From 12efb9d59429496c9a23ed487a0ce616036142e0 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Fri, 14 Jan 2022 16:29:45 +0100
Subject: [PATCH] remove filtering
---
droplet_growth/register.py | 75 ++++++++++++++++++++++----------------
1 file changed, 44 insertions(+), 31 deletions(-)
diff --git a/droplet_growth/register.py b/droplet_growth/register.py
index a02f6d6..a064b6d 100644
--- a/droplet_growth/register.py
+++ b/droplet_growth/register.py
@@ -5,6 +5,7 @@ import numpy as np
import scipy.ndimage as ndi
from droplet_growth import mic
from nd2tif.transform import to_8bits
+import os
grey = np.array([np.arange(256)] * 3, dtype='uint8')
red = np.array([np.arange(256), np.zeros((256,)), np.zeros((256,))], dtype='uint8')
@@ -24,7 +25,7 @@ META_ALIGNED = {'ImageJ': '1.53c',
'LUTs': [grey, green, blue]
}
-def align_stack(path, template16, mask2, plot=False, binnings=(1,16,2), suffix='.aligned.tif'):
+def align_stack(data_or_path, template16, mask2, plot=False, path=None, 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).
@@ -32,22 +33,29 @@ def align_stack(path, template16, mask2, plot=False, binnings=(1,16,2), suffix='
The output stack is of the same size as mask.
The resulting 3-layer stack will be returned and also saved with suffix ".aligned.tif"
'''
-
- stack = imread(path)
- print(path, stack.shape)
+ if isinstance(data_or_path, str):
+ path = data_or_path
+ stack = imread(path)
+ print(path, stack.shape)
+ else:
+ assert data_or_path.ndim == 3 and data_or_path.shape[0] == 2
+ assert path is not None
+ stack = data_or_path
bf, tritc = stack[:2]
stack_temp_scale = binnings[1] // binnings[0]
mask_temp_scale = binnings[1] // binnings[2]
stack_mask_scale = binnings[2] // binnings[0]
- f_bf = filter_by_fft(
- bf[::stack_temp_scale, ::stack_temp_scale],
- sigma=40,
- fix_horizontal_stripes=True,
- fix_vertical_stripes=True,
- highpass=True
- )
+ f_bf = bf[::stack_temp_scale, ::stack_temp_scale]
+
+ # f_bf = filter_by_fft(
+ # bf[::stack_temp_scale, ::stack_temp_scale],
+ # sigma=40,
+ # fix_horizontal_stripes=True,
+ # fix_vertical_stripes=True,
+ # highpass=True
+ # )
tvec8 = get_transform(f_bf, template16, plot=plot)
plt.show()
tvec = scale_tvec(tvec8, mask_temp_scale)
@@ -74,12 +82,12 @@ def align_stack(path, template16, mask2, plot=False, binnings=(1,16,2), suffix='
aligned_stack = np.stack((aligned_bf, aligned_tritc, mask2)).astype('uint16')
- imwrite((p:=path.replace('.tif', suffix)), aligned_stack, imagej=True, metadata=META_ALIGNED)
+ imwrite((p:="".join((*path.split('.')[:-1] , suffix))), aligned_stack, imagej=True, metadata=META_ALIGNED)
print(f'Saved aligned stack {p}')
return aligned_stack
-def align_stack_nd(stack, template16, mask2, plot=False, binnings=(1,16,2), suffix='.aligned.tif'):
+def align_stack_nd(stack, template16, mask2, path=None, plot=False, binnings=(1,16,2), suffix='.aligned.tif') -> (np.ndarray, dict):
'''
stack should contain two channels: bright field and fluorescence.
BF will be binned 8 times and registered with template8 (aligned BF).
@@ -92,19 +100,21 @@ def align_stack_nd(stack, template16, mask2, plot=False, binnings=(1,16,2), suff
bf, tritc = stack[:2]
- print('inputs: \n', *[f'{name}: {im.shape}, {bin}\n' for name, im, bin in zip(['bf', 'tmp', 'mask'], [bf, template16, mask2], binnings )])
+ print(f'Aligning {path}: \n', *[f'{name}: {im.shape}, {bin}\n' for name, im, bin in zip(['bf', 'tmp', 'mask'], [bf, template16, mask2], binnings )])
stack_temp_scale = binnings[1] // binnings[0]
mask_temp_scale = binnings[1] // binnings[2]
stack_mask_scale = binnings[2] // binnings[0]
- f_bf = filter_by_fft(
- bf[::stack_temp_scale, ::stack_temp_scale],
- sigma=40,
- fix_horizontal_stripes=True,
- fix_vertical_stripes=True,
- highpass=True
- )
+ f_bf = bf[::stack_temp_scale, ::stack_temp_scale]
+
+ #filter_by_fft(
+ # bf[::stack_temp_scale, ::stack_temp_scale],
+ # sigma=40,
+ # fix_horizontal_stripes=True,
+ # fix_vertical_stripes=True,
+ # highpass=True
+ # )
tvec8 = get_transform(f_bf, template16, plot=plot)
plt.show()
tvec = scale_tvec(tvec8, mask_temp_scale)
@@ -131,8 +141,9 @@ def align_stack_nd(stack, template16, mask2, plot=False, binnings=(1,16,2), suff
aligned_stack = np.stack((aligned_bf, aligned_tritc, mask2)).astype('uint16')
- # imwrite((p:=path.replace('.tif', suffix)), aligned_stack, imagej=True, metadata=META_ALIGNED)
- # print(f'Saved aligned stack {p}')
+ if path is not None:
+ imwrite((p:="".join((*path.split('.')[:-1] , suffix))), aligned_stack, imagej=True, metadata=META_ALIGNED)
+ print(f'Saved aligned stack {p}')
return aligned_stack, tvec
@@ -142,20 +153,22 @@ def align_timelapse(bf, fluo_stack, template16, mask2, plot=False, binnings=(4,1
BF will be binned 8 times and registered with template8 (aligned BF).
When the transformation verctor will be applied to the original data and stacked with the mask.
The output stack is of the same size as mask.
- The resulting 3-layer stack will be returned and also saved with suffix ".aligned.tif"
+ Return:
+ (aligned_bf, aligned_fluo, mask)
'''
stack_temp_scale = binnings[1] // binnings[0]
mask_temp_scale = binnings[1] // binnings[2]
mask_bf_scale = binnings[0] // binnings[2]
- f_bf = filter_by_fft(
- bf[::stack_temp_scale, ::stack_temp_scale],
- sigma=40,
- fix_horizontal_stripes=True,
- fix_vertical_stripes=True,
- highpass=True
- )
+ f_bf = bf[::stack_temp_scale, ::stack_temp_scale]
+ # f_bf = filter_by_fft(
+ # bf[::stack_temp_scale, ::stack_temp_scale],
+ # sigma=40,
+ # fix_horizontal_stripes=True,
+ # fix_vertical_stripes=True,
+ # highpass=True
+ # )
tvec8 = get_transform(f_bf, template16, plot=plot)
plt.show()
tvec = scale_tvec(tvec8, stack_temp_scale)
--
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