# DESCRIPTION: # A python script to measure thickness of small tissue mchanical testing samples. This scripts creates a GUI to # 1. pick the desired image from its location (this image will be taken using the Optical thickness measurement system set up and flycap camera software), # 2. calculate pixels from manually chosen ruler measurement, # 3. allow multiple thickness masurements on the sample, # 4. allow calculating average and standard deviation, and, # 5 save results in an xml file as well as save the final image with all the measurements overlaying on it. # # WRITTEN BY: Snehal Chokhandre # Computational Biomodeling (CoBi) Core # Department of Biomedical Engineering # The Cleveland Clinic Foundation import tkinter as tk import os import tkinter.filedialog from tkinter.filedialog import askopenfilename from tkinter import * from PIL import Image, ImageTk #import sys #import _imagingtk #import image import math import matplotlib.pyplot as plt import numpy as np import matplotlib.image as mpimg from scipy.misc import imread, imsave import statistics #from xml.etree.ElementTree import Element, SubElement, Comment import xml.etree.ElementTree as ET import lxml.etree as etree from xml.etree import ElementTree #import lxml.etree.XMLParser #from xml.etree import ElementTree #from xml.dom import minidom # #def prettify(elem): # """Return a pretty-printed XML string for the Element. # """ # rough_string = ElementTree.tostring(elem, 'utf-8') # reparsed = minidom.parseString(rough_string) # return reparsed.toprettyxml(indent=" ", encoding='UTF-8') import ntpath file_path = '' mm='' measurement= '' #filename='' #~~~~ FUNCTIONS~~~~ def browse_and_display_file(): global file_path global x global y global filename global scaled_image_data global image_data filename = askopenfilename() # infile = open(filename, 'r') file_path = os.path.abspath(filename) # display filepath in window entry.delete(0, END) entry.insert(0, file_path) image_data = imread(file_path).astype(np.float32) # display image in a new figure window scaled_image_data = image_data / 255. # imsave('test_out.png', scaled_image_data) plt.imshow(scaled_image_data) lines = [] # def draw_line(self): ax = plt.gca() # pick two points and draw a line xy = plt.ginput(n=2,timeout=0) # xy = plt.ginput(n=2, timeout=0, show_clicks=True, mouse_add=1, mouse_pop=3, mouse_stop=2) x = [p[0] for p in xy] y = [p[1] for p in xy] line = plt.plot(x,y) ax.figure.canvas.draw() lines.append(line) # print (x) # print (y) plt.draw() # im = Image.open(filename) # tkimage = PhotoImage(im) # tkinter.Label(root, image=tkimage).grid() # photo = ImageTk,PhotoImage(im) # photo_label = Label(root,image=photo) # photo_label.image = photo # photo_label.grid() # im=Image.open(filename) # im.show() def mm_to_pxl(): global mm global one_pxl_mm global MM global round_pxl global pxl # print (mm.get()) # get the user entered input mm value MM=mm.get() # pxl = y[1]-y[0] pxl=math.sqrt(math.pow((y[1]-y[0]),2)+math.pow((x[1]-x[0]),2)) print (pxl) round_pxl= round(pxl,1) # print (round_pxl) Label(f1,text=round_pxl).grid(row=5, column=1, sticky='we') one_pxl_mm= MM/pxl # print (one_pxl_mm) # def pick_measurement(): lines = [] global x_m global y_m ax = plt.gca() # pick two points and draw a line on sample xy = plt.ginput(n=2,timeout=0) x_m = [p[0] for p in xy] y_m = [p[1] for p in xy] line = plt.plot(x_m,y_m) ax.figure.canvas.draw() lines.append(line) plt.draw() def ok_measurement(row,column): global all_thickness # print (row) # info = tk.Button().grid_info() # print ('row='),row # print("row:", info["row"], "column:", info["column"]) # pxl = y_m[1]-y_m[0] # pixels for thickness measurement pxl= math.sqrt(math.pow((y_m[1]-y_m[0]),2)+math.pow((x_m[1]-x_m[0]),2)) # X= math.sqrt(math.pow((y_m[1]-y_m[0]),2)+math.pow((x_m[1]-x_m[0]),2)) # Y= math.sqrt(math.pow((y_m[0]-y_m[1]),2)+math.pow((x_m[1]-x_m[1]),2)) # pxl=math.sqrt(math.pow(X,2)+math.pow(Y,2)) pxl= round(pxl,1) thickness=pxl*one_pxl_mm # thickness in mm thickness=round(thickness,2) all_thickness.append(thickness) Label(f1,text=thickness).grid(row=row, column=15, sticky='we') # for children in f1.children.values(): # info = children.grid_info() # #note that rows and column numbers are stored as string # if info['row'] == str(row) and info['column'] == str(column): # return children # return None # print (info) def compute(): global average global std_dev global all_thickness average=sum(all_thickness)/len(all_thickness) Label(f1,text=average).grid(row=4, column=28, sticky='we') std_dev= statistics.stdev(all_thickness) Label(f1,text=std_dev).grid(row=5, column=28, sticky='we') def create_xml(): head, tail = ntpath.split(file_path) # works only for windows to split filename from path tail=tail[:-4] # root = ET.Element(tail) root = ET.Element('OTMS') ET.SubElement(root,'Sample').text=tail # ET.SubElement(sample_name,'Name').text=tail calib = ET.SubElement(root,"calibration") ET.SubElement(calib,"Physical",units="mm").text=str(MM) ET.SubElement(calib,"image",units="pixel").text= str(pxl) ET.SubElement(calib,"resolution",units="mm/pixel").text= str(one_pxl_mm) ET.SubElement(root,"Thickness",units="mm").text= str(all_thickness) stats= ET.SubElement(root,"Statistics",units="mm") ET.SubElement(stats,"average").text=str(average) ET.SubElement(stats,"std_dev").text=str(std_dev) tree = ET.ElementTree(root) tree.write( tail+ '.xml') # plt.savefig(tail+ '.png') #save figure with measurements prettyPrintXml(tail+ '.xml') def prettyPrintXml(xmlFilePathToPrettyPrint): assert xmlFilePathToPrettyPrint is not None parser = etree.XMLParser(resolve_entities=False, strip_cdata=False) document = etree.parse(xmlFilePathToPrettyPrint, parser) document.write(xmlFilePathToPrettyPrint, pretty_print=True, encoding='utf-8') # #~~~~~~ GUI ~~~~~~~~ root = Tk() root.title('Thickness measurement') root.geometry("500x400+250+100") mf = Frame(root) mf.grid() f1 = Frame(mf, width=500, height=250) f1.grid() f2 = Frame(mf, width=500, height=250) f2.grid() #f3 = Frame(mf, width=600, height=250) #f3.pack() #f4 = Frame(mf, width=600, height=250) #f4.pack() file_path = StringVar() mm= IntVar() all_thickness=[] #measurement=IntVar() Label(f1,text="Calibration",fg='blue').grid(row=3, column=1, sticky='we') Label(f1,text="Measurements (mm)",fg='blue').grid(row=3, column=15, sticky='we') Label(f1,text="Results",fg='blue').grid(row=3, column=27, sticky='we') Label(f1,text="mm").grid(row=4, column=0, sticky='we') entry = Entry(f1, width=5,textvariable=mm) # change filepath to measured mm on ruler entry.grid(row=4,column=1,padx=0,pady=0,sticky='we',columnspan=1) Label(f1,text="pixels").grid(row=5, column=0, sticky='we') #entry = Entry(f1, width=5) # replace filepath for measured pixels #entry.grid(row=5,column=1,padx=0,pady=0,sticky='we',columnspan=1) #--- #R=4 #for f in range(1,11): ## if i<=11: ## Label(f1,text=i).grid(row=R, column=14, sticky='we') ## entry = Entry(f1, width=5) # filepath replaced with measurement ## entry.grid(row=R,column=15,padx=0,pady=0,sticky='we',columnspan=1) # Button(f1, text="OK",command=lambda row=R, column=16: fourth_iter.ok_measurement(row,column)).grid(row=R, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement # Button(f1, text="Pick",command=third_iter.pick_measurement).grid(row=R, column=14, sticky='ew', padx=8, pady=4) # R+=1 # --- Button(f1, text="OK",command=lambda row=4, column=16: ok_measurement(row,column)).grid(row=4, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement Button(f1, text="Pick",command=pick_measurement).grid(row=4, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=5, column=16: ok_measurement(row,column)).grid(row=5, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=5, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=6, column=16: ok_measurement(row,column)).grid(row=6, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=6, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=7, column=16: ok_measurement(row,column)).grid(row=7, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=7, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=8, column=16: ok_measurement(row,column)).grid(row=8, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=8, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=9, column=16: ok_measurement(row,column)).grid(row=9, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=9, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=10, column=16: ok_measurement(row,column)).grid(row=10, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=10, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=11, column=16: ok_measurement(row,column)).grid(row=11, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=11, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=12, column=16: ok_measurement(row,column)).grid(row=12, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=12, column=14, sticky='ew', padx=8, pady=4) # #Button(f1, text="OK",command=lambda row=13, column=16: ok_measurement(row,column)).grid(row=13, column=16, sticky='ew', padx=8, pady=4) # command will be replaced with aafirmation of measurement #Button(f1, text="Pick",command=pick_measurement).grid(row=13, column=14, sticky='ew', padx=8, pady=4) Label(f1,text="Average=").grid(row=4, column=27, sticky='we') Label(f1,text="Std Dev=").grid(row=5, column=27, sticky='we') Label(f1,text="File").grid(row=0, column=0, sticky='e') entry = Entry(f1, width=50, textvariable=file_path) entry.grid(row=0,column=1,padx=2,pady=2,sticky='we',columnspan=25) Button(f1, text="Browse", command=browse_and_display_file).grid(row=0, column=27, sticky='ew', padx=8, pady=4) Button(f1, text="Compute",command=compute,fg='red').grid(row=6, column=28, sticky='ew', padx=8, pady=4) Button(f1, text="Calibrate",command=mm_to_pxl,fg='red').grid(row=6, column=1, sticky='ew', padx=8, pady=4) Button(f1, text="Save",command=create_xml,fg='red').grid(row=7, column=28, sticky='ew', padx=8, pady=4) root.mainloop() # starts the GUI # improvements needed # deselect measurements