added check for optics in etc to only move if not already there

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -356,18 +356,6 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
     # Logging helpers
     # ------------------------------------------------------------------
 
-    def write_to_spec_log(self, content):
-        try:
-            with open(
-                os.path.expanduser(
-                    "~/Data10/specES1/log-files/specES1_started_2022_11_30_1313.log"
-                ),
-                "a",
-            ) as log_file:
-                log_file.write(content)
-        except Exception:
-            logger.warning("Failed to write to spec log file (omny web page).")
-
     def write_to_scilog(self, content, tags: list = None):
         try:
             if tags is not None:
@@ -439,7 +427,6 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
                     f"{str(datetime.datetime.now())}: LamNI scan projection at angle {angle},"
                     f" scan number {bec.queue.next_scan_number}.\n"
                 )
-                self.write_to_spec_log(log_message)
                 corridor_size = self.corridor_size if self.corridor_size > 0 else None
                 scans.lamni_fermat_scan(
                     fov_size=[self.lamni_piezo_range_x, self.lamni_piezo_range_y],
@@ -779,7 +766,7 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
 
         user_input = input("Are these parameters correctly set for your scan? ")
         if user_input == "y":
-            print("good then")
+            print("OK. continue.")
             return
 
         self.tomo_countingtime = self._get_val("<ctime> s", self.tomo_countingtime, float)

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -5,7 +5,7 @@ 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
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put
 from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
 
 dev = builtins.__dict__.get("dev")
@@ -172,7 +172,7 @@ class LamNIOpticsMixin:
 
     def leye_out(self):
         self.loptics_in()
-        fshclose()
+        dev.omnyfsh.fshopen()
         leyey_out = self._get_user_param_safe("leyey", "out")
         umv(dev.leyey, leyey_out)
 

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -120,7 +120,7 @@ class FlomniInitStagesMixin:
 
 
         if self.OMNYTools.yesno("Init of foptz. Can the stage move to the upstream limit without collision?"):
-            print("good then")
+            print("OK. continue.")
         else:
             return
 
@@ -174,7 +174,7 @@ class FlomniInitStagesMixin:
         print("done")
 
         if self.OMNYTools.yesno("Init of tracking stages. Did you remove the outer laser flight tubes?"):
-            print("good then")
+            print("OK. continue.")
         else:
             print("Stopping.")
             return
@@ -190,7 +190,7 @@ class FlomniInitStagesMixin:
         print("done")
 
         if self.OMNYTools.yesno("Init of sample stage. Is the piezo at about 0 deg?"):
-            print("good then")
+            print("OK. continue.")
         else:
             print("Stopping.")
             return
@@ -207,7 +207,7 @@ class FlomniInitStagesMixin:
 
         print("Initializing UPR stage.")
         if self.OMNYTools.yesno("To ensure that the end switches work, please check that they are currently not pushed. Is everything okay?"):
-            print("good then")
+            print("OK. continue.")
         else:
             print("Stopping.")
             return
@@ -228,7 +228,7 @@ class FlomniInitStagesMixin:
                 continue
             break
         if self.OMNYTools.yesno("Shall I start the index search?"):
-            print("good then. Starting index search.")
+            print("OK. continue.. Starting index search.")
         else:
             print("Stopping.")
             return
@@ -247,7 +247,7 @@ class FlomniInitStagesMixin:
         print("done")
 
         if self.OMNYTools.yesno("Init of foptx. Can the stage move to the positive limit without collision? Attention: tracker flight tube!"):
-            print("good then")
+            print("OK. continue.")
         else:
             print("Stopping.")
             return
@@ -271,7 +271,7 @@ class FlomniInitStagesMixin:
             break
 
         if self.OMNYTools.yesno("Start limit switch search of fopty?"):
-            print("good then")
+            print("OK. continue.")
         else:
             print("Stopping.")
             return
@@ -438,7 +438,19 @@ class FlomniSampleTransferMixin:
         umv(dev.fsamx, fsamx_in)
         dev.fsamx.limits = [fsamx_in - 0.4, fsamx_in + 0.4]
 
-        #self.flomnigui_idle()
+        print("Moving X-ray eye in.")
+
+        if self.OMNYTools.yesno("Please confirm that this is ok with the flight tube. This check is to be removed after commissioning", "n"):
+            print("OK. continue.")
+        else:
+            print("Stopping.")
+            raise FlomniError("Manual abort of x-ray eye in.")
+
+        self.feye_in()
+        print("Moving X-ray optics out.")
+        self.foptics_out()
+        self.xrayeye_update_frame()
+
 
     def laser_tracker_show_all(self):
         dev.rtx.controller.laser_tracker_show_all()
@@ -543,12 +555,6 @@ class FlomniSampleTransferMixin:
         self.flomnigui_show_cameras()
 
 
-        if self.OMNYTools.yesno("Please confirm that there is currently no sample in the gripper. It would be dropped!", "y"):
-            print("good then")
-        else:
-            print("Stopping.")
-            raise FlomniError("The sample transfer was manually aborted.")
-
         self.ftransfer_gripper_move(position)
 
         self.ftransfer_controller_enable_mount_mode()
@@ -751,7 +757,7 @@ class FlomniSampleTransferMixin:
             return
 
         if self.OMNYTools.yesno("All OK? Continue?", "y"):
-            print("good then")
+            print("OK. continue.")
             dev.ftransy.controller.socket_put_confirmed("confirm=1")
         else:
             print("Stopping.")
@@ -785,7 +791,7 @@ class FlomniSampleTransferMixin:
         if position == 0 and fsamx_pos > -160:
 
             if self.OMNYTools.yesno("May the flomni stage be moved out for the sample change? Feedback will be disabled and alignment will be lost!", "y"):
-                print("good then")
+                print("OK. continue.")
                 self.ftransfer_flomni_stage_out()
             else:
                 print("Stopping.")
@@ -983,56 +989,63 @@ class FlomniAlignmentMixin:
 
     def read_alignment_offset(
         self,
-        dir_path=os.path.expanduser("~/Data10/specES1/internal/"),
+        dir_path=os.path.expanduser("~/data/raw/logs/"),
         setup="flomni",
         use_vertical_default_values=True,
+        get_data_from_gui=False,
     ):
-        """
-        Read the alignment parameters from xray eye fit.
 
-        """
         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()
+        if not get_data_from_gui:
+            """
+            Read the alignment parameters from xray eye fit.
 
-        # 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_Ax.txt"), "r") as file:
+                tomo_alignment_fit[0][0] = 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_Bx.txt"), "r") as file:
+                tomo_alignment_fit[0][1] = 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_Cx.txt"), "r") as file:
+                tomo_alignment_fit[0][2] = 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_Ay.txt"), "r") as file:
+                tomo_alignment_fit[1][0] = 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_By.txt"), "r") as file:
+                tomo_alignment_fit[1][1] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_Cy3.txt"), "r") as file:
-        #     tomo_alignment_fit[1][4] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Cy.txt"), "r") as file:
+                tomo_alignment_fit[1][2] = file.readline()
 
-        params = dev.omny_xray_gui.fit_params_x.get()
+            with open(os.path.join(dir_path, "ptychotomoalign_Ay3.txt"), "r") as file:
+                tomo_alignment_fit[1][3] = file.readline()
 
-        #amplitude
-        tomo_alignment_fit[0][0] = params['SineModel_0_amplitude']
-        #phase
-        tomo_alignment_fit[0][1] = params['SineModel_0_shift']
-        #offset
-        tomo_alignment_fit[0][2] = params['LinearModel_1_intercept']
-        print("applying vertical default values from mirror calibration, not from fit!")
-        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
+            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 from filesystem, meaning Matlab fit:")
+
+        else:
+            params = dev.omny_xray_gui.fit_params_x.get()
+
+            #amplitude
+            tomo_alignment_fit[0][0] = params['SineModel_0_amplitude']
+            #phase
+            tomo_alignment_fit[0][1] = params['SineModel_0_shift']
+            #offset
+            tomo_alignment_fit[0][2] = params['LinearModel_1_intercept']
+            print("applying vertical default values from mirror calibration, not from fit!")
+            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
+            print("New alignment parameters loaded based on Xray eye alignment GUI:")
 
 
-        print("New alignment parameters loaded:")
         print(
             f"X Amplitude {tomo_alignment_fit[0][0]}, "
             f"X Phase {tomo_alignment_fit[0][1]}, "
@@ -1441,18 +1454,6 @@ class Flomni(
     def sample_name(self):
         return self.sample_get_name(0)
 
-    def write_to_spec_log(self, content):
-        try:
-            with open(
-                os.path.expanduser(
-                    "~/Data10/specES1/log-files/specES1_started_2022_11_30_1313.log"
-                ),
-                "a",
-            ) as log_file:
-                log_file.write(content)
-        except Exception:
-            logger.warning("Failed to write to spec log file (omny web page).")
-
     def write_to_scilog(self, content, tags: list = None):
         try:
             if tags is not None:
@@ -1474,11 +1475,14 @@ class Flomni(
             return
         dev = builtins.__dict__.get("dev")
         bec = builtins.__dict__.get("bec")
+
+
+        self.feye_out()
         tags = ["BEC_alignment_tomo", self.sample_name]
         self.write_to_scilog(
             f"Starting alignment scan. First scan number: {bec.queue.next_scan_number}.", tags
         )
-
+    
         start_angle = 0
 
         angle_end = start_angle + 180
@@ -1507,9 +1511,8 @@ class Flomni(
                 for scan_nr in range(start_scan_number, end_scan_number):
                     self._write_tomo_scan_number(scan_nr, angle, 0)
 
-        print("Alignment scan finished. Please run SPEC_ptycho_align and load the new fit.")
-
         umv(dev.fsamroy, 0)
+        self.OMNYTools.printgreenbold("\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit.")
 
     def _write_subtomo_to_scilog(self, subtomo_number):
         dev = builtins.__dict__.get("dev")
@@ -1543,6 +1546,9 @@ class Flomni(
 
         self._write_subtomo_to_scilog(subtomo_number)
 
+        if start_angle is not None:
+            print(f"Sub tomo scan with start angle {start_angle} requested.")
+
         if start_angle is None:
             if subtomo_number == 1:
                 start_angle = 0
@@ -1561,29 +1567,94 @@ class Flomni(
             elif subtomo_number == 8:
                 start_angle = self.tomo_angle_stepsize / 8.0 * 7
 
+
         # _tomo_shift_angles (potential global variable)
         _tomo_shift_angles = 0
-        angle_end = start_angle + 180
+        # compute number of projections
+
+        start = start_angle + _tomo_shift_angles
+
+        if subtomo_number % 2:    # odd = forward
+            max_allowed_angle = 180.05 + self.tomo_angle_stepsize
+            proposed_end = start + 180
+            angle_end = min(proposed_end, max_allowed_angle)
+            span = angle_end - start
+
+        else:                     # even = reverse
+            min_allowed_angle = 0
+            proposed_end = start - 180
+            angle_end = max(proposed_end, min_allowed_angle)
+            span = start - angle_end
+
+        # number of projections needed to maintain step size
+        N = int(span / self.tomo_angle_stepsize) + 1
+
         angles = np.linspace(
-            start_angle + _tomo_shift_angles,
+            start,
             angle_end,
-            num=int(180 / self.tomo_angle_stepsize) + 1,
+            num=N,
             endpoint=True,
         )
-        # reverse even sub-tomograms
-        if not (subtomo_number % 2):
-            angles = np.flip(angles)
-        for angle in angles:
+
+        if subtomo_number % 2:    # odd subtomos → forward direction
+            # clamp end angle to max allowed
+            max_allowed_angle = 180.05 + self.tomo_angle_stepsize
+            proposed_end = start + 180
+            angle_end = min(proposed_end, max_allowed_angle)
+
+            angles = np.linspace(
+                start,
+                angle_end,
+                num=N,
+                endpoint=True,
+            )
+
+        else:                     # even subtomos → reverse direction
+            # go FROM start_angle down toward 0
+            min_allowed_angle = 0
+            proposed_end = start - 180
+            angle_end = max(proposed_end, min_allowed_angle)
+
+            angles = np.linspace(
+                start,
+                angle_end,
+                num=N,
+                endpoint=True,
+            )
+
+        for i, angle in enumerate(angles):
+
             self.progress["subtomo"] = subtomo_number
-            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"
-            ] + self.progress["subtomo_projection"]
+
+            # --- NEW LOGIC FOR OFFSET WHEN start_angle IS SPECIFIED ---
+            if i == 0:
+                step = self.tomo_angle_stepsize
+                sa = start_angle
+
+                if start_angle is None:
+                    # normal operation: always start at zero
+                    self._subtomo_offset = 0
+
+                else:
+                    if subtomo_number % 2:    # odd = forward direction
+                        self._subtomo_offset = round(sa / step)
+                    else:                     # even = reverse direction
+                        self._subtomo_offset = round((180 - sa) / step)
+
+            # progress index must always increase
+            self.progress["subtomo_projection"] = self._subtomo_offset + i
+            # ------------------------------------------------------------
+
+            # existing progress fields
+            self.progress["subtomo_total_projections"] = int(180 / self.tomo_angle_stepsize)
+            self.progress["projection"] = (subtomo_number - 1) * self.progress["subtomo_total_projections"] + self.progress["subtomo_projection"]
             self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
             self.progress["angle"] = angle
+
+            # finally do the scan at this angle
             self._tomo_scan_at_angle(angle, subtomo_number)
 
+
     def _tomo_scan_at_angle(self, angle, subtomo_number):
         successful = False
         error_caught = False
@@ -1591,7 +1662,7 @@ class Flomni(
             print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
             self._print_progress()
             while not successful:
-                self.bl_chk._bl_chk_start()
+                #self.bl_chk._bl_chk_start()
                 if not self.special_angles:
                     self._current_special_angles = []
                 if self._current_special_angles:
@@ -1614,10 +1685,10 @@ class Flomni(
                     else:
                         raise exc
 
-                if self.bl_chk._bl_chk_stop() and not error_caught:
-                    successful = True
-                else:
-                    self.bl_chk._bl_chk_wait_until_recovered()
+                # if self.bl_chk._bl_chk_stop() and not error_caught:
+                successful = True
+                # else:
+                #     self.bl_chk._bl_chk_wait_until_recovered()
             end_scan_number = bec.queue.next_scan_number
             for scan_nr in range(start_scan_number, end_scan_number):
                 self._write_tomo_scan_number(scan_nr, angle, subtomo_number)
@@ -1625,6 +1696,14 @@ class Flomni(
     def tomo_scan(self, subtomo_start=1, start_angle=None, projection_number=None):
         """start a tomo scan"""
 
+        if not self._check_eye_out_and_optics_in():
+            print("Attention: The setup is not in measurement condition.\nXray eye might be IN or the Xray optics OUT.")
+            if self.OMNYTools.yesno("Shall I continue?", "n"):
+            print("OK")
+        else:
+            print("Stopping.")
+            return
+
         self.flomnigui_show_progress()
 
         bec = builtins.__dict__.get("bec")
@@ -1638,19 +1717,19 @@ class Flomni(
         ):
 
             # pylint: disable=undefined-variable
-            if bec.active_account != "":
-                self.tomo_id = self.add_sample_database(
-                    self.sample_name,
-                    str(datetime.date.today()),
-                    bec.active_account.decode(),
-                    bec.queue.next_scan_number,
-                    "flomni",
-                    "test additional info",
-                    "BEC",
-                )
-                self.write_pdf_report()
-            else:
-                self.tomo_id = 0
+            # if bec.active_account != "":
+            #     self.tomo_id = self.add_sample_database(
+            #         self.sample_name,
+            #         str(datetime.date.today()),
+            #         bec.active_account,
+            #         bec.queue.next_scan_number,
+            #         "flomni",
+            #         "test additional info",
+            #         "BEC",
+            #     )
+            #     self.write_pdf_report()
+            # else:
+            self.tomo_id = 0
 
         with scans.dataset_id_on_hold:
             if self.tomo_type == 1:
@@ -1659,7 +1738,7 @@ class Flomni(
                 for ii in range(subtomo_start, 9):
                     self.sub_tomo_scan(ii, start_angle=start_angle)
                     start_angle = None
-
+    
             elif self.tomo_type == 2:
                 # Golden ratio tomography
                 previous_subtomo_number = -1
@@ -1755,6 +1834,11 @@ class Flomni(
             else:
                 raise FlomniError("undefined tomo type")
 
+        self.progress['projection'] = self.progress['total_projections']
+        self.progress["subtomo_projection"] = self.progress["subtomo_total_projections"]
+        self._print_progress()             
+        self.OMNYTools.printgreenbold("Tomoscan finished")
+
     def _print_progress(self):
         print("\x1b[95mProgress report:")
         print(f"Tomo type: ....................... {self.progress['tomo_type']}")
@@ -1836,7 +1920,7 @@ class Flomni(
 
         return angle, subtomo_number
 
-    def tomo_reconstruct(self, base_path="~/Data10/specES1"):
+    def tomo_reconstruct(self, base_path="~/data/raw/logs/reconstruction_queue"):
         """write the tomo reconstruct file for the reconstruction queue"""
         bec = builtins.__dict__.get("bec")
         self.reconstructor.write(
@@ -1847,7 +1931,7 @@ class Flomni(
 
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
         tomo_scan_numbers_file = os.path.expanduser(
-            "~/tomography_scannumbers.txt"
+            "~/data/raw/logs/tomography_scannumbers.txt"
         )
         with open(tomo_scan_numbers_file, "a+") as out_file:
             # pylint: disable=undefined-variable
@@ -1859,6 +1943,7 @@ class Flomni(
 
         dev.rtx.controller.laser_tracker_check_signalstrength()
 
+
         scans = builtins.__dict__.get("scans")
 
         # additional_correction = self.align.compute_additional_correction(angle)
@@ -1893,7 +1978,6 @@ class Flomni(
                     f"{str(datetime.datetime.now())}: flomni scan projection at angle {angle}, scan"
                     f" number {bec.queue.next_scan_number}.\n"
                 )
-                self.write_to_spec_log(log_message)
                 # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
                 scans.flomni_fermat_scan(
                     fovx=self.fovx,

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -1,10 +1,10 @@
 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
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put
 
 
 class FlomniOpticsMixin:
@@ -16,12 +16,18 @@ class FlomniOpticsMixin:
         return param.get(var)
 
     def feye_out(self):
-        fshclose()
+        dev.omnyfsh.fshclose()
         self.foptics_in()
+        self.flomnigui_show_xeyealign()
+        self.xrayeye_update_frame()
+        if self.OMNYTools.yesno("Did the direct beam on the xray eye disappear?"):
+            print("excellent.")
+        else:
+            print("Aborting. With visible parts of the direct beam on the xray eye, it cannot be removed.")
+            return
         feyex_out = self._get_user_param_safe("feyex", "out")
         umv(dev.feyex, feyex_out)
 
-        epics_put("XOMNYI-XEYE-ACQ:0", 2)
         # move rotation stage to zero to avoid problems with wires
         umv(dev.fsamroy, 0)
         # umv(dev.fttrx1, 9.2)
@@ -32,16 +38,39 @@ class FlomniOpticsMixin:
 
         feyex_in = self._get_user_param_safe("feyex", "in")
         feyey_in = self._get_user_param_safe("feyey", "in")
-        umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
-        #self.align.update_frame()
+
+        current_feyex = dev.feyex.readback.get()
+        current_feyey = dev.feyey.readback.get()
+
+        # check if both are close enough (within 0.01)
+        if np.isclose(current_feyex, feyex_in, atol=0.01) and np.isclose(current_feyey, feyey_in, atol=0.01):
+            # both already in position → do nothing
+            pass
+        else:
+            # move both axes to the desired "in" positions
+            umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
+
+        self.xrayeye_update_frame()
 
     def _ffzp_in(self):
         foptx_in = self._get_user_param_safe("foptx", "in")
         fopty_in = self._get_user_param_safe("fopty", "in")
-        umv(dev.foptx, foptx_in)
-        umv(
-            dev.fopty, fopty_in
-        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+
+        current_foptx = dev.foptx.readback.get()
+        current_fopty = dev.fopty.readback.get()
+
+        tol = 0.003
+
+        # if either axis is outside the tolerance → move both
+        need_move_optics = (
+            not np.isclose(current_foptx, foptx_in, atol=tol) or
+            not np.isclose(current_fopty, fopty_in, atol=tol)
+        )
+
+        if need_move_optics:
+            umv(dev.foptx, foptx_in, dev.fopty, fopty_in)  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+        else:
+            print("FZP is already at the in position.")
 
     def ffzp_in(self):
         """
@@ -84,19 +113,85 @@ class FlomniOpticsMixin:
         # umv(dev.losax, -1.4850, dev.losay, -0.1930)
         # umv(dev.losaz, 1.0000)
         # 7.2, 150
+
         fosax_in = self._get_user_param_safe("fosax", "in")
         fosay_in = self._get_user_param_safe("fosay", "in")
         fosaz_in = self._get_user_param_safe("fosaz", "in")
+
+        # tighten limits
         dev.fosax.limits = [fosax_in - 0.1, fosax_in + 0.1]
         dev.fosay.limits = [fosay_in - 0.1, fosay_in + 0.1]
         dev.fosaz.limits = [fosaz_in - 0.1, fosaz_in + 0.1]
-        umv(dev.fosax, fosax_in, dev.fosay, fosay_in)
-        umv(dev.fosaz, fosaz_in)
+
+        current_fosax = dev.fosax.readback.get()
+        current_fosay = dev.fosay.readback.get()
+        current_fosaz = dev.fosaz.readback.get()
+
+        # tolerance
+        tol = 0.003
+
+        need_move_osa = (
+            not np.isclose(current_fosax, fosax_in, atol=tol) or
+            not np.isclose(current_fosay, fosay_in, atol=tol) or
+            not np.isclose(current_fosaz, fosaz_in, atol=tol)
+        )
+
+        if need_move_osa:
+            umv(dev.fosax, fosax_in, dev.fosay, fosay_in)
+            umv(dev.fosaz, fosaz_in)
+        else:
+            print("OSA is already at the IN position.")
 
         # 11 kev
         # umv(dev.losax, -1.161000, dev.losay, -0.196)
         # umv(dev.losaz, 1.0000)
 
+    def _check_eye_out_and_optics_in(self, tol=0.003):
+        # --- expected IN positions ---
+        foptx_in = self._get_user_param_safe("foptx", "in")
+        fopty_in = self._get_user_param_safe("fopty", "in")
+        foptz_in = self._get_user_param_safe("foptz", "in")
+
+        # --- expected OUT condition for the X-ray eye ---
+        # eye is OUT when it is *not within tolerance* of its IN position
+        feyex_out = self._get_user_param_safe("feyex", "out")
+
+        # --- current positions ---
+        cx_feyex = dev.feyex.readback.get()
+
+        cx_foptx = dev.foptx.readback.get()
+        cx_fopty = dev.fopty.readback.get()
+        cx_foptz = dev.foptz.readback.get()
+
+        # --- check eye OUT ---
+        eye_out = (
+            np.isclose(cx_feyex, feyex_out, atol=tol)
+        )
+
+        # --- check optics IN ---
+        optics_in = (
+            np.isclose(cx_foptx, foptx_in, atol=tol) and
+            np.isclose(cx_fopty, fopty_in, atol=tol) and
+            np.isclose(cx_foptz, foptz_in, atol=tol)
+        )
+
+        fosax_in = self._get_user_param_safe("fosax", "in")
+        fosay_in = self._get_user_param_safe("fosay", "in")
+        fosaz_in = self._get_user_param_safe("fosaz", "in")
+
+        cx_fosax = dev.fosax.readback.get()
+        cx_fosay = dev.fosay.readback.get()
+        cx_fosaz = dev.fosaz.readback.get()
+
+        osa_in = (
+            np.isclose(cx_fosax, fosax_in, atol=tol) and
+            np.isclose(cx_fosay, fosay_in, atol=tol) and
+            np.isclose(cx_fosaz, fosaz_in, atol=tol)
+        )
+
+        return eye_out and optics_in and osa_in
+
+
     def fosa_out(self):
         self.ensure_fheater_up()
         curtain_is_triggered = dev.foptz.controller.fosaz_light_curtain_is_triggered()

csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py

@@ -1,4 +1,5 @@
 import builtins
+import time
 
 # from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
 
@@ -31,6 +32,7 @@ class flomniGuiTools:
             self.gui.flomni.raise_window()
         else:
             self.gui.new("flomni")
+            time.sleep(1)
 
     def flomnigui_stop_gui(self):
         self.gui.flomni.hide()
@@ -101,7 +103,8 @@ class flomniGuiTools:
         # dev.cam_flomni_overview.stop_live_mode()
         # dev.cam_flomni_gripper.stop_live_mode()
         # dev.cam_xeye.live_mode = False
-        self.gui.flomni.delete_all()
+        if hasattr(self.gui, "flomni"):
+            self.gui.flomni.delete_all()
         self.progressbar = None
         self.text_box = None
 
@@ -207,7 +210,16 @@ class flomniGuiTools:
             main_progress_ring.set_value(progress)
             subtomo_progress_ring.set_value(subtomo_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']}"
+            text = (
+                f"Progress report:\n"
+                f" Tomo type:  {self.progress['tomo_type']}\n"
+                f" Projection:  {self.progress['projection']:.0f}\n"
+                f" Total projections expected  {self.progress['total_projections']:.1f}\n"
+                f" Angle:  {self.progress['angle']:.1f}\n"
+                f" Current subtomo:  {self.progress['subtomo']}\n"
+                f" Current projection within subtomo: {self.progress['subtomo_projection']}\n"
+                f" Total projections per subtomo:  {int(self.progress['subtomo_total_projections'])}"
+            )
             self.progressbar.set_center_label(text)
 
 

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -231,10 +231,6 @@ class XrayEyeAlign:
         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)
-
         if keep_shutter_open:
             if self.flomni.OMNYTools.yesno("Close the shutter now?", "y"):
                 dev.omnyfsh.fshclose()
@@ -251,8 +247,11 @@ class XrayEyeAlign:
 
         print("Automatically loading new alignment parameters from xray eye alignment.\n")
 
-        self.flomni.read_alignment_offset()
+        self.flomni.read_alignment_offset(get_data_from_gui=True)
 
+        self.tomo_rotate(0)
+
+        umv(dev.rtx, 0)
         print("You are ready to remove the xray eye and start ptychography scans.")
 
     def write_output(self):

csaxs_bec/bec_ipython_client/plugins/omny/omny.py

@@ -852,18 +852,6 @@ class OMNY(
     def sample_name(self):
         return dev.omny_samples.get_sample_name_in_samplestage()
 
-    def write_to_spec_log(self, content):
-        try:
-            with open(
-                os.path.expanduser(
-                    "~/Data10/specES1/log-files/specES1_started_2022_11_30_1313.log"
-                ),
-                "a",
-            ) as log_file:
-                log_file.write(content)
-        except Exception:
-            logger.warning("Failed to write to spec log file (omny web page).")
-
     def write_to_scilog(self, content, tags: list = None):
         try:
             if tags is not None:
@@ -1288,7 +1276,6 @@ class OMNY(
                     f"{str(datetime.datetime.now())}: omny scan projection at angle {angle}, scan"
                     f" number {bec.queue.next_scan_number}.\n"
                 )
-                self.write_to_spec_log(log_message)
                 # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
                 scans.omny_fermat_scan(
                     fovx=self.fovx,

csaxs_bec/bec_ipython_client/plugins/omny/omny_optics_mixin.py

@@ -48,7 +48,7 @@ class OMNYOpticsMixin:
         dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
 
     def oeye_out(self):
-        fshclose()
+        dev.omnyfsh.fshclose()
         if self.OMNYTools.yesno("Did you move in the optics?"):
             umv(dev.oeyez, -2)
             self._oeyey_mv(-60.3)

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -227,7 +227,7 @@ ftransy:
   readoutPriority: baseline
   connectionTimeout: 20
   userParameter:
-    sensor_voltage: -2.4
+    sensor_voltage: -1.1
 ftransz:
   description: Sample transer Z
   deviceClass: csaxs_bec.devices.omny.galil.fgalil_ophyd.FlomniGalilMotor
@@ -344,6 +344,9 @@ rtx:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -200
+    - 200
     axis_Id: A
     host: mpc2844.psi.ch
     port: 2222
@@ -361,6 +364,9 @@ rty:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -100
+    - 100
     axis_Id: B
     host: mpc2844.psi.ch
     port: 2222
@@ -376,6 +382,9 @@ rtz:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -100
+    - 100
     axis_Id: C
     host: mpc2844.psi.ch
     port: 2222

csaxs_bec/devices/epics/delay_generator_csaxs/ddg_1.py

@@ -104,7 +104,7 @@ DEFAULT_REFERENCES: list[tuple[LiteralChannels, CHANNELREFERENCE]] = [
     ("B", CHANNELREFERENCE.A),
     ("C", CHANNELREFERENCE.T0),  # T0
     ("D", CHANNELREFERENCE.C),
-    ("E", CHANNELREFERENCE.D),  # D One extra pulse once shutter closes for MCS
+    ("E", CHANNELREFERENCE.B),  # B One extra pulse once shutter closes for MCS
     ("F", CHANNELREFERENCE.E),  # E + 1mu s
     ("G", CHANNELREFERENCE.T0),
     ("H", CHANNELREFERENCE.G),
@@ -213,8 +213,23 @@ class DDG1(PSIDeviceBase, DelayGeneratorCSAXS):
 
         # NOTE Burst delay should be set to 0, don't remove as this will not be checked
         # Also set the burst count to 1 to only have a single pulse for DDG1.
+        # As the IOC may be out of sync with the HW, we make sure that we set the default parameters
+        # in the IOC to the expected values. In the past, we've experienced that IOC and HW can go out
+        # of sync.
+        self.burst_delay.put(1)
+        time.sleep(0.02)  # Give HW time to process
         self.burst_delay.put(0)
+        time.sleep(0.02)
+
+        self.burst_count.put(2)
+        time.sleep(0.02)
         self.burst_count.put(1)
+        time.sleep(0.02)
+
+        self.burst_mode.put(1)
+        time.sleep(0.02)
+        self.burst_mode.put(0)
+        time.sleep(0.02)
 
     def keep_shutter_open_during_scan(self, open: True) -> None:
         """
@@ -291,17 +306,24 @@ class DDG1(PSIDeviceBase, DelayGeneratorCSAXS):
         # Burst Period DDG1
         # Set burst_period to shutter width
         # c/t0 + self._shutter_to_open_delay + exp_time * burst_count
-        shutter_width = (
-            self._shutter_to_open_delay + exp_time * frames_per_trigger
-        )  # Shutter starts closing at end of exposure
+        # SHUTTER WIDTH timing consists of the delay for the shutter to open
+        # + the exposure time * frames per trigger
+        shutter_width = self._shutter_to_open_delay + exp_time * frames_per_trigger
+        # TOTAL EXPOSURE accounts for the shutter to open AND close. In addition, we add
+        # a short additional delay of 3e-6 to allow for the extra trigger through 'ef'
+        # (delay of 1e-6, width of 1e-6)
+        total_exposure_time = 2 * self._shutter_to_open_delay + exp_time * frames_per_trigger + 3e-6
         if self.burst_period.get() != shutter_width:
-            self.burst_period.put(shutter_width)
+            # The burst_period has to be slightly longer
+            self.burst_period.put(total_exposure_time)
 
         # Trigger DDG2
         # a = t0 + 2ms, b = a + 1us
         # a has reference to t0, b has reference to a
-        # Add delay of self._shutter_to_open_delay to allow shutter to open
-        self.set_delay_pairs(channel="ab", delay=self._shutter_to_open_delay, width=1e-6)
+        # AB is delayed by the shutter opening time, and the falling edge indicates the shutter has
+        # fully closed, it has to be considered as the blocking signal for the next acquisition to start.
+        # PS: + 3e-6
+        self.set_delay_pairs(channel="ab", delay=self._shutter_to_open_delay, width=shutter_width)
 
         # Trigger shutter
         # d = c/t0 + self._shutter_to_open_delay + exp_time * burst_count + 1ms
@@ -321,7 +343,7 @@ class DDG1(PSIDeviceBase, DelayGeneratorCSAXS):
         if self.scan_info.msg.scan_type == "fly":
             self.set_delay_pairs(channel="ef", delay=0, width=0)
         else:
-            self.set_delay_pairs(channel="ef", delay=0, width=1e-6)
+            self.set_delay_pairs(channel="ef", delay=1e-6, width=1e-6)
 
         # NOTE Add additional sleep to make sure that the IOC and DDG HW process the values properly
         # This value has been choosen empirically after testing with the HW. It's

csaxs_bec/devices/epics/delay_generator_csaxs/ddg_2.py

@@ -29,6 +29,7 @@ from ophyd_devices import DeviceStatus, StatusBase
 from ophyd_devices.interfaces.base_classes.psi_device_base import PSIDeviceBase
 
 from csaxs_bec.devices.epics.delay_generator_csaxs.delay_generator_csaxs import (
+    BURSTCONFIG,
     CHANNELREFERENCE,
     OUTPUTPOLARITY,
     STATUSBITS,
@@ -37,7 +38,6 @@ from csaxs_bec.devices.epics.delay_generator_csaxs.delay_generator_csaxs import
     ChannelConfig,
     DelayGeneratorCSAXS,
     LiteralChannels,
-    BURSTCONFIG,
 )
 
 logger = bec_logger.logger
@@ -138,6 +138,24 @@ class DDG2(PSIDeviceBase, DelayGeneratorCSAXS):
         # Set burst config
         self.burst_config.put(BURSTCONFIG.FIRST_CYCLE.value)
 
+        # TODO As the IOC may be out of sync with the HW, we make sure that we set the default parameters
+        # in the IOC to the expected values. In the past, we've experienced that IOC and HW can go out
+        # of sync.
+        self.burst_delay.put(1)
+        time.sleep(0.02)  # Give HW time to process
+        self.burst_delay.put(0)
+        time.sleep(0.02)
+
+        self.burst_count.put(2)
+        time.sleep(0.02)
+        self.burst_count.put(1)
+        time.sleep(0.02)
+
+        self.burst_mode.put(1)
+        time.sleep(0.02)
+        self.burst_mode.put(0)
+        time.sleep(0.02)
+
     def on_stage(self) -> DeviceStatus | StatusBase | None:
         """
 

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

@@ -20,6 +20,7 @@ from typing import TYPE_CHECKING, Callable, Literal
 
 import numpy as np
 from bec_lib.logger import bec_logger
+from ophyd.utils.errors import WaitTimeoutError
 from ophyd import Component as Cpt
 from ophyd import EpicsSignalRO, Kind
 from ophyd_devices import (
@@ -316,6 +317,8 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         try:
             scan_done = bool(value == self._num_total_triggers)
             self.progress.put(value=value, max_value=self._num_total_triggers, done=scan_done)
+            if scan_done:
+                self._scan_done_event.set()
         except Exception:
             content = traceback.format_exc()
             logger.info(f"Device {self.name}  error: {content}")
@@ -390,7 +393,6 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         self._current_data_index = 0
 
         # NOTE Make sure that the signal that omits mca callbacks is cleared
-        # DO NOT REMOVE!!
         self._omit_mca_callbacks.clear()
 
         # For a fly scan we need to start the mcs card ourselves
@@ -512,7 +514,22 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         # that the acquisition finishes on the card and that data is emitted to BEC. If the acquisition
         # was already finished (i.e. normal step scan sends 1 extra pulse per burst cycle), this will
         # not have any effect as the card will already be in DONE state and signal.
-        self.software_channel_advance.put(1)
+        if self.scan_info.msg.scan_type == "fly":
+            expected_points = int(
+                        self.scan_info.msg.num_points
+                        * self.scan_info.msg.scan_parameters.get("frames_per_trigger", 1)
+                    )
+            
+            status = CompareStatus(self.current_channel, expected_points-1, operation_success=">=")
+            try:
+                status.wait(timeout=5)
+            except WaitTimeoutError:
+                text = f"Device {self.name} received num points {self.current_channel.get()} / {expected_points}. Device timed out after 5s."
+                logger.error(text)
+                raise TimeoutError(text)
+
+            # Manually set the last advance
+            self.software_channel_advance.put(1)
 
         # Prepare and register status callback for the async monitoring loop
         status_async_data = StatusBase(obj=self)
@@ -546,9 +563,8 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
 
     def on_stop(self) -> None:
         """Hook called when the device is stopped. In addition, any status that is registered through cancel_on_stop will be cancelled here."""
-        with suppress_mca_callbacks(self):
-            self.stop_all.put(1)
-            self.erase_all.put(1)
+        self.stop_all.put(1)
+        self.erase_all.put(1)
 
     def mcs_recovery(self, timeout: int = 1) -> None:
         """

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -92,7 +92,8 @@ class RtFlomniController(Controller):
             parent._min_scan_buffer_reached = False
             start_time = time.time()
             for pos_index, pos in enumerate(positions):
-                parent.socket_put_and_receive(f"s{pos[0]:.05f},{pos[1]:.05f},{pos[2]:.05f}")
+                cmd = f"s{pos[0]:.05f},{pos[1]:.05f},{pos[2]:.05f}"
+                parent.socket_put_and_receive(cmd)
                 if pos_index > 100:
                     parent._min_scan_buffer_reached = True
             parent._min_scan_buffer_reached = True
@@ -174,11 +175,12 @@ class RtFlomniController(Controller):
         self.set_device_read_write("foptx", False)
         self.set_device_read_write("fopty", False)
 
-    def move_samx_to_scan_region(self, fovx: float, cenx: float):
-        #new routine not using fovx anymore
-        self.device_manager.devices.rtx.obj.move(cenx, wait=True)
+    def move_samx_to_scan_region(self, cenx: float, move_in_this_routine: bool = False):
+        # attention. a movement will clear all positions in the rt trajectory generator!
+        if move_in_this_routine == True:
+            self.device_manager.devices.rtx.obj.move(cenx, wait=True)
         time.sleep(0.05)
-        #at cenx we expect the PID to be close to zero for a good fsamx position
+        # at cenx we expect the PID to be close to zero for a good fsamx position
         if self.rt_pid_voltage is None:
             rtx = self.device_manager.devices.rtx
             self.rt_pid_voltage = rtx.user_parameter.get("rt_pid_voltage")
@@ -188,29 +190,31 @@ class RtFlomniController(Controller):
                 )
             logger.info(f"Using PID voltage from rtx user parameter: {self.rt_pid_voltage}")
         expected_voltage = self.rt_pid_voltage
-        #logger.info(f"Expected PID voltage: {expected_voltage}")
+        # logger.info(f"Expected PID voltage: {expected_voltage}")
         logger.info(f"Current PID voltage: {self.get_pid_x()}")
         wait_on_exit = False
-        #we allow 2V range from center, this corresponds to 30 microns
+        # we allow 2V range from center, this corresponds to 30 microns
         if np.abs(self.get_pid_x() - expected_voltage) < 2:
             logger.info("No correction of fsamx needed")
         else:
             fsamx = self.device_manager.devices.fsamx
             fsamx.obj.controller.socket_put_confirmed("axspeed[4]=0.1*stppermm[4]")
             while True:
-                #when we correct, then to 1 V, within 15 microns
+                # when we correct, then to 1 V, within 15 microns
                 if np.abs(self.get_pid_x() - expected_voltage) < 1:
                     logger.info("No further correction needed")
                     break
                 wait_on_exit = True
-                #disable FZP piezo feedback
+                # disable FZP piezo feedback
                 self.socket_put("v0")
                 fsamx.read_only = False
                 logger.info(f"Current PID voltage: {self.get_pid_x()}")
-                #here we accumulate the correction
+                # here we accumulate the correction
                 fsamx.obj.pid_x_correction -= (self.get_pid_x() - expected_voltage) * 0.006
                 fsamx_in = fsamx.user_parameter.get("in")
-                logger.info(f"Moving fsamx to {cenx / 1000 * 0.7 + fsamx.obj.pid_x_correction}, PID portion of that {fsamx.obj.pid_x_correction}")
+                logger.info(
+                    f"Moving fsamx to {cenx / 1000 * 0.7 + fsamx.obj.pid_x_correction}, PID portion of that {fsamx.obj.pid_x_correction}"
+                )
                 fsamx.obj.move(fsamx_in + cenx / 1000 * 0.7 + fsamx.obj.pid_x_correction, wait=True)
                 fsamx.read_only = True
                 time.sleep(0.1)
@@ -219,7 +223,7 @@ class RtFlomniController(Controller):
 
         if wait_on_exit:
             time.sleep(1)
-        #enable fast FZP feedback again
+        # enable fast FZP feedback again
         self.socket_put("v1")
 
     @threadlocked
@@ -390,7 +394,7 @@ class RtFlomniController(Controller):
         val = float(self.socket_put_and_receive(f"j{axis_number}").strip())
         return val
 
-    def laser_tracker_check_signalstrength(self):
+    def laser_tracker_check_signalstrength(self, verbose=True):
         if not self.laser_tracker_check_enabled():
             returnval = "disabled"
         else:
@@ -401,9 +405,10 @@ class RtFlomniController(Controller):
             rtx = self.device_manager.devices.rtx
             min_signal = rtx.user_parameter.get("min_signal")
             low_signal = rtx.user_parameter.get("low_signal")
-            print(f"low signal: {low_signal}")
-            print(f"min signal: {min_signal}")
-            print(f"signal: {signal}")
+            if verbose:
+                print(f"low signal: {low_signal}")
+                print(f"min signal: {min_signal}")
+                print(f"signal: {signal}")
             if signal < min_signal:
                 time.sleep(1)
                 if signal < min_signal:
@@ -510,7 +515,7 @@ class RtFlomniController(Controller):
         # while scan is running
         while mode > 0:
 
-            #TODO here?: scan abortion if no progress in scan *raise error
+            # TODO here?: scan abortion if no progress in scan *raise error
 
             # logger.info(f"Current scan position {current_position_in_scan} out of {number_of_positions_planned}")
             mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
@@ -617,6 +622,18 @@ class RtFlomniSetpointSignal(RtSetpointSignal):
                 "The interferometer feedback is not running. Either it is turned off or and"
                 " interferometer error occured."
             )
+
+        tracker_status = self.parent.controller.laser_tracker_check_signalstrength()
+
+        if tracker_status == "toolow":
+            print(
+                "The interferometer signal is too low for movements. Realignment required."
+            )
+            raise RtError(
+                "The interferometer signal is too low for movements. Realignment required."
+            )
+
+
         self.set_with_feedback_disabled(val)
 
     def set_with_feedback_disabled(self, val):

csaxs_bec/devices/omny/shutter.py

@@ -48,6 +48,7 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshopen(self):
         """Open the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
+            self.shutter.put(1)
             return self.device_manager.devices["fsh"].fshopen()
         else:
             self.shutter.put(1)
@@ -55,6 +56,7 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshclose(self):
         """Close the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
+            self.shutter.put(0)
             return self.device_manager.devices["fsh"].fshclose()
         else:
             self.shutter.put(0)

csaxs_bec/scans/flomni_fermat_scan.py

@@ -165,7 +165,8 @@ class FlomniFermatScan(SyncFlyScanBase):
         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)
+        # rtx_status = yield from self.stubs.set(device="rtx", value=self.positions[0][0], wait=False)
+        rtx_status = yield from self.stubs.set(device="rtx", value=self.cenx, 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")
@@ -173,13 +174,15 @@ class FlomniFermatScan(SyncFlyScanBase):
         rtx_status.wait()
         rtz_status.wait()
 
+        # status = yield from self.stubs.send_rpc("rtx", "move", self.cenx)
+        # 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
-        )
         tracker_signal_status = yield from self.stubs.send_rpc_and_wait(
             "rtx", "controller.laser_tracker_check_signalstrength"
         )
+        yield from self.stubs.send_rpc_and_wait(
+            "rtx", "controller.move_samx_to_scan_region", self.cenx
+        )
         # self.device_manager.connector.send_client_info(tracker_signal_status)
         if tracker_signal_status == "low":
             error_info = messages.ErrorInfo(
@@ -313,7 +316,11 @@ class FlomniFermatScan(SyncFlyScanBase):
         # in flomni, we need to move to the start position of the next scan, which is the end position of the current scan
         # this method is called in finalize and overwrites the default move_to_start()
         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])
+            # yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=self.positions[-1])
+            # in x we move to cenx, then we avoid jumps in centering routine
+            value = self.positions[-1]
+            value[0] = self.cenx
+            yield from self.stubs.set(device=["rtx", "rty", "rtz"], value=value)
             return
 
         logger.warning("No positions found to return to start")

docs/user/ptychography/flomni.md

@@ -50,16 +50,15 @@ Manually move the gripper to a transfer position
 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. `flomni.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.
+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. The GUI will present a fit of this data, which is automatically loaded to BEC for aligning the sample.
 
 #### Fine alignment
 
 After the xrayeyealign, a fine alignment needs to be performed using ptychography.
-_To bypass the fine alignment: `feye_out`_
+_To bypass the fine alignment: `flomni.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.
@@ -71,13 +70,13 @@ _To bypass the fine alignment: `feye_out`_
 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.
+1. Before changing sample, verify that all subtomograms were completely acquired using the tomo_reconstruction 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`
+`~/data/raw/logs/tomography_scannumbers.txt`
 
 To continue an __interrupted tomography scan__:
 

docs/user/ptychography/lamni.md

@@ -26,7 +26,7 @@ The effective position of the axis of rotation shifts with sample thickness or m
 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()`
+1. close the shutter: `dev.omnyfsh.fshclose()`
 
 #### X-ray eye alignment
 

tests/tests_devices/test_delay_generator_csaxs.py

@@ -287,19 +287,20 @@ def test_ddg1_stage(mock_ddg1: DDG1):
     mock_ddg1.stage()
 
     shutter_width = mock_ddg1._shutter_to_open_delay + exp_time * frames_per_trigger
+    total_exposure = 2 * mock_ddg1._shutter_to_open_delay + exp_time * frames_per_trigger + 3e-6
 
     assert np.isclose(mock_ddg1.burst_mode.get(), 1)  # burst mode is enabled
     assert np.isclose(mock_ddg1.burst_delay.get(), 0)
-    assert np.isclose(mock_ddg1.burst_period.get(), shutter_width)
+    assert np.isclose(mock_ddg1.burst_period.get(), total_exposure)
 
     # Trigger DDG2 through EXT/EN
     assert np.isclose(mock_ddg1.ab.delay.get(), 2e-3)
-    assert np.isclose(mock_ddg1.ab.width.get(), 1e-6)
+    assert np.isclose(mock_ddg1.ab.width.get(), shutter_width)
     # Shutter channel cd
     assert np.isclose(mock_ddg1.cd.delay.get(), 0)
     assert np.isclose(mock_ddg1.cd.width.get(), shutter_width)
     # MCS channel ef or gate
-    assert np.isclose(mock_ddg1.ef.delay.get(), 0)
+    assert np.isclose(mock_ddg1.ef.delay.get(), 1e-6)
     assert np.isclose(mock_ddg1.ef.width.get(), 1e-6)
 
     assert mock_ddg1.staged == ophyd.Staged.yes

tests/tests_devices/test_mcs_card.py

@@ -217,16 +217,6 @@ def test_mcs_card_csaxs_complete_and_stop(mock_mcs_csaxs: MCSCardCSAXS):
     assert not mcs._start_monitor_async_data_emission.is_set()
 
 
-def test_mcs_on_stop(mock_mcs_csaxs: MCSCardCSAXS):
-    """Test that on stop sets the omit_mca_callbacks flag. Also test that on stage clears the omit_mca_callbacks flag."""
-    mcs = mock_mcs_csaxs
-    assert mcs._omit_mca_callbacks.is_set() is False
-    mcs.stop()
-    assert mcs._omit_mca_callbacks.is_set() is True
-    mcs.stage()
-    assert mcs._omit_mca_callbacks.is_set() is False
-
-
 def test_mcs_recovery(mock_mcs_csaxs: MCSCardCSAXS):
     mcs = mock_mcs_csaxs
     # Simulate ongoing acquisition