From 742fb2244e4ca0f7bce4ca52fe80102d190b73ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 15 Mar 2023 07:44:47 +0000
Subject: [PATCH] change(plot): remove and import stretch_image
---
src/aliby/utils/imageViewer.py | 33 +--------------------------------
1 file changed, 1 insertion(+), 32 deletions(-)
diff --git a/src/aliby/utils/imageViewer.py b/src/aliby/utils/imageViewer.py
index 7e723aba..044fef6a 100644
--- a/src/aliby/utils/imageViewer.py
+++ b/src/aliby/utils/imageViewer.py
@@ -30,6 +30,7 @@ from agora.io.cells import Cells
from agora.io.writer import load_attributes
from aliby.io.image import dispatch_image
from aliby.tile.tiler import Tiler, TilerParameters
+from aliby.utils.plot import stretch_image
default_colours = {
"Brightfield": "Greys_r",
@@ -443,35 +444,3 @@ 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
--
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