# HG changeset patch # User imgteam # Date 1645888570 0 # Node ID 589af0005df558d182511a3f631a1c570e311982 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c" diff -r 000000000000 -r 589af0005df5 overlay_images.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/overlay_images.py Sat Feb 26 15:16:10 2022 +0000 @@ -0,0 +1,95 @@ +""" +Copyright 2022 Biomedical Computer Vision Group, Heidelberg University. + +Distributed under the MIT license. +See file LICENSE for detail or copy at https://opensource.org/licenses/MIT + +""" + +import argparse + +import matplotlib.pyplot as plt +import numpy as np +import skimage.color +import skimage.io +import skimage.measure +import tifffile + + +def read_im_gray(fn): + img = skimage.io.imread(fn) + nDims = len(img.shape) + assert nDims in [2, 3], 'this tool only supports single 2D images' + if nDims == 3 and img.shape[-1] in [3, 4]: + img = skimage.color.rgb2gray(img) + if len(img.shape) == 3: + return img[:, :, 0] + else: + return img + + +def coloc_vis(in_red_fn, in_green_fn, out_fn): + im1 = read_im_gray(in_red_fn) + im2 = read_im_gray(in_green_fn) + assert im1.shape == im2.shape, 'Two images should have the same dimension' + + vmin = np.min([np.min(im1), np.min(im2)]) + scal = 255.0 / (np.max([np.max(im1), np.max(im2)]) - vmin) + + out_im = np.zeros(im1.shape + (3,), dtype=np.ubyte) + out_im[:, :, 0] = (im1 - vmin) * scal + out_im[:, :, 1] = (im2 - vmin) * scal + skimage.io.imsave(out_fn, out_im) # output is RGB + + +def blending(im1_fn, im2_fn, out_fn, alpha=0.5): + im1 = skimage.io.imread(im1_fn) + im2 = skimage.io.imread(im2_fn) + assert im1.shape == im2.shape, 'Two images should have the same dimension' + out_im = (1 - alpha) * im1 + alpha * im2 + if len(im1.shape) > 3: + tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True) + else: + skimage.io.imsave(out_fn, out_im.astype(im1.dtype)) # format of output is the same as input + + +def seg_contour(im1_fn, im2_fn, out_fn, linewidth=0.3, color='#ff0000', show_label=False): + img = skimage.io.imread(im1_fn) + label = skimage.io.imread(im2_fn) + + fig = plt.figure() + ax = fig.add_axes([0, 0, 1, 1]) + ax.axis('off') + if show_label: + for reg in skimage.measure.regionprops(label): + ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=color) + + if len(img.shape) == 2: + plt.imshow(img, cmap=plt.cm.gray) + else: + plt.imshow(img) + plt.contour(label, linewidths=linewidth, colors=color) + fig.canvas.print_png(out_fn) # output is RGB + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Overlay two images") + parser.add_argument("im1", help="The first image") + parser.add_argument("im2", help="The second image") + parser.add_argument("out", help="Output image") + parser.add_argument('--method', dest='method', default='coloc_vis', help='How to overlay images') + parser.add_argument('--alpha', dest='alpha', default=0.5, type=float, help='Blending weight') + parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='Contour thickness') + parser.add_argument('--color', dest='color', default='#FFFF00', help='Contour color') + parser.add_argument('--show_label', dest='show_label', action='store_true', help='Plot label') + args = parser.parse_args() + + if args.method == 'coloc_vis': + coloc_vis(args.im1, args.im2, args.out) + elif args.method == 'blending': + blending(args.im1, args.im2, args.out, alpha=args.alpha) + elif args.method == 'seg_contour': + seg_contour(args.im1, args.im2, args.out, + linewidth=args.thickness, + color=args.color, + show_label=args.show_label) diff -r 000000000000 -r 589af0005df5 overlay_images.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/overlay_images.xml Sat Feb 26 15:16:10 2022 +0000 @@ -0,0 +1,88 @@ + + for visualization + + scikit-image + matplotlib + tifffile + numpy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** + + This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. + + + + diff -r 000000000000 -r 589af0005df5 test-data/mask1.tif Binary file test-data/mask1.tif has changed diff -r 000000000000 -r 589af0005df5 test-data/mask1r.tif Binary file test-data/mask1r.tif has changed diff -r 000000000000 -r 589af0005df5 test-data/sample1.tif Binary file test-data/sample1.tif has changed diff -r 000000000000 -r 589af0005df5 test-data/test1.tif Binary file test-data/test1.tif has changed diff -r 000000000000 -r 589af0005df5 test-data/test2.tif Binary file test-data/test2.tif has changed diff -r 000000000000 -r 589af0005df5 test-data/test3.tif Binary file test-data/test3.tif has changed