Issue 122 Philips Multiframe dti with ADC

dicom2nifti/convert_philips.py

@@ -259,8 +259,9 @@ def _multiframe_to_nifti(dicom_input, output_file):
             logger.info('Creating bval en bvec files')
             bval_file = '%s/%s.bval' % (base_path, base_name)
             bvec_file = '%s/%s.bvec' % (base_path, base_name)
-        bval, bvec, bval_file, bvec_file = _create_bvals_bvecs(multiframe_dicom, bval_file, bvec_file, nii_image,
-                                                               output_file)
+        nii_image, bval, bvec, bval_file, bvec_file = _create_bvals_bvecs(
+            multiframe_dicom, bval_file, bvec_file, nii_image, output_file
+        )
 
         return {'NII_FILE': output_file,
                 'BVAL_FILE': bval_file,
@@ -433,15 +434,15 @@ def _create_bvals_bvecs(multiframe_dicom, bval_file, bvec_file, nifti, nifti_fil
         bvals = None
         bvecs = None
 
-    return bvals, bvecs, bval_file, bvec_file
+    return nifti, bvals, bvecs, bval_file, bvec_file
 
 
 def _fix_diffusion_images(bvals, bvecs, nifti, nifti_file):
     """
     This function will remove the last timepoint from the nifti, bvals and bvecs if the last vector is 0,0,0
     This is sometimes added at the end by philips
     """
-    # if all zero continue of if the last bvec is not all zero continue
+    # if all zero continue or if the last bvec is not all zero continue
     if numpy.count_nonzero(bvecs) == 0 or not numpy.count_nonzero(bvals[-1]) == 0:
         # nothing needs to be done here
         return nifti, bvals, bvecs

tests/data/philips_enhanced/dti/adc_ground_truth.bval

@@ -0,0 +1 @@
+0 1000 1000

tests/data/philips_enhanced/dti/adc_ground_truth.bvec

@@ -0,0 +1,3 @@
+0.0 -0.9939979910850525 -0.0821085199713707
+0.0 0.08382682502269745 -0.9962577819824219
+0.0 -0.07029245793819427 -0.02699320949614048

tests/test_data.py

@@ -95,6 +95,9 @@
 PHILIPS_ENHANCED_DTI_IMPLICIT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
                                              'data', 'philips_enhanced', 'dti', '001_implicit')
 
+PHILIPS_ENHANCED_DTI_ADC = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                            'data', 'philips_enhanced', 'dti', 'adc')
+
 PHILIPS_ENHANCED_FMRI = os.path.join(os.path.dirname(os.path.abspath(__file__)),
                                      'data', 'philips_enhanced', 'fmri', '001')
 

tests/test_philips.py

@@ -20,7 +20,7 @@
 import dicom2nifti.settings as settings
 from dicom2nifti.common import read_dicom_directory
 from dicom2nifti.exceptions import ConversionError
-from tests.test_tools import assert_compare_nifti, assert_compare_bval, assert_compare_bvec, ground_thruth_filenames
+from tests.test_tools import assert_compare_nifti, assert_compare_bval, assert_compare_bvec, ground_thruth_filenames, assert_compare_length_of_nii_to_bval
 
 
 class TestConversionPhilips(unittest.TestCase):
@@ -109,6 +109,22 @@ def test_diffusion_imaging(self):
                               read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI_IMPLICIT),
                               os.path.join(tmp_output_dir, 'test.nii.gz'))
 
+            # check PHILIPS_ENHANCED_ADC
+            results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI_ADC),
+                                                    os.path.join(tmp_output_dir, 'test.nii.gz'))
+            assert_compare_nifti(results['NII_FILE'],
+                                ground_thruth_filenames(test_data.PHILIPS_ENHANCED_DTI_ADC)[0])
+            self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
+            assert_compare_bval(results['BVAL_FILE'],
+                                ground_thruth_filenames(test_data.PHILIPS_ENHANCED_DTI_ADC)[2])
+            self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
+            assert_compare_bval(results['BVEC_FILE'],
+                                ground_thruth_filenames(test_data.PHILIPS_ENHANCED_DTI_ADC)[3])
+            self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
+            # Also check the length of the BVAL & BVEC
+            assert_compare_length_of_nii_to_bval(results['NII_FILE'],results['BVAL_FILE'])
+
+
         finally:
             shutil.rmtree(tmp_output_dir)
 

tests/test_tools.py

@@ -68,3 +68,11 @@ def assert_compare_bvec(bvec_file_1, bvec_file_2):
     equal = numpy.allclose(bvec_1, bvec_2)
     if not equal:
         raise Exception('bvecs not equal\n%s\n%s' %(numpy.array2string(bvec_1), numpy.array2string(bvec_2)))
+
+def assert_compare_length_of_nii_to_bval(nifti_file, bval_file):
+    nifti = nibabel.load(nifti_file)
+    nifti_num_of_directions = nifti.header['dim'][4]
+    bval_1 = numpy.loadtxt(bval_file)
+    bval_num_of_directions = len(bval_1)
+    if not nifti_num_of_directions == bval_num_of_directions:
+        raise Exception('BVAL not equal length to the NIfTI\n%s\n%s' %(bval_num_of_directions, nifti_num_of_directions))