diff --git a/__notations__.txt b/__notations__.txt new file mode 100644 index 0000000000000000000000000000000000000000..040f77271c75f3031406f29a63ec410e08e13bca --- /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 66db159d454364dfc89bc56ab55dd176859e8153..7f0eb85fbd5575480a307e59239f5aa27a309445 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 740f5d07b36235660b837360f64d53b7e0c368ea..ab971eb828073cb99dfbcc774e30c6ba35f7c183 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 50a2b3179bf1dc451f1cd9a32069929cec82389e..798b991fd753aafee3e4f3fff58cf272ee6c408d 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 39459bedca907a0bb421e6c6e5fa32966c78135a..d37492d3be2a3eb3fc8fe9320cd9ec00e3ec8aaa 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 7bad96613bed7fd3d5aaac4ba975a6ed274099e9..52e9d842d30e31d1b04ca1d6dacf2c009441cd71 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]