Merge pull request #147 from jhlegarreta/AllowTractogramDownsamplingR…

…eproducibility

ENH: Make tractogram downsampling results reproducible by default

bin/wm_preprocess_all.py

@@ -47,6 +47,9 @@ def main():
     parser.add_argument(
         '-retaindata', action='store_true', dest="flag_retaindata",
         help='If given, all point and cell data stored along the tractography will be retained.')
+    parser.add_argument(
+        '--nonidentical', action='store_true',
+        help='Obtain nonidentical results across runs for downsampling.')
 
     args = parser.parse_args()
 
@@ -88,7 +91,11 @@ def main():
     else:
         print("Remove all data stored along the tractography and only keep fiber streamlines.")
     retaindata = args.flag_retaindata
-
+
+    random_seed = 1234
+    if args.nonidentical:
+        random_seed = None
+
     print("==========================")
 
     # =======================================================================
@@ -154,7 +161,7 @@ def pipeline(inputPolyDatas, sidx, args):
             print(id_msg + msg)
 
             # , preserve_point_data=True needs editing of preprocess function to use mask function
-            wm3 = wma.filter.downsample(wm2, args.numberOfFibers, preserve_point_data=retaindata, preserve_cell_data=retaindata, verbose=False)
+            wm3 = wma.filter.downsample(wm2, args.numberOfFibers, preserve_point_data=retaindata, preserve_cell_data=retaindata, verbose=False, random_seed=random_seed)
             print("Number of fibers retained: ", wm3.GetNumberOfLines(), "/", num_lines)
 
         if wm3 is None:

whitematteranalysis/filter.py

@@ -250,7 +250,7 @@ def preprocess(inpd, min_length_mm,
         else:
             return outpd
 
-def downsample(inpd, output_number_of_lines, return_indices=False, preserve_point_data=False, preserve_cell_data=True, initial_indices=None, verbose=True, random_seed=None):
+def downsample(inpd, output_number_of_lines, return_indices=False, preserve_point_data=False, preserve_cell_data=True, initial_indices=None, verbose=True, random_seed=1234):
     """ Random (down)sampling of fibers without replacement. """
 
     if initial_indices is None: