Admin/cleanup instance segmentation (#299)

* remove omnipose * rename skoots -> instanceseg * cleanup comments * add astropy and edt * fix geomloss import * pre-commit * format * pin lightning and astropy --------- Co-authored-by: Benjamin Morris <[email protected]>
AllenCellModeling · Oct 19, 2023 · 7e7e8ae · 7e7e8ae
1 parent e5c64e9
commit 7e7e8ae
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Showing 19 changed files with 41 additions and 784 deletions.
diff --git a/Makefile b/Makefile
@@ -84,7 +84,6 @@ sync-reqs-files: requirements/$(PLATFORM)/requirements.txt \
                  requirements/$(PLATFORM)/torchserve-requirements.txt \
                  requirements/$(PLATFORM)/equiv-requirements.txt \
                  requirements/$(PLATFORM)/spharm-requirements.txt \
-                 requirements/$(PLATFORM)/omnipose-requirements.txt \
                  requirements/$(PLATFORM)/all-requirements.txt \
                  requirements/$(PLATFORM)/test-requirements.txt \
                  requirements/$(PLATFORM)/docs-requirements.txt
diff --git a/configs/data/im2im/skoots.yaml → configs/data/im2im/instance_seg.yaml b/configs/data/im2im/skoots.yaml → configs/data/im2im/instance_seg.yaml
@@ -35,7 +35,7 @@ transforms:
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
         zoom: 0.25
-      - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
+      - _target_: cyto_dl.models.im2im.utils.InstanceSegPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
       - _target_: monai.transforms.ToTensord
@@ -86,7 +86,7 @@ transforms:
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
         zoom: 0.25
-      - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
+      - _target_: cyto_dl.models.im2im.utils.InstanceSegPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
       - _target_: monai.transforms.ToTensord
@@ -141,7 +141,7 @@ transforms:
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
         zoom: 0.25
-      - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
+      - _target_: cyto_dl.models.im2im.utils.InstanceSegPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
       - _target_: monai.transforms.ToTensord

diff --git a/configs/data/im2im/omnipose.yaml b/configs/data/im2im/omnipose.yaml
diff --git a/configs/experiment/im2im/omnipose.yaml → configs/experiment/im2im/instance_seg.yaml b/configs/experiment/im2im/omnipose.yaml → configs/experiment/im2im/instance_seg.yaml
@@ -4,8 +4,8 @@
 # python train.py experiment=example
 
 defaults:
-  - override /data: im2im/omnipose.yaml
-  - override /model: im2im/omnipose.yaml
+  - override /data: im2im/instance_seg.yaml
+  - override /model: im2im/instance_seg.yaml
   - override /callbacks: default.yaml
   - override /trainer: gpu.yaml
   - override /logger: mlflow.yaml
@@ -30,6 +30,5 @@ data:
   path: ${paths.data_dir}/example_experiment_data/segmentation
   cache_dir: ${paths.data_dir}/example_experiment_data/cache
   batch_size: 1
-
   _aux:
     patch_shape: [16, 32, 32]
diff --git a/configs/experiment/im2im/skoots.yaml b/configs/experiment/im2im/skoots.yaml
diff --git a/configs/model/im2im/skoots.yaml → configs/model/im2im/instance_seg.yaml b/configs/model/im2im/skoots.yaml → configs/model/im2im/instance_seg.yaml
@@ -39,7 +39,7 @@ _aux:
     - - ${target_col}
       - _target_: cyto_dl.nn.BaseHead
         loss:
-          _target_: cyto_dl.models.im2im.utils.SkootsLoss
+          _target_: cyto_dl.models.im2im.utils.InstanceSegLoss
           dim: ${spatial_dims}
         save_raw: True
         postprocess:

diff --git a/configs/model/im2im/omnipose.yaml b/configs/model/im2im/omnipose.yaml
diff --git a/configs/model/test/omnipose.yaml b/configs/model/test/omnipose.yaml
diff --git a/configs/trainer/default.yaml b/configs/trainer/default.yaml
@@ -7,9 +7,8 @@ max_epochs: 10
 
 accelerator: cpu
 devices: 1
-
 # mixed precision for extra speed-up
-# precision: 16
+precision: 16
 
 # perform a validation loop every N training epochs
 check_val_every_n_epoch: 1

diff --git a/configs/trainer/gpu.yaml b/configs/trainer/gpu.yaml
@@ -1,5 +1,4 @@
 defaults:
   - default.yaml
-precision: 16
 accelerator: gpu
 devices: 1
diff --git a/cyto_dl/models/im2im/utils/__init__.py b/cyto_dl/models/im2im/utils/__init__.py
@@ -1,15 +1,12 @@
 try:
-    from .omnipose import OmniposeClustering, OmniposeLoss, OmniposePreprocessd
+    from .instance_seg import (
+        InstanceSegCluster,
+        InstanceSegLoss,
+        InstanceSegPreprocessd,
+    )
 except (ModuleNotFoundError, ImportError):
-    OmniposeClustering = None
-    OmniposeLoss = None
-    OmniposePreprocessd = None
-
-try:
-    from .skoots import SkootsCluster, SkootsLoss, SkootsPreprocessd
-except (ModuleNotFoundError, ImportError):
-    SkootsCluster = None
-    SkootsLoss = None
-    SkootsPreprocessd = None
+    InstanceSegCluster = None
+    InstanceSegLoss = None
+    InstanceSegPreprocessd = None
 
 from .postprocessing import ActThreshLabel, DictToIm, detach