update to new monai

configs/data/im2im/gan.yaml

@@ -31,7 +31,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -77,7 +78,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -110,7 +112,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${source_col}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -143,7 +146,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}

configs/data/im2im/labelfree.yaml

@@ -29,7 +29,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 5
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -76,7 +77,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -96,7 +98,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 5
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -125,7 +128,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}

configs/data/im2im/omnipose.yaml

@@ -29,7 +29,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -79,7 +80,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -103,7 +105,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 5
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -132,7 +135,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}

configs/data/im2im/segmentation.yaml

@@ -29,7 +29,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -81,7 +82,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -107,7 +109,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 5
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${source_col}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -136,7 +139,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}

configs/data/im2im/skoots.yaml

@@ -29,7 +29,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -79,7 +80,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -103,7 +105,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 5
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}
@@ -132,7 +135,8 @@ transforms:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: "ZYX"
             C: 0
-      - _target_: monai.transforms.AddChanneld
+      - _target_: monai.transforms.EnsureChannelFirstd
+        channel_dim: "no_channel"
         keys: ${data.columns}
       - _target_: monai.transforms.Zoomd
         keys: ${data.columns}

configs/data/private/variance_npm1.yaml

@@ -31,7 +31,8 @@ transforms:
     threshold: -2.
     above: true
     cval: -2.
-  - _target_: monai.transforms.AddChanneld
+  - _target_: monai.transforms.EnsureChannelFirstd
+    channel_dim: "no_channel"
     keys: image
   - _target_: monai.transforms.ToTensord
     keys: [image]

configs/experiment/private/lattice_nuc_sdf.yaml

@@ -33,7 +33,8 @@ data:
     - _target_: monai.transforms.Transposed
       keys: [image]
       indices: [2, 1, 0]
-    - _target_: monai.transforms.AddChanneld
+    - _target_: monai.transforms.EnsureChannelFirstd
+      channel_dim: "no_channel"
       keys: image
     - _target_: monai.transforms.ThresholdIntensityd
       keys: [image]

configs/experiment/private/npm1_classical_scale_inv.yaml

@@ -30,7 +30,8 @@ data:
     - _target_: cyto_dl.image.io.ReadNumpyFile
       keys: [image]
       remote: false
-    - _target_: monai.transforms.AddChanneld
+    - _target_: monai.transforms.EnsureChannelFirstd
+      channel_dim: "no_channel"
       keys: image
     - _target_: monai.transforms.NormalizeIntensityd
       keys: image

configs/experiment/private/npm1_scale_inv_canon_so3.yaml

@@ -30,7 +30,8 @@ data:
     - _target_: cyto_dl.image.io.ReadNumpyFile
       keys: [image]
       remote: false
-    - _target_: monai.transforms.AddChanneld
+    - _target_: monai.transforms.EnsureChannelFirstd
+      channel_dim: "no_channel"
       keys: image
     - _target_: monai.transforms.NormalizeIntensityd
       keys: image

configs/experiment/private/npm1_so2_scale_inv.yaml

@@ -33,7 +33,8 @@ data:
     - _target_: cyto_dl.image.io.ReadNumpyFile
       keys: [image]
       remote: false
-    - _target_: monai.transforms.AddChanneld
+    - _target_: monai.transforms.EnsureChannelFirstd
+      channel_dim: "no_channel"
       keys: image
     #    - _target_: monai.transforms.ThresholdIntensityd
     #      keys: image

configs/experiment/private/npm1_so3_scale_inv.yaml

@@ -30,7 +30,8 @@ data:
     - _target_: cyto_dl.image.io.ReadNumpyFile
       keys: [image]
       remote: false
-    - _target_: monai.transforms.AddChanneld
+    - _target_: monai.transforms.EnsureChannelFirstd
+      channel_dim: "no_channel"
       keys: image
     - _target_: monai.transforms.NormalizeIntensityd
       keys: image

cyto_dl/callbacks/outlier_detection.py

@@ -118,7 +118,7 @@ def on_predict_epoch_start(self, trainer, pl_module):
 
     def _inference_batch_end(self, batch):
         if self._run:
-            batch_names = batch["raw_meta_dict"]["filename_or_obj"]
+            batch_names = batch["raw"].meta["filename_or_obj"]
             # activations are saved per-patch
             distances_per_image = len(self.mahalanobis_distances[self.layer_names[0]]) // len(
                 batch_names

cyto_dl/datamodules/czi.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pandas as pd
 from aicsimageio.aics_image import AICSImage
-from monai.data import DataLoader, Dataset
+from monai.data import DataLoader, Dataset, MetaTensor
 from monai.transforms import Compose, apply_transform
 from omegaconf import ListConfig
 
@@ -129,13 +129,17 @@ def _transform(self, index: int):
         img.set_scene(img_data.pop("scene"))
         data_i = img.get_image_dask_data(**img_data).compute()
         data_i = self._ensure_channel_first(data_i)
+        output_img = (
+            apply_transform(self.transform, data_i) if self.transform is not None else data_i
+        )
+
         return {
-            self.out_key: apply_transform(self.transform, data_i)
-            if self.transform is not None
-            else data_i,
-            f"{self.out_key}_meta_dict": {
-                "filename_or_obj": original_path.replace(".", self._metadata_to_str(img_data))
-            },
+            self.out_key: MetaTensor(
+                output_img,
+                meta={
+                    "filename_or_obj": original_path.replace(".", self._metadata_to_str(img_data))
+                },
+            )
         }
 
     def __len__(self):

cyto_dl/image/io/aicsimage_loader.py

@@ -1,6 +1,7 @@
 from typing import List
 
 from aicsimageio import AICSImage
+from monai.data import MetaTensor
 from monai.transforms import Transform
 
 
@@ -52,7 +53,6 @@ def __call__(self, data):
             img.set_scene(data[self.scene_key])
         kwargs = {k: data[k] for k in self.kwargs_keys}
         img = img.get_image_dask_data(**kwargs).compute()
-        data[self.out_key] = img
-        data[f"{self.out_key}_meta_dict"] = {"filename_or_obj": path, "kwargs": kwargs}
+        data[self.out_key] = MetaTensor(img, meta={"filename_or_obj": path, "kwargs": kwargs})
 
         return data

cyto_dl/models/im2im/gan.py

@@ -174,6 +174,7 @@ def _extract_loss(self, outs, loss_type):
         return self._sum_losses(loss)
 
     def model_step(self, stage, batch, batch_idx):
+        batch["filenames"] = batch[self.hparams.x_key].meta["filename_or_obj"]
         # convert monai metatensors to tensors
         for k, v in batch.items():
             if isinstance(v, MetaTensor):
@@ -210,6 +211,7 @@ def model_step(self, stage, batch, batch_idx):
         return loss_dict, None, None
 
     def predict_step(self, batch, batch_idx):
+        batch["filenames"] = batch[self.hparams.x_key].meta["filename_or_obj"]
         # convert monai metatensors to tensors
         for k, v in batch.items():
             if isinstance(v, MetaTensor):

cyto_dl/models/im2im/multi_task.py

@@ -168,24 +168,21 @@ def _get_run_heads(self, batch, stage):
 
     def model_step(self, stage, batch, batch_idx):
         # convert monai metatensors to tensors
+        batch["filenames"] = batch[self.hparams.x_key].meta["filename_or_obj"]
         for k, v in batch.items():
             if isinstance(v, MetaTensor):
                 batch[k] = v.as_tensor()
 
         run_heads = self._get_run_heads(batch, stage)
         outs = self.run_forward(batch, stage, self.should_save_image(batch_idx, stage), run_heads)
 
-        if stage != "predict":
-            losses = {head_name: head_result["loss"] for head_name, head_result in outs.items()}
-            losses = self._sum_losses(losses)
-            return losses, None, None
-
-        preds = {head_name: head_result["y_hat_out"] for head_name, head_result in outs.items()}
-
-        return None, preds, None
+        losses = {head_name: head_result["loss"] for head_name, head_result in outs.items()}
+        losses = self._sum_losses(losses)
+        return losses, None, None
 
     def predict_step(self, batch, batch_idx):
         stage = "predict"
+        batch["filenames"] = batch[self.hparams.x_key].meta["filename_or_obj"]
         # convert monai metatensors to tensors
         for k, v in batch.items():
             if isinstance(v, MetaTensor):

cyto_dl/nn/head/base_head.py

@@ -68,15 +68,13 @@ def save_image(self, y_hat, batch, stage, global_step):
             if self.save_raw:
                 raw_out = self._postprocess(batch[self.x_key], img_type="input")
         try:
-            metadata_filenames = batch[f"{self.x_key}_meta_dict"]["filename_or_obj"]
+            metadata_filenames = batch["filenames"]
             filename_map = {"input": metadata_filenames, "output": []}
             metadata_filenames = [
                 f"{Path(fn).stem}_{self.head_name}.tif" for fn in metadata_filenames
             ]
         except KeyError:
-            raise ValueError(
-                f"Please ensure your batches contain key `{self.x_key}_meta_dict['filename_or_obj']`"
-            )
+            raise ValueError("Please ensure your batches have key `filenames`")
         save_name = (
             [f"{global_step}_{self.head_name}.tif"]
             if stage in ("train", "val")