Creating previews of dm3 files with Opencv v0

Author: Gabriel Ing

Image-previews_Opencv.py

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+import cv2 as cv
+import ncempy.io as nci
+import os
+import matplotlib.pyplot as plt
+import numpy as np 
+
+
+print('Dependancies imported')
+
+def Generate_preview_dm3(dm3_file, color='', textoff=False):
+    #make a folder called previews to save the folder 
+    foldername = 'previews'
+    if foldername not in os.listdir('.'):
+        os.mkdir(foldername)
+    
+    #read the dm3 fille with ncempy 
+    dm3_input = nci.dm.dmReader(dm3_file)
+    #extract image from ncempy read 
+    image = dm3_input['data']
+    
+    #extract x and y shapes
+    x = image.shape[1]
+    y = image.shape[0]
+
+    
+    #make coordinates for the scalebar, currently set to y-12.5%,x-5% of image size from the bottom right corner 
+    #of the image to bottom left of the scalebar - change this by editing /20 and /7.5 values (this just looked good to me)
+    
+    scalebar_y = y-int(image.shape[0]/20)
+    scalebar_x = x-int(image.shape[1]/7.5)
+    
+
+    #Save pixel size 
+    pixelSize=dm3_input['pixelSize'][0]
+    
+    #possible scalebar sizes are given here, if its >500nm it should be in unit micron, hopefully this should only fail with very extreme examples
+    possible_sizes = [1,2,5,10,25,50,100,250,500]
+    
+
+    #to select sizes, iterate through possible sizes, if the width of the resulting scalebar (n*pixelsize) 
+    #is over 15% of the image size, the size is chose, if none are over 15% of image size
+    #the largest size is chosen as default
+    
+    for n in possible_sizes:
+        width = n*pixelSize
+        #print(n, image.shape([0]/10)
+        if width>(x/15):
+            break
+    #print(n)
+    
+    #choose height of scalebar (default is scalebar width/6), convert width into an integer
+    height = int(y/60)
+    width = int(width)
+    
+    #apply median filter and gaussian blur
+    img_median = cv.medianBlur(image,5)
+    img_gauss = cv.GaussianBlur(img_median, (3,3),0)
+    
+    #Scale image between 0-255 (turn it into an 8bit greyscale image)
+    
+    new_arr = ((img_median - img_median.min()) * (1/(img_median.max() - img_median.min()) * 255)).astype('uint8')
+   
+    #these commands can increase contrast, by default the contrast is stretched to limits in previous line though
+    #new_image = cv.convertScaleAbs(img_gauss, alpha=alpha, beta=beta)
+    #new_image = cv.equalizeHist(new_arr)
+
+    #choose color - this can be given as black, white or grey in the function
+    if color=='black':
+        pixvalue = 0
+        textcolor = (0,0,0)
+    elif color=='white':
+        pixvalue = 255
+        textcolor=(255,255,255)
+    elif color=='grey':
+        pixvalue = 150
+        textcolor=(150,150,150)
+    else: #default is black, unless it is a particularly dark area - if the mean pixvalue of the scale bar region is significantly less than the overall image mean, the scalebar will be white
+        
+        if np.mean(new_arr[scalebar_y:scalebar_y+height,scalebar_x:scalebar_x+width])<np.mean(new_arr)/1.5:
+            pixvalue = 255
+            textcolor=(255,255,255)
+        else:
+            pixvalue = 0
+            textcolor = (0,0,0)
+    #add scalebar (set pixels to color)
+    
+    new_arr[scalebar_y:scalebar_y+height,scalebar_x:scalebar_x+width]=pixvalue
+    
+    #add label 
+    if textoff==False:
+        font= cv.FONT_HERSHEY_DUPLEX #can change to any opencv fonts, they're all quite rubbish 
+        fontsize = image.shape[0]/1200 #this fontsize looks good to me
+        text = '{}{}'.format(n,dm3_input['pixelUnit'][0]) 
+        cv.putText(new_arr, text, (scalebar_x+3,scalebar_y-int(height*3/5)),font,fontsize, color=textcolor, thickness=int(fontsize*2.5))#can change thickness, color and position here 
+
+
+    
+
+    
+    #Bin image to reduce filesize, comment out if you want full image size
+    new_arr = cv.resize(new_arr, (int(new_arr.shape[0]/2), int(new_arr.shape[1]/2)), interpolation=cv.INTER_CUBIC) 
+    #if you want to see it as it runs, can plot images heere
+    #plt.gray()
+    #plt.figure(figsize=(20,20))
+    #plt.imshow(new_arr)
+    #plt.show()
+    
+    #create filename(and path)
+    newname = foldername+'/'+dm3_file.strip('.dm3')+'{}{}'.format(n,dm3_input['pixelUnit'][0])+'scale.jpg'
+    status = cv.imwrite(newname, new_arr,[int(cv.IMWRITE_JPEG_QUALITY), 70])
+    print(newname, 'saved?: ',status)
+
+#collect the dm3 files in the folder and make a preview for them all 
+
+dm3_files = [x for x in os.listdir('.') if x[-3:]=='dm3']
+for file in dm3_files:
+    Generate_preview_dm3(file)
+