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)