Major organization changes

.travis.yml

@@ -19,7 +19,7 @@ script: tox
 deploy:
   provider: pypi
   distributions: sdist bdist_wheel
-  user: to specific regions of interest to the research question. Although widely applied, combining parcellations obtained with different approaches remains a challenging task. Here, we propose Chimera to flexibly integrate
+  user: yasseraleman
   password:
     secure: PLEASE_REPLACE_ME
   on:

MANIFEST.in

@@ -9,3 +9,7 @@ recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+
+packages = ['.','data','config','docs'],
+
+package_data={'data':['*'],'config':['*'],'docs':['*'],},

chimera/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Yasser Aleman Gomez"""
 __email__ = '[email protected]'
-__version__ = 'parcelations derived from different atlases and methodologies to produce a customized individual parcellation of the brain.'
+__version__ = '0.1.0'

chimera/chimera.py

@@ -80,8 +80,7 @@ def __init__(self, parc_code,
 
         """
 
-        cwd = os.path.dirname(os.path.abspath(__file__))
-        chim_dir = os.path.dirname(cwd)
+        chim_dir = os.path.dirname(os.path.abspath(__file__))
 
         # Rise an error if the parcellation code is not provided
         if parc_code is None:
@@ -1152,8 +1151,8 @@ def _build_parcellation1(self, t1:str, bids_dir:str,
             nmid_subc = len(mid_parc.index)
 
 
-        if "WhiteMatter" in supra_names:
-            self.supra_dict[supra][supra][atlas_code]["none"]["index"]
+        # if "WhiteMatter" in supra_names:
+            #self.supra_dict[supra][supra][atlas_code]["none"]["index"]
 
 
 
@@ -1383,7 +1382,7 @@ def _pipeline_info(pipe_json:str=None):
 
     """
     cwd = os.path.dirname(os.path.abspath(__file__))
-    cwd = os.path.dirname(cwd)
+
     # Get the absolute of this file
     if pipe_json is None:
 
@@ -1419,8 +1418,7 @@ def _load_parcellations_info(parc_json:str=None, supra_folder:str=None):
         Dictionary containing the supraregions information
 
     """
-    cwd = os.path.dirname(os.path.abspath(__file__))
-    chim_dir = os.path.dirname(cwd)
+    chim_dir = os.path.dirname(os.path.abspath(__file__))
 
     # Get the absolute of this file
     if parc_json is None:

config/supraregions_dictionary.json → chimera/config/supraregions_dictionary.json

@@ -423,6 +423,17 @@
                   "OutVolLocation":"freesurfer"}
       },
       "WhiteMatter": {
+      	    "F": {"atlas":"Aseg",
+                  "name":"Aseg",
+                  "description":"# 10. White matter parcellation (F): Aseg subcortical parcellation.",
+                  "citation":"(Fischl et al, 2002)",
+                  "source": "freesurfer",
+                  "reference":"conform",
+                  "parcels":"custom",
+                  "mask":"custom",
+                  "type":"custom",
+                  "deriv_volfold":"freesurfer"},
+
             "J": {"atlas":"Hua2008",
                   "name":"JHU",
                   "description":"# 10. Tract probability maps in stereotaxic spaces (J): White matter segmentation.",
@@ -433,5 +444,6 @@
                   "mask":"custom",
                   "type":"maxprob",
                   "OutVolLocation":"freesurfer"}
+
       }
-}
+}