Fixing issues with tenmap and tenmap2 both set by interface. Adding an input to select which one to generate.

Author: byvernault

nipype/interfaces/niftyfit/dwi.py

@@ -91,6 +91,12 @@ class FitDwiInputSpec(CommandLineInputSpec):
                               argstr='-rgbmap %s',
                               genfile=True,
                               requires=['dti_flag'])
+
+    desc = 'Use lower triangular (tenmap2) or diagonal, off-diagonal tensor \
+format'
+    ten_type = traits.Enum('lower-tri', 'diag-off-diag', desc=desc,
+                           usedefault=True)
+
     tenmap_file = traits.File(desc='Filename of tensor map [diag,offdiag].',
                               argstr='-tenmap %s',
                               genfile=True,
@@ -238,15 +244,22 @@ class FitDwi(NiftyFitCommand):
 -error .../dwi_error.nii.gz -famap .../dwi_famap.nii.gz \
 -mcmap .../dwi_mcmap.nii.gz -mdmap .../dwi_mdmap.nii.gz \
 -nodiff .../dwi_no_diff.nii.gz -res .../dwi_resmap.nii.gz \
--rgbmap rgb.nii.gz -syn .../dwi_syn.nii.gz -tenmap2 .../dwi_tenmap2.nii.gz \
--tenmap .../dwi_tenmap.nii.gz -v1map .../dwi_v1map.nii.gz'
+-rgbmap rgb.nii.gz -syn .../dwi_syn.nii.gz -tenmap2 .../dwi_tenmap2.nii.gz  \
+-v1map .../dwi_v1map.nii.gz'
 
     """
     _cmd = get_custom_path('fit_dwi')
     input_spec = FitDwiInputSpec
     output_spec = FitDwiOutputSpec
     _suffix = '_fit_dwi'
 
+    def _format_arg(self, name, trait_spec, value):
+        if name == 'tenmap_file' and self.inputs.ten_type != 'diag-off-diag':
+            return ""
+        if name == 'tenmap2_file' and self.inputs.ten_type != 'lower-tri':
+            return ""
+        return super(FitDwi, self)._format_arg(name, trait_spec, value)
+
     def _gen_filename(self, name):
         if name == 'mcmap_file':
             return self._gen_fname(self.inputs.source_file,
@@ -337,8 +350,8 @@ def _list_outputs(self):
         else:
             outputs['tenmap_file'] = self._gen_filename('tenmap_file')
 
-        if isdefined(self.inputs.tenmap_file):
-            outputs['tenmap2_file'] = self.inputs.tenmap_file
+        if isdefined(self.inputs.tenmap2_file):
+            outputs['tenmap2_file'] = self.inputs.tenmap2_file
         else:
             outputs['tenmap2_file'] = self._gen_filename('tenmap2_file')
 

nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py

@@ -120,6 +120,8 @@ def test_FitDwi_inputs():
     te_value=dict(argstr='-TE %s',
     xor=['te_file'],
     ),
+    ten_type=dict(usedefault=True,
+    ),
     tenmap2_file=dict(argstr='-tenmap2 %s',
     genfile=True,
     requires=['dti_flag'],

nipype/interfaces/niftyfit/tests/test_dwi.py

@@ -33,8 +33,7 @@ def test_fit_dwi():
 
     cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -dti \
 -error {error} -famap {fa} -mcmap {mc} -mdmap {md} -nodiff {nodiff} \
--res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2} \
--tenmap {ten} -v1map {v1}'
+-res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2}  -v1map {v1}'
 
     expected_cmd = cmd_tmp.format(
         cmd=get_custom_path('fit_dwi'),
@@ -50,9 +49,10 @@ def test_fit_dwi():
         rgb=os.path.join(os.getcwd(), 'dwi_rgbmap.nii.gz'),
         syn=os.path.join(os.getcwd(), 'dwi_syn.nii.gz'),
         ten2=os.path.join(os.getcwd(), 'dwi_tenmap2.nii.gz'),
-        v1=os.path.join(os.getcwd(), 'dwi_v1map.nii.gz'),
-        ten=os.path.join(os.getcwd(), 'dwi_tenmap.nii.gz'))
+        v1=os.path.join(os.getcwd(), 'dwi_v1map.nii.gz'))
 
+    print(fit_dwi.cmdline)
+    print(expected_cmd)
     assert fit_dwi.cmdline == expected_cmd