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stephen-riggsstephen-riggs
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Tabbing wasn't helpful
1 parent 5c90290 commit 0c84540

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+150
-153
lines changed

2 files changed

+150
-153
lines changed

‎src/murfey/client/contexts/spa.py‎

Lines changed: 104 additions & 106 deletions
Original file line numberDiff line numberDiff line change
@@ -678,120 +678,118 @@ def post_transfer(
678678
**kwargs,
679679
)
680680
data_suffixes = (".mrc", ".tiff", ".tif", ".eer")
681-
if "gain" in transferred_file.name:
682-
return True
683-
684-
if transferred_file.suffix in data_suffixes:
685-
if self._acquisition_software == "epu":
686-
if environment:
687-
machine_config = get_machine_config_client(
688-
str(environment.url.geturl()),
689-
instrument_name=environment.instrument_name,
690-
demo=environment.demo,
681+
if "gain" not in transferred_file.name:
682+
if transferred_file.suffix in data_suffixes:
683+
if self._acquisition_software == "epu":
684+
if environment:
685+
machine_config = get_machine_config_client(
686+
str(environment.url.geturl()),
687+
instrument_name=environment.instrument_name,
688+
demo=environment.demo,
689+
)
690+
else:
691+
machine_config = {}
692+
required_strings = (
693+
machine_config.get("data_required_substrings", {})
694+
.get("epu", {})
695+
.get(transferred_file.suffix, ["fractions"])
691696
)
692-
else:
693-
machine_config = {}
694-
required_strings = (
695-
machine_config.get("data_required_substrings", {})
696-
.get("epu", {})
697-
.get(transferred_file.suffix, ["fractions"])
698-
)
699697

700-
if not environment:
701-
logger.warning("No environment passed in")
702-
return True
703-
source = _get_source(transferred_file, environment)
704-
if not source:
705-
logger.warning(f"No source found for file {transferred_file}")
706-
return True
707-
708-
if required_strings and not any(
709-
r in transferred_file.name for r in required_strings
710-
):
711-
return True
712-
713-
if environment:
714-
file_transferred_to = _file_transferred_to(
715-
environment, source, transferred_file
716-
)
717-
if not environment.movie_counters.get(str(source)):
718-
movie_counts_get = capture_get(
719-
f"{str(environment.url.geturl())}/num_movies",
698+
if not environment:
699+
logger.warning("No environment passed in")
700+
return True
701+
source = _get_source(transferred_file, environment)
702+
if not source:
703+
logger.warning(f"No source found for file {transferred_file}")
704+
return True
705+
706+
if required_strings and not any(
707+
r in transferred_file.name for r in required_strings
708+
):
709+
return True
710+
711+
if environment:
712+
file_transferred_to = _file_transferred_to(
713+
environment, source, transferred_file
720714
)
721-
if movie_counts_get is not None:
722-
environment.movie_counters[str(source)] = count(
723-
movie_counts_get.json().get(str(source), 0) + 1
715+
if not environment.movie_counters.get(str(source)):
716+
movie_counts_get = capture_get(
717+
f"{str(environment.url.geturl())}/num_movies",
724718
)
725-
environment.movies[file_transferred_to] = MovieTracker(
726-
movie_number=next(environment.movie_counters[str(source)]),
727-
motion_correction_uuid=next(MurfeyID),
728-
)
719+
if movie_counts_get is not None:
720+
environment.movie_counters[str(source)] = count(
721+
movie_counts_get.json().get(str(source), 0) + 1
722+
)
723+
environment.movies[file_transferred_to] = MovieTracker(
724+
movie_number=next(environment.movie_counters[str(source)]),
725+
motion_correction_uuid=next(MurfeyID),
726+
)
729727

730-
eer_fractionation_file = None
731-
if file_transferred_to.suffix == ".eer":
732-
response = capture_post(
733-
f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/eer_fractionation_file",
728+
eer_fractionation_file = None
729+
if file_transferred_to.suffix == ".eer":
730+
response = capture_post(
731+
f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/eer_fractionation_file",
732+
json={
733+
"eer_path": str(file_transferred_to),
734+
"fractionation": environment.data_collection_parameters[
735+
"eer_fractionation"
736+
],
737+
"dose_per_frame": environment.data_collection_parameters[
738+
"dose_per_frame"
739+
],
740+
"fractionation_file_name": "eer_fractionation_spa.txt",
741+
},
742+
)
743+
if response is None:
744+
return False
745+
eer_fractionation_file = response.json()[
746+
"eer_fractionation_file"
747+
]
748+
749+
try:
750+
foil_hole: Optional[int] = self._position_analysis(
751+
transferred_file, environment, source, machine_config
752+
)
753+
except Exception:
754+
# try to continue if position information gathering fails so that movie is processed anyway
755+
foil_hole = None
756+
757+
preproc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/spa_preprocess"
758+
preproc_data = {
759+
"path": str(file_transferred_to),
760+
"description": "",
761+
"processing_job": None,
762+
"data_collection_id": None,
763+
"image_number": environment.movies[
764+
file_transferred_to
765+
].movie_number,
766+
"pixel_size": environment.data_collection_parameters.get(
767+
"pixel_size_on_image"
768+
),
769+
"autoproc_program_id": None,
770+
"dose_per_frame": environment.data_collection_parameters.get(
771+
"dose_per_frame"
772+
),
773+
"mc_binning": environment.data_collection_parameters.get(
774+
"motion_corr_binning", 1
775+
),
776+
"gain_ref": environment.data_collection_parameters.get(
777+
"gain_ref"
778+
),
779+
"extract_downscale": environment.data_collection_parameters.get(
780+
"downscale", True
781+
),
782+
"eer_fractionation_file": eer_fractionation_file,
783+
"tag": str(source),
784+
"foil_hole_id": foil_hole,
785+
}
786+
capture_post(
787+
preproc_url,
734788
json={
735-
"eer_path": str(file_transferred_to),
736-
"fractionation": environment.data_collection_parameters[
737-
"eer_fractionation"
738-
],
739-
"dose_per_frame": environment.data_collection_parameters[
740-
"dose_per_frame"
741-
],
742-
"fractionation_file_name": "eer_fractionation_spa.txt",
789+
k: None if v == "None" else v
790+
for k, v in preproc_data.items()
743791
},
744792
)
745-
if response is None:
746-
return False
747-
eer_fractionation_file = response.json()[
748-
"eer_fractionation_file"
749-
]
750-
751-
try:
752-
foil_hole: Optional[int] = self._position_analysis(
753-
transferred_file, environment, source, machine_config
754-
)
755-
except Exception:
756-
# try to continue if position information gathering fails so that movie is processed anyway
757-
foil_hole = None
758-
759-
preproc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/spa_preprocess"
760-
preproc_data = {
761-
"path": str(file_transferred_to),
762-
"description": "",
763-
"processing_job": None,
764-
"data_collection_id": None,
765-
"image_number": environment.movies[
766-
file_transferred_to
767-
].movie_number,
768-
"pixel_size": environment.data_collection_parameters.get(
769-
"pixel_size_on_image"
770-
),
771-
"autoproc_program_id": None,
772-
"dose_per_frame": environment.data_collection_parameters.get(
773-
"dose_per_frame"
774-
),
775-
"mc_binning": environment.data_collection_parameters.get(
776-
"motion_corr_binning", 1
777-
),
778-
"gain_ref": environment.data_collection_parameters.get(
779-
"gain_ref"
780-
),
781-
"extract_downscale": environment.data_collection_parameters.get(
782-
"downscale", True
783-
),
784-
"eer_fractionation_file": eer_fractionation_file,
785-
"tag": str(source),
786-
"foil_hole_id": foil_hole,
787-
}
788-
capture_post(
789-
preproc_url,
790-
json={
791-
k: None if v == "None" else v
792-
for k, v in preproc_data.items()
793-
},
794-
)
795793

796794
return True
797795

‎src/murfey/client/contexts/tomo.py‎

Lines changed: 46 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -561,55 +561,54 @@ def post_transfer(
561561
data_suffixes = (".mrc", ".tiff", ".tif", ".eer")
562562
completed_tilts = []
563563

564-
if "gain" in transferred_file.name:
565-
return []
566-
567-
if transferred_file.suffix in data_suffixes:
568-
if self._acquisition_software == "tomo":
569-
if environment:
570-
machine_config = get_machine_config_client(
571-
str(environment.url.geturl()),
572-
instrument_name=environment.instrument_name,
573-
demo=environment.demo,
564+
if "gain" not in transferred_file.name:
565+
if transferred_file.suffix in data_suffixes:
566+
if self._acquisition_software == "tomo":
567+
if environment:
568+
machine_config = get_machine_config_client(
569+
str(environment.url.geturl()),
570+
instrument_name=environment.instrument_name,
571+
demo=environment.demo,
572+
)
573+
else:
574+
machine_config = {}
575+
required_strings = (
576+
machine_config.get("data_required_substrings", {})
577+
.get("tomo", {})
578+
.get(transferred_file.suffix, ["fractions"])
574579
)
575-
else:
576-
machine_config = {}
577-
required_strings = (
578-
machine_config.get("data_required_substrings", {})
579-
.get("tomo", {})
580-
.get(transferred_file.suffix, ["fractions"])
581-
)
582-
completed_tilts = self._add_tomo_tilt(
583-
transferred_file,
584-
environment=environment,
585-
required_strings=kwargs.get("required_strings") or required_strings,
586-
)
587-
elif self._acquisition_software == "serialem":
588-
completed_tilts = self._add_serialem_tilt(
589-
transferred_file, environment=environment
590-
)
591-
if transferred_file.suffix == ".mdoc":
592-
with open(transferred_file, "r") as md:
593-
tilt_series = transferred_file.stem
594-
self._tilt_series_sizes[tilt_series] = get_num_blocks(md)
595-
if environment:
596-
source = self._get_source(transferred_file, environment)
597-
if source:
598-
completed_tilts = self._check_tilt_series(tilt_series)
599-
600-
# Always update the tilt series length in the database after an mdoc
601-
if environment.murfey_session is not None:
602-
length_url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/tilt_series_length"
603-
capture_post(
604-
length_url,
605-
json={
606-
"tags": [tilt_series],
607-
"source": str(transferred_file.parent),
608-
"tilt_series_lengths": [
609-
self._tilt_series_sizes[tilt_series]
610-
],
611-
},
580+
completed_tilts = self._add_tomo_tilt(
581+
transferred_file,
582+
environment=environment,
583+
required_strings=kwargs.get("required_strings")
584+
or required_strings,
585+
)
586+
elif self._acquisition_software == "serialem":
587+
completed_tilts = self._add_serialem_tilt(
588+
transferred_file, environment=environment
612589
)
590+
if transferred_file.suffix == ".mdoc":
591+
with open(transferred_file, "r") as md:
592+
tilt_series = transferred_file.stem
593+
self._tilt_series_sizes[tilt_series] = get_num_blocks(md)
594+
if environment:
595+
source = self._get_source(transferred_file, environment)
596+
if source:
597+
completed_tilts = self._check_tilt_series(tilt_series)
598+
599+
# Always update the tilt series length in the database after an mdoc
600+
if environment.murfey_session is not None:
601+
length_url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/tilt_series_length"
602+
capture_post(
603+
length_url,
604+
json={
605+
"tags": [tilt_series],
606+
"source": str(transferred_file.parent),
607+
"tilt_series_lengths": [
608+
self._tilt_series_sizes[tilt_series]
609+
],
610+
},
611+
)
613612

614613
if completed_tilts and environment:
615614
logger.info(

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