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Author: cesco345

ch3/contours.py

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+from PIL import Image
+from pylab import *
+import matplotlib.pyplot as plt
+
+
+im = array(Image.open('newport.png').convert('L'))
+im2 = array(Image.open('newport.png'))
+
+plt.figure(figsize=(10, 3.6))
+
+plt.subplot(131)
+plt.imshow(im2, cmap=plt.cm.gray)
+plt.title('Original', fontsize=12)
+plt.axis('off')
+
+plt.subplot(132)
+plt.imshow(im, cmap=plt.cm.gray, vmin=0, vmax=255)
+plt.title('Low Contrast', fontsize=12)
+plt.axis('off')
+
+plt.subplot(133)
+plt.imshow(im, cmap=plt.cm.gray, vmin=100, vmax=200)
+plt.title('High Contrast', fontsize=12)
+plt.axis('off')
+
+plt.subplots_adjust(wspace=0, hspace=0., top=0.99, bottom=0.01, left=0.05,
+                    right=0.99)
+
+figure('Contours')
+
+gray()
+contour(im, origin='image')
+axis('equal')
+axis('off')
+show()
+

ch3/cv2_display.py

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+#!/usr/bin/env python 
+
+import cv2 
+
+original = cv2.imread('home_tree.png') 
+
+gray = cv2.imread('home_tree.png', 0) 
+
+cv2.imshow('Original', original) 
+cv2.imshow('Gray', gray) 
+
+cv2.waitKey(0) 
+cv2.destroyAllWindows() 

ch3/gaussian_filter.py

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+import sys
+from PIL import Image
+import scipy
+from scipy.ndimage import gaussian_filter, label
+from pylab import *
+
+
+
+image = Image.open(sys.argv[1]).convert('L')
+img = np.array(image)
+
+im_g = gaussian_filter(img, 3)
+im_norm = (im_g - im_g.min()) / (float(im_g.max()) - im_g.min())
+im_norm[im_norm < 0.5] = 0
+im_norm[im_norm >= 0.5] = 1
+
+out = 255 - (im_norm * 255).astype(np.uint8)
+print u"\n\n**********  Cells Counted: %d  **********\n\n" % label(out)[1]
+
+print out
+
+figure()
+gray()
+imshow(out)
+
+
+show()

ch3/hough.py

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+import cv2
+import cv2.cv as cv
+import numpy as np
+
+
+
+img = cv2.imread('yeast2.png',0)
+
+cimg = cv2.cvtColor(img,cv2.COLOR_GRAY2BGR)
+
+circles = cv2.HoughCircles(img,cv.CV_HOUGH_GRADIENT,1,67,
+                            param1=5,param2=1,minRadius=4,maxRadius=20)
+
+circles = np.uint16(np.around(circles))
+ret2,th2 = cv2.threshold(img,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
+for i in circles[0,:]:
+    cv2.circle(cimg,(i[0],i[1]),i[2],(0,255,0),2)
+
+#cv2.imshow('Detected cells',cimg)
+cv2.imshow('detected circles',th2)
+cv2.waitKey(0)
+cv2.destroyAllWindows()

ch3/hough2.py

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+import cv2
+import cv2.cv as cv
+import numpy as np
+
+
+
+img = cv2.imread('yeast2.png',0)
+
+c_img = cv2.cvtColor(img,cv2.COLOR_GRAY2BGR)
+
+circles = cv2.HoughCircles(img,cv.CV_HOUGH_GRADIENT,1,67,
+                            param1=5,param2=1,minRadius=4,maxRadius=20)
+
+circles = np.uint16(np.around(circles))
+
+for i in circles[0,:]:
+    cv2.circle(c_img,(i[0],i[1]),i[2],(0,0,0),2)
+
+cv2.imshow('Detected Cells',c_img)
+cv2.waitKey(0)
+cv2.destroyAllWindows()

ch3/matplot_pil.py

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+#!/usr/bin/env python 
+
+import cv2
+from matplotlib import pyplot as plt 
+import matplotlib.image as mpimg 
+
+original = mpimg.imread('home_tree.png') 
+gray = cv2.imread('home_tree.png',0) 
+
+plt.subplot(131),plt.imshow(gray, cmap = 'gray'),plt.title('Grayscale Image')
+plt.xticks([]), plt.yticks([]) 
+
+plt.subplot(133),plt.imshow(original, cmap='gray'),plt.title('Original Image')
+plt.xticks([]), plt.yticks([])
+
+plt.show()

ch3/numpy_array.py

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+import numpy as np
+import cv2
+
+
+
+img = np.zeros((500,500), dtype=np.float)
+img[0:500, 0:500] = 1
+
+cv2.imshow('image',img)
+
+cv2.waitKey(0)
+cv2.destroyAllWindows()

ch3/numpy_mask.py

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+import numpy as np
+import cv2
+
+
+
+img = np.zeros((500,500), dtype=np.float)
+img[150:350, 150:350] = 1
+
+cv2.imshow('image',img)
+
+cv2.waitKey(0)
+cv2.destroyAllWindows()

ch3/numpy_mask2.py

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+import numpy as np
+import cv2
+from matplotlib import pyplot as plt
+
+
+img2 = np.zeros((500,500), np.int8)
+random = np.random.rand(500, 500)
+
+plt.subplot(131),plt.imshow(img2,'gray'),plt.title('Mask-0')
+plt.xticks([]),plt.yticks([])
+
+plt.subplot(133),plt.imshow(random,'gray'),plt.title('Random')
+plt.xticks([]),plt.yticks([])
+
+plt.show()

ch3/otsu2.py

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+import cv2
+
+img = cv2.imread('yeast2.png',0)
+
+ret2,th2 = cv2.threshold(img,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
+
+cv2.imshow('Detected Cells',th2)
+cv2.waitKey(0)
+cv2.destroyAllWindows()