = gripper`.
+You will be asked to enter a sample name. 
+
+To load a new sample in the sample stage, in principle only one command is needed  
+`flomni.ftransfer_sample_change(<position new sample>)`  
+You will be asked where the previous sample should go with a suggestion for an empty position in the tray.
+Other commands:  
+`ftransfer_tray_in /_out	 (not yet implemented).`
+
+__If something goes wrong__, there are additional commands to perform a manual operation of the gripper.
+
+| command | explanation |
+| --- | --- |
+| `flomni.ftransfer_get_sample(<position>)`  | Pick sample from <position> |
+| `flomni.ftransfer_put_sample(<position>)`  | Mount sample at <position> |
+| `flomni.ftransfer_flomni_stage_in()`       | stage to measurement position |
+| `flomni.ftransfer_flomni_stage_out()`      | stage to the sample change position |
+
+Manual operation of the gripper (do not leave it too long in open state)  
+`flomni.ftransfer_gripper_open()`  
+`flomni.ftransfer_gripper_close()`
+
+Manually move the gripper to a transfer position
+`flomni.ftransfer_gripper_move(<position>)`
+
+### Alignment of samples
+
+#### Coarse alignment
+
+After the sample transfer the sample stage moved to the measurement position with your new sample. The Xray eye will automatically move in and the shutter will open. You may already see the sample in the omny xeye interface running on the windows computer.
+If you see your sample already at the approximately correct height, you can skip steps 1 to 3. Otherwise adjust the height:
+
+1. `flomni.rt_feedback_disable()` disable the closed loop operation to allow movement of coarse stages
+1. `umvr(dev.fsamy, 0.01)`, attention: unit <mm>, move the sample stage relative up (positive) or down (negative) until the sample is approximately vertically centered in xray eye screen
+1. `flomni.xrayeye_update_frame()` will update the current image on the xray eye screen
+1. `flomni.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring (clicking in the X-ray eye software) the sample position at 0, 45, 90, 135, 180 degrees. Then use the matlab routine `SPEC_ptycho_align.m` to fit this data.
+1. `flomni.read_alignment_offset()` read the generated alignment data.
+
+#### Fine alignment
+
+After the xrayeyealign, a fine alignment needs to be performed using ptychography.
+_To bypass the fine alignment: `feye_out`_
+
+
+1. `flomni.tomo_parameters()` Adjust the  ptychographic scan parameters for performing an alignment scan. Typically FOVX = FOVX(Xrayeye)+20 mu, shell step = beamsize/2.5, number of projections and tomo mode are ignored in the alignment scans.
+1. `flomni.tomo_alignment_scan()` perform the alignment scan. When the first scan is running, switch to a matlab session and run `SPEC_ptycho_align` again. Click left and right. The third click can define the height of  the scan, but is not needed and ignored by default. The widest horizontal field of view will be printed at the end of the matlab session.
+1. `flomni.read_alignment_offset()` Load alignment parameters calculated in matlab.
+
+### Tomographic Measurement
+
+Now that the sample is aligned, the tomographic measurement can be performed.
+1. `flomni.tomo_parameters()` adjust the scan parameters for the tomographic scan. This includes the parameters for ptychographic scans of projections plus the strategy for angular sampling. The vertical shift adjusts the field of view, up (positive) or down (negative). After adjusting the numbers, type again `flomni.tomo_parameters()` and verify that they are correct.
+1. `flomni.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle <angle>. Launch the tomographic measurement by `flomni.tomo_scan()`. 
+1. Before changing sample, verify that all subtomograms were completely acquired using the `tomo_recons matlab` script.
+
+#### If something went wrong…
+
+A __single projection__ is to be repeated use
+`flomni.tomo_scan_projection(<angle>)`. The target angle of scans can be found in the second column of the file in 
+`~/Data10/specES1/dat-files/omni_scannumbers.txt`
+
+To continue an __interrupted tomography scan__:
+
+Depending on the tomo mode following parameters can be given to the `flomni.tomo_scan()` command:
+| tomo type | parameters and their defaults |
+| --- | --- |
+| 8 sub-tomograms | subtomo_start=1, start_angle=None |
+| Golden ratio tomography (sorted in bunches) | projection_number=None |
+| Equally spaced with golden starting angle | projection_number=None |
+
+## How to setup flOMNI (software)
+
+This part of the manual is intended for beamline staff and expert users
+
+The nano-positioning is controlled by a feedback loop running on a real-time linux based computer. With all related hardware connected, this loop has to be started manually.
+
+1. Login to the computer by `ssh control@mpc2680`. The password is "engine".
+1. `cd OMNY/flOMNI/`
+1. `./startflOMNI`
+
+Once the loop has started, it is possible to start bec with the flOMNI configuration file.
+
+Loading the flOMNI configuration (this command will load the OMNY configuration only - isolated from the beamline)  
+`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/flomni_config.yaml")`
+
+Loading the flOMNI scripts  
+`from csaxs_bec.bec_ipython_client.plugins.flomni import Flomni`  
+`flomni =  Flomni(bec)`
+
+If the realtime system is restarted, bec will lose communication. To restart:  
+`flomni.rt_off()` … then wait a few seconds  
+`flomni.rt_on()`
+
+### Initialization of the stages
+
+The stages of flOMNI are referenced in respect to their endswitches. The stages have to be initialized at the beginning of a run or when the Galil motor controllers have been reset or restarted. To see the status of the stages following commands are available:
+
+Show the status of all galil controllers (all stepper motors and the UPR rotation stage)  
+`dev.fsamx.controller.galil_show_all()`
+
+The same holds true for the Smaract stages which control the OSA position.  Their status can be checked by  
+`dev.fosax.controller.show_all()`
+
+In case referencing of the flOMNI stages is required, run  
+`flomni.flomni_init_stages()`  
+This script will first verify that the stages are not in an initialized state, and then reference all stages in a safe way. The user will be warned in case of a potentially risky situation. This mainly involves a collision risk upstream with the exposure box exit window. It might be worth to check clearance prior to calling the init skript.
+
+### X-ray optics alignment
+
+The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.  
+Example: The OSAx “in” position can be reviewed by `dev.fosax.user_parameter`  
+Update the value by (example "fosax", "in") by `dev.fosax.update_user_parameter({"in":value})`
+
+`flomni.ffzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter is the photon _energy_ in keV.  
+Example: `flomni.ffzp_info(6.2)`
+
+The [laser feedback](user.ptychography.flomni.laser_feedback) will be disabled and fine alignment lost if foptx/y are moved!
+
+Following functions exist to move the optics in and out, with self-explaining naming.
+- `flomni.ffzp_in()`
+- `flomni.foptics_in()`
+- `flomni.foptics_out()`
+- `flomni.fosa_in()`
+- `flomni.fosa_out()`
+
+### Interferometer
+
+The position feedback in flOMNI is controlled in closed loop to an interferometric position measurement. To show the signal of the interferometers:
+`flomni.show_signal_strength_interferometer()`  
+Typical values with proper alignment, sample stage at the measurement position and laser tracker running are  
+_TODO_
+
+#### Laser tracker commands
+
+The horizontal interferometer is built according to the [tracking interferometer](https://www.dora.lib4ri.ch/psi/islandora/object/psi:7524). The tracker can be controlled by following commands. During commissioning of the setup it is worthy to check the status, but during general operation these commands should not be required.
+
+- `flomni.laser_tracker_show_all()`
+- `flomni.laser_tracker_on()`
+- `flomni.laser_tracker_off()`
+
+(user.ptychography.flomni.laser_feedback)=
+#### Interferometer feedback commands
+
+The closed loop control of the Piezo stages can be controlled by  
+- `flomni.rt_feedback_enable_with_reset()`.  
+_There is also an enable without reset, which is used during tomography scans, when using coarse stages to increase the scan range. It should not be required to use manually._  
+- `flomni.rt_feedback_disable()`
+- `flomni.rt_feedback_status()`
+
+### Scanning in 2D and sample alignment
+
+#### flOMNI Fermat scan
+
+The basic scan function can be called by `scans.flomni_fermat_scan()` and offers a detailed doc string for further details (`scans.flomni_fermat_scan?`). A prerequisite for scanning is a running feedback system. The scan has following parameters.
+
+| Parameters |  |
+| --- | --- |
+| fovx (float) | Fov in the piezo plane (i.e. piezo range). Max 200 um |
+| fovy (float) | Fov in the piezo plane (i.e. piezo range). Max 100 um |
+| cenx (float) | center position in x |
+| ceny (float) | center position in y |
+| exp_time (float) | exposure time |
+| step (float) | stepsize |
+| zshift (float) | shift in z |
+| angle (float) | rotation angle (will rotate first) |
+| corridor_size (float) | corridor size for the corridor optimization. Default 3 um |
+
+Example:  
+`scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01)`
+
+#### Overview of the alignment steps
+
+There are several corrections applied to maintain the sample in the FOV:
+1. Mirror calibration
+1. X-ray eye alignment
+1. Ptychography fine alignment (improvement of the X-ray eye alignment step)
+1. Vertical shifts from tomography reconstruction (for very small vertical FOV)
+
+#### XrayEye and sample alignment
+
+The XrayEye can be moved in and out by  
+`flomni.feye_in()`  
+`flomni.feye_out()`
+
+The _in_ and _out_ positions are stored as user parameters in the stage definition. Get the values by  
+`dev.feyex.user_parameter`  
+`dev.feyey.user_parameter`
+
+Update the values by, example for feyex and in position,  
+`dev.feyex.update_user_parameter({"in":value})`
+
+To refresh the frame of the xray eye windows software  
+`flomni.xrayeye_update_frame()`
+
+To start the xray eye alignment (and clear any previous alignment)  
+`flomni.xrayeye_alignment_start()`
+
+To load the fit parameters from directory _dir_path_ computed by _SPEC_ptycho_align.m_ in Matlab run  
+`flomni.read_alignment_offset(dir_path='')`  
+The loading routine uses default values for the vertical alignment. This behavior can be changed (e.g. for getting new default values) by the parameter `use_vertical_default_values=False`.
+
+At each projection, the angular dependent is computed by  
+`flomni.get_alignment_offset(angle)`, with _angle_ in degrees.
+
+The alignment can be cleared by  
+`flomni.reset_tomo_alignment_fit()`
+
+#### Fine alignment
+
+The alginment obtained by the X-ray eye can be refinde by recording ptychography projections at 45 deg. intervals. For this, adjust the tomo parameters by  
+`flomni.tomo_parameters()`
+
+Next, run the alignment scan by
+`flomni.tomo_alignment_scan()`
+
+Reconstruct the scan and use SPEC_ptycho_align.m to obtain improved fit parameters. The new parameters can be loaded by  
+`flomni.read_alignment_offset()`
+
+For a __very__ tight vertical field of view, a fine vertical alignment based on outputs generated from early tomography reconstructions can be used. A corresponding file can be generated by the tomography reconstruction script and can be loaded by the following two methods:  
+`flomni.read_additional_correction_y()`  
+`flomni.read_additional_correction_y2()`  
+One __important__ note: The first method is by default loading a mirror correction file automatically. If the tomogram is using that data, do not overwrite it, use the secondary correction instead.
+
+The scan offsets are computed at each projection by  
+`flomni.compute_additional_correction_y(angle)`  
+`flomni.compute_additional_correction_y2(angle)`
+
+The additional correct can be __reset__ by  
+`flomni.reset_correction()`  
+It will automatically load the default mirror correction file as primary correction! To reset and not load any correction, which might be useful to obtain a new default correction file, run  
+`flomni.reset_correction(use_default_correction=False)`
+
+#### Scanning of projections
+
+At any stage of the alignment process it is possible to scan a projection.
+
+Define the scan parameters by `flomni.tomo_parameters()`
+
+Run a scan at _angle_ (in degrees) by `flomni.tomo_scan_projection(angle)`
+
+### Tomography
+
+The tomo parameters have to be set by  
+`flomni.tomo_parameters()`
+
+Once satisfied with the alignment, the tomography scan can be started by  
+`flomni.tomo_scan()`
+
+Three modes for angular sampling are implemented and they have different optional parameters for the tomo_scan method:
+| tomography mode | parameters and defaults |
+| --- | --- |
+| 8 sub-tomograms | subtomo_start=1, start_angle=None |
+| Golden ratio tomography (sorted in bunches) | projection_number=None |
+| Equally spaced with golden starting angle | projection_number=None |
+
+The parameters can be used to __restart an interrupted acquisition__. 
+In case of eight equally spaced sub-tomograms, an individual sub tomogram can be scanned by flomni.sub_tomo_scan(subtomo_number, start_angle). If the start angle is not specified, it will be computed depending on the subtomo_number, which is ranging from 1 to 8.
+
+### Sample storage and transfer
+
+[See short version](user.ptychography.flomni.transfer)
+
+### Heater
+
+The [heater](https://www.dora.lib4ri.ch/psi/islandora/object/psi:45302) can be moved up and down by
+flomni.move_fheater_down()
+flomni.move_fheater_up()
+
+The functions are safe in the sense that no collisions should occur. E.g. the OSA will be moved back before a movement of the heater.
+
+__The heater still needs commissioning in BEC!!!__
+

docs/user/ptychography/lamni.md

@@ -0,0 +1,173 @@
+(user.ptychography.lamni)=
+# LamNI
+
+LamNI is an instrument for 3D ptychography via ptychographic X-ray computed lamninography (PyXL). The instrument is described in detail [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:33067).
+
+## How to LamNI 
+
+… a step-by-step guide for _beamline staff and expert users_.
+
+### Sample change and alignment
+
+The access to the sample region is blocked by the flight tube during measurement. To get the flight tube out of the way use  
+`lamni.leye_in()`.  
+Mount the new sample. The X-ray eye is already in, but the X-ray optics needs to be moved out of the beam path by  
+`lamni.loptics_out()`. Potentially a larger area needs to be illuminated to properly see the sample, which can be done by
+`open slits`.
+
+#### Coarse axis alignment
+
+The effective position of the axis of rotation shifts with sample thickness or mounting position of the sample along the axis of rotation. The position of the axis of rotation is controlled by user parameters __center__ of the __lsamx__ and __lsamy__ stages. To observe the axis of rotation obtain the position of the Fresnel zone plate on the X-ray eye, possibly in the _ueye gui_ by:  
+1. `lamni.lfzp_in()`, move the FZP in
+1. `dev.rtx.controller.feedback_disable()`, disable feedback to allow lsam movements
+1. `fshopen()`, open the shutter
+1. `umv(dev.lsamrot,90)` to rotate the sample. One might observe the center of rotation at 0 and 180 degress.
+1. `umvr(dev.lsamx,0.01)` to move lsamx and lsamy such that the center of rotation is at the center of the X-ray beam
+1. `dev.lsamx` and `dev.lsamy` will print current position and the center value. Update the center value by  
+`dev.lsamx.update_user_parameter({'center':8.69})`  
+`dev.lsamy.update_user_parameter({'center':8.69})`  
+1. close the shutter: `fshclose()`
+
+#### X-ray eye alignment
+
+The GUI on the windows computer is used to obtain a coarse sample alignment. Start the alignment process (and clear any previous alignment) by  
+`lamni.align.align()`. With LamNI it can be very difficult to follow a region of interest as the sample rotates. Therefore the X-ray shutter will be open during the entire process. Therefore the windows software has to be set on __FORCE__ to continuously update frames and not freeze frames after rotation.  
+- run `SPEC_ptycho_align.m` (in matlab, use __force_ptychography = 0__)
+- `lamni.align.read_xray_eye_correction()` to read the alignment parameters. The correction is based on sinusoidal fits in x and y direction. The values are computed by
+`lamni_compute_additional_correction_xeye_mu(angle)`
+- If slits were opened during alignment, close the slits `slits 1 to around 0.3`
+- `lamni.leye_out()` remove the X-ray eye and move the flight tube in
+- _possibly check slit0wh, idgap_
+
+To only see one frame on the Windows GUI run `lamni.align.update_frame()`
+
+#### Fine alignment
+
+The sample fine alignment can be obtained using ptychography. For this a short laminogram has to be recorded.
+- `lamni.tomo_parameters()` adjust the parameters for a coarse scan: A large step size and large FOV. Especially select __FOV offset = 0__ and __number of projections = 96__ (only one sub-laminogram will be recorded).
+- `lamni.sub_tomo_scan(1,0)` record one sub-laminogram
+- use the corresponding scan numbers in `SPEC_ptycho_align.m`
+- Record a last projection for all scans to reconstruct `lamni.tomo_scan_projection(0)` and wait for the reconstructions to be complete
+- Run `SPEC_ptycho_align.m` (in Matlab, __force ptycho=1__, and __correct scan numbers__)
+- Click the sample position in the Matlab GUI and then load the generated file by, for example
+  `lamni.align.read_additional_correction('/sls/X12SA/data/e20632/Data10/cxs_software/ptycho/correction_lamni_um_S05389_lamni_fit.txt')`
+- With this alignment a second iteration could be performed. To read the second correction file use `lamni.align.read_additional_correction_2()`
+
+#### Shifting the FOV
+
+- `lamni.align.tomo_fovx/y_offset=value` [mm] will shift the field of view. Perform this adjustment from projections collected at __lsamrot 0 degrees__. 
+
+### Laminography scan
+
+Start the laminography scan by
+1. `lamni.tomo_parameters()` adjust the parameters to the desired settings.
+1. for test scans run  
+`lamni.tomo_scan_projection(angle)`  
+`lamni.tomo_reconstruct()`  
+1. `lamni.tomo_scan()` to start the lamninography scan
+
+### Tips and Tricks
+
+#### Reset corrections
+
+- `lamni.align.reset_correction()`
+- `lamni.align.reset_correction_2()`
+- `lamni.align.reset_xray_eye_correction()`
+
+#### Adjusting beam size with feedback running
+
+If the beam size needs to be changed with feedback running, e.g. to switch from near-field to far-field ptychography, following steps can be taken:  
+1. `dev.loptz.enable_set=True` to enable loptz movements with feedback running
+1. `umvr(dev.lopz,_value_)` move loptz to the desired position. 
+1. `lamni._manual_shift_x/y = _value_` correct the stage run out from motion along the optical axis (units of um). The exact value can be checked by comparing feature positions in projections before/after adjusting loptz.
+1. Potentially correct the alignment of the OSA
+
+#### BEC tips
+
+Print all global variables `bec.global_vars()`
+
+`dev.lsamx/y.wm` or `dev.lsamx/y` prints a motor position
+
+## How to setup LamNI (software)
+
+This part of the manual describes the software structure in more detail.
+
+### start the realtime feedback loop and BEC with OMNY
+
+The nano-positioning is controlled by a feedback loop running on a real-time linux based computer. With all related hardware connected, this loop has to be started manually.
+
+1. Login to the computer by `ssh control@mpc2680`. The password is "engine".
+1. `cd OMNY/lamni/`
+1. `./startLAMNI`
+
+Once the loop has started, it is possible to start bec with the LamNI configuration file.
+
+Loading the LamNI configuration (this command will load the LamNI configuration only - isolated from the beamline)  
+`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/lamni_config.yaml")`
+
+Loading the LamNI scripts  
+`from csaxs_bec.bec_ipython_client.plugins.LamNI import LamNI`
+`lamni = LamNI(bec)`
+
+If the realtime system is restarted, BEC will lose communication. To restart:  
+`lamni.rt_off()` … then wait a 10 seconds  
+`lamni.rt_on()`
+
+### Initialization of the stages
+
+The stages of LamNI are referenced in respect to their endswitches or reference marks. The stages have to be initialized at the beginning of a run or when the Galil motor controller has been reset or restarted. To see the status of the stages following commands are available:
+
+Show the status of all galil controllers (all stepper motors and the UPR rotation stage)  
+`dev.lsamx.controller.galil_show_all()`
+
+The same holds true for the Smaract stages which control the OSA position.  Their status can be checked by  
+`dev.losax.controller.show_all()`
+
+In case referencing of the LamNI stages is required, run  
+`lamni.init.lamni_init_stages()`
+This script will first verify that the stages are not in an initialized state, and then reference all stages in a safe way. The user will be warned in case of a potentially risky situation. This mainly involves a collision risk upstream with the exposure box exit window. It might be worth to check clearance prior to calling the init skript.
+
+### Interferometer
+
+The position feedback in LamNI is controlled in closed loop to an interferometric position measurement. To show the signal of the interferometers:
+`lamni.show_signal_strength_interferometer()`  
+Typical values with proper alignment are  
+_TODO_
+
+#### Interferometer feedback commands
+
+- `dev.rtx.feedback_enable_with_reset()`
+- `dev.rtx.feedback_disable()`
+- `dev.rtx.feedback_enable_without_reset()` *is only used internally by lamni methods
+- if reset of angle interferometer is required  
+`dev.rtx.feedback_disable_and_even_reset_lamni_angle_interferometer()`
+- `dev.rtx.feedback_enable_with_reset()`
+
+_ToDo Feedback status might be helpful. Plus make accessible via lamni.methods…_
+
+### Scanning in 2D and sample alignment
+
+The underlying scan function can be called as  
+`scans.lamni_fermat_scan()`
+
+Use `scans.lamni_fermat_scan?`for detailed information. A prerequisite for scanning is a running feedback system.
+
+### X-ray optics alignment
+
+The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.  
+Example: The OSAx “in” position can be reviewed by `dev.losax.user_parameter`  
+Update the value by (example "losax", "in") by `dev.losax.update_user_parameter({"in":value})`
+
+`lamni.lfzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter is the photon _energy_ in keV.  
+Example: `lamni.lfzp_info(6.2)`
+
+The laser feedback will be disabled and fine alignment lost if foptx/y are moved!
+
+Following functions exist to move the optics in and out, the naming is self-explaining.
+- `lamni.lfzp_in()`
+- `lamni.loptics_in()`
+- `lamni.loptics_out()`
+- `lamni.losa_in()`
+- `lamni.losa_out()`
+- `lamni.lfzp_in()`
+

docs/user/ptychography/omny.md

@@ -0,0 +1,434 @@
+(user.ptychography.omny)=
+# OMNY
+
+OMNY is a microscope setup for 3D mesurements via ptychographic X-ray computed tomography. The sample enviroment is in ultra-high vacuum and at a sample temperature of 90 K. The instrument is equipped with a load-lock system and allows loading and unloading of samples under cryogenic conditions. The setup is described in detail [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:4776). Samples have to be mounted on [OMNY pins](https://www.dora.lib4ri.ch/psi/islandora/object/psi:4528).
+
+## HowTo OMNY
+
+… a step-by-step guide for _beamline staff and expert users_.
+
+### Change to a new sample
+
+The sample storage, shuttles and parking positions are described in detail (here)[user.ptychography.omny.samples].
+
+1. `omny.otransfer_get_sample(0)` remove current sample from sample stage. Watch gripper action and be ready to ctrl+c in case something is wrong.  
+_If in doubt check that the correct sample shutte is in the active position by calling `omny.otransfer_storage()`. The slot can be selected by `omny.otransfer_park_slot(slot)`._
+1. `omny.otransfer_put_sample(position)` put the sample to the selected shuttle
+1. `omny.otransfer_get_sample(position) ` get the new sample from a shuttle
+1. `omny.otransfer_put_sample(0)`, mount the sample in the sample stage
+
+### Alignment of samples
+
+#### Coarse alignment
+
+After mounting a new sample, the Xray eye will automatically be at the correct position to collect X-ray data. It can also be manually moved to the correct position by `omny.oeye_xray_in()`.
+
+1. `omny.xrayeye_update_frame()` obtain a new frame that will be displayed on the Windows computer, OMNY software. If you see your sample already at the approximately correct height, you can skip step 2. Otherwise adjust the height:
+1. `umvr(dev.osamy, 0.01)`, attention: unit <mm>, move the sample stage relative up (positive) or down (negative) until the sample is approximately vertically centered in xray eye screen. After a move get a new frame by `omny.xrayeye_update_frame()`.
+1. `omny.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring (clicking in the X-ray eye software) the sample position at 0, 45, 90, 135, 180 degrees. Then use the matlab routine `SPEC_ptycho_align.m` to fit this data.
+1. `omny.read_alignment_offset()` read the generated alignment data.
+
+#### Fine alignment
+
+After the xrayeyealign, a fine alignment needs to be performed using ptychography.
+_To bypass the fine alignment skip steps_.
+
+1. `omny.tomo_parameters()` adjust the  ptychographic scan parameters for performing an alignment scan. Typically FOVX = FOVX(Xrayeye)+20 mu, shell step = beamsize/2.5, number of projections and tomo mode are ignored in the alignment scans.
+1. `omny.optics_in()` move the Fresnel zone plate and order sorting aperture into position for ptychographic measurements.
+1. `omny.oeye_out()` move the X-ray eye out of the beam path.
+1. `omny.tomo_alignment_scan()` perform the alignment scan. When the first scan is running, switch to a matlab session and run `SPEC_ptycho_align` again. Click left and right. The third click can define the height of  the scan, but is not needed and ignored by default. The widest horizontal field of view will be printed at the end of the matlab session.
+1. `omny.read_alignment_offset()` Load alignment parameters calculated in matlab.
+
+### Tomographic Measurement
+
+Now that the sample is aligned, the tomographic measurement can be performed.
+1. `omny.tomo_parameters()` adjust the scan parameters for the tomographic scan. This includes the parameters for ptychographic scans of projections plus the strategy for angular sampling. The vertical shift adjusts the field of view, up (positive) or down (negative). After adjusting the numbers, type again `omny.tomo_parameters()` and verify that they are correct.
+1. `omny.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle <angle>, e.g. at zero degrees. When happy with the scan parameters launch the tomographic measurement by `omny.tomo_scan()`.
+1. Before changing to the next sample sample, verify that all subtomograms were completely acquired using the `tomo_recons matlab` script.
+
+### If something went wrong…
+Special cases:
+If the gripper or another stage got stuck during transfer. Ctrl+c and then
+`umv(dev.otransy, -1.5)` followed by 
+`omny._otransfer_gripper_to_park_z()`, which will move the gripper to its parking position.
+
+If the above fails for the vertical movement of the gripper _Ctrl+C_. 
+Try moving up and down a bit `umvr(dev.otransy,0.5)`, `umvr(dev.otransy,-0.5)`, potentially requires a _ctrl+C_ again if stuck.
+Then, `umv(dev.ootransy,-1.5)` followed by 
+`omny._otransfer_gripper_to_park_z()`, which will move the gripper to its parking position.
+
+If this error happens after a sample was mounted or unmounted, it is important to chech that the sample storage is correct `omny.otransfer_storage()`.
+
+(user.ptychography.omny.samples)=
+### Sample storage and transfer
+
+Following commands will provide help within BEC:  
+- `omny.otransfer_help()`	print help related to sample transfer
+- `dev.omny_samples.help()` print help related to sample storage
+
+#### Managing sample storage
+
+The sample holders used are [OMNY pins](https://www.dora.lib4ri.ch/psi/islandora/object/psi:4528). These are instsalled in sample transfer shuttles, which can load up to six pins. These shuttles are transferred via a vacuum load lock to the vacuum chamber. The loading procedure can be handled at room temperature or under cryogenic conditions.  
+The thee __shuttles__ that exist are named __“A”, “B”, “C”__. The __pin positions__ within a shuttle are number __1 to 6__ according to the following sketch:
+
+```{figure} omny_shuttle.png
+OMNY sample shuttle
+```
+
+In addition to the shuttle positions, there are __fixed positions in OMNY__ which have numbers __larger than 10__. Such fixed positions are treated as system __“O”__.
+
+Each shuttle can be placed in a __parking slot__ in OMNY. The parking slots are numbered as displayed below (oparkz slot). Slots 1 and 2 are at room temperature. Slots 3 to 6 are at cryogenic temperature.
+
+```{figure} omny_parking.png
+OMNY parking station
+```
+
+The status of the sample storage has to be correct in BEC. This means that the status of OMNY pins within OMNY ("O") as well as the shuttles has to be correct, the pin status within the shuttles ("A", "B", "C"), as well as the status of the shuttles within the OMNY parking.  
+This loading status is handled via a OMNY samples device: `dev.omny_samples`
+
+Within the BEC client session `dev.omny_samples.help()` will display all required commands with a short explanation.
+
+To get an overview use `dev.omny_samples.show_all()` or `omny.otransfer_storage()`
+
+Modify a slot position of systems "A", "B", "C", "O":  
+`dev.omny_samples.unset_sample_slot('system',position)` free a sample position.  
+`dev.omny_samples.set_sample_slot('system',position,'name')` set a sample position. The sample has to get a _name_.  
+
+There are two __special sample slots__:  
+If a sample is in the __gripper__ and the information has to be manually changed use  
+`dev.omny_samples.unset_sample_in_gripper()`  
+`dev.omny_samples.set_sample_in_gripper('name')`
+
+In the case of the sample stage position, the commands are  
+`dev.omny_samples.unset_sample_in_samplestage()`  
+`dev.omny_samples.set_sample_in_samplestage('name')`
+
+The shuttles are mounted in the parking station. Typically oparkz slot 3 is used for shuttle A, slot 4 for shuttle B, slot 5 for shuttle C. If that status has to be modified, the following commands can be used:  
+`dev.omny_samples.unset_shuttle_slot(slot_nr)`  
+`dev.omny_samples.set_shuttle_slot(container, slot_nr)`  
+Here is an _example_: dev.omny_samples.set_shuttle_slot('A',2)
+
+#### Sample transfer
+
+Once the sample places are set correctly and checked by using `omny.otransfer_storage()`, the following commands are available for sample change. To pick a sample from a parking slot, the parking slot stage has to be moved to the correct parking slot position. If a parking position is active, this information is displayed in sample storage overview.
+
+| Command | Explanation |
+| --- | --- |
+| `omny.otransfer_help()` | print a brief help |
+| `omny.otransfer_park_slot(slot)` | drive the __parking station__ to place for sample transfer from _<slot>_ |
+| `omny.otransfer_park_loadlock_slot(slot)` | drive the __parking station__ to load _<slot>_ with the loadlock |
+| `omny.otransfer_get_sample(position)` | pick with the gripper from _<position>_ |
+| `omny.otransfer_put_sample(position)` | put with the gripper to _<position>_ |
+
+For transfer the __sample stage__ is refered to as _position_ 0.
+
+Advanced commands ... in case something goes wrong
+| Command | Explanation |
+| --- | --- |
+| `omny._otransfer_gripper_up()` | move gripper up |
+| `omny._otransfer_gripper_to_park_z()` | move gripper up and to parking position |
+| `omny._otransfer_ensure_shuttle_closed()` | close shuttle of parking station |
+| `omny._oshield_ST_close()` |  close shield of sample stage |
+
+When closing a shuttle of the shield, the gripper will be moved to the parking position prior closing.
+
+### Status of OMNY
+
+To see the status of the insrument, following commands can be used. Most of the components mentioned below are controlled via devices with naming starting with omny. TAB completion on dev.omny can be a quick way to find the commands.
+
+#### Cameras
+
+During operation the BEC GUI will show the relevant cameras or progress information. To manually switch view TAB completion on `omny.omnygui_` will show all options to control the GUI. Most useful 
+
+- `omny.omnygui_show_omnycam_parking()`  
+- `omny.omnygui_show_omnycam_samplestage()` 
+- `omny.omnygui_show_progress()`
+
+#### Vacuum status
+
+The status of the vacuum system of OMNY can be displayed by `omny.vcs_show_all()`.  
+`omny.vcs_valves_in_measurement_position()` will report if all valves are in the correct position for X-ray beam to enter and propagate to the detector.
+
+#### Temperatures
+
+The status of all temperature measurements can be displayed by `omny.temperatures_show_all()`
+
+It will display a table for the instrument and sample environment.
+
+Example in warm state
+
+| Channel | Name                  | Temperature | Setpoint | Unit  | AlarmState |
+|---------|-----------------------|-------------|----------|-------|------------|
+| 8       | XEye Chamber          | 22.60       |          | degC  |            |
+| 9       | Kuehlsystem RT ZufOSA | 22.80       | 23.00    | degC  |            |
+| 10      | OSA_HaltZul_517       | 384.15      |          | K     |            |
+| 16      | XEye Air              | 22.60       |          | degC  |            |
+| 17      | SampleShield_RT_440   | 23.00       | 23.00    | degC  |            |
+| 18      | DeltaA_RT             | 26.00       | 26.00    | degC  |            |
+| 19      | DeltaB_RT             | 26.00       | 26.00    | degC  |            |
+| 20      | DeltaC_RT             | 26.00       | 26.00    | degC  |            |
+| 21      | Haube_ST_RT           | 23.00       | 23.00    | degC  |            |
+| 22      | Delta_Basisplatte     | 21.40       |          | degC  |            |
+| 23      | InterfBridge          | 22.50       |          | degC  |            |
+| 24      | XEye Cam              | 23.30       |          | degC  |            |
+| 25      | OSA_HSupp_RT_403      | 25.00       | 25.00    | degC  |            |
+| 27      | OSA_Supp_RT_404       | 25.00       | 25.00    | degC  |            |
+| 28      | ST_Shield_1           | 384.15      |          | K     | Alarm      |
+| 29      | ST_Shield_2           | 384.15      |          | K     | Alarm      |
+| 30      | OSA_CoolConn_407      | 384.15      |          | K     | Alarm      |
+| 31      | OSA_Holder_406        | 384.15      |          | K     | Alarm      |
+| 35      | Gripper_Halter_460    | 25.40       | 25.00    | degC  |            |
+| 36      | Gripper_Flex_A        | -8999.00    | 25.00    | degC  | Alarm      |
+| 37      | Gripper_Flex_B        | 24.60       | 25.00    | degC  |            |
+| 38      | Gripper_A             | 384.15      |          | K     | Alarm      |
+| 39      | Gripper_B             | 384.15      |          | K     | Alarm      |
+| 41      | FZP                   | 30.00       | 30.00    | degC  |            |
+| 42      | Park_RT_A             | 25.10       | 25.00    | degC  |            |
+| 44      | Park_RT_B             | 25.30       | 25.00    | degC  |            |
+| 45      | BaseBlock             | 21.00       |          | degC  |            |
+| 46      | Park_Cryo_R           | 384.15      |          | K     | Alarm      |
+| 47      | Park_Cryo_L           | 384.15      |          | K     | Alarm      |
+
+OMNY Cryo Temperature Controller
+
+| Channel | Name  | Temperature | Setpoint | Unit |
+|---------|-------|-------------|----------|------|
+| 1       | ChanA | 297.95      | 300.00   | K    |
+| 2       | ChanB | 297.61      | 299.00   | K    |
+| 3       | ChanC | 0.00        | 0.00     | K    |
+| 4       | ChanD | 294.47      | 0.00     | K    |
+Cryo controller is running in open loop.
+
+ChanA and ChanD are sample temperatures, and ChanB is the bottom of the cryo link, meaning the head of the cryostat.
+
+
+#### Dewar
+
+The status of the dewar and nitrogen flow can be displayed by `omny.dewar_show_all()`
+
+## How to setup OMNY (software)
+
+This part of the manual describes the software structure in more detail.
+
+### start the realtime feedback loop and BEC with OMNY
+
+The nano-positioning is controlled by a feedback loop running on a real-time linux based computer. With all related hardware connected, this loop has to be started manually.
+
+1. Login to the computer by `ssh control@mpc3217`. The password is "engine".
+1. `cd OMNY/OMNY/`
+1. `./startOMNY`
+
+Once the loop has started, it is possible to start bec with the OMNY configuration file.
+
+Loading the OMNY configuration (this command will load the OMNY configuration only - isolated from the beamline)  
+`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/flomni_config.yaml")`
+
+Loading the OMNY scripts  
+`from csaxs_bec.bec_ipython_client.plugins.omny import OMNY`  
+`omny = OMNY(bec)`
+
+If the realtime system is restarted, BEC will lose communication. To restart:  
+`omny.rt_off()` … then wait a 10 seconds  
+`omny.rt_on()`
+
+### Initialization of the stages
+
+The stages of OMNY are referenced in respect to their endswitches and reference marks. The stages have to be initialized at the beginning of a run or when the Galil motor controllers have been reset or restarted. To see the status of the stages following commands are available:
+
+Show the status of all galil controllers (all stepper motor and rotation stage)  
+`dev.osamx.controller.galil_show_all()`
+
+In case referencing of the OMNY stages is required, run  
+`omny.omny_init_stages(autoconfirm, autoretry)`
+
+The process will regularly prompt the user for OK. At safe states this can be automatically done by setting _autoconfirm=1_.  
+In case referencing fails, another attempt will be made after prompting the user. This can also be automatically done for certain number of times using the parameter autoretry.
+We typically use  
+`omny.omny_init_stages(autoconfirm=1, autoretry=2)`
+
+### Interferometer
+
+If the realtime system is restarted, BEC will lose communication. To restart:  
+`omny.rt_off()` … then wait a 10 seconds  
+`omny.rt_on()`
+
+To show the signal of the interferometers:  
+`omny.show_signal_strength_interferometer()`  
+Typical values with proper alignment, sample stage at the measurement position and laser tracker running are  
+| Channel |    Name   |  Value   |
+|---------|-----------|----------|
+|    1    | OSA FZP Y |  5500  |
+|    2    |  ST OSA Y |  2500  |
+|    3    | OSA FZP X |  4000  |
+|    4    |  ST OSA X |  9000   |
+|    5    |   Angle   |  2500  |
+
+
+#### Laser tracker commands
+
+The horizontal interferometer is built according to the [tracking interferometer](https://www.dora.lib4ri.ch/psi/islandora/object/psi:7524). The tracker can be controlled by following commands. During commissioning of the setup it is worthy to check the status, but during general operation these commands should not be required.
+
+- `omny.laser_tracker_show_all()`
+- `omny.laser_tracker_on()`
+- `omny.laser_tracker_off()`
+
+When the PSD signal of the tracker (PSD not signalstrength!) is too low, enabling the laser tracker will not be successful. One can use `omny.interferometer_tweak_otrack()` to manually tweak the coarse stages of the tracker. Once signal is reached the tracker can be enabled. This should only be required during commissioning of OMNY.
+
+#### Interferometer alignment
+
+Several mirrors in OMNY are motorized. Aligning the interferometer can thus be done via software. To enter alignment mode use  
+`omny.interferometer_tweaking()`  
+Select the channel by using number keys __1 to 7__ and the __arrow keys__ to tweak.
+The tweaking mode can be exited by pressing __q to quit__.
+Some mirrors are regularly automatically aligned, such as the horizontal mirror of the OSA. This automatic alignment can also be manually executed by `omny.omny_interferometer_align_tracking()`
+
+#### Interferometer feedback commands
+
+The closed loop control of the Piezo stages can be controlled by  
+- `omny.feedback_enable_with_reset()`  
+_There is also an enable without reset, which is used during tomography scans, when using coarse stages to increase the scan range. It should not be required to use manually._
+- `omny.feedback_disable()`  
+- `omny.feedback_status()`
+
+
+### X-ray optics alignment, near-field and far-field ptychography
+
+The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.  
+Example: The OSAx “in” position can be reviewed by `dev.oosax.user_parameter`  
+Update the value by (example "oosax", "in") by `dev.oosax.update_user_parameter({"in":value})`
+
+For __near-field__ and __far-field__ separate optics parameters are stored. Example:  
+dev.oosax.user_parameter returns {'near_field_in': 3.2044, 'far_field_in': 3.022}  
+Update the value by (example "oosax", "near_field_in")
+dev.oosax.update_user_parameter({"near_field_in":value})
+
+The __global variable omny.near_field__ controls whether near- or far-field settings are used. To switch `omny.near-field=False` or `omny.near-field=True`.
+
+`omny.ofzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter energy in keV to get values at a different energy.  
+Example: `omny.ofzp_info(6.2)`
+
+__Laser feedback will be disabled and thus fine alignment lost if commands are used that move optics stages!__
+
+Following functions exist to move the optics in and out, with self-explaining naming.
+- `omny.optics_in()`
+- `omny.ofzp_in()`
+- `omny.ofzp_out()`
+- `omny.oosa_in()`
+- `omny.oosa_out()`
+- `omny.oosa_move_out_of_shield()`
+
+#### OMNY Fermat scan
+
+The basic scan function can be called by `scans.omny_fermat_scan()` and offers a detailed doc string for further details (`scans.omny_fermat_scan?`). A prerequisite for scanning is a running feedback system. The scan has following parameters.
+
+| Parameters |  |
+| --- | --- |
+| fovx (float) | Fov in the piezo plane (i.e. piezo range). Max 200 um |
+| fovy (float) | Fov in the piezo plane (i.e. piezo range). Max 100 um |
+| cenx (float) | center position in x |
+| ceny (float) | center position in y |
+| exp_time (float) | exposure time |
+| step (float) | stepsize |
+| zshift (float) | shift in z |
+| angle (float) | rotation angle (will rotate first) |
+| corridor_size (float) | corridor size for the corridor optimization. Default 3 um |
+
+Example:  
+`scans.omny_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01)`
+
+#### Overview of the alignment steps
+
+There are several corrections applied to maintain the sample in the FOV:
+1. Mirror calibration
+1. X-ray eye alignment
+1. Ptychography fine alignment (improvement of the X-ray eye alignment step)
+1. Vertical shifts from tomography reconstruction (for very small vertical FOV)
+
+#### XrayEye and sample alignment
+
+Within a usual work-flow the movement of the X-ray eye is mostly moved automatically to the correct position. For manual movements use
+| Command | Explanation |
+| --- | --- |
+| omny.oeye_xray_in() | move to the fluorescense microscope in |
+| omny.oeye_cam_in() | move the camera showing the samplestage from downstream in |
+| omny.oeye_out() | move out, X-rays can reach the X-ray detector |
+
+The _in_ and _out_ positions are stored as user parameters in the stage definition. Get the values by  
+`dev.oeyex.user_parameter`  
+`dev.oeyey.user_parameter`
+
+Update the values by, example for oeyex and in position  
+`dev.oeyex.update_user_parameter({"xray_in":value})`
+
+To refresh the frame of the xray eye windows software  
+`omny.xrayeye_update_frame()`
+
+To start the xray eye alignment (and clear any previous alignment)  
+`omny.xrayeye_alignment_start()`
+
+To load the fit parameters from directory _dir_path_ computed by _SPEC_ptycho_align.m_ in Matlab run  
+`omny.read_alignment_offset(dir_path='',setup="omny")`  
+
+To load from a specific directory, specify it as parameter. Example:  
+`omny.read_alignment_offset(dir_path="/bec/align",setup="omny")`
+
+The loading routine uses default values for the vertical alignment for setup. This behavior can be changed (e.g. for getting new default values) by the parameter `use_vertical_default_values=False`.
+
+At each projection, the angular dependent is computed by  
+`omny.get_alignment_offset(angle)`, with _angle_ in degrees.
+
+The alignment can be cleared by  
+`omny.reset_tomo_alignment_fit()`
+
+#### Fine alignment
+
+The alginment obtained by the X-ray eye can be refinde by recording ptychography projections at 45 deg. intervals. For this, adjust the tomo parameters by  
+`omny.tomo_parameters()`
+
+Next, run the alignment scan by
+`omny.tomo_alignment_scan()`
+
+Reconstruct the scan and use SPEC_ptycho_align.m to obtain improved fit parameters. The new parameters can be loaded by  
+`omny.read_alignment_offset()`
+
+For a __very__ tight vertical field of view, a fine vertical alignment based on outputs generated from early tomography reconstructions can be used. A corresponding file can be generated by the tomography reconstruction script and can be loaded by the following two methods:  
+`omny.read_additional_correction_y()`  
+`omny.read_additional_correction_y2()`  
+One __important__ note: The first method is by default loading a mirror correction file automatically. If the tomogram is using that data, do not overwrite it, use the secondary correction instead.
+
+The scan offsets are computed at each projection by  
+`omny.compute_additional_correction_y(angle)`
+`omny.compute_additional_correction_y2(angle)`
+
+The additional correct can be __reset__ by  
+`omny.reset_correction()`  
+It will automatically load the default mirror correction file as primary correction! To reset and not load any correction, which might be useful to obtain a new default correction file, run  
+`omny.reset_correction(use_default_correction=False)`
+
+#### Scanning of projections
+
+At any stage of the alignment process it is possible to scan a projection.
+
+Define the scan parameters by `omny.tomo_parameters()`
+
+Run a scan at _angle_ (in degrees, 0 to 180) by `omny.tomo_scan_projection(angle)`
+
+### Tomography
+
+The tomo parameters have to be set by  
+`omny.tomo_parameters()`
+
+Once satisfied with the alignment, the tomography scan can be started by  
+`omny.tomo_scan()`
+
+Three modes for angular sampling are implemented and they have different optional parameters for the tomo_scan method:
+| tomography mode | parameters and defaults |
+| --- | --- |
+| 2 sub-tomograms | subtomo_start=1, start_angle=None |
+| Golden ratio tomography (sorted in bunches) | projection_number=None |
+| Equally spaced with golden starting angle | projection_number=None |
+
+The parameters can be used to __restart an interrupted acquisition__. 
+In case of eight equally spaced sub-tomograms, an individual sub tomogram can be scanned by flomni.sub_tomo_scan(subtomo_number, start_angle). If the start angle is not specified, it will be computed depending on the subtomo_number, which is ranging from 1 to 2.
+
+__Mechanical wear is an issue with lifetime of dry vacuum stages. Thus for standard acquisitions that do not have VERY strong arguments that require a different mode, two sub-tomograms has to be performed.__

docs/user/ptychography/ptychography.md

@@ -0,0 +1,72 @@
+(user.ptychography)=
+# Ptychography
+Welcome to the ptychography section of the cSAXS beamline.
+
+```{toctree}
+---
+maxdepth: 2
+hidden: true
+---
+
+flomni/
+lamni/
+omny/
+reconstructions/
+
+```
+
+
+***
+
+````{grid} 2
+:gutter: 5
+
+```{grid-item-card}
+:link: user.ptychography.flomni
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## flOMNI
+
+All about the flOMNI instrument
+```
+
+```{grid-item-card}
+:link: user.ptychography.lamni
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## LamNI
+
+All about the LamNI instrument
+```
+
+```{grid-item-card}
+:link: user.ptychography.omny
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## OMNY
+
+All about the OMNY instrument
+```
+
+```{grid-item-card}
+:link: user.ptychography.reconstructions
+:link-type: ref
+:img-top: /assets/receipt_long.svg
+:text-align: center
+:class-item: index-card
+
+## Ptychoshelves
+
+All about ptychography reconstructions
+```
+
+````

docs/user/ptychography/reconstructions.md

@@ -0,0 +1,4 @@
+(user.ptychography.reconstructions)=
+# Ptychoshelves
+
+Check it out [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi%3A31264).

docs/user/saxs/saxs.md

@@ -0,0 +1,5 @@
+(user.saxs)=
+# Saxs
+
+
+## Beamtime allocation

docs/user/user.md

@@ -0,0 +1,59 @@
+(user)=
+# User
+Welcome to the User section of the cSAXS beamline.
+
+```{toctree}
+---
+maxdepth: 2
+hidden: true
+---
+
+before_you_arrive/before_you_arrive.md
+ptychography/ptychography.md
+saxs/saxs.md
+
+```
+
+
+***
+
+````{grid} 2
+:gutter: 5
+
+```{grid-item-card}
+:link: user.before_you_arrive
+:link-type: ref
+:img-top: /assets/receipt_long.svg
+:text-align: center
+:class-item: index-card
+
+## Before you arrive
+
+Learn what to do before you arrive to the beamline.
+```
+
+```{grid-item-card}
+:link: user.ptychography
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## Ptychography
+
+All about ptychography measurements and reconstructions.
+```
+
+```{grid-item-card}
+:link: user.saxs
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## SAXS
+
+All about SAXS measurements and analysis.
+```
+
+````

pyproject.toml

@@ -18,8 +18,11 @@ dependencies = [
     "bec_server",
     "ophyd_devices",
     "std_daq_client",
+    "jfjoch-client",
     "rich",
     "pyepics",
+    "pyueye",             # for the IDS uEye camera
+    "bec_widgets",
 ]
 
 [project.optional-dependencies]

tests/tests_devices/test_delay_generator_csaxs.py

@@ -2,21 +2,11 @@
 from unittest import mock
 
 import pytest
-from ophyd_devices.interfaces.base_classes.psi_delay_generator_base import TriggerSource
+from ophyd_devices.devices.delay_generator_645 import TriggerSource
 
 from csaxs_bec.devices.epics.delay_generator_csaxs import DDGSetup
 
 
-def patch_dual_pvs(device):
-    for walk in device.walk_signals():
-        if not hasattr(walk.item, "_read_pv"):
-            continue
-        if not hasattr(walk.item, "_write_pv"):
-            continue
-        if walk.item._read_pv.pvname.endswith("_RBV"):
-            walk.item._read_pv = walk.item._write_pv
-
-
 @pytest.fixture(scope="function")
 def mock_DDGSetup():
     mock_ddg = mock.MagicMock()
@@ -136,20 +126,6 @@ def channel_pairs(request):
     return request.param
 
 
-def test_check_scan_id(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan):
-    """Test the check_scan_id method."""
-    # Set first attributes of parent class
-    for k, v in scaninfo.items():
-        setattr(mock_DDGSetup.parent.scaninfo, k, v)
-    for k, v in ddg_config_defaults.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    for k, v in ddg_config_scan.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    # Call the function you want to test
-    mock_DDGSetup.check_scan_id()
-    mock_DDGSetup.parent.scaninfo.load_scan_metadata.assert_called_once()
-
-
 def test_on_pre_scan(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan):
     """Test the check_scan_id method."""
     # Set first attributes of parent class
@@ -165,27 +141,28 @@ def test_on_pre_scan(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_sc
         mock_DDGSetup.parent.trigger_shot.put.assert_called_once_with(1)
 
 
-@pytest.mark.parametrize("source", ["SINGLE_SHOT", "EXT_RISING_EDGE"])
-def test_on_trigger(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan, source):
-    """Test the on_trigger method."""
-    # Set first attributes of parent class
-    for k, v in scaninfo.items():
-        setattr(mock_DDGSetup.parent.scaninfo, k, v)
-    for k, v in ddg_config_defaults.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    for k, v in ddg_config_scan.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    # Call the function you want to test
-    mock_DDGSetup.parent.source.name = "source"
-    mock_DDGSetup.parent.source.read.return_value = {
-        mock_DDGSetup.parent.source.name: {"value": getattr(TriggerSource, source)}
-    }
-    mock_DDGSetup.on_trigger()
-    if source == "SINGLE_SHOT":
-        mock_DDGSetup.parent.trigger_shot.put.assert_called_once_with(1)
+# TODO put back once the logic is implemented
+# @pytest.mark.parametrize("source", ["SINGLE_SHOT", "EXT_RISING_EDGE"])
+# def test_on_trigger(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan, source):
+#     """Test the on_trigger method."""
+#     # Set first attributes of parent class
+#     for k, v in scaninfo.items():
+#         setattr(mock_DDGSetup.parent.scaninfo, k, v)
+#     for k, v in ddg_config_defaults.items():
+#         getattr(mock_DDGSetup.parent, k).get.return_value = v
+#     for k, v in ddg_config_scan.items():
+#         getattr(mock_DDGSetup.parent, k).get.return_value = v
+#     # Call the function you want to test
+#     mock_DDGSetup.parent.source.name = "source"
+#     mock_DDGSetup.parent.source.read.return_value = {
+#         mock_DDGSetup.parent.source.name: {"value": getattr(TriggerSource, source)}
+#     }
+#     mock_DDGSetup.on_trigger()
+#     if source == "SINGLE_SHOT":
+#         mock_DDGSetup.parent.trigger_shot.put.assert_called_once_with(1)
 
 
-def test_initialize_default_parameter(
+def test_on_wait_for_connection(
     mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan, channel_pairs
 ):
     """Test the initialize_default_parameter method."""
@@ -222,77 +199,78 @@ def test_initialize_default_parameter(
             )
         ]
     )
-    mock_DDGSetup.initialize_default_parameter()
+    mock_DDGSetup.on_wait_for_connection()
     mock_DDGSetup.parent.set_channels.assert_has_calls(calls)
 
 
-def test_prepare_ddg(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan, channel_pairs):
-    """Test the prepare_ddg method."""
-    # Set first attributes of parent class
-    for k, v in scaninfo.items():
-        setattr(mock_DDGSetup.parent.scaninfo, k, v)
-    for k, v in ddg_config_defaults.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    for k, v in ddg_config_scan.items():
-        getattr(mock_DDGSetup.parent, k).get.return_value = v
-    # Call the function you want to test
-    mock_DDGSetup.parent.all_channels = channel_pairs["all_channels"]
-    mock_DDGSetup.parent.all_delay_pairs = channel_pairs["all_delay_pairs"]
+# TODO put back once the logic is implemented
+# def test_on_stage(mock_DDGSetup, scaninfo, ddg_config_defaults, ddg_config_scan, channel_pairs):
+#     """Test the prepare_ddg method."""
+#     # Set first attributes of parent class
+#     for k, v in scaninfo.items():
+#         setattr(mock_DDGSetup.parent.scaninfo, k, v)
+#     for k, v in ddg_config_defaults.items():
+#         getattr(mock_DDGSetup.parent, k).get.return_value = v
+#     for k, v in ddg_config_scan.items():
+#         getattr(mock_DDGSetup.parent, k).get.return_value = v
+#     # Call the function you want to test
+#     mock_DDGSetup.parent.all_channels = channel_pairs["all_channels"]
+#     mock_DDGSetup.parent.all_delay_pairs = channel_pairs["all_delay_pairs"]
 
-    mock_DDGSetup.prepare_ddg()
-    mock_DDGSetup.parent.set_trigger.assert_called_once_with(
-        getattr(TriggerSource, ddg_config_scan["set_trigger_source"])
-    )
-    if scaninfo["scan_type"] == "step":
-        if ddg_config_scan["set_high_on_exposure"]:
-            num_burst_cycle = 1 + ddg_config_defaults["additional_triggers"]
-            exp_time = ddg_config_defaults["delta_width"] + scaninfo["frames_per_trigger"] * (
-                scaninfo["exp_time"] + scaninfo["readout_time"]
-            )
-            total_exposure = exp_time
-            delay_burst = ddg_config_defaults["delay_burst"]
-        else:
-            exp_time = ddg_config_defaults["delta_width"] + scaninfo["exp_time"]
-            total_exposure = exp_time + scaninfo["readout_time"]
-            delay_burst = ddg_config_defaults["delay_burst"]
-            num_burst_cycle = (
-                scaninfo["frames_per_trigger"] + ddg_config_defaults["additional_triggers"]
-            )
-    elif scaninfo["scan_type"] == "fly":
-        if ddg_config_scan["set_high_on_exposure"]:
-            num_burst_cycle = 1 + ddg_config_defaults["additional_triggers"]
-            exp_time = (
-                ddg_config_defaults["delta_width"]
-                + scaninfo["num_points"] * scaninfo["exp_time"]
-                + (scaninfo["num_points"] - 1) * scaninfo["readout_time"]
-            )
-            total_exposure = exp_time
-            delay_burst = ddg_config_defaults["delay_burst"]
-        else:
-            exp_time = ddg_config_defaults["delta_width"] + scaninfo["exp_time"]
-            total_exposure = exp_time + scaninfo["readout_time"]
-            delay_burst = ddg_config_defaults["delay_burst"]
-            num_burst_cycle = scaninfo["num_points"] + ddg_config_defaults["additional_triggers"]
+#     mock_DDGSetup.prepare_ddg()
+#     mock_DDGSetup.parent.set_trigger.assert_called_once_with(
+#         getattr(TriggerSource, ddg_config_scan["set_trigger_source"])
+#     )
+#     if scaninfo["scan_type"] == "step":
+#         if ddg_config_scan["set_high_on_exposure"]:
+#             num_burst_cycle = 1 + ddg_config_defaults["additional_triggers"]
+#             exp_time = ddg_config_defaults["delta_width"] + scaninfo["frames_per_trigger"] * (
+#                 scaninfo["exp_time"] + scaninfo["readout_time"]
+#             )
+#             total_exposure = exp_time
+#             delay_burst = ddg_config_defaults["delay_burst"]
+#         else:
+#             exp_time = ddg_config_defaults["delta_width"] + scaninfo["exp_time"]
+#             total_exposure = exp_time + scaninfo["readout_time"]
+#             delay_burst = ddg_config_defaults["delay_burst"]
+#             num_burst_cycle = (
+#                 scaninfo["frames_per_trigger"] + ddg_config_defaults["additional_triggers"]
+#             )
+#     elif scaninfo["scan_type"] == "fly":
+#         if ddg_config_scan["set_high_on_exposure"]:
+#             num_burst_cycle = 1 + ddg_config_defaults["additional_triggers"]
+#             exp_time = (
+#                 ddg_config_defaults["delta_width"]
+#                 + scaninfo["num_points"] * scaninfo["exp_time"]
+#                 + (scaninfo["num_points"] - 1) * scaninfo["readout_time"]
+#             )
+#             total_exposure = exp_time
+#             delay_burst = ddg_config_defaults["delay_burst"]
+#         else:
+#             exp_time = ddg_config_defaults["delta_width"] + scaninfo["exp_time"]
+#             total_exposure = exp_time + scaninfo["readout_time"]
+#             delay_burst = ddg_config_defaults["delay_burst"]
+#             num_burst_cycle = scaninfo["num_points"] + ddg_config_defaults["additional_triggers"]
 
-    # mock_DDGSetup.parent.burst_enable.assert_called_once_with(
-    #     mock.call(num_burst_cycle, delay_burst, total_exposure, config="first")
-    # )
-    mock_DDGSetup.parent.burst_enable.assert_called_once_with(
-        num_burst_cycle, delay_burst, total_exposure, config="first"
-    )
-    if not ddg_config_scan["trigger_width"]:
-        call = mock.call("width", exp_time)
-        assert call in mock_DDGSetup.parent.set_channels.mock_calls
-    else:
-        call = mock.call("width", ddg_config_scan["trigger_width"])
-        assert call in mock_DDGSetup.parent.set_channels.mock_calls
-    if ddg_config_scan["set_high_on_exposure"]:
-        calls = [
-            mock.call("width", value, channels=[channel])
-            for value, channel in zip(
-                ddg_config_scan["fixed_ttl_width"], channel_pairs["all_channels"]
-            )
-            if value != 0
-        ]
-        if calls:
-            assert all(calls in mock_DDGSetup.parent.set_channels.mock_calls)
+#     # mock_DDGSetup.parent.burst_enable.assert_called_once_with(
+#     #     mock.call(num_burst_cycle, delay_burst, total_exposure, config="first")
+#     # )
+#     mock_DDGSetup.parent.burst_enable.assert_called_once_with(
+#         num_burst_cycle, delay_burst, total_exposure, config="first"
+#     )
+#     if not ddg_config_scan["trigger_width"]:
+#         call = mock.call("width", exp_time)
+#         assert call in mock_DDGSetup.parent.set_channels.mock_calls
+#     else:
+#         call = mock.call("width", ddg_config_scan["trigger_width"])
+#         assert call in mock_DDGSetup.parent.set_channels.mock_calls
+#     if ddg_config_scan["set_high_on_exposure"]:
+#         calls = [
+#             mock.call("width", value, channels=[channel])
+#             for value, channel in zip(
+#                 ddg_config_scan["fixed_ttl_width"], channel_pairs["all_channels"]
+#             )
+#             if value != 0
+#         ]
+#         if calls:
+#             assert all(calls in mock_DDGSetup.parent.set_channels.mock_calls)

tests/tests_devices/test_eiger9m_csaxs.py

@@ -10,27 +10,17 @@ from bec_server.device_server.tests.utils import DMMock
 from ophyd_devices.tests.utils import MockPV
 
 from csaxs_bec.devices.epics.eiger9m_csaxs import Eiger9McSAXS
-
-
-def patch_dual_pvs(device):
-    for walk in device.walk_signals():
-        if not hasattr(walk.item, "_read_pv"):
-            continue
-        if not hasattr(walk.item, "_write_pv"):
-            continue
-        if walk.item._read_pv.pvname.endswith("_RBV"):
-            walk.item._read_pv = walk.item._write_pv
+from csaxs_bec.devices.tests_utils.utils import patch_dual_pvs
 
 
 @pytest.fixture(scope="function")
 def mock_det():
     name = "eiger"
     prefix = "X12SA-ES-EIGER9M:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
-            mock.patch("ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"),
+            mock.patch("ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"),
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
             ),
@@ -39,10 +29,9 @@ def mock_det():
                 mock_cl.get_pv = MockPV
                 mock_cl.thread_class = threading.Thread
                 with mock.patch.object(Eiger9McSAXS, "_init"):
-                    det = Eiger9McSAXS(
-                        name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode
-                    )
+                    det = Eiger9McSAXS(name=name, prefix=prefix, device_manager=dm)
                     patch_dual_pvs(det)
+                    det.TIMEOUT_FOR_SIGNALS = 0.1
                     yield det
 
 
@@ -50,11 +39,10 @@ def test_init():
     """Test the _init function:"""
     name = "eiger"
     prefix = "X12SA-ES-EIGER9M:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
-            mock.patch("ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"),
+            mock.patch("ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"),
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
             ),
@@ -72,7 +60,7 @@ def test_init():
                         "csaxs_bec.devices.epics.eiger9m_csaxs.Eiger9MSetup.initialize_detector_backend"
                     ) as mock_init_backend,
                 ):
-                    Eiger9McSAXS(name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode)
+                    Eiger9McSAXS(name=name, prefix=prefix, device_manager=dm)
                     mock_default.assert_called_once()
                     mock_init_det.assert_called_once()
                     mock_init_backend.assert_called_once()
@@ -236,8 +224,8 @@ def test_stage(
         mock_det.cam.beam_energy.put(scaninfo["mokev"])
         mock_det.stopped = stopped
         mock_det.cam.detector_state._read_pv.mock_data = detector_state
-        with mock.patch.object(mock_det.custom_prepare, "prepare_detector_backend") as mock_prep_fw:
-            mock_det.filepath = scaninfo["filepath"]
+        with mock.patch.object(mock_det.custom_prepare, "prepare_data_backend") as mock_prep_fw:
+            mock_det.filepath.set(scaninfo["filepath"]).wait()
             if expected_exception:
                 with pytest.raises(Exception):
                     mock_det.timeout = 0.1
@@ -251,7 +239,7 @@ def test_stage(
                 )
                 assert mock_det.cam.num_frames.get() == 1
 
-                mock_publish_file_location.assert_called_with(done=False)
+                mock_publish_file_location.assert_called_with(done=False, successful=False)
                 assert mock_det.cam.acquire.get() == 1
 
 
@@ -326,7 +314,7 @@ def test_prepare_detector_backend(mock_det, scaninfo, daq_status, expected_excep
 
 
 @pytest.mark.parametrize("stopped, expected_exception", [(False, False), (True, True)])
-def test_unstage(mock_det, stopped, expected_exception):
+def test_complete(mock_det, stopped, expected_exception):
     with (
         mock.patch.object(mock_det.custom_prepare, "finished") as mock_finished,
         mock.patch.object(
@@ -335,10 +323,10 @@ def test_unstage(mock_det, stopped, expected_exception):
     ):
         mock_det.stopped = stopped
         if expected_exception:
-            mock_det.unstage()
+            mock_det.complete()
             assert mock_det.stopped is True
         else:
-            mock_det.unstage()
+            mock_det.complete()
             mock_finished.assert_called_once()
             mock_publish_file_location.assert_called_with(done=True, successful=True)
             assert mock_det.stopped is False
@@ -357,12 +345,11 @@ def test_stop_detector_backend(mock_det):
     [
         ({"filepath": "test.h5", "successful": True, "done": False, "scan_id": "123"}),
         ({"filepath": "test.h5", "successful": False, "done": True, "scan_id": "123"}),
-        ({"filepath": "test.h5", "successful": None, "done": True, "scan_id": "123"}),
     ],
 )
 def test_publish_file_location(mock_det, scaninfo):
     mock_det.scaninfo.scan_id = scaninfo["scan_id"]
-    mock_det.filepath = scaninfo["filepath"]
+    mock_det.filepath.set(scaninfo["filepath"]).wait()
     mock_det.custom_prepare.publish_file_location(
         done=scaninfo["done"], successful=scaninfo["successful"]
     )

tests/tests_devices/test_falcon_csaxs.py

@@ -11,28 +11,18 @@ from bec_server.device_server.tests.utils import DMMock
 from ophyd_devices.tests.utils import MockPV
 
 from csaxs_bec.devices.epics.falcon_csaxs import FalconcSAXS, FalconTimeoutError
-
-
-def patch_dual_pvs(device):
-    for walk in device.walk_signals():
-        if not hasattr(walk.item, "_read_pv"):
-            continue
-        if not hasattr(walk.item, "_write_pv"):
-            continue
-        if walk.item._read_pv.pvname.endswith("_RBV"):
-            walk.item._read_pv = walk.item._write_pv
+from csaxs_bec.devices.tests_utils.utils import patch_dual_pvs
 
 
 @pytest.fixture(scope="function")
 def mock_det():
     name = "falcon"
     prefix = "X12SA-SITORO:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
             mock.patch(
-                "ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"
+                "ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"
             ) as filemixin,
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
@@ -42,10 +32,9 @@ def mock_det():
                 mock_cl.get_pv = MockPV
                 mock_cl.thread_class = threading.Thread
                 with mock.patch.object(FalconcSAXS, "_init"):
-                    det = FalconcSAXS(
-                        name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode
-                    )
+                    det = FalconcSAXS(name=name, prefix=prefix, device_manager=dm)
                     patch_dual_pvs(det)
+                    det.TIMEOUT_FOR_SIGNALS = 0.1
                     yield det
 
 
@@ -139,9 +128,9 @@ def test_stage(mock_det, scaninfo):
     This includes testing _prep_det
     """
     with (
-        mock.patch.object(mock_det, "set_trigger") as mock_set_trigger,
+        mock.patch.object(mock_det.custom_prepare, "set_trigger") as mock_set_trigger,
         mock.patch.object(
-            mock_det.custom_prepare, "prepare_detector_backend"
+            mock_det.custom_prepare, "prepare_data_backend"
         ) as mock_prep_data_backend,
         mock.patch.object(
             mock_det.custom_prepare, "publish_file_location"
@@ -158,7 +147,7 @@ def test_stage(mock_det, scaninfo):
             scaninfo["num_points"] * scaninfo["frames_per_trigger"]
         )
         mock_prep_data_backend.assert_called_once()
-        mock_publish_file_location.assert_called_once_with(done=False)
+        mock_publish_file_location.assert_called_once_with(done=False, successful=False)
         mock_arm_acquisition.assert_called_once()
 
 
@@ -204,12 +193,11 @@ def test_prepare_data_backend(mock_det, scaninfo):
     [
         ({"filepath": "test.h5", "successful": True, "done": False, "scan_id": "123"}),
         ({"filepath": "test.h5", "successful": False, "done": True, "scan_id": "123"}),
-        ({"filepath": "test.h5", "successful": None, "done": True, "scan_id": "123"}),
     ],
 )
 def test_publish_file_location(mock_det, scaninfo):
     mock_det.scaninfo.scan_id = scaninfo["scan_id"]
-    mock_det.filepath = scaninfo["filepath"]
+    mock_det.filepath.set(scaninfo["filepath"]).wait()
     mock_det.custom_prepare.publish_file_location(
         done=scaninfo["done"], successful=scaninfo["successful"]
     )
@@ -254,24 +242,18 @@ def test_trigger(mock_det):
         mock_on_trigger.assert_called_once()
 
 
-@pytest.mark.parametrize("stopped, expected_abort", [(False, False), (True, True)])
-def test_unstage(mock_det, stopped, expected_abort):
+def test_complete(mock_det):
     with (
         mock.patch.object(mock_det.custom_prepare, "finished") as mock_finished,
         mock.patch.object(
             mock_det.custom_prepare, "publish_file_location"
         ) as mock_publish_file_location,
     ):
-        mock_det.stopped = stopped
-        if expected_abort:
-            mock_det.unstage()
-            assert mock_det.stopped is stopped
-            assert mock_publish_file_location.call_count == 0
-        else:
-            mock_det.unstage()
-            mock_finished.assert_called_once()
-            mock_publish_file_location.assert_called_with(done=True, successful=True)
-            assert mock_det.stopped is stopped
+        mock_det.stopped = False
+        mock_det.complete()
+        assert mock_finished.call_count == 1
+        call = mock.call(done=True, successful=True)
+        assert mock_publish_file_location.call_args == call
 
 
 def test_stop(mock_det):

tests/tests_devices/test_jungfrau_joch.py

@@ -0,0 +1,54 @@
+import pytest
+from jfjoch_client.api_response import ApiResponse
+from jfjoch_client.models.broker_status import BrokerStatus
+from jfjoch_client.models.dataset_settings import DatasetSettings
+from jfjoch_client.models.detector_settings import DetectorSettings
+
+from csaxs_bec.devices.jungfraujoch.jungfrau_joch_client import DetectorState, ResponseWaitDone
+
+
+def test_jungfrau_joch_client_models_broker_status():
+    """Test BrokerStatus model from JJF client"""
+    # Test broker status model
+    broker_status = BrokerStatus
+    assert "state" in broker_status.model_fields
+    assert "progress" in broker_status.model_fields
+    # Test that all DetectorStates are valid BrokerStatus states. This will not raise if
+    for state in DetectorState:
+        broker_status = BrokerStatus(state=state.value)
+    # Test an invalid state
+    with pytest.raises(ValueError):
+        broker_status = BrokerStatus(state="wrong")
+
+
+def test_jungfrau_joch_client_models_dataset_settings():
+    """Test DatasetSettings model from JJF client"""
+    # Test detector state model
+    settings = {
+        "beam_x_pxl": 0,
+        "beam_y_pxl": 0,
+        "detector_distance_mm": 100,
+        "incident_energy_keV": 10.00,
+    }
+    # Try creating DatasetSettings object with minimal required settigns
+    dataset_settings = DatasetSettings(**settings)
+    # Test that image_time_ns and ntrigger are still available
+    settings["image_time_us"] = 1000
+    settings["ntrigger"] = 100
+    dataset_settings = DatasetSettings(**settings)
+
+
+def test_jungfrau_joch_client_models_api_response():
+    """Test APIResponse model from JJF client.
+    We can only check that all http status code responses are valid.
+    """
+    # Check if all ResponseWaitDone http status codes are valid for the APIResponse model
+    for state in ResponseWaitDone:
+        response = ApiResponse(status_code=state.value, data="", headers=None, raw_data=b"")
+
+
+def test_jungfrau_joch_client_models_detector_settigns():
+    """Test DetectorSettings model from JJF client"""
+    # Must be initialized with frame_time_us
+    settings = {"frame_time_us": 450}
+    DetectorSettings(**settings)  # type:ignore

tests/tests_devices/test_mcs_card.py

@@ -16,28 +16,18 @@ from csaxs_bec.devices.epics.mcs_csaxs import (
     ReadoutMode,
     TriggerSource,
 )
-
-
-def patch_dual_pvs(device):
-    for walk in device.walk_signals():
-        if not hasattr(walk.item, "_read_pv"):
-            continue
-        if not hasattr(walk.item, "_write_pv"):
-            continue
-        if walk.item._read_pv.pvname.endswith("_RBV"):
-            walk.item._read_pv = walk.item._write_pv
+from csaxs_bec.devices.tests_utils.utils import patch_dual_pvs
 
 
 @pytest.fixture(scope="function")
 def mock_det():
     name = "mcs"
     prefix = "X12SA-MCS:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
             mock.patch(
-                "ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"
+                "ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"
             ) as filemixin,
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
@@ -47,8 +37,9 @@ def mock_det():
                 mock_cl.get_pv = MockPV
                 mock_cl.thread_class = threading.Thread
                 with mock.patch.object(MCScSAXS, "_init"):
-                    det = MCScSAXS(name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode)
+                    det = MCScSAXS(name=name, prefix=prefix, device_manager=dm)
                     patch_dual_pvs(det)
+                    det.TIMEOUT_FOR_SIGNALS = 0.1
                     yield det
 
 
@@ -56,11 +47,10 @@ def test_init():
     """Test the _init function:"""
     name = "eiger"
     prefix = "X12SA-ES-EIGER9M:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
-            mock.patch("ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"),
+            mock.patch("ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"),
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
             ),
@@ -68,9 +58,6 @@ def test_init():
             with mock.patch.object(ophyd, "cl") as mock_cl:
                 mock_cl.get_pv = MockPV
                 with (
-                    mock.patch(
-                        "csaxs_bec.devices.epics.mcs_csaxs.MCSSetup.initialize_default_parameter"
-                    ) as mock_default,
                     mock.patch(
                         "csaxs_bec.devices.epics.mcs_csaxs.MCSSetup.initialize_detector"
                     ) as mock_init_det,
@@ -78,8 +65,7 @@ def test_init():
                         "csaxs_bec.devices.epics.mcs_csaxs.MCSSetup.initialize_detector_backend"
                     ) as mock_init_backend,
                 ):
-                    MCScSAXS(name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode)
-                    mock_default.assert_called_once()
+                    MCScSAXS(name=name, prefix=prefix, device_manager=dm)
                     mock_init_det.assert_called_once()
                     mock_init_backend.assert_called_once()
 
@@ -275,23 +261,10 @@ def test_prepare_detector_backend(mock_det):
     assert mock_det.read_mode.get() == ReadoutMode.EVENT
 
 
-@pytest.mark.parametrize("stopped, expected_exception", [(False, False), (True, True)])
-def test_unstage(mock_det, stopped, expected_exception):
-    with (
-        mock.patch.object(mock_det.custom_prepare, "finished") as mock_finished,
-        mock.patch.object(
-            mock_det.custom_prepare, "publish_file_location"
-        ) as mock_publish_file_location,
-    ):
-        mock_det.stopped = stopped
-        if expected_exception:
-            mock_det.unstage()
-            assert mock_det.stopped is True
-        else:
-            mock_det.unstage()
-            mock_finished.assert_called_once()
-            mock_publish_file_location.assert_called_with(done=True, successful=True)
-            assert mock_det.stopped is False
+def test_complete(mock_det):
+    with (mock.patch.object(mock_det.custom_prepare, "finished") as mock_finished,):
+        mock_det.complete()
+        assert mock_finished.call_count == 1
 
 
 def test_stop_detector_backend(mock_det):

tests/tests_devices/test_npoint_piezo.py

@@ -1,49 +1,43 @@
 import copy
+from unittest import mock
 
 import pytest
 
 from csaxs_bec.devices.npoint import NPointAxis, NPointController
 
+# pylint: disable=protected-access
+# pylint: disable=redefined-outer-name
 
-class SocketMock:
-    def __init__(self, sock=None):
-        self.buffer_put = ""
-        self.buffer_recv = ""
-        self.is_open = False
-        if sock is None:
-            self.open()
-        else:
-            self.sock = sock
 
-    def connect(self, host, port):
-        print(f"connecting to {host} port {port}")
-        # self.sock.create_connection((host, port))
-        # self.sock.connect((host, port))
+@pytest.fixture
+def controller():
+    """
+    Fixture to create a NPointController object.
+    """
+    with mock.patch("ophyd_devices.utils.socket.SocketIO") as socket_cls:
+        controller = NPointController(
+            socket_cls=socket_cls, socket_host="localhost", socket_port=1234
+        )
+        controller.on()
+        controller.sock.reset_mock()
+        yield controller
+        controller.off()
 
-    def _put(self, msg_bytes):
-        self.buffer_put = msg_bytes
-        print(self.buffer_put)
 
-    def _recv(self, buffer_length=1024):
-        print(self.buffer_recv)
-        return self.buffer_recv
-
-    def _initialize_socket(self):
-        pass
-
-    def put(self, msg):
-        return self._put(msg)
-
-    def receive(self, buffer_length=1024):
-        return self._recv(buffer_length=buffer_length)
-
-    def open(self):
-        self._initialize_socket()
-        self.is_open = True
-
-    def close(self):
-        self.sock = None
-        self.is_open = False
+@pytest.fixture
+def npointx():
+    """
+    Fixture to create a NPointAxis object.
+    """
+    controller = mock.MagicMock()
+    npointx = NPointAxis(
+        axis_Id="A", name="npointx", host="localhost", port=1234, socket_cls=controller
+    )
+    npointx.controller.on()
+    npointx.controller.sock.reset_mock()
+    npointx.controller.sock.receive.reset_mock()
+    yield npointx
+    npointx.controller.off()
 
 
 @pytest.mark.parametrize(
@@ -54,12 +48,29 @@ class SocketMock:
         (-5, b"\xa2\x18\x12\x83\x1133\xff\xffU"),
     ],
 )
-def test_axis_put(pos, msg):
-    controller = NPointController(SocketMock())
-    npointx = NPointAxis(controller, 0, "nx")
-    controller.on()
-    npointx.set(pos)
-    assert npointx.controller.socket.buffer_put == msg
+def test_axis_put(npointx, pos, msg):
+    """
+    Test that the set target position sends the correct message to the controller.
+    """
+    npointx.controller.set_target_pos(npointx.axis_Id_numeric, pos)
+    npointx.controller.sock.put.assert_called_with(msg)
+
+
+def test_npoint_axis_move(npointx):
+    """
+    Test that the move method sends the correct messages to the controller.
+    It should send the set target position, followed by 2 get current position messages.
+    """
+    npointx.controller.sock.receive.side_effect = [
+        b"\xa0\x34\x13\x83\x11\x00\x00\x00\x00U",  # pos 0
+        b"\xa0\x34\x13\x83\x11\xcd\xcc\x00\x00U",  # pos 5
+    ]
+    npointx.move(5)
+    assert (
+        mock.call(b"\xa2\x18\x12\x83\x11\xcd\xcc\x00\x00U")
+        in npointx.controller.sock.put.mock_calls
+    )
+    assert len(npointx.controller.sock.put.mock_calls) == 3
 
 
 @pytest.mark.parametrize(
@@ -70,13 +81,12 @@ def test_axis_put(pos, msg):
         (-5, b"\xa04\x13\x83\x11U", b"\xa0\x34\x13\x83\x1133\xff\xffU"),
     ],
 )
-def test_axis_get_out(pos, msg_in, msg_out):
-    controller = NPointController(SocketMock())
-    npointx = NPointAxis(controller, 0, "nx")
-    controller.on()
-    npointx.controller.socket.buffer_recv = msg_out
-    assert pytest.approx(npointx.get(), rel=0.01) == pos
-    # assert controller.socket.buffer_put == msg_in
+def test_axis_get_out(npointx, pos, msg_in, msg_out):
+    """
+    Test that the readback value is correctly read from the controller.
+    """
+    npointx.controller.sock.receive.side_effect = [msg_out]
+    assert pytest.approx(npointx.readback.get(), rel=0.01) == pos
 
 
 @pytest.mark.parametrize(
@@ -87,31 +97,40 @@ def test_axis_get_out(pos, msg_in, msg_out):
         (2, b"\xa043\x83\x11U", b"\xa0\x34\x13\x83\x1133\xff\xffU"),
     ],
 )
-def test_axis_get_in(axis, msg_in, msg_out):
-    controller = NPointController(SocketMock())
-    npointx = NPointAxis(controller, 0, "nx")
-    controller.on()
-    controller.socket.buffer_recv = msg_out
-    controller._get_current_pos(axis)
-    assert controller.socket.buffer_put == msg_in
+def test_axis_get_in(npointx, axis, msg_in, msg_out):
+    """
+    Test that the readback value is correctly read from the controller by directly calling the
+    controller's method.
+    """
+    npointx.controller.sock.receive.side_effect = [msg_out]
+    npointx.controller.get_current_pos(axis)
+    npointx.controller.sock.put.assert_called_once_with(msg_in)
 
 
-def test_axis_out_of_range():
-    controller = NPointController(SocketMock())
+def test_axis_out_of_range(controller):
+    """
+    Test that an error is raised when trying to create an NPointAxis object with an invalid axis ID.
+    """
     with pytest.raises(ValueError):
-        npointx = NPointAxis(controller, 3, "nx")
+        npointx = NPointAxis(
+            axis_Id="G", name="npointx", host="localhost", port=1234, socket_cls=mock.MagicMock()
+        )
 
 
-def test_get_axis_out_of_range():
-    controller = NPointController(SocketMock())
+def test_get_axis_out_of_range(controller):
+    """
+    Test that an error is raised when trying to get the current position of an invalid axis.
+    """
     with pytest.raises(ValueError):
-        controller._get_current_pos(3)
+        controller.get_current_pos(3)
 
 
-def test_set_axis_out_of_range():
-    controller = NPointController(SocketMock())
+def test_set_axis_out_of_range(controller):
+    """
+    Test that an error is raised when trying to set the target position of an invalid axis.
+    """
     with pytest.raises(ValueError):
-        controller._set_target_pos(3, 5)
+        controller.set_target_pos(3, 5)
 
 
 @pytest.mark.parametrize(
@@ -123,6 +142,9 @@ def test_set_axis_out_of_range():
     ],
 )
 def test_hex_list_to_int(in_buffer, byteorder, signed, val):
+    """
+    Test that the hex list is correctly converted to an integer
+    """
     assert (
         NPointController._hex_list_to_int(
             copy.deepcopy(in_buffer), byteorder=byteorder, signed=signed
@@ -139,10 +161,12 @@ def test_hex_list_to_int(in_buffer, byteorder, signed, val):
         (2, b"\xa0x0\x83\x11U", b"\xa0\x78\x13\x83\x11\x64\x00\x00\x00U"),
     ],
 )
-def test_get_range(axis, msg_in, msg_out):
-    controller = NPointController(SocketMock())
-    npointx = NPointAxis(controller, 0, "nx")
-    controller.on()
-    controller.socket.buffer_recv = msg_out
-    val = controller._get_range(axis)
-    assert controller.socket.buffer_put == msg_in and val == 100
+def test_get_range(npointx, axis, msg_in, msg_out):
+    """
+    Test that the range is correctly read from the controller by directly calling the
+    controller's method.
+    """
+    npointx.controller.sock.receive.side_effect = [msg_out]
+    val = npointx.controller._get_range(axis)
+    npointx.controller.sock.put.assert_called_once_with(msg_in)
+    assert val == 100

tests/tests_devices/test_pilatus_csaxs.py

@@ -11,27 +11,17 @@ from bec_server.device_server.tests.utils import DMMock
 from ophyd_devices.tests.utils import MockPV
 
 from csaxs_bec.devices.epics.pilatus_csaxs import PilatuscSAXS
-
-
-def patch_dual_pvs(device):
-    for walk in device.walk_signals():
-        if not hasattr(walk.item, "_read_pv"):
-            continue
-        if not hasattr(walk.item, "_write_pv"):
-            continue
-        if walk.item._read_pv.pvname.endswith("_RBV"):
-            walk.item._read_pv = walk.item._write_pv
+from csaxs_bec.devices.tests_utils.utils import patch_dual_pvs
 
 
 @pytest.fixture(scope="function")
 def mock_det():
     name = "pilatus"
     prefix = "X12SA-ES-PILATUS300K:"
-    sim_mode = False
     dm = DMMock()
     with mock.patch.object(dm, "connector"):
         with (
-            mock.patch("ophyd_devices.interfaces.base_classes.psi_detector_base.FileWriter"),
+            mock.patch("ophyd_devices.interfaces.base_classes.bec_device_base.FileWriter"),
             mock.patch(
                 "ophyd_devices.interfaces.base_classes.psi_detector_base.PSIDetectorBase._update_service_config"
             ),
@@ -40,9 +30,7 @@ def mock_det():
                 mock_cl.get_pv = MockPV
                 mock_cl.thread_class = threading.Thread
                 with mock.patch.object(PilatuscSAXS, "_init"):
-                    det = PilatuscSAXS(
-                        name=name, prefix=prefix, device_manager=dm, sim_mode=sim_mode
-                    )
+                    det = PilatuscSAXS(name=name, prefix=prefix, device_manager=dm)
                     patch_dual_pvs(det)
                     yield det
 
@@ -61,7 +49,7 @@ def test_init_detector(mock_det, trigger_source, detector_state):
     Validation upon setting the correct PVs
 
     """
-    mock_det.custom_prepare.initialize_detector()  # call the method you want to test
+    mock_det.custom_prepare.on_init()  # call the method you want to test
     assert mock_det.cam.acquire.get() == detector_state
     assert mock_det.cam.trigger_mode.get() == trigger_source
 
@@ -96,6 +84,8 @@ def test_init_detector(mock_det, trigger_source, detector_state):
     ],
 )
 def test_stage(mock_det, scaninfo, stopped, expected_exception):
+    path = "tmp"
+    mock_det.filepath_raw = path
     with mock.patch.object(
         mock_det.custom_prepare, "publish_file_location"
     ) as mock_publish_file_location:
@@ -105,14 +95,12 @@ def test_stage(mock_det, scaninfo, stopped, expected_exception):
         mock_det.device_manager.add_device("mokev", value=12.4)
         mock_det.stopped = stopped
         with (
-            mock.patch.object(
-                mock_det.custom_prepare, "prepare_detector_backend"
-            ) as mock_data_backend,
+            mock.patch.object(mock_det.custom_prepare, "prepare_data_backend") as mock_data_backend,
             mock.patch.object(
                 mock_det.custom_prepare, "update_readout_time"
             ) as mock_update_readout_time,
         ):
-            mock_det.filepath = scaninfo["filepath"]
+            mock_det.filepath.set(scaninfo["filepath"]).wait()
             if expected_exception:
                 with pytest.raises(Exception):
                     mock_det.timeout = 0.1
@@ -127,11 +115,13 @@ def test_stage(mock_det, scaninfo, stopped, expected_exception):
                 )
                 assert mock_det.cam.num_frames.get() == 1
 
-                mock_publish_file_location.assert_called_with(done=False)
+                mock_publish_file_location.assert_called_once_with(
+                    done=False, successful=False, metadata={"input_path": path}
+                )
 
 
 def test_pre_scan(mock_det):
-    mock_det.custom_prepare.pre_scan()
+    mock_det.custom_prepare.on_pre_scan()
     assert mock_det.cam.acquire.get() == 1
 
 
@@ -169,23 +159,16 @@ def test_update_readout_time(mock_det, readout_time, expected_value):
                 "scan_id": "123",
             }
         ),
-        (
-            {
-                "filepath": "test.h5",
-                "filepath_raw": "test5_raw.h5",
-                "successful": None,
-                "done": True,
-                "scan_id": "123",
-            }
-        ),
     ],
 )
 def test_publish_file_location(mock_det, scaninfo):
     mock_det.scaninfo.scan_id = scaninfo["scan_id"]
-    mock_det.filepath = scaninfo["filepath"]
+    mock_det.filepath.set(scaninfo["filepath"]).wait()
     mock_det.filepath_raw = scaninfo["filepath_raw"]
     mock_det.custom_prepare.publish_file_location(
-        done=scaninfo["done"], successful=scaninfo["successful"]
+        done=scaninfo["done"],
+        successful=scaninfo["successful"],
+        metadata={"input_path": scaninfo["filepath_raw"]},
     )
     if scaninfo["successful"] is None:
         msg = messages.FileMessage(
@@ -403,23 +386,19 @@ def test_prep_file_writer(mock_det, scaninfo, data_msgs, urls, requests_state, e
                 assert call == mock_call
 
 
-@pytest.mark.parametrize("stopped, expected_exception", [(False, False), (True, True)])
-def test_unstage(mock_det, stopped, expected_exception):
+def test_complete(mock_det):
+    path = "tmp"
+    mock_det.filepath_raw = path
     with (
         mock.patch.object(mock_det.custom_prepare, "finished") as mock_finished,
         mock.patch.object(
             mock_det.custom_prepare, "publish_file_location"
         ) as mock_publish_file_location,
     ):
-        mock_det.stopped = stopped
-        if expected_exception:
-            mock_det.unstage()
-            assert mock_det.stopped is True
-        else:
-            mock_det.unstage()
-            mock_finished.assert_called_once()
-            mock_publish_file_location.assert_called_with(done=True, successful=True)
-            assert mock_det.stopped is False
+        mock_det.complete()
+        assert mock_finished.call_count == 1
+        call = mock.call(done=True, successful=True, metadata={"input_path": path})
+        assert mock_publish_file_location.call_args == call
 
 
 def test_stop(mock_det):

tests/tests_scans/test_flomni_fermat_scan.py

@@ -2,15 +2,15 @@ from unittest import mock
 
 import pytest
 from bec_server.device_server.tests.utils import DMMock
+from bec_server.scan_server.tests.fixtures import *
 
 from csaxs_bec.scans.flomni_fermat_scan import FlomniFermatScan
 
 
 @pytest.fixture
-def scan_request():
-    device_manager = DMMock()
-    device_manager.producer = mock.MagicMock()
-    flomni_request = FlomniFermatScan(
+def scan_request(scan_assembler):
+    flomni_request = scan_assembler(
+        FlomniFermatScan,
         fovx=5,
         fovy=5,
         cenx=0.0,
@@ -19,7 +19,6 @@ def scan_request():
         step=1,
         zshift=0.0,
         angle=0.0,
-        device_manager=device_manager,
         metadata={"RID": "1234"},
     )
     yield flomni_request
@@ -31,7 +30,7 @@ def test_flomni_fermat_scan(scan_request):
 
 
 def test_flomni_rotation_no_rotation_required(scan_request):
-    with mock.patch.object(scan_request.stubs, "_get_from_rpc") as get_from_rpc_mock:
+    with mock.patch.object(scan_request.stubs, "_get_result_from_status") as get_from_rpc_mock:
         get_from_rpc_mock.return_value = 90
         with mock.patch.object(scan_request.stubs, "scan_report_instruction") as scan_report_mock:
             with mock.patch.object(scan_request.stubs, "set") as set_mock:
@@ -41,8 +40,7 @@ def test_flomni_rotation_no_rotation_required(scan_request):
 
 
 def test_flomni_rotation_rotation_required(scan_request):
-    with mock.patch.object(scan_request.stubs, "_get_from_rpc") as get_from_rpc_mock:
-        get_from_rpc_mock.return_value = 0
+    with mock.patch.object(scan_request.stubs, "_get_result_from_status", return_value=0):
         with mock.patch.object(scan_request.stubs, "scan_report_instruction") as scan_report_mock:
             with mock.patch.object(scan_request.stubs, "set") as set_mock:
                 list(scan_request.flomni_rotation(90))
@@ -56,6 +54,4 @@ def test_flomni_rotation_rotation_required(scan_request):
                         }
                     }
                 )
-                set_mock.assert_called_once_with(
-                    device="fsamroy", value=90, wait_group="flomni_rotation"
-                )
+                set_mock.assert_called_once_with(device="fsamroy", value=90, wait=False)

tests/tests_scans/test_lamni_fermat_scan.py

@@ -5,10 +5,33 @@ import pytest
 from bec_lib import messages
 from bec_server.device_server.tests.utils import DMMock
 from bec_server.scan_server.errors import ScanAbortion
+from bec_server.scan_server.tests.fixtures import (
+    DeviceMockType,
+    DMMock,
+    ScanStubStatusMock,
+    connector_mock,
+    instruction_handler_mock,
+    scan_assembler,
+)
 
 from csaxs_bec.scans.LamNIFermatScan import LamNIFermatScan
 
 
+@pytest.fixture
+def device_manager_mock():
+    device_manager = DMMock()
+    device_manager.add_device("lsamx")
+    device_manager.devices["lsamx"]._config["userParameter"] = {"center": 8.1}
+    device_manager.add_device("lsamy")
+    device_manager.devices["lsamy"]._config["userParameter"] = {"center": 10}
+    device_manager.add_device("samx")
+    device_manager.devices["samx"].read_buffer = {"value": 0}
+    device_manager.add_device("samy")
+    device_manager.devices["samy"].read_buffer = {"value": 0}
+    device_manager.add_device("bpm4i", dev_type=DeviceMockType.SIGNAL, readout_priority="monitored")
+    yield device_manager
+
+
 @pytest.mark.parametrize(
     "scan_msg,reference_scan_list",
     [
@@ -30,42 +53,49 @@ from csaxs_bec.scans.LamNIFermatScan import LamNIFermatScan
             ),
             [
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device=["rtx", "rty"],
                     action="read",
-                    parameter={"wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 0},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=["rtx", "rty"],
-                    action="wait",
-                    parameter={"type": "read", "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 1},
+                    parameter={},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="rpc",
                     parameter={
                         "device": "rtx",
                         "func": "controller.clear_trajectory_generator",
-                        "rpc_id": "e4897d7b-f8d9-4792-ac27-375d72d02aef",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 2, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="lsamrot",
                     action="rpc",
                     parameter={
                         "device": "lsamrot",
                         "func": "user_setpoint.get",
-                        "rpc_id": "7feb8d9e-b536-4958-9965-708a27c5e5f9",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 2, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={"readout_priority": "monitored", "RID": "1234"},
                     device=None,
                     action="scan_report_instruction",
                     parameter={
@@ -76,117 +106,147 @@ from csaxs_bec.scans.LamNIFermatScan import LamNIFermatScan
                             "end": [10],
                         }
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 0},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="lsamrot",
                     action="set",
-                    parameter={"value": 10, "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 3},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=["lsamrot"],
-                    action="wait",
-                    parameter={"type": "move", "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 4},
+                    parameter={"value": 10},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="rpc",
                     parameter={
                         "device": "rtx",
                         "func": "controller.feedback_disable",
-                        "rpc_id": "a5f5167b-61f2-4c24-8a08-698c0b52a971",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 5, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="rpc",
                     parameter={
                         "device": "rtx",
                         "func": "readback.get",
-                        "rpc_id": "409d1afc-39a5-442b-87e5-18145e59f367",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 6, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rty",
                     action="rpc",
                     parameter={
                         "device": "rty",
                         "func": "readback.get",
-                        "rpc_id": "80e560c8-c11a-4b6c-87e3-11addea3e80d",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 7, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="lsamx",
                     action="rpc",
                     parameter={
                         "device": "lsamx",
                         "func": "readback.get",
-                        "rpc_id": "5cef7087-3537-40fc-b558-8a2256019783",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 8, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="lsamy",
                     action="rpc",
                     parameter={
                         "device": "lsamy",
                         "func": "readback.get",
-                        "rpc_id": "61a7376c-36cf-41af-94b1-76c1ba821d47",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 9, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="rpc",
                     parameter={
                         "device": "rtx",
                         "func": "readback.get",
-                        "rpc_id": "a1d3c021-12fb-483e-a5b9-95a59d3c1304",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 10, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rty",
                     action="rpc",
                     parameter={
                         "device": "rty",
                         "func": "readback.get",
-                        "rpc_id": "bde7e130-b7b7-41d0-a56a-c83d740450df",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 11, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="rpc",
                     parameter={
                         "device": "rtx",
                         "func": "controller.feedback_enable_without_reset",
-                        "rpc_id": "aa2117b4-ef44-4c0d-8537-6b6ccea86d1e",
+                        "rpc_id": "rpc_id",
                         "args": (),
                         "kwargs": {},
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 12, "response": True},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={"readout_priority": "monitored", "RID": "1234"},
                     device=None,
                     action="open_scan",
                     parameter={
@@ -199,200 +259,163 @@ from csaxs_bec.scans.LamNIFermatScan import LamNIFermatScan
                         },
                         "num_points": 2,
                         "positions": [
-                            [1.3681828686580249, 2.1508313829565298],
+                            [1.3681828686580249, 2.1508313829565293],
                             [-0.7700589354581364, -0.8406005210092851],
                         ],
                         "scan_name": "lamni_fermat_scan",
                         "scan_type": "step",
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 13},
                 ),
                 messages.DeviceInstructionMessage(
-                    device=None,
+                    metadata={"device_instr_id": "diid"},
+                    device=["bpm4i", "lsamx", "lsamy", "samx", "samy"],
                     action="stage",
                     parameter={},
-                    metadata={"readout_priority": "monitored", "DIID": 14},
                 ),
                 messages.DeviceInstructionMessage(
-                    device=None,
-                    action="baseline_reading",
+                    metadata={
+                        "readout_priority": "baseline",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
+                    device=["lsamx", "lsamy", "samx", "samy"],
+                    action="read",
                     parameter={},
-                    metadata={"readout_priority": "baseline", "DIID": 15},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="set",
-                    parameter={"value": 1.3681828686580249, "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 17},
+                    parameter={"value": 1.3681828686580249},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rty",
                     action="set",
-                    parameter={"value": 2.1508313829565298, "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 18},
+                    parameter={"value": 2.1508313829565293},
                 ),
+                None,
                 messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "move", "group": "scan_motor", "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 19},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="trigger",
-                    parameter={"group": "trigger"},
-                    metadata={"readout_priority": "monitored", "DIID": 20, "point_id": 0},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "trigger", "group": "trigger", "time": 0.1},
-                    metadata={"readout_priority": "monitored", "DIID": 21},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="read",
-                    parameter={"group": "primary", "wait_group": "readout_primary"},
-                    metadata={"readout_priority": "monitored", "DIID": 22, "point_id": 0},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={
-                        "type": "read",
-                        "group": "scan_motor",
-                        "wait_group": "readout_primary",
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "point_id": 0,
+                        "device_instr_id": "diid",
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 23},
+                    device=["bpm4i"],
+                    action="read",
+                    parameter={"group": "monitored"},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rtx",
                     action="set",
-                    parameter={"value": -0.7700589354581364, "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 24},
+                    parameter={"value": -0.7700589354581364},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
                     device="rty",
                     action="set",
-                    parameter={"value": -0.8406005210092851, "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 25},
+                    parameter={"value": -0.8406005210092851},
                 ),
+                None,
                 messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "move", "group": "scan_motor", "wait_group": "scan_motor"},
-                    metadata={"readout_priority": "monitored", "DIID": 26},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "read", "group": "primary", "wait_group": "readout_primary"},
-                    metadata={"readout_priority": "monitored", "DIID": 27},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="trigger",
-                    parameter={"group": "trigger"},
-                    metadata={"readout_priority": "monitored", "DIID": 28, "point_id": 1},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "trigger", "group": "trigger", "time": 0.1},
-                    metadata={"readout_priority": "monitored", "DIID": 29},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="read",
-                    parameter={"group": "primary", "wait_group": "readout_primary"},
-                    metadata={"readout_priority": "monitored", "DIID": 30, "point_id": 1},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={
-                        "type": "read",
-                        "group": "scan_motor",
-                        "wait_group": "readout_primary",
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "point_id": 1,
+                        "device_instr_id": "diid",
                     },
-                    metadata={"readout_priority": "monitored", "DIID": 31},
+                    device=["bpm4i"],
+                    action="read",
+                    parameter={"group": "monitored"},
                 ),
                 messages.DeviceInstructionMessage(
-                    device=None,
-                    action="wait",
-                    parameter={"type": "read", "group": "primary", "wait_group": "readout_primary"},
-                    metadata={"readout_priority": "monitored", "DIID": 16},
+                    metadata={
+                        "readout_priority": "monitored",
+                        "RID": "1234",
+                        "device_instr_id": "diid",
+                    },
+                    device=["bpm4i", "lsamx", "lsamy", "samx", "samy"],
+                    action="complete",
+                    parameter={},
                 ),
                 messages.DeviceInstructionMessage(
-                    **{"device": None, "action": "complete", "parameter": {}},
-                    metadata={"readout_priority": "monitored", "DIID": 31},
-                ),
-                messages.DeviceInstructionMessage(
-                    device=None,
+                    metadata={"device_instr_id": "diid"},
+                    device=["bpm4i", "lsamx", "lsamy", "samx", "samy"],
                     action="unstage",
                     parameter={},
-                    metadata={"readout_priority": "monitored", "DIID": 17},
                 ),
                 messages.DeviceInstructionMessage(
+                    metadata={"readout_priority": "monitored", "RID": "1234"},
                     device=None,
                     action="close_scan",
                     parameter={},
-                    metadata={"readout_priority": "monitored", "DIID": 18},
                 ),
             ],
         )
     ],
 )
-def test_LamNIFermatScan(scan_msg, reference_scan_list):
-    device_manager = DMMock()
-    device_manager.add_device("lsamx")
-    device_manager.devices["lsamx"]._config["userParameter"] = {"center": 8.1}
-    device_manager.add_device("lsamy")
-    device_manager.devices["lsamy"]._config["userParameter"] = {"center": 10}
-    device_manager.add_device("samx")
-    device_manager.devices["samx"].read_buffer = {"value": 0}
-    device_manager.add_device("samy")
-    device_manager.devices["samy"].read_buffer = {"value": 0}
-    scan = LamNIFermatScan(
+def test_LamNIFermatScan(scan_msg, reference_scan_list, scan_assembler):
+    scan = scan_assembler(
+        LamNIFermatScan,
         parameter=scan_msg.content.get("parameter"),
-        device_manager=device_manager,
         metadata=scan_msg.metadata,
         **scan_msg.content["parameter"]["kwargs"],
     )
-    scan.stubs._get_from_rpc = lambda x: 0
-    with mock.patch.object(scan, "_check_min_positions") as check_min_pos:
-        scan_instructions = list(scan.run())
-        check_min_pos.assert_called_once()
-        scan_uid = scan_instructions[0].metadata.get("scan_id")
-        for ii, instr in enumerate(reference_scan_list):
+
+    with mock.patch.object(scan.stubs, "_get_result_from_status", return_value=0):
+        with mock.patch.object(scan, "_check_min_positions") as check_min_pos:
+            scan_instructions = list(scan.run())
+            check_min_pos.assert_called_once()
+
+        for ii, instr in enumerate(scan_instructions):
+            if instr is None:
+                continue
             if instr.metadata.get("scan_id") is not None:
-                instr.metadata["scan_id"] = scan_uid
-            instr.metadata["DIID"] = ii
-            instr.metadata["RID"] = scan.metadata.get("RID")
+                instr.metadata["scan_id"] = "scan_id"
+            if instr.metadata.get("RID") is not None:
+                instr.metadata["RID"] = scan.metadata.get("RID")
+            if instr.metadata.get("device_instr_id") is not None:
+                instr.metadata["device_instr_id"] = "diid"
             if instr.content["action"] == "rpc":
-                reference_scan_list[ii].content["parameter"]["rpc_id"] = scan_instructions[
-                    ii
-                ].content["parameter"]["rpc_id"]
+                instr.content["parameter"]["rpc_id"] = "rpc_id"
             if instr.content["parameter"].get("value"):
                 assert np.isclose(
                     instr.content["parameter"].get("value"),
-                    scan_instructions[ii].content["parameter"].get("value"),
+                    reference_scan_list[ii].content["parameter"].get("value"),
                 )
-                instr.content["parameter"]["value"] = scan_instructions[ii].content["parameter"][
+                instr.content["parameter"]["value"] = reference_scan_list[ii].content["parameter"][
                     "value"
                 ]
             if instr.content["parameter"].get("positions"):
                 assert np.isclose(
                     instr.content["parameter"].get("positions"),
-                    scan_instructions[ii].content["parameter"].get("positions"),
+                    reference_scan_list[ii].content["parameter"].get("positions"),
                 ).all()
-                instr.content["parameter"]["positions"] = scan_instructions[ii].content[
+                instr.content["parameter"]["positions"] = reference_scan_list[ii].content[
                     "parameter"
                 ]["positions"]
         assert scan_instructions == reference_scan_list
 
 
-def test_LamNIFermatScan_min_positions():
+def test_LamNIFermatScan_min_positions(scan_assembler):
     scan_msg = messages.ScanQueueMessage(
         scan_type="lamni_fermat_scan",
         parameter={
@@ -408,19 +431,12 @@ def test_LamNIFermatScan_min_positions():
         queue="primary",
         metadata={"RID": "1234"},
     )
-    device_manager = DMMock()
-    device_manager.add_device("lsamx")
-    device_manager.devices["lsamx"]._config["userParameter"] = {"center": 8.1}
-    device_manager.add_device("lsamy")
-    device_manager.devices["lsamy"]._config["userParameter"] = {"center": 10}
-    device_manager.add_device("samx")
-    device_manager.devices["samx"].read_buffer = {"value": 0}
-    device_manager.add_device("samy")
-    device_manager.devices["samy"].read_buffer = {"value": 0}
-    scan = LamNIFermatScan(
+
+    scan = scan_assembler(
+        LamNIFermatScan,
         parameter=scan_msg.content.get("parameter"),
-        device_manager=device_manager,
         metadata=scan_msg.metadata,
+        **scan_msg.content["parameter"]["kwargs"],
     )
     with pytest.raises(ScanAbortion):
         instructions = list(scan.run())

tests/tests_scans/test_owis_grid.py

@@ -3,6 +3,7 @@ from unittest import mock
 import numpy as np
 import pytest
 from bec_lib import messages
+from bec_server.scan_server.tests.fixtures import *
 
 from csaxs_bec.scans.owis_grid import OwisGrid
 
@@ -28,21 +29,29 @@ from csaxs_bec.scans.owis_grid import OwisGrid
         )
     ],
 )
-def test_owis_grid(scan_msg):
-    dm = mock.MagicMock()
-    request = OwisGrid(*scan_msg.content["parameter"]["args"].values(), device_manager=dm)
+def test_owis_grid(scan_msg, scan_assembler, ScanStubStatusMock):
+    request = scan_assembler(OwisGrid, *scan_msg.content["parameter"]["args"].values())
     request.high_velocity = 10
     request.high_acc_time = 0.2
     request.base_velocity = 0.0625
-    # pylint: disable=protected-access
-    request.stubs._get_from_rpc = lambda x: mock.MagicMock()
+
+    def fake_done():
+        yield False
+        yield True
+
+    def fake_set(*args, **kwargs):
+        yield "fake_set"
+        return ScanStubStatusMock(done_func=fake_done)
+
     with (
-        mock.patch.object(request.stubs, "get_req_status", return_value=1),
+        mock.patch.object(request.stubs, "set", side_effect=fake_set),
+        mock.patch.object(request.stubs, "_get_result_from_status"),
         mock.patch.object(
             request, "get_initial_motor_properties"
         ) as mock_get_init_motor_properties,
     ):
         scan_instructions = list(request.run())
+
         mock_get_init_motor_properties.assert_called_once()
         assert request.point_id == scan_msg.content["parameter"]["args"]["interval_x"]
         assert np.isclose(