Merge branch 'develop' into develop

payalcha · Dec 6, 2024 · cdce7bb · cdce7bb
2 parents ea7c509 + 2c7bd71
commit cdce7bb
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Showing 5 changed files with 15 additions and 16 deletions.
diff --git a/openfl-workspace/tf_3dunet_brats/plan/cols.yaml b/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
diff --git a/openfl-workspace/tf_3dunet_brats/plan/plan.yaml b/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
diff --git a/openfl-workspace/tf_3dunet_brats/requirements.txt b/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
diff --git a/openfl-workspace/tf_3dunet_brats/src/dataloader.py b/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):
         """

diff --git a/openfl-workspace/tf_3dunet_brats/src/tf_3dunet_model.py b/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]
                   )
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,3 @@
		# Licensed subject to the terms of the separately executed evaluation license agreement between Intel Corporation and you.

		collaborators:
		- one