antsCorticalThickness interface + example data for testing

Author: armaneshaghi

nipype/interfaces/afni/tests/test_auto_Volreg.py

@@ -32,11 +32,6 @@ def test_Volreg_inputs():
     name_source='in_file',
     name_template='%s.1D',
     ),
-    oned_matrix_save=dict(argstr='-1Dmatrix_save %s',
-    keep_extension=True,
-    name_source='in_file',
-    name_template='%s.aff12.1D',
-    ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
     name_template='%s_volreg',
@@ -62,7 +57,6 @@ def test_Volreg_inputs():
 def test_Volreg_outputs():
     output_map = dict(md1d_file=dict(),
     oned_file=dict(),
-    oned_matrix_save=dict(),
     out_file=dict(),
     )
     outputs = Volreg.output_spec()

nipype/interfaces/ants/segmentation.py

@@ -295,7 +295,7 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
     dimension=traits.Enum(3, 2, argstr= '-d %d', usedefault=True,
                            desc='image dimension (2 or 3)')
     anatomical_image=File(exists=True,
-                           argstr='-a %s', 
+                           argstr='-a %s',
                            desc='Structural *intensity* image, typically T1.'
                            'If more than one anatomical image is specified,'
                            'subsequently specified images are used during the'
@@ -308,41 +308,43 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
             argstr='-e %s',
             desc='Anatomical *intensity* template (possibly created using a'
             'population data set with buildtemplateparallel.sh in ANTs).'
-            'This template is  *not* skull-stripped.')
+            'This template is  *not* skull-stripped.',
+            mandatory=True)
     brain_probability_mask=File(exists=True,
             argstr='-m %s', desc='brain probability mask in template space',
-            mandatory=True, copyfile=False)
+            copyfile=False, mandatory=True)
     segmentation_priors = InputMultiPath(File(exists=True),
-            argstr='-p %s')
+            argstr='-p %s', mandatory=True)
     out_prefix = traits.Str('antsCT_', argstr='-o %s', usedefault=True,
                              desc=('Prefix that is prepended to all output'
                                    ' files (default = antsCT_)'))
     image_suffix=traits.Str('nii.gz', desc=('any of standard ITK formats,'
-        ' nii.gz is default'), mandatory = False, argstr='-s %s', 
+        ' nii.gz is default'), mandatory = False, argstr='-s %s',
         usedefault=True)
-    t1_registration_template = File(exists=True, 
+    t1_registration_template = File(exists=True,
             desc = ('Anatomical *intensity* template'
-           '(assumed to be skull-stripped). A common' 
+           '(assumed to be skull-stripped). A common'
            'case would be where this would be the same'
            'template as specified in the -e option which'
            'is not skull stripped.'),
-           mandatory=True, argstr='-t %s')
+           argstr='-t %s',
+           mandatory=True)
     extraction_registration_mask=File(exists=True, argstr='-f %s',
             mandatory=False, desc='Mask (defined in the template'
             'space) used during registration for brain extraction.')
-    keep_temporary_files=traits.Int(argstrr='-k %d', 
+    keep_temporary_files=traits.Int(argstrr='-k %d',
             desc='Keep brain extraction/segmentation'
             'warps, etc (default = 0).', mandatory=False)
-    max_iterations=traits.Int(argstr='-i %d', 
-            desc='ANTS registration max iterations' 
+    max_iterations=traits.Int(argstr='-i %d',
+            desc='ANTS registration max iterations'
             '(default = 100x100x70x20)',  mandatory=False)
     prior_segmentation_weight=traits.Float(mandatory=False, argstr='-w %f',
             desc='Atropos spatial prior *probability* weight for'
             'the segmentation')
     segmentation_iterations=traits.Int(argstr='-n %d', mandatory=False,
             desc='N4 -> Atropos -> N4 iterations during segmentation'
             '(default = 3)')
-    posterior_formulation=traits.Str(argstr='-b %s', mandatory=False, 
+    posterior_formulation=traits.Str(argstr='-b %s', mandatory=False,
             desc=('Atropos posterior formulation and whether or not'
                 'to use mixture model proportions.'
                    '''e.g 'Socrates[1]' (default) or 'Aristotle[1]'.'''
@@ -363,7 +365,7 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
     label_propagation=traits.Str(argstr='-l %s', mandatory=False,
             desc='Incorporate a distance prior one the posterior formulation.  Should be'
               '''of the form 'label[lambda,boundaryProbability]' where label'''
-              'is a value of 1,2,3,... denoting label ID.  The label' 
+              'is a value of 1,2,3,... denoting label ID.  The label'
               'probability for anything outside the current label'
               '  = boundaryProbability * exp( -lambda * distanceFromBoundary )'
               'Intuitively, smaller lambda values will increase the spatial capture'
@@ -372,7 +374,7 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
     quick_registration=traits.Bool(argstr='-q 1', mandatory=False,
             desc='If = 1, use antsRegistrationSyNQuick.sh as the basis for registration'
                   'during brain extraction, brain segmentation, and'
-                  '(optional) normalization to a template.' 
+                  '(optional) normalization to a template.'
                   'Otherwise use antsRegistrationSyN.sh (default = 0).')
     debug=traits.Bool(argstr='-z 1', mandatory=False,
             desc='If > 0, runs a faster version of the script.'
@@ -412,17 +414,17 @@ class antsCorticalThickness(ANTSCommand):
     Examples
     --------
     >>> from nipype.interfaces.ants.segmentation import antsCorticalThickness
-    >>> corticalthickness = anstCorticalThickness()
+    >>> corticalthickness = antsCorticalThickness()
     >>> corticalthickness.inputs.dimension = 3
     >>> corticalthickness.inputs.anatomical_image ='T1.nii.gz'
     >>> corticalthickness.inputs.brain_template = 'study_template.nii.gz'
     >>> corticalthickness.inputs.brain_probability_mask ='ProbabilityMaskOfStudyTemplate.nii.gz'
-    >>> corticalthickness.inputs.segmentation_priors =['CSF.nii.gz','WM.nii.gz','GM.nii.gz','DEEP_GM.nii.gz']
+    >>> corticalthickness.inputs.segmentation_priors = ['BrainSegmentationPrior01.nii.gz', 'BrainSegmentationPrior02.nii.gz', 'BrainSegmentationPrior03.nii.gz', 'BrainSegmentationPrior04.nii.gz']
     >>> corticalthickness.inputs.t1_registration_template = 'brain_study_template.nii.gz'
     >>> corticalthickness.cmdline
-   'antsCorticalThickness.sh -d 3 -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -o antsCT_ -p BrainSegmentationPrior%0d.nii.gz -t brain_study_template.nii.gz' 
+    'antsCorticalThickness.sh -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -d 3 -s nii.gz -o antsCT_ -p BrainSegmentationPrior%02d.nii.gz -t brain_study_template.nii.gz'
     """
-    
+
     input_spec = antsCorticalThicknessInputSpec
     output_spec = antsCorticalThicknessoutputSpec
     _cmd = 'antsCorticalThickness.sh'
@@ -444,7 +446,7 @@ def _format_arg(self, opt, spec, val):
             return retval
         if opt == 'segmentation_priors':
             _, _, ext = split_filename(self.inputs.segmentation_priors[0])
-            retval = "-p priors/BrainSegmentationPrior%02d"
+            retval = "-p BrainSegmentationPrior%02d"
             retval += ext
             return retval
         return super(ANTSCommand, self)._format_arg(opt, spec, val)
@@ -474,7 +476,7 @@ def _list_outputs(self):
                                              self.inputs.image_suffix)
         outputs['BrainSegmentationN4'] = os.path.join(os.getcwd(),
                                                      self.inputs.out_prefix +
-                                                     'BrainSegmentation0N4.' + 
+                                                     'BrainSegmentation0N4.' +
                                                      self.inputs.image_suffix)
         outputs['BrainSegmentationPosteriorsCSF'] = os.path.join(os.getcwd(),
                                                  self.inputs.out_prefix +
@@ -496,14 +498,14 @@ def _list_outputs(self):
                 os.getcwd(),
                 'TemplateToSubject1GenericAffine.mat')
         outputs['TemplateToSubject0Warp'] = os.path.join(os.getcwd(),
-               self.inputs.out_prefix + 'TemplateToSubject0Warp.'+ 
+               self.inputs.out_prefix + 'TemplateToSubject0Warp.'+
                self.inputs.image_suffix)
         outputs['SubjectToTemplate1Warp'] = os.path.join(os.getcwd(),
-               self.inputs.out_prefix + 'SubjectToTemplate1Warp' + 
+               self.inputs.out_prefix + 'SubjectToTemplate1Warp' +
                self.inputs.image_suffix)
         outputs['SubjectToTemplate0GenericAffine'] = os.path.join(os.getcwd(),
                 self.inputs.out_prefix + 'SubjectToTemplate0GenericAffine.mat')
-        outputs['TemplateToSubjectLogJacobian'] = os.path.join(os.getcwd(), 
+        outputs['TemplateToSubjectLogJacobian'] = os.path.join(os.getcwd(),
                self.inputs.out_prefix + 'subjectToTemplateLogJacobian.'+
                self.inputs.image_suffix)
         return outputs

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,18 +56,14 @@ def test_ProcStreamlines_inputs():
     position=-1,
     ),
     outputacm=dict(argstr='-outputacm',
-    requires=['outputroot', 'seedfile'],
     ),
     outputcbs=dict(argstr='-outputcbs',
-    requires=['outputroot', 'targetfile', 'seedfile'],
     ),
     outputcp=dict(argstr='-outputcp',
-    requires=['outputroot', 'seedfile'],
     ),
     outputroot=dict(argstr='-outputroot %s',
     ),
     outputsc=dict(argstr='-outputsc',
-    requires=['outputroot', 'seedfile'],
     ),
     outputtracts=dict(argstr='-outputtracts',
     ),
@@ -107,8 +103,7 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(outputroot_files=dict(),
-    proc=dict(),
+    output_map = dict(proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -16,28 +16,20 @@ def test_ApplyTOPUP_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_files=dict(argstr='--imain=%s',
+    in_files=dict(argstr='%s',
     mandatory=True,
-    sep=',',
     ),
-    in_index=dict(argstr='--inindex=%s',
+    in_index=dict(argstr='%s',
     mandatory=True,
-    sep=',',
     ),
-    in_topup_fieldcoef=dict(argstr='--topup=%s',
-    copyfile=False,
-    requires=['in_topup_movpar'],
-    ),
-    in_topup_movpar=dict(copyfile=False,
-    requires=['in_topup_fieldcoef'],
+    in_topup=dict(argstr='--topup=%s',
+    mandatory=True,
     ),
     interp=dict(argstr='--interp=%s',
     ),
     method=dict(argstr='--method=%s',
     ),
-    out_corrected=dict(argstr='--out=%s',
-    name_source=['in_files'],
-    name_template='%s_corrected',
+    out_base=dict(argstr='--out=%s',
     ),
     output_type=dict(),
     terminal_output=dict(mandatory=True,

nipype/interfaces/fsl/tests/test_auto_DTIFit.py

@@ -17,7 +17,7 @@ def test_DTIFit_inputs():
     mandatory=True,
     position=3,
     ),
-    cni=dict(argstr='--cni=%s',
+    cni=dict(argstr='-cni %s',
     ),
     dwi=dict(argstr='-k %s',
     mandatory=True,

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -33,12 +33,7 @@ def test_Eddy_inputs():
     in_mask=dict(argstr='--mask=%s',
     mandatory=True,
     ),
-    in_topup_fieldcoef=dict(argstr='--topup=%s',
-    copyfile=False,
-    requires=['in_topup_movpar'],
-    ),
-    in_topup_movpar=dict(copyfile=False,
-    requires=['in_topup_fieldcoef'],
+    in_topup=dict(argstr='--topup=%s',
     ),
     method=dict(argstr='--resamp=%s',
     ),

nipype/interfaces/fsl/tests/test_auto_FIRST.py

@@ -18,7 +18,6 @@ def test_FIRST_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-i %s',
-    copyfile=False,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/fsl/tests/test_auto_FUGUE.py

@@ -21,6 +21,7 @@ def test_FUGUE_inputs():
     fmap_in_file=dict(argstr='--loadfmap=%s',
     ),
     fmap_out_file=dict(argstr='--savefmap=%s',
+    hash_files=False,
     ),
     forward_warping=dict(usedefault=True,
     ),
@@ -52,23 +53,21 @@ def test_FUGUE_inputs():
     ),
     phase_conjugate=dict(argstr='--phaseconj',
     ),
-    phasemap_in_file=dict(argstr='--phasemap=%s',
+    phasemap_file=dict(argstr='--phasemap=%s',
     ),
     poly_order=dict(argstr='--poly=%d',
     ),
-    save_fmap=dict(xor=['save_unmasked_fmap'],
-    ),
-    save_shift=dict(xor=['save_unmasked_shift'],
-    ),
+    save_shift=dict(),
     save_unmasked_fmap=dict(argstr='--unmaskfmap',
-    xor=['save_fmap'],
+    requires=['fmap_out_file'],
     ),
     save_unmasked_shift=dict(argstr='--unmaskshift',
-    xor=['save_shift'],
+    requires=['shift_out_file'],
     ),
     shift_in_file=dict(argstr='--loadshift=%s',
     ),
     shift_out_file=dict(argstr='--saveshift=%s',
+    hash_files=False,
     ),
     smooth2d=dict(argstr='--smooth2=%.2f',
     ),
@@ -80,12 +79,11 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
-    requires=['in_file'],
-    xor=['warped_file'],
+    genfile=True,
+    hash_files=False,
     ),
     warped_file=dict(argstr='--warp=%s',
-    requires=['in_file'],
-    xor=['unwarped_file'],
+    hash_files=False,
     ),
     )
     inputs = FUGUE.input_spec()

nipype/interfaces/fsl/tests/test_auto_MELODIC.py

@@ -32,7 +32,6 @@ def test_MELODIC_inputs():
     in_files=dict(argstr='-i %s',
     mandatory=True,
     position=0,
-    sep=',',
     ),
     log_power=dict(argstr='--logPower',
     ),

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -8,14 +8,8 @@ def test_TOPUP_inputs():
     config=dict(argstr='--config=%s',
     usedefault=True,
     ),
-    encoding_direction=dict(argstr='--datain=%s',
-    mandatory=True,
-    requires=['readout_times'],
-    xor=['encoding_file'],
-    ),
+    encoding_direction=dict(),
     encoding_file=dict(argstr='--datain=%s',
-    mandatory=True,
-    xor=['encoding_direction'],
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -39,31 +33,15 @@ def test_TOPUP_inputs():
     numprec=dict(argstr='--numprec=%s',
     ),
     out_base=dict(argstr='--out=%s',
-    hash_files=False,
-    name_source=['in_file'],
-    name_template='%s_base',
     ),
     out_corrected=dict(argstr='--iout=%s',
-    hash_files=False,
-    name_source=['in_file'],
-    name_template='%s_corrected',
     ),
     out_field=dict(argstr='--fout=%s',
-    hash_files=False,
-    name_source=['in_file'],
-    name_template='%s_field',
     ),
     out_logfile=dict(argstr='--logout=%s',
-    hash_files=False,
-    keep_extension=True,
-    name_source=['in_file'],
-    name_template='%s_topup.log',
     ),
     output_type=dict(),
-    readout_times=dict(mandatory=True,
-    requires=['encoding_direction'],
-    xor=['encoding_file'],
-    ),
+    readout_times=dict(),
     regrid=dict(argstr='--regrid=%d',
     ),
     scale=dict(argstr='--scale=%d',
@@ -91,6 +69,7 @@ def test_TOPUP_outputs():
     out_fieldcoef=dict(),
     out_logfile=dict(),
     out_movpar=dict(),
+    out_topup=dict(),
     )
     outputs = TOPUP.output_spec()