Merge pull request #426 from dPys/development

Development

README.md

@@ -79,10 +79,10 @@ where the `-config` flag specifies that path to a .json configuration spec that
             "es": "['mean', 'median']" # Indicates the method(s) of nodal time-series signal extraction.
         },
     "dwi": { # dMRI options. If you only have structural (i.e. DWI) data, set each of the `func` options to "None"
-            "dg": "None",
-            "ml": "None",
-            "mod": "None",
-            "em": "None"
+            "dg": "det", # The directional assumptions of tractography (e.g. deterministic, probabilistic)
+            "ml": "40", # The minimum length criterion for streamlines in tractography
+            "mod": "csd", # The diffusion model type
+            "tol": "8" # The tolerance distance (in the units of the streamlines, usually mm). If any node in the streamline is within this distance from the center of any voxel in the ROI, then the connection is counted as an edge"
         },
     "gen": { # These are general options that apply to all modalities
             "a":  "['BrainnetomeAtlasFan2016', 'atlas_harvard_oxford', 'destrieux2009_rois']", # Anatomical atlases to define nodes.

pynets/__about__.py

@@ -6,7 +6,7 @@
 # from ._version import get_versions
 # __version__ = get_versions()['version']
 # del get_versions
-__version__ = "1.0.11"
+__version__ = "1.0.12"
 
 __packagename__ = "pynets"
 __copyright__ = "Copyright 2017, Derek Pisner"

pynets/cli/pynets_run.py

@@ -401,7 +401,7 @@ def get_parser():
              "minimums, separate the list by space (e.g. 10 30 50).\n",
     )
     parser.add_argument(
-        "-em",
+        "-tol",
         metavar="Error margin",
         default=8,
         nargs="+",
@@ -761,7 +761,7 @@ def build_workflow(args, retval):
                    int(list(psutil.virtual_memory())[4]/1000000000) - 2]
     else:
         procmem = list(eval(str(resources)))
-        procmem[1] = procmem[1] - 2
+        procmem[1] = procmem[1] - 1
     if args.thr is None:
         thr = float(1.0)
     else:
@@ -832,6 +832,8 @@ def build_workflow(args, retval):
     else:
         extract_strategy_list = None
     roi = args.roi
+    if isinstance(roi, list):
+        roi = roi[0]
     conn_model = args.mod
     if conn_model:
         if (isinstance(conn_model, list)) and (len(conn_model) > 1):
@@ -985,7 +987,7 @@ def build_workflow(args, retval):
             min_length_list = None
     else:
         min_length_list = None
-    error_margin = args.em
+    error_margin = args.tol
     if error_margin:
         if (isinstance(error_margin, list)) and (len(error_margin) > 1):
             error_margin_list = error_margin
@@ -1843,7 +1845,8 @@ def build_workflow(args, retval):
                         'roi_neighborhood_tol preset cannot be less than '
                         'the value of the structural connectome error_margin'
                         ' parameter.')
-            print(f"{Fore.GREEN}Iterating minimum streamline lengths:")
+            print(f"{Fore.GREEN}Iterating ROI-streamline intersection "
+                  f"tolerance:")
             print(f"{Fore.BLUE}{', '.join(error_margin_list)}")
 
         if target_samples:

pynets/config/bids_config.json

@@ -3,7 +3,7 @@
             "dg": "['prob', 'det']",
             "ml": "['10', '40']",
             "mod": "['csd', 'csa']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "['rena', 'ward', 'kmeans']",

pynets/config/bids_config_anatomical_atlases.json

@@ -3,7 +3,7 @@
             "dg": "['det', 'prob', 'clos']",
             "ml": "['0', '20', '40']",
             "mod": "['csd', 'csa', 'tensor', 'sfm']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_anatomical_atlases_test.json

@@ -3,7 +3,7 @@
             "dg": "['prob']",
             "ml": "['0']",
             "mod": "['csd']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_bold.json

@@ -2,7 +2,8 @@
     "dwi": {
             "dg": "None",
             "ml": "None",
-            "mod": "None"
+            "mod": "None",
+            "tol": "None"
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_clustering.json

@@ -3,7 +3,7 @@
             "dg": "None",
             "ml": "None",
             "mod": "None",
-            "em": "None"
+            "tol": "None"
         },
     "func": {
             "ct": "['rena']",

pynets/config/bids_config_dwi.json

@@ -3,7 +3,7 @@
             "dg": "['det', 'prob']",
             "ml": "['0', '20']",
             "mod": "['csa']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_embed.json

@@ -3,7 +3,7 @@
             "dg": "['clos']",
             "ml": "['0']",
             "mod": "['csa']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_rsns.json

@@ -3,7 +3,7 @@
             "dg": "['clos']",
             "ml": "['0']",
             "mod": "['csa']",
-            "em": 8
+            "tol": 8
         },
     "func": {
             "ct": "None",

pynets/config/bids_config_test.json

@@ -3,7 +3,7 @@
             "dg": "None",
             "ml": "None",
             "mod": "None",
-            "em": "None"
+            "tol": "None"
         },
     "func": {
             "ct": "None",