/tests/test_siemens.py

https://github.com/icometrix/dicom2nifti · Python · 206 lines · 170 code · 28 blank · 8 comment · 7 complexity · 144598d3c609a278b1d79109649aaf94 MD5 · raw file 

    

  1. # -*- coding: utf-8 -*-
    2. 

  2. """
    3. 

  3. dicom2nifti
    4. 

  4. 

  5. @author: abrys
    6. 

  6. """
    7. 

  7. import os
    8. 

  8. import shutil
    9. 

  9. import tempfile
    10. 

  10. import unittest
    11. 

  11. 

  12. import nibabel
    13. 

  13. import numpy
    14. 

  14. 

  15. import dicom2nifti.compressed_dicom as compressed_dicom
    16. 

  16. 

  17. import pydicom
    18. 

  18. 

  19. import tests.test_data as test_data
    20. 

  20. 

  21. import dicom2nifti.convert_siemens as convert_siemens
    22. 

  22. import dicom2nifti.common as common
    23. 

  23. from dicom2nifti.common import read_dicom_directory
    24. 

  24. from tests.test_tools import assert_compare_nifti, assert_compare_bval, assert_compare_bvec, ground_thruth_filenames
    25. 

  25. 

  26. 

  27. class TestConversionSiemens(unittest.TestCase):
    28. 

  28.     def test_diffusion_imaging(self):
    29. 

  29.         tmp_output_dir = tempfile.mkdtemp()
    30. 

  30.         try:
    31. 

  31. 

  32.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_DTI),
    33. 

  33.                                                      None)
    34. 

  34.             self.assertTrue(results.get('NII_FILE') is None)
    35. 

  35.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    36. 

  36.             self.assertTrue(results.get('BVAL_FILE') is None)
    37. 

  37.             self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
    38. 

  38.             self.assertTrue(results.get('BVEC_FILE') is None)
    39. 

  39.             self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
    40. 

  40. 

  41.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_DTI),
    42. 

  42.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    43. 

  43.             assert_compare_nifti(results['NII_FILE'],
    44. 

  44.                                         ground_thruth_filenames(test_data.SIEMENS_DTI)[0])
    45. 

  45.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    46. 

  46.             assert_compare_bval(results['BVAL_FILE'],
    47. 

  47.                                        ground_thruth_filenames(test_data.SIEMENS_DTI)[2])
    48. 

  48.             self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
    49. 

  49.             assert_compare_bval(results['BVEC_FILE'],
    50. 

  50.                                        ground_thruth_filenames(test_data.SIEMENS_DTI)[3])
    51. 

  51.             self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
    52. 

  52. 

  53.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_DTI_IMPLICIT),
    54. 

  54.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    55. 

  55.             assert_compare_nifti(results['NII_FILE'],
    56. 

  56.                                         ground_thruth_filenames(test_data.SIEMENS_DTI_IMPLICIT)[0])
    57. 

  57.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    58. 

  58.             assert_compare_bval(results['BVAL_FILE'],
    59. 

  59.                                        ground_thruth_filenames(test_data.SIEMENS_DTI_IMPLICIT)[2])
    60. 

  60.             self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
    61. 

  61.             assert_compare_bval(results['BVEC_FILE'],
    62. 

  62.                                        ground_thruth_filenames(test_data.SIEMENS_DTI_IMPLICIT)[3])
    63. 

  63.             self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
    64. 

  64. 

  65.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI),
    66. 

  66.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    67. 

  67.             assert_compare_nifti(results['NII_FILE'],
    68. 

  68.                                         ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI)[0])
    69. 

  69.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    70. 

  70.             assert_compare_bval(results['BVAL_FILE'],
    71. 

  71.                                        ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI)[2])
    72. 

  72.             self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
    73. 

  73.             assert_compare_bval(results['BVEC_FILE'],
    74. 

  74.                                        ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI)[3])
    75. 

  75.             self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
    76. 

  76. 

  77.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI_IMPLICIT),
    78. 

  78.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    79. 

  79.             assert_compare_nifti(results['NII_FILE'],
    80. 

  80.                                         ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[0])
    81. 

  81.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    82. 

  82.             assert_compare_bval(results['BVAL_FILE'],
    83. 

  83.                                        ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[2])
    84. 

  84.             self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
    85. 

  85.             assert_compare_bval(results['BVEC_FILE'],
    86. 

  86.                                        ground_thruth_filenames(test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[3])
    87. 

  87.             self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
    88. 

  88.         finally:
    89. 

  89.             shutil.rmtree(tmp_output_dir)
    90. 

  90. 

  91.     def test_4d(self):
    92. 

  92.         tmp_output_dir = tempfile.mkdtemp()
    93. 

  93.         try:
    94. 

  94.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
    95. 

  95.                                                      None)
    96. 

  96.             self.assertTrue(results.get('NII_FILE') is None)
    97. 

  97.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    98. 

  98. 

  99.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
    100. 

  100.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    101. 

  101.             assert_compare_nifti(results['NII_FILE'],
    102. 

  102.                                         ground_thruth_filenames(test_data.SIEMENS_FMRI)[0])
    103. 

  103.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    104. 

  104. 

  105.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT),
    106. 

  106.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    107. 

  107.             assert_compare_nifti(results['NII_FILE'],
    108. 

  108.                                         ground_thruth_filenames(test_data.SIEMENS_FMRI_IMPLICIT)[0])
    109. 

  109.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    110. 

  110. 

  111.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI),
    112. 

  112.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    113. 

  113.             assert_compare_nifti(results['NII_FILE'],
    114. 

  114.                                         ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI)[0])
    115. 

  115.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    116. 

  116. 

  117.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT),
    118. 

  118.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    119. 

  119.             assert_compare_nifti(results['NII_FILE'],
    120. 

  120.                                         ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0])
    121. 

  121.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    122. 

  122.         finally:
    123. 

  123.             shutil.rmtree(tmp_output_dir)
    124. 

  124. 

  125.     def test_anatomical(self):
    126. 

  126.         tmp_output_dir = tempfile.mkdtemp()
    127. 

  127.         try:
    128. 

  128.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_ANATOMICAL),
    129. 

  129.                                                      None)
    130. 

  130.             self.assertTrue(results.get('NII_FILE') is None)
    131. 

  131.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    132. 

  132. 

  133.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_ANATOMICAL),
    134. 

  134.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    135. 

  135.             assert_compare_nifti(results['NII_FILE'],
    136. 

  136.                                         ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0])
    137. 

  137.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    138. 

  138. 

  139.             results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_ANATOMICAL_IMPLICIT),
    140. 

  140.                                                      os.path.join(tmp_output_dir, 'test.nii.gz'))
    141. 

  141.             assert_compare_nifti(results['NII_FILE'],
    142. 

  142.                                         ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0])
    143. 

  143.             self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
    144. 

  144.         finally:
    145. 

  145.             shutil.rmtree(tmp_output_dir)
    146. 

  146. 

  147.     def test_is_mosaic(self):
    148. 

  148.         # test wit directory
    149. 

  149.         assert convert_siemens._is_mosaic(read_dicom_directory(test_data.SIEMENS_DTI))
    150. 

  150.         assert convert_siemens._is_mosaic(read_dicom_directory(test_data.SIEMENS_FMRI))
    151. 

  151.         assert not convert_siemens._is_mosaic(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI))
    152. 

  152.         assert not convert_siemens._is_mosaic(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI))
    153. 

  153.         assert not convert_siemens._is_mosaic(read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
    154. 

  154.         # test with grouped dicoms
    155. 

  155.         assert convert_siemens._is_mosaic(
    156. 

  156.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_DTI)))
    157. 

  157.         assert convert_siemens._is_mosaic(
    158. 

  158.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_FMRI)))
    159. 

  159.         assert not convert_siemens._is_mosaic(
    160. 

  160.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI)))
    161. 

  161.         assert not convert_siemens._is_mosaic(
    162. 

  162.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI)))
    163. 

  163.         assert not convert_siemens._is_mosaic(
    164. 

  164.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_ANATOMICAL)))
    165. 

  165. 

  166.     def test_is_4d(self):
    167. 

  167.         assert convert_siemens._is_4d(read_dicom_directory(test_data.SIEMENS_DTI))
    168. 

  168.         assert convert_siemens._is_4d(read_dicom_directory(test_data.SIEMENS_FMRI))
    169. 

  169.         assert not convert_siemens._is_4d(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI))
    170. 

  170.         assert not convert_siemens._is_4d(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI))
    171. 

  171.         assert not convert_siemens._is_4d(read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
    172. 

  172. 

  173.     def test_is_diffusion_imaging(self):
    174. 

  174.         assert convert_siemens._is_diffusion_imaging(read_dicom_directory(test_data.SIEMENS_DTI)[0])
    175. 

  175.         assert not convert_siemens._is_diffusion_imaging(read_dicom_directory(test_data.SIEMENS_FMRI)[0])
    176. 

  176.         assert convert_siemens._is_diffusion_imaging(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI)[0])
    177. 

  177.         assert not convert_siemens._is_diffusion_imaging(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI)[0])
    178. 

  178.         assert not convert_siemens._is_diffusion_imaging(read_dicom_directory(test_data.SIEMENS_ANATOMICAL)[0])
    179. 

  179. 

  180.     def test_is_classic_4d(self):
    181. 

  181.         assert not convert_siemens._is_classic_4d(
    182. 

  182.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_DTI)))
    183. 

  183.         assert not convert_siemens._is_classic_4d(
    184. 

  184.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_FMRI)))
    185. 

  185.         assert convert_siemens._is_classic_4d(
    186. 

  186.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI)))
    187. 

  187.         assert convert_siemens._is_classic_4d(
    188. 

  188.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI)))
    189. 

  189.         assert not convert_siemens._is_classic_4d(
    190. 

  190.             convert_siemens._classic_get_grouped_dicoms(read_dicom_directory(test_data.SIEMENS_ANATOMICAL)))
    191. 

  191. 

  192.     def test_is_siemens(self):
    193. 

  193.         assert not common.is_siemens(read_dicom_directory(test_data.PHILIPS_ANATOMICAL))
    194. 

  194.         assert common.is_siemens(read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
    195. 

  195.         assert not common.is_siemens(read_dicom_directory(test_data.GE_ANATOMICAL))
    196. 

  196.         assert not common.is_siemens(read_dicom_directory(test_data.GENERIC_ANATOMICAL))
    197. 

  197.         assert not common.is_siemens(read_dicom_directory(test_data.HITACHI_ANATOMICAL))
    198. 

  198. 

  199.     def test_get_asconv_headers(self):
    200. 

  200.         mosaic = compressed_dicom.read_file(os.path.join(test_data.SIEMENS_FMRI, 'IM-0001-0001.dcm'))
    201. 

  201.         asconv_headers = convert_siemens._get_asconv_headers(mosaic)
    202. 

  202.         assert len(asconv_headers) == 64022
    203. 

  203. 

  204. 

  205. if __name__ == '__main__':
    206. 

  206.     unittest.main()
    207.