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Author: Gregorio Flores

web: www.aniachitech.com

email: gregorio.flores

DICOM FILE VIEWER

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Categories

1. medical scientists
2. data scientific
3. nerds
4. technology enthusiasts
5. python developers
6. django developers

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What is a DICOM file

A DICOM file is an image saved in the Digital Imaging and Communications in Medicine (DICOM) format. It contains an image from a medical scan, such as an ultrasound or MRI. DICOM files may also include identification data for patients so that the image is linked to a specific individual.

Step by step Django tutorial

Running the Project

First, install python on your local computer:

brew install python3 tree 

Install the requirements:

pip install matplotlib numpy django termcolor imageio

Create a directory :

mkdir myproject
cd myproject

Create a new django project :

django-admin startproject myproject

Create a new django project :

django-admin startproject myproject

See and verify your directory structure

├── manage.py
└── myproject
    ├── __init__.py
    ├── settings.py
    ├── urls.py
    └── wsgi.py

Create a new django application :

 django-admin startapp dicom

See and verify your directory structure

.
├── dicom
│   ├── __init__.py
│   ├── admin.py
│   ├── apps.py
│   ├── migrations
│   │   └── __init__.py
│   ├── models.py
│   ├── tests.py
│   └── views.py
├── manage.py
└── myproject
    ├── __init__.py
    ├── settings.py
    ├── urls.py
    └── wsgi.py

Add dicom to setting.py

INSTALLED_APPS = [
    'django.contrib.admin',
    'django.contrib.auth',
    'django.contrib.contenttypes',
    'django.contrib.sessions',
    'django.contrib.messages',
    'django.contrib.staticfiles',
    'dicom',
]

Create 3 directories inside myproject

mkdir temp
mkdir static_content
mkdir templates

tree

    ├── static_content
    ├── temp
    ├── templates

Modiffy setting.py

#Add this lines
STATICFILES_DIRS = [(
    os.path.join(BASE_DIR, 'myproject/static_content')
),]


MEDIA_URL = '/media/'
MEDIA_ROOT = os.path.join(BASE_DIR, 'myproject/temp')
]

#And modiffy templates 
#Add 'DIRS': [os.path.join(BASE_DIR, 'myproject/templates')]',
TEMPLATES = [
    {
        'BACKEND': 'django.template.backends.django.DjangoTemplates',
        'DIRS': [os.path.join(BASE_DIR, 'myproject/templates')],
        'APP_DIRS': True,
        'OPTIONS': {
            'context_processors': [
                'django.template.context_processors.debug',
                'django.template.context_processors.request',
                'django.contrib.auth.context_processors.auth',
                'django.contrib.messages.context_processors.messages',
            ],
        },
    },
]

Put the static content

Create the template

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Run the development server:

python manage.py runserver

Verify the server status

curl -I  http://127.0.0.1:8000/static/img/logo.png 
response 
HTTP/1.1 200 OK
Date: Tue, 06 Nov 2018 23:20:11 GMT
Server: WSGIServer/0.2 CPython/3.7.0
Content-Type: image/png
Content-Length: 14235
Last-Modified: Mon, 21 May 2018 23:48:49 GMT

edit setting.py

remove 
    'django.middleware.csrf.CsrfViewMiddleware',

Crete views.py inside dicom directory

touch views.py

Add this two functions

import base64
import os
import time
import traceback
from io import BytesIO

import imageio
import matplotlib.pyplot as plt
from django.core.files.storage import FileSystemStorage
from django.http import JsonResponse
from django.shortcuts import redirect, render
from termcolor import colored

from myproject import settings

#our page
def app_render(request):
    print(settings.BASE_DIR)
    d = {'title': 'DICOM viewer','info':'DICOM SERVER SIDE RENDER'}
    return render(request, "main_template.html", d)
 

#just to redirect to the web app   
def send_to_dcom(request):
   return redirect('medical/app')

Modiffy urls.py

from dicom import views
from django.urls import path


urlpatterns = [
    path('', views.send_to_dcom),
    path('medical/app',views.app_render),
    

Test your app

add your webservice into views.py

def ajax_server(request):
    start = time.time()
    d = dict()
    generic = dict()
    medinfo = dict()

    try:

        print('FILE--->',str(request.FILES['imgInp'])[-3:])

        if request.method == 'POST' and ('imgInp' in request.FILES) and request.FILES['imgInp'] and  str(request.FILES['imgInp'])[-3:].upper() =='DCM':
            file = request.FILES['imgInp']
            fs = FileSystemStorage()
            filename = fs.save(file.name, file)
            full_path_file = os.path.join(settings.MEDIA_ROOT, filename)
            print(colored('path->', 'red'), full_path_file)

            generic['name'] = filename
            generic['size'] = os.path.getsize(full_path_file)
            try:
                if full_path_file[-3:].upper() == 'DCM':
                    dcpimg = imageio.imread(full_path_file)
                    for keys in dcpimg.meta:

                        medinfo[keys] = str(dcpimg.meta[keys])

                    if len(dcpimg.shape) ==4:
                        dcpimg = dcpimg[0,0]
                    elif len(dcpimg.shape) ==3:
                        dcpimg = dcpimg[0]

                    fig = plt.gcf()
                    fig.set_size_inches(18.5, 10.5)
                    plt.imshow(dcpimg, cmap='gray')
                    plt.colorbar()
                    figure = BytesIO()
                    plt.savefig(figure, format='jpg', dpi=300)

                    plt.close()
                    d['url'] = {'base64': 'data:image/png;base64,' + base64.b64encode(figure.getvalue()).decode()}

                # medinfo.update(dcpimg.meta)

            except Exception as e:

                traceback.print_tb(e)





            fs.delete(filename)
    except Exception as e:
        traceback.print_tb(e)




    generic['process time'] = time.time() - start
    d['generic'] = generic


    d['med'] = medinfo


    print(colored(d, 'red'))
    return JsonResponse(d)

    

add the url into. urls.py

path('medical/process.ajax',views.ajax_server),

The project will be available at 127.0.0.1:8000.

#Enjoy it