Merge pull request #437 from dPys/development

Development

Author: dPys

pynets/__about__.py

@@ -6,10 +6,10 @@
 # from ._version import get_versions
 # __version__ = get_versions()['version']
 # del get_versions
-__version__ = "1.0.13"
+__version__ = "1.0.14"
 
 __packagename__ = "pynets"
-__copyright__ = "Copyright 2017, Derek Pisner"
+__copyright__ = "Copyright 2016, Derek Pisner"
 __credits__ = (
     "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
     "of the repository")

pynets/cli/pynets_cloud.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Created on Tue Nov  7 10:40:07 2017
-Copyright (C) 2017
+Copyright (C) 2016
 @author: Derek Pisner (dPys)
 """
 import subprocess

pynets/cli/pynets_collect.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Created on Tue Nov  7 10:40:07 2017
-Copyright (C) 2017
+Copyright (C) 2016
 @author: Derek Pisner (dPys)
 """
 from nipype.interfaces import utility as niu
@@ -915,8 +915,9 @@ def main():
     args_dict_all['plug'] = 'MultiProc'
     args_dict_all['v'] = False
     args_dict_all['pm'] = '24,57'
-    args_dict_all['basedir'] = '/working/tuning_set/outputs_shaeffer/pynets'
+    #args_dict_all['basedir'] = '/working/tuning_set/outputs_shaeffer/pynets'
     #args_dict_all['basedir'] = '/scratch/04171/dpisner/HNU/HNU_outs/triple/pynets'
+    args_dict_all['basedir'] = '/scratch/04171/dpisner/HNU/HNU_outs/visual/pynets'
     args_dict_all['work'] = '/tmp/work/dwi'
     args_dict_all['modality'] = 'dwi'
     args_dict_all['dc'] = ['diversity_coefficient',
@@ -926,7 +927,8 @@ def main():
                            'average_local_clustering_nodewise',
                            'average_local_efficiency_nodewise',
                            'degree_centrality',
-                           "_minlength-0",
+                           'weighted_transitivity',
+                        #   "_minlength-0",
                            "_minlength-20", "_minlength-30", "variance",
                            "res-1000"]
     args = SimpleNamespace(**args_dict_all)

pynets/cli/pynets_run.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Created on Tue Nov  7 10:40:07 2017
-Copyright (C) 2017
+Copyright (C) 2016
 @author: Derek Pisner (dPys)
 """
 import warnings

pynets/core/cloud_utils.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Created on Tue Nov  7 10:40:07 2017
-Copyright (C) 2017
+Copyright (C) 2016
 @author: Derek Pisner (dPys)
 """
 from configparser import ConfigParser

pynets/core/interfaces.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 Created on Fri Nov 10 15:44:46 2017
-Copyright (C) 2017
+Copyright (C) 2016
 @author: Derek Pisner (dPys)
 """
 import warnings
@@ -107,9 +107,14 @@ def _run_interface(self, runtime):
                 else:
                     parcel_list = None
             else:
-                raise FileNotFoundError(
-                    f"\nAtlas file for {self.inputs.atlas} not found!"
-                )
+                try:
+                    raise FileNotFoundError(
+                        f"\nAtlas file for {self.inputs.atlas} not found!"
+                    )
+                except FileNotFoundError:
+                    import sys
+                    sys.exit(0)
+
             atlas = self.inputs.atlas
         elif (
             self.inputs.uatlas is None
@@ -159,8 +164,12 @@ def _run_interface(self, runtime):
                 else:
                     parcel_list = None
             else:
-                raise ValueError(
-                    f"\nAtlas file for {self.inputs.atlas} not found!")
+                try:
+                    raise FileNotFoundError(
+                        f"\nAtlas file for {self.inputs.atlas} not found!")
+                except FileNotFoundError:
+                    import sys
+                    sys.exit(0)
             par_max = None
             atlas = self.inputs.atlas
             label_intensities = None
@@ -194,14 +203,12 @@ def _run_interface(self, runtime):
                 # Describe user atlas coords
                 print(f"\n{self.inputs.atlas} comes with {par_max} parcels\n")
             except ValueError:
+                import sys
                 print(
                     "Either you have specified the name of an atlas that does"
                     " not exist in the nilearn or local repository or you have"
                     " not supplied a 3d atlas parcellation image!")
-                parcel_list = None
-                par_max = None
-                coords = None
-                label_intensities = None
+                sys.exit(0)
             labels = None
             networks_list = None
             atlas = self.inputs.atlas
@@ -242,24 +249,23 @@ def _run_interface(self, runtime):
                 # Describe user atlas coords
                 print(f"\n{atlas} comes with {par_max} parcels\n")
             except ValueError:
+                import sys
                 print(
                     "Either you have specified the name of an atlas that does"
                     " not exist in the nilearn or local repository or you have"
                     " not supplied a 3d atlas parcellation image!")
-                parcel_list = None
-                par_max = None
-                coords = None
-                atlas = None
-                uatlas = None
-                label_intensities = None
+                sys.exit(0)
             labels = None
             networks_list = None
         else:
-            raise ValueError(
-                "Either you have specified the name of an atlas that does not"
-                " exist in the nilearn or local repository or you have not"
-                " supplied a 3d atlas parcellation image!")
-
+            try:
+                raise ValueError(
+                    "Either you have specified the name of an atlas that does"
+                    " not exist in the nilearn or local repository or you have"
+                    " not supplied a 3d atlas parcellation image!")
+            except ValueError:
+                import sys
+                sys.exit(0)
         # Labels prep
         if atlas and not labels:
             if (self.inputs.ref_txt is not None) and (
@@ -748,11 +754,15 @@ def run_bs_iteration(i, ts_data, work_dir, local_corr,
                 parcellation.to_filename(out_path)
 
         else:
-            raise ValueError(
-                "Clustering method not recognized. See: "
-                "https://nilearn.github.io/modules/generated/"
-                "nilearn.regions.Parcellations."
-                "html#nilearn.regions.Parcellations")
+            try:
+                raise ValueError(
+                    "Clustering method not recognized. See: "
+                    "https://nilearn.github.io/modules/generated/"
+                    "nilearn.regions.Parcellations."
+                    "html#nilearn.regions.Parcellations")
+            except ValueError:
+                import sys
+                sys.exit(0)
 
         # Give it a minute
         ix = 0
@@ -762,8 +772,12 @@ def run_bs_iteration(i, ts_data, work_dir, local_corr,
             ix += 1
 
         if not os.path.isfile(nip.uatlas):
-            raise FileNotFoundError(f"Parcellation clustering failed for"
-                                    f" {nip.uatlas}")
+            try:
+                raise FileNotFoundError(f"Parcellation clustering failed for"
+                                        f" {nip.uatlas}")
+            except FileNotFoundError:
+                import sys
+                sys.exit(0)
 
         self._results["atlas"] = atlas
         self._results["uatlas"] = nip.uatlas
@@ -918,6 +932,7 @@ def _run_interface(self, runtime):
                 == te.ts_within_nodes.shape[1]
             )
         except AssertionError as e:
+            import sys
             e.args += ('Coords: ', len(self.inputs.coords),
                        self.inputs.coords, 'Labels:',
                        len(self.inputs.labels),
@@ -2293,8 +2308,10 @@ def _run_interface(self, runtime):
                         self.inputs.labels)
 
             except FileNotFoundError:
+                import sys
                 print('T1w-space parcellation not found. Did you delete '
                       'outputs?')
+                sys.exit(0)
         else:
             if self.inputs.uatlas is None:
                 uatlas_tmp_path = None
@@ -2455,10 +2472,12 @@ def _run_interface(self, runtime):
         try:
             assert len(coords) == len(labels) == len(intensities)
         except ValueError as err:
+            import sys
             print('Failed!')
             print(f"# Coords: {len(coords)}")
             print(f"# Labels: {len(labels)}")
             print(f"# Intensities: {len(intensities)}")
+            sys.exit(1)
 
         self._results["aligned_atlas_gm"] = aligned_atlas_gm
         self._results["coords"] = coords
@@ -2664,6 +2683,7 @@ class _TrackingOutputSpec(TraitedSpec):
     min_length = traits.Any()
     error_margin = traits.Any()
 
+
 class Tracking(SimpleInterface):
     """Interface wrapper for Tracking"""
 
@@ -2921,7 +2941,12 @@ def _run_interface(self, runtime):
                 f" Maximum"
             )
         else:
-            raise ValueError("Direction-getting type not recognized!")
+            try:
+                raise ValueError("Direction-getting type not recognized!")
+            except ValueError:
+                import sys
+                sys.exit(0)
+
         print(Style.RESET_ALL)
 
         # Commence Ensemble Tractography
@@ -3010,8 +3035,12 @@ def _run_interface(self, runtime):
                       f"streamlines output {namer_dir}/{op.basename(streams)}"
                       f" is recommended.")
             if len(streamlines) < 0.5*orig_count:
-                raise ValueError('LiFE revealed no plausible streamlines in '
-                                 'the tractogram!')
+                try:
+                    raise ValueError('LiFE revealed no plausible streamlines '
+                                     'in the tractogram!')
+                except ValueError:
+                    import sys
+                    sys.exit(0)
             del dwi_data, mask_data
 
         stf = StatefulTractogram(