From a9d87bf2ddb8c2e1ab58328b66e3ad8860b1fb5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Thu, 10 Feb 2022 11:34:11 +0000
Subject: [PATCH] add docs and limit all automatic function fetching
---
extraction/core/functions/loaders.py | 34 +++++++++++++++++++++++++---
1 file changed, 31 insertions(+), 3 deletions(-)
diff --git a/extraction/core/functions/loaders.py b/extraction/core/functions/loaders.py
index 9041b25a..7dc331de 100644
--- a/extraction/core/functions/loaders.py
+++ b/extraction/core/functions/loaders.py
@@ -17,9 +17,14 @@ def load_cellfuns_core():
def load_custom_args():
"""
- Load custom functions. If they have extra arguments also load these
+ Load custom functions. If they have extra arguments (starting at index 2,
+ after mask and image) also load these.
"""
- funs = {f[0]: f[1] for f in getmembers(localisation) if isfunction(f[1])}
+ funs = {
+ f[0]: f[1]
+ for f in getmembers(localisation)
+ if isfunction(f[1]) and f[1].__module__.startswith("extraction.core.functions")
+ }
args = {
k: getargspec(v).args[2:]
for k, v in funs.items()
@@ -30,6 +35,12 @@ def load_custom_args():
def load_cellfuns():
+ """
+ Input:
+
+ Returns:
+ Dict(str, function)
+ """
# Generate str -> trap_function dict from core.cell and core.trap functions
cell_funs = load_cellfuns_core()
CELLFUNS = {}
@@ -44,11 +55,22 @@ def load_cellfuns():
def load_trapfuns():
- TRAPFUNS = {f[0]: f[1] for f in getmembers(trap) if isfunction(f[1])}
+ """
+ Load functions that are applied to an entire trap (or tile, or subsection of a given image),
+ instead of being applied to single cells.
+ """
+ TRAPFUNS = {
+ f[0]: f[1]
+ for f in getmembers(trap)
+ if isfunction(f[1]) and f[1].__module__.startswith("extraction.core.functions")
+ }
return TRAPFUNS
def load_funs():
+ """
+ Combine all automatically-loaded functions
+ """
CELLFUNS = load_cellfuns()
TRAPFUNS = load_trapfuns()
@@ -56,6 +78,9 @@ def load_funs():
def load_redfuns(): # TODO make defining reduction functions more flexible
+ """
+ Load z-stack reduction functions.
+ """
RED_FUNS = {
"np_max": np.maximum,
"np_mean": np.mean,
@@ -66,5 +91,8 @@ def load_redfuns(): # TODO make defining reduction functions more flexible
def load_mergefuns():
+ """
+ Load functions to merge multiple channels
+ """
MERGE_FUNS = {"div0": div0, "np_add": np.add}
return MERGE_FUNS
--
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