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#!/usr/bin/env python |
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"""Tests for Image.""" |
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import copy |
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import torch |
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import pytest |
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import numpy as np |
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from torchio import ScalarImage, LabelMap, Subject, INTENSITY, LABEL, STEM |
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from ..utils import TorchioTestCase |
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from torchio import RandomFlip, RandomAffine |
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class TestImage(TorchioTestCase): |
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"""Tests for `Image`.""" |
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def test_image_not_found(self): |
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with self.assertRaises(FileNotFoundError): |
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ScalarImage('nopath') |
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def test_wrong_path_value(self): |
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with self.assertRaises(RuntimeError): |
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ScalarImage('~&./@#"!?X7=+') |
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def test_wrong_path_type(self): |
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with self.assertRaises(TypeError): |
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ScalarImage(5) |
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def test_wrong_affine(self): |
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with self.assertRaises(TypeError): |
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ScalarImage(5, affine=1) |
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def test_tensor_flip(self): |
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sample_input = torch.ones((4, 30, 30, 30)) |
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RandomFlip()(sample_input) |
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def test_tensor_affine(self): |
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sample_input = torch.ones((4, 10, 10, 10)) |
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RandomAffine()(sample_input) |
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def test_scalar_image_type(self): |
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data = torch.ones((1, 10, 10, 10)) |
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image = ScalarImage(tensor=data) |
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self.assertIs(image.type, INTENSITY) |
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def test_label_map_type(self): |
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data = torch.ones((1, 10, 10, 10)) |
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label = LabelMap(tensor=data) |
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self.assertIs(label.type, LABEL) |
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def test_wrong_scalar_image_type(self): |
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data = torch.ones((1, 10, 10, 10)) |
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with self.assertRaises(ValueError): |
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ScalarImage(tensor=data, type=LABEL) |
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def test_wrong_label_map_type(self): |
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data = torch.ones((1, 10, 10, 10)) |
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with self.assertRaises(ValueError): |
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LabelMap(tensor=data, type=INTENSITY) |
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def test_no_input(self): |
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with self.assertRaises(ValueError): |
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ScalarImage() |
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def test_bad_key(self): |
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with self.assertRaises(ValueError): |
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ScalarImage(path='', data=5) |
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def test_repr(self): |
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sample = Subject(t1=ScalarImage(self.get_image_path('repr_test'))) |
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assert 'shape' not in repr(sample['t1']) |
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sample.load() |
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assert 'shape' in repr(sample['t1']) |
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def test_data_tensor(self): |
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sample = copy.deepcopy(self.sample) |
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sample.load() |
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self.assertIs(sample.t1.data, sample.t1.tensor) |
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def test_bad_affine(self): |
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with self.assertRaises(ValueError): |
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ScalarImage(tensor=torch.rand(1, 2, 3, 4), affine=np.eye(3)) |
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def test_nans_tensor(self): |
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tensor = np.random.rand(1, 2, 3, 4) |
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tensor[0, 0, 0, 0] = np.nan |
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with self.assertWarns(UserWarning): |
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image = ScalarImage(tensor=tensor, check_nans=True) |
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image.set_check_nans(False) |
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def test_get_center(self): |
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tensor = torch.rand(1, 3, 3, 3) |
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image = ScalarImage(tensor=tensor) |
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ras = image.get_center() |
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lps = image.get_center(lps=True) |
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self.assertEqual(ras, (1, 1, 1)) |
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self.assertEqual(lps, (-1, -1, 1)) |
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def test_with_list_of_missing_files(self): |
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with self.assertRaises(FileNotFoundError): |
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ScalarImage(path=['nopath', 'error']) |
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def test_with_a_list_of_paths(self): |
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shape = (5, 5, 5) |
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path1 = self.get_image_path('path1', shape=shape) |
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path2 = self.get_image_path('path2', shape=shape) |
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image = ScalarImage(path=[path1, path2]) |
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self.assertEqual(image.shape, (2, 5, 5, 5)) |
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self.assertEqual(image[STEM], ['path1', 'path2']) |
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def test_with_a_list_of_images_with_different_shapes(self): |
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path1 = self.get_image_path('path1', shape=(5, 5, 5)) |
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path2 = self.get_image_path('path2', shape=(7, 5, 5)) |
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image = ScalarImage(path=[path1, path2]) |
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with self.assertRaises(RuntimeError): |
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image.load() |
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def test_with_a_list_of_images_with_different_affines(self): |
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path1 = self.get_image_path('path1', spacing=(1, 1, 1)) |
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path2 = self.get_image_path('path2', spacing=(1, 2, 1)) |
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image = ScalarImage(path=[path1, path2]) |
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with self.assertWarns(RuntimeWarning): |
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image.load() |
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def test_with_a_list_of_2d_paths(self): |
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shape = (5, 6) |
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path1 = self.get_image_path('path1', shape=shape, suffix='.nii') |
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path2 = self.get_image_path('path2', shape=shape, suffix='.img') |
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path3 = self.get_image_path('path3', shape=shape, suffix='.hdr') |
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image = ScalarImage(path=[path1, path2, path3]) |
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self.assertEqual(image.shape, (3, 5, 6, 1)) |
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self.assertEqual(image[STEM], ['path1', 'path2', 'path3']) |
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def test_axis_name_2d(self): |
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path = self.get_image_path('im2d', shape=(5, 6)) |
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image = ScalarImage(path) |
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height_idx = image.axis_name_to_index('t') |
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width_idx = image.axis_name_to_index('l') |
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self.assertEqual(image.height, image.shape[height_idx]) |
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self.assertEqual(image.width, image.shape[width_idx]) |
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def test_plot(self): |
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image = self.sample.t1 |
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image.plot(show=False, output_path=self.dir / 'image.png') |
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fepegar /
torchio
