How to use record_starttime method in Radish

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1_extractingrequiredsignalsandtimeoverlapwithicustay.py

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1# -*- coding: utf-8 -*-2"""1_ExtractingRequiredSignalsandTimeOverlapWithICUStay.ipynb3Automatically generated by Colaboratory.4Original file is located at5 https:/​/​colab.research.google.com/​drive/​1WlVZsHEAe1H4sLDaFeTUTI1lwymSx_X26"""7# This notebook does the following:8# 1. Extract the SUBJECT_IDs for whom a record edxists in the MIMIC matched waveform dataset (total number 4,653) from a 'df_waveform_exists.csv' CSV file into a dataframe9# 2. Extract all the unique signals that are recorded for above patients and generate a 'physio_signals.txt' file.10# 3. Check for which SUBJECT_IDs there exists all relevant signals i.e. HR, SPO2%, ABP SYS, ABP DIAS, ABP MEAN, and RESP. If there exists all signals11# insert '1' in the 'sig_exists' column for that particular patient in the dataframe.12# 4. Considering the SUBJECT_IDs for which there exists all relevant signals in the database, 13# check if the recordings in the database overlap with their ICU stays i.e. check if there is a overlap between the recording start date and end date 14# and ICU intime and outtime. If there exists a overlap, insert '1' in the 'timeoverlap' column for that particular patient in the dataframe.15# 5. Generate a final CSV 'df_TS_exists_withoutTEMP_overlapcount.csv'16# 6. There are a few sample records, 1 for once per second sampling frequency and 1 for once per minute frequency. Each of these are read from the17# matched waveform database and we extract only required HR, SPO2%, ABP SYS, ABP DIAS, ABP MEAN,& RESP signals and insert it into a dataframe. For sample18# with onec per second sampling frequency, the data is converted to once per minute by calculating average for each 60 secs.19# Commented out IPython magic to ensure Python compatibility.20!pip install wfdb21import io22import pandas as pd23from IPython.display import display24import matplotlib.pyplot as plt25# %matplotlib inline26import numpy as np27import os28import shutil29import posixpath30import wfdb31import urllib.request32import datetime33from google.colab import files34uploaded = files.upload()35df_csvdata = pd.read_csv(io.BytesIO(uploaded['df_waveform_exists.csv']))36# Dataset is now stored in a Pandas Dataframe37print (df_csvdata.shape)38df_csvdata['sig_exists']='';39df_csvdata['timeoverlap']='';40df_csvdata['Number_of_overlaping_records'] =''41print (df_csvdata.shape)42#To get a list of all the unique signals present in PHYSIOBANK43from collections import namedtuple44for index, row in df_csvdata.iterrows():45 #print(row['subject_id'], row['icustay_id'], row['sepsis_onsettime'],row['intime'],row['outtime'])46 signals_in_pyhisobank=[]47 wdb_dir_path = 'mimic3wdb/​matched/​p'+ str(row['subject_id']).zfill(6)[:2] + '/​p' + str(row['subject_id']).zfill(6) + '/​';48 wdb_path_toAllRecords = 'https:/​/​archive.physionet.org/​physiobank/​database/​'+ wdb_dir_path + 'RECORDS';49 wdb_records = urllib.request.urlopen(wdb_path_toAllRecords); 50 for lines in wdb_records.readlines():51 record = lines.decode("utf-8"); 52 record = str(record).rstrip()53 #print (record[-1:])54 if record[-1:] == 'n':55 #print(record);56 #print (wdb_dir_path);57 record = str(record).rstrip()58 try:59 print(row['subject_id'])60 signals,fields = wfdb.rdsamp(record, pb_dir=wdb_dir_path) ; 61 for i in fields['sig_name']:62 if i not in signals_in_pyhisobank:63 signals_in_pyhisobank.append(i);64 65 except ValueError:66 print('Error occured while reading waveform: ', record);67"""68#testing date part69 70 71 72 Range = namedtuple('Range', ['start', 'end'])73 print ('intime :', datetime.datetime.strptime(row['intime'],'%Y-%m-%d %H:%M:%S') ); 74 75 print ('outtime :', datetime.datetime.strptime(row['outtime'],'%Y-%m-%d %H:%M:%S') ); 76 print ('record starttime' , record_starttime);77 print ('record endtime' , record_endtime);78 r1 = Range(start= datetime.datetime.strptime(row['intime'],'%Y-%m-%d %H:%M:%S'), end= datetime.datetime.strptime(row['outtime'],'%Y-%m-%d %H:%M:%S'))79 r2 = Range(start= record_starttime, end = record_endtime)80 latest_start = max(r1.start, r2.start)81 earliest_end = min(r1.end, r2.end)82 delta = (earliest_end - latest_start).days + 183 if delta > 0 :84 print('NO OVERLAP BETWEEN RECORD DATETIME AND ICU STAY DATETIME')85 df_csvdata['TS_exists'] = 1;86 #overlap = max(0, delta) #to find exact overlap days87"""88print(len(signals_in_pyhisobank))89with open("physio_signals.txt", "w") as output:90 output.write(str(signals_in_pyhisobank))91from google.colab import files92files.download('physio_signals.txt')93#### IMPORTANT ! DO NOT DELETE94#To get patients for whom required signals exists and there are TS records for the ICU stay in consideration95from collections import namedtuple96for index, row in df_csvdata.iterrows():97 #print(row['subject_id'], row['icustay_id'], row['sepsis_onsettime'],row['intime'],row['outtime'])98 records_toRead=[]99 wdb_dir_path = 'mimic3wdb/​matched/​p'+ str(row['subject_id']).zfill(6)[:2] + '/​p' + str(row['subject_id']).zfill(6) + '/​';100 wdb_path_toAllRecords = 'https:/​/​archive.physionet.org/​physiobank/​database/​'+ wdb_dir_path + 'RECORDS';101 wdb_records = urllib.request.urlopen(wdb_path_toAllRecords); 102 count_overlaping_records = 0 103 for lines in wdb_records.readlines():104 record = lines.decode("utf-8"); 105 record = str(record).rstrip()106 #print (record[-1:])107 if record[-1:] == 'n':108 #print(record);109 #print (wdb_dir_path);110 record = str(record).rstrip()111 try:112 signals,fields = wfdb.rdsamp(record, pn_dir=wdb_dir_path) ; 113 #wfdb.plot_items(signal=signals, fs=fields['fs'])114 #display(signals)115 #display(fields)116 #print ('fs' , fields['fs']);117 #print ('signal length',fields['sig_len']);118 #print ('date' ,fields['base_date'] ); 119 #print ('time' ,fields['base_time'] );120 #print ('%.3f'%(fields['fs']))121 122 list_sig_name = [item.upper().replace(' ','') for item in fields['sig_name']]123 sig_exist_1 = all(x in list_sig_name for x in ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); #%SpO2124 sig_exist_2 = all(x in list_sig_name for x in ['HR', '%SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); 125 if ((sig_exist_1 == True) or (sig_exist_2 == True)) :126 df_csvdata.loc[index,'sig_exists'] = 1;127 record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;128 129 if '%.3f'%(fields['fs']) == '1.000' :130 record_endtime = record_starttime + datetime.timedelta(seconds= (fields['sig_len']-1)) ;131 elif '%.3f'%(fields['fs'])== '0.017' :132 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;133 else : 134 print('ERROR IN SAMPLING');135 print(record);136 print (wdb_dir_path);137 #Caculate if we have a recording for the time of icu stay138 Range = namedtuple('Range', ['start', 'end'])139 r1 = Range(start= datetime.datetime.strptime(row['intime'],'%Y-%m-%d %H:%M:%S'), end= datetime.datetime.strptime(row['outtime'],'%Y-%m-%d %H:%M:%S'))140 r2 = Range(start= record_starttime, end = record_endtime)141 latest_start = max(r1.start, r2.start)142 earliest_end = min(r1.end, r2.end)143 delta = (earliest_end - latest_start).days + 1144 if delta >= 0 :145 print('RECORD EXISTS FOR THE ICU STAYS WITH THE SIGNALS NEEDED : ', row['subject_id'])146 df_csvdata.loc[index,'timeoverlap'] = 1;147 count_overlaping_records = count_overlaping_records +1 ;148 #todo : adding new dataframe, exatracting required signals, computing avergage for per sminute values in case of per second sampling frequency149 else: 150 print('RECORD DOES NOT EXISTS FOR THE ICU STAYS WITH THE SIGNALS NEEDED : ', row['subject_id'])151 #df_csvdata.loc[index,'timeoverlap'] = 0;152 else:153 #df_csvdata.loc[index,'sig_exists'] = 0 ;154 print('DO NOT SELECT THIS RECORD', row['subject_id'])155 except ValueError:156 print('Error occured while reading waveform: ', record);157 df_csvdata.loc[index,'Number_of_overlaping_records'] = count_overlaping_records;158"""159#testing date part160 161 162 163 Range = namedtuple('Range', ['start', 'end'])164 print ('intime :', datetime.datetime.strptime(row['intime'],'%Y-%m-%d %H:%M:%S') ); 165 166 print ('outtime :', datetime.datetime.strptime(row['outtime'],'%Y-%m-%d %H:%M:%S') ); 167 print ('record starttime' , record_starttime);168 print ('record endtime' , record_endtime);169 r1 = Range(start= datetime.datetime.strptime(row['intime'],'%Y-%m-%d %H:%M:%S'), end= datetime.datetime.strptime(row['outtime'],'%Y-%m-%d %H:%M:%S'))170 r2 = Range(start= record_starttime, end = record_endtime)171 latest_start = max(r1.start, r2.start)172 earliest_end = min(r1.end, r2.end)173 delta = (earliest_end - latest_start).days + 1174 if delta > 0 :175 print('NO OVERLAP BETWEEN RECORD DATETIME AND ICU STAY DATETIME')176 df_csvdata['TS_exists'] = 1;177 #overlap = max(0, delta) #to find exact overlap days178"""179"""180# check dataframe 181print(df_csvdata[(df_csvdata['sig_exists'] == 1)].shape)182print(df_csvdata[(df_csvdata['timeoverlap'] == 1)].shape)183df_csvdata.to_csv ('df_TS_exists_withoutTEMP_overlapcount.csv', sep=',', index = False, header=True);184from google.colab import files185files.download('df_TS_exists_withoutTEMP_overlapcount.csv')186"""187# check dataframe 188print(df_csvdata[(df_csvdata['sig_exists'] == 1)].shape)189print(df_csvdata[(df_csvdata['timeoverlap'] == 1)].shape)190df_csvdata.to_csv ('df_TS_exists_withoutTEMP_overlapcount.csv', sep=',', index = False, header=True);191from google.colab import files192files.download('df_TS_exists_withoutTEMP_overlapcount.csv')193# Commented out IPython magic to ensure Python compatibility.194#example to send to Marcela195!pip install wfdb196import io197import pandas as pd198from IPython.display import display199import matplotlib.pyplot as plt200# %matplotlib inline201import numpy as np202import os203import shutil204import posixpath205import wfdb206import urllib.request207import datetime208"""209'HR',210 'PULSE', 211 'ABP SYS',212 'ABP DIAS',213"""214channels = ['ABP DIAS','ABP SYS','PULSE','temp','HR']215signals,fields = wfdb.rdsamp('p042930-2190-07-28-20-30n', pn_dir='mimic3wdb/​matched/​p04/​p042930/​', channel_names=['HR','ABP MEAN', 'ABP SYS','ABP DIAS'], sampfrom=100, sampto=120)216print(' ')217print(' ')218print(' ')219wfdb.plot_items(signal=signals, fs=fields['fs'])220print('Printing signals')221display(signals)222print('Printing fields')223display(fields)224print('------------------------------')225print ('fs' , fields['fs']);226print ('signal length',fields['sig_len']);227print ('date' ,fields['base_date'] ); 228print ('time' ,fields['base_time'] );229record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;230print ('%.3f'%(fields['fs']))231if '%.3f'%(fields['fs']) == '1.000':232 print ('Sampled once per second')233 record_endtime = record_starttime + datetime.timedelta(seconds = (fields['sig_len']-1)) ;234elif '%.3f'%(fields['fs'])== '0.017' :235 print('Sampled once per minute')236 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;237else :238 print('ERROR IN SAMPLING')239# Commented out IPython magic to ensure Python compatibility.240#### To show a sample of person suffereing from sepsis with high values for ABP Systolic (90 and less than 120) and low values for ABP diastolic (60 and less than 80)241# SAMPLE FREQUENCY: ONCE PER SECOND242#for i in subject_ids:243 # print (i.zfill(6)); --2186-01-26 14:13:07244!pip install wfdb245import io246import pandas as pd247from IPython.display import display248import matplotlib.pyplot as plt249# %matplotlib inline250import numpy as np251import os252import shutil253import posixpath254import wfdb255import urllib.request256import datetime257signals,fields = wfdb.rdsamp('p030582-2129-04-07-17-23n', pn_dir='mimic3wdb/​matched/​p03/​p030582/​')#sampfrom = 150 , sampto = 200258wfdb.plot_items(signal=signals, fs=fields['fs'])259#display(record.__dict__)260display(signals)261display(fields)262df_ts_records_columns = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP'] 263df_ts_records = pd.DataFrame(columns=df_ts_records_columns);264for i in fields['sig_name']:265 if i.upper().replace(' ','') == 'HR':266 idx_HR = fields['sig_name'].index(i);267 df_ts_records['HR']= signals[:,idx_HR ]268 elif (( i.upper().replace(' ','') == 'SPO2') or (i.upper().replace(' ','') =='%SPO2')):269 idx_SPO2 = fields['sig_name'].index(i);270 df_ts_records['SPO2']= signals[:,idx_SPO2]271 elif i.upper().replace(' ','') == 'ABPSYS' :272 idx_ABPSYS = fields['sig_name'].index(i);273 df_ts_records['ABPSYS']= signals[:,idx_ABPSYS]274 elif i.upper().replace(' ','') == 'ABPDIAS' :275 idx_ABPDIAS = fields['sig_name'].index(i);276 df_ts_records['ABPDIAS']= signals[:,idx_ABPDIAS]277 elif i.upper().replace(' ','') == 'ABPMEAN' :278 idx_ABPMEAN = fields['sig_name'].index(i);279 df_ts_records['ABPMEAN']= signals[:,idx_ABPMEAN]280 281 elif i.upper().replace(' ','') == 'RESP' :282 idx_RESP = fields['sig_name'].index(i);283 df_ts_records['RESP']= signals[:,idx_RESP]284 285record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;286if '%.3f'%(fields['fs']) == '1.000' :287 print ('Sampled once per second')288 record_endtime = record_starttime + datetime.timedelta(seconds = (fields['sig_len']-1)) ;289elif '%.3f'%(fields['fs'])== '0.017' :290 print('Sampled once per minute')291 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;292else :293 print('ERROR IN SAMPLING') 294print ('start time: ', record_starttime);295print ('end time: ', record_endtime);296""" START COMMENT297df_ts_records['TIME'] = pd.date_range( record_starttime , periods = fields['sig_len'], freq='S'); 298df_ts_records.TIME = pd.to_datetime(df_ts_records.TIME)299#dat['STA_STD_NEW'] = dat['STA_STD']300#dat.loc[dat['STA_STD'].dt.time == datetime.time(23,59), 'STA_STD_NEW'] += datetime.timedelta(minutes=1)301#In [5]: dat302df_ts_records['RECORD'] = 'p081193-2186-01-26-19-36n';303print(df_ts_records)304# to aggregate and convert per second values into per minute values305start_idx = 0;306df_ts_records_columns_new = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP'] 307df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns_new);308print('length of new df ' ,df_ts_records_new.shape[0] )309for index, rows in df_ts_records.iterrows():310 if start_idx >= df_ts_records.shape[0]:311 exit;312 else: 313 #print(df_ts_records.iloc[start_idx: (start_idx+2), 0:4])314 print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])315 array = np.array( df_ts_records.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))316 print('printing array of average')317 print (array)318 current_index = df_ts_records_new.shape[0]319 df_ts_records_new.loc[current_index ,'HR']= array[0]320 df_ts_records_new.loc[current_index,'SPO2']= array[1]321 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]322 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]323 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]324 df_ts_records_new.loc[current_index,'RESP']= array[5]325 print(df_ts_records_new)326 print('next average')327 start_idx = start_idx+60;328 #print('start index :: ' , start_idx)329df_ts_records_new['TIME'] = pd.date_range(record_starttime, periods=(fields['sig_len']/​60), freq='1min'); 330df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)331df_ts_records_new['RECORD'] = 'p081193-2186-01-26-19-36n';332print(df_ts_records_new)333 334""" #END COMMENT335# testing to convert per second data into per minute336"""337#df.iloc[1:3, 0:3]338mydict = [{'a': 1, 'b': 2, 'c': 3, 'd': 4},339 {'a': 100, 'b': 200, 'c': 300, 'd': 400},340 {'a': 1000, 'b': 2000, 'c': 3000, 'd': 4000 },341 {'a': 10, 'b': 30, 'c': 50, 'd': 70 },342 {'a': 20, 'b': 40, 'c': 60, 'd': 80 },343 {'a': 20, 'b': 40, 'c': 60, 'd': 80 },344 {'a': 20, 'b': 40, 'c': 60, 'd': 80 },345 {'a': 20, 'b': 40, 'c': 60, 'd': 80 },346 {'a': 20, 'b': 40, 'c': 60, 'd': 80 }347 ]348import numpy as np349df = pd.DataFrame(mydict)350print (df)351"""352"""353print(df.shape)354print('-----')355print(df.iloc[0:2, 0:4])356dd = pd.DataFrame( df.iloc[0:2, 0:4].mean(axis =0))357print(dd)358"""359"""360print('---------------------')361start_idx = 0 362new_df=pd.DataFrame(columns=['a','b','c','d']);363print(new_df)364print('length of new df ' ,new_df.shape[0] )365for index, rows in df.iterrows():366 if start_idx > df.shape[0]:367 exit;368 else: 369 print(df.iloc[start_idx: (start_idx+2), 0:4])370 print(df.iloc[start_idx: (start_idx+2), 0:4].mean(axis=0))371 array = np.array( df.iloc[start_idx: (start_idx+2), 0:4].mean(axis=0))372 print (array)373 374 current_index = new_df.shape[0]375 new_df.loc[current_index ,'a']= array[0]376 new_df.loc[current_index,'b']= array[1]377 new_df.loc[current_index,'c']= array[2]378 new_df.loc[current_index,'d']= array[3]379 print(new_df)380 print('next average')381 start_idx = start_idx+2;382 print('start index :: ' , start_idx)383 384"""385#### To show a sample of person NOT suffereing from sepsis 386##############################387################################388#for i in subject_ids:389 # print (i.zfill(6)); --2186-01-26 14:13:07390 391 392 # SAMPLE FREQUENCY: ONCE PER MINUTE393df_ts_records_columns = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP','TEMP'] 394sig_list_1 = ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP','TEMP'] 395sig_list_2 = ['HR', '%SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP','TEMP']396df_ts_records = pd.DataFrame(columns=df_ts_records_columns);397signals, fields = wfdb.rdsamp('p059864-2173-05-16-11-56n', pn_dir ='mimic3wdb/​matched/​p05/​p059864/​')398# signals, fields = wfdb.rdsamp('p042930-2190-07-28-20-30n', pn_dir='mimic3wdb/​matched/​p04/​p042930/​',sampfrom=0, sampto=10)399wfdb.plot_items(signal=signals, fs=fields['fs'])400display(signals)401print( signals.shape) ;402display(fields)403for i in fields['sig_name']:404 if i.upper().replace(' ','') == 'HR':405 idx_HR = fields['sig_name'].index(i);406 df_ts_records['HR']= signals[:,idx_HR ]407 elif (( i.upper().replace(' ','') == 'SPO2') or (i.upper().replace(' ','') =='%SPO2')):408 idx_SPO2 = fields['sig_name'].index(i);409 df_ts_records['SPO2']= signals[:,idx_SPO2]410 elif i.upper().replace(' ','') == 'ABPSYS' :411 idx_ABPSYS = fields['sig_name'].index(i);412 df_ts_records['ABPSYS']= signals[:,idx_ABPSYS]413 elif i.upper().replace(' ','') == 'ABPDIAS' :414 idx_ABPDIAS = fields['sig_name'].index(i);415 df_ts_records['ABPDIAS']= signals[:,idx_ABPDIAS]416 elif i.upper().replace(' ','') == 'ABPMEAN' :417 idx_ABPMEAN = fields['sig_name'].index(i);418 df_ts_records['ABPMEAN']= signals[:,idx_ABPMEAN]419 420 elif i.upper().replace(' ','') == 'RESP' :421 idx_RESP = fields['sig_name'].index(i);422 df_ts_records['RESP']= signals[:,idx_RESP]423 elif i.upper().replace(' ','') == 'TEMP':424 idx_TEMP = fields['sig_name'].index(i);425 df_ts_records['TEMP']= signals[:,idx_TEMP ]426 427print(df_ts_records);428record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;429if '%.3f'%(fields['fs']) == '1.000' :430 print ('Sampled once per second')431 record_endtime = record_starttime + datetime.timedelta(seconds = ( fields['sig_len']-1 )) ;432elif '%.3f'%(fields['fs'])== '0.017' :433 print('Sampled once per minute')434 record_endtime = record_starttime + datetime.timedelta(minutes = ( fields['sig_len']-1 )) ;435else :436 print('ERROR IN SAMPLING') 437print ('start time: ', record_starttime);438print ('end time: ', record_endtime);439df_ts_records['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 440df_ts_records.TIME = pd.to_datetime(df_ts_records.TIME)441df_ts_records['RECORD'] = 'p042930-2190-07-28-20-30n';442#print('--------#####-----')443#print(df_ts_records[ (df_ts_records['TIME'] >= '2151-10-06 05:25:35') & (df_ts_records['TIME'] <= '2151-10-06 05:29:35')])444#print('dropping all null')445#print(df_ts_records.dropna())446# Commented out IPython magic to ensure Python compatibility.447#### IMPORTANT ! DO NOT DELETE448#To get patient records if multiple ts existis 449!pip install wfdb450import io451import pandas as pd452from IPython.display import display453import matplotlib.pyplot as plt454# %matplotlib inline455import numpy as np456import os457import shutil458import posixpath459import wfdb460import urllib.request461import datetime462from collections import namedtuple463df_ts_records_columns = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP'] 464df_ts_records = pd.DataFrame(columns=df_ts_records_columns); 465#subject_id= 48149; # per second multiple 466#icu_intime = datetime.datetime(2127, 5, 25, 8, 34,39) # for 48149467#icu_outtime = datetime.datetime(2127, 6, 16, 1, 15,22) # for 4814946866965 23/​01/​2198 12:41 28/​01/​2198 19:16 22/​01/​2198 22:46 23/​01/​2198 13:46469subject_id= 55638; # per minute 470icu_intime = datetime.datetime(2106, 11, 25, 12, 37,32) # for 55638471icu_outtime = datetime.datetime(2106, 11, 27, 10, 49,33) # for 55638472print ('icu intime =', icu_intime)473print ('icu outtime', icu_outtime)474"""475subject_id= 59864;476icu_intime = datetime.datetime(2173, 5, 16, 12, 14,45)477print ('icu intime =', icu_intime)478icu_outtime = datetime.datetime(2173, 6, 8, 15, 45,23)479print ('icu outtime', icu_outtime)480#2173-05-16 12:14:45,2173-06-08 15:45:23,481"""482wdb_dir_path = 'mimic3wdb/​matched/​p'+ str(subject_id).zfill(6)[:2] + '/​p' + str(subject_id).zfill(6) + '/​';483wdb_path_toAllRecords = 'https:/​/​archive.physionet.org/​physiobank/​database/​'+ wdb_dir_path + 'RECORDS';484wdb_records = urllib.request.urlopen(wdb_path_toAllRecords); 485try:486 df_ts_records.drop(df_ts_records.index, inplace=True)487except:488 print('df_ts_records does not exist')489count_overlap = 0; 490for lines in wdb_records.readlines():491 record = lines.decode("utf-8"); 492 record = str(record).rstrip()493 #print (record[-1:])494 if record[-1:] == 'n':495 print(record);496 #print (wdb_dir_path);497 record = str(record).rstrip()498 499 500 #try:501 signals =''502 fields = ''503 signals,fields = wfdb.rdsamp(record, pn_dir=wdb_dir_path) ; 504 505 list_sig_name = [item.upper().replace(' ','') for item in fields['sig_name']]506 sig_exist_1 = all(x in list_sig_name for x in ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); #%SpO2507 sig_exist_2 = all(x in list_sig_name for x in ['HR', '%SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); 508 record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;509 510 if '%.3f'%(fields['fs']) == '1.000' :511 record_endtime = record_starttime + datetime.timedelta(seconds= (fields['sig_len']-1)) ;512 elif '%.3f'%(fields['fs'])== '0.017' :513 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;514 else : 515 print('ERROR IN SAMPLING');516 print(record);517 print(wdb_dir_path);518 print('record START time: ', record_starttime)519 print('record END time: ', record_endtime)520 Range = namedtuple('Range', ['start', 'end'])521 r1 = Range(start= icu_intime, end= icu_outtime)522 r2 = Range(start= record_starttime, end = record_endtime)523 latest_start = max(r1.start, r2.start)524 earliest_end = min(r1.end, r2.end)525 delta = (earliest_end - latest_start).days + 1526 #delta >= 0 :527 print('sig_exist_1 : ', sig_exist_1)528 print('sig_exist_2 : ', sig_exist_2)529 print('delta : ', delta)530 if ( ((sig_exist_1 == True) or (sig_exist_2 == True)) and (delta >= 0)):531 ###532 try:533 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True)534 except:535 print('individual record for a single patient df does not exists')536 537 df_ts_indv_record_temp = pd.DataFrame(columns = df_ts_records_columns ) # individual record for a single patient #safiya538 ###539 df_row_idx = df_ts_records.shape[0] ;540 print('length of signal: ', len(signals))541 print('index of dataframe before inserting into it: ', df_row_idx)542 543 for i in fields['sig_name']:544 545 if i.upper().replace(' ','') == 'HR':546 idx_HR = fields['sig_name'].index(i);547 elif (( i.upper().replace(' ','') == 'SPO2') or (i.upper().replace(' ','') =='%SPO2')):548 idx_SPO2 = fields['sig_name'].index(i);549 elif i.upper().replace(' ','') == 'ABPSYS' :550 idx_ABPSYS = fields['sig_name'].index(i);551 elif i.upper().replace(' ','') == 'ABPDIAS' :552 idx_ABPDIAS = fields['sig_name'].index(i);553 elif i.upper().replace(' ','') == 'ABPMEAN' :554 idx_ABPMEAN = fields['sig_name'].index(i);555 elif i.upper().replace(' ','') == 'RESP' :556 idx_RESP = fields['sig_name'].index(i);557 558 559 560 if count_overlap == 0 : 561 if record_starttime > icu_intime:562 print('inserting nulls before the record start time')563 #print( (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) ) #+ datetime.timedelta(seconds= int(record_starttime.strftime('%S'))) )564 #print(icu_intime.strftime('%Y-%m-%d %H:%M'))565 if '%.3f'%(fields['fs'])== '0.017' :566 minutes_to_insert_start = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))- (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))567 elif '%.3f'%(fields['fs'])== '1.000' :568 minutes_to_insert_start = record_starttime - icu_intime569 print('minutes_to_insert_start: ', minutes_to_insert_start)570 duration_in_s = minutes_to_insert_start.total_seconds()571 minutes_to_insert_start = divmod(duration_in_s, 60)[0] - 1 572 try:573 df_ts_records_time_temp_start.drop(df_ts_records_time_temp_start.index, inplace=True)574 except :575 print( 'df_ts_records_time_temp_start does not exist')576 577 df_ts_records_time_temp_start = pd.DataFrame(columns=df_ts_records_columns)578 if '%.3f'%(fields['fs'])== '0.017' :579 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(minutes=1), 580 periods=minutes_to_insert_start, freq='1min'); 581 elif '%.3f'%(fields['fs'])== '1.000' :582 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(seconds=1), 583 periods= (duration_in_s-1), freq='S'); 584 print ('INSERTING ONLY NULL IN START:')585 print (df_ts_records_time_temp_start)586 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp_start, ignore_index=True);587 print('inserting nulls in start IN INDV LEVEL')588 print(df_ts_indv_record_temp)589 try:590 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True)591 except:592 print( 'df_ts_records_temp does not exist')593 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)594 df_ts_records_temp['HR']= signals[:,idx_HR ] 595 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 596 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 597 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 598 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 599 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 600 if '%.3f'%(fields['fs'])== '0.017' :601 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 602 elif '%.3f'%(fields['fs'])== '1.000' :603 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 604 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)605 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True); #safiya606 print('inserting nulls in start + first record data')607 print(df_ts_indv_record_temp)608 if '%.3f'%(fields['fs'])== '1.000' : #safiya609 print("AGGREGATING")610 start_idx = 0;611 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);612 #print('length of new df ' , df_ts_records_new.shape[0] )613 for index, rows in df_ts_indv_record_temp.iterrows():614 print('start index for first: ', start_idx)615 if start_idx >= df_ts_indv_record_temp.shape[0]:616 exit;617 else: 618 619 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])620 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))621 #print('printing array of average')622 #print (array)623 current_index = df_ts_records_new.shape[0]624 df_ts_records_new.loc[current_index ,'HR']= array[0]625 df_ts_records_new.loc[current_index,'SPO2']= array[1]626 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]627 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]628 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]629 df_ts_records_new.loc[current_index,'RESP']= array[5]630 #print(df_ts_records_new)631 #print('next average')632 start_idx = start_idx+60;633 #print('start index :: ' , start_idx)634 print('# record time: ',df_ts_records_new.shape[0])635 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 636 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)637 #print(df_ts_records_new)638 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);639 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)640 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);641 print('only first record aggregated at individual record level: ')642 print(df_ts_records_new)643 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')644 print(df_ts_records)645 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)646 df_ts_records['RECORD'] = record 647 else:648 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);649 df_ts_records['RECORD'] = record 650 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')651 print(df_ts_records)652 653 654 else:655 if record_starttime <= icu_outtime :656 last_Record_time = df_ts_records.loc[(df_row_idx-1),'TIME']657 print('main DF last time record: ',last_Record_time )658 if '%.3f'%(fields['fs'])== '0.017' :659 minutes_to_insert = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((last_Record_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))660 elif '%.3f'%(fields['fs'])== '1.000' :661 minutes_to_insert = record_starttime - last_Record_time662 duration_in_s = minutes_to_insert.total_seconds()663 minutes_to_insert = divmod(duration_in_s, 60)[0] - 1664 print ('minutes_to_insert: ', minutes_to_insert);665 print('seconds to insert: ', duration_in_s)666 try:667 df_ts_records_time_temp.drop(df_ts_records_time_temp.index, inplace=True);668 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True);669 except:670 print ('df_ts_records_temp and df_ts_records_time_temp does not exits')671 df_ts_records_time_temp = pd.DataFrame(columns=df_ts_records_columns)672 if '%.3f'%(fields['fs'])== '0.017' :673 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(minutes=1), 674 periods=minutes_to_insert, freq='1min'); 675 elif '%.3f'%(fields['fs'])== '1.000' :676 print('last record time' , last_Record_time)677 print('(duration_in_s-1)' , (duration_in_s-1))678 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(seconds=1), 679 periods=(duration_in_s-1), freq='S'); 680 print ('INSERTING ONLY NULL UNTILL NEXT RECORD START TIME:')681 print (df_ts_records_time_temp)682 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp, ignore_index=True);683 print('inserting nulls UNTILL NEXT RECORD START TIME INTO INDV LEVEL')684 print(df_ts_indv_record_temp)685 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)686 687 df_ts_records_temp['HR']= signals[:,idx_HR ] 688 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 689 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 690 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 691 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 692 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 693 if '%.3f'%(fields['fs'])== '0.017' :694 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 695 elif '%.3f'%(fields['fs'])== '1.000' :696 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 697 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)698 699 print('before appending: ')700 701 print( df_ts_records_temp);702 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True);703 print('inserting nulls in start + SECOND record data')704 print(df_ts_indv_record_temp)705 if '%.3f'%(fields['fs'])== '1.000' : #safiya706 start_idx = 0;707 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);708 #print('length of new df ' , df_ts_records_new.shape[0] )709 for index, rows in df_ts_indv_record_temp.iterrows():710 if start_idx >= df_ts_indv_record_temp.shape[0]:711 exit;712 else: 713 714 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])715 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))716 #print('printing array of average')717 #print (array)718 current_index = df_ts_records_new.shape[0]719 df_ts_records_new.loc[current_index ,'HR']= array[0]720 df_ts_records_new.loc[current_index,'SPO2']= array[1]721 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]722 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]723 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]724 df_ts_records_new.loc[current_index,'RESP']= array[5]725 #print(df_ts_records_new)726 #print('next average')727 start_idx = start_idx+60;728 #print('start index :: ' , start_idx)729 print('# record time: ',df_ts_records_new.shape[0])730 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 731 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)732 #print(df_ts_records_new)733 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);734 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)735 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);736 737 print('only first record aggregated at individual record level: ')738 print(df_ts_records_new)739 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')740 print(df_ts_records)741 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)742 df_ts_records['RECORD'] = record 743 else:744 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);745 df_ts_records['RECORD'] = record 746 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')747 print(df_ts_records)748 749 750 count_overlap = count_overlap +1751 print('overlap count after all insertions: ', count_overlap )752 else:753 print('Either all 6 signals not exists or there is no overlapt with recording time and ICU in time and out time')754last_record_idx = df_ts_records.shape[0] - 1755all_records_end_time = df_ts_records.loc[last_record_idx,'TIME']756 757if (all_records_end_time < icu_outtime ):758 #print('INSERTING NULLS AT THE END')759 try:760 df_ts_records_time_temp_end.drop(df_ts_records_time_temp_end.index, inplace=True)761 except:762 print('df_ts_records_time_temp_end does not exists')763 #print('main DF last time record: ',last_Record_time )764 if '%.3f'%(fields['fs'])== '0.017' :765 minutes_to_insert_end = (datetime.datetime.strptime((icu_outtime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((all_records_end_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) 766 elif '%.3f'%(fields['fs'])== '1.000' :767 minutes_to_insert_end = icu_outtime - all_records_end_time;768 duration_in_s = minutes_to_insert_end.total_seconds()769 minutes_to_insert_end = divmod(duration_in_s, 60)[0] - 1770 df_ts_records_time_temp_end = pd.DataFrame(columns=df_ts_records_columns)771 772 df_ts_records_time_temp_end['TIME'] = pd.date_range(all_records_end_time + datetime.timedelta(minutes=1), 773 periods=minutes_to_insert_end, freq='1min'); 774 df_ts_records = df_ts_records.append(df_ts_records_time_temp_end, ignore_index=True);775 776 df_ts_records['RECORD'] = record777print('printing final data for this patient')778print(df_ts_records)779#print(df_ts_records)780df_ts_records.to_csv ('SampleRecordWith6SigalsExtracted.csv', sep=',', index = False, header=True);781from google.colab import files...

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12_after_caculation_of_shock_onsettimeto_check_waveforms_and_plot_for_sample_test_patients.py

Source:12_after_caculation_of_shock_onsettimeto_check_waveforms_and_plot_for_sample_test_patients.py Github

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1# -*- coding: utf-8 -*-2"""12_after caculation of shock onsettimeTo check waveforms and plot for sample test patients.ipynb3Automatically generated by Colaboratory.4Original file is located at5 https:/​/​colab.research.google.com/​drive/​1AmJmUX_2wyz2vJcyoXaXQnHin75KLwyR6"""7# Commented out IPython magic to ensure Python compatibility.8!pip install wfdb9import io10import pandas as pd11from IPython.display import display12import matplotlib.pyplot as plt13# %matplotlib inline14import numpy as np15import os16import shutil17import posixpath18import wfdb19import urllib.request20import datetime21from collections import namedtuple22import seaborn as sns23import matplotlib.ticker as ticker24from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,25 AutoMinorLocator)26from matplotlib.dates import DateFormatter27import matplotlib.dates as mdates28# Commented out IPython magic to ensure Python compatibility.29#to test sample patient suffereing from sepsis30#### IMPORTANT ! DO NOT DELETE31#To get patient records if multiple ts existis 32!pip install wfdb33import io34import pandas as pd35from IPython.display import display36import matplotlib.pyplot as plt37# %matplotlib inline38import numpy as np39import os40import shutil41import posixpath42import wfdb43import urllib.request44import datetime45from collections import namedtuple46df_ts_records_columns = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP'] 47df_ts_records = pd.DataFrame(columns=df_ts_records_columns); 48# 66965 only sepsis no septic shock'49# 51871 both sepsis and septic shock 07/​01/​2162 15:30 12/​01/​2162 02:5650# 61619 28/​11/​2121 21:04 03/​12/​2121 15:55 28/​11/​2121 22:23 28/​11/​2121 21:23 29/​11/​2121 05:5951subject_id= 61619 52icu_intime = datetime.datetime(2121, 11, 28, 21, 4,00) # for 6696553icu_outtime = datetime.datetime(2121, 12, 3, 4, 15,55) # for 6696554print ('icu intime =', icu_intime)55print ('icu outtime', icu_outtime)56"""57subject_id= 59864;58icu_intime = datetime.datetime(2173, 5, 16, 12, 14,45)59print ('icu intime =', icu_intime)60icu_outtime = datetime.datetime(2173, 6, 8, 15, 45,23)61print ('icu outtime', icu_outtime)62#2173-05-16 12:14:45,2173-06-08 15:45:23,63"""64wdb_dir_path = 'mimic3wdb/​matched/​p'+ str(subject_id).zfill(6)[:2] + '/​p' + str(subject_id).zfill(6) + '/​';65wdb_path_toAllRecords = 'https:/​/​archive.physionet.org/​physiobank/​database/​'+ wdb_dir_path + 'RECORDS';66wdb_records = urllib.request.urlopen(wdb_path_toAllRecords); 67try:68 df_ts_records.drop(df_ts_records.index, inplace=True)69except:70 print('df_ts_records does not exist')71count_overlap = 0; 72for lines in wdb_records.readlines():73 record = lines.decode("utf-8"); 74 record = str(record).rstrip()75 #print (record[-1:])76 if record[-1:] == 'n':77 print(record);78 #print (wdb_dir_path);79 record = str(record).rstrip()80 81 82 #try:83 signals =''84 fields = ''85 signals,fields = wfdb.rdsamp(record, pn_dir=wdb_dir_path) ; 86 87 list_sig_name = [item.upper().replace(' ','') for item in fields['sig_name']]88 sig_exist_1 = all(x in list_sig_name for x in ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); #%SpO289 sig_exist_2 = all(x in list_sig_name for x in ['HR', '%SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); 90 record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;91 92 if '%.3f'%(fields['fs']) == '1.000' :93 record_endtime = record_starttime + datetime.timedelta(seconds= (fields['sig_len']-1)) ;94 elif '%.3f'%(fields['fs'])== '0.017' :95 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;96 else : 97 print('ERROR IN SAMPLING');98 print(record);99 print(wdb_dir_path);100 print('record START time: ', record_starttime)101 print('record END time: ', record_endtime)102 Range = namedtuple('Range', ['start', 'end'])103 r1 = Range(start= icu_intime, end= icu_outtime)104 r2 = Range(start= record_starttime, end = record_endtime)105 latest_start = max(r1.start, r2.start)106 earliest_end = min(r1.end, r2.end)107 delta = (earliest_end - latest_start).days + 1108 #delta >= 0 :109 print('sig_exist_1 : ', sig_exist_1)110 print('sig_exist_2 : ', sig_exist_2)111 print('delta : ', delta)112 if ( ((sig_exist_1 == True) or (sig_exist_2 == True)) ) : #and (delta >= 0)):113 ###114 try:115 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True)116 except:117 print('individual record for a single patient df does not exists')118 119 df_ts_indv_record_temp = pd.DataFrame(columns = df_ts_records_columns ) # individual record for a single patient #safiya120 ###121 df_row_idx = df_ts_records.shape[0] ;122 print('length of signal: ', len(signals))123 print('index of dataframe before inserting into it: ', df_row_idx)124 125 for i in fields['sig_name']:126 127 if i.upper().replace(' ','') == 'HR':128 idx_HR = fields['sig_name'].index(i);129 elif (( i.upper().replace(' ','') == 'SPO2') or (i.upper().replace(' ','') =='%SPO2')):130 idx_SPO2 = fields['sig_name'].index(i);131 elif i.upper().replace(' ','') == 'ABPSYS' :132 idx_ABPSYS = fields['sig_name'].index(i);133 elif i.upper().replace(' ','') == 'ABPDIAS' :134 idx_ABPDIAS = fields['sig_name'].index(i);135 elif i.upper().replace(' ','') == 'ABPMEAN' :136 idx_ABPMEAN = fields['sig_name'].index(i);137 elif i.upper().replace(' ','') == 'RESP' :138 idx_RESP = fields['sig_name'].index(i);139 140 141 142 if count_overlap == 0 : 143 if record_starttime > icu_intime:144 print('inserting nulls before the record start time')145 #print( (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) ) #+ datetime.timedelta(seconds= int(record_starttime.strftime('%S'))) )146 #print(icu_intime.strftime('%Y-%m-%d %H:%M'))147 if '%.3f'%(fields['fs'])== '0.017' :148 minutes_to_insert_start = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))- (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))149 elif '%.3f'%(fields['fs'])== '1.000' :150 minutes_to_insert_start = record_starttime - icu_intime151 print('minutes_to_insert_start: ', minutes_to_insert_start)152 duration_in_s = minutes_to_insert_start.total_seconds()153 minutes_to_insert_start = divmod(duration_in_s, 60)[0] - 1 154 try:155 df_ts_records_time_temp_start.drop(df_ts_records_time_temp_start.index, inplace=True)156 except :157 print( 'df_ts_records_time_temp_start does not exist')158 159 df_ts_records_time_temp_start = pd.DataFrame(columns=df_ts_records_columns)160 if '%.3f'%(fields['fs'])== '0.017' :161 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(minutes=1), 162 periods=minutes_to_insert_start, freq='1min'); 163 elif '%.3f'%(fields['fs'])== '1.000' :164 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(seconds=1), 165 periods= (duration_in_s-1), freq='S'); 166 print ('INSERTING ONLY NULL IN START:')167 print (df_ts_records_time_temp_start)168 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp_start, ignore_index=True);169 print('inserting nulls in start IN INDV LEVEL')170 print(df_ts_indv_record_temp)171 try:172 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True)173 except:174 print( 'df_ts_records_temp does not exist')175 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)176 df_ts_records_temp['HR']= signals[:,idx_HR ] 177 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 178 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 179 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 180 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 181 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 182 if '%.3f'%(fields['fs'])== '0.017' :183 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 184 elif '%.3f'%(fields['fs'])== '1.000' :185 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 186 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)187 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True); #safiya188 print('inserting nulls in start + first record data')189 print(df_ts_indv_record_temp)190 if '%.3f'%(fields['fs'])== '1.000' : #safiya191 print("AGGREGATING")192 start_idx = 0;193 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);194 #print('length of new df ' , df_ts_records_new.shape[0] )195 for index, rows in df_ts_indv_record_temp.iterrows():196 print('start index for first: ', start_idx)197 if start_idx >= df_ts_indv_record_temp.shape[0]:198 exit;199 else: 200 201 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])202 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))203 #print('printing array of average')204 #print (array)205 current_index = df_ts_records_new.shape[0]206 df_ts_records_new.loc[current_index ,'HR']= array[0]207 df_ts_records_new.loc[current_index,'SPO2']= array[1]208 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]209 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]210 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]211 df_ts_records_new.loc[current_index,'RESP']= array[5]212 #print(df_ts_records_new)213 #print('next average')214 start_idx = start_idx+60;215 #print('start index :: ' , start_idx)216 print('# record time: ',df_ts_records_new.shape[0])217 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 218 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)219 #print(df_ts_records_new)220 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);221 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)222 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);223 print('only first record aggregated at individual record level: ')224 print(df_ts_records_new)225 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')226 print(df_ts_records)227 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)228 df_ts_records['RECORD'] = record 229 else:230 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);231 df_ts_records['RECORD'] = record 232 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')233 print(df_ts_records)234 235 236 else:237 if record_starttime <= icu_outtime :238 last_Record_time = df_ts_records.loc[(df_row_idx-1),'TIME']239 print('main DF last time record: ',last_Record_time )240 if '%.3f'%(fields['fs'])== '0.017' :241 minutes_to_insert = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((last_Record_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))242 elif '%.3f'%(fields['fs'])== '1.000' :243 minutes_to_insert = record_starttime - last_Record_time244 duration_in_s = minutes_to_insert.total_seconds()245 minutes_to_insert = divmod(duration_in_s, 60)[0] - 1246 print ('minutes_to_insert: ', minutes_to_insert);247 print('seconds to insert: ', duration_in_s)248 try:249 df_ts_records_time_temp.drop(df_ts_records_time_temp.index, inplace=True);250 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True);251 except:252 print ('df_ts_records_temp and df_ts_records_time_temp does not exits')253 df_ts_records_time_temp = pd.DataFrame(columns=df_ts_records_columns)254 if '%.3f'%(fields['fs'])== '0.017' :255 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(minutes=1), 256 periods=minutes_to_insert, freq='1min'); 257 elif '%.3f'%(fields['fs'])== '1.000' :258 print('last record time' , last_Record_time)259 print('(duration_in_s-1)' , (duration_in_s-1))260 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(seconds=1), 261 periods=(duration_in_s-1), freq='S'); 262 print ('INSERTING ONLY NULL UNTILL NEXT RECORD START TIME:')263 print (df_ts_records_time_temp)264 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp, ignore_index=True);265 print('inserting nulls UNTILL NEXT RECORD START TIME INTO INDV LEVEL')266 print(df_ts_indv_record_temp)267 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)268 269 df_ts_records_temp['HR']= signals[:,idx_HR ] 270 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 271 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 272 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 273 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 274 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 275 if '%.3f'%(fields['fs'])== '0.017' :276 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 277 elif '%.3f'%(fields['fs'])== '1.000' :278 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 279 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)280 281 print('before appending: ')282 283 print( df_ts_records_temp);284 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True);285 print('inserting nulls in start + SECOND record data')286 print(df_ts_indv_record_temp)287 if '%.3f'%(fields['fs'])== '1.000' : #safiya288 start_idx = 0;289 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);290 #print('length of new df ' , df_ts_records_new.shape[0] )291 for index, rows in df_ts_indv_record_temp.iterrows():292 if start_idx >= df_ts_indv_record_temp.shape[0]:293 exit;294 else: 295 296 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])297 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))298 #print('printing array of average')299 #print (array)300 current_index = df_ts_records_new.shape[0]301 df_ts_records_new.loc[current_index ,'HR']= array[0]302 df_ts_records_new.loc[current_index,'SPO2']= array[1]303 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]304 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]305 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]306 df_ts_records_new.loc[current_index,'RESP']= array[5]307 #print(df_ts_records_new)308 #print('next average')309 start_idx = start_idx+60;310 #print('start index :: ' , start_idx)311 print('# record time: ',df_ts_records_new.shape[0])312 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 313 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)314 #print(df_ts_records_new)315 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);316 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)317 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);318 319 print('only first record aggregated at individual record level: ')320 print(df_ts_records_new)321 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')322 print(df_ts_records)323 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)324 df_ts_records['RECORD'] = record 325 else:326 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);327 df_ts_records['RECORD'] = record 328 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')329 print(df_ts_records)330 331 332 count_overlap = count_overlap +1333 print('overlap count after all insertions: ', count_overlap )334 else:335 print('Either all 6 signals not exists or there is no overlapt with recording time and ICU in time and out time')336last_record_idx = df_ts_records.shape[0] - 1337all_records_end_time = df_ts_records.loc[last_record_idx,'TIME']338 339if (all_records_end_time < icu_outtime ):340 #print('INSERTING NULLS AT THE END')341 try:342 df_ts_records_time_temp_end.drop(df_ts_records_time_temp_end.index, inplace=True)343 except:344 print('df_ts_records_time_temp_end does not exists')345 #print('main DF last time record: ',last_Record_time )346 if '%.3f'%(fields['fs'])== '0.017' :347 minutes_to_insert_end = (datetime.datetime.strptime((icu_outtime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((all_records_end_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) 348 elif '%.3f'%(fields['fs'])== '1.000' :349 minutes_to_insert_end = icu_outtime - all_records_end_time;350 duration_in_s = minutes_to_insert_end.total_seconds()351 minutes_to_insert_end = divmod(duration_in_s, 60)[0] - 1352 df_ts_records_time_temp_end = pd.DataFrame(columns=df_ts_records_columns)353 354 df_ts_records_time_temp_end['TIME'] = pd.date_range(all_records_end_time + datetime.timedelta(minutes=1), 355 periods=minutes_to_insert_end, freq='1min'); 356 df_ts_records = df_ts_records.append(df_ts_records_time_temp_end, ignore_index=True);357 358 df_ts_records['RECORD'] = record359print('printing final data for this patient')360print(df_ts_records)361print(df_ts_records.columns)362#28/​11/​2121 21:23 29/​11/​2121 05:59363patient_sepsis_onsettime = datetime.datetime(2121, 11, 29, 5, 59,00) 364df_ts_records.TIME = pd.to_datetime(df_ts_records.TIME)365df_test_around_sepsis = df_ts_records[(df_ts_records['TIME'] >= (patient_sepsis_onsettime - datetime.timedelta(hours = 8)) )366 & (df_ts_records['TIME'] <= (patient_sepsis_onsettime + datetime.timedelta(hours= 8) ))]367from collections import namedtuple368import seaborn as sns369import matplotlib.ticker as ticker370from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,371 AutoMinorLocator)372from matplotlib.dates import DateFormatter373import matplotlib.dates as mdates374pd.set_option('display.max_rows', 2000)375pd.set_option('display.max_columns', 50)376pd.set_option('display.width', 1000)377pd.set_option('max_colwidth', 800)378df_test= df_test_around_sepsis379#df_test = df_ts_records[df_ts_records['SUBJECT_ID']== 40241] # 98930. 380# sepsis onset time for subject id 40241: 2192-03-15 13:20:59.000000381#Non septic subjectids 55563, 72269382#print(df_test)383print(df_test.RECORD.unique())384#print(df_test[['TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP','TEMP']])385date_form = DateFormatter('%Y-%m-%d %H:%M:%S')386sns.set(rc={'figure.figsize':(20, 10)})387cols_plot = ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']388df_test = df_test.set_index('TIME')389ax = df_test[cols_plot].plot(marker='.', alpha = 0.5,figsize=(50, 30), subplots=True, x_compat=True)390#print(ax)391count =0 392for i in ax: 393 i.xaxis.set_major_formatter(date_form)394 i.xaxis.set_major_locator(mdates.HourLocator(interval=1))395from matplotlib import pyplot as plt...

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Fetching6signalsforASamplePatientID_55638.py

Source:Fetching6signalsforASamplePatientID_55638.py Github

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1#### IMPORTANT ! DO NOT DELETE2#To get patient records if multiple ts existis 3!pip install wfdb4import io5import pandas as pd6from IPython.display import display7import matplotlib.pyplot as plt8%matplotlib inline9import numpy as np10import os11import shutil12import posixpath13import wfdb14import urllib.request15import datetime16from collections import namedtuple17df_ts_records_columns = ['RECORD','TIME','HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP'] 18df_ts_records = pd.DataFrame(columns=df_ts_records_columns); 19#subject_id= 48149; # per second multiple 20#icu_intime = datetime.datetime(2127, 5, 25, 8, 34,39) # for 4814921#icu_outtime = datetime.datetime(2127, 6, 16, 1, 15,22) # for 4814922subject_id= 55638; # per minute 23icu_intime = datetime.datetime(2106, 11, 25, 12, 37,32) # for 5563824icu_outtime = datetime.datetime(2106, 11, 27, 10, 49,33) # for 5563825print ('icu intime =', icu_intime)26print ('icu outtime', icu_outtime)27"""28subject_id= 59864;29icu_intime = datetime.datetime(2173, 5, 16, 12, 14,45)30print ('icu intime =', icu_intime)31icu_outtime = datetime.datetime(2173, 6, 8, 15, 45,23)32print ('icu outtime', icu_outtime)33#2173-05-16 12:14:45,2173-06-08 15:45:23,34"""35wdb_dir_path = 'mimic3wdb/​matched/​p'+ str(subject_id).zfill(6)[:2] + '/​p' + str(subject_id).zfill(6) + '/​';36wdb_path_toAllRecords = 'https:/​/​archive.physionet.org/​physiobank/​database/​'+ wdb_dir_path + 'RECORDS';37wdb_records = urllib.request.urlopen(wdb_path_toAllRecords); 38try:39 df_ts_records.drop(df_ts_records.index, inplace=True)40except:41 print('df_ts_records does not exist')42count_overlap = 0; 43for lines in wdb_records.readlines():44 record = lines.decode("utf-8"); 45 record = str(record).rstrip()46 #print (record[-1:])47 if record[-1:] == 'n':48 print(record);49 #print (wdb_dir_path);50 record = str(record).rstrip()51 52 53 #try:54 signals =''55 fields = ''56 signals,fields = wfdb.rdsamp(record, pn_dir=wdb_dir_path) ; 57 58 list_sig_name = [item.upper().replace(' ','') for item in fields['sig_name']]59 sig_exist_1 = all(x in list_sig_name for x in ['HR', 'SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); #%SpO260 sig_exist_2 = all(x in list_sig_name for x in ['HR', '%SPO2','ABPSYS','ABPDIAS','ABPMEAN','RESP']); 61 record_starttime = datetime.datetime.combine(fields['base_date'] ,fields['base_time'] ) ;62 63 if '%.3f'%(fields['fs']) == '1.000' :64 record_endtime = record_starttime + datetime.timedelta(seconds= (fields['sig_len']-1)) ;65 elif '%.3f'%(fields['fs'])== '0.017' :66 record_endtime = record_starttime + datetime.timedelta(minutes = (fields['sig_len']-1)) ;67 else : 68 print('ERROR IN SAMPLING');69 print(record);70 print(wdb_dir_path);71 print('record START time: ', record_starttime)72 print('record END time: ', record_endtime)73 Range = namedtuple('Range', ['start', 'end'])74 r1 = Range(start= icu_intime, end= icu_outtime)75 r2 = Range(start= record_starttime, end = record_endtime)76 latest_start = max(r1.start, r2.start)77 earliest_end = min(r1.end, r2.end)78 delta = (earliest_end - latest_start).days + 179 #delta >= 0 :80 print('sig_exist_1 : ', sig_exist_1)81 print('sig_exist_2 : ', sig_exist_2)82 print('delta : ', delta)83 if ( ((sig_exist_1 == True) or (sig_exist_2 == True)) and (delta >= 0)):84 ###85 try:86 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True)87 except:88 print('individual record for a single patient df does not exists')89 90 df_ts_indv_record_temp = pd.DataFrame(columns = df_ts_records_columns ) # individual record for a single patient #safiya91 ###92 df_row_idx = df_ts_records.shape[0] ;93 print('length of signal: ', len(signals))94 print('index of dataframe before inserting into it: ', df_row_idx)95 96 for i in fields['sig_name']:97 98 if i.upper().replace(' ','') == 'HR':99 idx_HR = fields['sig_name'].index(i);100 elif (( i.upper().replace(' ','') == 'SPO2') or (i.upper().replace(' ','') =='%SPO2')):101 idx_SPO2 = fields['sig_name'].index(i);102 elif i.upper().replace(' ','') == 'ABPSYS' :103 idx_ABPSYS = fields['sig_name'].index(i);104 elif i.upper().replace(' ','') == 'ABPDIAS' :105 idx_ABPDIAS = fields['sig_name'].index(i);106 elif i.upper().replace(' ','') == 'ABPMEAN' :107 idx_ABPMEAN = fields['sig_name'].index(i);108 elif i.upper().replace(' ','') == 'RESP' :109 idx_RESP = fields['sig_name'].index(i);110 111 112 113 if count_overlap == 0 : 114 if record_starttime > icu_intime:115 print('inserting nulls before the record start time')116 #print( (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) ) #+ datetime.timedelta(seconds= int(record_starttime.strftime('%S'))) )117 #print(icu_intime.strftime('%Y-%m-%d %H:%M'))118 if '%.3f'%(fields['fs'])== '0.017' :119 minutes_to_insert_start = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))- (datetime.datetime.strptime((icu_intime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))120 elif '%.3f'%(fields['fs'])== '1.000' :121 minutes_to_insert_start = record_starttime - icu_intime122 print('minutes_to_insert_start: ', minutes_to_insert_start)123 duration_in_s = minutes_to_insert_start.total_seconds()124 minutes_to_insert_start = divmod(duration_in_s, 60)[0] - 1 125 try:126 df_ts_records_time_temp_start.drop(df_ts_records_time_temp_start.index, inplace=True)127 except :128 print( 'df_ts_records_time_temp_start does not exist')129 130 df_ts_records_time_temp_start = pd.DataFrame(columns=df_ts_records_columns)131 if '%.3f'%(fields['fs'])== '0.017' :132 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(minutes=1), 133 periods=minutes_to_insert_start, freq='1min'); 134 elif '%.3f'%(fields['fs'])== '1.000' :135 df_ts_records_time_temp_start['TIME'] = pd.date_range(icu_intime + datetime.timedelta(seconds=1), 136 periods= (duration_in_s-1), freq='S'); 137 print ('INSERTING ONLY NULL IN START:')138 print (df_ts_records_time_temp_start)139 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp_start, ignore_index=True);140 print('inserting nulls in start IN INDV LEVEL')141 print(df_ts_indv_record_temp)142 try:143 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True)144 except:145 print( 'df_ts_records_temp does not exist')146 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)147 df_ts_records_temp['HR']= signals[:,idx_HR ] 148 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 149 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 150 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 151 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 152 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 153 if '%.3f'%(fields['fs'])== '0.017' :154 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 155 elif '%.3f'%(fields['fs'])== '1.000' :156 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 157 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)158 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True); #safiya159 print('inserting nulls in start + first record data')160 print(df_ts_indv_record_temp)161 if '%.3f'%(fields['fs'])== '1.000' : #safiya162 print("AGGREGATING")163 start_idx = 0;164 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);165 #print('length of new df ' , df_ts_records_new.shape[0] )166 for index, rows in df_ts_indv_record_temp.iterrows():167 print('start index for first: ', start_idx)168 if start_idx >= df_ts_indv_record_temp.shape[0]:169 exit;170 else: 171 172 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])173 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))174 #print('printing array of average')175 #print (array)176 current_index = df_ts_records_new.shape[0]177 df_ts_records_new.loc[current_index ,'HR']= array[0]178 df_ts_records_new.loc[current_index,'SPO2']= array[1]179 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]180 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]181 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]182 df_ts_records_new.loc[current_index,'RESP']= array[5]183 #print(df_ts_records_new)184 #print('next average')185 start_idx = start_idx+60;186 #print('start index :: ' , start_idx)187 print('# record time: ',df_ts_records_new.shape[0])188 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 189 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)190 #print(df_ts_records_new)191 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);192 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)193 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);194 print('only first record aggregated at individual record level: ')195 print(df_ts_records_new)196 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')197 print(df_ts_records)198 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)199 df_ts_records['RECORD'] = record 200 else:201 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);202 df_ts_records['RECORD'] = record 203 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')204 print(df_ts_records)205 206 207 else:208 if record_starttime <= icu_outtime :209 last_Record_time = df_ts_records.loc[(df_row_idx-1),'TIME']210 print('main DF last time record: ',last_Record_time )211 if '%.3f'%(fields['fs'])== '0.017' :212 minutes_to_insert = (datetime.datetime.strptime((record_starttime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((last_Record_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M'))213 elif '%.3f'%(fields['fs'])== '1.000' :214 minutes_to_insert = record_starttime - last_Record_time215 duration_in_s = minutes_to_insert.total_seconds()216 minutes_to_insert = divmod(duration_in_s, 60)[0] - 1217 print ('minutes_to_insert: ', minutes_to_insert);218 print('seconds to insert: ', duration_in_s)219 try:220 df_ts_records_time_temp.drop(df_ts_records_time_temp.index, inplace=True);221 df_ts_records_temp.drop(df_ts_records_temp.index, inplace=True);222 except:223 print ('df_ts_records_temp and df_ts_records_time_temp does not exits')224 df_ts_records_time_temp = pd.DataFrame(columns=df_ts_records_columns)225 if '%.3f'%(fields['fs'])== '0.017' :226 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(minutes=1), 227 periods=minutes_to_insert, freq='1min'); 228 elif '%.3f'%(fields['fs'])== '1.000' :229 print('last record time' , last_Record_time)230 print('(duration_in_s-1)' , (duration_in_s-1))231 df_ts_records_time_temp['TIME'] = pd.date_range(last_Record_time + datetime.timedelta(seconds=1), 232 periods=(duration_in_s-1), freq='S'); 233 print ('INSERTING ONLY NULL UNTILL NEXT RECORD START TIME:')234 print (df_ts_records_time_temp)235 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_time_temp, ignore_index=True);236 print('inserting nulls UNTILL NEXT RECORD START TIME INTO INDV LEVEL')237 print(df_ts_indv_record_temp)238 df_ts_records_temp = pd.DataFrame(columns=df_ts_records_columns)239 240 df_ts_records_temp['HR']= signals[:,idx_HR ] 241 df_ts_records_temp['SPO2']= signals[:,idx_SPO2 ] 242 df_ts_records_temp['ABPSYS']= signals[:,idx_ABPSYS ] 243 df_ts_records_temp['ABPDIAS']= signals[:,idx_ABPDIAS ] 244 df_ts_records_temp['ABPMEAN']= signals[:,idx_ABPMEAN ] 245 df_ts_records_temp['RESP']= signals[:,idx_RESP ] 246 if '%.3f'%(fields['fs'])== '0.017' :247 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='1min'); 248 elif '%.3f'%(fields['fs'])== '1.000' :249 df_ts_records_temp['TIME'] = pd.date_range(record_starttime, periods=fields['sig_len'], freq='S'); 250 df_ts_records_temp.TIME = pd.to_datetime(df_ts_records_temp.TIME)251 252 print('before appending: ')253 254 print( df_ts_records_temp);255 df_ts_indv_record_temp = df_ts_indv_record_temp.append(df_ts_records_temp, ignore_index=True);256 print('inserting nulls in start + SECOND record data')257 print(df_ts_indv_record_temp)258 if '%.3f'%(fields['fs'])== '1.000' : #safiya259 start_idx = 0;260 df_ts_records_new = pd.DataFrame(columns=df_ts_records_columns);261 #print('length of new df ' , df_ts_records_new.shape[0] )262 for index, rows in df_ts_indv_record_temp.iterrows():263 if start_idx >= df_ts_indv_record_temp.shape[0]:264 exit;265 else: 266 267 #print(df_ts_records.iloc[start_idx: (start_idx+60), 2:8])268 array = np.array( df_ts_indv_record_temp.iloc[start_idx: (start_idx+60), 2:8].mean(axis=0))269 #print('printing array of average')270 #print (array)271 current_index = df_ts_records_new.shape[0]272 df_ts_records_new.loc[current_index ,'HR']= array[0]273 df_ts_records_new.loc[current_index,'SPO2']= array[1]274 df_ts_records_new.loc[current_index,'ABPSYS']= array[2]275 df_ts_records_new.loc[current_index,'ABPDIAS']= array[3]276 df_ts_records_new.loc[current_index,'ABPMEAN']= array[4]277 df_ts_records_new.loc[current_index,'RESP']= array[5]278 #print(df_ts_records_new)279 #print('next average')280 start_idx = start_idx+60;281 #print('start index :: ' , start_idx)282 print('# record time: ',df_ts_records_new.shape[0])283 df_ts_records_new['TIME'] = pd.date_range(df_ts_indv_record_temp.loc[0,'TIME'], periods= df_ts_records_new.shape[0], freq='1min'); 284 df_ts_records_new.TIME = pd.to_datetime(df_ts_records_new.TIME)285 #print(df_ts_records_new)286 df_ts_indv_record_temp.drop(df_ts_indv_record_temp.index, inplace=True);287 #df_ts_records = pd.DataFrame(columns=df_ts_records_columns)288 df_ts_records = df_ts_records.append(df_ts_records_new, ignore_index=True);289 290 print('only first record aggregated at individual record level: ')291 print(df_ts_records_new)292 print('inserting aggregated first record into FINAL SUBJEC DATAFRAME')293 print(df_ts_records)294 df_ts_records_new.drop(df_ts_records_new.index, inplace=True)295 df_ts_records['RECORD'] = record 296 else:297 df_ts_records = df_ts_records.append(df_ts_indv_record_temp, ignore_index=True);298 df_ts_records['RECORD'] = record 299 print('inserting nulls in start + first record data into FINAL SUBJEC DATAFRAME')300 print(df_ts_records)301 302 303 count_overlap = count_overlap +1304 print('overlap count after all insertions: ', count_overlap )305 else:306 print('Either all 6 signals not exists or there is no overlapt with recording time and ICU in time and out time')307last_record_idx = df_ts_records.shape[0] - 1308all_records_end_time = df_ts_records.loc[last_record_idx,'TIME']309 310if (all_records_end_time < icu_outtime ):311 #print('INSERTING NULLS AT THE END')312 try:313 df_ts_records_time_temp_end.drop(df_ts_records_time_temp_end.index, inplace=True)314 except:315 print('df_ts_records_time_temp_end does not exists')316 #print('main DF last time record: ',last_Record_time )317 if '%.3f'%(fields['fs'])== '0.017' :318 minutes_to_insert_end = (datetime.datetime.strptime((icu_outtime.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) - (datetime.datetime.strptime((all_records_end_time.strftime('%Y-%m-%d %H:%M' )), '%Y-%m-%d %H:%M')) 319 elif '%.3f'%(fields['fs'])== '1.000' :320 minutes_to_insert_end = icu_outtime - all_records_end_time;321 duration_in_s = minutes_to_insert_end.total_seconds()322 minutes_to_insert_end = divmod(duration_in_s, 60)[0] - 1323 df_ts_records_time_temp_end = pd.DataFrame(columns=df_ts_records_columns)324 325 df_ts_records_time_temp_end['TIME'] = pd.date_range(all_records_end_time + datetime.timedelta(minutes=1), 326 periods=minutes_to_insert_end, freq='1min'); 327 df_ts_records = df_ts_records.append(df_ts_records_time_temp_end, ignore_index=True);328 329 df_ts_records['RECORD'] = record330print('printing final data for this patient')...

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spl_recorder_hd.py

Source:spl_recorder_hd.py Github

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1#!/​usr/​bin/​env python2# -*- coding: utf-8 -*-3from directorymapper import DirectoryMapper4from splthread import SplThread5from messagehandler import Query6from classes import MovieInfo7import defaults8from defaults import Record_States9from scheduler import Scheduler10from jsonstorage import JsonStorage11import json12import os13import sys14import time15import threading16import base6417import subprocess18from urllib.parse import urlparse19# Standard module20# Non standard modules (install with pip)21# own local modules22ScriptPath = os.path.realpath(os.path.join(23 os.path.dirname(__file__), "../​../​../​common"))24# Add the directory containing your module to the Python path (wants absolute paths)25sys.path.append(os.path.abspath(ScriptPath))26import schnipsllogger27logger = schnipsllogger.getLogger(__name__)28class SplPlugin(SplThread):29 plugin_id = 'record_hd'30 plugin_names = ['HD Recorder']31 def __init__(self, modref):32 ''' inits the plugin33 '''34 self.modref = modref35 # do the plugin specific initialisation first36 self.origin_dir = os.path.dirname(__file__)37 self.config = JsonStorage(self.plugin_id, 'backup', "config.json", {'path': DirectoryMapper.abspath(self.plugin_id, 'videos','', True), 'www-root': 'http:/​/​schnipsl:9092/​'})38 self.records = JsonStorage(self.plugin_id, 'runtime', "records.json", {})39 self.record_threats={} # we need to store the thread pointers seperate from self.records, as we can't store them as json40 self.last_recorded_time = 0 # remembers how long the last recording action is away41 # at last announce the own plugin42 super().__init__(modref.message_handler, self)43 modref.message_handler.add_event_handler(44 self.plugin_id, 0, self.event_listener)45 modref.message_handler.add_query_handler(46 self.plugin_id, 0, self.query_handler)47 self.runFlag = True48 def event_listener(self, queue_event):49 if queue_event.type == defaults.TIMER_RECORD_REQUEST:50 self.timer_record_request(queue_event.data)51 # for further pocessing, do not forget to return the queue event52 return queue_event53 def query_handler(self, queue_event, max_result_count):54 ''' try to send simulated answers55 '''56 # logger.info(f"hd_recorder query handler" {queue_event.type} {queue_event.user} {max_result_count"})57 if queue_event.type == defaults.QUERY_MOVIE_ID:58 new_uri=queue_event.params59 for record_movie in self.records.read('all',{}).values(): # 'all': read the whole config60 if record_movie['new_uri']==new_uri:61 return [MovieInfo(62 source=self.plugin_names[0],63 source_type=defaults.MOVIE_TYPE_RECORD,64 provider=record_movie['new_uri'].split(':')[1], # extracts the original provider back out of the uri65 category=record_movie['category'],66 title=record_movie['title'],67 timestamp=record_movie['timestamp'],68 duration=record_movie['duration'],69 description=record_movie['description'],70 url=record_movie['new_url'],71 mime=record_movie['mime']72 )]73 return[]74 def _run(self):75 ''' starts the server76 '''77 scheduler = Scheduler(78 [(self.check_for_records, 10), (self.cleanup_records, 60)])79 while self.runFlag:80 scheduler.execute()81 time.sleep(2)82 def _stop(self):83 self.runFlag = False84 def timer_record_request(self, data):85 uri = data['uri']86 uuid = data['uuid']87 movie_info_list = self.modref.message_handler.query(88 Query(None, defaults.QUERY_MOVIE_ID, uri))89 if movie_info_list:90 movie_info = movie_info_list[0]91 uri = movie_info['uri']92 # do we have that record request already93 existing_record = self.records.read(uri)94 if not existing_record:95 uri_base64 = base64_encode(uri)96 ext='.mp4'97 if movie_info['mime']=='video/​MP2T':98 ext='.mp4'99 file_path = DirectoryMapper.abspath('','videos', self.config.read('path')+ uri_base64+ext)100 if movie_info['source_type'] == defaults.MOVIE_TYPE_RECORD:101 self.records.write(uri, {102 # in case of a record we set start and duration to 0 to indicate that the recording can start immediadly & has no duration103 'record_starttime': 0,104 'record_duration': 0,105 'provider': movie_info['provider'],106 'category': movie_info['category'],107 'title': movie_info['title'],108 'timestamp': movie_info['timestamp'],109 'duration': movie_info['duration'],110 'description': movie_info['description'],111 'url': movie_info['url'],112 'mime': movie_info['mime'],113 'uri': uri,114 'new_uri': self.plugin_names[0]+':'+':'.join(movie_info['uri'].split(':')[1:]),115 'new_url': self.config.read('www-root')+uri_base64+ext,116 'uuid': uuid,117 'file_path': file_path,118 'state': Record_States.WAIT_FOR_RECORDING,119 'errorcount': 4 # try to start the record up to 4 times before it finally failes120 })121 if movie_info['source_type'] == defaults.MOVIE_TYPE_STREAM:122 # recording a stream with a duration of 0 is a very bad idea, because it would never stop..123 if movie_info['duration']:124 self.records.write(uri, {125 'record_starttime': movie_info['timestamp'],126 'record_duration': movie_info['duration'],127 'category': movie_info['category'],128 'title': movie_info['title'],129 'timestamp': movie_info['timestamp'],130 'duration': movie_info['duration'],131 'description': movie_info['description'],132 'url': movie_info['url'],133 'mime': movie_info['mime'],134 'uri': uri,135 'new_uri': self.plugin_names[0]+':'+':'.join(movie_info['uri'].split(':')[1:]),136 'new_url': self.config.read('www-root')+uri_base64+ext,137 'uuid': uuid,138 'file_path': file_path,139 'state': Record_States.WAIT_FOR_RECORDING,140 'errorcount': 4 # try to start the record up to 4 times before it finally failes141 })142 143 def check_for_records(self):144 act_time = time.time()145 for uri, record in self.records.read('all','').items():146 if record['state'] == Record_States.WAIT_FOR_RECORDING:147 if record['record_duration'] == 0: # this is a record, which can be recorded immediadly148 record['state'] = Record_States.ACTUAL_RECORDING149 self.records.write(uri, record)150 self.recording(record)151 continue152 # something went wrong, the record time was in the past. Mark the entry as failed153 if record['record_starttime']+record['record_duration'] < act_time:154 record['state'] = Record_States.RECORDING_FAILED155 # something went wrong during recording156 if record['state'] == Record_States.RECORDING_FAILED:157 self.records.write(uri, record)158 self.deploy_record_result(record, record['state'])159 continue160 # it's time to start161 if record['record_starttime']-self.config.read('padding_secs', 300) <= act_time and record['record_starttime']+record['record_duration'] > act_time:162 # in case the movie has already started, we correct starttime and duration to show the real values163 if record['record_starttime'] < act_time:164 record['starttime'] = str(act_time)165 record['duration'] = record['duration'] - (act_time - record['record_starttime'])166 record['state'] = Record_States.ACTUAL_RECORDING167 self.records.write(uri, record)168 self.recording(record)169 continue170 def cleanup_records(self):171 records_to_delete={}172 act_time=time.time()173 # request which movies are still in the UI list174 valid_movieuri_list = self.modref.message_handler.query(175 Query(None, defaults.QUERY_VALID_MOVIE_RECORDS, {'source':self.plugin_names[0]}))176 for uri, record in self.records.config.items():177 if uri in self.record_threats:178 # recording is finished, so deploy the result179 if not self.record_threats[uri].is_alive():180 del(self.record_threats[uri]) # we destroy the thread181 self.deploy_record_result(record,182 record['state'] )183 self.last_recorded_time=act_time184 if self.last_recorded_time> act_time-5*60:185 return # don't do any delete action if the last record is just 5 mins ago to give the UI some time to adapt the new movie186 if record['state'] == Record_States.ACTUAL_RECORDING and not uri in self.record_threats: # seems to be a zombie record187 records_to_delete[uri]=record188 self.deploy_record_result(record,189 Record_States.RECORDING_FAILED )190 if record['state'] == Record_States.RECORDING_FINISHED or record['state'] == Record_States.RECORDING_FAILED:191 new_uri=record['new_uri']192 #logger.info(f'Record on disk: {new_uri}') 193 if not new_uri in valid_movieuri_list:194 records_to_delete[uri]=record195 # some debug output196 #for uri in valid_movieuri_list:197 # logger.info(f'recoder uri: {uri}')198 if records_to_delete:199 # go through the list of records to be deleted200 for uri, record in records_to_delete.items():201 # delete the file202 file_path=record['file_path']203 logger.info(f'try to delete file {file_path}' )204 if os.path.exists(file_path):205 try:206 os.remove(file_path)207 logger.info(f'file deleted {file_path}' )208 except Exception as ex:209 logger.warning("Cant delete record file {0}. Error: {1}".format(file_path,str(ex)))210 else:211 # remove the entry212 logger.info(f'file not found, just remove the entry {uri}' )213 del(self.records.config[uri])214 self.records.save()215 def deploy_record_result(self, record, record_state):216 # save changes217 self.records.write(record['uri'], record)218 self.modref.message_handler.queue_event(None, defaults.TIMER_RECORD_RESULT, {219 'new_uri':record['new_uri'], 'new_url':record['new_url'], 'uuid': record['uuid'], 'record_state': record_state})220 def recording(self, record):221 uri=record['uri']222 logger.info(f'try to record {uri}')223 threat = threading.Thread(target=record_thread, args=(224 record, self.config.read('padding_secs', 300)))225 self.record_threats[uri] = threat226 threat.start()227def record_thread(record, padding_time):228 file_path = record['file_path']229 url = record['url']230 act_time = time.time()231 remaining_time = record['record_starttime']+record['record_duration']-act_time232 ################ debug tweak to keep the records short - reduce the records to 30 secs.233 if False:234 remaining_time=25235 padding_time=5236 attr = None237 # does the record has a duration? then we've use ffmeg to limit the duration238 if record['record_duration']:239 # attr = ['ffmpeg', '-y', '-i', url, '-vcodec', 'copy', '-acodec', 'copy', '-map', '0:v', '-map', '0:a', '-t', str(remaining_time+padding_time), '-f', 'ts' , file_path]240 attr = ['ffmpeg', '-y', '-rw_timeout', '5000', '-i', url, '-vcodec', 'copy', '-acodec', 'copy', '-t', str(remaining_time+padding_time), file_path]241 else:242 attr = ['curl', '-s', url, '-o', file_path] # process arguments243 if attr:244 logger.info(f"recorder started {repr(attr)}" )245 try:246 completed_process = subprocess.run(attr)247 if completed_process.returncode:248 logger.warning("recorder ended with an error:\n%s" %249 (completed_process.returncode))250 try:251 record['errorcount']-=1252 except:253 record['errorcount']=4 # just a temporary fix to avoid a crash on older configs254 if record['errorcount']<=0:255 record['state'] = Record_States.RECORDING_FAILED256 logger.info(f"recorder max error count reached, recording finally failed" )257 else: # give it another try258 record['state'] =Record_States.WAIT_FOR_RECORDING259 logger.info(f"recorder error count {record['errorcount']}, try it again soon.." )260 else:261 logger.info("recorder ended")262 record['state'] = Record_States.RECORDING_FINISHED263 except Exception as ex:264 logger.warning("recorder could not be started. Error: %s" % (ex))265 else:266 record['state'] = Record_States.RECORDING_FAILED267def base64_encode(string):268 """269 Removes any `=` used as padding from the encoded string.270 """271 encoded = base64.urlsafe_b64encode(string.encode())272 return encoded.decode().replace('=', '')273def base64_decode(string):274 """275 Adds back in the required padding before decoding.276 """277 padding = 4 - (len(string) % 4)278 string = string + ("=" * padding)...

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