refactors FetalPlaneDataset adding downsampling_factor and tested in …

…notebooks (#4)
budai4medtech · Jul 2, 2023 · 2ef338b · 2ef338b
1 parent 1f0bbf2
commit 2ef338b
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Showing 3 changed files with 23 additions and 15 deletions.
diff --git a/examples/difussion-super-resolution-gan/DSRGAN.ipynb b/examples/difussion-super-resolution-gan/DSRGAN.ipynb
@@ -64,7 +64,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {
     "id": "RjqaHOU9UiCn"
    },
@@ -132,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -166,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "id": "6O8mjlKLI23w"
    },
@@ -179,7 +179,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {
     "id": "2HMQVMOsUxqN"
    },
@@ -287,6 +287,9 @@
     "# batch_size = 16\n",
     "# batch_size = 128\n",
     "\n",
+    "\n",
+    "downsampling_factor = 2\n",
+    "\n",
     "# # Data augmentation and preprocessing \n",
     "# monai_transform_operations=transforms.Compose([\n",
     "#                         transforms.ToTensor(),\n",
@@ -318,7 +321,8 @@
     "                            #transform=monai_transform_operations,\n",
     "                            transform=transform_operations,  \n",
     "                            train=True,\n",
-    "                            train_size=256\n",
+    "                            train_size=256,\n",
+    "                            downsampling_factor=downsampling_factor\n",
     "                            )\n",
     "\n",
     "train_size = 12\n",

diff --git a/examples/preparing_dataset_fetal_planes.ipynb b/examples/preparing_dataset_fetal_planes.ipynb
diff --git a/medisynth/medisynth.py b/medisynth/medisynth.py
@@ -16,7 +16,8 @@ def __init__(self, root_dir, ref,
                  operator_number=None,
                  transform=None,
                  train=None,
-                 train_size=100
+                 train_size=100,
+                 downsampling_factor=2
                  ):
         """
         Args:
@@ -33,6 +34,7 @@ def __init__(self, root_dir, ref,
         return image
         """
         self.transform = transform
+        self.downsampling_factor = downsampling_factor
         self.root_dir = root_dir
         self.ref = pd.read_csv(ref, sep=';')
         self.ref = self.ref[self.ref['Plane'] == plane]
@@ -72,10 +74,9 @@ def __getitem__(self, idx):
             image = self.transform(image)
 
         ## Make a half sized image for SRGAN
-        downsampling = 2
         ds_image = resize(
             image.cpu().numpy(),
-            (image.shape[0], image.shape[1] / downsampling, image.shape[2] / downsampling)
+            (image.shape[0], image.shape[1] / self.downsampling_factor, image.shape[2] / self.downsampling_factor)
         )
         # .cpu().numpy()#TypeError: Cannot interpret 'torch.float32' as a data type