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Examples5DBs_4algo.py
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Examples5DBs_4algo.py
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import platform
import os
import wfdb
import glob
import numpy as np
import pandas as pd
from os.path import join
from biosppy.signals import ecg
from Helpers.Physionet import LoadFile, PhysionetConstants
from Helpers.Metrices import *
from subprocess import call
from collections import namedtuple
import traceback
import csv
import h5py
import Helpers.ECGprocessing as fcg
import matplotlib.pyplot as plt
ChannelDescription = namedtuple('ChannelDescription',['blocks','annotations'])
#segmenters = [ecg.hamilton_segmenter, ecg.engzee_segmenter]
segmenters = [ecg.engzee_segmenter]
# databases = ["cinc1"]*100 +["cinc2"]*100+["mitdb"]*48+["qtdb"]*82+["ludb"]*200
# patients = [str(i) for i in list(range(100,200))] + [
# '1003', '1009', '1016', '1019', '1020', '1022', '1023', '1028', '1032',
# '1033', '1036', '1043', '1069', '1071', '1073', '1077', '1169', '1195',
# '1242', '1284', '1354', '1376', '1388', '1447', '1456', '1485', '1503',
# '1522', '1565', '1584', '1683', '1686', '1715', '1742', '1774', '1804',
# '1807', '1821', '1858', '1866', '1900', '1906', '1954', '1993', '1998',
# '2041', '2063', '2132', '2164', '2174', '2201', '2203', '2209', '2247',
# '2277', '2279', '2283', '2296', '2327', '2370', '2384', '2397', '2469',
# '2527', '2552', '2556', '2602', '2639', '2664', '2714', '2728', '2732',
# '2733', '2798', '2800', '2812', '2839', '2850', '2879', '2885', '2886',
# '2907', '2923', '2970', '3188', '3266', '41024', '41025', '41081',
# '41164', '41173', '41180', '41566', '41778', '41951', '42228', '42511',
# '42878', '42961', '43247'
# ] + ['100', '101', '102', '103', '104', '105', '106', '107', '108', '109',
# '111', '112', '113', '114', '115', '116', '117', '118', '119', '121',
# '122', '123', '124', '200', '201', '202', '203', '205', '207', '208',
# '209', '210', '212', '213', '214', '215', '217', '219', '220', '221',
# '222', '223', '228', '230', '231', '232', '233', '234'
# ] + ['sel14046', 'sel14157', 'sel14172', 'sel15814', 'sel16265', 'sel16272',
# 'sel16273', 'sel16420', 'sel16483', 'sel16539', 'sel16773', 'sel16786',
# 'sel16795', 'sel17152', 'sel17453', 'sele0104', 'sele0106', 'sele0107',
# 'sele0110', 'sele0111', 'sele0112', 'sele0114', 'sele0116', 'sele0121',
# 'sele0122', 'sele0124', 'sele0126', 'sele0129', 'sele0133', 'sele0136',
# 'sele0166', 'sele0170', 'sele0203', 'sele0210', 'sele0211', 'sele0303',
# 'sele0405', 'sele0406', 'sele0409', 'sele0411', 'sele0509', 'sele0603',
# 'sele0604', 'sele0606', 'sele0607', 'sele0609', 'sele0612', 'sele0704',
# 'sel100', 'sel102', 'sel103', 'sel104', 'sel114', 'sel116', 'sel117',
# 'sel123', 'sel213', 'sel221', 'sel223', 'sel230', 'sel231', 'sel232',
# 'sel233', 'sel301', 'sel302', 'sel306', 'sel307', 'sel308', 'sel310',
# 'sel803', 'sel808', 'sel811', 'sel820', 'sel821', 'sel840', 'sel847',
# 'sel853', 'sel871', 'sel872', 'sel873', 'sel883', 'sel891'
# ] + [str(item) for item in list(range(1,201))]
databases = ["qtdb"]*82
#patients = [str(i) for i in list(range(100,200))]
patients = ['sel14046', 'sel14157', 'sel14172', 'sel15814', 'sel16265', 'sel16272',
'sel16273', 'sel16420', 'sel16483', 'sel16539', 'sel16773', 'sel16786',
'sel16795', 'sel17152', 'sel17453', 'sele0104', 'sele0106', 'sele0107',
'sele0110', 'sele0111', 'sele0112', 'sele0114', 'sele0116', 'sele0121',
'sele0122', 'sele0124', 'sele0126', 'sele0129', 'sele0133', 'sele0136',
'sele0166', 'sele0170', 'sele0203', 'sele0210', 'sele0211', 'sele0303',
'sele0405', 'sele0406', 'sele0409', 'sele0411', 'sele0509', 'sele0603',
'sele0604', 'sele0606', 'sele0607', 'sele0609', 'sele0612', 'sele0704',
'sel100', 'sel102', 'sel103', 'sel104', 'sel114', 'sel116', 'sel117',
'sel123', 'sel213', 'sel221', 'sel223', 'sel230', 'sel231', 'sel232',
'sel233', 'sel301', 'sel302', 'sel306', 'sel307', 'sel308', 'sel310',
'sel803', 'sel808', 'sel811', 'sel820', 'sel821', 'sel840', 'sel847',
'sel853', 'sel871', 'sel872', 'sel873', 'sel883', 'sel891'
]
def processECGFile(data):
exec_path = join(os.getcwd(), "Binaries/App/demo.exe" )
ecg_path = join(os.getcwd(), "Temp/AppTemp/ecg_file.csv" )
beat_path = join(os.getcwd(), "Temp/AppTemp/beat_file.txt" )
block_path = join(os.getcwd(), "Temp/AppTemp/block_file.txt" )
#for each channel
retDict = {}
#right now only channel [0]
for channel in [0]:
pd.DataFrame({'ecg': data.data[:,channel]}).to_csv(ecg_path)
prev_wd = os.getcwd()
try:
os.chdir(os.path.dirname(exec_path))
execution_result = call([exec_path, str(data.getFreq()), ecg_path, beat_path, block_path])
finally:
os.chdir(prev_wd)
if execution_result == 0:
#read output files
blocksAnn = pd.read_csv(block_path, sep = ";",
names = ["start_T","end_T","start","end","bpm","type"])
beatsAnnRaw = pd.read_csv(beat_path, sep = "\t",
names = ["raw"])
beatsAnn = beatsAnnRaw.raw.str.strip().str.split(" ", expand = True)
beatsAnn.columns = ["idx","annotation"]
beatsAnn = beatsAnn[beatsAnn['annotation'].isnull() == False]
beatsAnn['idx'] = pd.to_numeric(beatsAnn['idx'], errors = 'coerce')
retDict[channel] = ChannelDescription(blocksAnn, beatsAnn)
else:
retDict[channel] = None
return retDict
def check_segmentation(dbcode, patient_nr):
ret = []
if(platform.system() == "Linux"):
base_dir_raw = os.path.join(os.getcwd(),"Datasets/"+dbcode+"/data_raw")
else:
base_dir_raw = os.path.join(os.getcwd(),"Datasets\\"+dbcode+"\\data_raw")
if (dbcode=='ludb'):
data = LoadFile(join(base_dir_raw, patient_nr), "atr_ii")
else:
data = LoadFile(join(base_dir_raw, patient_nr))
#ecg segmenters
for segmenter in segmenters:
rpeaks = segmenter(data.data[:,0], data.freq)[0]
ann_selector = [x in PhysionetConstants.all_beats for x in data.annotations.anntype]
anntype_selected = np.array(data.annotations.anntype)[ann_selector]
annsamp_selected = data.annotations.annsamp[ann_selector]
ref_peaks = sample_to_time(annsamp_selected, data.freq)
pred_peaks = sample_to_time(rpeaks, data.freq)
try:
peaks_matching = match_peaks(ref_peaks, pred_peaks)
ret_qrs_scores = qrs_detection_scores( ref_peaks, pred_peaks, peaks_matching)
ret.append([dbcode] + [patient_nr] + [segmenter.__name__] + [len(ref_peaks)] +
[len(pred_peaks)] + [len(peaks_matching)] + list(ret_qrs_scores))
except Exception:
traceback.print_exc()
print("---")
ret.append([dbcode] + [patient_nr] + [segmenter.__name__] + [-1]*7)
# WTDelin
# rpeaks = fcg.delineateMultiLeadECG(data.data[:,0][:,np.newaxis],data.freq)[0][:,4]
# try:
# ann_selector = [x in PhysionetConstants.all_beats for x in data.annotations.anntype]
# anntype_selected = np.array(data.annotations.anntype)[ann_selector]
# annsamp_selected = data.annotations.annsamp[ann_selector]
# ref_peaks = sample_to_time(annsamp_selected, data.freq)
# pred_peaks = sample_to_time(rpeaks, data.freq)
# peaks_matching = match_peaks(ref_peaks, pred_peaks)
# ret_qrs_scores = qrs_detection_scores( ref_peaks, pred_peaks, peaks_matching)
# ret.append([dbcode] + [patient_nr] + ["WTDelin"] + [len(ref_peaks)] +
# [len(pred_peaks)] + [len(peaks_matching)] + list(ret_qrs_scores))
# except Exception:
# traceback.print_exc()
# print("---")
# ret.append([dbcode] + [patient_nr] + ["WTDelin"] + [-1]*7)
return ret
#print(from_3dbs("cinc1", "101"))
#print(from_3dbs("mitdb", "100"))
#print(from_3dbs("cinc2", "1003"))
resultsdf = pd.DataFrame(columns=['dbcode', 'patient_nr', 'segmenter',
'ref_peaks', 'pred_peaks', 'peaks_matching',
'mu', 'sigma', 'TPR', 'PPV'])
#for j in range(len(databases)):
#for j in range(330,333):
#for j in [10, 58, 74, 109, 122, 142, 154, 190, 196, 197, 250]:
#for j in ([190, 196, 197, 249, 250] + list(range(251,248+82))):
#for j in range(248, 248+82):
#for j in range(248+82+34, 248+82+200):
#for j in range(248+82+200):
for j in range(len(databases)):
print(j, databases[j], patients[j])
a=check_segmentation(databases[j], patients[j])
for i in range(len(a)):
resultsdf.loc[len(resultsdf)] = a[i]
#print(databases[58], patients[58])