Merge remote-tracking branch 'upstream/maint/1.5.x'

Author: effigies

.travis.yml

@@ -71,7 +71,7 @@ install:
 script:
 - |
     if [ "$CHECK_TYPE" = "test" ]; then
-        py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
+        py.test -sv --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n 2
     fi
 - |
     if [ "$CHECK_TYPE" = "specs" ]; then

.zenodo.json

@@ -115,16 +115,16 @@
       "name": "Hamalainen, Carlo",
       "orcid": "0000-0001-7655-3830"
     },
-    {
-      "affiliation": "Stanford University",
-      "name": "\u0106iri\u0107 , Rastko",
-      "orcid": "0000-0001-6347-7939"
-    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "\u0106iri\u0107 , Rastko",
+      "orcid": "0000-0001-6347-7939"
+    },
     {
       "name": "Dubois, Mathieu"
     },
@@ -225,6 +225,11 @@
     {
       "name": "Millman, Jarrod"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
+    },
     {
       "affiliation": "National Institute of Mental Health",
       "name": "Nielson, Dylan M.",
@@ -241,11 +246,6 @@
     {
       "name": "Mordom, David"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Mancini, Matteo",
-      "orcid": "0000-0001-7194-4568"
-    },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Je\u0301re\u0301my",

doc/changelog/1.X.X-changelog.rst

@@ -1,5 +1,21 @@
+1.5.1 (August 16, 2020)
+=======================
+
+Bug-fix release in the 1.5.x series.
+
+This release includes small updates to ANTs utilities that lie somewhere
+between bug fixes and enhancements.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.5.1?closed=1>`__)
+
+  * FIX: Warn for min/max_ver traits when tool version can't be parsed (https://github.com/nipy/nipype/pull/3241)
+  * FIX: Serialize all interface arguments when exporting workflows (https://github.com/nipy/nipype/pull/3240)
+  * FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (https://github.com/nipy/nipype/pull/3237)
+  * FIX: ANTs' utilities revision - bug fixes and add more operations to ``ants.ImageMath`` (https://github.com/nipy/nipype/pull/3236)
+  * DOC: Skip BIDSDataGrabber doctest if pybids is missing (https://github.com/nipy/nipype/pull/3224)
+
 1.5.0 (June 03, 2020)
-=========================
+=====================
 
 New feature release in the 1.5.x series.
 

doc/interfaces.rst

@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.4.2 <http://nipype.readthedocs.io/en/1.4.2/>`_ `1.4.1 <http://nipype.readthedocs.io/en/1.4.1/>`_
+Previous versions: `1.5.1 <http://nipype.readthedocs.io/en/1.5.1/>`_ `1.5.0 <http://nipype.readthedocs.io/en/1.5.0/>`_
 
 Workflows
 ---------

nipype/conftest.py

@@ -17,6 +17,7 @@
 def add_np(doctest_namespace):
     doctest_namespace["np"] = numpy
     doctest_namespace["os"] = os
+    doctest_namespace["pytest"] = pytest
     doctest_namespace["datadir"] = data_dir
 
 

nipype/interfaces/ants/registration.py

@@ -592,7 +592,8 @@ class RegistrationOutputSpec(TraitedSpec):
         File(exists=True), desc="List of output transforms for forward registration"
     )
     reverse_forward_transforms = traits.List(
-        File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform"
+        File(exists=True),
+        desc="List of output transforms for forward registration reversed for antsApplyTransform",
     )
     reverse_transforms = traits.List(
         File(exists=True), desc="List of output transforms for reverse registration"
@@ -601,7 +602,8 @@ class RegistrationOutputSpec(TraitedSpec):
         traits.Bool(), desc="List of flags corresponding to the forward transforms"
     )
     reverse_forward_invert_flags = traits.List(
-        traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform"
+        traits.Bool(),
+        desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform",
     )
     reverse_invert_flags = traits.List(
         traits.Bool(), desc="List of flags corresponding to the reverse transforms"

nipype/interfaces/ants/resampling.py

@@ -4,7 +4,7 @@
 import os
 
 from .base import ANTSCommand, ANTSCommandInputSpec
-from ..base import TraitedSpec, File, traits, isdefined, InputMultiPath
+from ..base import TraitedSpec, File, traits, isdefined, InputMultiObject
 from ...utils.filemanip import split_filename
 
 
@@ -52,7 +52,7 @@ class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec):
     use_bspline = traits.Bool(
         argstr="--use-Bspline", desc="Use 3rd order B-Spline interpolation"
     )
-    transformation_series = InputMultiPath(
+    transformation_series = InputMultiObject(
         File(exists=True),
         argstr="%s",
         desc="transformation file(s) to be applied",
@@ -204,7 +204,7 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
     use_bspline = traits.Bool(
         argstr="--use-BSpline", desc="Use 3rd order B-Spline interpolation"
     )
-    transformation_series = InputMultiPath(
+    transformation_series = InputMultiObject(
         File(exists=True),
         argstr="%s",
         desc="transformation file(s) to be applied",
@@ -369,15 +369,14 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
             traits.Float(), traits.Float()  # Gaussian/MultiLabel (sigma, alpha)
         ),
     )
-    transforms = traits.Either(
-        InputMultiPath(File(exists=True)),
-        "identity",
+    transforms = InputMultiObject(
+        traits.Either(File(exists=True), "identity"),
         argstr="%s",
         mandatory=True,
         desc="transform files: will be applied in reverse order. For "
         "example, the last specified transform will be applied first.",
     )
-    invert_transform_flags = InputMultiPath(traits.Bool())
+    invert_transform_flags = InputMultiObject(traits.Bool())
     default_value = traits.Float(0.0, argstr="--default-value %g", usedefault=True)
     print_out_composite_warp_file = traits.Bool(
         False,
@@ -411,7 +410,7 @@ class ApplyTransforms(ANTSCommand):
     >>> at.cmdline
     'antsApplyTransforms --default-value 0 --float 0 --input moving1.nii \
 --interpolation Linear --output moving1_trans.nii \
---reference-image fixed1.nii -t identity'
+--reference-image fixed1.nii --transform identity'
 
     >>> at = ApplyTransforms()
     >>> at.inputs.dimension = 3
@@ -421,11 +420,11 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.interpolation = 'Linear'
     >>> at.inputs.default_value = 0
     >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
-    >>> at.inputs.invert_transform_flags = [False, False]
+    >>> at.inputs.invert_transform_flags = [False, True]
     >>> at.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
 --interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii \
---transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
+--transform ants_Warp.nii.gz --transform [ trans.mat, 1 ]'
 
     >>> at1 = ApplyTransforms()
     >>> at1.inputs.dimension = 3
@@ -440,7 +439,23 @@ class ApplyTransforms(ANTSCommand):
     >>> at1.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
 --interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii \
---transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
+--transform ants_Warp.nii.gz --transform trans.mat'
+
+    Identity transforms may be used as part of a chain:
+
+    >>> at2 = ApplyTransforms()
+    >>> at2.inputs.dimension = 3
+    >>> at2.inputs.input_image = 'moving1.nii'
+    >>> at2.inputs.reference_image = 'fixed1.nii'
+    >>> at2.inputs.output_image = 'deformed_moving1.nii'
+    >>> at2.inputs.interpolation = 'BSpline'
+    >>> at2.inputs.interpolation_parameters = (5,)
+    >>> at2.inputs.default_value = 0
+    >>> at2.inputs.transforms = ['identity', 'ants_Warp.nii.gz', 'trans.mat']
+    >>> at2.cmdline
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
+--interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii \
+--transform identity --transform ants_Warp.nii.gz --transform trans.mat'
     """
 
     _cmd = "antsApplyTransforms"
@@ -458,25 +473,20 @@ def _gen_filename(self, name):
 
     def _get_transform_filenames(self):
         retval = []
-        for ii in range(len(self.inputs.transforms)):
-            if isdefined(self.inputs.invert_transform_flags):
-                if len(self.inputs.transforms) == len(
-                    self.inputs.invert_transform_flags
-                ):
-                    invert_code = 1 if self.inputs.invert_transform_flags[ii] else 0
-                    retval.append(
-                        "--transform [ %s, %d ]"
-                        % (self.inputs.transforms[ii], invert_code)
-                    )
-                else:
-                    raise Exception(
-                        (
-                            "ERROR: The useInverse list must have the same number "
-                            "of entries as the transformsFileName list."
-                        )
-                    )
+        invert_flags = self.inputs.invert_transform_flags
+        if not isdefined(invert_flags):
+            invert_flags = [False] * len(self.inputs.transforms)
+        elif len(self.inputs.transforms) != len(invert_flags):
+            raise ValueError(
+                "ERROR: The invert_transform_flags list must have the same number "
+                "of entries as the transforms list."
+            )
+
+        for transform, invert in zip(self.inputs.transforms, invert_flags):
+            if invert:
+                retval.append(f"--transform [ {transform}, 1 ]")
             else:
-                retval.append("--transform %s" % self.inputs.transforms[ii])
+                retval.append(f"--transform {transform}")
         return " ".join(retval)
 
     def _get_output_warped_filename(self):
@@ -492,8 +502,6 @@ def _format_arg(self, opt, spec, val):
         if opt == "output_image":
             return self._get_output_warped_filename()
         elif opt == "transforms":
-            if val == "identity":
-                return "-t identity"
             return self._get_transform_filenames()
         elif opt == "interpolation":
             if self.inputs.interpolation in [

nipype/interfaces/ants/segmentation.py

@@ -543,6 +543,7 @@ def _list_outputs(self):
             outputs["bias_image"] = os.path.abspath(self._out_bias_file)
         return outputs
 
+
 class CorticalThicknessInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(
         3, 2, argstr="-d %d", usedefault=True, desc="image dimension (2 or 3)"

nipype/interfaces/ants/utils.py

@@ -138,18 +138,18 @@ class ImageMath(ANTSCommand, CopyHeaderInterface):
 
     def __init__(self, **inputs):
         super(ImageMath, self).__init__(**inputs)
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
         self.inputs.on_trait_change(self._operation_update, "operation")
         self.inputs.on_trait_change(self._copyheader_update, "copy_header")
 
     def _operation_update(self):
-        if self.inputs.operation in ("PadImage", ):
+        if self.inputs.operation in ("PadImage",):
             self.inputs.copy_header = False
 
     def _copyheader_update(self):
-        if self.inputs.copy_header and self.inputs.operation in ("PadImage", ):
+        if self.inputs.copy_header and self.inputs.operation in ("PadImage",):
             warn("copy_header cannot be updated to True with PadImage as operation.")
             self.inputs.copy_header = False
 

nipype/interfaces/base/core.py

@@ -276,7 +276,18 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
             version = LooseVersion(str(self.version))
             for name in names:
                 min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
-                if min_ver > version:
+                try:
+                    too_old = min_ver > version
+                except TypeError as err:
+                    msg = (
+                        f"Nipype cannot validate the package version {version!r} for "
+                        f"{self.__class__.__name__}. Trait {name} requires version >={min_ver}."
+                    )
+                    iflogger.warning(f"{msg}. Please verify validity.")
+                    if config.getboolean("execution", "stop_on_unknown_version"):
+                        raise ValueError(msg) from err
+                    continue
+                if too_old:
                     unavailable_traits.append(name)
                     if not isdefined(getattr(trait_object, name)):
                         continue
@@ -293,7 +304,18 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
             version = LooseVersion(str(self.version))
             for name in names:
                 max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
-                if max_ver < version:
+                try:
+                    too_new = max_ver < version
+                except TypeError as err:
+                    msg = (
+                        f"Nipype cannot validate the package version {version!r} for "
+                        f"{self.__class__.__name__}. Trait {name} requires version <={max_ver}."
+                    )
+                    iflogger.warning(f"{msg}. Please verify validity.")
+                    if config.getboolean("execution", "stop_on_unknown_version"):
+                        raise ValueError(msg) from err
+                    continue
+                if too_new:
                     unavailable_traits.append(name)
                     if not isdefined(getattr(trait_object, name)):
                         continue

nipype/interfaces/base/tests/test_core.py

@@ -3,6 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import os
 import simplejson as json
+import logging
 
 import pytest
 from unittest import mock
@@ -236,6 +237,41 @@ class DerivedInterface1(nib.BaseInterface):
     obj._check_version_requirements(obj.inputs)
 
 
+def test_input_version_missing(caplog):
+    class DerivedInterface(nib.BaseInterface):
+        class input_spec(nib.TraitedSpec):
+            foo = nib.traits.Int(min_ver="0.9")
+            bar = nib.traits.Int(max_ver="0.9")
+
+        _version = "misparsed-garbage"
+
+    obj = DerivedInterface()
+    obj.inputs.foo = 1
+    obj.inputs.bar = 1
+    with caplog.at_level(logging.WARNING, logger="nipype.interface"):
+        obj._check_version_requirements(obj.inputs)
+    assert len(caplog.records) == 2
+
+
+def test_input_version_missing_error():
+    from nipype import config
+
+    class DerivedInterface(nib.BaseInterface):
+        class input_spec(nib.TraitedSpec):
+            foo = nib.traits.Int(min_ver="0.9")
+            bar = nib.traits.Int(max_ver="0.9")
+
+        _version = "misparsed-garbage"
+
+    with mock.patch.object(config, "getboolean", return_value=True):
+        obj = DerivedInterface(foo=1)
+        with pytest.raises(ValueError):
+            obj._check_version_requirements(obj.inputs)
+        obj = DerivedInterface(bar=1)
+        with pytest.raises(ValueError):
+            obj._check_version_requirements(obj.inputs)
+
+
 def test_output_version():
     class InputSpec(nib.TraitedSpec):
         foo = nib.traits.Int(desc="a random int")
@@ -457,7 +493,7 @@ def test_global_CommandLine_output(tmpdir):
     ci = BET()
     assert ci.terminal_output == "stream"  # default case
 
-    with mock.patch.object(nib.CommandLine, '_terminal_output'):
+    with mock.patch.object(nib.CommandLine, "_terminal_output"):
         nib.CommandLine.set_default_terminal_output("allatonce")
         ci = nib.CommandLine(command="ls -l")
         assert ci.terminal_output == "allatonce"

nipype/interfaces/freesurfer/base.py

@@ -76,7 +76,7 @@ def looseversion(cls):
                 vstr = "6.0.0-dev" + githash
             elif vinfo[5][0] == "v":
                 vstr = vinfo[5][1:]
-            elif len([1 for val in vinfo[3] if val == '.']) == 2:
+            elif len([1 for val in vinfo[3] if val == "."]) == 2:
                 "version string: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b"
                 vstr = vinfo[3]
             else: