from __future__ import division, print_function
import json
# coding=utf-8
import sys
import os
import glob
import re
import numpy as np
import cv2
import pandas as pd
import numpy as np
import biosppy
import matplotlib.pyplot as plt
# Keras
from keras.applications.imagenet_utils import preprocess_input, decode_predictions
from keras.models import load_model
from keras.preprocessing import image
# Flask utils
from flask import Flask, redirect, url_for, request, render_template
from werkzeug.utils import secure_filename
from gevent.pywsgi import WSGIServer
# Define a flask app
app = Flask(__name__)
# Model saved with Keras model.save()
# Load your trained model
model = load_model('path to the model')
model._make_predict_function() # Necessary
print('Model loaded. Start serving...')
output = []
# You can also use pretrained model from Keras
# Check https://keras.io/applications/
#from keras.applications.resnet50 import ResNet50
#model = ResNet50(weights='imagenet')
#print('Model loaded. Check http://127.0.0.1:5000/')
def model_predict(uploaded_files, model):
flag = 1
for path in uploaded_files:
#index1 = str(path).find('sig-2') + 6
#index2 = -4
#ts = int(str(path)[index1:index2])
APC, NORMAL, LBB, PVC, PAB, RBB, VEB = [], [], [], [], [], [], []
output.append(str(path))
result = {"APC": APC, "Normal": NORMAL, "LBB": LBB, "PAB": PAB, "PVC": PVC, "RBB": RBB, "VEB": VEB}
indices = []
kernel = np.ones((4,4),np.uint8)
csv = pd.read_csv(path)
csv_data = csv[' Sample Value']
data = np.array(csv_data)
signals = []
count = 1
peaks = biosppy.signals.ecg.christov_segmenter(signal=data, sampling_rate = 200)[0]
for i in (peaks[1:-1]):
diff1 = abs(peaks[count - 1] - i)
diff2 = abs(peaks[count + 1]- i)
x = peaks[count - 1] + diff1//2
y = peaks[count + 1] - diff2//2
signal = data[x:y]
signals.append(signal)
count += 1
indices.append((x,y))
for count, i in enumerate(signals):
fig = plt.figure(frameon=False)
plt.plot(i)
plt.xticks([]), plt.yticks([])
for spine in plt.gca().spines.values():
spine.set_visible(False)
filename = 'fig' + '.png'
fig.savefig(filename)
im_gray = cv2.imread(filename, cv2.IMREAD_GRAYSCALE)
im_gray = cv2.erode(im_gray,kernel,iterations = 1)
im_gray = cv2.resize(im_gray, (128, 128), interpolation = cv2.INTER_LANCZOS4)
cv2.imwrite(filename, im_gray)
im_gray = cv2.imread(filename)
pred = model.predict(im_gray.reshape((1, 128, 128, 3)))
pred_class = pred.argmax(axis=-1)
if pred_class == 0:
APC.append(indices[count])
elif pred_class == 1:
NORMAL.append(indices[count])
elif pred_class == 2:
LBB.append(indices[count])
elif pred_class == 3:
PAB.append(indices[count])
elif pred_class == 4:
PVC.append(indices[count])
elif pred_class == 5:
RBB.append(indices[count])
elif pred_class == 6:
VEB.append(indices[count])
result = sorted(result.items(), key = lambda y: len(y[1]))[::-1]
output.append(result)
data = {}
data['filename'+ str(flag)] = str(path)
data['result'+str(flag)] = str(result)
json_filename = 'data.txt'
with open(json_filename, 'a+') as outfile:
json.dump(data, outfile)
flag+=1
with open(json_filename, 'r') as file:
filedata = file.read()
filedata = filedata.replace('}{', ',')
with open(json_filename, 'w') as file:
file.write(filedata)
os.remove('fig.png')
return output
@app.route('/', methods=['GET'])
def index():
# Main page
return render_template('index.html')
@app.route('/predict', methods=['GET', 'POST'])
def upload():
if request.method == 'POST':
# Get the file from post request
uploaded_files = []
# Save the file to ./uploads
print(uploaded_files)
for f in request.files.getlist('file'):
basepath = os.path.dirname(__file__)
file_path = os.path.join(
basepath, 'uploads', secure_filename(f.filename))
print(file_path)
if file_path[-4:] == '.csv':
uploaded_files.append(file_path)
f.save(file_path)
print(uploaded_files)
# Make prediction
pred = model_predict(uploaded_files, model)
# Process your result for human
# Simple argmax
#pred_class = decode_predictions(pred, top=1) # ImageNet Decode
#result = str(pred_class[0][0][1]) # Convert to string
result = str(pred)
return result
return None
if __name__ == '__main__':
# app.run(port=5002, debug=True)
# Serve the app with gevent
http_server = WSGIServer(('', 5000), app)
http_server.serve_forever()