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Restore code to register tomo data collections post mdoc #498

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Merged
d-j-hatton merged 1 commit into from
Feb 17, 2025
Merged

Restore code to register tomo data collections post mdoc #498

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152 changes: 88 additions & 64 deletions src/murfey/client/contexts/tomo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,84 @@ def __init__(self, acquisition_software: str, basepath: Path):
self._processing_job_stash: dict = {}
self._lock: RLock = RLock()

def register_tomography_data_collections(
self,
file_extension: str,
image_directory: str,
environment: MurfeyInstanceEnvironment | None = None,
):
if not environment:
logger.error(
"No environment passed to register tomography data collections"
)
return
try:
dcg_url = f"{str(environment.url.geturl())}/visits/{str(environment.visit)}/{environment.murfey_session}/register_data_collection_group"
dcg_data = {
"experiment_type": "tomo",
"experiment_type_id": 36,
"tag": str(self._basepath),
"atlas": "",
"sample": None,
}
capture_post(dcg_url, json=dcg_data)

for tilt_series in self._tilt_series.keys():
dc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/start_data_collection"
dc_data = {
"experiment_type": "tomography",
"file_extension": file_extension,
"acquisition_software": self._acquisition_software,
"image_directory": image_directory,
"data_collection_tag": tilt_series,
"source": str(self._basepath),
"tag": tilt_series,
}
if (
environment.data_collection_parameters
and environment.data_collection_parameters.get("voltage")
):
# Once mdoc parameters are known register processing jobs
dc_data.update(
{
"voltage": environment.data_collection_parameters[
"voltage"
],
"pixel_size_on_image": environment.data_collection_parameters[
"pixel_size_on_image"
],
"image_size_x": environment.data_collection_parameters[
"image_size_x"
],
"image_size_y": environment.data_collection_parameters[
"image_size_y"
],
"magnification": environment.data_collection_parameters[
"magnification"
],
}
)
capture_post(dc_url, json=dc_data)

proc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_processing_job"
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
capture_post(
proc_url,
json={
"tag": tilt_series,
"source": str(self._basepath),
"recipe": recipe,
"experiment_type": "tomography",
},
)
else:
logger.info(
"Cannot register data collection yet as no values from mdoc"
)

except Exception as e:
logger.error(f"ERROR {e}, {environment.data_collection_parameters}")

def _file_transferred_to(
self, environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
):
Expand Down Expand Up @@ -201,71 +279,17 @@ def _add_tilt(
capture_post(ts_url, json=ts_data)
if not self._tilt_series_sizes.get(tilt_series):
self._tilt_series_sizes[tilt_series] = 0
try:
if environment:
dcg_url = f"{str(environment.url.geturl())}/visits/{str(environment.visit)}/{environment.murfey_session}/register_data_collection_group"
dcg_data = {
"experiment_type": "tomo",
"experiment_type_id": 36,
"tag": str(self._basepath),
"atlas": "",
"sample": None,
}
capture_post(dcg_url, json=dcg_data)

dc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/start_data_collection"
dc_data = {
"experiment_type": "tomography",
"file_extension": file_path.suffix,
"acquisition_software": self._acquisition_software,
"image_directory": str(
environment.default_destinations.get(
file_path.parent, file_path.parent
)
),
"data_collection_tag": tilt_series,
"source": str(self._basepath),
"tag": tilt_series,
}
if (
environment.data_collection_parameters
and environment.data_collection_parameters.get("voltage")
):
dc_data.update(
{
"voltage": environment.data_collection_parameters[
"voltage"
],
"pixel_size_on_image": environment.data_collection_parameters[
"pixel_size_on_image"
],
"image_size_x": environment.data_collection_parameters[
"image_size_x"
],
"image_size_y": environment.data_collection_parameters[
"image_size_y"
],
"magnification": environment.data_collection_parameters[
"magnification"
],
}
)
capture_post(dc_url, json=dc_data)

proc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_processing_job"
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
capture_post(
proc_url,
json={
"tag": tilt_series,
"source": str(self._basepath),
"recipe": recipe,
"experiment_type": "tomography",
},
)

except Exception as e:
logger.error(f"ERROR {e}, {environment.data_collection_parameters}")
# Will register processing jobs for all tilt series except the first one
self.register_tomography_data_collections(
file_extension=file_path.suffix,
image_directory=str(
environment.default_destinations.get(
file_path.parent, file_path.parent
)
),
environment=environment,
)
else:
if file_path not in self._tilt_series[tilt_series]:
for p in self._tilt_series[tilt_series]:
Expand Down
6 changes: 6 additions & 0 deletions src/murfey/client/multigrid_control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -377,6 +377,12 @@ def _start_dc(self, json, from_form: bool = False):
)

source = Path(json["source"])
context.register_tomography_data_collections(
file_extension=json["file_extension"],
image_directory=str(self._environment.default_destinations[source]),
environment=self._environment,
)

log.info("Registering tomography processing parameters")
if self._environment.data_collection_parameters.get("num_eer_frames"):
eer_response = requests.post(
Expand Down
6 changes: 6 additions & 0 deletions src/murfey/client/tui/app.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -478,6 +478,12 @@ def _start_dc(self, json, from_form: bool = False):
context = self.analysers[source]._context
if isinstance(context, TomographyContext):
source = Path(json["source"])
context.register_tomography_data_collections(
file_extension=json["file_extension"],
image_directory=str(self._environment.default_destinations[source]),
environment=self._environment,
)

log.info("Registering tomography processing parameters")
if self.app._environment.data_collection_parameters.get("num_eer_frames"):
eer_response = requests.post(
Expand Down
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