added demo.py

Former-commit-id: fcd6610 [formerly b644919]
Former-commit-id: 64a7701

.gitignore

@@ -201,5 +201,4 @@ examples/process_one.py
 
 tests/temp_folder*
 examples/data_test
-data
-demo.py
+data

demo.py

@@ -0,0 +1,57 @@
+from imgtools.io import Dataset
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.optim as optim
+import numpy as np
+import torchio as tio
+import os
+from torch.utils.data import DataLoader
+from typing import List
+import re
+
+class select_roi_names(tio.LabelTransform):
+    """
+    Based on the given roi names, selects from the given set
+    """
+    def __init__(
+            self,
+            roi_names: List[str] = None,
+            **kwargs
+            ) -> None:
+        super().__init__(**kwargs)
+        self.kwargs = kwargs
+        self.roi_names = roi_names
+
+    def apply_transform(self,subject):
+        #list of roi_names
+        metadata = subject["metadata_RTSTRUCT_CT"]
+        for image in self.get_images(subject):
+            patterns = self.roi_names
+            mask = torch.empty_like(image.data)[:len(patterns)]
+            for j,pat in enumerate(patterns):
+                k = []
+                for i,col in enumerate(metadata):
+                    if re.match(pat,col,flags=re.IGNORECASE):
+                        k.append(i)
+                        print(col)
+                mask[j] = (image.data[k].sum(axis=0)>0)*1    
+            image.set_data(mask)
+        return subject
+
+    def is_invertible(self):
+        return False
+
+
+#Data directory
+output_directory = "/cluster/projects/radiomics/Temp/vishwesh/demo_data"
+transforms = tio.Compose([
+    tio.ToCanonical(),
+    tio.Resample(4),
+    tio.CropOrPad((96,96,40))],
+    select_roi_names(["^Body$"]),
+    tio.RandomFlip(),
+    tio.OneHot())
+subjects_dataset = Dataset.load_from_nrrd(output_directory,transform=transforms,ignore_multi=True)
+training_loader = DataLoader(subjects_dataset, batch_size=4)
+

requirements.txt

@@ -8,4 +8,6 @@ pytest
 scikit-image
 SimpleITK
 tqdm
+torch
 torchio
+pyvis