registration routines

droplet_growth/register.py

+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

requirements.txt

@@ -12,3 +12,4 @@ seaborn
 statannot
 jupyterlab
 czifile
+imreg-dft

setup.py

@@ -22,7 +22,8 @@ setup(
         "pandas",
         "seaborn",
         "statannot",
-        "click"
+        "click",
+        "imreg-dft"
     ],
     python_requires=">=3.8",
     packages=find_packages(),