Merge pull request #372 into main

This adds support for reading FLAC compressed signal files (indicated
by format codes 508, 516, and 524, which were added in libwfdb version
10.7.0.)

Reading FLAC files uses the Python soundfile package, which in turn
requires the libsndfile and libFLAC C libraries to be installed.
soundfile is now included as a dependency of wfdb; you can install it
even if you don't have libsndfile, but trying to 'import soundfile'
will fail in that case.  Consequently, wfdb will only try to import
soundfile when you actually try to read a FLAC signal file.

Note that most desktop Linux systems include libsndfile by default,
and the soundfile wheel packages include libsndfile binaries for
x86-64 Windows and Mac OS platforms.

Author: Benjamin Moody

.github/workflows/run-tests.yml

@@ -28,6 +28,10 @@ jobs:
         run: |
           python -m pip install --upgrade pip poetry
           pip install ".[dev]"
+      - name: Install libsndfile
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          sudo apt-get install -y libsndfile1
       - name: Run tests
         run: pytest
       - name: Validate poetry file
@@ -48,6 +52,7 @@ jobs:
                   python3-pandas \
                   python3-requests \
                   python3-scipy \
+                  python3-soundfile \
                   python3-pytest \
                   git
 

README.md

@@ -35,6 +35,8 @@ pip install wfdb
 poetry add wfdb
 ```
 
+On Linux systems, accessing *compressed* WFDB signal files requires installing `libsndfile`, by running `sudo apt-get install libsndfile1` or `sudo yum install libsndfile`.  Support for Apple M1 systems is a work in progess (see <https://github.com/bastibe/python-soundfile/issues/310> and <https://github.com/bastibe/python-soundfile/issues/325>).
+
 The development version is hosted at: <https://github.com/MIT-LCP/wfdb-python>. This repository also contains demo scripts and example data. To install the development version, clone or download the repository, navigate to the base directory, and run:
 
 ```sh

pyproject.toml

@@ -10,6 +10,7 @@ python = "^3.7"
 numpy = "^1.10.1"
 scipy = "^1.0.0"
 pandas = "^1.0.0"
+SoundFile = ">=0.10.0, <0.12.0"
 matplotlib = "^3.2.2"
 requests = "^2.8.1"
 pytest = {version = "^7.1.1", optional = true}

sample-data/flacformats.d0

@@ -0,0 +1,4 @@
+flacformats 3 200 499
+flacformats.d0 508 200/mV 8 0 -127 -484 0 sig 0, fmt 508
+flacformats.d1 516 200/mV 16 0 -32766 -750 0 sig 1, fmt 516
+flacformats.d2 524 200/mV 24 0 -8388605 8721 0 sig 2, fmt 524

sample-data/flacformats.d1

@@ -0,0 +1,7 @@
+mixedsignals 6 62.4725/999.56 14400
+mixedsignals_e.dat 516x4 200/mV 14 8192 0 24460 0 II
+mixedsignals_e.dat 516x4 200/mV 14 8192 0 19772 0 III
+mixedsignals_e.dat 516x4 200/mV 14 8192 0 22261 0 V
+mixedsignals_p.dat 516x2 16(800)/mmHg 12 2048 0 49347 0 ABP
+mixedsignals_p.dat 516x2 4096(0)/NU 12 2048 0 36026 0 Pleth
+mixedsignals_r.dat 516 4093(2)/Ohm 12 2048 0 35395 0 Resp