search all tvtk imports and fix ETS_TOOLKIT

doc/users/config_file.rst

@@ -139,11 +139,6 @@ Execution
 *xvfb_max_wait*
     Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x parameter of an Interface is True.
 
-*ets_toolkit*
-    This sets the backend for the Enthought traits (should be ``'null'`` in headless
-    settings).
-
-
 Example
 ~~~~~~~
 

nipype/algorithms/mesh.py

@@ -25,7 +25,6 @@
 
 oldets = os.getenv('ETS_TOOLKIT')
 have_tvtk = False
-
 try:
     os.environ['ETS_TOOLKIT'] = 'null'
     from tvtk.api import tvtk

nipype/algorithms/tests/test_mesh_ops.py

@@ -13,15 +13,24 @@
 
 from nipype.algorithms import mesh as m
 
-notvtk = True
 import platform
+
+notvtk = True
 if 'darwin' not in platform.system().lower():
+    oldets = os.getenv('ETS_TOOLKIT')
+    have_tvtk = False
     try:
+        os.environ['ETS_TOOLKIT'] = 'null'
         from tvtk.api import tvtk
         notvtk = False
     except ImportError:
         pass
 
+    if oldets is not None:
+        os.environ['ETS_TOOLKIT'] = oldets
+    else:
+        del os.environ['ETS_TOOLKIT']
+
 @skipif(notvtk)
 def test_ident_distances():
     tempdir = mkdtemp()

nipype/interfaces/fsl/utils.py

@@ -1854,11 +1854,20 @@ def _parse_inputs(self, skip=None):
         return first_args + [ second_args ]
 
     def _vtk_to_coords(self, in_file, out_file=None):
+        import os
         import os.path as op
+
+        oldets = os.getenv('ETS_TOOLKIT')
         try:
+            os.environ['ETS_TOOLKIT'] = 'null'
             from tvtk.api import tvtk
         except ImportError:
             raise ImportError('This interface requires tvtk to run.')
+        finally:
+            if oldets is not None:
+                os.environ['ETS_TOOLKIT'] = oldets
+            else:
+                del os.environ['ETS_TOOLKIT']
 
         reader = tvtk.PolyDataReader(file_name=in_file+'.vtk')
         reader.update()
@@ -1871,11 +1880,20 @@ def _vtk_to_coords(self, in_file, out_file=None):
         return out_file
 
     def _coords_to_vtk(self, points, out_file):
+        import os
         import os.path as op
+
+        oldets = os.getenv('ETS_TOOLKIT')
         try:
+            os.environ['ETS_TOOLKIT'] = 'null'
             from tvtk.api import tvtk
         except ImportError:
             raise ImportError('This interface requires tvtk to run.')
+        finally:
+            if oldets is not None:
+                os.environ['ETS_TOOLKIT'] = oldets
+            else:
+                del os.environ['ETS_TOOLKIT']
 
         reader = tvtk.PolyDataReader(file_name=self.inputs.in_file)
         reader.update()

nipype/pipeline/plugins/base.py

@@ -54,8 +54,8 @@ def report_crash(node, traceback=None, hostname=None):
     timeofcrash = strftime('%Y%m%d-%H%M%S')
     login_name = getpass.getuser()
     crashfile = 'crash-%s-%s-%s.pklz' % (timeofcrash,
-                                         login_name,
-                                         name)
+                                        login_name,
+                                        name)
     crashdir = node.config['execution']['crashdump_dir']
     if crashdir is None:
         crashdir = os.getcwd()
@@ -106,10 +106,10 @@ def create_pyscript(node, updatehash=False, store_exception=True):
     pkl_file = os.path.join(batch_dir, 'node_%s.pklz' % suffix)
     savepkl(pkl_file, dict(node=node, updatehash=updatehash))
     mpl_backend = node.config["execution"]["matplotlib_backend"]
-    ets_toolkit = node.config["execution"]["ets_toolkit"]
     # create python script to load and trap exception
     cmdstr = """import os
 import sys
+
 can_import_matplotlib = True #Silently allow matplotlib to be ignored
 try:
     import matplotlib
@@ -118,8 +118,6 @@ def create_pyscript(node, updatehash=False, store_exception=True):
     can_import_matplotlib = False
     pass
 
-os.environ['ETS_TOOLKIT'] = '%s'
-
 from nipype import config, logging
 from nipype.utils.filemanip import loadpkl, savepkl
 from socket import gethostname
@@ -133,12 +131,9 @@ def create_pyscript(node, updatehash=False, store_exception=True):
         from collections import OrderedDict
     config_dict=%s
     config.update_config(config_dict)
-
-    ## Only configure matplotlib if it was successfully imported, matplotlib is
-    ## an optional component to nipype
+    ## Only configure matplotlib if it was successfully imported, matplotlib is an optional component to nipype
     if can_import_matplotlib:
         config.update_matplotlib()
-    config.update_ets()
     logging.update_logging(config)
     traceback=None
     cwd = os.getcwd()
@@ -170,8 +165,7 @@ def create_pyscript(node, updatehash=False, store_exception=True):
         report_crash(info['node'], traceback, gethostname())
     raise Exception(e)
 """
-    cmdstr = cmdstr % (mpl_backend, ets_toolkit, pkl_file,
-                       batch_dir, node.config, suffix)
+    cmdstr = cmdstr % (mpl_backend, pkl_file, batch_dir, node.config, suffix)
     pyscript = os.path.join(batch_dir, 'pyscript_%s.py' % suffix)
     fp = open(pyscript, 'wt')
     fp.writelines(cmdstr)
@@ -180,7 +174,6 @@ def create_pyscript(node, updatehash=False, store_exception=True):
 
 
 class PluginBase(object):
-
     """Base class for plugins"""
 
     def __init__(self, plugin_args=None):
@@ -195,7 +188,6 @@ def run(self, graph, config, updatehash=False):
 
 
 class DistributedPluginBase(PluginBase):
-
     """Execute workflow with a distribution engine
     """
 
@@ -238,7 +230,7 @@ def run(self, graph, config, updatehash=False):
         # setup polling - TODO: change to threaded model
         notrun = []
         while np.any(self.proc_done == False) | \
-                np.any(self.proc_pending == True):
+                    np.any(self.proc_pending == True):
             toappend = []
             # trigger callbacks for any pending results
             while self.pending_tasks:
@@ -316,7 +308,7 @@ def _submit_mapnode(self, jobid):
         self.procs.extend(mapnodesubids)
         self.depidx = ssp.vstack((self.depidx,
                                   ssp.lil_matrix(np.zeros(
-                                      (numnodes, self.depidx.shape[1])))),
+                                  (numnodes, self.depidx.shape[1])))),
                                  'lil')
         self.depidx = ssp.hstack((self.depidx,
                                   ssp.lil_matrix(
@@ -365,23 +357,23 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
                     self.proc_pending[jobid] = True
                     # Send job to task manager and add to pending tasks
                     logger.info('Executing: %s ID: %d' %
-                                (self.procs[jobid]._id, jobid))
+                               (self.procs[jobid]._id, jobid))
                     if self._status_callback:
                         self._status_callback(self.procs[jobid], 'start')
                     continue_with_submission = True
                     if str2bool(self.procs[jobid].config['execution']
-                                ['local_hash_check']):
+                                                          ['local_hash_check']):
                         logger.debug('checking hash locally')
                         try:
                             hash_exists, _, _, _ = self.procs[
                                 jobid].hash_exists()
                             logger.debug('Hash exists %s' % str(hash_exists))
                             if (hash_exists and
-                                    (self.procs[jobid].overwrite == False or
-                                     (self.procs[jobid].overwrite == None and
-                                              not self.procs[jobid]._interface.always_run)
-                                     )
-                                    ):
+                                 (self.procs[jobid].overwrite == False or
+                                   (self.procs[jobid].overwrite == None and
+                                    not self.procs[jobid]._interface.always_run)
+                                 )
+                               ):
                                 continue_with_submission = False
                                 self._task_finished_cb(jobid)
                                 self._remove_node_dirs()
@@ -473,7 +465,6 @@ def _remove_node_dirs(self):
 
 
 class SGELikeBatchManagerBase(DistributedPluginBase):
-
     """Execute workflow with SGE/OGE/PBS like batch system
     """
 
@@ -536,7 +527,7 @@ def _get_result(self, taskid):
                                  'seconds. Batch dir contains crashdump file '
                                  'if node raised an exception.\n'
                                  'Node working directory: ({2}) '.format(
-                                     taskid, timeout, node_dir))
+                                 taskid,timeout,node_dir) )
                 raise IOError(error_message)
             except IOError, e:
                 result_data['traceback'] = format_exc()
@@ -583,7 +574,6 @@ def _clear_task(self, taskid):
 
 
 class GraphPluginBase(PluginBase):
-
     """Base class for plugins that distribute graphs to workflows
     """
 
@@ -613,19 +603,19 @@ def _get_args(self, node, keywords):
             if keyword == "template" and os.path.isfile(value):
                 value = open(value).read()
             if (hasattr(node, "plugin_args") and
-                isinstance(node.plugin_args, dict) and
-                    keyword in node.plugin_args):
-                if (keyword == "template" and
-                        os.path.isfile(node.plugin_args[keyword])):
-                    tmp_value = open(node.plugin_args[keyword]).read()
-                else:
-                    tmp_value = node.plugin_args[keyword]
-
-                if ('overwrite' in node.plugin_args and
-                        node.plugin_args['overwrite']):
-                    value = tmp_value
-                else:
-                    value += tmp_value
+                    isinstance(node.plugin_args, dict) and
+                        keyword in node.plugin_args):
+                    if (keyword == "template" and
+                            os.path.isfile(node.plugin_args[keyword])):
+                        tmp_value = open(node.plugin_args[keyword]).read()
+                    else:
+                        tmp_value = node.plugin_args[keyword]
+
+                    if ('overwrite' in node.plugin_args and
+                            node.plugin_args['overwrite']):
+                        value = tmp_value
+                    else:
+                        value += tmp_value
             values += (value, )
         return values
 
@@ -636,13 +626,16 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
         """
         raise NotImplementedError
 
+
+
     def _get_result(self, taskid):
         if taskid not in self._pending:
             raise Exception('Task %d not found' % taskid)
         if self._is_pending(taskid):
             return None
         node_dir = self._pending[taskid]
 
+
         logger.debug(os.listdir(os.path.realpath(os.path.join(node_dir,
                                                               '..'))))
         logger.debug(os.listdir(node_dir))
@@ -663,3 +656,4 @@ def _get_result(self, taskid):
             result_out['result'] = result_data
 
         return result_out
+

nipype/utils/config.py

@@ -40,7 +40,6 @@
 keep_inputs = false
 local_hash_check = true
 matplotlib_backend = Agg
-ets_toolkit = null
 plugin = Linear
 remove_node_directories = false
 remove_unnecessary_outputs = true
@@ -71,7 +70,6 @@ def mkdir_p(path):
 
 
 class NipypeConfig(object):
-
     """Base nipype config class
     """
 
@@ -84,12 +82,12 @@ def __init__(self, *args, **kwargs):
         # To be deprecated in two releases
         if os.path.exists(old_config_file):
             if os.path.exists(new_config_file):
-                msg = ("Detected presence of both old (%s, used by versions "
-                       "< 0.5.2) and new (%s) config files.  This version will "
-                       "proceed with the new one. We advise to merge settings "
-                       "and remove old config file if you are not planning to "
-                       "use previous releases of nipype.") % (old_config_file,
-                                                              new_config_file)
+                msg=("Detected presence of both old (%s, used by versions "
+                     "< 0.5.2) and new (%s) config files.  This version will "
+                     "proceed with the new one. We advise to merge settings "
+                     "and remove old config file if you are not planning to "
+                     "use previous releases of nipype.") % (old_config_file,
+                                                            new_config_file)
                 warn(msg)
             else:
                 warn("Moving old config file from: %s to %s" % (old_config_file,
@@ -167,10 +165,7 @@ def update_matplotlib(self):
         import matplotlib
         matplotlib.use(self.get('execution', 'matplotlib_backend'))
 
-    def update_ets(self):
-        import os
-        os.environ['ETS_TOOLKIT'] = '%s' % self.get('execution', 'ets_toolkit')
-
     def enable_provenance(self):
         self._config.set('execution', 'write_provenance', 'true')
         self._config.set('execution', 'hash_method', 'content')
+