Merge branch 'master' of git://github.com/nipy/nipype into rel/1.0

Author: mgxd

.zenodo.json

@@ -530,6 +530,11 @@
     {
       "name": "Arias, Jaime"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "CEA",
       "name": "Papadopoulos Orfanos, Dimitri",

nipype/interfaces/afni/model.py

@@ -36,7 +36,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         argstr='-input %s',
         copyfile=False,
         sep=" ",
-        position=0)
+        position=1)
     sat = traits.Bool(
         desc='check the dataset time series for initial saturation transients,'
         ' which should normally have been excised before data analysis.',
@@ -57,10 +57,11 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         '* If the auto-catenation feature isn\'t used, then this option '
         'has no effect, no how, no way.',
         argstr='-noblock')
-    force_TR = traits.Int(
+    force_TR = traits.Float(
         desc='use this value instead of the TR in the \'input\' '
-        'dataset. (It\'s better to fix the input using Refit.)',
-        argstr='-force_TR %d')
+             'dataset. (It\'s better to fix the input using Refit.)',
+        argstr='-force_TR %f',
+        position=0)
     input1D = File(
         desc='filename of single (fMRI) .1D time series where time runs down '
         'the column.',
@@ -294,7 +295,11 @@ def _list_outputs(self):
 
         outputs['reml_script'] = self._gen_fname(
             suffix='.REML_cmd', **_gen_fname_opts)
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        # remove out_file from outputs if x1d_stop set to True
+        if self.inputs.x1D_stop:
+            del outputs['out_file']
+        else:
+            outputs['out_file'] = os.path.abspath(self.inputs.out_file)
 
         return outputs
 

nipype/interfaces/afni/tests/test_auto_Deconvolve.py

@@ -18,7 +18,10 @@ def test_Deconvolve_inputs():
             nohash=True,
             usedefault=True,
         ),
-        force_TR=dict(argstr='-force_TR %d', ),
+        force_TR=dict(
+            argstr='-force_TR %f',
+            position=0,
+        ),
         fout=dict(argstr='-fout', ),
         global_times=dict(
             argstr='-global_times',
@@ -42,7 +45,7 @@ def test_Deconvolve_inputs():
         in_files=dict(
             argstr='-input %s',
             copyfile=False,
-            position=0,
+            position=1,
             sep=' ',
         ),
         input1D=dict(argstr='-input1D %s', ),

nipype/interfaces/afni/tests/test_extra_Deconvolve.py

@@ -0,0 +1,10 @@
+"""Test afni deconvolve"""
+
+from ..model import Deconvolve
+
+def test_x1dstop():
+    deconv = Deconvolve()
+    deconv.inputs.out_file = 'file.nii'
+    assert 'out_file' in deconv._list_outputs()
+    deconv.inputs.x1D_stop = True
+    assert not 'out_file' in deconv._list_outputs()

nipype/interfaces/base/core.py

@@ -33,7 +33,7 @@
 
 from ... import config, logging, LooseVersion
 from ...utils.provenance import write_provenance
-from ...utils.misc import trim, str2bool
+from ...utils.misc import trim, str2bool, rgetcwd
 from ...utils.filemanip import (FileNotFoundError, split_filename, read_stream,
                                 which, get_dependencies, canonicalize_env as
                                 _canonicalize_env)
@@ -438,14 +438,16 @@ def _duecredit_cite(self):
             r['path'] = self.__module__
             due.cite(**r)
 
-    def run(self, **inputs):
+    def run(self, cwd=None, **inputs):
         """Execute this interface.
 
         This interface will not raise an exception if runtime.returncode is
         non-zero.
 
         Parameters
         ----------
+
+        cwd : specify a folder where the interface should be run
         inputs : allows the interface settings to be updated
 
         Returns
@@ -455,6 +457,13 @@ def run(self, **inputs):
         """
         from ...utils.profiler import ResourceMonitor
 
+        # Tear-up: get current and prev directories
+        syscwd = rgetcwd(error=False)  # Recover when wd does not exist
+        if cwd is None:
+            cwd = syscwd
+
+        os.chdir(cwd)  # Change to the interface wd
+
         enable_rm = config.resource_monitor and self.resource_monitor
         force_raise = not getattr(self.inputs, 'ignore_exception', False)
         self.inputs.trait_set(**inputs)
@@ -471,7 +480,8 @@ def run(self, **inputs):
             env['DISPLAY'] = config.get_display()
 
         runtime = Bunch(
-            cwd=os.getcwd(),
+            cwd=cwd,
+            prevcwd=syscwd,
             returncode=None,
             duration=None,
             environ=env,
@@ -556,6 +566,7 @@ def run(self, **inputs):
                         'rss_GiB': (vals[:, 2] / 1024).tolist(),
                         'vms_GiB': (vals[:, 3] / 1024).tolist(),
                     }
+            os.chdir(syscwd)
 
         return results
 

nipype/interfaces/dtitk/__init__.py

@@ -0,0 +1,15 @@
+"""The dtitk module provides classes for interfacing with the `Diffusion
+Tensor Imaging Toolkit (DTI-TK)
+<http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
+
+Top-level namespace for dti-tk.
+"""
+
+# from .base import ()
+from .registration import (RigidTask, AffineTask, DiffeoTask,
+                           ComposeXfmTask, diffeoSymTensor3DVolTask,
+                           affSymTensor3DVolTask, affScalarVolTask,
+                           diffeoScalarVolTask)
+from .utils import (TVAdjustOriginTask, TVAdjustVoxSpTask,
+                    SVAdjustVoxSpTask, TVResampleTask, SVResampleTask,
+                    TVtoolTask, BinThreshTask)

nipype/interfaces/dtitk/base.py

@@ -0,0 +1,81 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""The dtitk module provides classes for interfacing with the `DTITK
+<http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
+
+These are the base tools for working with DTITK.
+Preprocessing tools are found in dtitk/preprocess.py
+Registration tools are found in dtitk/registration.py
+
+Currently these tools are supported:
+
+* Rigid Tensor Registration
+* Affine Tensor Registration
+* Diffeomorphic Tensor Registration
+
+Examples
+--------
+See the docstrings of the individual classes for examples.
+
+"""
+from __future__ import print_function, division, unicode_literals, \
+    absolute_import
+
+import os
+
+from ... import logging
+from ...utils.filemanip import fname_presuffix
+from ..base import CommandLine
+from nipype.interfaces.fsl.base import Info
+
+LOGGER = logging.getLogger('interface')
+
+
+class CommandLineDtitk(CommandLine):
+
+    def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
+                   ext=None):
+        """Generate a filename based on the given parameters.
+
+        The filename will take the form: cwd/basename<suffix><ext>.
+        If change_ext is True, it will use the extentions specified in
+        <instance>intputs.output_type.
+
+        Parameters
+        ----------
+        basename : str
+            Filename to base the new filename on.
+        cwd : str
+            Path to prefix to the new filename. (default is os.getcwd())
+        suffix : str
+            Suffix to add to the `basename`.  (defaults is '' )
+        change_ext : bool
+            Flag to change the filename extension to the FSL output type.
+            (default True)
+
+        Returns
+        -------
+        fname : str
+            New filename based on given parameters.
+
+        """
+
+        if basename == '':
+            msg = 'Unable to generate filename for command %s. ' % self.cmd
+            msg += 'basename is not set!'
+            raise ValueError(msg)
+        if cwd is None:
+            cwd = os.getcwd()
+        if ext is None:
+            ext = Info.output_type_to_ext(self.inputs.output_type)
+        if change_ext:
+            if suffix:
+                suffix = ''.join((suffix, ext))
+            else:
+                suffix = ext
+        if suffix is None:
+            suffix = ''
+        fname = fname_presuffix(basename, suffix=suffix,
+                                use_ext=False, newpath=cwd)
+        return fname