Merge pull request #478 from mdesco/fixel_rd_map_remove

remove fixel rd_map... not doing what it should...

scripts/scil_compute_mean_fixel_afd_from_bundles.py

@@ -7,11 +7,6 @@
 
 This is the "real" fixel-based fODF amplitude along every streamline
 of the bundle provided, averaged at every voxel.
-Radial fODF comes for free from the mathematics, it is the great circle
-integral of the fODF orthogonal to the fixel of interest, similar to
-a Funk-Radon transform. Hence, radfODF is the fixel-based or HARDI-based
-generalization of the DTI radial diffusivity and AFD
-the generalization of axial diffusivity.
 
 Please use a bundle file rather than a whole tractogram.
 """
@@ -45,8 +40,6 @@ def _build_arg_parser():
                    help='Path of the fODF volume in spherical harmonics (SH).')
     p.add_argument('afd_mean_map',
                    help='Path of the output mean AFD map.')
-    p.add_argument('rd_mean_map',
-                   help='Path of the output mean radfODF map.')
 
     p.add_argument('--length_weighting', action='store_true',
                    help='If set, will weigh the AFD values according to '
@@ -63,7 +56,7 @@ def main():
     args = parser.parse_args()
 
     assert_inputs_exist(parser, [args.in_bundle, args.in_fodf])
-    assert_outputs_exist(parser, args, [args.afd_mean_map, args.rd_mean_map])
+    assert_outputs_exist(parser, args, [args.afd_mean_map])
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)
     fodf_img = nib.load(args.in_fodf)
@@ -76,8 +69,6 @@ def main():
     nib.Nifti1Image(afd_mean_map.astype(np.float32),
                     fodf_img.affine).to_filename(args.afd_mean_map)
 
-    nib.Nifti1Image(rd_mean_map.astype(np.float32),
-                    fodf_img.affine).to_filename(args.rd_mean_map)
 
 
 if __name__ == '__main__':

scripts/scil_compute_mean_fixel_afd_from_hdf5.py

@@ -7,11 +7,6 @@
 
 This is the "real" fixel-based fODF amplitude along every streamline
 of the bundle provided, averaged at every voxel.
-Radial fODF comes for free from the mathematics, it is the great circle
-integral of the fODF orthogonal to the fixel of interest, similar to
-a Funk-Radon transform. Hence, radfODF is the fixel-based or HARDI-based
-generalization of the DTI radial diffusivity and AFD
-the generalization of axial diffusivity.
 
 Please use a bundle file rather than a whole tractogram.
 """
@@ -69,9 +64,8 @@ def _afd_rd_wrapper(args):
                                                           sh_basis,
                                                           length_weighting)
     afd_mean = np.average(afd_mean_map[afd_mean_map > 0])
-    rd_mean = np.average(rd_mean_map[rd_mean_map > 0])
 
-    return key, afd_mean, rd_mean
+    return key, afd_mean
 
 
 def _build_arg_parser():
@@ -140,14 +134,11 @@ def main():
 
     shutil.copy(args.in_hdf5, args.out_hdf5)
     with h5py.File(args.out_hdf5, 'a') as out_hdf5_file:
-        for key, afd_fixel, rd_fixel in results_list:
+        for key, afd_fixel in results_list:
             group = out_hdf5_file[key]
             if 'afd_fixel' in group:
                 del group['afd_fixel']
             group.create_dataset('afd_fixel', data=afd_fixel)
-            if 'rd_fixel' in group:
-                del group['rd_fixel']
-            group.create_dataset('rd_fixel', data=rd_fixel)
 
 
 if __name__ == '__main__':

scripts/tests/test_compute_mean_fixel_afd_from_bundles.py

@@ -25,6 +25,6 @@ def test_execution_processing(script_runner):
                            'fodf_descoteaux07.nii.gz')
     ret = script_runner.run('scil_compute_mean_fixel_afd_from_bundles.py',
                             in_tracking, in_fodf,
-                            'afd_test.nii.gz', 'rd_test.nii.gz',
+                            'afd_test.nii.gz',
                             '--sh_basis', 'descoteaux07', '--length_weighting')
     assert ret.success

scripts/tests/test_compute_mean_fixel_afd_from_hdf5.py

@@ -25,7 +25,7 @@ def test_execution_connectivity(script_runner):
     in_fodf = os.path.join(get_home(), 'connectivity',
                            'fodf.nii.gz')
     ret = script_runner.run('scil_compute_mean_fixel_afd_from_hdf5.py',
-                            in_h5, in_fodf, 'decompose_afd_rd.nii.gz',
+                            in_h5, in_fodf, 'decompose_afd.nii.gz',
                             '--length_weighting', '--sh_basis', 'descoteaux07',
                             '--processes', '1')
     assert ret.success