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Use safe placholder atlas name if atlas XML not found #734

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Use safe placholder atlas name if atlas XML not found #734

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80 changes: 44 additions & 36 deletions src/murfey/client/context.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,31 +94,6 @@ def ensure_dcg_exists(
logger.info(
f"Looking for atlas XML file in metadata directory {str((source_visit_dir / partial_path).parent)}"
)
atlas_xml_path = list(
(source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
)[0]
logger.info(f"Atlas XML path {str(atlas_xml_path)} found")
with open(atlas_xml_path, "rb") as atlas_xml:
atlas_xml_data = xmltodict.parse(atlas_xml)
atlas_original_pixel_size = float(
atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
"numericValue"
]
)
# need to calculate the pixel size of the downscaled image
atlas_pixel_size = atlas_original_pixel_size * 7.8
logger.info(f"Atlas image pixel size determined to be {atlas_pixel_size}")

for p in partial_path.split("/"):
if p.startswith("Sample"):
sample = int(p.replace("Sample", ""))
break
else:
logger.warning(f"Sample could not be identified for {metadata_source}")
return None
environment.samples[metadata_source] = SampleInfo(
atlas=Path(partial_path), sample=sample
)

dcg_search_dir = (
str(metadata_source).replace(f"/{environment.visit}", "").replace("//", "/")
Expand All @@ -137,17 +112,50 @@ def ensure_dcg_exists(
dcg_images_dirs = [Path(dcg_search_dir) / "Images-Disc1"]
dcg_tag = str(dcg_images_dirs[-1])

dcg_data = {
"experiment_type_id": experiment_type_id,
"tag": dcg_tag,
"atlas": str(
_atlas_destination(environment, metadata_source, token)
/ environment.samples[metadata_source].atlas.parent
/ atlas_xml_path.with_suffix(".jpg").name
).replace("//", "/"),
"sample": environment.samples[metadata_source].sample,
"atlas_pixel_size": atlas_pixel_size,
}
for p in partial_path.split("/"):
if p.startswith("Sample"):
sample = int(p.replace("Sample", ""))
break
else:
logger.warning(f"Sample could not be identified for {metadata_source}")
return None
environment.samples[metadata_source] = SampleInfo(
atlas=Path(partial_path), sample=sample
)

if atlas_xml_search := list(
(source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
):
atlas_xml_path = atlas_xml_search[0]
logger.info(f"Atlas XML path {str(atlas_xml_path)} found")
with open(atlas_xml_path, "rb") as atlas_xml:
atlas_xml_data = xmltodict.parse(atlas_xml)
atlas_original_pixel_size = float(
atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
"numericValue"
]
)
# need to calculate the pixel size of the downscaled image
atlas_pixel_size = atlas_original_pixel_size * 7.8
logger.info(f"Atlas image pixel size determined to be {atlas_pixel_size}")

dcg_data = {
"experiment_type_id": experiment_type_id,
"tag": dcg_tag,
"atlas": str(
_atlas_destination(environment, metadata_source, token)
/ environment.samples[metadata_source].atlas.parent
/ atlas_xml_path.with_suffix(".jpg").name
).replace("//", "/"),
"sample": environment.samples[metadata_source].sample,
"atlas_pixel_size": atlas_pixel_size,
}
else:
dcg_data = {
"experiment_type_id": experiment_type_id,
"tag": dcg_tag,
"sample": environment.samples[metadata_source].sample,
}
capture_post(
base_url=str(environment.url.geturl()),
router_name="workflow.router",
Expand Down