Merge pull request #637 from mwaskom/enh/selectfiles_forcelist

Enhance flexibiliy of SelectFiles output list coercion

Author: satra

nipype/interfaces/io.py

@@ -562,8 +562,12 @@ class SelectFilesInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
         desc="When matching mutliple files, return them in sorted order.")
     raise_on_empty = traits.Bool(True, usedefault=True,
         desc="Raise an exception if a template pattern matches no files.")
-    force_lists = traits.Bool(False, usedefault=True,
-        desc="Return all values as lists even when matching a single file.")
+    force_lists = traits.Either(traits.Bool(), traits.List(traits.Str()),
+        default=False, usedefault=True,
+        desc=("Whether to return outputs as a list even when only one file "
+              "matches the template. Either a boolean that applies to all "
+              "output fields or a list of output field names to coerce to "
+              " a list"))
 
 
 class SelectFiles(IOBase):
@@ -646,6 +650,18 @@ def _list_outputs(self):
         info = dict([(k, v) for k, v in self.inputs.__dict__.items()
                      if k in self._infields])
 
+        force_lists = self.inputs.force_lists
+        if isinstance(force_lists, bool):
+            force_lists = self._outfields if force_lists else []
+        bad_fields = set(force_lists) - set(self._outfields)
+        if bad_fields:
+            bad_fields = ", ".join(list(bad_fields))
+            plural = "s" if len(bad_fields) > 1 else ""
+            verb = "were" if len(bad_fields) > 1 else "was"
+            msg = ("The field%s '%s' %s set in 'force_lists' and not in "
+                   "'templates'.") % (plural, bad_fields, verb)
+            raise ValueError(msg)
+
         for field, template in self._templates.iteritems():
 
             # Build the full template path
@@ -673,7 +689,7 @@ def _list_outputs(self):
                 filelist.sort()
 
             # Handle whether this must be a list or not
-            if not self.inputs.force_lists:
+            if field not in force_lists:
                 filelist = list_to_filename(filelist)
 
             outputs[field] = filelist

nipype/interfaces/tests/test_io.py

@@ -6,6 +6,7 @@
 import os.path as op
 from tempfile import mkstemp, mkdtemp
 
+from nose.tools import assert_raises
 import nipype
 from nipype.testing import assert_equal, assert_true, assert_false
 import nipype.interfaces.io as nio
@@ -43,6 +44,16 @@ def test_selectfiles():
                      "interfaces/spm/preprocess.py")
     yield assert_equal, res.outputs.preprocess, [wanted]
 
+    dg.inputs.package = "fsl"
+    dg.inputs.force_lists = ["model"]
+    res = dg.run()
+    preproc = op.join(op.dirname(nipype.__file__),
+                      "interfaces/fsl/preprocess.py")
+    model = [op.join(op.dirname(nipype.__file__),
+                     "interfaces/fsl/model.py")]
+    yield assert_equal, res.outputs.preprocess, preproc
+    yield assert_equal, res.outputs.model, model
+
     templates = {"converter": "interfaces/dcm{to!s}nii.py"}
     dg = nio.SelectFiles(templates, base_directory=base_dir)
     dg.inputs.to = 2
@@ -51,6 +62,17 @@ def test_selectfiles():
     yield assert_equal, res.outputs.converter, wanted
 
 
+def test_selectfiles_valueerror():
+    """Test ValueError when force_lists has field that isn't in template."""
+    base_dir = op.dirname(nipype.__file__)
+    templates = {"model": "interfaces/{package}/model.py",
+                 "preprocess": "interfaces/{package}/pre*.py"}
+    force_lists = ["model", "preprocess", "registration"]
+    sf = nio.SelectFiles(templates, base_directory=base_dir,
+                         force_lists=force_lists)
+    yield assert_raises, ValueError, sf.run
+
+
 def test_datagrabber_order():
     tempdir = mkdtemp()
     file1 = mkstemp(prefix='sub002_L1_R1.q', dir=tempdir)