tests.data.test_image

Complexity

Total Complexity

75

Size/Duplication

Total Lines	338
Duplicated Lines	0 %

Importance

Changes

0

45 Methods

Rating	Name	Duplication	Size	Complexity
A	TestImage.test_repr()	0	7	1
A	TestImage.test_bad_key()	0	3	2
A	TestImage.test_wrong_label_map_type()	0	4	2
A	TestImage.test_image_not_found()	0	3	2
A	TestImage.test_with_sequences_of_paths()	0	10	2
A	TestImage.test_wrong_path_type()	0	3	2
A	TestImage.test_wrong_affine()	0	3	2
A	TestImage.test_with_list_of_missing_files()	0	3	2
A	TestImage.test_get_center()	0	7	1
A	TestImage.test_tensor_flip()	0	3	1
A	TestImage.test_wrong_scalar_image_type()	0	4	2
A	TestImage.test_axis_name_2d()	0	7	1
A	TestImage.test_bad_affine()	0	3	2
A	TestImage.test_data_tensor()	0	4	1
A	TestImage.test_no_input()	0	3	2
A	TestImage.test_with_a_list_of_2d_paths()	0	8	1
A	TestImage.test_nans_tensor()	0	6	2
A	TestImage.test_with_a_list_of_images_with_different_affines()	0	6	2
A	TestImage.test_tensor_affine()	0	3	1
A	TestImage.test_wrong_path_value()	0	4	2
A	TestImage.test_with_a_list_of_images_with_different_shapes()	0	6	2
A	TestImage.test_save_image_with_data_type_boolean()	0	4	1
A	TestImage.test_copy_no_data()	0	13	1
A	TestImage.test_set_data()	0	4	2
A	TestImage.test_hist()	0	4	1
A	TestImage.test_unload_no_path()	0	5	2
A	TestImage.test_pil_3()	0	2	1
A	TestImage.test_plot()	0	5	1
A	TestImage.test_data_type_uint16_array()	0	4	1
A	TestImage.test_pil_1()	0	2	1
A	TestImage.test_pil_3d()	0	3	2
A	TestImage.test_load_uint()	0	8	3
A	TestImage.test_no_type()	0	3	2
A	TestImage.test_affine_multipath()	0	7	1
A	TestImage.test_gif_rgb()	0	3	2
A	TestImage.test_custom_reader()	0	17	1
A	TestImage.test_bad_numpy_type_reader()	0	10	1
A	TestImage.test_load_unload()	0	12	2
A	TestImage.test_slicing()	0	23	4
A	TestImage.test_verify_path()	0	16	2
A	TestImage.test_different_shape()	0	7	2
A	TestImage.test_count()	0	9	1
A	TestImage.test_data_type_uint32_array()	0	4	1
A	TestImage.test_pil_2()	0	3	2
A	TestImage.test_fast_gif()	0	4	3

#!/usr/bin/env python
"""Tests for Image."""

import copy
import sys
import tempfile
from pathlib import Path

import nibabel as nib
import numpy as np
import pytest
import torch

import torchio as tio

from ..utils import TorchioTestCase


class TestImage(TorchioTestCase):
    """Tests for `Image`."""

    def test_image_not_found(self):
        with pytest.raises(FileNotFoundError):
            tio.ScalarImage('nopath')

    @pytest.mark.skipif(sys.platform == 'win32', reason='Path not valid')
    def test_wrong_path_value(self):
        with pytest.raises(RuntimeError):
            tio.ScalarImage('~&./@#"!?X7=+')

    def test_wrong_path_type(self):
        with pytest.raises(TypeError):
            tio.ScalarImage(5)

    def test_wrong_affine(self):
        with pytest.raises(TypeError):
            tio.ScalarImage(5, affine=1)

    def test_tensor_flip(self):
        sample_input = torch.ones((4, 30, 30, 30))
        tio.RandomFlip()(sample_input)

    def test_tensor_affine(self):
        sample_input = torch.ones((4, 10, 10, 10))
        tio.RandomAffine()(sample_input)

    def test_wrong_scalar_image_type(self):
        data = torch.ones((1, 10, 10, 10))
        with pytest.raises(ValueError):
            tio.ScalarImage(tensor=data, type=tio.LABEL)

    def test_wrong_label_map_type(self):
        data = torch.ones((1, 10, 10, 10))
        with pytest.raises(ValueError):
            tio.LabelMap(tensor=data, type=tio.INTENSITY)

    def test_no_input(self):
        with pytest.raises(ValueError):
            tio.ScalarImage()

    def test_bad_key(self):
        with pytest.raises(ValueError):
            tio.ScalarImage(path='', data=5)

    def test_repr(self):
        subject = tio.Subject(
            t1=tio.ScalarImage(self.get_image_path('repr_test')),
        )
        assert 'memory' not in repr(subject['t1'])
        subject.load()
        assert 'memory' in repr(subject['t1'])

    def test_data_tensor(self):
        subject = copy.deepcopy(self.sample_subject)
        subject.load()
        assert subject.t1.data is subject.t1.tensor

    def test_bad_affine(self):
        with pytest.raises(ValueError):
            tio.ScalarImage(tensor=torch.rand(1, 2, 3, 4), affine=np.eye(3))

    def test_nans_tensor(self):
        tensor = np.random.rand(1, 2, 3, 4)
        tensor[0, 0, 0, 0] = np.nan
        with pytest.warns(RuntimeWarning):
            image = tio.ScalarImage(tensor=tensor, check_nans=True)
        image.set_check_nans(False)

    def test_get_center(self):
        tensor = torch.rand(1, 3, 3, 3)
        image = tio.ScalarImage(tensor=tensor)
        ras = image.get_center()
        lps = image.get_center(lps=True)
        assert ras == (1, 1, 1)
        assert lps == (-1, -1, 1)

    def test_with_list_of_missing_files(self):
        with pytest.raises(FileNotFoundError):
            tio.ScalarImage(path=['nopath', 'error'])

    def test_with_sequences_of_paths(self):
        shape = (5, 5, 5)
        path1 = self.get_image_path('path1', shape=shape)
        path2 = self.get_image_path('path2', shape=shape)
        paths_tuple = path1, path2
        paths_list = list(paths_tuple)
        for sequence in (paths_tuple, paths_list):
            image = tio.ScalarImage(path=sequence)
            assert image.shape == (2, 5, 5, 5)
            assert image[tio.STEM] == ['path1', 'path2']

    def test_with_a_list_of_images_with_different_shapes(self):
        path1 = self.get_image_path('path1', shape=(5, 5, 5))
        path2 = self.get_image_path('path2', shape=(7, 5, 5))
        image = tio.ScalarImage(path=[path1, path2])
        with pytest.raises(RuntimeError):
            image.load()

    def test_with_a_list_of_images_with_different_affines(self):
        path1 = self.get_image_path('path1', spacing=(1, 1, 1))
        path2 = self.get_image_path('path2', spacing=(1, 2, 1))
        image = tio.ScalarImage(path=[path1, path2])
        with pytest.warns(RuntimeWarning):
            image.load()

    def test_with_a_list_of_2d_paths(self):
        shape = (5, 6)
        path1 = self.get_image_path('path1', shape=shape, suffix='.nii')
        path2 = self.get_image_path('path2', shape=shape, suffix='.img')
        path3 = self.get_image_path('path3', shape=shape, suffix='.hdr')
        image = tio.ScalarImage(path=[path1, path2, path3])
        assert image.shape == (3, 5, 6, 1)
        assert image[tio.STEM] == ['path1', 'path2', 'path3']

    def test_axis_name_2d(self):
        path = self.get_image_path('im2d', shape=(5, 6))
        image = tio.ScalarImage(path)
        height_idx = image.axis_name_to_index('t')
        width_idx = image.axis_name_to_index('l')
        assert image.height == image.shape[height_idx]
        assert image.width == image.shape[width_idx]

    def test_different_shape(self):
        path_1 = self.get_image_path('im_shape1', shape=(5, 5, 5))
        path_2 = self.get_image_path('im_shape2', shape=(7, 5, 5))

        image = tio.ScalarImage([path_1, path_2])
        with pytest.raises(RuntimeError):
            image.load()

    @pytest.mark.slow
    @pytest.mark.skipif(sys.platform == 'win32', reason='Unstable on Windows')
    def test_plot(self):
        image = self.sample_subject.t1
        image.plot(show=False, output_path=self.dir / 'image.png')

    def test_data_type_uint16_array(self):
        tensor = np.random.rand(1, 3, 3, 3).astype(np.uint16)
        image = tio.ScalarImage(tensor=tensor)
        assert image.data.dtype == torch.int32

    def test_data_type_uint32_array(self):
        tensor = np.random.rand(1, 3, 3, 3).astype(np.uint32)
        image = tio.ScalarImage(tensor=tensor)
        assert image.data.dtype == torch.int64

    def test_save_image_with_data_type_boolean(self):
        tensor = np.random.rand(1, 3, 3, 3).astype(bool)
        image = tio.ScalarImage(tensor=tensor)
        image.save(self.dir / 'image.nii')

    def test_load_uint(self):
        affine = np.eye(4)
        for dtype in np.uint16, np.uint32:
            data = np.ones((3, 3, 3), dtype=dtype)
            img = nib.Nifti1Image(data, affine)
            with tempfile.NamedTemporaryFile(suffix='.nii', delete=False) as f:
                nib.save(img, f.name)
                tio.ScalarImage(f.name).load()

    def test_pil_3d(self):
        with pytest.raises(RuntimeError):
            tio.ScalarImage(tensor=torch.rand(1, 2, 3, 4)).as_pil()

    def test_pil_1(self):
        tio.ScalarImage(tensor=torch.rand(1, 2, 3, 1)).as_pil()

    def test_pil_2(self):
        with pytest.raises(RuntimeError):
            tio.ScalarImage(tensor=torch.rand(2, 2, 3, 1)).as_pil()

    def test_pil_3(self):
        tio.ScalarImage(tensor=torch.rand(3, 2, 3, 1)).as_pil()

    def test_set_data(self):
        im = self.sample_subject.t1
        with pytest.deprecated_call():
            im.data = im.data

    def test_no_type(self):
        with pytest.warns(FutureWarning):
            tio.Image(tensor=torch.rand(1, 2, 3, 4))

    def test_custom_reader(self):
        path = self.dir / 'im.npy'

        def numpy_reader(path):
            return np.load(path), np.eye(4)

        def assert_shape(shape_in, shape_out):
            np.save(path, np.random.rand(*shape_in))
            image = tio.ScalarImage(path, reader=numpy_reader)
            assert image.shape == shape_out

        assert_shape((5, 5), (1, 5, 5, 1))
        assert_shape((5, 5, 3), (3, 5, 5, 1))
        assert_shape((3, 5, 5), (3, 5, 5, 1))
        assert_shape((5, 5, 5), (1, 5, 5, 5))
        assert_shape((1, 5, 5, 5), (1, 5, 5, 5))
        assert_shape((4, 5, 5, 5), (4, 5, 5, 5))

    def test_fast_gif(self):
        with pytest.warns(RuntimeWarning):
            with tempfile.NamedTemporaryFile(suffix='.gif', delete=False) as f:
                self.sample_subject.t1.to_gif(0, 0.0001, f.name)

    def test_gif_rgb(self):
        with tempfile.NamedTemporaryFile(suffix='.gif', delete=False) as f:
            tio.ScalarImage(tensor=torch.rand(3, 4, 5, 6)).to_gif(0, 1, f.name)

    @pytest.mark.slow
    def test_hist(self):
        self.sample_subject.t1.hist(density=False, show=False)
        self.sample_subject.t1.hist(density=True, show=False)

    def test_count(self):
        image = self.sample_subject.label
        max_n = image.data.numel()
        nonzero = image.count_nonzero()
        assert 0 <= nonzero <= max_n
        counts = image.count_labels()
        assert tuple(counts) == (0, 1)
        assert 0 <= counts[0] <= max_n
        assert 0 <= counts[1] <= max_n

    def test_affine_multipath(self):
        # https://github.com/TorchIO-project/torchio/issues/762
        path1 = self.get_image_path('multi1')
        path2 = self.get_image_path('multi2')
        paths = path1, path2
        image = tio.ScalarImage(paths)
        self.assert_tensor_equal(image.affine, np.eye(4))

    def test_bad_numpy_type_reader(self):
        # https://github.com/TorchIO-project/torchio/issues/764
        def numpy_reader(path):
            return np.load(path), np.eye(4)

        tensor = np.random.rand(1, 2, 3, 4).astype(np.uint16)
        test_path = self.dir / 'test_image.npy'
        np.save(test_path, tensor)
        image = tio.ScalarImage(test_path, reader=numpy_reader)
        image.load()

    def test_load_unload(self):
        path = self.get_image_path('unload')
        image = tio.ScalarImage(path)
        with self.assertRaises(RuntimeError):
            image.unload()
        image.load()
        assert image._loaded
        image.unload()
        assert not image._loaded
        assert image[tio.DATA] is None
        assert image[tio.AFFINE] is None
        assert not image._loaded

    def test_unload_no_path(self):
        tensor = torch.rand(1, 2, 3, 4)
        image = tio.ScalarImage(tensor=tensor)
        with self.assertRaises(RuntimeError):
            image.unload()

    def test_copy_no_data(self):
        # https://github.com/TorchIO-project/torchio/issues/974
        path = self.get_image_path('im_copy')
        my_image = tio.LabelMap(path)
        assert not my_image._loaded
        new_image = copy.copy(my_image)
        assert not my_image._loaded
        assert not new_image._loaded

        my_image.load()
        new_image = copy.copy(my_image)
        assert my_image._loaded
        assert new_image._loaded

    def test_slicing(self):
        path = self.get_image_path('im_slicing')
        image = tio.ScalarImage(path)

        assert image.shape == (1, 10, 20, 30)

        cropped = image[0]
        assert cropped.shape == (1, 1, 20, 30)

        cropped = image[:, 2:-3]
        assert cropped.shape == (1, 10, 15, 30)

        cropped = image[-5:, 5:]
        assert cropped.shape == (1, 5, 15, 30)

        with pytest.raises(NotImplementedError):
            image[..., 5]

        with pytest.raises(ValueError):
            image[0:8:-1]

        with pytest.raises(ValueError):
            image[3::-1]

    def test_verify_path(self):
        path = Path(self.get_image_path('im_verify'))

        image = tio.ScalarImage(path, verify_path=False)
        assert image.path == path

        image = tio.ScalarImage(path, verify_path=True)
        assert image.path == path

        fake_path = Path('fake_path.nii')

        image = tio.ScalarImage(fake_path, verify_path=False)
        assert image.path == fake_path

        with pytest.raises(FileNotFoundError):
            tio.ScalarImage(fake_path, verify_path=True)