Merge branch 'main' into fix/minimal-safeguard-for-progress-update
This commit is contained in:
@@ -9,12 +9,13 @@ import numpy as np
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from bec_lib import bec_logger
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from bec_lib.alarm_handler import AlarmBase
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from bec_lib.pdf_writer import PDFWriter
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from bec_lib.scan_repeat import scan_repeat
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from typeguard import typechecked
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from csaxs_bec.bec_ipython_client.plugins.cSAXS import cSAXSBeamlineChecks
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from csaxs_bec.bec_ipython_client.plugins.flomni.flomni_optics_mixin import FlomniOpticsMixin
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from csaxs_bec.bec_ipython_client.plugins.flomni.x_ray_eye_align import XrayEyeAlign
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from csaxs_bec.bec_ipython_client.plugins.flomni.gui_tools import flomniGuiTools
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from csaxs_bec.bec_ipython_client.plugins.flomni.x_ray_eye_align import XrayEyeAlign
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from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import (
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OMNYTools,
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PtychoReconstructor,
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@@ -786,9 +787,7 @@ class FlomniSampleTransferMixin:
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dev.ftransy.controller.socket_put_confirmed("confirm=1")
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else:
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print("Stopping.")
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raise FlomniError(
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"User abort sample transfer."
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)
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raise FlomniError("User abort sample transfer.")
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def ftransfer_gripper_is_open(self) -> bool:
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status = bool(float(dev.ftransy.controller.socket_put_and_receive("MG @OUT[9]").strip()))
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@@ -811,7 +810,7 @@ class FlomniSampleTransferMixin:
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def ftransfer_gripper_move(self, position: int):
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self.check_position_is_valid(position)
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#this is not used for sample stage position!
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# this is not used for sample stage position!
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self._ftransfer_shiftx = -0.15
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self._ftransfer_shiftz = -0.5
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@@ -1237,6 +1236,7 @@ class _ProgressProxy:
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"tomo_type": 0,
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"tomo_start_time": None,
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"estimated_remaining_time": None,
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"estimated_finish_time": None,
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"heartbeat": None,
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}
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@@ -1314,12 +1314,13 @@ class Flomni(
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from csaxs_bec.bec_ipython_client.plugins.flomni.flomni_webpage_generator import (
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FlomniWebpageGenerator,
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)
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self._webpage_gen = FlomniWebpageGenerator(
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bec_client=client,
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output_dir="~/data/raw/webpage/",
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#upload_url="http://s1090968537.online.de/upload.php", # optional
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# upload_url="http://s1090968537.online.de/upload.php", # optional
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upload_url="https://v1p0zyg2w9n2k9c1.myfritz.net/upload.php",
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local_port=8080
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local_port=8080,
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)
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self._webpage_gen.start()
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@@ -1578,6 +1579,22 @@ class Flomni(
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def tomo_stitch_overlap(self, val: float):
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self.client.set_global_var("tomo_stitch_overlap", val)
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@property
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def tomo_angle_range(self):
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"""Total angular sweep in degrees for tomo_type 1 (equally spaced
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sub-tomograms), inclusive of the upper bound. Either 180 (default,
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original behaviour) or 360."""
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val = self.client.get_global_var("tomo_angle_range")
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if val is None:
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return 180
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return val
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@tomo_angle_range.setter
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def tomo_angle_range(self, val: float):
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if val not in (180, 360):
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raise ValueError("tomo_angle_range must be 180 or 360 degrees.")
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self.client.set_global_var("tomo_angle_range", val)
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@property
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def golden_projections_at_0_deg_for_damage_estimation(self):
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val = self.client.get_global_var("golden_projections_at_0_deg_for_damage_estimation")
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@@ -1600,6 +1617,39 @@ class Flomni(
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def golden_ratio_bunch_size(self, val: float):
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self.client.set_global_var("golden_ratio_bunch_size", val)
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@property
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def frames_per_trigger(self):
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"""Number of burst frames acquired per point/projection. Used both
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by scans.flomni_fermat_scan (via tomo_scan_projection) and by
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tomo_acquire_at_angle (scans.acquire)."""
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val = self.client.get_global_var("frames_per_trigger")
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if val is None:
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return 1
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return val
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@frames_per_trigger.setter
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def frames_per_trigger(self, val: int):
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if isinstance(val, bool) or not isinstance(val, int):
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raise ValueError("frames_per_trigger must be a positive integer.")
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if val <= 0:
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raise ValueError("frames_per_trigger must be a positive integer.")
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self.client.set_global_var("frames_per_trigger", val)
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@property
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def single_point_instead_of_fermat_scan(self):
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"""If True, tomo_scan acquires a single point (or burst) at each
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angle via scans.acquire instead of running scans.flomni_fermat_scan.
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Applies to all tomo_types, since it only changes how a given angle
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is acquired, not which angles are visited."""
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val = self.client.get_global_var("single_point_instead_of_fermat_scan")
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if val is None:
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return False
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return val
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@single_point_instead_of_fermat_scan.setter
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def single_point_instead_of_fermat_scan(self, val: bool):
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self.client.set_global_var("single_point_instead_of_fermat_scan", val)
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@property
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def sample_name(self):
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return self.sample_get_name(0)
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@@ -1645,7 +1695,7 @@ class Flomni(
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end_scan_number = bec.queue.next_scan_number
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for scan_nr in range(start_scan_number, end_scan_number):
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#self._write_tomo_scan_number(scan_nr, angle, 0)
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# self._write_tomo_scan_number(scan_nr, angle, 0)
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alignment_scan_numbers.append(scan_nr)
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umv(dev.fsamroy, 0)
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@@ -1655,7 +1705,7 @@ class Flomni(
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# summary of alignment scan numbers
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scan_list_str = ", ".join(str(s) for s in alignment_scan_numbers)
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#print(f"\nAlignment scan numbers ({len(alignment_scan_numbers)} total): {scan_list_str}")
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# print(f"\nAlignment scan numbers ({len(alignment_scan_numbers)} total): {scan_list_str}")
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# BEC scilog entry (no logo)
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scilog_content = (
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@@ -1665,7 +1715,9 @@ class Flomni(
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f"Alignment scan numbers: {scan_list_str}\n"
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)
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print(scilog_content)
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bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "<br>")).add_tags("alignmentscan").send()
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bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "<br>")).add_tags(
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"alignmentscan"
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).send()
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def write_alignment_scan_numbers(self, first_scan):
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import os
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@@ -1691,8 +1743,6 @@ class Flomni(
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f.write(" ".join(map(str, x_vals)) + "\n")
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f.write(" ".join(map(str, zeros)) + "\n")
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def sub_tomo_scan(self, subtomo_number, start_angle=None):
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"""
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Performs a sub tomogram scan.
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@@ -1729,14 +1779,14 @@ class Flomni(
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start = start_angle + _tomo_shift_angles
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if subtomo_number % 2: # odd = forward
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max_allowed_angle = 180.05 + self.tomo_angle_stepsize
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proposed_end = start + 180
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max_allowed_angle = self.tomo_angle_range + 0.05 + self.tomo_angle_stepsize
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proposed_end = start + self.tomo_angle_range
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angle_end = min(proposed_end, max_allowed_angle)
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span = angle_end - start
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else: # even = reverse
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min_allowed_angle = 0
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proposed_end = start - 180
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proposed_end = start - self.tomo_angle_range
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angle_end = max(proposed_end, min_allowed_angle)
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span = start - angle_end
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@@ -1747,8 +1797,8 @@ class Flomni(
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if subtomo_number % 2: # odd subtomos → forward direction
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# clamp end angle to max allowed
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max_allowed_angle = 180.05 + self.tomo_angle_stepsize
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proposed_end = start + 180
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max_allowed_angle = self.tomo_angle_range + 0.05 + self.tomo_angle_stepsize
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proposed_end = start + self.tomo_angle_range
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angle_end = min(proposed_end, max_allowed_angle)
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angles = np.linspace(start, angle_end, num=N, endpoint=True)
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@@ -1756,7 +1806,7 @@ class Flomni(
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else: # even subtomos → reverse direction
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# go FROM start_angle down toward 0
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min_allowed_angle = 0
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proposed_end = start - 180
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proposed_end = start - self.tomo_angle_range
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angle_end = max(proposed_end, min_allowed_angle)
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angles = np.linspace(start, angle_end, num=N, endpoint=True)
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@@ -1778,58 +1828,48 @@ class Flomni(
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if subtomo_number % 2: # odd = forward direction
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self._subtomo_offset = round(sa / step)
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else: # even = reverse direction
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self._subtomo_offset = round((180 - sa) / step)
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self._subtomo_offset = round((self.tomo_angle_range - sa) / step)
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# progress index must always increase
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self.progress["subtomo_projection"] = self._subtomo_offset + i
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# ------------------------------------------------------------
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# existing progress fields
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self.progress["subtomo_total_projections"] = int(180 / self.tomo_angle_stepsize)
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self.progress["subtomo_total_projections"] = int(
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self.tomo_angle_range / self.tomo_angle_stepsize
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)
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self.progress["projection"] = (subtomo_number - 1) * self.progress[
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"subtomo_total_projections"
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] + self.progress["subtomo_projection"]
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self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
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self.progress["total_projections"] = (
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self.tomo_angle_range / self.tomo_angle_stepsize
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) * 8
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self.progress["angle"] = angle
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# finally do the scan at this angle
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self._tomo_scan_at_angle(angle, subtomo_number)
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@scan_repeat(max_repeats=10, default=True)
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def _tomo_scan_at_angle(self, angle, subtomo_number):
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successful = False
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error_caught = False
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if 0 <= angle < 180.05:
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if 0 <= angle < self.tomo_angle_range + 0.05:
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self.progress["heartbeat"] = datetime.datetime.now().isoformat()
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print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
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self._print_progress()
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while not successful:
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# self.bl_chk._bl_chk_start()
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if not self.special_angles:
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self._current_special_angles = []
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if self._current_special_angles:
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next_special_angle = self._current_special_angles[0]
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if np.isclose(angle, next_special_angle, atol=0.5):
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self._current_special_angles.pop(0)
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num_repeats = self.special_angle_repeats
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else:
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num_repeats = 1
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try:
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start_scan_number = bec.queue.next_scan_number
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for i in range(num_repeats):
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self._at_each_angle(angle)
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error_caught = False
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except AlarmBase as exc:
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if exc.alarm_type == "TimeoutError":
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bec.queue.request_queue_reset()
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time.sleep(2)
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error_caught = True
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else:
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raise exc
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# if self.bl_chk._bl_chk_stop() and not error_caught:
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successful = True
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# else:
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# self.bl_chk._bl_chk_wait_until_recovered()
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if not self.special_angles:
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self._current_special_angles = []
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if self._current_special_angles:
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next_special_angle = self._current_special_angles[0]
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if np.isclose(angle, next_special_angle, atol=0.5):
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self._current_special_angles.pop(0)
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num_repeats = self.special_angle_repeats
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else:
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num_repeats = 1
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start_scan_number = bec.queue.next_scan_number
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for i in range(num_repeats):
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self._at_each_angle(angle)
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||||
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||||
end_scan_number = bec.queue.next_scan_number
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for scan_nr in range(start_scan_number, end_scan_number):
|
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self._write_tomo_scan_number(scan_nr, angle, subtomo_number)
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@@ -1851,6 +1891,10 @@ class Flomni(
|
||||
|
||||
bec = builtins.__dict__.get("bec")
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scans = builtins.__dict__.get("scans")
|
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bec.builtin_actors.scan_interlock.trigger_setting = "restart_scan"
|
||||
bec.builtin_actors.scan_interlock.enabled = True
|
||||
|
||||
self._current_special_angles = self.special_angles.copy()
|
||||
# a new tomo scan was started
|
||||
if (
|
||||
@@ -1859,7 +1903,7 @@ class Flomni(
|
||||
or (self.tomo_type == 3 and projection_number == None)
|
||||
):
|
||||
|
||||
#pylint: disable=undefined-variable
|
||||
# pylint: disable=undefined-variable
|
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if bec.active_account != "":
|
||||
self.tomo_id = self.add_sample_database(
|
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self.sample_name,
|
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@@ -1875,6 +1919,11 @@ class Flomni(
|
||||
self.tomo_id = 0
|
||||
self.write_pdf_report()
|
||||
self.progress["tomo_start_time"] = datetime.datetime.now().isoformat()
|
||||
# reset stale estimates from any previous scan, otherwise the GUI
|
||||
# would keep showing a leftover ETA from before this scan has
|
||||
# accumulated enough projections to compute a fresh one
|
||||
self.progress["estimated_remaining_time"] = None
|
||||
self.progress["estimated_finish_time"] = None
|
||||
|
||||
with scans.dataset_id_on_hold:
|
||||
if self.tomo_type == 1:
|
||||
@@ -2000,15 +2049,18 @@ class Flomni(
|
||||
projection = self.progress["projection"]
|
||||
total = self.progress["total_projections"]
|
||||
if start_str is not None and total > 0 and projection > 9:
|
||||
elapsed = (
|
||||
datetime.datetime.now() - datetime.datetime.fromisoformat(start_str)
|
||||
).total_seconds()
|
||||
now = datetime.datetime.now()
|
||||
elapsed = (now - datetime.datetime.fromisoformat(start_str)).total_seconds()
|
||||
rate = projection / elapsed # projections per second
|
||||
remaining_s = (total - projection) / rate
|
||||
self.progress["estimated_remaining_time"] = remaining_s
|
||||
eta_str = self._format_duration(remaining_s)
|
||||
finish_dt = now + datetime.timedelta(seconds=remaining_s)
|
||||
self.progress["estimated_finish_time"] = finish_dt.isoformat()
|
||||
finish_str = finish_dt.strftime("%Y-%m-%d %H:%M:%S")
|
||||
else:
|
||||
eta_str = "N/A"
|
||||
finish_str = "N/A"
|
||||
# ----------------------------------------------------------------------
|
||||
print("\x1b[95mProgress report:")
|
||||
print(f"Tomo type: ....................... {self.progress['tomo_type']}")
|
||||
@@ -2017,7 +2069,8 @@ class Flomni(
|
||||
print(f"Angle: ........................... {self.progress['angle']}")
|
||||
print(f"Current subtomo: ................. {self.progress['subtomo']}")
|
||||
print(f"Current projection within subtomo: {self.progress['subtomo_projection']}")
|
||||
print(f"Estimated remaining time: ........ {eta_str}\x1b[0m")
|
||||
print(f"Estimated remaining time: ........ {eta_str}")
|
||||
print(f"Estimated finish time: ........... {finish_str}\x1b[0m")
|
||||
self._flomnigui_update_progress()
|
||||
|
||||
def add_sample_database(
|
||||
@@ -2040,6 +2093,10 @@ class Flomni(
|
||||
flomni_at_each_angle(self, angle)
|
||||
return
|
||||
|
||||
if self.single_point_instead_of_fermat_scan:
|
||||
self.tomo_acquire_at_angle(angle)
|
||||
return
|
||||
|
||||
self.tomo_scan_projection(angle)
|
||||
|
||||
def _golden(self, ii, howmany_sorted, maxangle, reverse=False):
|
||||
@@ -2123,6 +2180,7 @@ class Flomni(
|
||||
offsets[1]
|
||||
- self.compute_additional_correction_y(angle)
|
||||
- self.compute_additional_correction_y_2(angle)
|
||||
+ self.manual_shift_y
|
||||
)
|
||||
sum_offset_z = offsets[2]
|
||||
|
||||
@@ -2155,6 +2213,7 @@ class Flomni(
|
||||
zshift=sum_offset_z,
|
||||
angle=angle,
|
||||
exp_time=self.tomo_countingtime,
|
||||
frames_per_trigger=self.frames_per_trigger,
|
||||
)
|
||||
|
||||
if self.corridor_size > 0:
|
||||
@@ -2164,6 +2223,67 @@ class Flomni(
|
||||
|
||||
self.tomo_reconstruct()
|
||||
|
||||
def tomo_acquire_at_angle(self, angle: float, frames_per_trigger: int | None = None):
|
||||
"""
|
||||
Move fsamroy to `angle`, then move rtx/rty/rtz to the alignment-corrected
|
||||
scan center (same alignment-offset logic as tomo_scan_projection, but
|
||||
without stitching), and acquire a single frame or a burst via
|
||||
scans.acquire instead of running a fermat scan.
|
||||
|
||||
This mirrors the positioning sequence used internally by
|
||||
flomni_fermat_scan (rotation, then rtx/rty/rtz with laser-tracker
|
||||
on/check/move-to-region), but executes it as plain blocking
|
||||
client-side calls, since this runs in the BEC client, not on the
|
||||
scan server.
|
||||
|
||||
Args:
|
||||
angle (float): rotation angle [deg] to move fsamroy to.
|
||||
frames_per_trigger (int, optional): number of burst frames for
|
||||
this acquisition. Defaults to self.frames_per_trigger.
|
||||
"""
|
||||
scans = builtins.__dict__.get("scans")
|
||||
|
||||
# --- rotation ---
|
||||
fsamroy_current_setpoint = dev.fsamroy.user_setpoint.get()
|
||||
if angle != fsamroy_current_setpoint:
|
||||
umv(dev.fsamroy, angle)
|
||||
else:
|
||||
print("No rotation required")
|
||||
|
||||
# --- alignment offset (same as tomo_scan_projection, no stitching) ---
|
||||
offsets = self.get_alignment_offset(angle)
|
||||
sum_offset_x = offsets[0]
|
||||
sum_offset_y = (
|
||||
offsets[1]
|
||||
- self.compute_additional_correction_y(angle)
|
||||
- self.compute_additional_correction_y_2(angle)
|
||||
+ self.manual_shift_y
|
||||
)
|
||||
sum_offset_z = offsets[2]
|
||||
|
||||
# --- positioning + laser tracker, mirroring
|
||||
# flomni_fermat_scan._prepare_setup_part2 ---
|
||||
dev.rtx.controller.laser_tracker_on()
|
||||
umv(dev.rtx, sum_offset_x, dev.rty, sum_offset_y, dev.rtz, sum_offset_z)
|
||||
tracker_signal = dev.rtx.controller.laser_tracker_check_signalstrength()
|
||||
# checks that the fsamx coarse stage is at a position that leaves
|
||||
# sufficient piezo range on the fine (rtx) stage
|
||||
dev.rtx.controller.move_samx_to_scan_region(sum_offset_x)
|
||||
|
||||
if tracker_signal == "low":
|
||||
logger.warning(
|
||||
"Signal strength of the laser tracker is low. Realignment recommended!"
|
||||
)
|
||||
elif tracker_signal == "toolow":
|
||||
raise FlomniError(
|
||||
"Signal strength of the laser tracker is too low for scanning. Realignment required!"
|
||||
)
|
||||
|
||||
# --- 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)
|
||||
|
||||
def tomo_parameters(self):
|
||||
"""print and update the tomo parameters"""
|
||||
@@ -2174,12 +2294,19 @@ class Flomni(
|
||||
print(f"Stitching number x,y = {self.stitch_x}, {self.stitch_y}")
|
||||
print(f"Stitching overlap = {self.tomo_stitch_overlap}")
|
||||
print(f"Reconstruction queue name = {self.ptycho_reconstruct_foldername}")
|
||||
print(f" _manual_shift_y <mm> = {self.manual_shift_y}")
|
||||
print(f" _manual_shift_y <um> = {self.manual_shift_y}")
|
||||
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"Total number of projections: {180/self.tomo_angle_stepsize*8}")
|
||||
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")
|
||||
print(
|
||||
"Angular step of the final (combined) tomogram:"
|
||||
f" {self.tomo_angle_range/((self.tomo_angle_range/self.tomo_angle_stepsize)*8)} degrees"
|
||||
)
|
||||
if self.tomo_type == 2:
|
||||
print("\x1b[1mTomo type 2:\x1b[0m Golden ratio tomography")
|
||||
print(f"Sorted in bunches of: {self.golden_ratio_bunch_size}")
|
||||
@@ -2214,11 +2341,38 @@ class Flomni(
|
||||
self.tomo_shellstep = self._get_val("<step size> um", self.tomo_shellstep, float)
|
||||
self.fovx = self._get_val("<FOV X (max 200)> um", self.fovx, float)
|
||||
self.fovy = self._get_val("<FOV Y (max 100)> um", self.fovy, float)
|
||||
self.stitch_x = self._get_val("<stitch X>", self.stitch_x, int)
|
||||
self.stitch_y = self._get_val("<stitch Y>", self.stitch_y, int)
|
||||
if self.single_point_instead_of_fermat_scan:
|
||||
print(
|
||||
"Stitching is disabled while single point instead of fermat scan is"
|
||||
" active; stitch X/Y forced to 0."
|
||||
)
|
||||
self.stitch_x = 0
|
||||
self.stitch_y = 0
|
||||
else:
|
||||
self.stitch_x = self._get_val("<stitch X>", self.stitch_x, int)
|
||||
self.stitch_y = self._get_val("<stitch Y>", self.stitch_y, int)
|
||||
self.ptycho_reconstruct_foldername = self._get_val(
|
||||
"Reconstruction queue ", self.ptycho_reconstruct_foldername, str
|
||||
)
|
||||
self.frames_per_trigger = self._get_val(
|
||||
"Frames per trigger (burst)", self.frames_per_trigger, int
|
||||
)
|
||||
self.single_point_instead_of_fermat_scan = bool(
|
||||
self._get_val(
|
||||
"Single point instead of fermat scan (acquire at angle) 1/0?",
|
||||
int(self.single_point_instead_of_fermat_scan),
|
||||
int,
|
||||
)
|
||||
)
|
||||
if self.single_point_instead_of_fermat_scan and (
|
||||
self.stitch_x != 0 or self.stitch_y != 0
|
||||
):
|
||||
print(
|
||||
"Stitching is not supported with single point instead of fermat scan;"
|
||||
" stitch X/Y forced to 0."
|
||||
)
|
||||
self.stitch_x = 0
|
||||
self.stitch_y = 0
|
||||
|
||||
print("Tomography type:")
|
||||
print(" 1: 8 equally spaced sub-tomograms")
|
||||
@@ -2227,12 +2381,22 @@ class Flomni(
|
||||
self.tomo_type = self._get_val("Tomography type", self.tomo_type, int)
|
||||
|
||||
if self.tomo_type == 1:
|
||||
self.tomo_angle_range = self._get_val(
|
||||
"Angular range (180 or 360)", self.tomo_angle_range, int
|
||||
)
|
||||
tomo_numberofprojections = self._get_val(
|
||||
"Total number of projections", 180 / self.tomo_angle_stepsize * 8, int
|
||||
"Total number of projections",
|
||||
(self.tomo_angle_range / self.tomo_angle_stepsize) * 8,
|
||||
int,
|
||||
)
|
||||
self.tomo_angle_stepsize = (self.tomo_angle_range / tomo_numberofprojections) * 8
|
||||
print(
|
||||
f"The angular step within a sub-tomogram will be {self.tomo_angle_stepsize} degrees"
|
||||
)
|
||||
print(
|
||||
"The angular step of the final (combined) tomogram will be"
|
||||
f" {self.tomo_angle_range / tomo_numberofprojections} degrees"
|
||||
)
|
||||
print(f"The angular step will be {180/tomo_numberofprojections}")
|
||||
self.tomo_angle_stepsize = 180 / tomo_numberofprojections * 8
|
||||
print(f"The angular step in a subtomogram it will be {self.tomo_angle_stepsize}")
|
||||
|
||||
if self.tomo_type == 2:
|
||||
self.golden_ratio_bunch_size = self._get_val(
|
||||
@@ -2313,11 +2477,11 @@ class Flomni(
|
||||
f"{'Dataset ID:':<{padding}}{dataset_id:>{padding}}\n",
|
||||
f"{'Sample Info:':<{padding}}{'Sample Info':>{padding}}\n",
|
||||
f"{'e-account:':<{padding}}{str(account):>{padding}}\n",
|
||||
f"{'Number of projections:':<{padding}}{int(180 / self.tomo_angle_stepsize * 8):>{padding}}\n",
|
||||
f"{'Number of projections:':<{padding}}{int((self.tomo_angle_range / self.tomo_angle_stepsize) * 8):>{padding}}\n",
|
||||
f"{'First scan number:':<{padding}}{self.client.queue.next_scan_number:>{padding}}\n",
|
||||
f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int(180 / self.tomo_angle_stepsize * 8) + 10:>{padding}}\n",
|
||||
f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int((self.tomo_angle_range / self.tomo_angle_stepsize) * 8) + 10:>{padding}}\n",
|
||||
f"{'Current photon energy:':<{padding}}To be implemented\n",
|
||||
#f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
|
||||
# f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
|
||||
f"{'Exposure time:':<{padding}}{self.tomo_countingtime:>{padding}.2f}\n",
|
||||
f"{'Fermat spiral step size:':<{padding}}{self.tomo_shellstep:>{padding}.2f}\n",
|
||||
f"{'FOV:':<{padding}}{fovxy:>{padding}}\n",
|
||||
@@ -2326,7 +2490,9 @@ class Flomni(
|
||||
f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n",
|
||||
]
|
||||
content = "".join(content)
|
||||
user_target = os.path.expanduser(f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
|
||||
user_target = os.path.expanduser(
|
||||
f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf"
|
||||
)
|
||||
with PDFWriter(user_target) as file:
|
||||
file.write(header)
|
||||
file.write(content)
|
||||
@@ -2342,7 +2508,6 @@ class Flomni(
|
||||
# self.client.tomo_progress.send_tomo_progress_message("~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf").send()
|
||||
import csaxs_bec
|
||||
|
||||
|
||||
# Ensure this is a Path object, not a string
|
||||
csaxs_bec_basepath = Path(csaxs_bec.__file__)
|
||||
|
||||
@@ -2350,14 +2515,12 @@ class Flomni(
|
||||
|
||||
# Build the absolute path correctly
|
||||
logo_file = (
|
||||
csaxs_bec_basepath.parent
|
||||
/ "bec_ipython_client"
|
||||
/ "plugins"
|
||||
/ "flomni"
|
||||
/ logo_file_rel
|
||||
csaxs_bec_basepath.parent / "bec_ipython_client" / "plugins" / "flomni" / logo_file_rel
|
||||
).resolve()
|
||||
print(logo_file)
|
||||
bec.messaging.scilog.new().add_attachment(logo_file, width=200).add_text(content.replace("\n", "<br>")).add_tags("tomoscan").send()
|
||||
bec.messaging.scilog.new().add_attachment(logo_file, width=200).add_text(
|
||||
content.replace("\n", "<br>")
|
||||
).add_tags("tomoscan").send()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
@@ -13,8 +13,8 @@ eiger_9:
|
||||
description: Eiger 9M detector
|
||||
deviceClass: csaxs_bec.devices.jungfraujoch.eiger_9m.Eiger9M
|
||||
deviceConfig:
|
||||
detector_distance: 100
|
||||
beam_center: [0, 0]
|
||||
detector_distance: 2200
|
||||
beam_center: [870, 1203]
|
||||
onFailure: raise
|
||||
enabled: True
|
||||
readoutPriority: async
|
||||
|
||||
@@ -1089,47 +1089,47 @@ bim_xbox3_slowrb:
|
||||
|
||||
|
||||
|
||||
# ####################
|
||||
# ### Beamstop diode control for flight tube
|
||||
# ### This requires galilrioft device. On top of that the gain control device is built as well as a slow voltage readback.
|
||||
# ####################
|
||||
####################
|
||||
### Beamstop diode control for flight tube
|
||||
### This requires galilrioft device. On top of that the gain control device is built as well as a slow voltage readback.
|
||||
####################
|
||||
|
||||
# galilrioesft:
|
||||
# description: Galil RIO for remote gain switching and slow reading FlightTube
|
||||
# deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
|
||||
# deviceConfig:
|
||||
# host: galilrioesft.psi.ch
|
||||
# enabled: true
|
||||
# onFailure: retry
|
||||
# readOnly: false
|
||||
# readoutPriority: baseline
|
||||
# connectionTimeout: 20
|
||||
galilrioesft:
|
||||
description: Galil RIO for remote gain switching and slow reading FlightTube
|
||||
deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
|
||||
deviceConfig:
|
||||
host: galilrioesft.psi.ch
|
||||
enabled: true
|
||||
onFailure: retry
|
||||
readOnly: false
|
||||
readoutPriority: baseline
|
||||
connectionTimeout: 20
|
||||
|
||||
# gain_beamstop_diode:
|
||||
# description: Gain control for beamstop flightube
|
||||
# deviceClass: csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl
|
||||
# deviceConfig:
|
||||
# gain_lsb: galilrioesft.digital_out.ch0 # Pin 10 -> Galil ch0
|
||||
# gain_mid: galilrioesft.digital_out.ch1 # Pin 11 -> Galil ch1
|
||||
# gain_msb: galilrioesft.digital_out.ch2 # Pin 12 -> Galil ch2
|
||||
# coupling: galilrioesft.digital_out.ch3 # Pin 13 -> Galil ch3
|
||||
# speed_mode: galilrioesft.digital_out.ch4 # Pin 14 -> Galil ch4
|
||||
# enabled: true
|
||||
# readoutPriority: baseline
|
||||
# onFailure: retry
|
||||
# needs:
|
||||
# - galilrioesft
|
||||
gain_beamstop_diode:
|
||||
description: Gain control for beamstop flightube
|
||||
deviceClass: csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl
|
||||
deviceConfig:
|
||||
gain_lsb: galilrioesft.digital_out.ch0 # Pin 10 -> Galil ch0
|
||||
gain_mid: galilrioesft.digital_out.ch1 # Pin 11 -> Galil ch1
|
||||
gain_msb: galilrioesft.digital_out.ch2 # Pin 12 -> Galil ch2
|
||||
coupling: galilrioesft.digital_out.ch3 # Pin 13 -> Galil ch3
|
||||
speed_mode: galilrioesft.digital_out.ch4 # Pin 14 -> Galil ch4
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
onFailure: retry
|
||||
needs:
|
||||
- galilrioesft
|
||||
|
||||
# beamstop_intensity:
|
||||
# description: Beamstop intensity from Galil analog input ch6
|
||||
# deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
# deviceConfig:
|
||||
# signal: galilrioesft.analog_in.ch0
|
||||
# enabled: true
|
||||
# readoutPriority: baseline
|
||||
# onFailure: retry
|
||||
# needs:
|
||||
# - galilrioesft
|
||||
beamstop_intensity:
|
||||
description: Beamstop intensity from Galil analog input ch6
|
||||
deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
deviceConfig:
|
||||
signal: galilrioesft.analog_in.ch0
|
||||
enabled: true
|
||||
readoutPriority: monitored
|
||||
onFailure: retry
|
||||
needs:
|
||||
- galilrioesft
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -264,6 +264,7 @@ scinx:
|
||||
# bl_smar_stage to use csaxs reference method. assign number according to axis channel
|
||||
init_position: -23
|
||||
bl_smar_stage: 2
|
||||
in_position: -12.5
|
||||
|
||||
poly:
|
||||
description: polarizer holder in OPbox
|
||||
@@ -328,25 +329,25 @@ polrot:
|
||||
# readOnly: false
|
||||
# softwareTrigger: false
|
||||
|
||||
# ####################
|
||||
# ### BPM and polarization diag XBox1 (optics hutch)
|
||||
# ### This requires galilrioop device. On top of that the gain control devices and slow readback devices are built.
|
||||
# ### dev.galilrioop.read() shows the analog inputs
|
||||
# ### another example ...analog_in.ch0.get()
|
||||
# ### dev.galilrioop.read_configuration() shows the digital channels
|
||||
# ### example for direct access dev.galilrioesxbox.digital_out.ch1.put(0)
|
||||
# ####################
|
||||
####################
|
||||
### BPM and polarization diag XBox1 (optics hutch)
|
||||
### This requires galilrioop device. On top of that the gain control devices and slow readback devices are built.
|
||||
### dev.galilrioop.read() shows the analog inputs
|
||||
### another example ...analog_in.ch0.get()
|
||||
### dev.galilrioop.read_configuration() shows the digital channels
|
||||
### example for direct access dev.galilrioesxbox.digital_out.ch1.put(0)
|
||||
####################
|
||||
|
||||
# galilrioop:
|
||||
# description: Galil RIO for remote gain switching and slow reading XBox OP
|
||||
# deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
|
||||
# deviceConfig:
|
||||
# host: galilrioop.psi.ch
|
||||
# enabled: true
|
||||
# onFailure: retry
|
||||
# readOnly: false
|
||||
# readoutPriority: monitored
|
||||
# connectionTimeout: 20
|
||||
galilrioop:
|
||||
description: Galil RIO for remote gain switching and slow reading XBox OP
|
||||
deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
|
||||
deviceConfig:
|
||||
host: galilrioop.psi.ch
|
||||
enabled: true
|
||||
onFailure: retry
|
||||
readOnly: false
|
||||
readoutPriority: monitored
|
||||
connectionTimeout: 20
|
||||
|
||||
# gain_bpm_xbox1:
|
||||
# description: Gain control for BPM XBox1 (OP hutch)
|
||||
@@ -377,42 +378,42 @@ polrot:
|
||||
# needs:
|
||||
# - galilrioop
|
||||
|
||||
# gain_diodes_xbox1:
|
||||
# description: Gain control for diodes (horizontal and vertical) XBox1
|
||||
# deviceClass: csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl
|
||||
# deviceConfig:
|
||||
# gain_lsb: galilrioop.digital_out.ch6 # Pin 10 -> Galil ch0
|
||||
# gain_mid: galilrioop.digital_out.ch7 # Pin 11 -> Galil ch1
|
||||
# gain_msb: galilrioop.digital_out.ch8 # Pin 12 -> Galil ch2
|
||||
# coupling: galilrioop.digital_out.ch9 # Pin 13 -> Galil ch3
|
||||
# speed_mode: galilrioop.digital_out.ch10 # Pin 14 -> Galil ch4
|
||||
# enabled: true
|
||||
# readoutPriority: baseline
|
||||
# onFailure: retry
|
||||
# needs:
|
||||
# - galilrioop
|
||||
gain_diodes_xbox1:
|
||||
description: Gain control for diodes (horizontal and vertical) XBox1
|
||||
deviceClass: csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl
|
||||
deviceConfig:
|
||||
gain_lsb: galilrioop.digital_out.ch6 # Pin 10 -> Galil ch0
|
||||
gain_mid: galilrioop.digital_out.ch7 # Pin 11 -> Galil ch1
|
||||
gain_msb: galilrioop.digital_out.ch8 # Pin 12 -> Galil ch2
|
||||
coupling: galilrioop.digital_out.ch9 # Pin 13 -> Galil ch3
|
||||
speed_mode: galilrioop.digital_out.ch10 # Pin 14 -> Galil ch4
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
onFailure: retry
|
||||
needs:
|
||||
- galilrioop
|
||||
|
||||
# diode_horizontal_xbox1_slowrb:
|
||||
# description: Slow readback diode horizontal XBox OP (polarization diagnostics)
|
||||
# deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
# deviceConfig:
|
||||
# signal: galilrioop.analog_in.ch6
|
||||
# enabled: true
|
||||
# readoutPriority: baseline
|
||||
# onFailure: retry
|
||||
# needs:
|
||||
# - galilrioop
|
||||
diode_horizontal_xbox1_slowrb:
|
||||
description: Slow readback diode horizontal XBox OP (polarization diagnostics)
|
||||
deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
deviceConfig:
|
||||
signal: galilrioop.analog_in.ch6
|
||||
enabled: true
|
||||
readoutPriority: monitored
|
||||
onFailure: retry
|
||||
needs:
|
||||
- galilrioop
|
||||
|
||||
# diode_vertical_xbox1_slowrb:
|
||||
# description: Slow readback diode vertical XBox OP (polarization diagnostics)
|
||||
# deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
# deviceConfig:
|
||||
# signal: galilrioop.analog_in.ch7
|
||||
# enabled: true
|
||||
# readoutPriority: baseline
|
||||
# onFailure: retry
|
||||
# needs:
|
||||
# - galilrioop
|
||||
diode_vertical_xbox1_slowrb:
|
||||
description: Slow readback diode vertical XBox OP (polarization diagnostics)
|
||||
deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
|
||||
deviceConfig:
|
||||
signal: galilrioop.analog_in.ch7
|
||||
enabled: true
|
||||
readoutPriority: monitored
|
||||
onFailure: retry
|
||||
needs:
|
||||
- galilrioop
|
||||
|
||||
sl3xi:
|
||||
description: "slit 2 (optics) x ring"
|
||||
@@ -525,3 +526,339 @@ sl3ys:
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvbendu:
|
||||
description: "KB Vertical Focusing Mirror, bender upstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:BNDU"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvbendd:
|
||||
description: "KB Vertical Focusing Mirror, bender downstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:BNDD"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtrx:
|
||||
description: "KB Vertical Focusing Mirror, translation X"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRX"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtry:
|
||||
description: "KB Vertical Focusing Mirror, translation Y"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRY"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvyaw:
|
||||
description: "KB Vertical Focusing Mirror, yaw"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:YAW"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvroll:
|
||||
description: "KB Vertical Focusing Mirror, roll"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:ROLL"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvpitch:
|
||||
description: "KB Vertical Focusing Mirror, pitch"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:PITCH"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtrxu:
|
||||
description: "KB Vertical Focusing Mirror, translation X upstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRXU"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtrxd:
|
||||
description: "KB Vertical Focusing Mirror, translation X downstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRXD"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtryur:
|
||||
description: "KB Vertical Focusing Mirror, translation Y upstream ring"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRYUR"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtryw:
|
||||
description: "KB Vertical Focusing Mirror, translation Y wall"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRYW"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbvtrydr:
|
||||
description: "KB Vertical Focusing Mirror, translation Y downstream ring"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-VFM:TRYDR"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhbendu:
|
||||
description: "KB Horizontal Focusing Mirror, bender upstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:BNDU"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhbendd:
|
||||
description: "KB Horizontal Focusing Mirror, bender downstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:BNDD"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtrx:
|
||||
description: "KB Horizontal Focusing Mirror, translation X"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRX"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtry:
|
||||
description: "KB Horizontal Focusing Mirror, translation Y"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRY"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhyaw:
|
||||
description: "KB Horizontal Focusing Mirror, yaw"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:YAW"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhroll:
|
||||
description: "KB Horizontal Focusing Mirror, roll"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:ROLL"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhpitch:
|
||||
description: "KB Horizontal Focusing Mirror, pitch"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:PITCH"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtrxu:
|
||||
description: "KB Horizontal Focusing Mirror, translation X upstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRXU"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtrxd:
|
||||
description: "KB Horizontal Focusing Mirror, translation X downstream"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRXD"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtryuw:
|
||||
description: "KB Horizontal Focusing Mirror, translation Y upstream wall"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRYUW"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtryr:
|
||||
description: "KB Horizontal Focusing Mirror, translation Y ring"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRYR"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
kbhtrydw:
|
||||
description: "KB Horizontal Focusing Mirror, translation Y downstream wall"
|
||||
deviceClass: ophyd_devices.EpicsMotorEC
|
||||
deviceConfig:
|
||||
prefix: "X12SA-OP-HFM:TRYDW"
|
||||
onFailure: raise
|
||||
enabled: true
|
||||
readoutPriority: baseline
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
deviceTags:
|
||||
- cSAXS
|
||||
- optics
|
||||
|
||||
@@ -437,7 +437,7 @@ cam_xeye:
|
||||
description: Camera flOMNI Xray eye ID1
|
||||
deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
|
||||
deviceConfig:
|
||||
camera_id: 1
|
||||
camera_id: 11
|
||||
bits_per_pixel: 24
|
||||
num_rotation_90: 3
|
||||
transpose: false
|
||||
@@ -511,33 +511,33 @@ calculated_signal:
|
||||
############################################################
|
||||
#################### OMNY Pandabox #########################
|
||||
############################################################
|
||||
omny_panda:
|
||||
readoutPriority: async
|
||||
deviceClass: csaxs_bec.devices.panda_box.panda_box_omny.PandaBoxOMNY
|
||||
deviceConfig:
|
||||
host: omny-panda.psi.ch
|
||||
signal_alias:
|
||||
FMC_IN.VAL1.Min: cap_voltage_fzp_y_min
|
||||
FMC_IN.VAL1.Max: cap_voltage_fzp_y_max
|
||||
FMC_IN.VAL1.Mean: cap_voltage_fzp_y_mean
|
||||
FMC_IN.VAL2.Min: cap_voltage_fzp_x_min
|
||||
FMC_IN.VAL2.Max: cap_voltage_fzp_x_max
|
||||
FMC_IN.VAL2.Mean: cap_voltage_fzp_x_mean
|
||||
INENC1.VAL.Max: interf_st_fzp_y_max
|
||||
INENC1.VAL.Mean: interf_st_fzp_y_mean
|
||||
INENC1.VAL.Min: interf_st_fzp_y_min
|
||||
INENC2.VAL.Max: interf_st_fzp_x_max
|
||||
INENC2.VAL.Mean: interf_st_fzp_x_mean
|
||||
INENC2.VAL.Min: interf_st_fzp_x_min
|
||||
INENC3.VAL.Max: interf_st_rotz_max
|
||||
INENC3.VAL.Mean: interf_st_rotz_mean
|
||||
INENC3.VAL.Min: interf_st_rotz_min
|
||||
INENC4.VAL.Max: interf_st_rotx_max
|
||||
INENC4.VAL.Mean: interf_st_rotx_mean
|
||||
INENC4.VAL.Min: interf_st_rotx_min
|
||||
PCAP.GATE_DURATION.Value: pcap_gate_duration_value
|
||||
deviceTags:
|
||||
- detector
|
||||
enabled: true
|
||||
readOnly: false
|
||||
softwareTrigger: false
|
||||
# omny_panda:
|
||||
# readoutPriority: async
|
||||
# deviceClass: csaxs_bec.devices.panda_box.panda_box_omny.PandaBoxOMNY
|
||||
# deviceConfig:
|
||||
# host: omny-panda.psi.ch
|
||||
# signal_alias:
|
||||
# FMC_IN.VAL1.Min: cap_voltage_fzp_y_min
|
||||
# FMC_IN.VAL1.Max: cap_voltage_fzp_y_max
|
||||
# FMC_IN.VAL1.Mean: cap_voltage_fzp_y_mean
|
||||
# FMC_IN.VAL2.Min: cap_voltage_fzp_x_min
|
||||
# FMC_IN.VAL2.Max: cap_voltage_fzp_x_max
|
||||
# FMC_IN.VAL2.Mean: cap_voltage_fzp_x_mean
|
||||
# INENC1.VAL.Max: interf_st_fzp_y_max
|
||||
# INENC1.VAL.Mean: interf_st_fzp_y_mean
|
||||
# INENC1.VAL.Min: interf_st_fzp_y_min
|
||||
# INENC2.VAL.Max: interf_st_fzp_x_max
|
||||
# INENC2.VAL.Mean: interf_st_fzp_x_mean
|
||||
# INENC2.VAL.Min: interf_st_fzp_x_min
|
||||
# INENC3.VAL.Max: interf_st_rotz_max
|
||||
# INENC3.VAL.Mean: interf_st_rotz_mean
|
||||
# INENC3.VAL.Min: interf_st_rotz_min
|
||||
# INENC4.VAL.Max: interf_st_rotx_max
|
||||
# INENC4.VAL.Mean: interf_st_rotx_mean
|
||||
# INENC4.VAL.Min: interf_st_rotx_min
|
||||
# PCAP.GATE_DURATION.Value: pcap_gate_duration_value
|
||||
# deviceTags:
|
||||
# - detector
|
||||
# enabled: true
|
||||
# readOnly: false
|
||||
# softwareTrigger: false
|
||||
|
||||
@@ -18,4 +18,7 @@ fsh:
|
||||
readoutPriority: monitored
|
||||
|
||||
flomni:
|
||||
- !include ../ptycho_flomni.yaml
|
||||
- !include ../ptycho_flomni.yaml
|
||||
|
||||
machine:
|
||||
- !include ../machine.yml
|
||||
|
||||
@@ -36,6 +36,7 @@ import os
|
||||
import time
|
||||
from typing import TYPE_CHECKING, Literal
|
||||
|
||||
import numpy as np
|
||||
import yaml
|
||||
from bec_lib.file_utils import get_full_path
|
||||
from bec_lib.logger import bec_logger
|
||||
@@ -117,6 +118,8 @@ class Eiger(PSIDeviceBase):
|
||||
self._full_path = ""
|
||||
self._num_triggers = 0
|
||||
self._wait_for_on_complete = 20 # seconds
|
||||
# Initial incident energy in keV, if restarted None
|
||||
self._incident_energy: float | None = None
|
||||
if self.device_manager is not None:
|
||||
self.device_manager: DeviceManagerDS
|
||||
self.scan_parameters: ScanServerScanInfo | None = None
|
||||
@@ -272,7 +275,25 @@ class Eiger(PSIDeviceBase):
|
||||
|
||||
# TODO: Check mono energy from device in BEC
|
||||
# Setting incident energy in keV
|
||||
incident_energy = 12.0
|
||||
|
||||
try:
|
||||
incident_energy = self._get_beam_energy(self.device_manager)
|
||||
if self._incident_energy is None:
|
||||
self._incident_energy = round(float(incident_energy), 3)
|
||||
elif not np.isclose(
|
||||
self._incident_energy, incident_energy, atol=0.01
|
||||
): # 10 keV tolerance
|
||||
logger.warning(
|
||||
f"Incident energy changed from {self._incident_energy} keV to {incident_energy} keV for device {self.name}. "
|
||||
)
|
||||
self._incident_energy = round(float(incident_energy), 3)
|
||||
except Exception as e:
|
||||
logger.warning(f"Failed to set up beam energy for {self.name}: {e}")
|
||||
incident_energy = 12.0 # default to 12 keV if error occurs
|
||||
self._incident_energy = round(float(incident_energy), 3)
|
||||
|
||||
logger.info(f"Device {self.name} uses incident energy of {self._incident_energy} keV.")
|
||||
|
||||
# Setting up exp_time and num_triggers acquisition parameter
|
||||
exp_time = self.scan_parameters.exp_time
|
||||
if exp_time <= self._readout_time: # Exp_time must be at least the readout time
|
||||
@@ -417,3 +438,20 @@ class Eiger(PSIDeviceBase):
|
||||
self.jfj_preview_client.stop()
|
||||
self.on_stop()
|
||||
return super().on_destroy()
|
||||
|
||||
def _get_beam_energy(self, device_manager: DeviceManagerDS) -> float:
|
||||
"""
|
||||
Fetch the beam energy from the device manager.
|
||||
|
||||
Args:
|
||||
device_manager (DeviceManagerDS): The device manager to fetch the beam energy from.
|
||||
|
||||
Returns:
|
||||
float: The beam energy in keV.
|
||||
"""
|
||||
if hasattr(device_manager, "devices") and hasattr(device_manager.devices, "ccm_energy"):
|
||||
energy = device_manager.devices.ccm_energy.read()[
|
||||
device_manager.devices.ccm_energy.name
|
||||
]["value"]
|
||||
|
||||
return energy
|
||||
|
||||
Reference in New Issue
Block a user