nuclei_area = 0.0 mitosis_area = 0.0 num = 0 for img in images: cntr = Controller(img) if normalized: img, _, __, __ = macenko(cntr) plt.imsave('data/imagemap' + str(num) + ".png", img) num += 1 print ("making nuclei map") nimg, nuclei_map = nuclei_detect_pipeline(img) print ('created') print('synthesizing image through reflection') img2 = np.append(img, np.append(img, img, axis = 0), axis = 0) img3 = np.append(img2, np.append(img2, img2, axis = 1), axis = 1) print('synthesized -- ', img3.shape) def get_patches(coords, patchsize=PATCH_SIZE): patches = np.zeros((len(coords), patchsize, patchsize, 3)) i = 0 for (x, y) in coords: x += SIZE y += SIZE #print x, y #print (x - patchsize/2), (x + patchsize/2 + 1), (y - patchsize/2), (y + patchsize/2 + 1)
#generate ICPR heatmap files import numpy as np import matplotlib import matplotlib.pyplot as plt import glob, sys, os, csv import scipy.io, scipy.misc from nuclei_detect import nuclei_detect_pipeline for image_file, csv_file in zip(sorted(glob.glob("icpr/train/*.bmp")), sorted(glob.glob("icpr/train/*.csv"))): print (image_file, csv_file) img = scipy.misc.imread(image_file) hmap = nuclei_detect_pipeline(img) print (hmap) scipy.misc.imsave(image_file[:-4] + "_image.jpg", img) scipy.misc.imsave(image_file[:-4] + "_heatmap.jpg", hmap)