changes in Interfaces base (closes #2320)

nipype/algorithms/confounds.py

@@ -27,7 +27,7 @@
 from ..external.due import BibTeX
 from ..interfaces.base import (traits, TraitedSpec, BaseInterface,
                                BaseInterfaceInputSpec, File, isdefined,
-                               InputMultiPath, OutputMultiPath)
+                               InputMultiObject, OutputMultiObject)
 from ..utils import NUMPY_MMAP
 from ..utils.misc import normalize_mc_params
 
@@ -360,7 +360,7 @@ def _list_outputs(self):
 class CompCorInputSpec(BaseInterfaceInputSpec):
     realigned_file = File(
         exists=True, mandatory=True, desc='already realigned brain image (4D)')
-    mask_files = InputMultiPath(
+    mask_files = InputMultiObject(
         File(exists=True),
         desc=('One or more mask files that determines '
               'ROI (3D). When more that one file is '
@@ -649,7 +649,7 @@ class TCompCorInputSpec(CompCorInputSpec):
 
 class TCompCorOutputSpec(CompCorOutputSpec):
     # and all the fields in CompCorOutputSpec
-    high_variance_masks = OutputMultiPath(
+    high_variance_masks = OutputMultiObject(
         File(exists=True),
         desc=(("voxels exceeding the variance"
                " threshold")))
@@ -714,7 +714,7 @@ def _list_outputs(self):
 
 
 class TSNRInputSpec(BaseInterfaceInputSpec):
-    in_file = InputMultiPath(
+    in_file = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc='realigned 4D file or a list of 3D files')

nipype/algorithms/metrics.py

@@ -29,7 +29,7 @@
 from ..utils.misc import package_check
 
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
-                               InputMultiPath, BaseInterfaceInputSpec,
+                               InputMultiObject, BaseInterfaceInputSpec,
                                isdefined)
 from ..utils import NUMPY_MMAP
 
@@ -382,11 +382,11 @@ def _list_outputs(self):
 
 
 class FuzzyOverlapInputSpec(BaseInterfaceInputSpec):
-    in_ref = InputMultiPath(
+    in_ref = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc='Reference image. Requires the same dimensions as in_tst.')
-    in_tst = InputMultiPath(
+    in_tst = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc='Test image. Requires the same dimensions as in_ref.')

nipype/algorithms/misc.py

@@ -31,7 +31,7 @@
 from .. import logging
 from . import metrics as nam
 from ..interfaces.base import (
-    BaseInterface, traits, TraitedSpec, File, InputMultiPath, OutputMultiPath,
+    BaseInterface, traits, TraitedSpec, File, InputMultiObject, OutputMultiObject,
     BaseInterfaceInputSpec, isdefined, DynamicTraitedSpec, Undefined)
 from ..utils.filemanip import fname_presuffix, split_filename, filename_to_list
 from ..utils import NUMPY_MMAP
@@ -124,7 +124,7 @@ def _list_outputs(self):
 
 
 class SimpleThresholdInputSpec(BaseInterfaceInputSpec):
-    volumes = InputMultiPath(
+    volumes = InputMultiObject(
         File(exists=True), desc='volumes to be thresholded', mandatory=True)
     threshold = traits.Float(
         desc='volumes to be thresholdedeverything below this value will be set\
@@ -133,7 +133,7 @@ class SimpleThresholdInputSpec(BaseInterfaceInputSpec):
 
 
 class SimpleThresholdOutputSpec(TraitedSpec):
-    thresholded_volumes = OutputMultiPath(
+    thresholded_volumes = OutputMultiObject(
         File(exists=True), desc="thresholded volumes")
 
 
@@ -170,7 +170,7 @@ def _list_outputs(self):
 
 
 class ModifyAffineInputSpec(BaseInterfaceInputSpec):
-    volumes = InputMultiPath(
+    volumes = InputMultiObject(
         File(exists=True),
         desc='volumes which affine matrices will be modified',
         mandatory=True)
@@ -183,7 +183,7 @@ class ModifyAffineInputSpec(BaseInterfaceInputSpec):
 
 
 class ModifyAffineOutputSpec(TraitedSpec):
-    transformed_volumes = OutputMultiPath(File(exist=True))
+    transformed_volumes = OutputMultiObject(File(exist=True))
 
 
 class ModifyAffine(BaseInterface):
@@ -328,7 +328,7 @@ class Matlab2CSVInputSpec(TraitedSpec):
 
 
 class Matlab2CSVOutputSpec(TraitedSpec):
-    csv_files = OutputMultiPath(
+    csv_files = OutputMultiObject(
         File(desc='Output CSV files for each variable saved in the input .mat\
         file'))
 
@@ -503,7 +503,7 @@ def makefmtlist(output_array, typelist, rowheadingsBool, shape,
 
 
 class MergeCSVFilesInputSpec(TraitedSpec):
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc='Input comma-separated value (CSV) files')
@@ -1046,14 +1046,14 @@ def gen_noise(self,
 
 
 class NormalizeProbabilityMapSetInputSpec(TraitedSpec):
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(exists=True, mandatory=True, desc='The tpms to be normalized'))
     in_mask = File(
         exists=True, desc='Masked voxels must sum up 1.0, 0.0 otherwise.')
 
 
 class NormalizeProbabilityMapSetOutputSpec(TraitedSpec):
-    out_files = OutputMultiPath(File(exists=True), desc="normalized maps")
+    out_files = OutputMultiObject(File(exists=True), desc="normalized maps")
 
 
 class NormalizeProbabilityMapSet(BaseInterface):
@@ -1099,10 +1099,10 @@ class SplitROIsInputSpec(TraitedSpec):
 
 
 class SplitROIsOutputSpec(TraitedSpec):
-    out_files = OutputMultiPath(File(exists=True), desc='the resulting ROIs')
-    out_masks = OutputMultiPath(
+    out_files = OutputMultiObject(File(exists=True), desc='the resulting ROIs')
+    out_masks = OutputMultiObject(
         File(exists=True), desc='a mask indicating valid values')
-    out_index = OutputMultiPath(
+    out_index = OutputMultiObject(
         File(exists=True), desc='arrays keeping original locations')
 
 
@@ -1148,9 +1148,9 @@ def _list_outputs(self):
 
 
 class MergeROIsInputSpec(TraitedSpec):
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(exists=True, mandatory=True, desc='files to be re-merged'))
-    in_index = InputMultiPath(
+    in_index = InputMultiObject(
         File(exists=True, mandatory=True),
         desc='array keeping original locations')
     in_reference = File(exists=True, desc='reference file')
@@ -1421,7 +1421,7 @@ def merge_rois(in_files, in_idxs, in_ref, dtype=None, out_file=None):
 
 
 class CalculateMedianInputSpec(BaseInterfaceInputSpec):
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(
             exists=True,
             mandatory=True,
@@ -1432,7 +1432,7 @@ class CalculateMedianInputSpec(BaseInterfaceInputSpec):
 
 
 class CalculateMedianOutputSpec(TraitedSpec):
-    median_files = OutputMultiPath(
+    median_files = OutputMultiObject(
         File(exists=True), desc="One or more median images")
 
 

nipype/algorithms/modelgen.py

@@ -30,7 +30,7 @@
 from scipy.special import gammaln
 
 from ..utils import NUMPY_MMAP
-from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath,
+from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiObject,
                                traits, File, Bunch, BaseInterfaceInputSpec,
                                isdefined)
 from ..utils.filemanip import filename_to_list
@@ -182,22 +182,22 @@ def gen_info(run_event_files):
 
 
 class SpecifyModelInputSpec(BaseInterfaceInputSpec):
-    subject_info = InputMultiPath(
+    subject_info = InputMultiObject(
         Bunch,
         mandatory=True,
         xor=['subject_info', 'event_files'],
         desc='Bunch or List(Bunch) subject-specific '
         'condition information. see '
         ':ref:`SpecifyModel` or '
         'SpecifyModel.__doc__ for details')
-    event_files = InputMultiPath(
+    event_files = InputMultiObject(
         traits.List(File(exists=True)),
         mandatory=True,
         xor=['subject_info', 'event_files'],
         desc='List of event description files 1, 2 or 3 '
         'column format corresponding to onsets, '
         'durations and amplitudes')
-    realignment_parameters = InputMultiPath(
+    realignment_parameters = InputMultiObject(
         File(exists=True),
         desc='Realignment parameters returned '
         'by motion correction algorithm',
@@ -210,12 +210,12 @@ class SpecifyModelInputSpec(BaseInterfaceInputSpec):
         "NIPY",
         usedefault=True,
         desc="Source of motion parameters")
-    outlier_files = InputMultiPath(
+    outlier_files = InputMultiObject(
         File(exists=True),
         desc='Files containing scan outlier indices '
         'that should be tossed',
         copyfile=False)
-    functional_runs = InputMultiPath(
+    functional_runs = InputMultiObject(
         traits.Either(traits.List(File(exists=True)), File(exists=True)),
         mandatory=True,
         desc='Data files for model. List of 4D '

nipype/algorithms/rapidart.py

@@ -31,8 +31,8 @@
 import scipy.io as sio
 
 from ..utils import NUMPY_MMAP
-from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
-                               OutputMultiPath, TraitedSpec, File,
+from ..interfaces.base import (BaseInterface, traits, InputMultiObject,
+                               OutputMultiObject, TraitedSpec, File,
                                BaseInterfaceInputSpec, isdefined)
 from ..utils.filemanip import filename_to_list, save_json, split_filename
 from ..utils.misc import find_indices, normalize_mc_params
@@ -163,12 +163,12 @@ def _calc_norm_affine(affines, use_differences, brain_pts=None):
 
 
 class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
-    realigned_files = InputMultiPath(
+    realigned_files = InputMultiObject(
         File(exists=True),
         desc=("Names of realigned functional data "
               "files"),
         mandatory=True)
-    realignment_parameters = InputMultiPath(
+    realignment_parameters = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc=("Names of realignment "
@@ -267,22 +267,22 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
 
 
 class ArtifactDetectOutputSpec(TraitedSpec):
-    outlier_files = OutputMultiPath(
+    outlier_files = OutputMultiObject(
         File(exists=True),
         desc=("One file for each functional run "
               "containing a list of 0-based indices"
               " corresponding to outlier volumes"))
-    intensity_files = OutputMultiPath(
+    intensity_files = OutputMultiObject(
         File(exists=True),
         desc=("One file for each functional run "
               "containing the global intensity "
               "values determined from the "
               "brainmask"))
-    norm_files = OutputMultiPath(
+    norm_files = OutputMultiObject(
         File,
         desc=("One file for each functional run "
               "containing the composite norm"))
-    statistic_files = OutputMultiPath(
+    statistic_files = OutputMultiObject(
         File(exists=True),
         desc=("One file for each functional run "
               "containing information about the "
@@ -291,16 +291,16 @@ class ArtifactDetectOutputSpec(TraitedSpec):
               "details of stimulus correlated "
               "motion and a listing or artifacts "
               "by event type."))
-    plot_files = OutputMultiPath(
+    plot_files = OutputMultiObject(
         File,
         desc=("One image file for each functional run "
               "containing the detected outliers"))
-    mask_files = OutputMultiPath(
+    mask_files = OutputMultiObject(
         File,
         desc=("One image file for each functional run "
               "containing the mask used for global "
               "signal calculation"))
-    displacement_files = OutputMultiPath(
+    displacement_files = OutputMultiObject(
         File,
         desc=("One image file for each "
               "functional run containing the "
@@ -631,13 +631,13 @@ def _run_interface(self, runtime):
 
 
 class StimCorrInputSpec(BaseInterfaceInputSpec):
-    realignment_parameters = InputMultiPath(
+    realignment_parameters = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc=("Names of realignment "
               "parameters corresponding to "
               "the functional data files"))
-    intensity_values = InputMultiPath(
+    intensity_values = InputMultiObject(
         File(exists=True),
         mandatory=True,
         desc=("Name of file containing intensity "
@@ -653,7 +653,7 @@ class StimCorrInputSpec(BaseInterfaceInputSpec):
 
 
 class StimCorrOutputSpec(TraitedSpec):
-    stimcorr_files = OutputMultiPath(
+    stimcorr_files = OutputMultiObject(
         File(exists=True),
         desc=("List of files containing "
               "correlation values"))

nipype/interfaces/afni/model.py

@@ -18,15 +18,15 @@
 import os
 
 from ..base import (CommandLineInputSpec, CommandLine, Directory, TraitedSpec,
-                    traits, isdefined, File, InputMultiPath, Undefined, Str)
+                    traits, isdefined, File, InputMultiObject, Undefined, Str)
 from ...external.due import BibTeX
 
 from .base import (AFNICommandBase, AFNICommand, AFNICommandInputSpec,
                    AFNICommandOutputSpec)
 
 
 class DeconvolveInputSpec(AFNICommandInputSpec):
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(exists=True),
         desc='filenames of 3D+time input datasets. More than one filename can '
         'be given and the datasets will be auto-catenated in time. '
@@ -306,7 +306,7 @@ def _list_outputs(self):
 
 class RemlfitInputSpec(AFNICommandInputSpec):
     # mandatory files
-    in_files = InputMultiPath(
+    in_files = InputMultiObject(
         File(exists=True),
         desc='Read time series dataset',
         argstr='-input "%s"',
@@ -353,7 +353,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         '(only with \'mask\' or \'automask\' options).',
         argstr='-STATmask %s',
         exists=True)
-    addbase = InputMultiPath(
+    addbase = InputMultiObject(
         File(
             exists=True,
             desc='file containing columns to add to regression matrix'),
@@ -364,7 +364,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         copyfile=False,
         sep=" ",
         argstr='-addbase %s')
-    slibase = InputMultiPath(
+    slibase = InputMultiObject(
         File(
             exists=True,
             desc='file containing columns to add to regression matrix'),
@@ -381,7 +381,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         'will slow the program down, and make it use a lot more memory '
         '(to hold all the matrix stuff).',
         argstr='-slibase %s')
-    slibase_sm = InputMultiPath(
+    slibase_sm = InputMultiObject(
         File(
             exists=True,
             desc='file containing columns to add to regression matrix'),