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stephen-riggsstephen-riggs
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Rename json variable
1 parent 5f7e5c8 commit c3e628d

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2 files changed

+66
-56
lines changed

2 files changed

+66
-56
lines changed

‎src/murfey/client/multigrid_control.py‎

Lines changed: 33 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -412,29 +412,31 @@ def _data_collection_form(self, response: dict):
412412
elif self._register_dc is None:
413413
self._data_collection_form_complete = True
414414

415-
def _start_dc(self, json, from_form: bool = False):
415+
def _start_dc(self, metadata_json, from_form: bool = False):
416416
if self.dummy_dc:
417417
return
418418
# for multigrid the analyser sends the message straight to _start_dc by-passing user input
419419
# it is then necessary to extract the data from the message
420420
if from_form:
421-
json = json.get("form", {})
421+
metadata_json = metadata_json.get("form", {})
422422
# Safely convert all entries into strings, but leave None as-is
423-
json = {k: str(v) if v is not None else None for k, v in json.items()}
424-
self._environment.dose_per_frame = json.get("dose_per_frame")
425-
self._environment.gain_ref = json.get("gain_ref")
426-
self._environment.symmetry = json.get("symmetry")
427-
self._environment.eer_fractionation = json.get("eer_fractionation")
428-
source = Path(json["source"])
423+
metadata_json = {
424+
k: str(v) if v is not None else None for k, v in metadata_json.items()
425+
}
426+
self._environment.dose_per_frame = metadata_json.get("dose_per_frame")
427+
self._environment.gain_ref = metadata_json.get("gain_ref")
428+
self._environment.symmetry = metadata_json.get("symmetry")
429+
self._environment.eer_fractionation = metadata_json.get("eer_fractionation")
430+
source = Path(metadata_json["source"])
429431
context = self.analysers[source]._context
430432
if context:
431433
context.data_collection_parameters = {
432-
k: None if v == "None" else v for k, v in json.items()
434+
k: None if v == "None" else v for k, v in metadata_json.items()
433435
}
434436
if isinstance(context, TomographyContext):
435-
source = Path(json["source"])
437+
source = Path(metadata_json["source"])
436438
context.register_tomography_data_collections(
437-
file_extension=json["file_extension"],
439+
file_extension=metadata_json["file_extension"],
438440
image_directory=str(self._environment.default_destinations[source]),
439441
environment=self._environment,
440442
)
@@ -453,10 +455,10 @@ def _start_dc(self, json, from_form: bool = False):
453455
},
454456
)
455457
eer_fractionation_file = eer_response.json()["eer_fractionation_file"]
456-
json.update({"eer_fractionation_file": eer_fractionation_file})
458+
metadata_json.update({"eer_fractionation_file": eer_fractionation_file})
457459
capture_post(
458460
f"{self._environment.url.geturl()}{url_path_for('workflow.tomo_router', 'register_tomo_proc_params', session_id=self._environment.murfey_session)}",
459-
json=json,
461+
json=metadata_json,
460462
)
461463
capture_post(
462464
f"{self._environment.url.geturl()}{url_path_for('workflow.tomo_router', 'flush_tomography_processing', visit_name=self._environment.visit, session_id=self._environment.murfey_session)}",
@@ -484,24 +486,24 @@ def _start_dc(self, json, from_form: bool = False):
484486
capture_post(url, json=dcg_data)
485487
if from_form:
486488
data = {
487-
"voltage": json["voltage"],
488-
"pixel_size_on_image": json["pixel_size_on_image"],
489-
"experiment_type": json["experiment_type"],
490-
"image_size_x": json["image_size_x"],
491-
"image_size_y": json["image_size_y"],
492-
"file_extension": json["file_extension"],
493-
"acquisition_software": json["acquisition_software"],
489+
"voltage": metadata_json["voltage"],
490+
"pixel_size_on_image": metadata_json["pixel_size_on_image"],
491+
"experiment_type": metadata_json["experiment_type"],
492+
"image_size_x": metadata_json["image_size_x"],
493+
"image_size_y": metadata_json["image_size_y"],
494+
"file_extension": metadata_json["file_extension"],
495+
"acquisition_software": metadata_json["acquisition_software"],
494496
"image_directory": str(
495497
self._environment.default_destinations[source]
496498
),
497499
"tag": str(source),
498500
"source": str(source),
499-
"magnification": json["magnification"],
500-
"total_exposed_dose": json.get("total_exposed_dose"),
501-
"c2aperture": json.get("c2aperture"),
502-
"exposure_time": json.get("exposure_time"),
503-
"slit_width": json.get("slit_width"),
504-
"phase_plate": json.get("phase_plate", False),
501+
"magnification": metadata_json["magnification"],
502+
"total_exposed_dose": metadata_json.get("total_exposed_dose"),
503+
"c2aperture": metadata_json.get("c2aperture"),
504+
"exposure_time": metadata_json.get("exposure_time"),
505+
"slit_width": metadata_json.get("slit_width"),
506+
"phase_plate": metadata_json.get("phase_plate", False),
505507
}
506508
capture_post(
507509
f"{str(self._environment.url.geturl())}{url_path_for('workflow.router', 'start_dc', visit_name=self._environment.visit, session_id=self.session_id)}",
@@ -522,11 +524,14 @@ def _start_dc(self, json, from_form: bool = False):
522524
"recipe": recipe,
523525
},
524526
)
525-
log.info(f"Posting SPA processing parameters: {json}")
527+
log.info(f"Posting SPA processing parameters: {metadata_json}")
526528
response = capture_post(
527529
f"{self._environment.url.geturl()}{url_path_for('workflow.spa_router', 'register_spa_proc_params', session_id=self.session_id)}",
528530
json={
529-
**{k: None if v == "None" else v for k, v in json.items()},
531+
**{
532+
k: None if v == "None" else v
533+
for k, v in metadata_json.items()
534+
},
530535
"tag": str(source),
531536
},
532537
)

‎src/murfey/client/tui/app.py‎

Lines changed: 33 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -460,28 +460,30 @@ def _start_dc_confirm_prompt(self, json: dict):
460460
)
461461
)
462462

463-
def _start_dc(self, json, from_form: bool = False):
463+
def _start_dc(self, metadata_json, from_form: bool = False):
464464
if self._dummy_dc:
465465
return
466466
# for multigrid the analyser sends the message straight to _start_dc by-passing user input
467467
# it is then necessary to extract the data from the message
468468
if from_form:
469-
json = json.get("form", {})
470-
json = {k: v if v is None else str(v) for k, v in json.items()}
471-
self._environment.dose_per_frame = json.get("dose_per_frame")
472-
self._environment.gain_ref = json.get("gain_ref")
473-
self._environment.symmetry = json.get("symmetry")
474-
self._environment.eer_fractionation = json.get("eer_fractionation")
475-
source = Path(json["source"])
469+
metadata_json = metadata_json.get("form", {})
470+
metadata_json = {
471+
k: v if v is None else str(v) for k, v in metadata_json.items()
472+
}
473+
self._environment.dose_per_frame = metadata_json.get("dose_per_frame")
474+
self._environment.gain_ref = metadata_json.get("gain_ref")
475+
self._environment.symmetry = metadata_json.get("symmetry")
476+
self._environment.eer_fractionation = metadata_json.get("eer_fractionation")
477+
source = Path(metadata_json["source"])
476478
context = self.analysers[source]._context
477479
if context:
478480
context.data_collection_parameters = {
479-
k: None if v == "None" else v for k, v in json.items()
481+
k: None if v == "None" else v for k, v in metadata_json.items()
480482
}
481483
if isinstance(context, TomographyContext):
482-
source = Path(json["source"])
484+
source = Path(metadata_json["source"])
483485
context.register_tomography_data_collections(
484-
file_extension=json["file_extension"],
486+
file_extension=metadata_json["file_extension"],
485487
image_directory=str(self._environment.default_destinations[source]),
486488
environment=self._environment,
487489
)
@@ -500,10 +502,10 @@ def _start_dc(self, json, from_form: bool = False):
500502
},
501503
)
502504
eer_fractionation_file = eer_response.json()["eer_fractionation_file"]
503-
json.update({"eer_fractionation_file": eer_fractionation_file})
505+
metadata_json.update({"eer_fractionation_file": eer_fractionation_file})
504506
requests.post(
505507
f"{self.app._environment.url.geturl()}{url_path_for('workflow.tomo_router', 'register_tomo_proc_params', session_id=self.app._environment.murfey_session)}",
506-
json=json,
508+
json=metadata_json,
507509
)
508510
capture_post(
509511
f"{self.app._environment.url.geturl()}{url_path_for('workflow.tomo_router', 'flush_tomography_processing', visit_name=self._visit, session_id=self.app._environment.murfey_session)}",
@@ -530,24 +532,24 @@ def _start_dc(self, json, from_form: bool = False):
530532
capture_post(url, json=dcg_data)
531533
if from_form:
532534
data = {
533-
"voltage": json["voltage"],
534-
"pixel_size_on_image": json["pixel_size_on_image"],
535-
"experiment_type": json["experiment_type"],
536-
"image_size_x": json["image_size_x"],
537-
"image_size_y": json["image_size_y"],
538-
"file_extension": json["file_extension"],
539-
"acquisition_software": json["acquisition_software"],
535+
"voltage": metadata_json["voltage"],
536+
"pixel_size_on_image": metadata_json["pixel_size_on_image"],
537+
"experiment_type": metadata_json["experiment_type"],
538+
"image_size_x": metadata_json["image_size_x"],
539+
"image_size_y": metadata_json["image_size_y"],
540+
"file_extension": metadata_json["file_extension"],
541+
"acquisition_software": metadata_json["acquisition_software"],
540542
"image_directory": str(
541543
self._environment.default_destinations[source]
542544
),
543545
"tag": str(source),
544546
"source": str(source),
545-
"magnification": json["magnification"],
546-
"total_exposed_dose": json.get("total_exposed_dose"),
547-
"c2aperture": json.get("c2aperture"),
548-
"exposure_time": json.get("exposure_time"),
549-
"slit_width": json.get("slit_width"),
550-
"phase_plate": json.get("phase_plate", False),
547+
"magnification": metadata_json["magnification"],
548+
"total_exposed_dose": metadata_json.get("total_exposed_dose"),
549+
"c2aperture": metadata_json.get("c2aperture"),
550+
"exposure_time": metadata_json.get("exposure_time"),
551+
"slit_width": metadata_json.get("slit_width"),
552+
"phase_plate": metadata_json.get("phase_plate", False),
551553
}
552554
capture_post(
553555
f"{str(self._url.geturl())}{url_path_for('workflow.router', 'start_dc', visit_name=self._visit, session_id=self._environment.murfey_session)}",
@@ -568,11 +570,14 @@ def _start_dc(self, json, from_form: bool = False):
568570
"recipe": recipe,
569571
},
570572
)
571-
log.info(f"Posting SPA processing parameters: {json}")
573+
log.info(f"Posting SPA processing parameters: {metadata_json}")
572574
response = capture_post(
573575
f"{self.app._environment.url.geturl()}{url_path_for('workflow.spa_router', 'register_spa_proc_params', session_id=self.app._environment.murfey_session)}",
574576
json={
575-
**{k: None if v == "None" else v for k, v in json.items()},
577+
**{
578+
k: None if v == "None" else v
579+
for k, v in metadata_json.items()
580+
},
576581
"tag": str(source),
577582
},
578583
)

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