Question/suggestions about benchmark files about biopeaks HOT 3 CLOSED

I cannot find "signal" and "annotations" as required in benchmark_PPG.py. where am I going wrong?

@sappelhoff, you're right. I didn't document that the "signal" and "annotations" need to be extracted from the .mat files before running benchmark_PPG. I updated the script such that the PPG benchmark can now be run directly on TBME2013-PPGRR-Benchmark_R3/data (the extraction of "signal" and "annotations" is now taken care of in the script). See 41d7a6f.

I removed the commented code from benchmark_ECG_local (I only used it for debugging).

Will address the module level docstrings once I get around to #11.

from biopeaks.

One more question about benchmark_PPG.py --> according to the docs, I should first download the data from http://www.capnobase.org/index.php?id=857

I did that (specifically: TBME2013-PPGRR-Benchmark_R3.zip), and the data looks like the following. I cannot find "signal" and "annotations" as required in benchmark_PPG.py. where am I going wrong?

TBME2013-PPGRR-Benchmark_R3
├── data
│   ├── 0009_8min.mat
│   ├── 0015_8min.mat
│   ├── 0016_8min.mat
│   ├── 0018_8min.mat
│   ├── 0023_8min.mat
│   ├── 0028_8min.mat
│   ├── 0029_8min.mat
│   ├── 0030_8min.mat
│   ├── 0031_8min.mat
│   ├── 0032_8min.mat
│   ├── 0035_8min.mat
│   ├── 0038_8min.mat
│   ├── 0103_8min.mat
│   ├── 0104_8min.mat
│   ├── 0105_8min.mat
│   ├── 0115_8min.mat
│   ├── 0121_8min.mat
│   ├── 0122_8min.mat
│   ├── 0123_8min.mat
│   ├── 0125_8min.mat
│   ├── 0127_8min.mat
│   ├── 0128_8min.mat
│   ├── 0133_8min.mat
│   ├── 0134_8min.mat
│   ├── 0142_8min.mat
│   ├── 0147_8min.mat
│   ├── 0148_8min.mat
│   ├── 0149_8min.mat
│   ├── 0150_8min.mat
│   ├── 0309_8min.mat
│   ├── 0311_8min.mat
│   ├── 0312_8min.mat
│   ├── 0313_8min.mat
│   ├── 0322_8min.mat
│   ├── 0325_8min.mat
│   ├── 0328_8min.mat
│   ├── 0329_8min.mat
│   ├── 0330_8min.mat
│   ├── 0331_8min.mat
│   ├── 0332_8min.mat
│   ├── 0333_8min.mat
│   └── 0370_8min.mat
└── README.txt

1 directory, 43 files

from biopeaks.

great, I was able to run all benchmarks now. Thanks a bunch.

The performance details you describe in the paper match approximately with what I can reproduce on my machine (slight rounding deviations are to be expected I guess.)

from biopeaks.