From a58f3f33f945e6e962b8fb9066bee733de47e396 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Mon, 9 Nov 2020 16:04:17 +0100
Subject: [PATCH] registration routines
---
droplet_growth/register.py | 43 ++++++++++++++++++++++++++++++++++++++
requirements.txt | 1 +
setup.py | 3 ++-
3 files changed, 46 insertions(+), 1 deletion(-)
create mode 100644 droplet_growth/register.py
diff --git a/droplet_growth/register.py b/droplet_growth/register.py
new file mode 100644
index 0000000..b336e56
--- /dev/null
+++ b/droplet_growth/register.py
@@ -0,0 +1,43 @@
+from tifffile import imread, imwrite
+import matplotlib.pyplot as plt
+import imreg_dft as reg
+import numpy as np
+import scipy.ndimage as ndi
+
+
+def calculate_padding(image, template):
+ shi = np.array(image.shape)
+ sht = np.array(template.shape)
+ dif = shi - sht
+ mid = dif // 2
+ rest = dif - mid
+ return (tuple((mid[0], rest[0])), tuple((mid[1],rest[1])))
+
+
+def pad_template(image, template, padding=None):
+ if padding is None:
+ padding = calculate_padding(image, template)
+ padded_template = np.pad(template, padding, 'median')
+ return padded_template
+
+
+def unpad_image(image, template=None, padding=None):
+ if padding is None:
+ padding = calculate_padding(image, template)
+ return image[padding[0][0]:-padding[0][1], padding[1][0]:-padding[1][1]]
+
+
+def scale_tvec(tvec, scale=8):
+ tvec_8x = tvec.copy()
+ tvec_8x['tvec'] = tvec['tvec'] * scale
+ try:
+ tvec_8x['timg'] = None
+ except KeyError:
+ pass
+ finally:
+ return tvec_8x
+
+
+def transform(image, tvec):
+ fluo = reg.transform_img_dict(image, tvec)
+ return fluo.astype('uint')
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 787d9f8..c5eac49 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,3 +12,4 @@ seaborn
statannot
jupyterlab
czifile
+imreg-dft
diff --git a/setup.py b/setup.py
index 6506773..58ce40c 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,8 @@ setup(
"pandas",
"seaborn",
"statannot",
- "click"
+ "click",
+ "imreg-dft"
],
python_requires=">=3.8",
packages=find_packages(),
--
GitLab