Merge pull request #1 from satra/antsct

Antsct

.travis.yml

@@ -4,7 +4,7 @@ python:
   - 2.7
 # Setup anaconda
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.0.0-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda/bin:$PATH

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.
 * ENH: New Freesurfer interface: MRIPretess
 * ENH: New miscelaneous interface: AddCSVRow
 * ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 

nipype/interfaces/afni/tests/test_auto_Volreg.py

@@ -32,6 +32,11 @@ 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',
@@ -57,6 +62,7 @@ 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

@@ -319,8 +319,7 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
                              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',
-        usedefault=True)
+        ' nii.gz is default'),  argstr='-s %s', usedefault=True)
     t1_registration_template = File(exists=True,
             desc = ('Anatomical *intensity* template'
            '(assumed to be skull-stripped). A common'
@@ -330,56 +329,54 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
            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',
-            desc='Keep brain extraction/segmentation'
-            'warps, etc (default = 0).', mandatory=False)
+                        desc=('Mask (defined in the template space) used during'
+                              ' registration for brain extraction.'))
+    keep_temporary_files=traits.Int(argstr='-k %d',
+            desc='Keep brain extraction/segmentation warps, etc (default = 0).')
     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',
+            '(default = 100x100x70x20)')
+    prior_segmentation_weight=traits.Float(argstr='-w %f',
             desc='Atropos spatial prior *probability* weight for'
             'the segmentation')
-    segmentation_iterations=traits.Int(argstr='-n %d', mandatory=False,
+    segmentation_iterations=traits.Int(argstr='-n %d',
             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',
             desc=('Atropos posterior formulation and whether or not'
                 'to use mixture model proportions.'
                    '''e.g 'Socrates[1]' (default) or 'Aristotle[1]'.'''
                    'Choose the latter if you'
                    'want use the distance priors (see also the -l option'
                    'for label propagation control).'))
     use_floatingpoint_precision=traits.Enum(0, 1, argstr='-j %d',
-            mandatory=False,
             desc='Use floating point precision in registrations (default = 0)')
-    use_random_seeding=traits.Enum(0, 1, argstr='-u %d', mandatory=False,
-            desc='Use random number generated from system clock in Atropos'
-            '(default = 1)')
-    b_spline_smoothing=traits.Bool(argst='-v', mandatory=False,
-            desc='Use B-spline SyN for registrations and B-spline'
-            'exponential mapping in DiReCT.')
-    cortical_label_image=File(exists=True, mandatory=False,
+    use_random_seeding=traits.Enum(0, 1, argstr='-u %d',
+            desc=('Use random number generated from system clock in Atropos'
+            '(default = 1)'))
+    b_spline_smoothing=traits.Bool(argstr='-v',
+            desc=('Use B-spline SyN for registrations and B-spline'
+            'exponential mapping in DiReCT.'))
+    cortical_label_image=File(exists=True,
             desc='Cortical ROI labels to use as a prior for ATITH.')
-    label_propagation=traits.Str(argstr='-l %s', mandatory=False,
-            desc='Incorporate a distance prior one the posterior formulation.  Should be'
+    label_propagation=traits.Str(argstr='-l %s',
+            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'
               'probability for anything outside the current label'
               '  = boundaryProbability * exp( -lambda * distanceFromBoundary )'
               'Intuitively, smaller lambda values will increase the spatial capture'
               'range of the distance prior.  To apply to all label values, simply omit'
-              'specifying the label, i.e. -l [lambda,boundaryProbability].')
-    quick_registration=traits.Bool(argstr='-q 1', mandatory=False,
-            desc='If = 1, use antsRegistrationSyNQuick.sh as the basis for registration'
+              'specifying the label, i.e. -l [lambda,boundaryProbability].'))
+    quick_registration=traits.Bool(argstr='-q 1',
+            desc=('If = 1, use antsRegistrationSyNQuick.sh as the basis for registration'
                   'during brain extraction, brain segmentation, and'
                   '(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.'
+                  'Otherwise use antsRegistrationSyN.sh (default = 0).'))
+    debug=traits.Bool(argstr='-z 1',
+            desc=('If > 0, runs a faster version of the script.'
             'Only for testing. Implies -u 0.'
-            'Requires single thread computation for complete reproducibility.')
+            'Requires single thread computation for complete reproducibility.'))
 
 class antsCorticalThicknessoutputSpec(TraitedSpec):
     BrainExtractionMask=File(exists=True,
@@ -450,6 +447,7 @@ def _format_arg(self, opt, spec, val):
             retval += ext
             return retval
         return super(ANTSCommand, self)._format_arg(opt, spec, val)
+
     def _run_interface(self, runtime):
         priors_directory = os.path.join(os.getcwd(), "priors")
         if not os.path.exists(priors_directory):

nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py

@@ -56,14 +56,18 @@ 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',
     ),
@@ -103,7 +107,8 @@ def test_ProcStreamlines_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ProcStreamlines_outputs():
-    output_map = dict(proc=dict(),
+    output_map = dict(outputroot_files=dict(),
+    proc=dict(),
     )
     outputs = ProcStreamlines.output_spec()
 

nipype/interfaces/elastix/registration.py

@@ -6,7 +6,7 @@
 # @Author: oesteban - code@oscaresteban.es
 # @Date:   2014-06-02 12:06:50
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-17 10:19:23
+# @Last Modified time: 2014-09-01 21:03:57
 """
 Interfaces to perform image registrations and to apply the resulting
 displacement maps to images and points.
@@ -18,8 +18,6 @@
 
 from ..base import (CommandLine, CommandLineInputSpec, isdefined,
                     TraitedSpec, File, traits, InputMultiPath)
-
-
 from base import ElastixBaseInputSpec
 
 from ... import logging
@@ -31,10 +29,8 @@ class RegistrationInputSpec(ElastixBaseInputSpec):
            desc='fixed image')
     moving_image = File(exists=True, mandatory=True, argstr='-m %s',
            desc='moving image')
-
     parameters = InputMultiPath(File(exists=True), mandatory=True, argstr='-p %s...',
                                 desc='parameter file, elastix handles 1 or more -p')
-
     fixed_mask = File(exists=True, argstr='-fMask %s', desc='mask for fixed image')
     moving_mask = File(exists=True, argstr='-mMask %s', desc='mask for moving image')
     initial_transform = File(exists=True, argstr='-t0 %s',
@@ -51,7 +47,8 @@ class RegistrationOutputSpec(TraitedSpec):
 
 
 class Registration(CommandLine):
-    """Elastix nonlinear registration interface
+    """
+    Elastix nonlinear registration interface
 
     Example
     -------
@@ -63,6 +60,8 @@ class Registration(CommandLine):
     >>> reg.inputs.parameters = ['elastix.txt']
     >>> reg.cmdline
     'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt'
+
+
     """
 
     _cmd = 'elastix'
@@ -140,17 +139,21 @@ class ApplyWarpOutputSpec(TraitedSpec):
     warped_file = File(desc='input moving image warped to fixed image')
 
 class ApplyWarp(CommandLine):
-    """Use `transformix` to apply a transform on an input image.
+    """
+    Use ``transformix`` to apply a transform on an input image.
     The transform is specified in the transform-parameter file.
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import ApplyWarp
     >>> reg = ApplyWarp()
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix'
@@ -170,22 +173,26 @@ class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
 
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
-    disp_field = File(exists=True, desc='displacements field')
-    jacdet_map = File(exists=True, desc='det(Jacobian) map')
-    jacmat_map = File(exists=True, desc='Jacobian matrix map')
+    disp_field = File(desc='displacements field')
+    jacdet_map = File(desc='det(Jacobian) map')
+    jacmat_map = File(desc='Jacobian matrix map')
 
 class AnalyzeWarp(CommandLine):
-    """Use `transformix` to get details from the input transform (generate
+    """
+    Use transformix to get details from the input transform (generate
     the corresponding deformation field, generate the determinant of the
     Jacobian map or the Jacobian map itself)
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import AnalyzeWarp
     >>> reg = AnalyzeWarp()
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix -def all -jac all -jacmat all'
@@ -213,17 +220,20 @@ class PointsWarpOutputSpec(TraitedSpec):
     warped_file = File(desc='input points displaced in fixed image domain')
 
 class PointsWarp(CommandLine):
-    """Use `transformix` to apply a transform on an input point set.
+    """Use ``transformix`` to apply a transform on an input point set.
     The transform is specified in the transform-parameter file.
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import PointsWarp
     >>> reg = PointsWarp()
     >>> reg.inputs.points_file = 'surf1.vtk'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix'

nipype/interfaces/elastix/utils.py

@@ -6,7 +6,7 @@
 # @Author: oesteban - code@oscaresteban.es
 # @Date:   2014-06-17 10:17:07
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-27 10:25:36
+# @Last Modified time: 2014-09-01 21:05:33
 """
 Generic interfaces to manipulate registration parameters files, including
 transform files (to configure warpings)
@@ -51,14 +51,17 @@ class EditTransform(BaseInterface):
     """
     Manipulates an existing transform file generated with elastix
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import EditTransform
     >>> tfm = EditTransform()
     >>> tfm.inputs.transform_file = 'TransformParameters.0.txt'
     >>> tfm.inputs.reference_image = 'fixed1.nii'
     >>> tfm.inputs.output_type = 'unsigned char'
     >>> tfm.run() # doctest: +SKIP
+
+
     """
 
     input_spec = EditTransformInputSpec

nipype/interfaces/fsl/__init__.py

@@ -16,7 +16,7 @@
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,
-                    Complex, InvWarp, WarpUtils, ConvertWarp)
+                    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect)