Added arguments parsing, tested with range of images, fixed bugs with micron symbol by using pillow to add text, corrected scalebar length

Author: Gabriel Ing

Image-previews_Opencv.py

@@ -3,11 +3,22 @@
 import os
 import matplotlib.pyplot as plt
 import numpy as np 
+from PIL import Image, ImageOps, ImageFont, ImageDraw, ImageFilter
+import time 
+import argparse
+
+parser = argparse.ArgumentParser(description='add additional arguments here')
+parser.add_argument('--file', help='if you only want one file processed, add this argment followed by the file')
+parser.add_argument('--color', help='If you want to specify the color of the scalebar, use this', default=None)
+parser.add_argument('--xybin', help='Default is to bin the image on xy by 2, if you want to change this, use this flag + integer', default=2, type=int)
+parser.add_argument('--textoff', help='if you dont want the text, use this followed by any integer', default=0)
+parser.add_argument('--quality', help='Default jpg quality is 80%, use this flag follwed by an integer to change this',default=80, type=int)
+args = parser.parse_args()
 
 
 print('Dependancies imported')
 
-def Generate_preview_dm3(dm3_file, color='', textoff=False):
+def Generate_preview_dm3(dm3_file, color='', textoff=0, xybin=2, quality=80):
     #make a folder called previews to save the folder 
     foldername = 'previews'
     if foldername not in os.listdir('.'):
@@ -27,22 +38,22 @@ def Generate_preview_dm3(dm3_file, color='', textoff=False):
     #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)
+    scalebar_x = x-int(image.shape[1]/6)
 
 
     #Save pixel size 
     pixelSize=dm3_input['pixelSize'][0]
-    
+    pixelUnit = dm3_input['pixelUnit'][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]
+    possible_sizes = [0.5, 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
+        width = n*(1/pixelSize)
         #print(n, image.shape([0]/10)
         if width>(x/15):
             break
@@ -54,7 +65,7 @@ def Generate_preview_dm3(dm3_file, color='', textoff=False):
 
     #apply median filter and gaussian blur
     img_median = cv.medianBlur(image,5)
-    img_gauss = cv.GaussianBlur(img_median, (3,3),0)
+    #img_gauss = cv.GaussianBlur(img_median, (3,3),0)
 
     #Scale image between 0-255 (turn it into an 8bit greyscale image)
 
@@ -67,52 +78,85 @@ def Generate_preview_dm3(dm3_file, color='', textoff=False):
     #choose color - this can be given as black, white or grey in the function
     if color=='black':
         pixvalue = 0
-        textcolor = (0,0,0)
+        textcolor = 'black'
     elif color=='white':
         pixvalue = 255
-        textcolor=(255,255,255)
+        textcolor='white'
     elif color=='grey':
         pixvalue = 150
-        textcolor=(150,150,150)
+        textcolor='grey'
     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)
+            textcolor='white'
         else:
             pixvalue = 0
-            textcolor = (0,0,0)
+            textcolor = 'black'
     #add scalebar (set pixels to color)
 
+
+
     new_arr[scalebar_y:scalebar_y+height,scalebar_x:scalebar_x+width]=pixvalue
-    
+    #Bin image to reduce filesize, comment out if you want full image size
+    new_arr = cv.resize(new_arr, (int(new_arr.shape[0]/xybin), int(new_arr.shape[1]/xybin)), interpolation=cv.INTER_CUBIC) 
+
+    textposition = ((scalebar_x+width/2)/xybin,scalebar_y/xybin +20)
     #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
+
+    if pixelUnit!='nm':
+        #print('yes')
+        Utext = str(n)+u'\u00b5'+ 'm'
+        text = str(n)+'microns'
+    else:
+        #print('no')
         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 
+        Utext=  text
+    newname = foldername+'/'+dm3_file.strip('.dm3')+'_'+text+'scale.jpg'
+    pil_image = Image.fromarray(new_arr)
 
+    if textoff==0:
+        draw = ImageDraw.Draw(pil_image)        
+ 
+        fontsize=int(x/(40*xybin))
+        font = ImageFont.truetype("/Library/fonts/Arial.ttf", fontsize)
+        draw.text(textposition, Utext, anchor ='rm', fill=textcolor, font=font, stroke_width=1)
+    
+    pil_image.save(newname, quality=quality)
 
 
 
 
-    #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)
+    
+    #status = cv.imwrite(newname, new_arr,[int(cv.IMWRITE_JPEG_QUALITY), 70])
+    print(newname, 'Done!')
 
 #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)
 
+
+start_time = time.time()
+if args.file==None:
+    dm3_files = [x for x in os.listdir('.') if x[-3:]=='dm3']
+
+    for file in dm3_files:
+        # if you have a scalebar color preference (black, white or grey) add it here, also turn off text by replacing false with True or ''
+        Generate_preview_dm3(file, color=args.color, textoff=args.textoff,xybin=args.xybin,quality=args.quality)
+        running_time = (time.time() - start_time)
+    print("--- {} seconds ---".format(running_time))
+    print('---{} seconds per file ---'.format(str(running_time/len(dm3_files))))
+else:
+    Generate_preview_dm3(args.file, color=args.color, textoff=args.textoff,xybin=args.xybin,quality=args.quality)
+
+    running_time = (time.time() - start_time)
+    print("--- {} seconds ---".format(running_time))
+#print(len(dm3_file))