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added cdp tomogram filter for no_processing and added environment to … #118

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added cdp tomogram filter for no_processing and added environment to … #118

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5 changes: 5 additions & 0 deletions environment.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,5 +17,10 @@ dependencies:
- torchvision
- trimesh
- zarr < 3
- ome-zarr
- s3fs
- botocore=1.37.1
- aiobotocore=2.21.1
- pip:
- napari-skimage-regionprops
- cryoet_data_portal
13 changes: 9 additions & 4 deletions synapse_net/file_utils.py
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Expand Up @@ -178,7 +178,7 @@ def read_data_from_cryo_et_portal_run(
The data read from the run.
The voxel size read from the run.
"""
assert id_field in ("id", "run_id")
assert id_field in ("id", "run_id", "deposition_id")
if output_path is not None and os.path.exists(output_path):
return read_ome_zarr(output_path) if use_zarr_format else read_mrc(output_path)

Expand All @@ -190,9 +190,14 @@ def read_data_from_cryo_et_portal_run(
client = cdp.Client()

fs = s3fs.S3FileSystem(anon=True)
tomograms = cdp.Tomogram.find(
client, [getattr(cdp.Tomogram, id_field) == run_id, cdp.Tomogram.processing == processing_type]
)
if processing_type is not None:
tomograms = cdp.Tomogram.find(
client, [getattr(cdp.Tomogram, id_field) == run_id, cdp.Tomogram.processing == processing_type]
)
else:
tomograms = cdp.Tomogram.find(
client, [getattr(cdp.Tomogram, id_field) == run_id]
)
if len(tomograms) == 0:
return None, None
if len(tomograms) > 1:
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