csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXS.py

@@ -1,23 +1,21 @@
-# import builtins
-# import datetime
-# import os
-# import subprocess
-# import time
-# from pathlib import Path
+import inspect
 
-# import numpy as np
 from bec_lib import bec_logger
-# from bec_lib.alarm_handler import AlarmBase
-# from bec_lib.pdf_writer import PDFWriter
 from typeguard import typechecked
 
-
+from csaxs_bec.bec_ipython_client.plugins.cSAXS.diagnostics import cSAXSDiagnostics
+from csaxs_bec.bec_ipython_client.plugins.cSAXS.filter_transmission import cSAXSFilterTransmission
+from csaxs_bec.bec_ipython_client.plugins.cSAXS.intensity_map_predict_gap import (
+    predict_gap as _predict_gap,
+)
+from csaxs_bec.bec_ipython_client.plugins.cSAXS.slits import cSAXSSlits
 from csaxs_bec.bec_ipython_client.plugins.cSAXS.smaract import cSAXSInitSmaractStages
 from csaxs_bec.bec_ipython_client.plugins.cSAXS.smaract import cSAXSSmaract
 from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.filter_transmission import cSAXSFilterTransmission
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.diagnostics import cSAXSDiagnostics
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.slits import cSAXSSlits
+
+logger = bec_logger.logger
+
+
 class cSAXSError(Exception):
     pass
 
@@ -36,6 +34,80 @@ class cSAXS(
         self.diagnostics = cSAXSDiagnostics()
         super().__init__(client=client)
 
+    # ------------------------------------------------------------------
+    # Undulator
+    # ------------------------------------------------------------------
+
+    def predict_gap(self, energy: float, n: int = 3) -> None:
+        """Print the predicted undulator gap for *energy* [keV] on harmonic *n*.
+
+        Examples
+        --------
+        csaxs.predict_gap(6.2)        # h=3 (default)
+        csaxs.predict_gap(10.0, n=5)  # explicit harmonic
+        """
+        import math
+
+        gap = float(_predict_gap(energy, n=n))
+        if math.isnan(gap):
+            print(f"Energy {energy:.3f} keV is unreachable on harmonic {n}.")
+        else:
+            print(f"Predicted gap for {energy:.3f} keV (h={n}): {gap:.4f} mm")
+
+    # ------------------------------------------------------------------
+    # Help / discovery
+    # ------------------------------------------------------------------
+
+    def commands(self) -> None:
+        """Print a table of all available cSAXS commands and sub-namespaces."""
+        from rich import box
+        from rich.console import Console
+        from rich.table import Table
+
+        console = Console()
+
+        entries: list[tuple[str, str]] = []
+        seen: set[str] = set()
+
+        for cls in type(self).__mro__:
+            if cls is object:
+                continue
+            module = getattr(cls, "__module__", "") or ""
+            if "csaxs_bec" not in module:
+                continue
+            for name, func in inspect.getmembers(cls, predicate=inspect.isfunction):
+                if name.startswith("_") or name in seen:
+                    continue
+                seen.add(name)
+                doc = (inspect.getdoc(func) or "").split("\n")[0].strip()
+                entries.append((name, doc))
+
+        entries.sort(key=lambda x: x[0])
+
+        tbl = Table(title="cSAXS Commands", box=box.SQUARE, show_lines=False)
+        tbl.add_column("Command", style="cyan bold", no_wrap=True, min_width=46)
+        tbl.add_column("Description")
+        for name, doc in entries:
+            tbl.add_row(f"csaxs.{name}()", doc)
+        console.print(tbl)
+        console.print("")
+
+        ns = Table(title="Sub-namespaces", box=box.SQUARE, show_lines=False)
+        ns.add_column("Access", style="cyan bold", no_wrap=True, min_width=46)
+        ns.add_column("Description")
+        for access, desc in [
+            ("csaxs.diagnostics.show_all()", "All diagnostic device readbacks"),
+            (
+                "csaxs.diagnostics.bpm_xbox1 / .bpm_xbox2",
+                "BPM diagnostics — .show_all(), .gain(val)",
+            ),
+            ("csaxs.diagnostics.bim", "BIM diagnostics — .show_all(), .gain(val)"),
+            ("csaxs.diagnostics.beamstop", "Beamstop diode — .show_all(), .gain(val)"),
+            ("csaxs.diagnostics.polarization", "Polarization diodes — .show_all(), .gain(val)"),
+            ("csaxs.OMNYTools.*", "OMNY instrument tools"),
+        ]:
+            ns.add_row(access, desc)
+        console.print(ns)
 
 
 # this is the csaxs master file that imports all routines from csaxs
@@ -45,4 +117,6 @@ class cSAXS(
 # csaxs = cSAXS(bec)
 #
 # then all commands can be accessed by for example
-# csaxs._cSAXS_smaract_stages_.....
+# csaxs.commands()
+# csaxs.predict_gap(6.2)
+# csaxs._cSAXS_smaract_stages_...

csaxs_bec/bec_ipython_client/plugins/cSAXS/intensity_map_predict_gap.py

@@ -0,0 +1,26 @@
+"""Undulator gap predictor emitted by plot_intensity_map.py.
+Edit the fitted constants in the signature to retune."""
+
+import numpy as np
+
+
+def predict_gap(energy, n=3, gap_min=5.0,
+                E_inf=3.2878, c0=2.46086, c1=-0.468091, c2=0.0):
+    """Undulator gap [mm] to place `energy` [keV] on harmonic `n`.
+    Fitted constants are the defaults below; edit them to retune.
+    Returns NaN where the energy is unreachable on that harmonic."""
+    energy = np.asarray(energy, float)
+    arg = E_inf * n / energy - 1.0          # required K^2/2; must be > 0
+    with np.errstate(invalid="ignore", divide="ignore"):
+        y = np.log(arg)
+    if abs(c2) < 1e-12:
+        g = (y - c0) / c1
+    else:
+        disc = c1 * c1 - 4.0 * c2 * (c0 - y)
+        sq = np.sqrt(np.where(disc >= 0, disc, np.nan))
+        r1 = (-c1 + sq) / (2.0 * c2)
+        r2 = (-c1 - sq) / (2.0 * c2)
+        g = np.where(c1 + 2.0 * c2 * r1 < 0, r1, r2)
+    g = np.where(arg > 0, g, np.nan)         # above harmonic cutoff
+    g = np.where(g >= gap_min, g, np.nan)    # below mechanical minimum
+    return g

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -2560,6 +2560,10 @@ class Flomni(
             + self.manual_shift_y
         )
         sum_offset_z = offsets[2]
+        
+        # TODO this fix is while the tracker z is broken
+        probe_propagation = -sum_offset_z * 1e-6
+        sum_offset_z = 0
 
         # --- positioning + laser tracker, mirroring
         # flomni_fermat_scan._prepare_setup_part2 ---
@@ -2580,6 +2584,7 @@ class Flomni(
         # --- acquire ---
         n_frames = frames_per_trigger if frames_per_trigger is not None else self.frames_per_trigger
         scans.acquire(exp_time=self.tomo_countingtime, frames_per_trigger=n_frames)
+        self.tomo_reconstruct(probe_propagation=probe_propagation)
 
     def _tomo_type1_actual_grid(self) -> tuple[int, float, int]:
         """Compute the actual (achievable) tomo_type==1 grid from the
@@ -2618,13 +2623,17 @@ class Flomni(
         print(f"Frames per trigger (burst)       =  {self.frames_per_trigger}")
         print(f"Single point instead of fermat   =  {self.single_point_instead_of_fermat_scan}")
         print("")
+
         if self.tomo_type == 1:
             print("\x1b[1mTomo type 1:\x1b[0m 8 equally spaced sub-tomograms")
             print(f"Angular range                    =  {self.tomo_angle_range} degrees")
-            print(
-                f"Total number of projections: {(self.tomo_angle_range/self.tomo_angle_stepsize)*8}"
-            )
-            print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
+            # N, step, total_projections all come from the same helper
+            # sub_tomo_scan() effectively uses internally - see
+            # _tomo_type1_actual_grid() for why this can't just read
+            # self.tomo_angle_stepsize directly.
+            _, achievable_step, total_projections = self._tomo_type1_actual_grid()
+            print(f"Total number of projections: {total_projections}")
+            print(f"Angular step within sub-tomogram:   {achievable_step:.3f} degrees")
             print(
                 "Angular step of the final (combined) tomogram:"
                 f"   {self.tomo_angle_range / total_projections:.3f} degrees"

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -98,8 +98,9 @@ class FlomniOpticsMixin:
             dev.rtx.controller.feedback_disable()
 
         self.fosa_out()
+        foptx_out = self._get_user_param_safe("foptx", "out")
         fopty_out = self._get_user_param_safe("fopty", "out")
-        umv(dev.fopty, fopty_out)
+        umv(dev.foptx, foptx_out, dev.fopty, fopty_out)
 
         if "rtx" in dev and dev.rtx.enabled:
             time.sleep(1)
@@ -237,7 +238,7 @@ class FlomniOpticsMixin:
 
         console.print(table)
 
-        diameters = [150e-6, 250e-6]
+        diameters = [140e-6, 170e-6, 200e-6, 250e-6]
 
         console = Console()
         table = Table(title="Outermost zone width \033[1m30 nm\033[0m", box=box.SQUARE)

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -70,14 +70,26 @@ class XrayEyeAlign:
         # so a second submission at step==1 is treated as the real angle-0
         # fit point instead of triggering another height correction.
         self._height_centered = False
+        # Raw pixel coords + ROI size collected at each submit:
+        # [[step_k, x_px, y_px, w_px, h_px, image_idx], ...]
+        # image_idx refers to alignment_images[image_idx], i.e. the last
+        # frame captured before that submit (shutter is closed at submit time).
+        self.roi_pixel_data = []
 
-    def _save_alignment_data(self, file_path: str):
-        os.makedirs(os.path.dirname(file_path), exist_ok=True)
-        with h5py.File(os.path.expanduser(file_path), "w") as f:
+    def _save_alignment_data(self, file_path: str, fit_data: np.ndarray | None = None):
+        expanded = os.path.expanduser(file_path)
+        os.makedirs(os.path.dirname(expanded), exist_ok=True)
+        with h5py.File(expanded, "w") as f:
             f.create_dataset(
                 "alignment_values", data=np.array(list(self.alignment_values.values()))
             )
             f.create_dataset("alignment_images", data=np.array(self.alignment_images))
+            if self.roi_pixel_data:
+                ds = f.create_dataset("roi_pixel_data", data=np.array(self.roi_pixel_data))
+                ds.attrs["columns"] = ["step_k", "x_px", "y_px", "w_px", "h_px", "image_idx"]
+            if fit_data is not None:
+                ds = f.create_dataset("alignment_fit", data=fit_data)
+                ds.attrs["rows"] = ["angles_deg", "offsets_um", "zeros"]
 
     def update_frame(self, keep_shutter_open=False):
         if self.flomni._flomnigui_check_attribute_not_exists("xeyegui"):
@@ -220,6 +232,20 @@ class XrayEyeAlign:
                 # reset submit channel
                 dev.omny_xray_gui.submit.set(0)
 
+                # Raw pixel position and ROI size at submit time.
+                # The relevant image is the last captured frame (shutter is
+                # closed by the time the user clicks submit).
+                _raw_x = getattr(dev.omny_xray_gui, f"xval_x_{k}").get()
+                _raw_y = getattr(dev.omny_xray_gui, f"yval_y_{k}").get()
+                _raw_w = getattr(dev.omny_xray_gui, f"width_x_{k}").get()
+                _raw_h = getattr(dev.omny_xray_gui, f"width_y_{k}").get()
+                _img_idx = len(self.alignment_images) - 1
+                print(
+                    f"  Submit k={k}: px x={_raw_x:.1f} y={_raw_y:.1f} "
+                    f"w={_raw_w:.1f} h={_raw_h:.1f} img={_img_idx}"
+                )
+                self.roi_pixel_data.append([k, _raw_x, _raw_y, _raw_w, _raw_h, _img_idx])
+
                 # Controls whether `k` advances to the next step below. Left
                 # True except for the height-centering submission, which
                 # reuses k==1 for a second, real submission afterwards.
@@ -252,9 +278,13 @@ class XrayEyeAlign:
                     self.gui.show_crosshair()
 
                     self.send_message(
-                                            "Adjust sample height with the arrows if needed, then mark "
-                                            "the sample and submit - height will be centered automatically"
-                                        )
+<<<<<<< Updated upstream
+                        "Submit height. Use arrows if far off."
+=======
+                        "Adjust sample height with the arrows if needed, then mark "
+                        "the sample and submit - height will be centered automatically"
+>>>>>>> Stashed changes
+                    )
                     self.gui.enable_submit_button(True)
                     self.movement_buttons_enabled(True, True)
 
@@ -373,37 +403,22 @@ class XrayEyeAlign:
         )
 
     def write_output(self):
-        file = os.path.expanduser("~/data/raw/logs/xrayeye_alignmentvalues/xrayeye_alignmentvalues")
         timestamp = time.strftime("%Y%m%d_%H%M%S")
-        self._save_alignment_data(file + f"_image_data_{timestamp}.h5")
-        if not os.path.exists(file):
-            os.makedirs(os.path.dirname(file), exist_ok=True)
+        file_h5 = f"~/data/raw/logs/xrayeye_alignmentvalues/xrayeye_alignmentvalues_{timestamp}.h5"
 
-        with open(file, "w") as alignment_values_file:
-            alignment_values_file.write("angle\thorizontal\n")
+        fovx_offsets = np.zeros(5)
+        for k in range(1, 6):
+            fovx_offset = self.alignment_values[0] - self.alignment_values[k]
+            fovx_offsets[k - 1] = fovx_offset
+            print(f"Alignment number {k}, value x {fovx_offset}")
 
-            # Initialize an empty list to store fovx values
-            fovx_list = []
-            fovx_offsets = np.zeros(5)  # holds offsets for k = 1..5
-
-            for k in range(1, 6):
-                fovx_offset = self.alignment_values[0] - self.alignment_values[k]
-                fovx_offsets[k - 1] = fovx_offset  # store in array
-
-                fovx_x = (k - 1) * 45
-                fovx_list.append([fovx_x, fovx_offset * 1000])  # Append the data to the list
-
-                print(f"Alignment number {k}, value x {fovx_offset}")
-                alignment_values_file.write(f"{fovx_x}\t{fovx_offset * 1000}\n")
-
-            # Now build final numpy array:
-            data = np.array(
-                [
-                    [0, 45, 90, 135, 180],  # angles
-                    fovx_offsets * 1000,  # fovx_offset values
-                    [0, 0, 0, 0, 0],
-                ]
-            )
+        data = np.array(
+            [
+                [0, 45, 90, 135, 180],  # angles
+                fovx_offsets * 1000,  # fovx_offset values
+                [0, 0, 0, 0, 0],
+            ]
+        )
+        self._save_alignment_data(file_h5, fit_data=data)
         self.gui.submit_fit_array(data)
-        print(f"fit submited with {data}")
-        # self.flomni.flomnigui_show_xeyealign_fittab()
+        print(f"fit submited with {data}")

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -76,7 +76,10 @@ foptx:
   connectionTimeout: 20
   userParameter:
     #170 micron, 60 nm
-    in: -13.831
+    #in: -13.831
+    #250 micron, 30 nm, Abe structures
+    in: -13.8809375
+    out: -14.1809
 fopty:
   description: Optics Y
   deviceClass: csaxs_bec.devices.omny.galil.fgalil_ophyd.FlomniGalilMotor
@@ -95,8 +98,11 @@ fopty:
   connectionTimeout: 20
   userParameter:
     #170 micron, 60 nm
-    in: 0.42
-    out: 0.57
+    #in: 0.42
+    #out: 0.57
+    #250 micron, 30 nm, Abe structures
+    in: 2.8299
+    out: 2.8299
 foptz:
   description: Optics Z
   deviceClass: csaxs_bec.devices.omny.galil.fgalil_ophyd.FlomniGalilMotor
@@ -157,7 +163,7 @@ fsamy:
     host: mpc2844.psi.ch
     limits:
     - 2
-    - 3.3
+    - 3.8
     port: 8081
     sign: 1
   enabled: true
@@ -305,7 +311,10 @@ fosax:
     #in: 8.7568
     #out: 5.1
     #170 micron, 60 nm, 7.9 kev
-    in: 8.731922
+    # in: 8.731922
+    # out: 5.1
+    #250 micron, 30 nm, Abe structures
+    in: 8.755141
     out: 5.1
 fosay:
   description: OSA Y
@@ -327,8 +336,9 @@ fosay:
     #170 micron, 60 nm, 7.6 kev
     #in: -0.0235
     #170 micron, 60 nm, 7.6 kev
-    in: -0.0422
-
+    #in: -0.0422
+    #250 micron, 30 nm, Abe structures
+    in: -2.357436
 fosaz:
   description: OSA Z
   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
@@ -350,8 +360,11 @@ fosaz:
     #in: 8.5
     #out: 6
     #170 micron, 60 nm, 7.9 kev, foptz 15.9
-    in: 11.9
-    out: 6
+    # in: 11.9
+    # out: 6
+    # micron, 30 nm, 7.9 kev, foptz 32 //abe's fzp's
+    in: -2
+    out: -5
 
 ############################################################
 #################### flOMNI RT motors ######################