From 535287a23248de10deb1f6da9bd3e009301266a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 14 Feb 2023 13:04:09 +0000
Subject: [PATCH] refactor/docs(utils): move and autodoc stretch_img
---
src/aliby/tile/traps.py | 15 ---------------
src/aliby/utils/imageViewer.py | 32 ++++++++++++++++++++++++++++++++
2 files changed, 32 insertions(+), 15 deletions(-)
diff --git a/src/aliby/tile/traps.py b/src/aliby/tile/traps.py
index 65b21b9c..49b07a9b 100644
--- a/src/aliby/tile/traps.py
+++ b/src/aliby/tile/traps.py
@@ -227,18 +227,3 @@ def identify_trap_locations(
exclude_border=(trap_size // 3),
)
return coordinates
-
-
-###############################################################
-# functions below here do not appear to be used any more
-###############################################################
-
-
-def stretch_image(image):
- # FIXME Used in aliby.utils.imageViewer
- image = ((image - image.min()) / (image.max() - image.min())) * 255
- minval = np.percentile(image, 2)
- maxval = np.percentile(image, 98)
- image = np.clip(image, minval, maxval)
- image = (image - minval) / (maxval - minval)
- return image
diff --git a/src/aliby/utils/imageViewer.py b/src/aliby/utils/imageViewer.py
index 67490812..af82ad96 100644
--- a/src/aliby/utils/imageViewer.py
+++ b/src/aliby/utils/imageViewer.py
@@ -405,3 +405,35 @@ def concat_pad(a: np.array, width, nrows):
axis=1,
)
)
+
+
+def stretch_image(image):
+ """
+ Performs contrast stretching on an input image.
+
+ This function takes an array-like input image and enhances its contrast by adjusting
+ the dynamic range of pixel values. It first scales the pixel values between 0 and 255,
+ then clips the values that are below the 2nd percentile or above the 98th percentile.
+ Finally, the pixel values are scaled to the range between 0 and 1.
+
+ Parameters
+ ----------
+ image : array-like
+ Input image.
+
+ Returns
+ -------
+ stretched : ndarray
+ Contrast-stretched version of the input image.
+
+ Examples
+ --------
+ FIXME: Add docs.
+ FIXME: GTP-generated. Confirm manually.
+ """
+ image = ((image - image.min()) / (image.max() - image.min())) * 255
+ minval = np.percentile(image, 2)
+ maxval = np.percentile(image, 98)
+ image = np.clip(image, minval, maxval)
+ image = (image - minval) / (maxval - minval)
+ return image
--
GitLab