Merge remote-tracking branch 'upstream/master' into fix/1795

Author: oesteban

.travis.yml

@@ -28,13 +28,11 @@ before_install:
   export PATH=/home/travis/anaconda/bin:$PATH &&
   conda config --append channels conda-forge &&
   conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
-  conda install -y icu numpy scipy traits &&
-  if [ "${TRAVIS_PYTHON_VERSION:0:1}" -gt "2" ]; then
-    conda install -y boto3;
-  fi }
+  conda install -y nipype icu==56.1 &&
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
+  rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*}
 - travis_retry bef_inst
 install:
-#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
 - travis_retry pip install -e .[$NIPYPE_EXTRAS]
 script:
 - py.test --doctest-modules nipype

CHANGES

@@ -29,6 +29,7 @@ Upcoming release 0.13
 * ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
 * ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
        (https://github.com/nipy/nipype/pull/1654)
+* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 
 Release 0.12.1 (August 3, 2016)
 ===============================

doc/devel/interface_specs.rst

@@ -353,7 +353,7 @@ CommandLine
 	be fixed it's recommended to just use ``usedefault``.
 
 ``sep``
-	For List traits the string with witch elements of the list will be joined.
+	For List traits the string with which elements of the list will be joined.
 
 ``name_source``
     Indicates the list of input fields from which the value of the current File

nipype/interfaces/freesurfer/preprocess.py

@@ -454,6 +454,20 @@ class EddyOutputSpec(TraitedSpec):
     out_parameter = File(exists=True,
                          desc=('text file with parameters definining the '
                                'field and movement for each scan'))
+    out_rotated_bvecs = File(exists=True,
+                             desc=('File containing rotated b-values for all volumes'))
+    out_movement_rms = File(exists=True,
+                            desc=('Summary of the "total movement" in each volume'))
+    out_restricted_movement_rms = File(exists=True,
+                                       desc=('Summary of the "total movement" in each volume '
+                                             'disregarding translation in the PE direction'))
+    out_shell_alignment_parameters = File(exists=True,
+                                          desc=('File containing rigid body movement parameters '
+                                                'between the different shells as estimated by a '
+                                                'post-hoc mutual information based registration'))
+    out_outlier_report = File(exists=True,
+                              desc=('Text-file with a plain language report '
+                                    'on what outlier slices eddy has found'))
 
 
 class Eddy(FSLCommand):
@@ -526,6 +540,30 @@ def _list_outputs(self):
             '%s.nii.gz' % self.inputs.out_base)
         outputs['out_parameter'] = os.path.abspath(
             '%s.eddy_parameters' % self.inputs.out_base)
+
+        # File generation might depend on the version of EDDY
+        out_rotated_bvecs = os.path.abspath(
+            '%s.eddy_rotated_bvecs' % self.inputs.out_base)
+        out_movement_rms = os.path.abspath(
+            '%s.eddy_movement_rms' % self.inputs.out_base)
+        out_restricted_movement_rms = os.path.abspath(
+            '%s.eddy_restricted_movement_rms' % self.inputs.out_base)
+        out_shell_alignment_parameters = os.path.abspath(
+            '%s.eddy_post_eddy_shell_alignment_parameters' % self.inputs.out_base)
+        out_outlier_report = os.path.abspath(
+            '%s.eddy_outlier_report' % self.inputs.out_base)
+
+        if os.path.exists(out_rotated_bvecs):
+            outputs['out_rotated_bvecs'] = out_rotated_bvecs
+        if os.path.exists(out_movement_rms):
+            outputs['out_movement_rms'] = out_movement_rms
+        if os.path.exists(out_restricted_movement_rms):
+            outputs['out_restricted_movement_rms'] = out_restricted_movement_rms
+        if os.path.exists(out_shell_alignment_parameters):
+            outputs['out_shell_alignment_parameters'] = out_shell_alignment_parameters
+        if os.path.exists(out_outlier_report):
+            outputs['out_outlier_report'] = out_outlier_report
+
         return outputs
 
 

nipype/interfaces/fsl/epi.py

@@ -25,7 +25,7 @@
 from ..base import (TraitedSpec, File, InputMultiPath,
                     OutputMultiPath, Undefined, traits,
                     isdefined)
-from .base import FSLCommand, FSLCommandInputSpec
+from .base import FSLCommand, FSLCommandInputSpec, Info
 
 
 class BETInputSpec(FSLCommandInputSpec):
@@ -750,10 +750,12 @@ class FNIRTInputSpec(FSLCommandInputSpec):
                        desc='name of file containing affine transform')
     inwarp_file = File(exists=True, argstr='--inwarp=%s',
                        desc='name of file containing initial non-linear warps')
-    in_intensitymap_file = File(exists=True, argstr='--intin=%s',
-                                desc=('name of file/files containing initial '
-                                      'intensity maping usually generated by '
-                                      'previous fnirt run'))
+    in_intensitymap_file = traits.List(File(exists=True), argstr='--intin=%s',
+                                       copyfiles=False, minlen=1, maxlen=2,
+                                       desc=('name of file/files containing '
+                                             'initial intensity mapping '
+                                             'usually generated by previous '
+                                             'fnirt run'))
     fieldcoeff_file = traits.Either(
         traits.Bool, File, argstr='--cout=%s',
         desc='name of output file with field coefficients or true')
@@ -907,8 +909,9 @@ class FNIRTOutputSpec(TraitedSpec):
     field_file = File(desc='file with warp field')
     jacobian_file = File(desc='file containing Jacobian of the field')
     modulatedref_file = File(desc='file containing intensity modulated --ref')
-    out_intensitymap_file = File(
-        desc='file containing info pertaining to intensity mapping')
+    out_intensitymap_file = traits.List(
+        File, minlen=2, maxlen=2,
+        desc='files containing info pertaining to intensity mapping')
     log_file = File(desc='Name of log-file')
 
 
@@ -975,9 +978,23 @@ def _list_outputs(self):
                                                        change_ext=change_ext)
                 else:
                     outputs[key] = os.path.abspath(inval)
+
+            if key == 'out_intensitymap_file' and isdefined(outputs[key]):
+                basename = FNIRT.intensitymap_file_basename(outputs[key])
+                outputs[key] = [
+                    outputs[key],
+                    '%s.txt' % basename,
+                ]
         return outputs
 
     def _format_arg(self, name, spec, value):
+        if name in ('in_intensitymap_file', 'out_intensitymap_file'):
+            if name == 'out_intensitymap_file':
+                value = self._list_outputs()[name]
+            value = [FNIRT.intensitymap_file_basename(v) for v in value]
+            assert len(set(value)) == 1, (
+                'Found different basenames for {}: {}'.format(name, value))
+            return spec.argstr % value[0]
         if name in list(self.filemap.keys()):
             return spec.argstr % self._list_outputs()[name]
         return super(FNIRT, self)._format_arg(name, spec, value)
@@ -1005,6 +1022,17 @@ def write_config(self, configfile):
             fid.write('%s\n' % (item))
         fid.close()
 
+    @classmethod
+    def intensitymap_file_basename(cls, f):
+        """Removes valid intensitymap extensions from `f`, returning a basename
+        that can refer to both intensitymap files.
+        """
+        for ext in list(Info.ftypes.values()) + ['.txt']:
+            if f.endswith(ext):
+                return f[:-len(ext)]
+        # TODO consider warning for this case
+        return f
+
 
 class ApplyWarpInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',

nipype/interfaces/fsl/preprocess.py

@@ -353,6 +353,7 @@ def test_mcflirt(setup_flirt):
 def test_fnirt(setup_flirt):
 
     tmpdir, infile, reffile = setup_flirt
+    os.chdir(tmpdir)
     fnirt = fsl.FNIRT()
     assert fnirt.cmd == 'fnirt'
 
@@ -404,64 +405,81 @@ def test_fnirt(setup_flirt):
         fnirt.run()
     fnirt.inputs.in_file = infile
     fnirt.inputs.ref_file = reffile
+    intmap_basename = '%s_intmap' % fsl.FNIRT.intensitymap_file_basename(infile)
+    intmap_image = fsl_name(fnirt, intmap_basename)
+    intmap_txt = '%s.txt' % intmap_basename
+    # doing this to create the file to pass tests for file existence
+    with open(intmap_image, 'w'):
+        pass
+    with open(intmap_txt, 'w'):
+        pass
 
     # test files
-    opt_map = {
-        'affine_file': ('--aff='),
-        'inwarp_file': ('--inwarp='),
-        'in_intensitymap_file': ('--intin='),
-        'config_file': ('--config='),
-        'refmask_file': ('--refmask='),
-        'inmask_file': ('--inmask='),
-        'field_file': ('--fout='),
-        'jacobian_file': ('--jout='),
-        'modulatedref_file': ('--refout='),
-        'out_intensitymap_file': ('--intout='),
-        'log_file': ('--logout=')}
-
-    for name, settings in list(opt_map.items()):
+    opt_map = [
+        ('affine_file', '--aff=%s' % infile, infile),
+        ('inwarp_file', '--inwarp=%s' % infile, infile),
+        ('in_intensitymap_file', '--intin=%s' % intmap_basename, [intmap_image]),
+        ('in_intensitymap_file',
+            '--intin=%s' % intmap_basename,
+            [intmap_image, intmap_txt]),
+        ('config_file', '--config=%s' % infile, infile),
+        ('refmask_file', '--refmask=%s' % infile, infile),
+        ('inmask_file', '--inmask=%s' % infile, infile),
+        ('field_file', '--fout=%s' % infile, infile),
+        ('jacobian_file', '--jout=%s' % infile, infile),
+        ('modulatedref_file', '--refout=%s' % infile, infile),
+        ('out_intensitymap_file',
+            '--intout=%s' % intmap_basename, True),
+        ('out_intensitymap_file', '--intout=%s' % intmap_basename, intmap_image),
+        ('fieldcoeff_file', '--cout=%s' % infile, infile),
+        ('log_file', '--logout=%s' % infile, infile)]
+
+    for (name, settings, arg) in opt_map:
         fnirt = fsl.FNIRT(in_file=infile,
                           ref_file=reffile,
-                          **{name: infile})
+                          **{name: arg})
 
-        if name in ('config_file', 'affine_file', 'field_file'):
-            cmd = 'fnirt %s%s --in=%s '\
+        if name in ('config_file', 'affine_file', 'field_file', 'fieldcoeff_file'):
+            cmd = 'fnirt %s --in=%s '\
                   '--logout=%s '\
-                  '--ref=%s --iout=%s' % (settings, infile, infile, log,
+                  '--ref=%s --iout=%s' % (settings, infile, log,
                                           reffile, iout)
         elif name in ('refmask_file'):
             cmd = 'fnirt --in=%s '\
                   '--logout=%s --ref=%s '\
-                  '%s%s '\
+                  '%s '\
                   '--iout=%s' % (infile, log,
                                  reffile,
-                                 settings, infile,
+                                 settings,
                                  iout)
         elif name in ('in_intensitymap_file', 'inwarp_file', 'inmask_file', 'jacobian_file'):
             cmd = 'fnirt --in=%s '\
-                  '%s%s '\
+                  '%s '\
                   '--logout=%s --ref=%s '\
                   '--iout=%s' % (infile,
-                                 settings, infile,
+                                 settings,
                                  log,
                                  reffile,
                                  iout)
         elif name in ('log_file'):
             cmd = 'fnirt --in=%s '\
-                  '%s%s --ref=%s '\
+                  '%s --ref=%s '\
                   '--iout=%s' % (infile,
-                                 settings, infile,
+                                 settings,
                                  reffile,
                                  iout)
         else:
             cmd = 'fnirt --in=%s '\
-                  '--logout=%s %s%s '\
+                  '--logout=%s %s '\
                   '--ref=%s --iout=%s' % (infile, log,
-                                          settings, infile,
+                                          settings,
                                           reffile, iout)
 
         assert fnirt.cmdline == cmd
 
+        if name == 'out_intensitymap_file':
+            assert fnirt._list_outputs()['out_intensitymap_file'] == [
+                intmap_image, intmap_txt]
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_applywarp(setup_flirt):

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -447,6 +447,19 @@ def list_to_filename(filelist):
     else:
         return filelist[0]
 
+
+def check_depends(targets, dependencies):
+    """Return true if all targets exist and are newer than all dependencies.
+
+    An OSError will be raised if there are missing dependencies.
+    """
+    tgts = filename_to_list(targets)
+    deps = filename_to_list(dependencies)
+    return all(map(os.path.exists, tgts)) and \
+        min(map(os.path.getmtime, tgts)) > \
+        max(list(map(os.path.getmtime, deps)) + [0])
+
+
 def save_json(filename, data):
     """Save data to a json file
 

nipype/utils/filemanip.py

@@ -5,7 +5,9 @@
 from builtins import open
 
 import os
-from tempfile import mkstemp
+import time
+from tempfile import mkstemp, mkdtemp
+import shutil
 import warnings
 
 import pytest
@@ -15,6 +17,7 @@
                                 hash_rename, check_forhash,
                                 copyfile, copyfiles,
                                 filename_to_list, list_to_filename,
+                                check_depends,
                                 split_filename, get_related_files)
 
 import numpy as np
@@ -271,6 +274,41 @@ def test_list_to_filename(list, expected):
     assert x == expected
 
 
+def test_check_depends():
+    def touch(fname):
+        with open(fname, 'a'):
+            os.utime(fname, None)
+
+    tmpdir = mkdtemp()
+
+    dependencies = [os.path.join(tmpdir, str(i)) for i in range(3)]
+    targets = [os.path.join(tmpdir, str(i)) for i in range(3, 6)]
+
+    # Targets newer than dependencies
+    for dep in dependencies:
+        touch(dep)
+    time.sleep(1)
+    for tgt in targets:
+        touch(tgt)
+    assert check_depends(targets, dependencies)
+
+    # Targets older than newest dependency
+    time.sleep(1)
+    touch(dependencies[0])
+    assert not check_depends(targets, dependencies)
+
+    # Missing dependency
+    os.unlink(dependencies[0])
+    try:
+        check_depends(targets, dependencies)
+    except OSError as e:
+        pass
+    else:
+        assert False, "Should raise OSError on missing dependency"
+
+    shutil.rmtree(tmpdir)   
+
+
 def test_json():
     # Simple roundtrip test of json files, just a sanity check.
     adict = dict(a='one', c='three', b='two')