added notation file

__notations__.txt

+som=soma
+ext=extension
+
+map=binary, int8 or uint8 array (/!\ python keyword; map_ used instead)
+bmp=boolean map
+lmp=labeled map (intXX or uintXX array)
+
+ep=extension end point, or extremity (e.g. ep_bmp)
+
+n=number of (e.g. n_somas)
+nfo=info (e.g. som_nfo)
+
+tintegers=tuple of integers

extension.py

@@ -19,12 +19,7 @@ min_area_c = 100
 
 class extension_t(glial_cmp_t):
     #
-    # bmp=boolean map
-    # lmp=labeled map (intXX or uintXX array)
-    # map=extension map (map=binary, int8 or uint8 array))
-    # ep_=end point
-    # soma_uid: connected to a soma somewhere upstream (as opposed to downstream extensions)
-    # extensions: downstream (as opposed to being upstreamed connected)
+    # soma_uid: connected to a soma somewhere upstream
     #
     __slots__ = ("scales", "end_points", "soma_uid", "__cache__")
 

glial_cmp.py

@@ -8,6 +8,8 @@ import numpy as np_
 
 
 class glial_cmp_t:
+    #
+    # extensions: connected downstream (i.e. going away from the soma)
     #
     __slots__ = ("uid", "sites", "connection_path", "extensions", "img_shape")
 

main.py

@@ -32,8 +32,8 @@ costs = 1.0 / (image + 1.0)
 
 
 # --- Initialization
-som_nfo = {}  # som=soma, nfo=info
-ext_nfo = {}  # ext=extension, nfo=info
+som_nfo = {}
+ext_nfo = {}
 axes = {}
 
 # n_somas = 0

soma.py

@@ -19,10 +19,6 @@ som_ext_path_t = namedtuple_t("som_ext_path_t", "extension length path idx")
 
 
 class soma_t(glial_cmp_t):
-    #
-    # bmp=boolean map
-    # lmp=labeled map (intXX or uintXX array)
-    # map=extension map (map=binary, int8 or uint8 array))
     #
     __slots__ = ("contour_points",)
 

type.py

@@ -5,7 +5,7 @@ import numpy as np_
 
 array_t = np_.ndarray
 
-tintegers_h = Tuple[int, ...] # tintegers=tuple of integers
+tintegers_h = Tuple[int, ...]
 
 number_h = Union[int, float]