app.py

import os
import wfdb
import shutil
import numpy as np
import gradio as gr
from models.inception import *
from scipy.signal import resample
import pandas as pd



def load_apple_data():
    return None



# load wfdb data
def load_data(sample_data):
    ecg, meta_data = wfdb.rdsamp(sample_data)
    lead_I = ecg[:,0]
    sample_frequency = meta_data["fs"]
    return lead_I, sample_frequency



def preprocess_ecg(ecg,fs):
    if fs != 100:
        ecg = resample(ecg, int(len(ecg)*(100/fs)))
    else:
        pass
    if len(ecg) > 1000:
        ecg = ecg[:1000]
    else:
        pass
    return ecg

def load_age_model(sample_frequency,recording_time, num_leads):
    cwd = os.getcwd()
    weights = f"{cwd}/models/weights/model_weights_leadI_age.h5"
    model = build_age_model((sample_frequency * recording_time, num_leads), 1)
    model.load_weights(weights)
    return model


def load_gender_model(sample_frequency,recording_time, num_leads):
    cwd = os.getcwd()
    weights = f"{cwd}/models/weights/model_weights_leadI_gender.h5"
    model = build_gender_model((sample_frequency * recording_time, num_leads), 1)
    model.load_weights(weights)
    return model

def run(header_file, data_file):
    SAMPLE_FREQUENCY = 100
    TIME = 10
    NUM_LEADS = 1
    NEW_SAMPLE_FREQUENCY = 100
    demo_dir = f"{CWD}/sample_data"

    if data_file.name.endswith(".csv"):
        _, data_basename = os.path.split(data_file.name)
        shutil.copyfile(data_file.name, f"{demo_dir}/{data_basename}")
        df= pd.read_csv(f"{demo_dir}/{data_basename}", skiprows=12, sep=";", header=None,  decimal=',')
        ecg = np.asarray(df[0].str.replace(',', '.').str.replace('−', '-').astype(float))
        ecg = resample(ecg[(TIME*SAMPLE_FREQUENCY):(TIME*SAMPLE_FREQUENCY*2)],TIME * NEW_SAMPLE_FREQUENCY)
        ecg = ecg/1000
    else:
        _, hdr_basename = os.path.split(header_file.name)
        _, data_basename = os.path.split(data_file.name)
        shutil.copyfile(data_file.name, f"{demo_dir}/{data_basename}")
        shutil.copyfile(header_file.name, f"{demo_dir}/{hdr_basename}")
        data, fs = load_data(f"{demo_dir}/{hdr_basename.split('.')[0]}")
        ecg = preprocess_ecg(data,fs)
    age_model = load_age_model(sample_frequency=SAMPLE_FREQUENCY,recording_time=TIME,num_leads=NUM_LEADS)
    gender_model = load_gender_model(sample_frequency=SAMPLE_FREQUENCY,recording_time=TIME,num_leads=NUM_LEADS)
    age_estimate = age_model.predict(np.expand_dims(ecg,0)).ravel()[0]
    gender_prediction = gender_model.predict(np.expand_dims(ecg,0)).ravel()[0]
    return str(round(age_estimate,1)), {"Male": 1- gender_prediction, "Female": gender_prediction}

# Give credit to https://huggingface.co/spaces/Tej3/ECG_Classification/blob/main/app.py for interface

CWD = os.getcwd()

with gr.Blocks() as demo:
    #with  gr.Row():
    #    pred_type = gr.Radio(['Age', 'Gender'], label= "Select Model")
    with gr.Row():
        with gr.Column(scale=1):
            header_file = gr.File(label = "header_file", file_types=[".hea"],)
            data_file = gr.File(label = "data_file", file_types=[".dat",".csv"])
        with gr.Column(scale=1):
            output_age = gr.Textbox(label = "Estimated age")
            output_gender = gr.Label( label = "Predicted gender")
    #with gr.Row():
    #    ecg_graph = gr.Plot(label = "ECG Signal Visualisation")
    with gr.Row():    
        predict_btn = gr.Button("Predict")
        predict_btn.click(fn= run, inputs = [#pred_type, 
                                            header_file, data_file], outputs=[output_age,output_gender])
    with gr.Row():    
        gr.Examples(examples=[[f"{CWD}/sample_data/ath_001.hea", f"{CWD}/sample_data/ath_001.dat"],\
    #                          [f"{CWD}/demo_data/test/00008_lr.hea", f"{CWD}/demo_data/test/00008_lr.dat", "sinusrhythmus linkstyp qrs(t) abnormal    inferiorer infarkt     alter unbest."], \
    #                          [f"{CWD}/demo_data/test/00045_lr.hea", f"{CWD}/demo_data/test/00045_lr.dat", "sinusrhythmus unvollstÄndiger rechtsschenkelblock sonst normales ekg"],\
    #                          [f"{CWD}/demo_data/test/00257_lr.hea", f"{CWD}/demo_data/test/00257_lr.dat", "premature atrial contraction(s). sinus rhythm. left atrial enlargement. qs complexes in v2. st segments are slightly elevated in v2,3. st segments are depressed in i, avl. t waves are low or flat in i, v5,6 and inverted in avl. consistent with ischaemic h"],\
                                ],
                    inputs = [header_file, data_file])
        gr.Examples(examples=[[f"{CWD}/sample_data/ecg_2021-10-16.csv", ]], inputs=[data_file])
#
if __name__ == "__main__":
    demo.launch(share=True)

#iface = gr.Interface(fn=run, inputs="text", outputs="text")
#iface.launch()