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Remove the client-side stashing for tomography #473

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Merged
d-j-hatton merged 3 commits into from
Jan 31, 2025
Merged

Remove the client-side stashing for tomography #473

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8daaa4f
Remove the client-side data collection stash
stephen-riggs Jan 28, 2025
44e4db2
Remove dcg_ids
stephen-riggs Jan 28, 2025
40ddb49
Slightly cleaner posts
stephen-riggs Jan 29, 2025
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84 changes: 17 additions & 67 deletions src/murfey/client/contexts/tomo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,31 +92,6 @@ def __init__(self, acquisition_software: str, basepath: Path):
self._processing_job_stash: dict = {}
self._lock: RLock = RLock()

def _flush_data_collections(self):
logger.info(
f"Flushing {len(self._data_collection_stash)} data collection API calls"
)
for dc_data in self._data_collection_stash:
data = {
**dc_data[2],
**{
k: v
for k, v in dc_data[1].data_collection_parameters.items()
if k != "tag"
},
}
capture_post(dc_data[0], json=data)
self._data_collection_stash = []

def _flush_processing_jobs(self):
logger.info(
f"Flushing {len(self._processing_job_stash.keys())} processing job API calls"
)
for v in self._processing_job_stash.values():
for pd in v:
requests.post(pd[0], json=pd[1])
self._processing_job_stash = {}

def _file_transferred_to(
self, environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
):
Expand Down Expand Up @@ -227,8 +202,18 @@ def _add_tilt(
self._tilt_series_sizes[tilt_series] = 0
try:
if environment:
url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/start_data_collection"
data = {
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,
Expand All @@ -245,7 +230,7 @@ def _add_tilt(
environment.data_collection_parameters
and environment.data_collection_parameters.get("voltage")
):
data.update(
dc_data.update(
{
"voltage": environment.data_collection_parameters[
"voltage"
Expand All @@ -264,51 +249,16 @@ def _add_tilt(
],
}
)
capture_post(dc_url, json=dc_data)

proc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_processing_job"
if (
environment.data_collection_group_ids.get(str(self._basepath))
is None
):
self._data_collection_stash.append((url, environment, data))
self._processing_job_stash[tilt_series] = [
(
proc_url,
{
"tag": tilt_series,
"source": str(self._basepath),
"recipe": "em-tomo-preprocess",
"experiment_type": "tomography",
},
)
]
self._processing_job_stash[tilt_series].append(
(
proc_url,
{
"tag": tilt_series,
"source": str(self._basepath),
"recipe": "em-tomo-align",
"experiment_type": "tomography",
},
)
)
else:
capture_post(url, json=data)
capture_post(
proc_url,
json={
"tag": tilt_series,
"source": str(self._basepath),
"recipe": "em-tomo-preprocess",
"experiment_type": "tomography",
},
)
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
capture_post(
proc_url,
json={
"tag": tilt_series,
"source": str(self._basepath),
"recipe": "em-tomo-align",
"recipe": recipe,
"experiment_type": "tomography",
},
)
Expand Down
2 changes: 0 additions & 2 deletions src/murfey/client/instance_environment.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ class MurfeyInstanceEnvironment(BaseModel):
destination_registry: Dict[str, str] = {}
watchers: Dict[Path, DirWatcher] = {}
demo: bool = False
data_collection_group_ids: Dict[str, int] = {}
data_collection_parameters: dict = {}
movies: Dict[Path, MovieTracker] = {}
movie_tilt_pair: Dict[Path, str] = {}
Expand All @@ -64,7 +63,6 @@ def clear(self):
for w in self.watchers.values():
w.stop()
self.watchers = {}
self.data_collection_group_ids = {}
self.data_collection_parameters = {}
self.movies = {}
self.movie_tilt_pair = {}
Expand Down
42 changes: 0 additions & 42 deletions src/murfey/client/multigrid_control.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -369,46 +369,6 @@ def _start_dc(self, json, from_form: bool = False):
)

source = Path(json["source"])

url = f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/{self.session_id}/register_data_collection_group"
dcg_data = {
"experiment_type": "tomo",
"experiment_type_id": 36,
"tag": str(source),
}
requests.post(url, json=dcg_data)

data = {
"voltage": json["voltage"],
"pixel_size_on_image": json["pixel_size_on_image"],
"experiment_type": json["experiment_type"],
"image_size_x": json["image_size_x"],
"image_size_y": json["image_size_y"],
"file_extension": json["file_extension"],
"acquisition_software": json["acquisition_software"],
"image_directory": str(self._environment.default_destinations[source]),
"tag": json["tilt_series_tag"],
"source": str(source),
"magnification": json["magnification"],
"total_exposed_dose": json.get("total_exposed_dose"),
"c2aperture": json.get("c2aperture"),
"exposure_time": json.get("exposure_time"),
"slit_width": json.get("slit_width"),
"phase_plate": json.get("phase_plate", False),
}
capture_post(
f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/{self._environment.murfey_session}/start_data_collection",
json=data,
)
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
capture_post(
f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/{self._environment.murfey_session}/register_processing_job",
json={
"tag": json["tilt_series_tag"],
"source": str(source),
"recipe": recipe,
},
)
log.info("Registering tomography processing parameters")
if self._environment.data_collection_parameters.get("num_eer_frames"):
eer_response = requests.post(
Expand All @@ -432,8 +392,6 @@ def _start_dc(self, json, from_form: bool = False):
f"{self._environment.url.geturl()}/sessions/{self._environment.murfey_session}/tomography_preprocessing_parameters",
json=json,
)
context._flush_data_collections()
context._flush_processing_jobs()
capture_post(
f"{self._environment.url.geturl()}/visits/{self._environment.visit}/{self._environment.murfey_session}/flush_tomography_processing",
json={"rsync_source": str(source)},
Expand Down
50 changes: 0 additions & 50 deletions src/murfey/client/tui/app.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -474,54 +474,6 @@ def _start_dc(self, json, from_form: bool = False):
context = self.analysers[source]._context
if isinstance(context, TomographyContext):
source = Path(json["source"])
url = f"{str(self._url.geturl())}/visits/{str(self._visit)}/{self._environment.murfey_session}/register_data_collection_group"
dcg_data = {
"experiment_type": "tomo",
"experiment_type_id": 36,
"tag": str(source),
"atlas": (
str(self._environment.samples[source].atlas)
if self._environment.samples.get(source)
else ""
),
"sample": (
self._environment.samples[source].sample
if self._environment.samples.get(source)
else None
),
}
capture_post(url, json=dcg_data)
data = {
"voltage": json["voltage"],
"pixel_size_on_image": json["pixel_size_on_image"],
"experiment_type": json["experiment_type"],
"image_size_x": json["image_size_x"],
"image_size_y": json["image_size_y"],
"file_extension": json["file_extension"],
"acquisition_software": json["acquisition_software"],
"image_directory": str(self._environment.default_destinations[source]),
"tag": json["tilt_series_tag"],
"source": str(source),
"magnification": json["magnification"],
"total_exposed_dose": json.get("total_exposed_dose"),
"c2aperture": json.get("c2aperture"),
"exposure_time": json.get("exposure_time"),
"slit_width": json.get("slit_width"),
"phase_plate": json.get("phase_plate", False),
}
capture_post(
f"{str(self._url.geturl())}/visits/{str(self._visit)}/{self._environment.murfey_session}/start_data_collection",
json=data,
)
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
capture_post(
f"{str(self._url.geturl())}/visits/{str(self._visit)}/{self._environment.murfey_session}/register_processing_job",
json={
"tag": json["tilt_series_tag"],
"source": str(source),
"recipe": recipe,
},
)
log.info("Registering tomography processing parameters")
if self.app._environment.data_collection_parameters.get("num_eer_frames"):
eer_response = requests.post(
Expand All @@ -545,8 +497,6 @@ def _start_dc(self, json, from_form: bool = False):
f"{self.app._environment.url.geturl()}/sessions/{self.app._environment.murfey_session}/tomography_preprocessing_parameters",
json=json,
)
context._flush_data_collections()
context._flush_processing_jobs()
capture_post(
f"{self.app._environment.url.geturl()}/visits/{self._visit}/{self.app._environment.murfey_session}/flush_tomography_processing",
json={"rsync_source": str(source)},
Expand Down