diff overlay_images.py @ 0:589af0005df5 draft

"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"

--- /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)