T-DOSE 2015: Using Python, PHP, JQuery and Linux to visualize the heartrate and blood oxygen saturation level of my stepdaughter

1
Using Python, PHP, JQuery and Linux to visualize oxygen saturation levels
Using Python, PHP, JQuery and Linux to
visualize the heartrate and blood oxygen
saturation level of my stepdaughter
Jeroen Baten
T-DOSE 2015

2
TOC
Who am I
Who is Anouschka?
What happened
What I did
How it worked out
The end...

3
Who am I?
●
Jeroen Baten
●
Open Source geek since 1997
●
Sofar 9 books and 2 columns
●
Job title : all-round IT problem fixer
●
(former) Volunteer Firefighter
●
Scouting

4
Who am I ? (in pics)

5
Who the f*ck is this Anouschka?
Name: Anouschka van G.
DOB: 18-1-1997
Current age: 18 years
Diagnosis:
Spina Bifida Aperta L3-L5
Arnold Chiari Malformation
Hydrocephalus
Number of surgeries till today: 43
Number of hospital sessions: stopped counting

6
Hospital life….

7
Some surgery examples

8
The surgery session where our journey starts
Reason: chronic pain in hip joint
Cause: insufficient joint development
Post surgery:
Low oxygen levels during sleep
Questions:
Source/origin?
How severe?
How to fix?

9
Actions taken by pediatrician at WKZ
Polysomnografy at AMC. This takes 24 hours.
Result: varying (85-90%) O2-levels at night.
Values found are in “grey” area.
Oxygen measures introduced at home.
Pediatrician: “If only we had more data….”
“But please not a huge table with data.”

10
Oxygen concentrator + saturation measurement
Oxygen concentrator for producing O2:
Philips Everflo oxygen concentrator
No matter what people say: these
things are loud at night!
Saturation measurement for correct level
feedback + alarm:
Masimo RAD-8 saturation
measurement device.
And so we begin
But what is that I see on the back of the
Rad-8?

11
RS-232!
That looks like….
No, it IS an RS-232 port!
Google….
Masimo-Rad-8-User-Manual.pdf

12
Manual adventures
What does the manual say?
09/01/14 04:01:41 SN=0000051252 SPO2=092% BPM=086 PI=01.03%
SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000800
What do we get….?

13
Step 1: make database
Use simple database: MySQL
Make simple table:
CREATE TABLE `data` (
ìd` int(11) NOT NULL AUTO_INCREMENT,
`tijd` datetime DEFAULT NULL,
`data` varchar(150) DEFAULT NULL,
`spo2` int(11) DEFAULT NULL,
`bpm` int(11) DEFAULT NULL,
`session` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
`tijd3` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
KEY ìd` (ìd`),
KEY `session_index` (`session`),
KEY `tijd_index` (`tijd`),
KEY `spo2_index` (`spo2`)
)

14
Step 2: python
#!/usr/bin/python
print "Loading libraries"
import serial, time, os
import logging
import logging.handlers
import MySQLdb
import datetime
version="1.0"
def log(msg):
print msg
my_logger.debug(os.path.basename(__file__)+":"+msg)
print "Initialising logging"
my_logger = logging.getLogger('MyLogger')
my_logger.setLevel(logging.DEBUG)
handler = logging.handlers.SysLogHandler(address = '/dev/log')
my_logger.addHandler(handler)
log("Log-RAD-8 version "+version)
log("Copyright 2014 J. Baten")
log("")
log("Logging serial data from Masimo RAD-8 serial port")
log("Note: Works only with RAD-8 serial port set to 'ASC1'")
log("")
#my_logger.debug('this is debug')
#my_logger.critical('this is critical')
log("Initialising database connection")
#setting up database connection
#create table data (id int auto_increment, tijd timestamp, data varchar(150), key(id) );
#+-------+--------------+------+-----+-------------------+-----------------------------+
#| Field | Type | Null | Key | Default | Extra |
#+-------+--------------+------+-----+-------------------+-----------------------------+
#| id | int(11) | NO | MUL | NULL | auto_increment |
#| tijd | timestamp | NO | | CURRENT_TIMESTAMP | on update CURRENT_TIMESTAMP |
#| data | varchar(150) | YES | | NULL | |
#+-------+--------------+------+-----+-------------------+-----------------------------+
try:
conn = MySQLdb.connect(host= "10.1.1.1", user="lograd8", passwd="lograd8", db="lograd8")
except MySQLdb.Error, e:
log( "ERROR %d IN CONNECTION: %s" % (e.args[0], e.args[1]))
#except MySQLdb.Error:
#log("ERROR IN CONNECTION")
exit(2)
x = conn.cursor()
#x.execute("SELECT * FROM anooog1")
#x.execute (" INSERT INTO anooog1 VALUES ('%s','%s') ", (188,90))
#row = x.fetchall()
now = datetime.datetime.now()
#print now
log("Program started at "+str(now))
#today8am = now.replace(hour=8, minute=0, second=0, microsecond=0)
today = datetime.datetime.today()
#print today
one_day = datetime.timedelta(days=1)
tomorrow = today + one_day
#print 'Tomorrow :', tomorrow
endtime= tomorrow.replace(hour=8, minute=0, second=0, microsecond=0)
log("Logging should stop at "+ str(endtime))
#initialization and open the port
#possible timeout values:
# 1. None: wait forever, block call
# 2. 0: non-blocking mode, return immediately
# 3. x, x is bigger than 0, float allowed, timeout block call
log( "Initializing port")
ser = serial.Serial()
#ser.port = "/dev/ttyUSB0"
ser.port = "/dev/ttyS0"
#ser.port = "/dev/ttyS2"
ser.baudrate = 9600
ser.bytesize = serial.EIGHTBITS #number of bits per bytes
ser.parity = serial.PARITY_NONE #set parity check: no parity
ser.stopbits = serial.STOPBITS_ONE #number of stop bits
#ser.timeout = None #block read
ser.timeout = 1 #non-block read
#ser.timeout = 2 #timeout block read
ser.xonxoff = False #disable software flow control
ser.rtscts = False #disable hardware (RTS/CTS) flow control
ser.dsrdtr = False #disable hardware (DSR/DTR) flow control
ser.writeTimeout = 2 #timeout for write
try:
log( "Trying to open serial port")
ser.open()
except Exception, e:
log( "error open serial port: " + str(e))
exit(1)
if ser.isOpen():
log( "Port succesfully opened")
try:
log( "Flushing port data")
ser.flushInput() #flush input buffer, discarding all its contents
ser.flushOutput()#flush output buffer, aborting current output
#and discard all that is in buffer
#write data
#ser.write("AT+CSQ")
#time.sleep(0.5) #give the serial port sometime to receive the data
while True:
response = ser.readline()
print response
response = MySQLdb.escape_string(response)
print(response)
if (len(response)>5):
try:
x.execute ("INSERT INTO data (tijd,data) VALUES (now(),%s) ", response)
conn.commit()
except MySQLdb.Error, e:
log( "ERROR %d IN CONNECTION: %s" % (e.args[0], e.args[1]))
log( "Last query was: "+ x._last_executed )
# Is it time to stop yet?
#endtime= now+ datetime.timedelta(seconds=5)
now = datetime.datetime.now()
if (now > endtime):
break
ser.close()
except Exception, e1:
log( "error communicating...: " + str(e1))
else:
log( "cannot open serial port ")
conn.close()

15
Step 3:
What do we have?
MySQL [(none)]> use lograd8
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
MySQL [lograd8]> show tables;
+-------------------+
| Tables_in_lograd8 |
+-------------------+
| data |
+-------------------+
1 row in set (0.00 sec)
MySQL [lograd8]> select count(*) from data;
+----------+
| count(*) |
+----------+
| 717298 |
+----------+
1 row in set (0.68 sec)
MySQL [lograd8]>
select * from data limit 5;
+----+---------------------+-----------------------------------------------------------------------------------------------------------------------------------+------+------+---------------------+---------------------+
| id | tijd | data | spo2 | bpm | session | tijd3 |
+----+---------------------+-----------------------------------------------------------------------------------------------------------------------------------+------+------+---------------------+---------------------+
| 9 | 2014-09-02 15:00:18 | 00/00/00 00:00:03 SN=0000051252 SPO2=---% BPM=--- PI=--.--% SPCO=--.-% SPMET=--.-% DESAT=-- PIDELTA=+-- ALARM=0000 EXC=000000rn | 0 | 0 | 2014-09-02 03:00:18 | 0000-00-00 00:00:00 |
+----+---------------------+-----------------------------------------------------------------------------------------------------------------------------------+------+------+---------------------+---------------------+
5 rows in set (0.02 sec)
MySQL [lograd8]>
MySQL [lograd8]> select count(*),date_format(session,"%d/%m/%Y") from data group
by date(session);
+----------+---------------------------------+
| count(*) | date_format(session,"%d/%m/%Y") |
+----------+---------------------------------+
| 181711 | 00/00/0000 |
| 11200 | 02/09/2014 |
| 36399 | 03/09/2014 |
| 34166 | 04/09/2014 |
| 42495 | 05/09/2014 |
| 38313 | 09/09/2014 |
| 37392 | 10/09/2014 |
| 37279 | 11/09/2014 |
| 35972 | 12/09/2014 |
| 35467 | 13/09/2014 |
| 35761 | 14/09/2014 |
| 34845 | 15/09/2014 |
| 36510 | 16/09/2014 |
| 38400 | 17/09/2014 |
| 37797 | 18/09/2014 |
| 23 | 23/09/2014 |
| 43568 | 26/09/2014 |
+----------+---------------------------------+
17 rows in set (0.65 sec)
MySQL [lograd8]>

16
Step 4: turn raw data into usefull data
Need to get BPM and O2 from string.
And fix the date!
update data set spo2=substring(data,38,3);
update data set bpm=substring(data,47,3);
update data set session=DATE_SUB(tijd, INTERVAL 12 HOUR);

17
Step 4: visualize quick and dirty => PHP!
Use PHP and Jquery (for date selection)
Find easy PHP visualisation lib...
JpGraph?
No longer leading.
Google Charts javascript lib can't be wrong right?
Wrong!
DyGraph! Send it CSV formatted data. Done!
Including zoom functionality. Yay!

18
The result
First results...

19
Results: DyGraph to the rescue
Working with small range averages

20
Results: graphing ALL data...
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Saturatie weergave</title>
<link rel="stylesheet" href="jquery/jquery-ui.min.css">
<link rel="stylesheet" href="get-sat.css">
<script type="text/javascript" src="dygraph-combined.js"></script>
</head>
<body>
<div class="box" id="spo2_div" style="width:95%">
<h3>SPO2</h3>
</div>
<div class="box" id="bpm_div" style="width:95%">
<h3>SPO2</h3>
</div>
<script>

g = new Dygraph(
document.getElementById("spo2_div"),
"get-data3spo.php", // path to CSV file
{ // rollPeriod: 7,
legend: 'always',
animatedZooms: true,
showRoller: true
//errorBars: true,
//valueRange: [40,100]} // options
}
);
g = new Dygraph(
document.getElementById("bpm_div"),
"get-data3bpm.php", // path to CSV file
{ // rollPeriod: 7,
legend: 'always',
animatedZooms: true,
showRoller: true
//errorBars: true,
//valueRange: [40,100]} // options
}
);
</script>
</body>
</html>
<?php
ini_set("error_reporting",E_ALL);
syslog(LOG_DEBUG,"Start get-data.php");
# set db connection parameters
$dbhost="10.1.1.1";
#$dbhost="127.0.0.1";
$dblogin="lograd8";
$dbpwd="secret";
$dbname="lograd8";
$db = mysql_connect($dbhost,$dblogin,$dbpwd);
mysql_select_db($dbname);
$rows = "DatumTijd,gem_SPO2,spreiding_SPO2,max_SPO2,min_SPO2n";
#$startdate = $_POST['startdate'];
$former=0;
$query = "select date_format(tijd,'%Y/%m/%d %H:00') as datum, avg(spo2)
as gem_spo2, std(spo2) as spreiding_spo2, max(spo2) as max_spo2,
min(spo2) as min_spo2 from data group by date_format(session,'%d/%m/%Y
%H');";
# +---------------+----------+----------------+----------+----------+
# | datum_uur | gem_spo2 | spreiding_spo2 | max_spo2 | min_spo2 |
# +---------------+----------+----------+----------------+----------+
syslog(LOG_DEBUG,"$query");
$result = mysql_query($query);
while($r = mysql_fetch_array($result)){
#syslog(LOG_DEBUG,print_r($r,TRUE));
$rij="";
# vervangen min=0 door min=avg bij spo2 en bpm
if ($r[4]==0) $r[4]=$r[1];
for ($i=0;$i<=4;$i++) {
$rij = $rij.$r[$i].",";
}
$rij=substr($rij,0,strlen($rij)-1);
$rows = $rows.$rij."n";
}
#syslog(LOG_DEBUG,print_r($rows,TRUE));
#echo $cols . '"rows":[',$google_JSON_row ."]}";
# output off json string to caller.
echo $rows;
# saving of cvs string for debugging purposes
#$fh=fopen("/tmp/get-data.cvs","w");
#fwrite($fh,$rows);
#fclose($fh);
mysql_close($db);
syslog(LOG_DEBUG,"Einde get-data.phpnn");
?>
<?php
ini_set("error_reporting",E_ALL);
syslog(LOG_DEBUG,"Start get-data.php");
# set db connection parameters
$dbhost="10.1.1.1";
#$dbhost="127.0.0.1";
$dblogin="lograd8";
$dbpwd="secret";
$dbname="lograd8";
$db = mysql_connect($dbhost,$dblogin,$dbpwd);
mysql_select_db($dbname);
$rows = "DatumTijd,gem_BPM,spreiding_BPM,max_BPM,min_BPMn";
$former=0;
$query = "select date_format(tijd,'%Y/%m/%d %H:00') as datum, avg(bpm)
as gem_bpm, std(bpm) as spreiding_bpm, max(bpm) as max_bpm, min(bpm)
as min_bpm from data group by date_format(session,'%d/%m/%Y %H');";
# +---------------+----------+---------------+---------+---------+
# | datum_uur | gem_bpm | spreiding_bpm | max_bpm | min_bpm |
# +---------------+----------+---------------+---------+---------+
syslog(LOG_DEBUG,"$query");
$result = mysql_query($query);
while($r = mysql_fetch_array($result)){
#syslog(LOG_DEBUG,print_r($r,TRUE));
#syslog(LOG_DEBUG,print_r($tijd,TRUE));
$rij="";
# replace min=0 by min=avg for spo2 and bpm
if ($r[4]==0) $r[4]=$r[1];
for ($i=0;$i<=4;$i++) {
$rij = $rij.$r[$i].",";
}
$rij=substr($rij,0,strlen($rij)-1);
$rows = $rows.$rij."n";
}
#echo $cols . '"rows":[',$google_JSON_row ."]}";
# output off json string to caller.
echo $rows;
# saving of cvs string for debugging purposes
#$fh=fopen("/tmp/get-data2.cvs","w");
#fwrite($fh,$rows);
#fclose($fh);
mysql_close($db);
syslog(LOG_DEBUG,"Einde get-data.phpnn");
?>
Index.php
oxygen.php bpm.php

21
New result
Can you see the problem?

22
New result
Let me show you...

23
Findings
Medical:
When not connected to O2 during the night the minimum
rates will continue to drop during several days.
Ergo: O2 always needed.
Techical:
Next time make a stored procedure and a trigger to update
records upon creation.

24
Anouschka thanks you …
Thanks for your attention.
Any questions?

T-DOSE 2015: Using Python, PHP, JQuery and Linux to visualize the heartrate and blood oxygen saturation level of my stepdaughter

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Similar to T-DOSE 2015: Using Python, PHP, JQuery and Linux to visualize the heartrate and blood oxygen saturation level of my stepdaughter

Similar to T-DOSE 2015: Using Python, PHP, JQuery and Linux to visualize the heartrate and blood oxygen saturation level of my stepdaughter (20)

More from Jeroen Baten

More from Jeroen Baten (6)

Recently uploaded

Recently uploaded (20)

T-DOSE 2015: Using Python, PHP, JQuery and Linux to visualize the heartrate and blood oxygen saturation level of my stepdaughter