Update to the new PhysioNet site

ikarosilva / wfdb-app-toolbox

The WFDB Toolbox for MATLAB/Octave is a collection of functions for reading, writing, and processing physiologic signals in the formats used by PhysioNet (see README for details).

http://physionet.org/physiotools/matlab/wfdb-app-matlab/

GNU General Public License v3.0

92 stars 45 forks source link

Update to the new PhysioNet site #175

Open Lucas-Mc opened 3 years ago

Lucas-Mc commented 3 years ago

In this change, I update the toolbox to work with the new PhysioNet site which, in the process, allows users to use even the most recent submissions rather than only those available on Physiobank (nearly 3x more datasets now plus the old content is still available on the new PhysioNet site). Updates to the relevant documentation is also done to fix broken links, fix typos, and update docstrings to refer to the most recent changes.

Some major changes include:

Updating the PhysioNet database list to now come from the new site's REST API
Including version numbers in reference to databases to reflect the new syntax on PhysioNet
Parsing the header file along with using: wfdb_extensions={'.dat','.atr','.edf','.rec','.hea','.hea-','.trigger','.mat'}; (this helps with some situations where one of the following extensions may not be present such as various new annotation types)
Updating from MIMIC-II to MIMIC-III (which is now a superset of MIMIC-II)
Fixing the examples and Unit Tests to work for the updated PhysioNet
Updating the HTML documentation for the website
Updating some syntax for the most recent Matlab version
Fixing the broken links and image in the README

Fixes to current issues include (possibly): #158, #149, #130, #112

bemoody commented 3 years ago

Would you please redo this without re-indenting the entire Java source? Your re-indentation of those four files makes it impossible to see at a glance what you've changed, and makes them inconsistent with the indentation of the other Java files.

I realize we do need to add support on PhysioNet for reading new project files via http; this is something that should have been done a long time ago and dropped off the radar...

Lucas-Mc commented 3 years ago

Yeah no problem, it must have automatically been done by my IDE... it has spaces as default since tabs cause problems with display. Thanks! On it!

xaishu commented 3 years ago

Thanks, Lucas for the update.

How can I use it? Do I need to delete the whole toolbox and download the updated one? Where is the download link?

Lucas-Mc commented 3 years ago

Hey @xaishu! You should be able to download the original from the instructions here then overwrite the files in your MATLAB/wfdb/mcode with the ones from my fork, probably using a git clone to another folder, here.

The final step is to run make package in the same directory as the Makefile from the folder where you git clone my fork. This should generate a wfdb-app-****.jar file which you can copy to the MATLAB/wfdb/mcode folder. It's kind of hard to explain great and I'm sure there's a better way but let me know if you need more help!

EDIT: I suppose the alternate is to run Matlab out of the git clone directory but I haven't tried this though it seems much easier.