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import copy |
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import shutil |
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3
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import random |
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4
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import tempfile |
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5
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import unittest |
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6
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from pathlib import Path |
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8
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import torch |
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import numpy as np |
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import nibabel as nib |
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from numpy.testing import assert_array_equal, assert_raises |
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from torchio.datasets import IXITiny |
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from torchio import DATA, AFFINE, ScalarImage, LabelMap, SubjectsDataset, Subject |
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class TorchioTestCase(unittest.TestCase): |
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def setUp(self): |
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"""Set up test fixtures, if any.""" |
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self.dir = Path(tempfile.gettempdir()) / '.torchio_tests' |
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self.dir.mkdir(exist_ok=True) |
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random.seed(42) |
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np.random.seed(42) |
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25
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registration_matrix = np.array([ |
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[1, 0, 0, 10], |
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[0, 1, 0, 0], |
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[0, 0, 1.2, 0], |
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[0, 0, 0, 1] |
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]) |
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31
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32
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subject_a = Subject( |
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t1=ScalarImage(self.get_image_path('t1_a')), |
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) |
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subject_b = Subject( |
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t1=ScalarImage(self.get_image_path('t1_b')), |
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label=LabelMap(self.get_image_path('label_b', binary=True)), |
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) |
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subject_c = Subject( |
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label=LabelMap(self.get_image_path('label_c', binary=True)), |
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) |
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subject_d = Subject( |
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t1=ScalarImage( |
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self.get_image_path('t1_d'), |
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pre_affine=registration_matrix, |
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46
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), |
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t2=ScalarImage(self.get_image_path('t2_d')), |
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label=LabelMap(self.get_image_path('label_d', binary=True)), |
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) |
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subject_a4 = Subject( |
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t1=ScalarImage(self.get_image_path('t1_a'), components=2), |
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) |
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self.subjects_list = [ |
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subject_a, |
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subject_a4, |
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subject_b, |
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subject_c, |
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subject_d, |
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] |
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self.dataset = SubjectsDataset(self.subjects_list) |
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self.sample = self.dataset[-1] # subject_d |
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63
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def make_2d(self, sample): |
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sample = copy.deepcopy(sample) |
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for image in sample.get_images(intensity_only=False): |
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image[DATA] = image[DATA][..., :1] |
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return sample |
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69
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def make_4d(self, sample): |
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sample = copy.deepcopy(sample) |
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for image in sample.get_images(intensity_only=False): |
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image[DATA] = torch.cat(4 * (image[DATA],)) |
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return sample |
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def flip_affine_x(self, sample): |
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sample = copy.deepcopy(sample) |
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for image in sample.get_images(intensity_only=False): |
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image[AFFINE] = np.diag((-1, 1, 1, 1)) @ image[AFFINE] |
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return sample |
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81
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def get_inconsistent_sample(self): |
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"""Return a sample containing images of different shape.""" |
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subject = Subject( |
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t1=ScalarImage(self.get_image_path('t1_inc')), |
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t2=ScalarImage( |
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self.get_image_path('t2_inc', shape=(10, 20, 31))), |
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label=LabelMap( |
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self.get_image_path( |
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'label_inc', |
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shape=(8, 17, 25), |
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binary=True, |
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), |
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), |
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label2=LabelMap( |
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self.get_image_path( |
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'label2_inc', |
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shape=(18, 17, 25), |
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binary=True, |
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), |
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), |
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) |
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return subject |
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104
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def get_reference_image_and_path(self): |
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"""Return a reference image and its path""" |
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path = self.get_image_path('ref', shape=(10, 20, 31), spacing=(1, 1, 2)) |
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image = ScalarImage(path) |
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return image, path |
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110
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def get_sample_with_partial_volume_label_map(self, components=1): |
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"""Return a sample with a partial-volume label map.""" |
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return Subject( |
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t1=ScalarImage( |
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self.get_image_path('t1_d'), |
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), |
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label=LabelMap( |
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self.get_image_path( |
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'label_d2', binary=False, components=components |
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) |
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120
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), |
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) |
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123
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def tearDown(self): |
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"""Tear down test fixtures, if any.""" |
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shutil.rmtree(self.dir) |
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def get_ixi_tiny(self): |
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root_dir = Path(tempfile.gettempdir()) / 'torchio' / 'ixi_tiny' |
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return IXITiny(root_dir, download=True) |
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def get_image_path( |
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self, |
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stem, |
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binary=False, |
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shape=(10, 20, 30), |
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spacing=(1, 1, 1), |
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components=1, |
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add_nans=False, |
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suffix=None, |
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): |
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shape = (*shape, 1) if len(shape) == 2 else shape |
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data = np.random.rand(components, *shape) |
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if binary: |
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data = (data > 0.5).astype(np.uint8) |
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if add_nans: |
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data[:] = np.nan |
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affine = np.diag((*spacing, 1)) |
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if suffix is None: |
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suffix = random.choice(('.nii.gz', '.nii', '.nrrd', '.img')) |
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path = self.dir / f'{stem}{suffix}' |
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if np.random.rand() > 0.5: |
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path = str(path) |
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image = ScalarImage(tensor=data, affine=affine, check_nans=not add_nans) |
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image.save(path) |
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return path |
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157
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def assertTensorNotEqual(self, *args, **kwargs): |
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assert_raises(AssertionError, assert_array_equal, *args, **kwargs) |
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160
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def assertTensorEqual(self, *args, **kwargs): |
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assert_array_equal(*args, **kwargs) |
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fepegar /
torchio
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