Merge branch 'master' into enh/add-masks-overlap

Author: effigies

nipype/algorithms/metrics.py

@@ -19,12 +19,12 @@
 from scipy.ndimage.measurements import center_of_mass, label
 
 from .. import config, logging
-from ..utils.misc import package_check
 
 from ..interfaces.base import (
     SimpleInterface, BaseInterface, traits, TraitedSpec, File,
     InputMultiPath, BaseInterfaceInputSpec,
     isdefined)
+from ..interfaces.nipy.base import NipyBaseInterface
 
 iflogger = logging.getLogger('interface')
 
@@ -645,7 +645,7 @@ class SimilarityOutputSpec(TraitedSpec):
         traits.Float(desc="Similarity between volume 1 and 2, frame by frame"))
 
 
-class Similarity(BaseInterface):
+class Similarity(NipyBaseInterface):
     """Calculates similarity between two 3D or 4D volumes. Both volumes have to be in
     the same coordinate system, same space within that coordinate system and
     with the same voxel dimensions.
@@ -668,19 +668,8 @@ class Similarity(BaseInterface):
 
     input_spec = SimilarityInputSpec
     output_spec = SimilarityOutputSpec
-    _have_nipy = True
-
-    def __init__(self, **inputs):
-        try:
-            package_check('nipy')
-        except Exception:
-            self._have_nipy = False
-        super(Similarity, self).__init__(**inputs)
 
     def _run_interface(self, runtime):
-        if not self._have_nipy:
-            raise RuntimeError('nipy is not installed')
-
         from nipy.algorithms.registration.histogram_registration import HistogramRegistration
         from nipy.algorithms.registration.affine import Affine
 

nipype/algorithms/misc.py

@@ -26,7 +26,7 @@
 from ..interfaces.base import (
     BaseInterface, traits, TraitedSpec, File, InputMultiPath, OutputMultiPath,
     BaseInterfaceInputSpec, isdefined, DynamicTraitedSpec, Undefined)
-from ..utils.filemanip import fname_presuffix, split_filename, filename_to_list
+from ..utils.filemanip import fname_presuffix, split_filename, ensure_list
 from ..utils import NUMPY_MMAP
 
 from . import confounds
@@ -1479,7 +1479,7 @@ def _gen_fname(self, suffix, idx=None, ext=None):
     def _run_interface(self, runtime):
         total = None
         self._median_files = []
-        for idx, fname in enumerate(filename_to_list(self.inputs.in_files)):
+        for idx, fname in enumerate(ensure_list(self.inputs.in_files)):
             img = nb.load(fname, mmap=NUMPY_MMAP)
             data = np.median(img.get_data(), axis=3)
             if self.inputs.median_per_file:

nipype/algorithms/modelgen.py

@@ -26,7 +26,7 @@
 from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath,
                                traits, File, Bunch, BaseInterfaceInputSpec,
                                isdefined)
-from ..utils.filemanip import filename_to_list
+from ..utils.filemanip import ensure_list
 from ..utils.misc import normalize_mc_params
 from .. import config, logging
 iflogger = logging.getLogger('interface')
@@ -383,7 +383,7 @@ def _generate_standard_design(self,
         if outliers is not None:
             for i, out in enumerate(outliers):
                 numscans = 0
-                for f in filename_to_list(sessinfo[i]['scans']):
+                for f in ensure_list(sessinfo[i]['scans']):
                     shape = load(f, mmap=NUMPY_MMAP).shape
                     if len(shape) == 3 or shape[3] == 1:
                         iflogger.warning('You are using 3D instead of 4D '
@@ -580,7 +580,7 @@ def _generate_design(self, infolist=None):
         else:
             infolist = gen_info(self.inputs.event_files)
         concatlist, nscans = self._concatenate_info(infolist)
-        functional_runs = [filename_to_list(self.inputs.functional_runs)]
+        functional_runs = [ensure_list(self.inputs.functional_runs)]
         realignment_parameters = []
         if isdefined(self.inputs.realignment_parameters):
             realignment_parameters = []

nipype/algorithms/rapidart.py

@@ -28,7 +28,7 @@
 from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
                                OutputMultiPath, TraitedSpec, File,
                                BaseInterfaceInputSpec, isdefined)
-from ..utils.filemanip import filename_to_list, save_json, split_filename
+from ..utils.filemanip import ensure_list, save_json, split_filename
 from ..utils.misc import find_indices, normalize_mc_params
 from .. import logging, config
 iflogger = logging.getLogger('interface')
@@ -376,7 +376,7 @@ def _list_outputs(self):
                 outputs['displacement_files'] = []
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             outputs['plot_files'] = []
-        for i, f in enumerate(filename_to_list(self.inputs.realigned_files)):
+        for i, f in enumerate(ensure_list(self.inputs.realigned_files)):
             (outlierfile, intensityfile, statsfile, normfile, plotfile,
              displacementfile, maskfile) = \
                 self._get_output_filenames(f, os.getcwd())
@@ -616,8 +616,8 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
     def _run_interface(self, runtime):
         """Execute this module.
         """
-        funcfilelist = filename_to_list(self.inputs.realigned_files)
-        motparamlist = filename_to_list(self.inputs.realignment_parameters)
+        funcfilelist = ensure_list(self.inputs.realigned_files)
+        motparamlist = ensure_list(self.inputs.realignment_parameters)
         for i, imgf in enumerate(funcfilelist):
             self._detect_outliers_core(
                 imgf, motparamlist[i], i, cwd=os.getcwd())

nipype/interfaces/afni/preprocess.py

@@ -218,7 +218,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
     out_file = File(
         desc='output file from 3dAllineate',
         argstr='-prefix %s',
-        genfile=True,
+        name_template='%s_allineate',
+        name_source='in_file',
+        hash_files=False,
         xor=['allcostx'])
     out_param_file = File(
         argstr='-1Dparam_save %s',
@@ -424,11 +426,11 @@ class AllineateInputSpec(AFNICommandInputSpec):
     _dirs = ['X', 'Y', 'Z', 'I', 'J', 'K']
     nwarp_fixmot = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixmot%s',
+        argstr='-nwarp_fixmot%s...',
         desc='To fix motion along directions.')
     nwarp_fixdep = traits.List(
         traits.Enum(*_dirs),
-        argstr='-nwarp_fixdep%s',
+        argstr='-nwarp_fixdep%s...',
         desc='To fix non-linear warp dependency along directions.')
     verbose = traits.Bool(
         argstr='-verb', desc='Print out verbose progress reports.')
@@ -465,31 +467,29 @@ class Allineate(AFNICommand):
     '3dAllineate -source functional.nii -prefix functional_allineate.nii -1Dmatrix_apply cmatrix.mat'
     >>> res = allineate.run()  # doctest: +SKIP
 
-    >>> from nipype.interfaces import afni
     >>> allineate = afni.Allineate()
     >>> allineate.inputs.in_file = 'functional.nii'
     >>> allineate.inputs.reference = 'structural.nii'
     >>> allineate.inputs.allcostx = 'out.allcostX.txt'
     >>> allineate.cmdline
     '3dAllineate -source functional.nii -base structural.nii -allcostx |& tee out.allcostX.txt'
     >>> res = allineate.run()  # doctest: +SKIP
+
+    >>> allineate = afni.Allineate()
+    >>> allineate.inputs.in_file = 'functional.nii'
+    >>> allineate.inputs.reference = 'structural.nii'
+    >>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
+    >>> allineate.cmdline
+    '3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
+    >>> res = allineate.run()  # doctest: +SKIP
     """
 
     _cmd = '3dAllineate'
     input_spec = AllineateInputSpec
     output_spec = AllineateOutputSpec
 
-    def _format_arg(self, name, trait_spec, value):
-        if name == 'nwarp_fixmot' or name == 'nwarp_fixdep':
-            arg = ' '.join([trait_spec.argstr % v for v in value])
-            return arg
-        return super(Allineate, self)._format_arg(name, trait_spec, value)
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        if self.inputs.out_file:
-            outputs['out_file'] = op.abspath(self.inputs.out_file)
+        outputs = super(Allineate, self)._list_outputs()
 
         if self.inputs.out_weight_file:
             outputs['out_weight_file'] = op.abspath(
@@ -512,16 +512,10 @@ def _list_outputs(self):
                 outputs['out_param_file'] = op.abspath(
                     self.inputs.out_param_file)
 
-        if isdefined(self.inputs.allcostx):
-            outputs['allcostX'] = os.path.abspath(
-                os.path.join(os.getcwd(), self.inputs.allcostx))
+        if self.inputs.allcostx:
+            outputs['allcostX'] = os.path.abspath(self.inputs.allcostx)
         return outputs
 
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._list_outputs()[name]
-        return None
-
 
 class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     in_file = File(
@@ -2510,7 +2504,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
                rather than the value stored in the dataset header.""",
         argstr='-TR %g')
     mask = File(
-        exist=True,
+        exists=True,
         desc="""Only operate on voxels nonzero in the mset dataset.
                 ++ Voxels outside the mask will be filled with zeros.
                 ++ If no masking option is given, then all voxels

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -61,12 +61,14 @@ def test_Allineate_inputs():
             usedefault=True,
         ),
         nwarp=dict(argstr='-nwarp %s', ),
-        nwarp_fixdep=dict(argstr='-nwarp_fixdep%s', ),
-        nwarp_fixmot=dict(argstr='-nwarp_fixmot%s', ),
+        nwarp_fixdep=dict(argstr='-nwarp_fixdep%s...', ),
+        nwarp_fixmot=dict(argstr='-nwarp_fixmot%s...', ),
         one_pass=dict(argstr='-onepass', ),
         out_file=dict(
             argstr='-prefix %s',
-            genfile=True,
+            hash_files=False,
+            name_source='in_file',
+            name_template='%s_allineate',
             xor=['allcostx'],
         ),
         out_matrix=dict(

nipype/interfaces/afni/tests/test_auto_TProject.py

@@ -32,10 +32,7 @@ def test_TProject_inputs():
             mandatory=True,
             position=1,
         ),
-        mask=dict(
-            argstr='-mask %s',
-            exist=True,
-        ),
+        mask=dict(argstr='-mask %s', ),
         noblock=dict(argstr='-noblock', ),
         norm=dict(argstr='-norm', ),
         num_threads=dict(

nipype/interfaces/ants/registration.py

@@ -7,7 +7,7 @@
 from builtins import range, str
 import os
 
-from ...utils.filemanip import filename_to_list
+from ...utils.filemanip import ensure_list
 from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined
 from .base import ANTSCommand, ANTSCommandInputSpec, LOCAL_DEFAULT_NUMBER_OF_THREADS
 
@@ -1088,14 +1088,14 @@ def _format_registration(self):
             if any((isdefined(self.inputs.fixed_image_masks),
                     isdefined(self.inputs.moving_image_masks))):
                 if isdefined(self.inputs.fixed_image_masks):
-                    fixed_masks = filename_to_list(
+                    fixed_masks = ensure_list(
                         self.inputs.fixed_image_masks)
                     fixed_mask = fixed_masks[ii if len(fixed_masks) > 1 else 0]
                 else:
                     fixed_mask = 'NULL'
 
                 if isdefined(self.inputs.moving_image_masks):
-                    moving_masks = filename_to_list(
+                    moving_masks = ensure_list(
                         self.inputs.moving_image_masks)
                     moving_mask = moving_masks[ii
                                                if len(moving_masks) > 1 else 0]
@@ -1556,7 +1556,7 @@ class RegistrationSynQuick(ANTSCommand):
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.num_threads = 2
     >>> reg.cmdline
-    'antsRegistrationSynQuick.sh -d 3 -f fixed1.nii -m moving1.nii -n 2 -o transform -p d -t s'
+    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -m moving1.nii -n 2 -o transform -p d -t s'
     >>> reg.run()  # doctest: +SKIP
 
     example for multiple images
@@ -1567,19 +1567,18 @@ class RegistrationSynQuick(ANTSCommand):
     >>> reg.inputs.moving_image = ['moving1.nii', 'moving2.nii']
     >>> reg.inputs.num_threads = 2
     >>> reg.cmdline
-    'antsRegistrationSynQuick.sh -d 3 -f fixed1.nii -f fixed2.nii -m moving1.nii -m moving2.nii -n 2 -o transform -p d -t s'
+    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -f fixed2.nii -m moving1.nii -m moving2.nii -n 2 -o transform -p d -t s'
     >>> reg.run()  # doctest: +SKIP
     """
 
-
-    _cmd = 'antsRegistrationSynQuick.sh'
+    _cmd = 'antsRegistrationSyNQuick.sh'
     input_spec = RegistrationSynQuickInputSpec
     output_spec = RegistrationSynQuickOutputSpec
 
     def _num_threads_update(self):
         """
-        antsRegistrationSynQuick.sh ignores environment variables,
-        so override environment update frm ANTSCommand class
+        antsRegistrationSyNQuick.sh ignores environment variables,
+        so override environment update from ANTSCommand class
         """
         pass
 

nipype/interfaces/base/__init__.py

@@ -10,15 +10,16 @@
 """
 from .core import (Interface, BaseInterface, SimpleInterface, CommandLine,
                    StdOutCommandLine, MpiCommandLine, SEMLikeCommandLine,
-                   PackageInfo)
+                   LibraryBaseInterface, PackageInfo)
 
 from .specs import (BaseTraitedSpec, TraitedSpec, DynamicTraitedSpec,
                     BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec)
 
 from .traits_extension import (
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
-    File, Directory, Str, DictStrStr, has_metadata, ImageFile, MultiPath,
+    File, Directory, Str, DictStrStr, has_metadata, ImageFile,
+    OutputMultiObject, InputMultiObject,
     OutputMultiPath, InputMultiPath)
 
 from .support import (Bunch, InterfaceResult, load_template,

nipype/interfaces/base/core.py

@@ -1072,6 +1072,12 @@ def _filename_from_source(self, name, chain=None):
         if not isdefined(retval) or "%s" in retval:
             if not trait_spec.name_source:
                 return retval
+
+            # Do not generate filename when excluded by other inputs
+            if trait_spec.xor and any(isdefined(getattr(self.inputs, field))
+                                      for field in trait_spec.xor):
+                return retval
+
             if isdefined(retval) and "%s" in retval:
                 name_template = retval
             else:
@@ -1133,7 +1139,7 @@ def _list_outputs(self):
         metadata = dict(name_source=lambda t: t is not None)
         traits = self.inputs.traits(**metadata)
         if traits:
-            outputs = self.output_spec().get()
+            outputs = self.output_spec().trait_get()
             for name, trait_spec in list(traits.items()):
                 out_name = name
                 if trait_spec.output_name is not None:
@@ -1237,7 +1243,7 @@ class SEMLikeCommandLine(CommandLine):
     """
 
     def _list_outputs(self):
-        outputs = self.output_spec().get()
+        outputs = self.output_spec().trait_get()
         return self._outputs_from_inputs(outputs)
 
     def _outputs_from_inputs(self, outputs):
@@ -1267,6 +1273,35 @@ def _format_arg(self, name, spec, value):
         return super(SEMLikeCommandLine, self)._format_arg(name, spec, value)
 
 
+class LibraryBaseInterface(BaseInterface):
+    _pkg = None
+    imports = ()
+
+    def __init__(self, check_import=True, *args, **kwargs):
+        super(LibraryBaseInterface, self).__init__(*args, **kwargs)
+        if check_import:
+            import importlib
+            failed_imports = []
+            for pkg in (self._pkg,) + tuple(self.imports):
+                try:
+                    importlib.import_module(pkg)
+                except ImportError:
+                    failed_imports.append(pkg)
+            if failed_imports:
+                iflogger.warn('Unable to import %s; %s interface may fail to '
+                              'run', failed_imports, self.__class__.__name__)
+
+    @property
+    def version(self):
+        if self._version is None:
+            import importlib
+            try:
+                self._version = importlib.import_module(self._pkg).__version__
+            except (ImportError, AttributeError):
+                pass
+        return super(LibraryBaseInterface, self).version
+
+
 class PackageInfo(object):
     _version = None
     version_cmd = None