def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_ANATOMICAL), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GE_ANATOMICAL)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GE_ANATOMICAL_IMPLICIT)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_4d(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_FMRI)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_FMRI_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_4d(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_FMRI)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_FMRI_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_ANATOMICAL)[0]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_ANATOMICAL_IMPLICIT)[0]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_ENHANCED_ANATOMICAL)[0]) is True self.assertRaises( ConversionError, convert_philips.dicom_to_nifti, read_dicom_directory( test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) finally: shutil.rmtree(tmp_output_dir)
def test_4d(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_siemens.dicom_to_nifti( read_dicom_directory(test_data.SIEMENS_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_FMRI)[0]) is True results = convert_siemens.dicom_to_nifti( read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_FMRI_IMPLICIT)[0]) is True results = convert_siemens.dicom_to_nifti( read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_CLASSIC_FMRI)[0]) is True results = convert_siemens.dicom_to_nifti( read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0]) is True finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_ANATOMICAL)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_ANATOMICAL_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_ENHANCED_ANATOMICAL)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) self.assertRaises(ConversionError, convert_philips.dicom_to_nifti, read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_ANATOMICAL)[0]) == True results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_ANATOMICAL_IMPLICIT)[0]) == True finally: shutil.rmtree(tmp_output_dir)
def test_diffusion_images_old(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_OLD), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI_OLD)[0]) is True finally: shutil.rmtree(tmp_output_dir)
def test_diffusion_images_old(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_OLD), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI_OLD)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_4d(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_FMRI), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_FMRI)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_FMRI_IMPLICIT)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_ENHANCED_FMRI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_ENHANCED_FMRI)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) self.assertRaises( ConversionError, convert_philips.dicom_to_nifti, read_dicom_directory(test_data.PHILIPS_ENHANCED_FMRI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) finally: shutil.rmtree(tmp_output_dir)
def test_anatomical_implicit(self): tmp_output_dir = tempfile.mkdtemp() try: settings.disable_validate_multiframe_implicit() results = convert_philips.dicom_to_nifti(read_dicom_directory( test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) settings.enable_validate_multiframe_implicit() finally: shutil.rmtree(tmp_output_dir)
def test_anatomical_implicit(self): tmp_output_dir = tempfile.mkdtemp() try: settings.disable_validate_multiframe_implicit() results = convert_philips.dicom_to_nifti( read_dicom_directory( test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0]) is True settings.enable_validate_multiframe_implicit() finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_ANATOMICAL)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_single_slice(self): tmp_output_dir = tempfile.mkdtemp() try: settings.disable_validate_slicecount() results = convert_generic.dicom_to_nifti( read_dicom_directory(test_data.GE_ANATOMICAL_SINGLE_SLICE), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GE_ANATOMICAL_SINGLE_SLICE)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: settings.enable_validate_slicecount() shutil.rmtree(tmp_output_dir)
def test_inconsistent_slice_increment_resampling(self): tmp_output_dir = tempfile.mkdtemp() try: settings.disable_validate_orthogonal() settings.disable_validate_slice_increment() settings.enable_resampling() settings.set_resample_padding(0) settings.set_resample_spline_interpolation_order(1) results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: settings.disable_resampling() settings.enable_validate_slice_increment() settings.enable_validate_orientation() shutil.rmtree(tmp_output_dir)
def test_inconsistent_slice_increment_resampling(self): tmp_output_dir = tempfile.mkdtemp() try: settings.disable_validate_orthogonal() settings.disable_validate_slice_increment() settings.enable_resampling() settings.set_resample_padding(0) settings.set_resample_spline_interpolation_order(1) results = convert_generic.dicom_to_nifti( read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: settings.disable_resampling() settings.enable_validate_slice_increment() settings.enable_validate_orientation() shutil.rmtree(tmp_output_dir)
def test_diffusion_images(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_DTI), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) self.assertTrue(results.get('BVAL_FILE') is None) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) self.assertTrue(results.get('BVEC_FILE') is None) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) results = convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_DTI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) assert_compare_bval(results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI)[2]) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) assert_compare_bval(results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI)[3]) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) convert_ge.dicom_to_nifti( read_dicom_directory(test_data.GE_DTI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) assert_compare_bval( results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2]) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) assert_compare_bval( results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3]) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) finally: shutil.rmtree(tmp_output_dir)
def test_diffusion_images(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI)[0]) == True assert compare_bval(results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI)[2]) == True assert compare_bvec(results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI)[3]) == True convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0]) == True assert compare_bval(results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2]) == True assert compare_bvec(results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3]) == True finally: shutil.rmtree(tmp_output_dir)
def test_diffusion_images(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI), None) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) self.assertTrue(results.get('BVAL_FILE') is None) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) self.assertTrue(results.get('BVEC_FILE') is None) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) assert_compare_bval(results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI)[2]) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) assert_compare_bval(results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI)[3]) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0]) self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) assert_compare_bval(results['BVAL_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2]) self.assertTrue(isinstance(results['BVAL'], numpy.ndarray)) assert_compare_bval(results['BVEC_FILE'], ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3]) self.assertTrue(isinstance(results['BVEC'], numpy.ndarray)) finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL)[0]) is True results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL)[1]) is True results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) is True results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL)[0]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL)[1]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_COMPRESSED)[0]) is True results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_COMPRESSED)[1]) is True results = convert_dicom.dicom_series_to_nifti( test_data.HITACHI_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.HITACHI_ANATOMICAL)[1]) is True finally: shutil.rmtree(tmp_output_dir)
def test_anatomical(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, None, False) self.assertTrue(results.get('NII_FILE') is None) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_NON_ISOTROPIC, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_NON_ISOTROPIC)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) results = convert_dicom.dicom_series_to_nifti( test_data.HITACHI_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.HITACHI_ANATOMICAL)[1]) self.assertTrue( isinstance(results['NII'], nibabel.nifti1.Nifti1Image)) finally: shutil.rmtree(tmp_output_dir)
def test_main_function(self): tmp_output_dir = tempfile.mkdtemp() try: results = dicom2nifti.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0]) results = dicom2nifti.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1]) results = dicom2nifti.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) results = dicom2nifti.dicom_series_to_nifti( test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0]) results = dicom2nifti.dicom_series_to_nifti( test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1]) finally: shutil.rmtree(tmp_output_dir)
def test_diffusion_imaging(self): tmp_output_dir = tempfile.mkdtemp() try: results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_DTI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI)[0]) is True assert compare_bval( results['BVAL_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI)[2]) is True assert compare_bvec( results['BVEC_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI)[3]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_DTI_002), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI_002)[0]) is True assert compare_bval( results['BVAL_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI_002)[2]) is True assert compare_bvec( results['BVEC_FILE'], ground_thruth_filenames(test_data.PHILIPS_DTI_002)[3]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_ENHANCED_DTI)[0]) is True assert compare_bval( results['BVAL_FILE'], ground_thruth_filenames( test_data.PHILIPS_ENHANCED_DTI)[2]) is True assert compare_bvec( results['BVEC_FILE'], ground_thruth_filenames( test_data.PHILIPS_ENHANCED_DTI)[3]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_DTI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT)[0]) is True assert compare_bval( results['BVAL_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT)[2]) is True assert compare_bvec( results['BVEC_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT)[3]) is True results = convert_philips.dicom_to_nifti( read_dicom_directory(test_data.PHILIPS_DTI_IMPLICIT_002), os.path.join(tmp_output_dir, 'test.nii.gz')) assert compare_nifti( results['NII_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT_002)[0]) is True assert compare_bval( results['BVAL_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT_002)[2]) is True assert compare_bvec( results['BVEC_FILE'], ground_thruth_filenames( test_data.PHILIPS_DTI_IMPLICIT_002)[3]) is True self.assertRaises( ConversionError, convert_philips.dicom_to_nifti, read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI_IMPLICIT), os.path.join(tmp_output_dir, 'test.nii.gz')) finally: shutil.rmtree(tmp_output_dir)
def test_main_function(self): tmp_output_dir = tempfile.mkdtemp() try: results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0]) results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1]) results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL_IMPLICIT, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), False) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0]) results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_COMPRESSED, os.path.join(tmp_output_dir, 'test.nii.gz'), True) assert_compare_nifti(results['NII_FILE'], ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1]) finally: shutil.rmtree(tmp_output_dir)