briangow
commented
7 months ago Thanks @bemoody , this is running on my mac (though there is a RuntimeWarning). Here is the output for reference:
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Format: waveform_benchmark.formats.wfdb.WFDBFormat516
(WFDB with FLAC compression)
Record: /Users/briangow/Dropbox/MIT/chorus/repos/chorus_waveform/physionet.org/files/mimic4wdb/0.1.0/waves/p100/p10014354/81739927/81739927
106625 seconds x 7 channels
153205760 timepoints, 99842432 samples (65.2%)
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/Users/briangow/Dropbox (MIT)/MIT/chorus/repos/chorus_waveform/env/lib/python3.10/site-packages/wfdb/io/_signal.py:578: RuntimeWarning: invalid value encountered in cast
ch_d_signal = ch_d_signal.astype(intdtype, copy=False)
Output size: 47043 KiB (3.86 bits/sample)
Time to output: 13 sec
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Read performance (median of N trials):
#seek #read KiB sec [N]
nan nan nan 1.5564 [7] read 1 x 106625s, all channels
nan nan nan 0.0468 [172] read 5 x 500s, all channels
nan nan nan 0.1635 [41] read 50 x 50s, all channels
nan nan nan 1.3392 [5] read 500 x 5s, all channels
nan nan nan 1.1852 [12] read 1 x 106625s, one channel
nan nan nan 0.0318 [260] read 5 x 500s, one channel
nan nan nan 0.1225 [56] read 50 x 50s, one channel
nan nan nan 1.0367 [7] read 500 x 5s, one channel
Try to make the waveform_benchmark script work at a basic level on non-Linux systems - where currently we don't have a way to gather I/O performance numbers, but it's useful to see that the code runs and measure execution time.