Coverage for src/pytribeam/workflow.py: 68%
188 statements
« prev ^ index » next coverage.py v7.6.1, created at 2026-09-03 19:02 +0000
1#!/usr/bin/python3
2"""High-level experiment workflow orchestration.
4This module coordinates complete `pytribeam` serial-sectioning experiments from
5a YAML configuration file. It performs pre-flight validation, initializes the
6microscope and experiment settings, prepares the log file, retracts insertable
7devices, moves the stage to each step's slice-dependent position, dispatches the
8configured operation, records position metadata, and runs the main slice/step
9experiment loop.
11Most users should enter this module through `run_experiment_cli`, which is used
12by the command-line interface. Programmatic workflows may call
13`setup_experiment` and `perform_step` directly when more control over execution
14is needed.
16## Typical usage
18Run an experiment from a YAML configuration file:
20```python
21from pathlib import Path
22from pytribeam import workflow
24workflow.run_experiment_cli(
25 start_slice=1,
26 start_step=1,
27 yml_path=Path("experiment.yml"),
28)
29```
31Set up an experiment and manually perform a step:
33```python
34from pathlib import Path
35from pytribeam import workflow
37experiment = workflow.setup_experiment(Path("experiment.yml"))
39workflow.perform_step(
40 slice_number=1,
41 step_number=1,
42 experiment_settings=experiment,
43)
44```
46## Main entry points
48- `run_experiment_cli`: run the full command-line experiment loop.
49- `setup_experiment`: validate configuration, create the log file, link the
50 stage, and retract insertable devices.
51- `pre_flight_check`: parse and validate the YAML file, connect to hardware, and
52 construct `tbt.ExperimentSettings`.
53- `perform_step`: execute one configured step for one slice.
54- `perform_operation`: dispatch operation execution based on the step settings
55 type.
56- `ebsd_eds_conflict_free`: validate EBSD/EDS step compatibility constraints.
58## Workflow sequence
60The command-line workflow proceeds as follows:
621. Read the YAML configuration file.
632. Determine the supported YAML schema version.
643. Parse and validate general experiment settings.
654. Enable or validate EBSD/EDS control when configured.
665. Connect to the microscope.
676. Parse and validate the configured step sequence.
687. Check for unsupported EBSD/EDS step conflicts.
698. Create the experiment log file.
709. Link the stage to free working distance.
7110. Retract all available and enabled insertable devices.
7211. Log the experiment configuration.
7312. Iterate over slices and steps.
7413. For each executed step:
75 - log the pre-operation stage position,
76 - retract insertable devices,
77 - move to the step start position,
78 - perform the step operation,
79 - log the post-operation stage position,
80 - retract insertable devices again.
8114. Disconnect from the microscope when the experiment completes.
83## Operation dispatch
85`perform_operation` is implemented with `functools.singledispatch`. Dispatch is
86based on the type of `step.operation_settings`.
88| Settings type | Operation |
89| --- | --- |
90| `tbt.ImageSettings` | Acquire an image using `pytribeam.image.image_operation`. |
91| `tbt.FIBSettings` | Acquire an associated ion image, then run FIB milling. |
92| `tbt.LaserSettings` | Run a laser milling operation. |
93| `tbt.EBSDSettings` | Insert EBSD, optionally insert EDS, measure current, image, and map EBSD. |
94| `tbt.EDSSettings` | Insert EDS, measure current, image, and map EDS. |
95| `tbt.CustomSettings` | Execute a user-specified external script. |
97Unsupported operation settings types raise `NotImplementedError`.
99## Slice and step numbering
101Slice and step numbers are user-facing and one-indexed. Step sequences are stored
102internally as Python lists, so `perform_step` converts the requested
103`step_number` to a zero-indexed list index.
105Step frequency is evaluated relative to slice 1. A step with frequency `n` runs
106on slice 1 and then every `n` slices thereafter.
108## Logging
110The workflow logs:
112- experiment settings at the beginning of the run,
113- stage position before each executed step,
114- stage position after each executed step,
115- specimen current for EBSD and EDS operations,
116- laser power before and after laser operations.
118Dataset names and HDF5 dtypes are defined in `pytribeam.constants.Constants`.
120## Safety behavior
122Before and after each step, all available and enabled insertable devices are
123retracted. Stage movement is delegated to `pytribeam.stage`, which checks stage
124limits and verifies final position. Detector insertion, EBSD/EDS control, laser
125patterning, FIB milling, and imaging are delegated to their subsystem modules.
127> **Warning**
128>
129> Functions in this module orchestrate microscope motion, detector insertion,
130> FIB milling, laser firing, EBSD/EDS mapping, and external script execution.
131> Confirm that the configuration file, microscope state, sample geometry,
132> detector positions, laser state, and stage limits are safe before running an
133> experiment.
135<hr style="height: 12px; background-color: #333; border: none;">
136"""
138__all__ = [
139 "perform_operation",
140 "ebsd_eds_conflict_free",
141 "pre_flight_check",
142 "setup_experiment",
143 "perform_step",
144 "run_experiment_cli",
145]
147# Default python modules
148# from functools import singledispatch
149from pathlib import Path
150import sys
151from typing import List
152from functools import singledispatch
153import subprocess
155# 3rd party module
157# Local scripts
158import pytribeam.constants as cs
159import pytribeam.insertable_devices as devices
160import pytribeam.factory as factory
161import pytribeam.types as tbt
162import pytribeam.utilities as ut
163import pytribeam.stage as stage
164import pytribeam.log as log
165import pytribeam.laser as laser
166import pytribeam.image as img
167import pytribeam.fib as fib
170@singledispatch
171def perform_operation(
172 step_settings,
173 step: tbt.Step,
174 general_settings: tbt.GeneralSettings,
175 slice_number: int,
176) -> bool:
177 """
178 Perform the operation for the specified step settings.
180 This function performs the operation for the specified step settings, including validation.
182 ## Parameters
184 - `step_settings` (`Any`): The step settings for the operation.
185 - `step` (`tbt.Step`): The step object containing the operation settings.
186 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
187 - `slice_number` (`int`): The slice number for the operation.
189 ## Returns
191 - `bool`: True if the operation is performed successfully.
193 ## Raises
195 - `NotImplementedError`: If no handler is available for the provided step settings type.
196 """
197 _ = step_settings
198 __ = step
199 ___ = general_settings
200 ____ = slice_number
201 raise NotImplementedError(f"No handler for type {type(step_settings)}")
204@perform_operation.register
205def _perform_image_operation(
206 step_settings: tbt.ImageSettings,
207 step: tbt.Step,
208 general_settings: tbt.GeneralSettings,
209 slice_number: int,
210) -> bool:
211 """
212 Perform the image operation for the specified step settings.
214 ## Parameters
216 - `step_settings` (`tbt.ImageSettings`): The image settings for the operation.
217 - `step` (`tbt.Step`): The step object containing the operation settings.
218 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
219 - `slice_number` (`int`): The slice number for the operation.
221 ## Returns
223 - `bool`: True if the image operation is performed successfully.
224 """
225 return img.image_operation(
226 step=step,
227 image_settings=step.operation_settings,
228 general_settings=general_settings,
229 slice_number=slice_number,
230 )
233@perform_operation.register
234def _perform_fib_operation(
235 step_settings: tbt.FIBSettings,
236 step: tbt.Step,
237 general_settings: tbt.GeneralSettings,
238 slice_number: int,
239) -> bool:
240 """
241 Perform the FIB operation for the specified step settings.
243 ## Parameters
245 - `step_settings` (`tbt.FIBSettings`): The FIB settings for the operation.
246 - `step` (`tbt.Step`): The step object containing the operation settings.
247 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
248 - `slice_number` (`int`): The slice number for the operation.
250 ## Returns
252 - `bool`: True if the FIB operation is performed successfully.
253 """
254 # collect image
255 image_step = tbt.Step(
256 type=tbt.StepType.IMAGE,
257 name=step.name,
258 number=step.number,
259 frequency=step.frequency,
260 stage=step.stage,
261 operation_settings=step_settings.image,
262 )
263 type(image_step.operation_settings)
264 perform_operation(
265 image_step.operation_settings,
266 step=image_step,
267 general_settings=general_settings,
268 slice_number=slice_number,
269 )
270 # mill pattern
271 fib.mill_operation(
272 step=step,
273 fib_settings=step_settings,
274 general_settings=general_settings,
275 slice_number=slice_number,
276 )
278 return True
281@perform_operation.register
282def _perform_custom_operation(
283 step_settings: tbt.CustomSettings,
284 step: tbt.Step,
285 general_settings: tbt.GeneralSettings,
286 slice_number: int,
287) -> bool:
288 """
289 Perform the custom operation for the specified step settings.
291 ## Parameters
293 - `step_settings` (`tbt.CustomSettings`): The custom settings for the operation.
294 - `step` (`tbt.Step`): The step object containing the operation settings.
295 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
296 - `slice_number` (`int`): The slice number for the operation.
298 ## Returns
300 - `bool`: True if the custom operation is performed successfully.
301 """
302 # dump out .yml with experiment info
303 slice_info_path = Path.joinpath(general_settings.exp_dir, "slice_info.yml")
304 db = {"exp_dir": str(general_settings.exp_dir), "slice_number": slice_number}
305 ut.dict_to_yml(db=db, file_path=slice_info_path)
307 output = subprocess.run(
308 [step_settings.executable_path, step_settings.script_path],
309 capture_output=True,
310 )
311 stdout, stderr = output.stdout.decode("utf-8"), output.stderr.decode("utf-8")
312 if stdout: 312 ↛ 315line 312 didn't jump to line 315 because the condition on line 312 was always true
313 print(f"\nCustom script output: {stdout}\n")
315 if output.returncode != 0: 315 ↛ 316line 315 didn't jump to line 316 because the condition on line 315 was never true
316 if stderr:
317 print(f"\nCustom script errors: {stderr}\n")
318 raise ValueError(
319 f"Subprocess call for script {step_settings.script_path} using executable {step_settings.executable_path} did not execute correctly."
320 )
322 slice_info_path.unlink()
323 return True
326@perform_operation.register
327def _perform_ebsd_operation(
328 step_settings: tbt.EBSDSettings,
329 step: tbt.Step,
330 general_settings: tbt.GeneralSettings,
331 slice_number: int,
332) -> bool:
333 """
334 Perform the EBSD operation for the specified step settings.
336 ## Parameters
338 - `step_settings` (`tbt.EBSDSettings`): The EBSD settings for the operation.
339 - `step` (`tbt.Step`): The step object containing the operation settings.
340 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
341 - `slice_number` (`int`): The slice number for the operation.
343 ## Returns
345 - `bool`: True if the EBSD operation is performed successfully.
346 """
347 image_settings = step_settings.image
348 microscope = image_settings.microscope
350 # insert detector
351 devices.insert_EBSD(microscope=microscope)
352 if step_settings.enable_eds:
353 devices.insert_EDS(microscope=microscope)
355 # measure and log specimen current
356 found_current_na = devices.specimen_current(microscope=microscope)
357 log.specimen_current(
358 step_number=step.number,
359 step_name=step.name,
360 slice_number=slice_number,
361 log_filepath=general_settings.log_filepath,
362 dataset_name=cs.Constants.specimen_current_dataset_name,
363 specimen_current_na=found_current_na,
364 )
366 # take image
367 img.image_operation(
368 step=step,
369 image_settings=image_settings,
370 general_settings=general_settings,
371 slice_number=slice_number,
372 )
374 # set dynamic focus/tilt correction
375 dynamic_focus = image_settings.beam.settings.dynamic_focus
376 tilt_correction = image_settings.beam.settings.tilt_correction
377 img.beam_angular_correction(
378 microscope=microscope,
379 dynamic_focus=dynamic_focus,
380 tilt_correction=tilt_correction,
381 )
383 # take map
384 laser.map_ebsd()
386 # retract detector(s)
387 devices.retract_EBSD(microscope=microscope)
388 if step_settings.enable_eds: 388 ↛ 389, 388 ↛ 3912 missed branches: 1) line 388 didn't jump to line 389 because the condition on line 388 was never true, 2) line 388 didn't jump to line 391 because the condition on line 388 was always true
389 devices.retract_EDS(microscope=microscope)
391 return True
394@perform_operation.register
395def _perform_eds_operation(
396 step_settings: tbt.EDSSettings,
397 step: tbt.Step,
398 general_settings: tbt.GeneralSettings,
399 slice_number: int,
400) -> bool:
401 """
402 Perform the EDS operation for the specified step settings.
404 ## Parameters
406 - `step_settings` (`tbt.EDSSettings`): The EDS settings for the operation.
407 - `step` (`tbt.Step`): The step object containing the operation settings.
408 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
409 - `slice_number` (`int`): The slice number for the operation.
411 ## Returns
413 - `bool`: True if the EDS operation is performed successfully.
414 """
415 image_settings = step_settings.image
416 microscope = image_settings.microscope
418 # insert detector
419 devices.insert_EDS(microscope=microscope)
421 # measure and log specimen current
422 found_current_na = devices.specimen_current(microscope=microscope)
423 log.specimen_current(
424 step_number=step.number,
425 step_name=step.name,
426 slice_number=slice_number,
427 log_filepath=general_settings.log_filepath,
428 dataset_name=cs.Constants.specimen_current_dataset_name,
429 specimen_current_na=found_current_na,
430 )
432 # take image
433 img.image_operation(
434 step=step,
435 image_settings=image_settings,
436 general_settings=general_settings,
437 slice_number=slice_number,
438 )
440 # set dynamic focus/tilt correction
441 dynamic_focus = image_settings.beam.settings.dynamic_focus
442 tilt_correction = image_settings.beam.settings.tilt_correction
443 img.beam_angular_correction(
444 microscope=microscope,
445 dynamic_focus=dynamic_focus,
446 tilt_correction=tilt_correction,
447 )
449 # take map
450 laser.map_eds()
452 # retract detector
453 devices.retract_EDS(microscope=microscope)
455 return True
458@perform_operation.register
459def _perform_laser_operation(
460 step_settings: tbt.LaserSettings,
461 step: tbt.Step,
462 general_settings: tbt.GeneralSettings,
463 slice_number: int,
464) -> bool:
465 """
466 Perform the laser operation for the specified step settings.
468 ## Parameters
470 - `step_settings` (`tbt.LaserSettings`): The laser settings for the operation.
471 - `step` (`tbt.Step`): The step object containing the operation settings.
472 - `general_settings` (`tbt.GeneralSettings`): The general settings object.
473 - `slice_number` (`int`): The slice number for the operation.
475 ## Returns
477 - `bool`: True if the laser operation is performed successfully.
478 """
479 return laser.laser_operation(
480 step=step,
481 general_settings=general_settings,
482 slice_number=slice_number,
483 )
486def ebsd_eds_conflict_free(step_sequence: List[tbt.Step]) -> bool:
487 """
488 Check if the step sequence is free of EBSD and EDS conflicts.
490 This function checks if the step sequence is free of EBSD and EDS conflicts.
492 ## Parameters
494 - `step_sequence` (`List[tbt.Step]`): The step sequence to check.
496 ## Returns
498 - `bool`: True if the step sequence is free of EBSD and EDS conflicts.
500 ## Raises
502 - `ValueError`: If an EBSD or EDS conflict is found in the step sequence.
503 """
504 EBSD_EDS_conflict_msg = "Due to current limitations in 3rd party EBSD/EDS integration with the TriBeam, only one of these step types is allowed as only one map can be configured for an experiment, but EDS can be configured to be included with an EBSD type step. See User Guide for more details."
506 found_EBSD = False
507 found_EDS = False
509 for step in step_sequence:
510 if step.type == tbt.StepType.EBSD: 510 ↛ 511line 510 didn't jump to line 511 because the condition on line 510 was never true
511 if found_EDS == True:
512 raise ValueError(
513 f"EBSD step found in sequence after EDS step was already defined. {EBSD_EDS_conflict_msg}"
514 )
515 found_EBSD = True
517 if step.type == tbt.StepType.EDS: 517 ↛ 518line 517 didn't jump to line 518 because the condition on line 517 was never true
518 if found_EBSD == True:
519 raise ValueError(
520 f"EDS step found in sequence after EBSD step was already defined. {EBSD_EDS_conflict_msg}"
521 )
522 found_EDS = True
524 return True
527def pre_flight_check(yml_path: Path) -> tbt.ExperimentSettings:
528 """
529 Perform a pre-flight check for the experiment.
531 This function performs a pre-flight check for the experiment by validating the YAML configuration, connecting to the microscope, and validating the step sequence.
533 ## Parameters
535 - `yml_path` (`Path`): The path to the YAML configuration file.
537 ## Returns
539 - `tbt.ExperimentSettings`: The validated experiment settings.
541 ## Raises
543 - `SystemError`: If there are issues with the EBSD or EDS camera, or if the laser control is not enabled.
544 - `ValueError`: If the step sequence is not parsed correctly or if there are EBSD/EDS conflicts.
545 """
546 # get configuration from yml
547 yml_version = ut.yml_version(yml_path)
548 experiment_settings = ut.yml_to_dict(
549 yml_path_file=yml_path,
550 version=yml_version,
551 required_keys=(
552 "general",
553 "config_file_version",
554 ),
555 )
556 yml_format = ut.yml_format(version=yml_version)
558 # get general settings and validate them
559 general_db = ut.general_settings(
560 exp_settings=experiment_settings, yml_format=yml_format
561 )
562 general_settings = factory.general(
563 general_db=general_db,
564 yml_format=yml_format,
565 )
567 # whether to enable EBSD and EDS control
568 enable_EBSD = ut.enable_external_device(general_settings.EBSD_OEM)
569 enable_EDS = ut.enable_external_device(general_settings.EDS_OEM)
570 if enable_EBSD: 570 ↛ 571line 570 didn't jump to line 571 because the condition on line 570 was never true
571 status = devices.connect_EBSD()
572 if status == tbt.RetractableDeviceState.ERROR: 572 ↛ 573, 572 ↛ 5742 missed branches: 1) line 572 didn't jump to line 573 because the condition on line 572 was never true, 2) line 572 didn't jump to line 574 because the condition on line 572 was always true
573 raise SystemError("EBSD camera is connected but in error state.")
574 if enable_EDS: 574 ↛ 575line 574 didn't jump to line 575 because the condition on line 574 was never true
575 status = devices.connect_EDS()
576 if status == tbt.RetractableDeviceState.ERROR:
577 raise SystemError("EDS camera is connected but in error state.")
579 # connect to microscope:
580 connection = general_settings.connection
581 microscope = tbt.Microscope()
582 ut.connect_microscope(
583 microscope=microscope,
584 quiet_output=True,
585 connection_host=connection.host,
586 connection_port=connection.port,
587 )
589 # get step_count and validate settings
590 num_steps = ut.step_count(exp_settings=experiment_settings, yml_format=yml_format)
591 step_sequence = [] # empty list of tbt.Step type objects
592 for step in range(1, num_steps + 1):
593 step_name, step_settings = ut.step_settings(
594 exp_settings=experiment_settings,
595 step_number_key=yml_format.step_number_key,
596 step_number_val=step,
597 yml_format=yml_format,
598 )
599 if not step_name: 599 ↛ 600line 599 didn't jump to line 600 because the condition on line 599 was never true
600 raise KeyError(
601 f"Step name for step {step} of {num_steps} is empty. Please provide a unique name for each step in your configuration."
602 )
603 step_type = ut.step_type(
604 settings=step_settings,
605 yml_format=yml_format,
606 )
608 # validate connections for specific step types
609 if step_type == tbt.StepType.LASER: 609 ↛ 610line 609 didn't jump to line 610 because the condition on line 609 was never true
610 laser_enabled = laser.laser_connected()
611 if not laser_enabled: 611 ↛ 615line 611 didn't jump to line 615 because the condition on line 611 was always true
612 raise SystemError(
613 f"Step name '{step_name}' is a Laser step type but Laser control is not currently enabled. Ensure TFS laser API is installed, Laser Control application is open."
614 )
615 if (step_type == tbt.StepType.EDS) and (not enable_EDS): 615 ↛ 616line 615 didn't jump to line 616 because the condition on line 615 was never true
616 raise SystemError(
617 f"Step name '{step_name}' is an EDS step type but EDS control is not currently enabled."
618 )
619 if (step_type == tbt.StepType.EBSD) and (not enable_EBSD): 619 ↛ 620line 619 didn't jump to line 620 because the condition on line 619 was never true
620 raise SystemError(
621 f"Step name '{step_name}' is an EBSD step type but EDS control is not currently enabled."
622 )
623 # if (step_type == tbt.StepType.EBSD_EDS) and (
624 # (not enable_EBSD) or (not enable_EDS)
625 # ):
626 # raise SystemError(
627 # f"Step name '{step_name}' is an EBSD_EDS step type but EBSD and EDS control are not both currently enabled."
628 # )
629 # create the step settings
630 step = factory.step(
631 microscope=microscope,
632 step_name=step_name,
633 step_settings=step_settings,
634 general_settings=general_settings,
635 yml_format=yml_format,
636 )
638 step_sequence.append(step)
640 if len(step_sequence) != num_steps: 640 ↛ 641line 640 didn't jump to line 641 because the condition on line 640 was never true
641 raise ValueError(
642 f"Settings not parsed correctly, expected {num_steps} but only {len(step_sequence)} have been parsed."
643 )
645 # ensure only EBSD or EDS step type exists
646 ebsd_eds_conflict_free(step_sequence=step_sequence)
648 experiment_settings = tbt.ExperimentSettings(
649 microscope=microscope,
650 general_settings=general_settings,
651 step_sequence=step_sequence,
652 enable_EBSD=enable_EBSD,
653 enable_EDS=enable_EDS,
654 )
655 # print("Pre-flight check complete.")
656 return experiment_settings
659def setup_experiment(
660 yml_path: Path,
661) -> tbt.ExperimentSettings:
662 """
663 Set up the experiment based on the YAML configuration.
665 This function sets up the experiment by validating the YAML configuration, creating the log file, linking the stage, and retracting all devices.
667 ## Parameters
669 - `yml_path` (`Path`): The path to the YAML configuration file.
671 ## Returns
673 - `tbt.ExperimentSettings`: The experiment settings.
674 """
675 # validate yml
676 experiment_settings = pre_flight_check(yml_path=yml_path)
678 log_filepath = experiment_settings.general_settings.log_filepath
679 log.create_file(log_filepath)
681 # link stage to free working distance
682 experiment_settings.microscope.specimen.stage.link()
684 # retract all devices
685 print("\tRetracting all devices...")
686 devices.retract_all_devices(
687 microscope=experiment_settings.microscope,
688 enable_EBSD=experiment_settings.enable_EBSD,
689 enable_EDS=experiment_settings.enable_EDS,
690 )
692 return experiment_settings
695def perform_step(
696 slice_number: int,
697 step_number: int,
698 experiment_settings: tbt.ExperimentSettings,
699) -> None:
700 """
701 Perform a step in the experiment.
703 This function performs a step in the experiment based on the slice number, step number, and experiment settings.
705 ## Parameters
707 - `slice_number` (`int`): The slice number for the step.
708 - `step_number` (`int`): The step number for the experiment.
709 - `experiment_settings` (`tbt.ExperimentSettings`): The experiment settings.
711 ## Returns
713 - `bool`: True if the step is performed successfully.
714 """
715 # # breakout experiment settings elements
716 microscope = experiment_settings.microscope
717 general_settings = experiment_settings.general_settings
718 step_sequence = experiment_settings.step_sequence
719 enable_EBSD = experiment_settings.enable_EBSD
720 enable_EDS = experiment_settings.enable_EDS
722 # get operation settings, execute operation.
723 operation = step_sequence[step_number - 1] # list is 0-indexed
724 print(
725 f"Slice {slice_number}, Step {step_number} of {general_settings.step_count}, '{operation.name}', a {operation.type.value} type step."
726 )
727 # slices start at 1, perform all steps on slice 1.
728 if (slice_number - 1) % operation.frequency != 0: 728 ↛ 729line 728 didn't jump to line 729 because the condition on line 728 was never true
729 print(
730 f"\tStep frequency is every {operation.frequency} slices, starting on slice 1. Skipping step on this slice.\n"
731 )
732 return
734 # log step_start position
735 log.position(
736 step_number=step_number,
737 step_name=operation.name,
738 slice_number=slice_number,
739 log_filepath=general_settings.log_filepath,
740 dataset_name=cs.Constants.pre_position_dataset_name,
741 current_position=factory.active_stage_position_settings(
742 microscope=microscope,
743 ),
744 )
746 # retract all devices
747 print("\tRetracting all devices...")
748 # with ut.nostdout():
749 devices.retract_all_devices(
750 microscope=microscope,
751 enable_EBSD=enable_EBSD,
752 enable_EDS=enable_EDS,
753 )
754 print("\tDevices retracted.")
756 # move stage to starting position for slice
757 stage.step_start_position(
758 microscope=microscope,
759 slice_number=slice_number,
760 operation=operation,
761 general_settings=general_settings,
762 )
764 # perform specific operation
765 perform_operation(
766 operation.operation_settings,
767 step=operation,
768 general_settings=general_settings,
769 slice_number=slice_number,
770 )
772 # log step end position
773 log.position(
774 step_number=step_number,
775 step_name=operation.name,
776 slice_number=slice_number,
777 log_filepath=general_settings.log_filepath,
778 dataset_name=cs.Constants.post_position_dataset_name,
779 current_position=factory.active_stage_position_settings(
780 microscope=microscope,
781 ),
782 )
784 # retract all devices
785 print("\tRetracting all devices...")
786 # with ut.nostdout():
787 devices.retract_all_devices(
788 microscope=microscope,
789 enable_EBSD=enable_EBSD,
790 enable_EDS=enable_EDS,
791 )
792 print("\tDevices retracted. Step Complete.\n")
795def run_experiment_cli(
796 start_slice: int,
797 start_step: int,
798 yml_path: Path,
799) -> None:
800 """
801 Main loop for the experiment, accessed through the command line.
803 This function runs the main loop for the experiment based on the specified start slice, start step, and YAML configuration file.
805 ## Parameters
807 - `start_slice` (`int`): The starting slice number for the experiment.
808 - `start_step` (`int`): The starting step number for the experiment.
809 - `yml_path` (`Path`): The path to the YAML configuration file.
811 ## Returns
813 - `None`
814 """
816 experiment_settings = setup_experiment(yml_path=yml_path)
818 # warn user of any EBSD/EDS lack of control
819 warning_text = """is not enabled, you will not have access to safety
820 checking and these modalities during data collection. Please ensure
821 this detector is retracted before proceeding."""
822 if not experiment_settings.enable_EBSD: 822 ↛ 827line 822 didn't jump to line 827 because the condition on line 822 was always true
823 print(f"\nWARNING: EBSD {warning_text}")
824 if not ut.yes_no("Continue?"): 824 ↛ 825line 824 didn't jump to line 825 because the condition on line 824 was never true
825 print("\nExiting now...")
826 sys.exit()
827 if not experiment_settings.enable_EDS: 827 ↛ 834line 827 didn't jump to line 834 because the condition on line 827 was always true
828 print(f"\nWARNING: EDS {warning_text}")
829 if not ut.yes_no("Continue?"): 829 ↛ 830line 829 didn't jump to line 830 because the condition on line 829 was never true
830 print("\nExiting now...")
831 sys.exit()
833 # main loop
834 log.experiment_settings(
835 slice_number=start_slice,
836 step_number=start_step,
837 log_filepath=experiment_settings.general_settings.log_filepath,
838 yml_path=yml_path,
839 )
840 num_steps = len(experiment_settings.step_sequence)
841 print(
842 f"\n\nBeginning serial sectioning experiment on slice {start_slice}, step {start_step} of {num_steps}.\n"
843 )
845 for slice_number in range(
846 start_slice, experiment_settings.general_settings.max_slice_number + 1
847 ): # inclusive of max slice number
848 for step_number in range(start_step, num_steps + 1): # list is 1-indexed
849 perform_step(
850 slice_number=slice_number,
851 step_number=step_number,
852 experiment_settings=experiment_settings,
853 )
855 # reset start_step to 1 at end of slice
856 start_step = 1
858 ut.disconnect_microscope(
859 microscope=experiment_settings.microscope,
860 quiet_output=True,
861 )
863 print("\n\nExperiment complete.")