setting up and testing pypi delivery

MANIFEST.in

@@ -0,0 +1,2 @@
+include versioneer.py
+include conwhat/_version.py

conwhat/__init__.py

@@ -1,10 +1,9 @@
 
+__all__ = [ 'VolTractAtlas', 'VolConnAtlas', 'StreamTractAtlas', 'StreamConnAtlas' ]
 
-
-__version__ = '0.1.dev0'
-
-
-from atlas import (VolTractAtlas,VolConnAtlas,
+from .atlas import (VolTractAtlas,VolConnAtlas,
                    StreamTractAtlas,StreamConnAtlas)
 
-
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions

conwhat/__main__.py

@@ -0,0 +1,15 @@
+
+
+
+def main():
+    "Entry point."
+
+    raise NotImplementedError('The command line interface for ConWhAt is not currently supported. '
+                              'Please use it via API in a script or jupyter notebook. \n'
+                              'Example usages : \n'
+                              'from conwhat import StreamConnAtlas \n'
+                              'from conwhat import VolConnAtlas \n'
+                              '')
+
+if __name__ == '__main__':
+    main()

conwhat/atlas.py

@@ -4,6 +4,7 @@
 
 # Author: John Griffiths
 # License: simplified BSD
+from __future__ import print_function
 
 import os
 
@@ -14,17 +15,17 @@
 
 from nilearn.plotting import plot_glass_brain
 
-from utils.readers import (load_connectivity,load_vol_file_mappings,load_vol_bboxes,
+from .utils.readers import (load_connectivity,load_vol_file_mappings,load_vol_bboxes,
                            load_stream_file_mappings,load_stream_bboxes,
                            make_nx_graph,dpy_to_trk)
 
-from utils.stats import (compute_vol_hit_stats,compute_vol_scalar_stats,
+from .utils.stats import (compute_vol_hit_stats,compute_vol_scalar_stats,
                          compute_streams_in_roi,#compute_stream_hit_stats,compute_stream_scalar_stats,
                          hit_stats_to_nx)
 
-#from viz.network import plot_network,plot_matrix
-#from viz.volume import plot_vol_cnxn,plot_vol_tract
-#from viz.streams import plot_stream_cnxn,plot_stream_tract
+from .viz.network import plot_network, plot_matrix
+from .viz.volume import plot_vol_cnxn, plot_vol_tract
+from .viz.streams import plot_stream_cnxn, plot_stream_tract
 
 
 
@@ -38,7 +39,7 @@ class _Atlas(): # object):
 
   def __init__(self):
 
-    print 'blah'
+    print('blah')
 
 
 class _VolAtlas(_Atlas):
@@ -61,6 +62,7 @@ def __init__(self,atlas_name=None,atlas_dir=None):
     self.vfms,self.atlas_dir = load_vol_file_mappings(atlas_name=atlas_name,atlas_dir=atlas_dir)
     self.bbox = load_vol_bboxes(atlas_name=atlas_name,atlas_dir=atlas_dir)
 
+    self.scalar_stats = dict()
 
   def get_vol_from_vfm(self,idx):		
     """ 		
@@ -79,10 +81,10 @@ def get_vol_from_vfm(self,idx):
 
     if os.path.isfile(nii_file):		
       if (np.isnan(volnum) or volnum == 'nan'):		
-        print 'getting atlas entry %s: image file %s'  %(idx,nii_file)		
+        print('getting atlas entry {}: image file {} ' % (idx,nii_file))
         img = nib.load(nii_file)		
       else:		
-        print 'getting atlas entry %s: volume %s from image file %s'  %(idx,volnum,nii_file)		
+        print('getting atlas entry {}: volume %s from image file {}' % (idx,volnum,nii_file))
         img = index_img(nii_file,volnum)		
 
     return img
@@ -174,7 +176,8 @@ def compute_hit_stats(self,roi,idxs,n_jobs=1,run_type='simple',joblib_cache_dir=
   def plot_tract(self,atlas_name):
 
     # (uses plotting param defaults tuned to JHU atlas)
-    plot_tract()
+    # plot_tract()
+    raise NotImplementedError
 
 
 
@@ -207,6 +210,8 @@ def __init__(self,atlas_dir=None,atlas_name=None):
     # Compile node and connectivity info into a networkx graph
     self.Gnx = make_nx_graph(self.vfms,self.bbox,ws,rls,hs,ctx)
 
+    self.modcons = dict()
+
 
   @property
   def weights(self):
@@ -282,13 +287,17 @@ def get_vol_from_rois(self,roi1,roi2):
     return img
 
 
+  def modify_vol_connectome(self):
+
+    raise NotImplementedError
+
   def modify_connectome(self, name='mc1',function=''):
     """
     Modify canonical connectome using hit or scalar 
     stats, and store in this obj
     """
 
-    res = modify_vol_connectome()
+    res = self.modify_vol_connectome()
 
     self.modcons[name] = res
 
@@ -398,7 +407,7 @@ def __init__(self,atlas_name=None,atlas_dir=None):
 
   def write_subset_to_trk(self,ref_file,outfile,stream_inds='all'):
 
-    print 'writing streams to trk file: %s' %outfile
+    print('writing streams to trk file: {}' % outfile)
     dpy_to_trk(self.dpy_file,ref_file,outfile,inds=stream_inds)
 
 
@@ -444,6 +453,8 @@ def __init__(self,atlas_name=None,atlas_dir=None):
     # Compile node and connectivity info into a networkx graph
     self.Gnx = make_nx_graph(self.sfms,self.bbox,ws,rls,hs,ctx)
 
+    self.modcons = dict()
+
 
 
   def get_rois_from_idx(self,idx):
@@ -484,15 +495,16 @@ def compute_hit_stats(self,roi,idxs,n_jobs=1,run_type='simple',joblib_cache_dir=
 
 
 
-
+  def modify_stream_connectome(self):
+    raise NotImplementedError
 
   def modify_connectome(self, name='mc1',function=''):
     """
     Modify canonical connectome using hit or scalar 
     stats, and store in this obj
     """
 
-    res = modify_stream_connectome()
+    res = self.modify_stream_connectome()
 
     self.modcons[name] = res
 
@@ -521,7 +533,7 @@ def plot_matrix(self):
 
   def plot_cnxns(self):
 
-    plot_stream_cnxns()
+    plot_stream_cnxn()
 
 
 

conwhat/utils/stats.py

@@ -388,20 +388,23 @@ def calc_streams_in_roi(dpy_file,roi_dat,stream_idxs):
 
 
 
-def compute_vol_scalar_stats():
+def compute_vol_scalar_stats(params):
 
-  print 'computing vol scalar stats'
+  print('computing vol scalar stats')
+  raise NotImplementedError
 
 
-def compute_stream_hit_stats():
+def compute_stream_hit_stats(params):
 
-  print 'computing stream hit stats'
+  print('computing stream hit stats')
+  raise NotImplementedError
 
 
-def compute_stream_scalar_stats():
+def compute_stream_scalar_stats(params):
 
+  print('computing stream scalar stats')
+  raise NotImplementedError
 
-  print 'computing stream scalar stats'
 
 
 

conwhat/viz/network.py

@@ -9,13 +9,16 @@
 
 def plot_network():
 
-  print 'plotting network'
+  print('plotting network')
 
+  return
 
 
 def plot_matrix():
 
-  print 'plotting matrix'
+  print('plotting matrix')
+
+  return
 
 
 

conwhat/viz/streams.py

@@ -54,7 +54,7 @@ def get_track_vis_pic(trk_file, length=None,bg_image=None,bz=None, sc='/tmp/movi
   if tr: 
     cmd += ' -s -r %s' %tr
 
-  if tc: 
+  if tc:
     cmd += ' -c %s ' %tc
   if aa: cmd+= ' -aa '
 
@@ -74,11 +74,13 @@ def get_track_vis_pic(trk_file, length=None,bg_image=None,bz=None, sc='/tmp/movi
 
 def plot_stream_cnxn():
 
-  print 'plotting streamlinetric connection'
+  print('plotting streamlinetric connection')
+  raise NotImplementedError
 
 
 def plot_stream_tract():
 
-  print 'plotting streamlinetric tract'
+  print('plotting streamlinetric tract')
+  raise NotImplementedError
 
 

conwhat/viz/volume.py

@@ -157,3 +157,11 @@ def plot_vol_and_rois_nilearn(vol,labels,roi1_img=None,roi2_img=None,
   return display
 
 
+def plot_vol_cnxn():
+  ""
+
+  raise NotImplementedError
+
+def plot_vol_tract():
+
+  raise NotImplementedError

requirements.txt

@@ -5,3 +5,7 @@ nilearn
 dipy
 joblib
 matplotlib
+sklearn
+pyyaml
+networkx
+indexed_gzip

setup.cfg

@@ -2,6 +2,6 @@
 VCS = git
 style = pep440
 versionfile_source = conwhat/_version.py
-versionfile_build = _version.py
+versionfile_build = conwhat/_version.py
 tag_prefix =
 parentdir_prefix = conwhat-