From 109ae09c646739833dca4ca99a625e0308a0f507 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Wed, 5 Apr 2023 15:16:04 +0200
Subject: [PATCH] tighten constraints
---
src/droplet_growth/register.py | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/src/droplet_growth/register.py b/src/droplet_growth/register.py
index 0203af9..e7096cd 100644
--- a/src/droplet_growth/register.py
+++ b/src/droplet_growth/register.py
@@ -25,6 +25,13 @@ META_ALIGNED = {'ImageJ': '1.53c',
'LUTs': [grey, green, blue]
}
+constraints={
+ "scale": [1, 0.1],
+ "tx": [0, 150],
+ "ty": [0, 150],
+ "angle": [0, 10],
+}
+
def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None, binnings=(1,16,2), suffix='.aligned.tif'):
'''
stack should contain two channels: bright field and fluorescence.
@@ -94,7 +101,7 @@ def align_stack(data_or_path, template16, mask2, plot=False, path_to_save=None,
return aligned_stack, tvec
-def align_stack_nd(stack, template16, mask2, path=None, plot=False, binnings=(1,16,2), suffix='.aligned.tif') -> tuple(np.ndarray, dict):
+def align_stack_nd(stack, template16, mask2, path=None, plot=False, binnings=(1,16,2), suffix='.aligned.tif'):
'''
stack should contain two channels: bright field and fluorescence.
BF will be binned 8 times and registered with template8 (aligned BF).
@@ -279,7 +286,7 @@ def register(image, template):
'''
assert np.array_equal(image.shape, template.shape), \
f'unequal shapes {(image.shape, template.shape)}'
- return reg.similarity(template, image, constraints={'scale': [1,0.2], 'tx': [0, 500], 'ty': [0, 500], 'angle': [0, 30]})
+ return reg.similarity(template, image, constraints=constraints)
def filter_by_fft(
--
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