Merge pull request #2196 from satra/fix/timeout

fix for networkx and afni

Author: satra

doc/users/install.rst

@@ -47,7 +47,7 @@ use the following command::
 While `all` installs everything, one can also install select components as
 listed below::
 
-    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'tests': ['pytest-cov', 'codecov'],
     'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],

examples/dmri_dtk_dti.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/dmri_dtk_odf.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/dmri_fsl_dti.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 

examples/fmri_slicer_coregistration.py

@@ -37,7 +37,6 @@
 
 package_check('numpy', '1.3', 'tutorial1')
 package_check('scipy', '0.7', 'tutorial1')
-package_check('networkx', '1.0', 'tutorial1')
 package_check('IPython', '0.10', 'tutorial1')
 
 """The nipype tutorial contains data for two subjects.  Subject data

nipype/info.py

@@ -107,6 +107,7 @@ def get_nipype_gitversion():
 SIMPLEJSON_MIN_VERSION = '3.8.0'
 PROV_VERSION = '1.5.0'
 CLICK_MIN_VERSION = '6.6.0'
+PYDOT_MIN_VERSION = '1.2.3'
 
 NAME = 'nipype'
 MAINTAINER = 'nipype developers'
@@ -142,6 +143,7 @@ def get_nipype_gitversion():
     'pytest>=%s' % PYTEST_MIN_VERSION,
     'mock',
     'pydotplus',
+    'pydot>=%s' % PYDOT_MIN_VERSION,
     'packaging',
 ]
 
@@ -154,7 +156,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
-    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'tests': TESTS_REQUIRES,
     'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],

nipype/interfaces/afni/base.py

@@ -10,7 +10,7 @@
 from sys import platform
 from distutils import spawn
 
-from ... import logging
+from ... import logging, LooseVersion
 from ...utils.filemanip import split_filename, fname_presuffix
 
 from ..base import (
@@ -44,32 +44,25 @@ def version():
 
         """
         try:
-            clout = CommandLine(command='afni_vcheck',
+            clout = CommandLine(command='afni --version',
                                 terminal_output='allatonce').run()
-
-            # Try to parse the version number
-            currv = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
         except IOError:
             # If afni_vcheck is not present, return None
-            IFLOGGER.warn('afni_vcheck executable not found.')
+            IFLOGGER.warn('afni executable not found.')
             return None
-        except RuntimeError as e:
-            # If AFNI is outdated, afni_vcheck throws error.
-            # Show new version, but parse current anyways.
-            currv = str(e).split('\n')[4].split('=', 1)[1].strip()
-            nextv = str(e).split('\n')[6].split('=', 1)[1].strip()
-            IFLOGGER.warn(
-                'AFNI is outdated, detected version %s and %s is available.' % (currv, nextv))
-
-        if currv.startswith('AFNI_'):
-            currv = currv[5:]
-
-        v = currv.split('.')
-        try:
-            v = [int(n) for n in v]
-        except ValueError:
-            return currv
-        return tuple(v)
+
+        version_stamp = clout.runtime.stdout.split('\n')[0].split('Version ')[1]
+        if version_stamp.startswith('AFNI'):
+            version_stamp = version_stamp.split('AFNI_')[1]
+        elif version_stamp.startswith('Debian'):
+            version_stamp = version_stamp.split('Debian-')[1].split('~')[0]
+        else:
+            return None
+
+        version = LooseVersion(version_stamp.replace('_', '.')).version[:3]
+        if version[0] < 1000:
+            version[0] = version[0] + 2000
+        return tuple(version)
 
     @classmethod
     def output_type_to_ext(cls, outputtype):

nipype/interfaces/afni/preprocess.py

@@ -1457,7 +1457,7 @@ def __init__(self, **inputs):
             version = Info.version()
 
             # As of AFNI 16.0.00, redirect_x is not needed
-            if isinstance(version[0], int) and version[0] > 15:
+            if version[0] > 2015:
                 self._redirect_x = False
 
     def _parse_inputs(self, skip=None):
@@ -2150,7 +2150,7 @@ def __init__(self, **inputs):
             v = Info.version()
 
             # As of AFNI 16.0.00, redirect_x is not needed
-            if isinstance(v[0], int) and v[0] > 15:
+            if v[0] > 2015:
                 self._redirect_x = False
 
 

nipype/interfaces/cmtk/cmtk.py

@@ -214,16 +214,16 @@ def cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_
     nROIs = len(gp.nodes())
 
     # add node information from parcellation
-    if 'dn_position' in gp.node[gp.nodes()[0]]:
+    if 'dn_position' in gp.nodes[list(gp.nodes())[0]]:
         G = gp.copy()
     else:
         G = nx.Graph()
-        for u, d in gp.nodes_iter(data=True):
-            G.add_node(int(u), d)
+        for u, d in gp.nodes(data=True):
+            G.add_node(int(u), **d)
             # compute a position for the node based on the mean position of the
             # ROI in voxel coordinates (segmentation volume )
             xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])), axis=1))
-            G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]])
+            G.nodes[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]])
 
     if intersections:
         iflogger.info("Filtering tractography from intersections")
@@ -304,7 +304,7 @@ def cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_
     fibmean = numfib.copy()
     fibmedian = numfib.copy()
     fibdev = numfib.copy()
-    for u, v, d in G.edges_iter(data=True):
+    for u, v, d in G.edges(data=True):
         G.remove_edge(u, v)
         di = {}
         if 'fiblist' in d:
@@ -319,7 +319,7 @@ def cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_
             di['fiber_length_median'] = 0
             di['fiber_length_std'] = 0
         if not u == v:  # Fix for self loop problem
-            G.add_edge(u, v, di)
+            G.add_edge(u, v, **di)
             if 'fiblist' in d:
                 numfib.add_edge(u, v, weight=di['number_of_fibers'])
                 fibmean.add_edge(u, v, weight=di['fiber_length_mean'])
@@ -747,10 +747,10 @@ def create_nodes(roi_file, resolution_network_file, out_filename):
     roi_image = nb.load(roi_file, mmap=NUMPY_MMAP)
     roiData = roi_image.get_data()
     nROIs = len(gp.nodes())
-    for u, d in gp.nodes_iter(data=True):
-        G.add_node(int(u), d)
+    for u, d in gp.nodes(data=True):
+        G.add_node(int(u), **d)
         xyz = tuple(np.mean(np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])), axis=1))
-        G.node[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]])
+        G.nodes[int(u)]['dn_position'] = tuple([xyz[0], xyz[2], -xyz[1]])
     nx.write_gpickle(G, out_filename)
     return out_filename
 

nipype/interfaces/cmtk/nbs.py

@@ -113,9 +113,9 @@ def _run_interface(self, runtime):
         node_network = nx.read_gpickle(node_ntwk_name)
         iflogger.info('Populating node dictionaries with attributes from {node}'.format(node=node_ntwk_name))
 
-        for nid, ndata in node_network.nodes_iter(data=True):
-            nbsgraph.node[nid] = ndata
-            nbs_pval_graph.node[nid] = ndata
+        for nid, ndata in node_network.nodes(data=True):
+            nbsgraph.nodes[nid] = ndata
+            nbs_pval_graph.nodes[nid] = ndata
 
         path = op.abspath('NBS_Result_' + details)
         iflogger.info(path)