Fix get_subjects_from_batch ignoring metadata (#1131)

* added test that shows metadata issues

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* Fix get_subjects_from_batch ignoring metadata

---------

Co-authored-by: Max Konowski <max.konowski@uni-muenster.de>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Fernando Pérez-García <fepegar@gmail.com>

src/torchio/utils.py

@@ -248,17 +248,17 @@ def get_batch_images_and_size(batch: Dict) -> Tuple[List[str], int]:
 
     Args:
         batch: Dictionary generated by a :class:`torch.utils.data.DataLoader`
-        extracting data from a :class:`torchio.SubjectsDataset`.
+            extracting data from a :class:`torchio.SubjectsDataset`.
 
     Raises:
         RuntimeError: If the batch does not seem to contain any dictionaries
-        that seem to represent a :class:`torchio.Image`.
+            that seem to represent a :class:`torchio.Image`.
     """
     names = []
-    for image_name, image_dict in batch.items():
-        if constants.DATA in image_dict:  # assume it is a TorchIO Image
-            size = len(image_dict[constants.DATA])
-            names.append(image_name)
+    for key, value in batch.items():
+        if isinstance(value, dict) and constants.DATA in value:
+            size = len(value[constants.DATA])
+            names.append(key)
     if not names:
         raise RuntimeError('The batch does not seem to contain any images')
     return names, size
@@ -269,28 +269,38 @@ def get_subjects_from_batch(batch: Dict) -> List:
 
     Args:
         batch: Dictionary generated by a :class:`torch.utils.data.DataLoader`
-        extracting data from a :class:`torchio.SubjectsDataset`.
+            extracting data from a :class:`torchio.SubjectsDataset`.
     """
     from .data import ScalarImage, LabelMap, Subject
 
     subjects = []
     image_names, batch_size = get_batch_images_and_size(batch)
+
     for i in range(batch_size):
         subject_dict = {}
-        for image_name in image_names:
-            image_dict = batch[image_name]
-            data = image_dict[constants.DATA][i]
-            affine = image_dict[constants.AFFINE][i]
-            path = Path(image_dict[constants.PATH][i])
-            is_label = image_dict[constants.TYPE][i] == constants.LABEL
-            klass = LabelMap if is_label else ScalarImage
-            image = klass(tensor=data, affine=affine, filename=path.name)
-            subject_dict[image_name] = image
+
+        for key, value in batch.items():
+            if key in image_names:
+                image_name = key
+                image_dict = value
+                data = image_dict[constants.DATA][i]
+                affine = image_dict[constants.AFFINE][i]
+                path = Path(image_dict[constants.PATH][i])
+                is_label = image_dict[constants.TYPE][i] == constants.LABEL
+                klass = LabelMap if is_label else ScalarImage
+                image = klass(tensor=data, affine=affine, filename=path.name)
+                subject_dict[image_name] = image
+            else:
+                instance_value = value[i]
+                subject_dict[key] = instance_value
+
         subject = Subject(subject_dict)
+
         if constants.HISTORY in batch:
             applied_transforms = batch[constants.HISTORY][i]
             for transform in applied_transforms:
                 transform.add_transform_to_subject_history(subject)
+
         subjects.append(subject)
     return subjects
 

tests/test_utils.py

@@ -48,6 +48,33 @@ def test_subjects_from_batch(self):
         subjects = tio.utils.get_subjects_from_batch(batch)
         assert isinstance(subjects[0], tio.Subject)
 
+    def test_subjects_from_batch_with_string_metadata(self):
+        subject_c_with_string_metadata = tio.Subject(
+            name='John Doe',
+            label=tio.LabelMap(self.get_image_path('label_c', binary=True)),
+        )
+
+        dataset = tio.SubjectsDataset(4 * [subject_c_with_string_metadata])
+        loader = torch.utils.data.DataLoader(dataset, batch_size=4)
+        batch = tio.utils.get_first_item(loader)
+        subjects = tio.utils.get_subjects_from_batch(batch)
+        assert isinstance(subjects[0], tio.Subject)
+        assert 'label' in subjects[0]
+        assert 'name' in subjects[0]
+
+    def test_subjects_from_batch_with_int_metadata(self):
+        subject_c_with_int_metadata = tio.Subject(
+            age=45,
+            label=tio.LabelMap(self.get_image_path('label_c', binary=True)),
+        )
+        dataset = tio.SubjectsDataset(4 * [subject_c_with_int_metadata])
+        loader = torch.utils.data.DataLoader(dataset, batch_size=4)
+        batch = tio.utils.get_first_item(loader)
+        subjects = tio.utils.get_subjects_from_batch(batch)
+        assert isinstance(subjects[0], tio.Subject)
+        assert 'label' in subjects[0]
+        assert 'age' in subjects[0]
+
     def test_add_images_from_batch(self):
         subject = copy.deepcopy(self.sample_subject)
         subjects = 4 * [subject]