Merge 169c235 into ac86f80

docs/source/index.rst

@@ -9,6 +9,7 @@
    data/dataset.rst
    data/patch_based.rst
    transforms/transforms.rst
+   reproducibility.rst
    datasets.rst
    cli.rst
    slicer.rst

docs/source/reproducibility.rst

@@ -0,0 +1,3 @@
+###############
+Reproducibility
+###############

tests/transforms/augmentation/test_random_elastic_deformation.py

@@ -11,11 +11,10 @@ def test_random_elastic_deformation(self):
         transform = RandomElasticDeformation(
             num_control_points=5,
             max_displacement=(2, 3, 5),  # half grid spacing is (3.3, 3.3, 5)
-            seed=42,
         )
         keys = ('t1', 't2', 'label')
         fixtures = 2916.7192, 2955.1265, 2950
-        transformed = transform(self.sample)
+        transformed = transform(self.sample, seed=42)
         for key, fixture in zip(keys, fixtures):
             sample_data = self.sample[key].numpy()
             transformed_data = transformed[key].numpy()

tests/transforms/preprocessing/test_crop_pad.py

@@ -24,42 +24,43 @@ def test_no_changes_mask(self):
         transform = CropOrPad(shape, mask_name='label')
         with self.assertWarns(UserWarning):
             transformed = transform(self.sample)
-        for key in transformed:
-            image_dict = self.sample[key]
-            assert_array_equal(image_dict[DATA], transformed[key][DATA])
-            assert_array_equal(image_dict[AFFINE], transformed[key][AFFINE])
+        iterable = transformed.get_images_dict(intensity_only=False).items()
+        for image_name, image in iterable:
+            image = self.sample[image_name]
+            assert_array_equal(image[DATA], transformed[image_name][DATA])
+            assert_array_equal(image[AFFINE], transformed[image_name][AFFINE])
 
     def test_different_shape(self):
         shape = self.sample['t1'].spatial_shape
         target_shape = 9, 21, 30
         transform = CropOrPad(target_shape)
         transformed = transform(self.sample)
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             self.assertNotEqual(shape, result_shape)
 
     def test_shape_right(self):
         target_shape = 9, 21, 30
         transform = CropOrPad(target_shape)
         transformed = transform(self.sample)
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             self.assertEqual(target_shape, result_shape)
 
     def test_only_pad(self):
         target_shape = 11, 22, 30
         transform = CropOrPad(target_shape)
         transformed = transform(self.sample)
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             self.assertEqual(target_shape, result_shape)
 
     def test_only_crop(self):
         target_shape = 9, 18, 30
         transform = CropOrPad(target_shape)
         transformed = transform(self.sample)
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             self.assertEqual(target_shape, result_shape)
 
     def test_shape_negative(self):
@@ -77,8 +78,8 @@ def test_shape_string(self):
     def test_shape_one(self):
         transform = CropOrPad(1)
         transformed = transform(self.sample)
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             self.assertEqual((1, 1, 1), result_shape)
 
     def test_wrong_mask_name(self):
@@ -106,17 +107,15 @@ def test_mask_only_pad(self):
         mask [0, 4:6, 5:8, 3:7] = 1
         transformed = transform(self.sample)
         shapes = []
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             shapes.append(result_shape)
         set_shapes = set(shapes)
         message = f'Images have different shapes: {set_shapes}'
         assert len(set_shapes) == 1, message
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
-            self.assertEqual(target_shape, result_shape,
-                f'Wrong shape for image: {key}',
-            )
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
+            self.assertEqual(target_shape, result_shape)
 
     def test_mask_only_crop(self):
         target_shape = 9, 18, 30
@@ -126,17 +125,15 @@ def test_mask_only_crop(self):
         mask [0, 4:6, 5:8, 3:7] = 1
         transformed = transform(self.sample)
         shapes = []
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
             shapes.append(result_shape)
         set_shapes = set(shapes)
         message = f'Images have different shapes: {set_shapes}'
         assert len(set_shapes) == 1, message
-        for key in transformed:
-            result_shape = transformed[key].spatial_shape
-            self.assertEqual(target_shape, result_shape,
-                f'Wrong shape for image: {key}',
-            )
+        for image in transformed.get_images(intensity_only=False):
+            result_shape = image.spatial_shape
+            self.assertEqual(target_shape, result_shape)
 
     def test_center_mask(self):
         """The mask bounding box and the input image have the same center"""
@@ -148,8 +145,9 @@ def test_center_mask(self):
         mask[0, 4:6, 9:11, 14:16] = 1
         transformed_center = transform_center(self.sample)
         transformed_mask = transform_mask(self.sample)
-        zipped = zip(transformed_center.values(), transformed_mask.values())
-        for image_center, image_mask in zipped:
+        tc_images = transformed_center.get_images(intensity_only=False)
+        tm_images = transformed_mask.get_images(intensity_only=False)
+        for image_center, image_mask in zip(tc_images, tm_images):
             assert_array_equal(
                 image_center[DATA], image_mask[DATA],
                 'Data is different after cropping',
@@ -171,8 +169,9 @@ def test_mask_corners(self):
         mask[0, -1, -1, -1] = 1
         transformed_center = transform_center(self.sample)
         transformed_mask = transform_mask(self.sample)
-        zipped = zip(transformed_center.values(), transformed_mask.values())
-        for image_center, image_mask in zipped:
+        tc_images = transformed_center.get_images(intensity_only=False)
+        tm_images = transformed_mask.get_images(intensity_only=False)
+        for image_center, image_mask in zip(tc_images, tm_images):
             assert_array_equal(
                 image_center[DATA], image_mask[DATA],
                 'Data is different after cropping',
@@ -193,8 +192,9 @@ def test_mask_origin(self):
         mask[0, 0, 0, 0] = 1
         transformed_center = transform_center(self.sample)
         transformed_mask = transform_mask(self.sample)
-        zipped = zip(transformed_center.values(), transformed_mask.values())
-        for image_center, image_mask in zipped:
+        tc_images = transformed_center.get_images(intensity_only=False)
+        tm_images = transformed_mask.get_images(intensity_only=False)
+        for image_center, image_mask in zip(tc_images, tm_images):
             # Arrays are different
             assert not np.array_equal(image_center[DATA], image_mask[DATA])
             # Rotation matrix doesn't change

tests/transforms/preprocessing/test_resample.py

@@ -13,33 +13,32 @@ def test_spacing(self):
         spacing = 2
         transform = Resample(spacing)
         transformed = transform(self.sample)
-        for image_dict in transformed.values():
-            image = image_dict.as_sitk()
+        for image in transformed.get_images(intensity_only=False):
+            image = image.as_sitk()
             self.assertEqual(image.GetSpacing(), 3 * (spacing,))
 
     def test_reference_name(self):
         sample = self.get_inconsistent_sample()
         reference_name = 't1'
         transform = Resample(reference_name)
         transformed = transform(sample)
-        ref_image_dict = sample[reference_name]
-        for image_dict in transformed.values():
-            self.assertEqual(
-                ref_image_dict.shape, image_dict.shape)
-            assert_array_equal(ref_image_dict[AFFINE], image_dict[AFFINE])
+        ref_image = sample[reference_name]
+        for image in transformed.get_images(intensity_only=False):
+            self.assertEqual(ref_image.shape, image.shape)
+            assert_array_equal(ref_image[AFFINE], image[AFFINE])
 
     def test_affine(self):
         spacing = 1
         affine_name = 'pre_affine'
         transform = Resample(spacing, pre_affine_name=affine_name)
         transformed = transform(self.sample)
-        for image_dict in transformed.values():
-            if affine_name in image_dict.keys():
+        for image in transformed.get_images(intensity_only=False):
+            if affine_name in image.keys():
                 new_affine = np.eye(4)
                 new_affine[0, 3] = 10
-                assert_array_equal(image_dict[AFFINE], new_affine)
+                assert_array_equal(image[AFFINE], new_affine)
             else:
-                assert_array_equal(image_dict[AFFINE], np.eye(4))
+                assert_array_equal(image[AFFINE], np.eye(4))
 
     def test_missing_affine(self):
         transform = Resample(1, pre_affine_name='missing')
@@ -50,7 +49,7 @@ def test_reference_path(self):
         reference_image, reference_path = self.get_reference_image_and_path()
         transform = Resample(reference_path)
         transformed = transform(self.sample)
-        for image in transformed.values():
+        for image in transformed.get_images(intensity_only=False):
             self.assertEqual(reference_image.shape, image.shape)
             assert_array_equal(reference_image.affine, image.affine)
 

tests/transforms/test_reproducibility.py

@@ -0,0 +1,89 @@
+import warnings
+import torch
+import torchio
+from torchio import Subject, Image, INTENSITY
+from torchio.transforms import RandomNoise
+from ..utils import TorchioTestCase
+
+
+class TestReproducibility(TorchioTestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.subject = Subject(img=Image(tensor=torch.ones(4, 4, 4)))
+
+    def random_stuff(self, seed=None):
+        transform = RandomNoise(std=(100, 100))#, seed=seed)
+        transformed = transform(self.subject, seed=seed)
+        value = transformed.img.data.sum().item()
+        _, seed = transformed.get_applied_transforms()[0]
+        return value, seed
+
+    def test_reproducibility_no_seed(self):
+        a, seed_a = self.random_stuff()
+        b, seed_b = self.random_stuff()
+        self.assertNotEqual(a, b)
+        c, seed_c = self.random_stuff(seed_a)
+        self.assertEqual(c, a)
+        self.assertEqual(seed_c, seed_a)
+
+    def test_reproducibility_seed(self):
+        torch.manual_seed(42)
+        a, seed_a = self.random_stuff()
+        b, seed_b = self.random_stuff()
+        self.assertNotEqual(a, b)
+        c, seed_c = self.random_stuff(seed_a)
+        self.assertEqual(c, a)
+        self.assertEqual(seed_c, seed_a)
+
+        torch.manual_seed(42)
+        a2, seed_a2 = self.random_stuff()
+        self.assertEqual(a2, a)
+        self.assertEqual(seed_a2, seed_a)
+        b2, seed_b2 = self.random_stuff()
+        self.assertNotEqual(a2, b2)
+        self.assertEqual(b2, b)
+        self.assertEqual(seed_b2, seed_b)
+        c2, seed_c2 = self.random_stuff(seed_a2)
+        self.assertEqual(c2, a2)
+        self.assertEqual(seed_c2, seed_a2)
+        self.assertEqual(c2, c)
+        self.assertEqual(seed_c2, seed_c)
+
+    # def test_all_random_transforms(self):
+    #     sample = Subject(
+    #         t1=Image(tensor=torch.rand(20, 20, 20)),
+    #         seg=Image(tensor=torch.rand(20, 20, 20) > 1, type=INTENSITY)
+    #     )
+
+    #     transforms_names = [
+    #         name
+    #         for name in dir(torchio)
+    #         if name.startswith('Random')
+    #     ]
+
+    #     # Downsample at the end so that the image shape is not modified
+    #     transforms_names.remove('RandomDownsample')
+    #     transforms_names.append('RandomDownsample')
+
+    #     transforms = []
+    #     for transform_name in transforms_names:
+    #         transform = getattr(torchio, transform_name)()
+    #         transforms.append(transform)
+    #     composed_transform = torchio.Compose(transforms)
+    #     with warnings.catch_warnings():  # ignore elastic deformation warning
+    #         warnings.simplefilter('ignore', UserWarning)
+    #         transformed = composed_transform(sample)
+
+    #     new_transforms = []
+    #     for transform_name, params_dict in transformed.history:
+    #         transform_class = getattr(torchio, transform_name)
+    #         transform = transform_class(seed=params_dict['seed'])
+    #         new_transforms.append(transform)
+    #     composed_transform = torchio.Compose(transforms)
+    #     with warnings.catch_warnings():  # ignore elastic deformation warning
+    #         warnings.simplefilter('ignore', UserWarning)
+    #         new_transformed = composed_transform(sample)
+
+    #     self.assertTensorEqual(transformed.t1.data, new_transformed.t1.data)
+    #     self.assertTensorEqual(transformed.seg.data, new_transformed.seg.data)

tests/utils.py

@@ -4,6 +4,7 @@
 import tempfile
 import unittest
 from pathlib import Path
+import torch
 import numpy as np
 import nibabel as nib
 from torchio.datasets import IXITiny
@@ -54,6 +55,14 @@ def setUp(self):
         self.dataset = ImagesDataset(self.subjects_list)
         self.sample = self.dataset[-1]
 
+    def tearDown(self):
+        """Tear down test fixtures, if any."""
+        print('Deleting', self.dir)
+        shutil.rmtree(self.dir)
+
+    def assertTensorEqual(self, a, b):
+        assert torch.all(torch.eq(a, b))
+
     def make_2d(self, sample):
         sample = copy.deepcopy(sample)
         for image in sample.get_images(intensity_only=False):
@@ -85,11 +94,6 @@ def get_reference_image_and_path(self):
         image = Image(path, INTENSITY)
         return image, path
 
-    def tearDown(self):
-        """Tear down test fixtures, if any."""
-        print('Deleting', self.dir)
-        shutil.rmtree(self.dir)
-
     def get_ixi_tiny(self):
         root_dir = Path(tempfile.gettempdir()) / 'torchio' / 'ixi_tiny'
         return IXITiny(root_dir, download=True)

torchio/cli.py

@@ -51,14 +51,13 @@ def apply_transform(
         raise ValueError(message) from error
 
     params_dict = get_params_dict_from_kwargs(kwargs)
-    if issubclass(transform_class, RandomTransform):
-        params_dict['seed'] = seed
     transform = transform_class(**params_dict)
     apply_transform_to_file(
         input_path,
         transform,
         output_path,
         verbose=verbose,
+        seed=seed,
     )
     return 0
 

torchio/data/queue.py

@@ -54,7 +54,7 @@ class Queue(Dataset):
     >>> patch_size = 96
     >>> queue_length = 300
     >>> samples_per_volume = 10
-    >>> sample = torchio.data.UniformSampler(patch_size)
+    >>> sampler = torchio.data.UniformSampler(patch_size)
     >>> patches_queue = torchio.Queue(
     ...     subjects_dataset,  # instance of torchio.ImagesDataset
     ...     queue_length,