app.py

import math
import cv2
import numpy as np
from matplotlib import pyplot as plt
from scipy import ndimage
from skimage import measure, color, io
from tensorflow.keras.preprocessing import image
from scipy import ndimage

#Function that predicts on only 1 sample 
def predict_sample(image):
  prediction = model.predict(image[tf.newaxis, ...])
  prediction[prediction > 0.5 ] = 1
  prediction[prediction !=1] = 0
  result = prediction[0]*255
  return result




def create_input_image(data, visualize=False):
  #Initialize input matrix
  input = np.ones((256,256))

  #Fill matrix with data point values
  for i in range(0,len(data)):
    if math.floor(data[i][0]) < 256 and math.floor(data[i][1]) < 256:
      input[math.floor(data[i][0])][math.floor(data[i][1])] = 0
    elif math.floor(data[i][0]) >= 256:
      input[255][math.floor(data[i][1])] = 0
    elif math.floor(data[i][1]) >= 256:
      input[math.floor(data[i][0])][255] = 0
  
  #Visualize
  if visualize == True:
    plt.imshow(input.T, cmap='gray')
    plt.gca().invert_yaxis()

  return input




def get_instances(prediction, data, max_filter_size=1):
  #Adjust format (clusters to be 255 and rest is 0)
  prediction[prediction == 255] = 3
  prediction[prediction == 0] = 4
  prediction[prediction == 3] = 0
  prediction[prediction == 4] = 255

  #Convert to 8-bit image
  prediction = image.img_to_array(prediction, dtype='uint8')
  
  #Get 1 color channel
  cells=prediction[:,:,0]
  #Threshold
  ret1, thresh = cv2.threshold(cells, 0, 255, cv2.THRESH_BINARY)
  #Filter to remove noise
  kernel = np.ones((3,3),np.uint8)
  opening = cv2.morphologyEx(thresh,cv2.MORPH_OPEN,kernel, iterations = 2)

  #Get the background
  background = cv2.dilate(opening,kernel,iterations=5)
  dist_transform = cv2.distanceTransform(opening,cv2.DIST_L2,5)
  ret2, foreground = cv2.threshold(dist_transform,0.04*dist_transform.max(),255,0)
  foreground = np.uint8(foreground)
  unknown = cv2.subtract(background,foreground)

  #Connected Component Analysis
  ret3, markers = cv2.connectedComponents(foreground)
  markers = markers+10
  markers[unknown==255] = 0

  #Watershed
  img = cv2.merge((prediction,prediction,prediction))
  markers = cv2.watershed(img,markers)
  img[markers == -1] = [0,255,255]  

  #Maximum filtering
  markers = ndimage.maximum_filter(markers, size=max_filter_size)
  # plt.imshow(markers.T, cmap='gray')
  # plt.gca().invert_yaxis()

  #Get an RGB colored image
  img2 = color.label2rgb(markers, bg_label=1)
  # plt.imshow(img2)
  # plt.gca().invert_yaxis()

  #Get regions
  regions = measure.regionprops(markers, intensity_image=cells)

  #Get Cluster IDs
  cluster_ids = np.zeros(len(data))

  for i in range(0,len(cluster_ids)):
    row = math.floor(data[i][0])
    column = math.floor(data[i][1])
    if row < 256 and column < 256:
      cluster_ids[i] = markers[row][column] - 10
    elif row >= 256:
      # cluster_ids[i] = markers[255][column]
      cluster_ids[i] = 0
    elif column >= 256:
      # cluster_ids[i] = markers[row][255] 
      cluster_ids[i] = 0

  cluster_ids = cluster_ids.astype('int8')
  cluster_ids[cluster_ids == -11] = 0
    
  return cluster_ids