rdsamp fails when attempting to read local data
mr.fabi...@gmail.com
I'm running a test script which worked fine for the last months using wfdb version 0.9.9.
After having updated to version 0.10.0 due to the error described here (https://github.com/ikarosilva/wfdb-app-toolbox/issues/160) rdsamp() does not work anymore as before.
Before I could read local data files (*.dat, *.atr) via rdsamp() and rdann().
With the updated wfdb version 0.10 it does not work anymore:
Could not find record:
C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\..\database\\tmpEcgR\100.
Search path is set to: '.
C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\..\database\
http://physionet.org/physiobank/database/'
I've copied the files into config.CACHE_DEST but this didn't solve my issue.
Any idea how this can be fixed?
Thanks a lot for your help!
Cheers,
Fab
PS: my configuration is as follows:
>> [~,config]=wfdbloadlib()
config =
struct with fields:
MATLAB_VERSION: '9.5.0.944444 (R2018b)'
inOctave: 0
WFDB_VERSION: '[10.5.25]'
WFDB_JAVA_HOME: ' C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\'
WFDB_NATIVE_BIN: ' C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\nativelibs\windows\'
EXECUTING_DIR: ' null'
osName: 'windows'
fullOsName: ' Windows 10'
osArch: ' amd64'
customArchFlag: ' false'
OSVersion: ' 10.0'
JVMVersion: ' 1.8.0_152]'
MATLAB_PATH: 'C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\'
WFDB_JAVA_VERSION: 'wfdb-app-JVM7-0-10-0.jar'
DEBUG_LEVEL: 0
NETWORK_WAIT_TIME: 1000
MATLAB_ARCH: 'win64'
WFDB_PATH: '. C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\..\database\ http://physionet.org/physiobank/database/'
WFDBCAL: ' C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\\database\wfdbcal'
WFDB_CUSTOMLIB: 0
CACHE_SOURCE: 'http://physionet.org/physiobank/database/'
CACHE_DEST: 'C:\xxx\GIT\libecg-matlab-perf\wfdb-toolbox-matlab\..\database\'
CACHE: 1
>> ver
-----------------------------------------------------------------------------------------------------
MATLAB Version: 9.5.0.944444 (R2018b)
MATLAB License Number: 663530
Operating System: Microsoft Windows 10 Enterprise Version 10.0 (Build 17134)
Java Version: Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
-----------------------------------------------------------------------------------------------------
MATLAB Version 9.5 (R2018b)
Signal Processing Toolbox Version 8.1 (R2018b)
mr.fabi...@gmail.com
I just gave it a try on another machine with Win10 and ML R2016b (java JRE version 1.7.0).
WFDB 0.10 still fails, however when downgrading to 0.9.10 I can successfully read a *.dat file from local storage:
a) This configuration (wfdb 0.10.0) does NOT work :
>> cd C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\
>> [~, config] = wfdbloadlib
config =
struct with fields:
MATLAB_VERSION: '9.1.0.441655 (R2016b)'
inOctave: 0
WFDB_VERSION: '[10.5.25]'
WFDB_JAVA_HOME: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\'
WFDB_NATIVE_BIN: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\nativelibs\windows\'
EXECUTING_DIR: ' null'
osName: 'windows'
fullOsName: ' Windows 8'
osArch: ' amd64'
customArchFlag: ' false'
OSVersion: ' 6.2'
JVMVersion: ' 1.7.0_60]'
MATLAB_PATH: 'C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\'
WFDB_JAVA_VERSION: 'wfdb-app-JVM7-0-10-0.jar'
DEBUG_LEVEL: 0
NETWORK_WAIT_TIME: 1000
MATLAB_ARCH: 'win64'
WFDB_PATH: '. C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\..\database\ http://physionet.org/physiobank/database/'
WFDBCAL: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\\database\wfdbcal'
WFDB_CUSTOMLIB: 0
CACHE_SOURCE: 'http://physionet.org/physiobank/database/'
CACHE_DEST: 'C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\..\database\'
CACHE: 1
>> rdsamp('C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\database\mitdb\100.dat');
Error using rdsamp (line 203)
Could not find record: C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\database\mitdb\100. Search path is set to: '.
C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\mcode\..\database\ http://physionet.org/physiobank/database/'
b) This configuration configuration (wfdb 0.9.10) DOES work WELL!
>> cd C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\
>> [~, config] = wfdbloadlib
config =
struct with fields:
MATLAB_VERSION: '9.1.0.441655 (R2016b)'
inOctave: 0
WFDB_VERSION: '[10.5.24]'
WFDB_JAVA_HOME: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\'
WFDB_NATIVE_BIN: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\nativelibs\windows\'
EXECUTING_DIR: ' null'
osName: 'windows'
fullOsName: ' Windows 8'
osArch: ' amd64'
customArchFlag: ' false'
OSVersion: ' 6.2'
JVMVersion: ' 1.7.0_60]'
MATLAB_PATH: 'C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\'
SUPPORT_EMAIL: 'wfdb-matl...@physionet.org'
WFDB_JAVA_VERSION: 'wfdb-app-JVM7-0-9-9.jar'
DEBUG_LEVEL: 0
NETWORK_WAIT_TIME: 1000
MATLAB_ARCH: 'win64'
WFDB_PATH: '. file:// C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\database http://physionet.org/physiobank/database'
WFDBCAL: ' C:\Users\Fab\Downloads\wfdb-app-toolbox-0-9-10\mcode\\database\wfdbcal'
WFDB_CUSTOMLIB: 0
>> rdsamp('C:\Users\Fab\Downloads\wfdb-app-toolbox-0-10-0\database\mitdb\100.dat');
>>
petru...@gmail.com
I am currently facing the same problem. Could, you, please advise me, how to downgrade the version of the toolbox? I am new to it...
This is my configuration:
[~,config]=wfdbloadlib()
config =
struct with fields:
MATLAB_VERSION: '9.5.0.944444 (R2018b)'
inOctave: 0
WFDB_VERSION: '[10.5.25]'
WFDB_JAVA_HOME: ' C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\'
WFDB_NATIVE_BIN: ' C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\nativelibs\windows\'
EXECUTING_DIR: ' null'
osName: 'windows'
fullOsName: ' Windows 10'
osArch: ' amd64'
customArchFlag: ' false'
OSVersion: ' 10.0'
JVMVersion: ' 1.8.0_152]'
MATLAB_PATH: 'C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\'
WFDB_JAVA_VERSION: 'wfdb-app-JVM7-0-10-0.jar'
DEBUG_LEVEL: 0
NETWORK_WAIT_TIME: 1000
MATLAB_ARCH: 'win64'
WFDB_PATH: '. C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\..\database\ http://physionet.org/physiobank/database/'
WFDBCAL: ' C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\\database\wfdbcal'
WFDB_CUSTOMLIB: 0
CACHE_SOURCE: 'http://physionet.org/physiobank/database/'
CACHE_DEST: 'C:\Users\Petra Novotna\iCloudDrive\PhD\Pepe_Lecture_2\Funciones\mcode\..\database\'
CACHE: 1
Thank you very much!
mr.fabi...@gmail.com
mr.fabi...@gmail.com
novo...@vutbr.cz
I don't know why I was searching for the appropriate master branch in the GitHub (*facepalm*).
Also, I have also Matlab 2016b on Mac and 2015b on Win10, so I will try at either of them.
Thanks!
Petra
kimra...@gmail.com
I had the same problem (the function rdsamp not working due the same error, eventhough it was working yesterday), so I thought I must have somehow changed the search path for the function.
It turned out the problem was that I have deleted the .hea file from my folder (the .hea file had the same name as the .dat file), and when I downloaded it again from the PhysioNet database, the function started working again (toolbox version 0.10).