coreslicer-plugin.py

from flask import Flask, request, send_file
import numpy as np, os, json
from scipy.misc import imsave
from coreslicer import read_dcm

app = Flask(__name__)

APP_ROOT = os.path.dirname(os.path.abspath(__file__))
UPLOAD_FOLDER = os.path.join(APP_ROOT, '../tmp/coreslicer')
app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER

def import_slice_file(request, index, upload_folder):
  
  slices = json.loads(request.form['slices'])
  slice_name = slices[index]['filename']
  
  slices_data = request.files
  
  slice_data = slices_data[slice_name]
  
  slice_filename = os.path.join(upload_folder, slice_data.filename)
  slice_data.save(slice_filename)
  slice_data.stream.seek(0)
  
  return slice_filename
  
def export_slice_file(mask, upload_folder):
  
  image_filename = os.path.join(upload_folder, 'result.png')
  imsave(image_filename, mask)

  return image_filename
  
@app.route('/endpoint', methods = ['POST'])
  
def segmentation_function():
  
  slice_filename = import_slice_file(request, 0, app.config['UPLOAD_FOLDER'])
  
  dcm_image, grayscale, pixel_spacing = read_dcm(slice_filename)

  mask = np.zeros((dcm_image.shape[0], dcm_image.shape[1], 4))
  mask[dcm_image > 0] = (1, 1, 1, 1)

  return send_file(
    export_slice_file(mask, app.config['UPLOAD_FOLDER']),
    attachment_filename='result.png', mimetype='image/png')

if __name__ == '__main__':
    port = 8000
    app.run(host='0.0.0.0', port=port)