Merge branch 'master' of https://github.com/armaneshaghi/nipype

armaneshaghi · armaneshaghi · commit 3c7fe610e664 · 2014-08-31T07:39:18.000Z
diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/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()
diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/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()
 
diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/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,
diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/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,
diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/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',
     ),
diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/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,
     ),
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/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()
diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/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',
     ),
diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/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()
 
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py
@@ -16,13 +16,12 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    xor=['exclude_file', 'exclude_spec'],
+    position=2,
     ),
-    exclude_spec=dict(argstr='-exclude %s',
+    exclude_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['exclude_file', 'exclude_spec'],
     ),
     gradient_encoding_file=dict(argstr='-grad %s',
     mandatory=True,
@@ -36,13 +35,12 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    xor=['include_file', 'include_spec'],
+    position=2,
     ),
-    include_spec=dict(argstr='-include %s',
+    include_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -54,14 +52,13 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-mask %s',
-    xor=['mask_file', 'mask_spec'],
+    mask_file=dict(argstr='-exclude %s',
+    position=2,
     ),
-    mask_spec=dict(argstr='-mask %s',
+    mask_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -77,24 +74,21 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    name_source=['in_file'],
-    name_template='%s_tracked.tck',
-    output_name='tracked',
+    genfile=True,
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    xor=['seed_file', 'seed_spec'],
+    position=2,
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-stop',
+    stop=dict(argstr='-gzip',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py
@@ -23,9 +23,8 @@ def test_GenerateDirections_inputs():
     ),
     out_file=dict(argstr='%s',
     hash_files=False,
-    name_source=['num_dirs'],
-    name_template='directions_%d.txt',
     position=-1,
+    usedefault=True,
     ),
     power=dict(argstr='-power %s',
     ),
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py
@@ -16,13 +16,12 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     usedefault=True,
     ),
     exclude_file=dict(argstr='-exclude %s',
-    xor=['exclude_file', 'exclude_spec'],
+    position=2,
     ),
-    exclude_spec=dict(argstr='-exclude %s',
+    exclude_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['exclude_file', 'exclude_spec'],
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -32,13 +31,12 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     position=-2,
     ),
     include_file=dict(argstr='-include %s',
-    xor=['include_file', 'include_spec'],
+    position=2,
     ),
-    include_spec=dict(argstr='-include %s',
+    include_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['include_file', 'include_spec'],
     ),
     initial_cutoff_value=dict(argstr='-initcutoff %s',
     units='NA',
@@ -50,14 +48,13 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     position=-3,
     usedefault=True,
     ),
-    mask_file=dict(argstr='-mask %s',
-    xor=['mask_file', 'mask_spec'],
+    mask_file=dict(argstr='-exclude %s',
+    position=2,
     ),
-    mask_spec=dict(argstr='-mask %s',
+    mask_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['mask_file', 'mask_spec'],
     ),
     maximum_number_of_tracks=dict(argstr='-maxnum %d',
     ),
@@ -75,24 +72,21 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    name_source=['in_file'],
-    name_template='%s_tracked.tck',
-    output_name='tracked',
+    genfile=True,
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',
-    xor=['seed_file', 'seed_spec'],
+    position=2,
     ),
     seed_spec=dict(argstr='-seed %s',
     position=2,
     sep=',',
     units='mm',
-    xor=['seed_file', 'seed_spec'],
     ),
     step_size=dict(argstr='-step %s',
     units='mm',
     ),
-    stop=dict(argstr='-stop',
+    stop=dict(argstr='-gzip',
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py
diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py
diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py
diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py
