Merge remote-tracking branch 'upstream/master' into bf-nopytest

Author: effigies

.travis.yml

@@ -60,6 +60,9 @@ matrix:
           NIPYPE_EXTRAS="doc,tests,nipy,profiler"
           EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
           CI_SKIP_TEST=1
+  allow_failures:
+    - python: 2.7
+      env: INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,nipy,profiler" EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS" CI_SKIP_TEST=1
 
 addons:
   apt:

nipype/info.py

@@ -105,6 +105,7 @@ def get_nipype_gitversion():
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = '1.15.3'
+NUMPY_BAD_VERSION_27 = '1.16.0'
 SCIPY_MIN_VERSION = '0.14'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
@@ -136,7 +137,8 @@ def get_nipype_gitversion():
 REQUIRES = [
     'nibabel>=%s' % NIBABEL_MIN_VERSION,
     'networkx>=%s' % NETWORKX_MIN_VERSION,
-    'numpy>=%s ; python_version < "3.7"' % NUMPY_MIN_VERSION,
+    'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
+    'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
     'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
     'scipy>=%s' % SCIPY_MIN_VERSION,

nipype/interfaces/ants/__init__.py

@@ -5,7 +5,7 @@
 
 # Registraiton programs
 from .registration import (ANTS, Registration, RegistrationSynQuick,
-                           MeasureImageSimilarity)
+                           CompositeTransformUtil, MeasureImageSimilarity)
 
 # Resampling Programs
 from .resampling import (ApplyTransforms, ApplyTransformsToPoints,

nipype/interfaces/ants/registration.py

@@ -1596,3 +1596,77 @@ def _list_outputs(self):
             outputs['forward_warp_field'] = out_base + '1Warp.nii.gz'
             outputs['inverse_warp_field'] = out_base + '1InverseWarp.nii.gz'
         return outputs
+
+class CompositeTransformUtilInputSpec(ANTSCommandInputSpec):
+    process = traits.Enum('assemble', 'disassemble', argstr='--%s',
+        position=1, usedefault=True,
+        desc='What to do with the transform inputs (assemble or disassemble)',
+        )
+    out_file = File(exists=False, argstr='%s', position=2,
+          desc='Output file path (only used for disassembly).')
+    in_file = InputMultiPath(File(exists=True), mandatory=True, argstr='%s...',
+        position=3, desc='Input transform file(s)')
+    output_prefix = Str("transform", usedefault=True, argstr='%s', position=4,
+          desc="A prefix that is prepended to all output files (only used for assembly).")
+
+class CompositeTransformUtilOutputSpec(TraitedSpec):
+    affine_transform = File(desc="Affine transform component")
+    displacement_field = File(desc="Displacement field component")
+    out_file = File(desc="Compound transformation file")
+
+class CompositeTransformUtil(ANTSCommand):
+    """
+    ANTs utility which can combine or break apart transform files into their individual
+    constituent components.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.ants import CompositeTransformUtil
+    >>> tran = CompositeTransformUtil()
+    >>> tran.inputs.process = 'disassemble'
+    >>> tran.inputs.in_file = 'output_Composite.h5'
+    >>> tran.cmdline
+    'CompositeTransformUtil --disassemble output_Composite.h5 transform'
+    >>> tran.run()  # doctest: +SKIP
+
+    example for assembling transformation files
+
+    >>> from nipype.interfaces.ants import CompositeTransformUtil
+    >>> tran = CompositeTransformUtil()
+    >>> tran.inputs.process = 'assemble'
+    >>> tran.inputs.out_file = 'my.h5'
+    >>> tran.inputs.in_file = ['AffineTransform.mat', 'DisplacementFieldTransform.nii.gz']
+    >>> tran.cmdline
+    'CompositeTransformUtil --assemble my.h5 AffineTransform.mat DisplacementFieldTransform.nii.gz '
+    >>> tran.run()  # doctest: +SKIP
+    """
+
+    _cmd = 'CompositeTransformUtil'
+    input_spec = CompositeTransformUtilInputSpec
+    output_spec = CompositeTransformUtilOutputSpec
+
+    def _num_threads_update(self):
+        """
+        CompositeTransformUtil ignores environment variables,
+        so override environment update from ANTSCommand class
+        """
+        pass
+
+    def _format_arg(self, name, spec, value):
+        if name == 'output_prefix' and self.inputs.process == 'assemble':
+            return ''
+        if name == 'out_file' and self.inputs.process == 'disassemble':
+            return ''
+        return super(CompositeTransformUtil, self)._format_arg(name, spec, value)
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if self.inputs.process == 'disassemble':
+            outputs['affine_transform'] = os.path.abspath(
+                '00_{}_AffineTransform.mat'.format(self.inputs.output_prefix))
+            outputs['displacement_field'] = os.path.abspath(
+                '01_{}_DisplacementFieldTransform.nii.gz'.format(self.inputs.output_prefix))
+        if self.inputs.process == 'assemble':
+            outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        return outputs

nipype/interfaces/ants/segmentation.py

@@ -207,13 +207,27 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
         name_template='%s_thickness',
         keep_extension=True,
         hash_files=False)
-    smooth_param = traits.Float(argstr='smoothparam=%d', desc='', position=4)
+    smooth_param = traits.Float(
+        argstr='%f',
+        desc='Sigma of the Laplacian Recursive Image Filter (defaults to 1)',
+        position=4)
     prior_thickness = traits.Float(
-        argstr='priorthickval=%d', desc='', position=5)
-    dT = traits.Float(argstr='dT=%d', desc='', position=6)
-    sulcus_prior = traits.Bool(argstr='use-sulcus-prior', desc='', position=7)
-    opt_tolerance = traits.Float(
-        argstr='optional-laplacian-tolerance=%d', desc='', position=8)
+        argstr='%f',
+        desc='Prior thickness (defaults to 500)',
+        position=5)
+    dT = traits.Float(
+        argstr='%f',
+        desc='Time delta used during integration (defaults to 0.01)',
+        position=6)
+    sulcus_prior = traits.Float(
+        argstr='%f',
+        desc='Positive floating point number for sulcus prior. '
+             'Authors said that 0.15 might be a reasonable value',
+        position=7)
+    tolerance = traits.Float(
+        argstr='%f',
+        desc='Tolerance to reach during optimization (defaults to 0.001)',
+        position=8)
 
 
 class LaplacianThicknessOutputSpec(TraitedSpec):

nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py

@@ -0,0 +1,52 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..registration import CompositeTransformUtil
+
+
+def test_CompositeTransformUtil_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        in_file=dict(
+            argstr='%s...',
+            mandatory=True,
+            position=3,
+        ),
+        num_threads=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        out_file=dict(
+            argstr='%s',
+            position=2,
+        ),
+        output_prefix=dict(
+            argstr='%s',
+            position=4,
+            usedefault=True,
+        ),
+        process=dict(
+            argstr='--%s',
+            position=1,
+            usedefault=True,
+        ),
+    )
+    inputs = CompositeTransformUtil.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_CompositeTransformUtil_outputs():
+    output_map = dict(
+        affine_transform=dict(),
+        displacement_field=dict(),
+        out_file=dict(),
+    )
+    outputs = CompositeTransformUtil.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py

@@ -7,7 +7,7 @@ def test_LaplacianThickness_inputs():
     input_map = dict(
         args=dict(argstr='%s', ),
         dT=dict(
-            argstr='dT=%d',
+            argstr='%f',
             position=6,
         ),
         environ=dict(
@@ -30,10 +30,6 @@ def test_LaplacianThickness_inputs():
             nohash=True,
             usedefault=True,
         ),
-        opt_tolerance=dict(
-            argstr='optional-laplacian-tolerance=%d',
-            position=8,
-        ),
         output_image=dict(
             argstr='%s',
             hash_files=False,
@@ -43,17 +39,21 @@ def test_LaplacianThickness_inputs():
             position=3,
         ),
         prior_thickness=dict(
-            argstr='priorthickval=%d',
+            argstr='%f',
             position=5,
         ),
         smooth_param=dict(
-            argstr='smoothparam=%d',
+            argstr='%f',
             position=4,
         ),
         sulcus_prior=dict(
-            argstr='use-sulcus-prior',
+            argstr='%f',
             position=7,
         ),
+        tolerance=dict(
+            argstr='%f',
+            position=8,
+        ),
     )
     inputs = LaplacianThickness.input_spec()
 

nipype/testing/data/AffineTransform.mat

@@ -41,6 +41,7 @@
         '\.pipeline\.s3_node_wrapper$',
         '\.testing',
         '\.scripts',
+        '\.conftest',
     ]
     docwriter.class_skip_patterns += [
         'AFNICommand',