Merge branch 'master' into enh/rapidart

* master:
  Removed unnecessary usedefault.
  fixed typo in a file name
  fix: github authentication
  Going back to distinguishing affine transformations by names. Improved docs.
  fixed typo in randomize parameters
  Removed unnecessary copyfiles and added output_image option.
  BF: Pass plugin_args to child nodes of MapNode
  ENH: Don't require ordereddict for python < 2.7
  BF: Fix for plugins when using python2.7
  Fixed parenthesis.
  Fix fslreorient2std output collection
  Allow FNIRT to take standard names as reference.
  BF: Check plugin_args is not None before accessing it like a dict.

Author: satra

nipype/interfaces/ants/resampling.py

@@ -103,12 +103,14 @@ def _list_outputs(self):
 class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=True,
                             desc='image dimension (2 or 3)', position=1)
-    input_image = File(argstr='%s', mandatory=True, copyfile=True,
+    input_image = File(argstr='%s', mandatory=True,
                         desc=('image to apply transformation to (generally a '
-                              'coregistered functional)') )
-    out_postfix = traits.Str('_wimt', argstr='%s', usedefault=True,
-                             desc=('Postfix that is prepended to all output '
-                                   'files (default = _wimt)'))
+                              'coregistered functional)'), position=2)
+    output_image = File(genfile=True, hash_files=False, argstr='%s', 
+                        desc=('name of the output warped image'), position = 3, xor=['out_postfix'])
+    out_postfix = File("_wimt", usedefault=True, hash_files=False, 
+                        desc=('Postfix that is prepended to all output '
+                                   'files (default = _wimt)'), xor=['output_image'])
     reference_image = File(argstr='-R %s', xor=['tightest_box'],
                        desc='reference image space that you wish to warp INTO')
     tightest_box = traits.Bool(argstr='--tightest-bounding-box',
@@ -123,13 +125,16 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
                               desc='Use nearest neighbor interpolation')
     use_bspline = traits.Bool(argstr='--use-Bspline',
                               desc='Use 3rd order B-Spline interpolation')
-    transformation_series = InputMultiPath(File(exists=True, copyfile=False), argstr='%s',
+    transformation_series = InputMultiPath(File(exists=True), argstr='%s',
                              desc='transformation file(s) to be applied',
-                             mandatory=True, copyfile=False)
+                             mandatory=True)
     invert_affine = traits.List(traits.Int,
-                    desc=('List of Affine transformations to invert. '
+                    desc=('List of Affine transformations to invert.'
                           'E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines '
-                          'found in transformation_series'))
+                          'found in transformation_series. Note that indexing '
+                          'starts with 1 and does not include warp fields. Affine '
+                          'transformations are distinguished '
+                          'from warp fields by the word "affine" included in their filenames.'))
 
 class WarpImageMultiTransformOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc='Warped image')
@@ -161,16 +166,19 @@ class WarpImageMultiTransform(ANTSCommand):
     _cmd = 'WarpImageMultiTransform'
     input_spec = WarpImageMultiTransformInputSpec
     output_spec = WarpImageMultiTransformOutputSpec
+    
+    def _gen_filename(self, name):
+        if name == 'output_image':
+            _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
+            return ''.join((name, self.inputs.out_postfix, ext))
+        return None
 
     def _format_arg(self, opt, spec, val):
-        if opt == 'out_postfix':
-            _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-            return name + val + ext
         if opt == 'transformation_series':
             series = []
             affine_counter = 0
             for transformation in val:
-                if 'Affine' in transformation and \
+                if "affine" in transformation.lower() and \
                     isdefined(self.inputs.invert_affine):
                     affine_counter += 1
                     if affine_counter in self.inputs.invert_affine:
@@ -181,11 +189,10 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-        outputs['output_image'] = os.path.join(os.getcwd(),
-                                             ''.join((name,
-                                                      self.inputs.out_postfix,
-                                                      ext)))
+        if isdefined(self.inputs.output_image):
+            outputs['output_image'] = os.path.abspath(self.inputs.output_image)
+        else:
+            outputs['output_image'] = os.path.abspath(self._gen_filename('output_image'))
         return outputs
 
 

nipype/interfaces/fsl/model.py

@@ -1403,15 +1403,15 @@ def _format_arg(self, name, spec, value):
 class RandomiseInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, desc='4D input file', argstr='-i %s', position=0, mandatory=True)
     base_name = traits.Str('tbss_', desc='the rootname that all generated files will have',
-                          argstr='-o %s', position=1, usedefault=True)
-    design_mat = File(exists=True, desc='design matrix file', argstr='-d %s', position=2, mandatory=True)
-    tcon = File(exists=True, desc='t contrasts file', argstr='-t %s', position=3, mandatory=True)
+                          argstr='-o "%s"', position=1, usedefault=True)
+    design_mat = File(exists=True, desc='design matrix file', argstr='-d %s', position=2)
+    tcon = File(exists=True, desc='t contrasts file', argstr='-t %s', position=3)
     fcon = File(exists=True, desc='f contrasts file', argstr='-f %s')
     mask = File(exists=True, desc='mask image', argstr='-m %s')
     x_block_labels = File(exists=True, desc='exchangeability block labels file', argstr='-e %s')
     demean = traits.Bool(desc='demean data temporally before model fitting', argstr='-D')
     one_sample_group_mean = traits.Bool(desc='perform 1-sample group-mean test instead of generic permutation test',
-                                  argstr='-l')
+                                  argstr='-1')
     show_total_perms = traits.Bool(desc='print out how many unique permutations would be generated and exit',
                                  argstr='-q')
     show_info_parallel_mode = traits.Bool(desc='print out information required for parallel mode and exit',

nipype/interfaces/fsl/preprocess.py

@@ -690,7 +690,7 @@ class FNIRTInputSpec(FSLCommandInputSpec):
                                           'to intensity mapping', hash_files=False)
     log_file = File(argstr='--logout=%s',
                              desc='Name of log-file', genfile=True, hash_files=False)
-    config_file = File(exists=True, argstr='--config=%s',
+    config_file = traits.Either(traits.Enum("T1_2_MNI152_2mm", "FA_2_FMRIB58_1mm"), File(exists=True), argstr='--config=%s',
                        desc='Name of config file specifying command line arguments')
     refmask_file = File(exists=True, argstr='--refmask=%s',
                         desc='name of file with mask in reference space')

nipype/interfaces/fsl/utils.py

@@ -1187,3 +1187,4 @@ def _list_outputs(self):
             outputs['out_file'] = self._gen_filename('out_file')
         else:
             outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        return outputs

nipype/pipeline/engine.py

@@ -1596,6 +1596,7 @@ def _make_nodes(self, cwd=None):
             node = Node(deepcopy(self._interface), name=nodename)
             node.overwrite = self.overwrite
             node.run_without_submitting = self.run_without_submitting
+            node.plugin_args = self.plugin_args
             node._interface.inputs.set(**deepcopy(self._interface.inputs.get()))
             for field in self.iterfield:
                 fieldvals = filename_to_list(getattr(self.inputs, field))

nipype/pipeline/plugins/base.py

@@ -108,21 +108,20 @@ def create_pyscript(node, updatehash=False, store_exception=True):
     # create python script to load and trap exception
     cmdstr = """import os
 import sys
+from nipype import config, logging
+from nipype.utils.filemanip import loadpkl, savepkl
 from socket import gethostname
 from traceback import format_exception
 info = None
 pklfile = '%s'
 batchdir = '%s'
 try:
-    from nipype import config, logging
-    import sys
     if not sys.version_info < (2, 7):
-        from ordereddict import OrderedDict
+        from collections import OrderedDict
     config_dict=%s
     config.update_config(config_dict)
     config.update_matplotlib()
     logging.update_logging(config)
-    from nipype.utils.filemanip import loadpkl, savepkl
     traceback=None
     cwd = os.getcwd()
     info = loadpkl(pklfile)

nipype/pipeline/plugins/dagman.py

@@ -35,7 +35,7 @@ def __init__(self, **kwargs):
         self._template = "universe = vanilla\nnotification = Never"
         self._submit_specs = ""
         self._dagman_args = ""
-        if 'plugin_args' in kwargs:
+        if 'plugin_args' in kwargs and not kwargs['plugin_args'] is None:
             plugin_args = kwargs['plugin_args']
             if 'template' in plugin_args:
                 self._template = plugin_args['template']

tools/github.py

@@ -42,7 +42,12 @@ def create_hash_map():
     """
 
     hashmap = {}
+    from base64 import encodestring as base64
+    import pwd
+    login_name = pwd.getpwuid(os.geteuid())[0]
     conn = httplib.HTTPSConnection("api.github.com")
+    conn.request("GET", "/repos/nipy/nipype",
+                 headers={'Authorization': 'Basic %s' % base64(login_name)})
     try:
         conn.request("GET", "/repos/nipy/nipype/git/trees/master?recursive=1")
     except: