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🚀 Added plugin support for multi-channel segmentations #388

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merged 2 commits into from
Jun 27, 2024
Merged

🚀 Added plugin support for multi-channel segmentations #388

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64d2279
:rocket: Added plugin support for multi-channel segmentations
amilworks Jun 11, 2024
ba76e97
Added top level overrides for multi-channel segs
amilworks Jun 25, 2024
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18 changes: 12 additions & 6 deletions configs/data/im2im/segmentation_plugin.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,16 @@ transforms:
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [TRAIN] Exposing C as a configurable param for multi-channel segs
C: ${target_col1_channel}
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- _target_: monai.transforms.LoadImaged
keys: ${target_col2}
allow_missing_keys: True
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [TRAIN] Exposing C as a configurable param for multi-channel segs
C: ${target_col2_channel}
- _target_: monai.transforms.ThresholdIntensityd
allow_missing_keys: True
keys:
Expand Down Expand Up @@ -108,14 +110,16 @@ transforms:
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [TEST] Exposing C as a configurable param for multi-channel segs
C: ${target_col1_channel}
- _target_: monai.transforms.LoadImaged
keys: ${target_col2}
allow_missing_keys: True
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [TEST] Exposing C as a configurable param for multi-channel segs
C: ${target_col2_channel}
# load merging mask - assumed not to exist by default
- _target_: cyto_dl.image.io.PolygonLoaderd
keys:
Expand Down Expand Up @@ -184,14 +188,16 @@ transforms:
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [VAL] Exposing C as a configurable param for multi-channel segs
C: ${target_col1_channel}
- _target_: monai.transforms.LoadImaged
keys: ${target_col2}
allow_missing_keys: True
reader:
- _target_: cyto_dl.image.io.MonaiBioReader
dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
C: 0
# [VAL] Exposing C as a configurable param for multi-channel segs
C: ${target_col2_channel}

- _target_: monai.transforms.ThresholdIntensityd
allow_missing_keys: True
Expand Down
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