Feature/update transforms (#293)

* off by one * add non-dict resize * fix configs * delete resize --------- Co-authored-by: Benjamin Morris <[email protected]>
AllenCellModeling · Sep 25, 2023 · a9be90c · a9be90c
1 parent 6ca7278
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Showing 8 changed files with 62 additions and 179 deletions.
diff --git a/configs/data/im2im/gan.yaml b/configs/data/im2im/gan.yaml
@@ -33,12 +33,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       # GANs use Tanh as final activation, target has to be in range [-1,1]
@@ -82,12 +79,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       # GANs use Tanh as final activation, target has to be in range [-1,1]
@@ -118,11 +112,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${source_col}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${source_col}
       # input to synthetic image generation model is a semantic segmentation
@@ -153,12 +145,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       # GANs use Tanh as final activation, target has to be in range [-1,1]

diff --git a/configs/data/im2im/labelfree.yaml b/configs/data/im2im/labelfree.yaml
@@ -31,12 +31,9 @@ transforms:
             C: 5
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -81,12 +78,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -104,6 +98,9 @@ transforms:
             C: 5
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${source_col}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -130,12 +127,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd

diff --git a/configs/data/im2im/omnipose.yaml b/configs/data/im2im/omnipose.yaml
@@ -31,12 +31,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.omnipose.OmniposePreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
@@ -84,12 +81,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.omnipose.OmniposePreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
@@ -111,6 +105,9 @@ transforms:
             C: 5
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${source_col}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -137,12 +134,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.omnipose.OmniposePreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}

diff --git a/configs/data/im2im/segmentation.yaml b/configs/data/im2im/segmentation.yaml
@@ -31,12 +31,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -86,12 +83,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -115,6 +109,9 @@ transforms:
             C: 5
       - _target_: monai.transforms.AddChanneld
         keys: ${source_col}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${source_col}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -141,12 +138,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${data.columns}
       - _target_: monai.transforms.NormalizeIntensityd

diff --git a/configs/data/im2im/skoots.yaml b/configs/data/im2im/skoots.yaml
@@ -31,12 +31,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
@@ -84,12 +81,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}
@@ -111,6 +105,9 @@ transforms:
             C: 5
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: monai.transforms.ToTensord
         keys: ${source_col}
       - _target_: monai.transforms.NormalizeIntensityd
@@ -137,12 +134,9 @@ transforms:
             C: 0
       - _target_: monai.transforms.AddChanneld
         keys: ${data.columns}
-      - _target_: cyto_dl.image.transforms.Resized
-        keys:
-          - ${source_col}
-          - ${target_col}
-        scale_factor: 0.25
-        spatial_dims: ${spatial_dims}
+      - _target_: monai.transforms.Zoomd
+        keys: ${data.columns}
+        zoom: 0.25
       - _target_: cyto_dl.models.im2im.utils.SkootsPreprocessd
         label_keys: ${target_col}
         dim: ${spatial_dims}

diff --git a/cyto_dl/image/transforms/__init__.py b/cyto_dl/image/transforms/__init__.py
@@ -2,7 +2,7 @@
 from .contrastadjust import ContrastAdjustd
 from .multiscale_cropper import RandomMultiScaleCropd
 from .project import MaxProjectd
-from .resize import Resized
+from .resize import Resize, Resized
 from .save import Save, Saved
 
 try:

diff --git a/cyto_dl/image/transforms/multiscale_cropper.py b/cyto_dl/image/transforms/multiscale_cropper.py
@@ -109,7 +109,7 @@ def _get_max_start_indices(self, image_dict: Dict):
             max_start_indices = np.minimum(max_start_indices_img, max_start_indices)
             if np.any(max_start_indices < 0):
                 raise ValueError(f"Crop size {roi_size} is too large for image size {shape}")
-        return max_start_indices
+        return max_start_indices + 1  # range doesn't include end
 
     def generate_slices(self, image_dict: Dict) -> Dict:
         """Generate dictionary of slices at all scales starting at random point."""

diff --git a/cyto_dl/image/transforms/resize.py b/cyto_dl/image/transforms/resize.py