Merge pull request #2517 from effigies/enh/multi_object

ENH: Add MultiObject, ensure/simplify_list; alias old names for 1.x compatibility

Author: effigies

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/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]

nipype/interfaces/base/__init__.py

@@ -18,7 +18,8 @@
 
 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/traits_extension.py

@@ -315,8 +315,8 @@ def has_metadata(trait, metadata, value=None, recursive=True):
     return count > 0
 
 
-class MultiPath(traits.List):
-    """ Abstract class - shared functionality of input and output MultiPath
+class MultiObject(traits.List):
+    """ Abstract class - shared functionality of input and output MultiObject
     """
 
     def validate(self, object, name, value):
@@ -335,18 +335,18 @@ def validate(self, object, name, value):
         inner_trait = self.inner_traits()[0]
         if not isinstance(value, list) \
             or (isinstance(inner_trait.trait_type, traits.List) and
-                not isinstance(inner_trait.trait_type, InputMultiPath) and
+                not isinstance(inner_trait.trait_type, InputMultiObject) and
                 not isinstance(value[0], list)):
             newvalue = [value]
-        value = super(MultiPath, self).validate(object, name, newvalue)
+        value = super(MultiObject, self).validate(object, name, newvalue)
 
         if value:
             return value
 
         self.error(object, name, value)
 
 
-class OutputMultiPath(MultiPath):
+class OutputMultiObject(MultiObject):
     """ Implements a user friendly traits that accepts one or more
     paths to files or directories. This is the output version which
     return a single string whenever possible (when it was set to a
@@ -358,9 +358,9 @@ class OutputMultiPath(MultiPath):
 
     XXX This needs to be vetted by somebody who understands traits
 
-    >>> from nipype.interfaces.base import OutputMultiPath, TraitedSpec
+    >>> from nipype.interfaces.base import OutputMultiObject, TraitedSpec
     >>> class A(TraitedSpec):
-    ...     foo = OutputMultiPath(File(exists=False))
+    ...     foo = OutputMultiObject(File(exists=False))
     >>> a = A()
     >>> a.foo
     <undefined>
@@ -392,7 +392,7 @@ def set(self, object, name, value):
         self.set_value(object, name, value)
 
 
-class InputMultiPath(MultiPath):
+class InputMultiObject(MultiObject):
     """ Implements a user friendly traits that accepts one or more
     paths to files or directories. This is the input version which
     always returns a list. Default value of this trait
@@ -403,9 +403,9 @@ class InputMultiPath(MultiPath):
 
     XXX This needs to be vetted by somebody who understands traits
 
-    >>> from nipype.interfaces.base import InputMultiPath, TraitedSpec
+    >>> from nipype.interfaces.base import InputMultiObject, TraitedSpec
     >>> class A(TraitedSpec):
-    ...     foo = InputMultiPath(File(exists=False))
+    ...     foo = InputMultiObject(File(exists=False))
     >>> a = A()
     >>> a.foo
     <undefined>
@@ -424,3 +424,6 @@ class InputMultiPath(MultiPath):
 
     """
     pass
+
+InputMultiPath = InputMultiObject
+OutputMultiPath = OutputMultiObject

nipype/interfaces/fsl/model.py

@@ -18,7 +18,7 @@
 from nibabel import load
 
 from ... import LooseVersion
-from ...utils.filemanip import list_to_filename, filename_to_list
+from ...utils.filemanip import simplify_list, ensure_list
 from ...utils.misc import human_order_sorted
 from ...external.due import BibTeX
 from ..base import (File, traits, isdefined, TraitedSpec, BaseInterface,
@@ -493,7 +493,7 @@ def _get_design_root(self, infile):
     def _list_outputs(self):
         # TODO: figure out file names and get rid off the globs
         outputs = self._outputs().get()
-        root = self._get_design_root(list_to_filename(self.inputs.fsf_file))
+        root = self._get_design_root(simplify_list(self.inputs.fsf_file))
         design_file = glob(os.path.join(os.getcwd(), '%s*.mat' % root))
         assert len(design_file) == 1, 'No mat file generated by FEAT Model'
         outputs['design_file'] = design_file[0]
@@ -890,7 +890,7 @@ def _run_interface(self, runtime):
             num_runs=num_runs,
             regimage=self.inputs.reg_image,
             regdof=self.inputs.reg_dof)
-        for i, rundir in enumerate(filename_to_list(self.inputs.feat_dirs)):
+        for i, rundir in enumerate(ensure_list(self.inputs.feat_dirs)):
             fsf_txt += fsf_dirs.substitute(
                 runno=i + 1, rundir=os.path.abspath(rundir))
         fsf_txt += fsf_footer.substitute()

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -10,7 +10,7 @@
 
 import pytest
 import pdb
-from nipype.utils.filemanip import split_filename, filename_to_list
+from nipype.utils.filemanip import split_filename, ensure_list
 from .. import preprocess as fsl
 from nipype.interfaces.fsl import Info
 from nipype.interfaces.base import File, TraitError, Undefined, isdefined
@@ -164,7 +164,7 @@ def _run_and_test(opts, output_base):
         outputs = fsl.FAST(**opts)._list_outputs()
         for output in outputs.values():
             if output:
-                for filename in filename_to_list(output):
+                for filename in ensure_list(output):
                     assert os.path.realpath(filename).startswith(
                         os.path.realpath(output_base))
 

nipype/interfaces/io.py

@@ -33,7 +33,7 @@
 
 from .. import config, logging
 from ..utils.filemanip import (
-    copyfile, list_to_filename, filename_to_list,
+    copyfile, simplify_list, ensure_list,
     get_related_files, related_filetype_sets)
 from ..utils.misc import human_order_sorted, str2bool
 from .base import (
@@ -721,7 +721,7 @@ def _list_outputs(self):
             if not isdefined(files):
                 continue
             iflogger.debug("key: %s files: %s", key, str(files))
-            files = filename_to_list(files)
+            files = ensure_list(files)
             tempoutdir = outdir
             if s3_flag:
                 s3tempoutdir = s3dir
@@ -738,7 +738,7 @@ def _list_outputs(self):
                     files = [item for sublist in files for item in sublist]
 
             # Iterate through passed-in source files
-            for src in filename_to_list(files):
+            for src in ensure_list(files):
                 # Format src and dst files
                 src = os.path.abspath(src)
                 if not os.path.isfile(src):
@@ -938,7 +938,7 @@ def _list_outputs(self):
                 else:
                     if self.inputs.sort_filelist:
                         filelist = human_order_sorted(filelist)
-                    outputs[key] = list_to_filename(filelist)
+                    outputs[key] = simplify_list(filelist)
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
@@ -987,7 +987,7 @@ def _list_outputs(self):
                     else:
                         if self.inputs.sort_filelist:
                             outfiles = human_order_sorted(outfiles)
-                        outputs[key].append(list_to_filename(outfiles))
+                        outputs[key].append(simplify_list(outfiles))
             if any([val is None for val in outputs[key]]):
                 outputs[key] = []
             if len(outputs[key]) == 0:
@@ -1195,7 +1195,7 @@ def _list_outputs(self):
                 else:
                     if self.inputs.sort_filelist:
                         filelist = human_order_sorted(filelist)
-                    outputs[key] = list_to_filename(filelist)
+                    outputs[key] = simplify_list(filelist)
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
@@ -1241,7 +1241,7 @@ def _list_outputs(self):
                     else:
                         if self.inputs.sort_filelist:
                             outfiles = human_order_sorted(outfiles)
-                        outputs[key].append(list_to_filename(outfiles))
+                        outputs[key].append(simplify_list(outfiles))
             if self.inputs.drop_blank_outputs:
                 outputs[key] = [x for x in outputs[key] if x is not None]
             else:
@@ -1409,7 +1409,7 @@ def _list_outputs(self):
 
             # Handle whether this must be a list or not
             if field not in force_lists:
-                filelist = list_to_filename(filelist)
+                filelist = simplify_list(filelist)
 
             outputs[field] = filelist
 
@@ -1750,7 +1750,7 @@ def _get_files(self, path, key, dirval, altkey=None):
                 globprefix = self.inputs.hemi + '.'
             else:
                 globprefix = '*'
-        keys = filename_to_list(altkey) if altkey else [key]
+        keys = ensure_list(altkey) if altkey else [key]
         globfmt = os.path.join(path, dirval, ''.join((globprefix, '{}',
                                                       globsuffix)))
         return [
@@ -1768,7 +1768,7 @@ def _list_outputs(self):
                                   output_traits.traits()[k].loc,
                                   output_traits.traits()[k].altkey)
             if val:
-                outputs[k] = list_to_filename(val)
+                outputs[k] = simplify_list(val)
         return outputs
 
 
@@ -1909,7 +1909,7 @@ def _list_outputs(self):
                 file_objects = xnat.select(template).get('obj')
                 if file_objects == []:
                     raise IOError('Template %s returned no files' % template)
-                outputs[key] = list_to_filename([
+                outputs[key] = simplify_list([
                     str(file_object.get()) for file_object in file_objects
                     if file_object.exists()
                 ])
@@ -1944,7 +1944,7 @@ def _list_outputs(self):
                             raise IOError('Template %s '
                                           'returned no files' % target)
 
-                        outfiles = list_to_filename([
+                        outfiles = simplify_list([
                             str(file_object.get())
                             for file_object in file_objects
                             if file_object.exists()
@@ -1956,7 +1956,7 @@ def _list_outputs(self):
                             raise IOError('Template %s '
                                           'returned no files' % template)
 
-                        outfiles = list_to_filename([
+                        outfiles = simplify_list([
                             str(file_object.get())
                             for file_object in file_objects
                             if file_object.exists()
@@ -2079,7 +2079,7 @@ def _list_outputs(self):
         # gather outputs and upload them
         for key, files in list(self.inputs._outputs.items()):
 
-            for name in filename_to_list(files):
+            for name in ensure_list(files):
 
                 if isinstance(name, list):
                     for i, file_name in enumerate(name):
@@ -2205,7 +2205,7 @@ def __init__(self, input_names, **inputs):
 
         super(SQLiteSink, self).__init__(**inputs)
 
-        self._input_names = filename_to_list(input_names)
+        self._input_names = ensure_list(input_names)
         add_traits(self.inputs, [name for name in self._input_names])
 
     def _list_outputs(self):
@@ -2263,7 +2263,7 @@ def __init__(self, input_names, **inputs):
 
         super(MySQLSink, self).__init__(**inputs)
 
-        self._input_names = filename_to_list(input_names)
+        self._input_names = ensure_list(input_names)
         add_traits(self.inputs, [name for name in self._input_names])
 
     def _list_outputs(self):
@@ -2463,7 +2463,7 @@ def _get_files_over_ssh(self, template):
                         iflogger.info('remote file %s not found' % f)
 
             # return value
-            outfiles = list_to_filename(outfiles)
+            outfiles = simplify_list(outfiles)
 
         return outfiles
 

nipype/interfaces/mne/base.py

@@ -7,7 +7,7 @@
 import glob
 
 from ... import logging
-from ...utils.filemanip import list_to_filename
+from ...utils.filemanip import simplify_list
 from ..base import (traits, File, Directory, TraitedSpec, OutputMultiPath)
 from ..freesurfer.base import FSCommand, FSTraitedSpec
 
@@ -120,7 +120,7 @@ def _list_outputs(self):
                                       output_traits.traits()[k].loc,
                                       output_traits.traits()[k].altkey)
                 if val:
-                    value_list = list_to_filename(val)
+                    value_list = simplify_list(val)
                     if isinstance(value_list, list):
                         out_files = []
                         for value in value_list: