Unable to read ECG data in either Matlab or Octave. New to WFDB.

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Barbara Presley

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Mar 25, 2016, 2:17:38 AM3/25/16
to wfdb-app-toolbox
Any help would be greatly appreciated.  I am unable to read ECG data either in Matlab or Octave.

I believe Matlab R2015a is not supported, but it worked fine on wfdbdemo.  I ran
[tm,sig]=rdsamp('mitdb/100',1);
plot(tm,sig);

and that worked fine.  I don't understand how the program works.  I read through many of the functions, such as rdsamp.  Apparently it's a wrapper for http://www.physionet.org/physiotools/wag/rdsamp-1.htm.  I went to that site and did not find any references to 'mitdb/100', so I don't where that comes from.  I only know it works. 

I would like to read http://physionet.org/physiobank/database/nsrdb/16265.dat from  I downloaded the files (.dat, .hea, atr, xws) and put them in the folder that contains the toolbox m files.  I ran  wfdb2mat('16265', 1, 100, 1).  There were no crashes, but no results.  So I ran b.mat=wfdb2mat('16265', 1, 100, 1) and got an error message:

Error in wfdb2mat (line 54)
persistent javaWfdbExec config
Output argument "varargout" (and maybe
others) not assigned during call to
"wfdb2mat".


I tried

wfdb_url='http://physionet.org/physiobank/database/pbi/nsrdb/16265.dat';
[filestr,status] = urlwrite(wfdb_url,'16265.dat');

and

wfdb_url='http://physionet.org/physiobank/database/pbi/nsrdb/16265.dat';
[filestr,status] = urlwrite(wfdb_url,'16265');

filestr returned empty and status was 0.

I tried removing 'pbi' to be consistent with the database listing I got in matlab.  Same results, nothing.

for

> wfdbtest
***Starting test of the WFDB Application Toolbox
***If you experience any issues, please see our FAQ at:
http://physionet.org/physiotools/matlab/wfdb-app-matlab/faq.shtml
**Printing Configuration Settings:
**    WFDB App Toolbox Path is:
        C:\Users\Barb\OneDrive\WFDBToolbox\wfdb-app-toolbox-0-9-9\mcode\wfdbloadlib.m
config =
       MATLAB_VERSION: '8.5.0.1...'
             inOctave: 0
         WFDB_VERSION: '[10.5.24]'
       WFDB_JAVA_HOME: ' C:\Use...'
      WFDB_NATIVE_BIN: ' C:\Use...'
        EXECUTING_DIR: ' null'
               osName: 'windows'
           fullOsName: ' Windows 8'
               osArch: ' amd64'
       customArchFlag: ' false'
            OSVersion: ' 6.2'
           JVMVersion: ' 1.7.0_60]'
          MATLAB_PATH: 'C:\User...'
        SUPPORT_EMAIL: 'wfdb-ma...'
    WFDB_JAVA_VERSION: 'wfdb-ap...'
          DEBUG_LEVEL: 0
    NETWORK_WAIT_TIME: 1000
          MATLAB_ARCH: 'win64'
            WFDB_PATH: '. file:...'
              WFDBCAL: ' C:\Use...'
       WFDB_CUSTOMLIB: 0
Warning: You are using an
unsupported version of MATLAB:
8.5.0.197613 (R2015a)
> In wfdbtest (line 71)
**Querying PhysioNet for available databases...
    99 databases available for download (type 'help physionetdb' for more info).
**Reading local example data and annotation...
**Calculating maternal QRS sample data ...
**Reading data from PhysioNet...
***Finished testing WFDB App Toolbox!
***Note: You currently have access to 99 databases for download via PhysioNet:
     Type 'physionetdb' for a list of the databases or 'help physionetdb' for more info.

**Reading local example data and annotation...
Warning: Objects of
org/physionet/wfdb/Wfdbexec class exist -
not clearing java
> In javaclasspath>local_javapath (line 190)
  In javaclasspath (line 119)
  In javaaddpath (line 71)
  In wfdbloadlib (line 100)
  In getWfdbClass (line 21)
  In rdsamp (line 87)
  In wfdbtest (line 110)
**Calculating maternal QRS sample data ...
**Reading data from PhysioNet...
***Finished testing WFDB App Toolbox!
***Note: You currently have access to 99 databases for download via PhysioNet:
     Type 'physionetdb' for a list of the databases or 'help physionetdb' for more info.




So, I tried using the latest version of Octave.  I was unable to run the demo, and wfdbtest did not go well:


wfdbdemo
error: unable to find Java Runtime Environment: software\javasoft\java runtime environment::Currentversion
error: called from
    wfdbloadlib at line 89 column 23
    wfdbdemo at line 8 column 10

>> wfdbtest

***Starting test of the WFDB Application Toolbox
***If you experience any issues, please see our FAQ at:
http://physionet.org/physiotools/matlab/wfdb-app-matlab/faq.shtml
warning: MATLAB JVM is not properly configured for toolbox
warning: called from
    wfdbtest at line 50 column 5
**Printing Configuration Settings:
**      WFDB App Toolbox Path is:
                C:\Users\Barb\OneDrive\WFDBToolbox\wfdb-app-toolbox-0-9-9\mcode\wfdbloadlib.m
error: unable to find Java Runtime Environment: software\javasoft\java runtime environment::Currentversion
error: called from
    wfdbloadlib at line 89 column 23
    wfdbtest at line 63 column 17


I had installed java, so I checked the version with a cmd prompt:
C:\Users\Barb>java -version
java version "1.8.0_77"
Java(TM) SE Runtime Environment (build.1.80.0_77-b03)
Java HotSpot(TM) 64-Bit Server VM (build 27.77-b03, mixed mode)


Thanks.

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