Merge branch 'master' of git://github.com/nipy/nipype into fix/py2functions

Author: mgxd

nipype/interfaces/afni/preprocess.py

@@ -15,7 +15,8 @@
 import os
 import os.path as op
 
-from ...utils.filemanip import (load_json, save_json, split_filename)
+from ...utils.filemanip import (load_json, save_json, split_filename,
+                                fname_presuffix)
 from ..base import (
     CommandLineInputSpec, CommandLine, TraitedSpec,
     traits, isdefined, File, InputMultiPath, Undefined, Str)
@@ -3131,7 +3132,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
              'Note that the source dataset in the second run is the SAME as'
              'in the first run.  If you don\'t see why this is necessary,'
              'then you probably need to seek help from an AFNI guru.',
-        argstr='-inlev %d',
+        argstr='-inilev %d',
         xor=['duplo'])
     minpatch = traits.Int(
         desc='* The value of mm should be an odd integer.'
@@ -3462,7 +3463,7 @@ class Qwarp(AFNICommand):
     >>> qwarp2.inputs.inilev = 7
     >>> qwarp2.inputs.iniwarp = ['Q25_warp+tlrc.HEAD']
     >>> qwarp2.cmdline  # doctest: +ALLOW_UNICODE
-    '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inlev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
+    '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
     >>> res2 = qwarp2.run()  # doctest: +SKIP
     """
     _cmd = '3dQwarp'
@@ -3475,29 +3476,38 @@ def _list_outputs(self):
         if not isdefined(self.inputs.out_file):
             prefix = self._gen_fname(self.inputs.in_file, suffix='_QW')
             ext = '.HEAD'
+            suffix ='+tlrc'
         else:
             prefix = self.inputs.out_file
             ext_ind = max([prefix.lower().rfind('.nii.gz'),
                            prefix.lower().rfind('.nii.')])
             if ext_ind == -1:
                 ext = '.HEAD'
+                suffix = '+tlrc'
             else:
                 ext = prefix[ext_ind:]
+                suffix = ''
         print(ext,"ext")
-        outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='+tlrc')+ext)
+        outputs['warped_source'] = fname_presuffix(prefix, suffix=suffix,
+                                                   use_ext=False) + ext
         if not self.inputs.nowarp:
-            outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARP+tlrc')+ext)
+            outputs['source_warp'] = fname_presuffix(prefix,
+                suffix='_WARP' + suffix, use_ext=False) + ext
         if self.inputs.iwarp:
-            outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARPINV+tlrc')+ext)
+            outputs['base_warp'] = fname_presuffix(prefix,
+                suffix='_WARPINV' + suffix, use_ext=False) + ext
         if isdefined(self.inputs.out_weight_file):
             outputs['weights'] = os.path.abspath(self.inputs.out_weight_file)
 
         if self.inputs.plusminus:
-            outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS+tlrc')+ext)
-            outputs['warped_base'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS+tlrc')+ext)
-            outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS_WARP+tlrc')+ext)
-            outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS_WARP+tlrc',)+ext)
-
+            outputs['warped_source'] = fname_presuffix(prefix,
+                suffix='_PLUS' + suffix, use_ext=False) + ext
+            outputs['warped_base'] = fname_presuffix(prefix,
+                suffix='_MINUS' + suffix, use_ext=False) + ext
+            outputs['source_warp'] = fname_presuffix(prefix,
+                suffix='_PLUS_WARP' + suffix, use_ext=False) + ext
+            outputs['base_warp'] = fname_presuffix(prefix,
+                suffix='_MINUS_WARP' + suffix, use_ext=False) + ext
         return outputs
 
     def _gen_filename(self, name):

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -51,7 +51,7 @@ def test_Qwarp_inputs():
     copyfile=False,
     mandatory=True,
     ),
-    inilev=dict(argstr='-inlev %d',
+    inilev=dict(argstr='-inilev %d',
     xor=['duplo'],
     ),
     iniwarp=dict(argstr='-iniwarp %s',

nipype/interfaces/ants/resampling.py

@@ -243,13 +243,15 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
                                 'Gaussian',
                                 'BSpline',
                                 argstr='%s', usedefault=True)
-    interpolation_parameters = traits.Either(traits.Tuple(traits.Int()),  # BSpline (order)
-                                             traits.Tuple(traits.Float(),  # Gaussian/MultiLabel (sigma, alpha)
-                                                          traits.Float())
-                                            )
-    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
-                                desc='transform files: will be applied in reverse order. For '
-                                'example, the last specified transform will be applied first.')
+    interpolation_parameters = traits.Either(
+        traits.Tuple(traits.Int()),  # BSpline (order)
+        traits.Tuple(traits.Float(),  # Gaussian/MultiLabel (sigma, alpha)
+                     traits.Float())
+    )
+    transforms = traits.Either(
+        InputMultiPath(File(exists=True)), 'identity', argstr='%s', mandatory=True,
+        desc='transform files: will be applied in reverse order. For '
+             'example, the last specified transform will be applied first.')
     invert_transform_flags = InputMultiPath(traits.Bool())
     default_value = traits.Float(0.0, argstr='--default-value %g', usedefault=True)
     print_out_composite_warp_file = traits.Bool(False, requires=["output_image"],
@@ -269,6 +271,15 @@ class ApplyTransforms(ANTSCommand):
     --------
 
     >>> from nipype.interfaces.ants import ApplyTransforms
+    >>> at = ApplyTransforms()
+    >>> at.inputs.input_image = 'moving1.nii'
+    >>> at.inputs.reference_image = 'fixed1.nii'
+    >>> at.inputs.transforms = 'identity'
+    >>> at.cmdline # doctest: +ALLOW_UNICODE
+    'antsApplyTransforms --default-value 0 --input moving1.nii \
+--interpolation Linear --output moving1_trans.nii \
+--reference-image fixed1.nii -t identity'
+
     >>> at = ApplyTransforms()
     >>> at.inputs.dimension = 3
     >>> at.inputs.input_image = 'moving1.nii'
@@ -338,6 +349,8 @@ def _format_arg(self, opt, spec, val):
         if opt == "output_image":
             return self._get_output_warped_filename()
         elif opt == "transforms":
+            if val == 'identity':
+                return '-t identity'
             return self._get_transform_filenames()
         elif opt == 'interpolation':
             if self.inputs.interpolation in ['BSpline', 'MultiLabel', 'Gaussian'] and \

nipype/interfaces/base.py

@@ -38,7 +38,7 @@
 from ..utils.provenance import write_provenance
 from ..utils.misc import is_container, trim, str2bool
 from ..utils.filemanip import (md5, hash_infile, FileNotFoundError, hash_timestamp,
-                               split_filename, to_str)
+                               split_filename, to_str, read_stream)
 from .traits_extension import (
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
     File, Directory, DictStrStr, has_metadata, ImageFile)
@@ -1268,9 +1268,7 @@ def __init__(self, name, impl):
         self._buf = ''
         self._rows = []
         self._lastidx = 0
-        self.default_encoding = locale.getdefaultlocale()[1]
-        if self.default_encoding is None:
-            self.default_encoding = 'UTF-8'
+        self.default_encoding = locale.getdefaultlocale()[1] or 'UTF-8'
 
     def fileno(self):
         "Pass-through for file descriptor."
@@ -1349,10 +1347,6 @@ def run_command(runtime, output=None, timeout=0.01):
     cmdline = runtime.cmdline
     env = _canonicalize_env(runtime.environ)
 
-    default_encoding = locale.getdefaultlocale()[1]
-    if default_encoding is None:
-        default_encoding = 'UTF-8'
-
     errfile = None
     outfile = None
     stdout = sp.PIPE
@@ -1420,19 +1414,22 @@ def _process(drain=0):
 
     if output == 'allatonce':
         stdout, stderr = proc.communicate()
-        result['stdout'] = stdout.decode(default_encoding).split('\n')
-        result['stderr'] = stderr.decode(default_encoding).split('\n')
+        result['stdout'] = read_stream(stdout, logger=iflogger)
+        result['stderr'] = read_stream(stderr, logger=iflogger)
 
     elif output.startswith('file'):
         proc.wait()
         if outfile is not None:
             stdout.flush()
-            result['stdout'] = [line.decode(default_encoding).strip()
-                                for line in open(outfile, 'rb').readlines()]
+            with open(outfile, 'rb') as ofh:
+                stdoutstr = ofh.read()
+            result['stdout'] = read_stream(stdoutstr, logger=iflogger)
+
         if errfile is not None:
             stderr.flush()
-            result['stderr'] = [line.decode(default_encoding).strip()
-                                for line in open(errfile, 'rb').readlines()]
+            with open(errfile, 'rb') as efh:
+                stderrstr = efh.read()
+            result['stderr'] = read_stream(stderrstr, logger=iflogger)
 
         if output == 'file':
             result['merged'] = result['stdout']

nipype/interfaces/cmtk/nbs.py

@@ -32,7 +32,10 @@ def ntwks_to_matrices(in_files, edge_key):
     for idx, name in enumerate(in_files):
         graph = nx.read_gpickle(name)
         for u, v, d in graph.edges(data=True):
-            graph[u][v]['weight'] = d[edge_key]  # Setting the edge requested edge value as weight value
+            try:
+                graph[u][v]['weight'] = d[edge_key]  # Setting the edge requested edge value as weight value
+            except:
+                raise KeyError("the graph edges do not have {} attribute".format(edge_key))
         matrix[:, :, idx] = nx.to_numpy_matrix(graph)  # Retrieve the matrix
     return matrix
 
@@ -77,6 +80,10 @@ class NetworkBasedStatistic(BaseInterface):
     output_spec = NetworkBasedStatisticOutputSpec
 
     def _run_interface(self, runtime):
+
+        if not have_cv:
+            raise ImportError("cviewer library is not available")
+
         THRESH = self.inputs.threshold
         K = self.inputs.number_of_permutations
         TAIL = self.inputs.t_tail

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -0,0 +1,58 @@
+from __future__ import unicode_literals
+from ..nbs import NetworkBasedStatistic
+from ....utils.misc import package_check
+import numpy as np
+import networkx as nx
+import pytest
+
+have_cv = True
+try:
+    package_check('cviewer')
+except Exception as e:
+    have_cv = False
+
+@pytest.fixture()
+def creating_graphs(tmpdir):
+    graphlist = []
+    graphnames = ["name"+str(i) for i in range(6)]
+    for idx, name in enumerate(graphnames):
+        graph = np.random.rand(10,10)
+        G = nx.from_numpy_matrix(graph)
+        out_file = str(tmpdir) + graphnames[idx] + '.pck'
+        # Save as pck file
+        nx.write_gpickle(G, out_file)
+        graphlist.append(out_file)
+    return graphlist
+
+
+@pytest.mark.skipif(have_cv, reason="tests for import error, cviewer available")
+def test_importerror(creating_graphs):
+    graphlist = creating_graphs
+    group1 = graphlist[:3]
+    group2 = graphlist[3:]
+    
+    nbs = NetworkBasedStatistic()
+    nbs.inputs.in_group1 = group1
+    nbs.inputs.in_group2 = group2
+    nbs.inputs.edge_key = "weight"
+    
+    with pytest.raises(ImportError) as e:
+        nbs.run()
+    assert "cviewer library is not available" == str(e.value)
+
+
+@pytest.mark.skipif(not have_cv, reason="cviewer has to be available")
+def test_keyerror(creating_graphs):
+    graphlist =creating_graphs
+
+    group1 = graphlist[:3]
+    group2 = graphlist[3:]
+
+    nbs = NetworkBasedStatistic()
+    nbs.inputs.in_group1 = group1
+    nbs.inputs.in_group2 = group2
+    nbs.inputs.edge_key = "Your_edge"
+
+    with pytest.raises(KeyError) as e:
+        nbs.run()
+    assert "the graph edges do not have Your_edge attribute" in str(e.value)

nipype/interfaces/freesurfer/preprocess.py

@@ -2387,8 +2387,8 @@ class ConcatenateLTAInputSpec(FSTraitedSpec):
         File(exists=True), 'identity.nofile', argstr='%s', position=-2,
         mandatory=True, desc='maps dst1(src2) to dst2')
     out_file = File(
-        'concat.lta', usedefault=True, position=-1, argstr='%s',
-        hash_files=False,
+        position=-1, argstr='%s', hash_files=False, name_source=['in_lta1'],
+        name_template='%s_concat', keep_extension=True,
         desc='the combined LTA maps: src1 to dst2 = LTA2*LTA1')
 
     # Inversion and transform type
@@ -2434,7 +2434,7 @@ class ConcatenateLTA(FSCommand):
     >>> conc_lta.inputs.in_lta1 = 'lta1.lta'
     >>> conc_lta.inputs.in_lta2 = 'lta2.lta'
     >>> conc_lta.cmdline # doctest: +ALLOW_UNICODE
-    'mri_concatenate_lta lta1.lta lta2.lta concat.lta'
+    'mri_concatenate_lta lta1.lta lta2.lta lta1_concat.lta'
 
     You can use 'identity.nofile' as the filename for in_lta2, e.g.:
 
@@ -2459,8 +2459,3 @@ def _format_arg(self, name, spec, value):
         if name == 'out_type':
             value = {'VOX2VOX': 0, 'RAS2RAS': 1}[value]
         return super(ConcatenateLTA, self)._format_arg(name, spec, value)
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
-        return outputs

nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py

@@ -28,8 +28,10 @@ def test_ConcatenateLTA_inputs():
     ),
     out_file=dict(argstr='%s',
     hash_files=False,
+    keep_extension=True,
+    name_source=['in_lta1'],
+    name_template='%s_concat',
     position=-1,
-    usedefault=True,
     ),
     out_type=dict(argstr='-out_type %d',
     ),

nipype/interfaces/fsl/epi.py

@@ -592,7 +592,7 @@ def _run_interface(self, runtime):
         cmd = self._cmd
         if all((FSLDIR != '',
                 cmd == 'eddy_openmp',
-                not os.path.exists(os.path.join(FSLDIR, cmd)))):
+                not os.path.exists(os.path.join(FSLDIR, 'bin', cmd)))):
             self._cmd = 'eddy'
         runtime = super(Eddy, self)._run_interface(runtime)
 

nipype/pipeline/engine/nodes.py

@@ -633,7 +633,7 @@ def _run_command(self, execute, copyfiles=True):
             if copyfiles:
                 self._copyfiles_to_wd(cwd, execute)
 
-            message = 'Running node "%s" (a "%s" interface)'
+            message = 'Running node "%s" ("%s.%s")'
             if issubclass(self._interface.__class__, CommandLine):
                 try:
                     cmd = self._interface.cmdline
@@ -644,7 +644,7 @@ def _run_command(self, execute, copyfiles=True):
                 with open(cmdfile, 'wt') as fd:
                     print(cmd + "\n", file=fd)
                 message += ', a CommandLine Interface with command:\n%s' % cmd
-            logger.info(message + '.', self.name,
+            logger.info(message + '.', self.name, self._interface.__module__,
                         self._interface.__class__.__name__)
             try:
                 result = self._interface.run()