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import tempfile |
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2
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import unittest |
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3
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from pathlib import Path |
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4
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import torch |
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5
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import numpy as np |
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6
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import SimpleITK as sitk |
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7
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from ..utils import TorchioTestCase |
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8
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from torchio.data import io |
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9
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10
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11
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class TestIO(TorchioTestCase): |
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12
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"""Tests for `io` module.""" |
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def setUp(self): |
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super().setUp() |
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15
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self.write_dicom() |
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16
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string = ( |
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17
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'1.5 0.18088 -0.124887 0.65072 ' |
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18
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'-0.20025 0.965639 -0.165653 -11.6452 ' |
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'0.0906326 0.18661 0.978245 11.4002 ' |
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'0 0 0 1 ' |
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21
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) |
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22
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tensor = torch.from_numpy(np.fromstring(string, sep=' ').reshape(4, 4)) |
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23
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self.matrix = tensor |
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24
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25
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def write_dicom(self): |
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26
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self.dicom_dir = self.dir / 'dicom' |
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self.dicom_dir.mkdir(exist_ok=True) |
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28
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self.dicom_path = self.dicom_dir / 'dicom.dcm' |
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29
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self.nii_path = self.get_image_path('read_image') |
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30
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writer = sitk.ImageFileWriter() |
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31
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writer.SetFileName(str(self.dicom_path)) |
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32
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image = sitk.ReadImage(str(self.nii_path)) |
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33
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image = sitk.Cast(image, sitk.sitkUInt16) |
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34
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image = image[0] # dicom reader supports 2D only |
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writer.Execute(image) |
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36
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37
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def test_read_image(self): |
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38
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# I need to find something readable by nib but not sitk |
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39
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io.read_image(self.nii_path) |
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40
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io.read_image(self.nii_path, itk_first=True) |
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41
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42
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def test_read_dicom_file(self): |
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io.read_image(self.dicom_path) |
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45
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def test_read_dicom_dir(self): |
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io.read_image(self.dicom_dir) |
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47
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48
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def test_dicom_dir_missing(self): |
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49
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with self.assertRaises(FileNotFoundError): |
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io._read_dicom('missing') |
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51
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52
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def test_dicom_dir_no_files(self): |
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empty = self.dir / 'empty' |
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empty.mkdir() |
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55
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with self.assertRaises(FileNotFoundError): |
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56
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io._read_dicom(empty) |
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57
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58
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def write_read_matrix(self, suffix): |
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59
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out_path = self.dir / f'matrix{suffix}' |
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60
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io.write_matrix(self.matrix, out_path) |
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61
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matrix = io.read_matrix(out_path) |
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assert torch.allclose(matrix, self.matrix) |
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63
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64
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def test_matrix_itk(self): |
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self.write_read_matrix('.tfm') |
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66
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self.write_read_matrix('.h5') |
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67
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68
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def test_matrix_txt(self): |
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69
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self.write_read_matrix('.txt') |
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70
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fepegar /
torchio
