Fix for tf_3dunet_barts workspace (#1197)

Signed-off-by: yes <[email protected]>

Author: tanwarsh

openfl-workspace/tf_3dunet_brats/plan/cols.yaml

@@ -2,4 +2,3 @@
 # Licensed subject to the terms of the separately executed evaluation license agreement between Intel Corporation and you.
 
 collaborators:
-   - one

openfl-workspace/tf_3dunet_brats/plan/plan.yaml

@@ -36,15 +36,6 @@ data_loader:
   template: src.tf_brats_dataloader.TensorFlowBratsDataLoader
 network:
   defaults: plan/defaults/network.yaml
-  settings:
-    agg_addr: DESKTOP-AOKV1IJ.localdomain
-    agg_port: auto
-    cert_folder: cert
-    client_reconnect_interval: 5
-    disable_client_auth: false
-    disable_tls: false
-    hash_salt: auto
-  template: openfl.federation.Network
 task_runner:
   defaults: plan/defaults/task_runner.yaml
   settings:
@@ -80,4 +71,3 @@ tasks:
       epochs: 1
       metrics:
       - loss
-      num_batches: 1

openfl-workspace/tf_3dunet_brats/requirements.txt

@@ -1,5 +1,6 @@
+keras==2.13.1
 nibabel
 numpy
 
 setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability
-tensorflow>=2
+tensorflow==2.13.0

openfl-workspace/tf_3dunet_brats/src/dataloader.py

@@ -53,15 +53,24 @@ def create_file_list(self):
 
         Split into training and testing sets.
         """
-        searchpath = os.path.join(self.data_path, '*/*_seg.nii.gz')
+        extension = '_seg.nii.gz'
+        flair_extension = '_flair.nii.gz'
+        searchpath = os.path.join(self.data_path, "*/*" + extension)
         filenames = tf.io.gfile.glob(searchpath)
 
+        # check for uncompressed files
+        if not filenames:
+            extension = '_seg.nii'
+            flair_extension = '_flair.nii'
+            searchpath = os.path.join(self.data_path, "*/*" + extension)
+            filenames = tf.io.gfile.glob(searchpath)
+
         # Create a dictionary of tuples with image filename and label filename
 
         self.num_files = len(filenames)
         self.filenames = {}
         for idx, filename in enumerate(filenames):
-            self.filenames[idx] = [filename.replace('_seg.nii.gz', '_flair.nii.gz'), filename]
+            self.filenames[idx] = [filename.replace(extension, flair_extension), filename]
 
     def z_normalize_img(self, img):
         """

openfl-workspace/tf_3dunet_brats/src/tf_3dunet_model.py

@@ -80,7 +80,7 @@ def create_model(self,
                             initial_filters=initial_filters,
                             batch_norm=batch_norm)
 
-        self.optimizer = tf.keras.optimizers.Adam()
+        self.optimizer = tf.keras.optimizers.legacy.Adam()
 
         model.compile(
             loss=dice_loss,
@@ -193,7 +193,7 @@ def create_model(self,
                         )
 
     model.compile(loss=dice_loss,
-                  optimizer=tf.keras.optimizers.Adam(learning_rate=0.01),
+                  optimizer=tf.keras.optimizers.legacy.Adam(learning_rate=0.01),
                   metrics=[dice_coef, soft_dice_coef]
                   )