A dialog-based DICOM to video converter.
DICOM (Digital Imaging and Communications in Medicine) is a standard for handling, storing, printing, and transmitting information in medical imaging. DICOM files can be exchanged between two entities that are capable of receiving image and patient data in DICOM format by following network communications protocol. DICOM has been widely adopted by hospitals and is making inroads in smaller applications like dentists' and doctors' offices.
This project is to implement the process of conversion from DICOM format to video format (avi) in order to meet the needs and requirements for universal computer systems (PC, Mac, Linux, etc.). So the ordinary users of such systems can use the converted file to present, communicate and store the universal files. Case reports in medical conferences, educations of clinical medicine will become more convenient to use universal video formats in the slide presentations.
In [1]:
import SimpleITK as sitk
import cv2
import pydicom
import numpy as np
import tkinter as tk
from tkinter import ttk
from tkinter import messagebox
from tkinter import filedialog
In [ ]:
def loadFile(filename):
ds = sitk.ReadImage(filename)
img_array = sitk.GetArrayFromImage(ds)
frame_num, width, height = img_array.shape
return img_array, frame_num, width, height
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def loadFileInformation(filename):
information = {}
ds = pydicom.read_file(filename)
information['PatientID'] = ds.PatientID
information['PatientName'] = ds.PatientName
information['PatientBirthDate'] = ds.PatientBirthDate
information['PatientSex'] = ds.PatientSex
information['StudyID'] = ds.StudyID
information['StudyDate'] = ds.StudyDate
information['StudyTime'] = ds.StudyTime
information['InstitutionName'] = ds.InstitutionName
information['Manufacturer'] = ds.Manufacturer
information['NumberOfFrames'] =ds.NumberOfFrames
return information
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def autoEqualize(img_array):
img_array_list = []
for img in img_array:
img_array_list.append(cv2.equalizeHist(img))
img_array_equalized = np.array(img_array_list)
return img_array_equalized
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def limitedEqualize(img_array, limit=4.0):
img_array_list = []
for img in img_array:
clahe = cv2.createCLAHE(clipLimit=limit, tileGridSize=(8,8)) #CLAHE (Contrast Limited Adaptive Histogram Equalization)
img_array_list.append(clahe.apply(img))
img_array_limited_equalized = np.array(img_array_list, dtype=np.uint8)
return img_array_limited_equalized
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def writeVideo(img_array, directory):
frame_num, width, height = img_array.shape
filename_output = directory + '/' + filename.split('.')[0].split('/')[-1] + '.avi'
#fourcc = cv2.VideoWriter_fourcc(*'XVID')
#video = cv2.VideoWriter(filename_output, fourcc, 15, (width, height))
# Above is for Mac OSX use only./////////////////////////////////////////////////////////////
video = cv2.VideoWriter(filename_output, -1, 15, (width, height)) # Initialize Video File
for img in img_array:
img_rgb = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
video.write(img_rgb) # Write video file frame by frame
video.release()
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def browseFileButton():
global filename
try:
filename = filedialog.askopenfilename(filetypes=(('DICOM files', '*.dcm'), ('All files', '*.*')))
information = loadFileInformation(filename)
text_filename.delete('1.0', tk.END)
text_filename.insert('1.0', filename)
text_PatientID.delete('1.0', tk.END)
text_PatientID.insert('1.0', information['PatientID'])
text_PatientName.delete('1.0', tk.END)
text_PatientName.insert('1.0', information['PatientName'])
text_PatientSex.delete('1.0', tk.END)
text_PatientSex.insert('1.0', information['PatientSex'])
text_PatientBirthDate.delete('1.0', tk.END)
text_PatientBirthDate.insert('1.0', information['PatientBirthDate'])
text_StudyID.delete('1.0', tk.END)
text_StudyID.insert('1.0', information['StudyID'])
text_StudyDate.delete('1.0', tk.END)
text_StudyDate.insert('1.0', information['StudyDate'])
text_StudyTime.delete('1.0', tk.END)
text_StudyTime.insert('1.0', information['StudyTime'])
text_InstitutionName.delete('1.0', tk.END)
text_InstitutionName.insert('1.0', information['InstitutionName'])
text_Manufacturer.delete('1.0', tk.END)
text_Manufacturer.insert('1.0', information['Manufacturer'])
text_NumberOfFrames.delete('1.0', tk.END)
text_NumberOfFrames.insert('1.0', information['NumberOfFrames'])
except:
filename = ''
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def loadFileButton():
global img_array, frame_num, width, height, information, isLoad
if filename == '':
messagebox.showwarning("No File", "Sorry, no file loaded! Please choose DICOM file first.")
else:
try:
img_array, frame_num, width, height = loadFile(filename)
information = loadFileInformation(filename)
isLoad = 1
messagebox.showinfo("DICOM File Loaded", "DICOM file successfully loaded!")
except:
messagebox.showwarning("File Loading Failed", "Sorry, file loading failed! Please check the file format.")
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def convertVideoButton():
global isLoad, clipLimit
clipLimit = float(text_clipLimit.get('1.0', tk.END))
directory = filedialog.askdirectory()
if filename == '':
messagebox.showwarning("No File to be Converted", "Sorry, no file to be converted! Please choose a DICOM file first.")
elif isLoad == 0:
messagebox.showwarning("No File Loaded", "Sorry, no file loaded! Please load the chosen DICOM file.")
elif directory == '':
messagebox.showwarning("No Directory", "Sorry, no directory shown! Please specify the output directory.")
else:
img_array_limited_equalized = limitedEqualize(img_array, clipLimit)
writeVideo(img_array_limited_equalized, directory)
messagebox.showinfo("Video File Converted", "Video file successfully generated!")
isLoad = 0
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def about():
about_root=tk.Tk()
w = 367 # width for the Tk root
h = 230 # height for the Tk root
# get screen width and height
ws = about_root.winfo_screenwidth() # width of the screen
hs = about_root.winfo_screenheight() # height of the screen
# calculate x and y coordinates for the Tk root window
x = (ws/2) - (w/2)
y = (hs/2) - (h/2)
# set the dimensions of the screen
# and where it is placed
about_root.geometry('%dx%d+%d+%d' % (w, h, x, y))
about_root.title('About Willowbend DICOM')
about_root.iconbitmap('Heart.ico')
label_author=tk.Label(about_root,text='Willowbend DICOM Version 1.0', font=('tahoma', 9))
label_author.place(x=90,y=30)
label_author=tk.Label(about_root,text='Copyright (C) 2016', font=('tahoma', 9))
label_author.place(x=125,y=60)
label_author=tk.Label(about_root,text='Author: Chuan Yang', font=('tahoma', 9))
label_author.place(x=125,y=90)
label_author=tk.Label(about_root,text='Shengjing Hospital of China Medical University', font=('tahoma', 9))
label_author.place(x=50,y=120)
button_refresh=ttk.Button(about_root, width=15, text='OK', command=about_root.destroy)
button_refresh.place(x=135, y=170)
about_root.mainloop()
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# Main Frame////////////////////////////////////////////////////////////////////////////////////////
root = tk.Tk()
w = 930 # width for the Tk root
h = 660 # height for the Tk root
# get screen width and height
ws = root.winfo_screenwidth() # width of the screen
hs = root.winfo_screenheight() # height of the screen
# calculate x and y coordinates for the Tk root window
x = (ws/2) - (w/2)
y = (hs/2) - (h/2)
# set the dimensions of the screen
# and where it is placed
root.geometry('%dx%d+%d+%d' % (w, h, x, y))
#root.attributes('-fullscreen', True)
root.title('Willowbend DICOM')
root.iconbitmap('Heart.ico')
isLoad = 0
clipLimit = 3.0
filename = ''
#///////////Image Title///////////////////////////////
photo=tk.PhotoImage(file='Title.png')
label_photo=tk.Label(root, image=photo, relief='sunken', borderwidth=3)
label_photo.place(x=260,y=35)
#/////////////Text///////////////////////////////////////////////////////////////////
text_PatientID=tk.Text(root, width=20,height=1, font=('tahoma', 9), bd=2)
text_PatientID.place(x=60, y=90)
label_PatientID=tk.Label(root, text='Patient ID', font=('tahoma', 9))
label_PatientID.place(x=60,y=60)
#//////////////////
y_position = 180
text_PatientName=tk.Text(root, width=30,height=1, font=('tahoma', 9), bd=2)
text_PatientName.place(x=60, y=y_position)
label_PatientName=tk.Label(root, text='Patient\'s Name:', font=('tahoma', 9))
label_PatientName.place(x=60,y=y_position-30)
text_PatientSex=tk.Text(root, width=15,height=1, font=('tahoma', 9), bd=2)
text_PatientSex.place(x=360, y=y_position)
label_PatientSex=tk.Label(root, text='Gender:', font=('tahoma', 9))
label_PatientSex.place(x=360,y=y_position-30)
text_PatientBirthDate=tk.Text(root, width=25,height=1, font=('tahoma', 9), bd=2)
text_PatientBirthDate.place(x=560, y=y_position)
label_PatientBirthDate=tk.Label(root, text='Birth Date:', font=('tahoma', 9))
label_PatientBirthDate.place(x=560,y=y_position-30)
#//////////////////////////////////////////////////////////////////////////////////
y_position = 260
text_StudyID=tk.Text(root, width=25,height=1, font=('tahoma', 9), bd=2)
text_StudyID.place(x=60, y=y_position)
label_StudyID=tk.Label(root, text='Study ID:', font=('tahoma', 9))
label_StudyID.place(x=60,y=y_position-30)
text_StudyDate=tk.Text(root, width=25,height=1, font=('tahoma', 9), bd=2)
text_StudyDate.place(x=340, y=y_position)
label_StudyDate=tk.Label(root, text='Study Date:', font=('tahoma', 9))
label_StudyDate.place(x=340,y=y_position-30)
text_StudyTime=tk.Text(root, width=25,height=1, font=('tahoma', 9), bd=2)
text_StudyTime.place(x=600, y=y_position)
label_StudyTime=tk.Label(root, text='Study Time:', font=('tahoma', 9))
label_StudyTime.place(x=600,y=y_position-30)
#////////////////////////////////////
y_position = 340
text_InstitutionName=tk.Text(root, width=50,height=1, font=('tahoma', 9), bd=2)
text_InstitutionName.place(x=60, y=y_position)
label_InstitutionName=tk.Label(root, text='Institution Name:', font=('tahoma', 9))
label_InstitutionName.place(x=60,y=y_position-30)
text_Manufacturer=tk.Text(root, width=38,height=1, font=('tahoma', 9), bd=2)
text_Manufacturer.place(x=560, y=y_position)
label_Manufacturer=tk.Label(root, text='Manufacturer:', font=('tahoma', 9))
label_Manufacturer.place(x=560,y=y_position-30)
# File Name
text_filename=tk.Text(root, width=100,height=1, font=('tahoma', 9), bd=2)
text_filename.place(x=60, y=450)
label_filename=tk.Label(root, text='DICOM File:', font=('tahoma', 9))
label_filename.place(x=60,y=420)
text_NumberOfFrames=tk.Text(root, width=10,height=1, font=('tahoma', 9), bd=2)
text_NumberOfFrames.place(x=660, y=400)
label_NumberOfFrames=tk.Label(root, text='Frames', font=('tahoma', 9))
label_NumberOfFrames.place(x=760,y=400)
text_clipLimit=tk.Text(root, width=8,height=1, font=('tahoma', 9), bd=2)
text_clipLimit.place(x=580, y=510)
label_clipLimit=tk.Label(root, text='Clip Limit:', font=('tahoma', 9))
label_clipLimit.place(x=500,y=510)
text_clipLimit.delete('1.0', tk.END)
text_clipLimit.insert('1.0', clipLimit)
#/////////////Button///////////////////////////////////////////////////////////////
button_browse=ttk.Button(root, text='Browse...', width=20, command=browseFileButton)
button_browse.place(x=60, y=510)
button_load=ttk.Button(root, text='Load', width=20, command=loadFileButton)
button_load.place(x=260, y=510)
button_convert=ttk.Button(root, text='Convert', width=20, command=convertVideoButton)
button_convert.place(x=700, y=510)
button_about=ttk.Button(root, text='About...', width=20, command=about)
button_about.place(x=260, y=580)
button_close=ttk.Button(root, width=20, text='Exit', command=root.destroy)
button_close.place(x=700, y=580)
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cv2.destroyAllWindows()
In [ ]:
root.mainloop()
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### To install the SimpleITK package with conda run:
```powershell
conda install --channel https://conda.anaconda.org/SimpleITK SimpleITK
```