From 249c17f45dcf05372eccf86ddca39f451ef3eb61 Mon Sep 17 00:00:00 2001
From: DEBREUVE Eric <eric.debreuve@inria.fr>
Date: Tue, 1 Oct 2019 14:15:27 +0200
Subject: [PATCH] added notation file
---
__notations__.txt | 13 +++++++++++++
extension.py | 7 +------
glial_cmp.py | 2 ++
main.py | 4 ++--
soma.py | 4 ----
type.py | 2 +-
6 files changed, 19 insertions(+), 13 deletions(-)
create mode 100644 __notations__.txt
diff --git a/__notations__.txt b/__notations__.txt
new file mode 100644
index 0000000..040f772
--- /dev/null
+++ b/__notations__.txt
@@ -0,0 +1,13 @@
+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
diff --git a/extension.py b/extension.py
index 66db159..7f0eb85 100644
--- a/extension.py
+++ b/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__")
diff --git a/glial_cmp.py b/glial_cmp.py
index 740f5d0..ab971eb 100644
--- a/glial_cmp.py
+++ b/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")
diff --git a/main.py b/main.py
index 50a2b31..798b991 100644
--- a/main.py
+++ b/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
diff --git a/soma.py b/soma.py
index 39459be..d37492d 100644
--- a/soma.py
+++ b/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",)
diff --git a/type.py b/type.py
index 7bad966..52e9d84 100644
--- a/type.py
+++ b/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]
--
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