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Return NAN when downsampling singlechan SDDB dataset #249

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Yosafat1997 opened this issue Aug 20, 2020 · 1 comment · Fixed by #250
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Return NAN when downsampling singlechan SDDB dataset #249

Yosafat1997 opened this issue Aug 20, 2020 · 1 comment · Fixed by #250
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@Lucas-Mc
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@Yosafat1997
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Yosafat1997 commented Aug 20, 2020 •
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Dear devs,

I try to downsample one of SDDB signal from 250Hz to 128 Hz due i need to compare it with NSR-DB. Here what I do to downsample it:

import wfdb
from wfdb import processing as proc
#this is from sddb
sig,fields=wfdb.rdsamp(r'C:\Users\Yosafat VS\PycharmProjects\Paper Reproduce\dataset\sddb\30',channels=[0])

ann = wfdb.rdann(r'C:\Users\Yosafat VS\PycharmProjects\Paper Reproduce\dataset\sddb\30',extension='atr')

#this is from nsr_db
nsig,nfields=wfdb.rdsamp(r'C:\Users\Yosafat VS\PycharmProjects\Paper Reproduce\dataset\nsr\16265',channels=[0])
# print(nsig)
nann = wfdb.rdann(r'C:\Users\Yosafat VS\PycharmProjects\Paper Reproduce\dataset\nsr\16265',extension='atr')

print(sig[:,0])
print(lambda sig: [item for sublist in sig for item in sublist])
# print(ann.fs)
# print(nann.fs)
new_sig,new_ann= proc.resample_singlechan(sig[:,0],ann,fields['fs'],nfields['fs'])
print(new_x,new_t)

But when i run it, it return nan for new signal. For record number 30 to 35, it generate nan operation for record number 30 and 34.
@Lucas-Mc Lucas-Mc self-assigned this Aug 20, 2020
@Lucas-Mc Lucas-Mc added the bug label Aug 20, 2020
@Lucas-Mc
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Hey @Yosafat1997, it looks like it was a Scipy issue where it would return all NaNs if there were any NaN values in the input array when attempting to resample. I am pushing a new pull request now to fix this. Thanks for catching this! 👍

Lucas-Mc added a commit that referenced this issue Aug 20, 2020
@Lucas-Mc
Fixes downsample error #249
3fd3cc7 
Fixes error when downsampling single channel if NaN values are present. This was a Scipy issue so extra pre-processing and input validation was done to help safe-guard against this issue re-occuring in the future. Fixes #249.
@Lucas-Mc Lucas-Mc mentioned this issue Aug 20, 2020
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Lucas-Mc added a commit that referenced this issue Aug 20, 2020
@Lucas-Mc
Merge pull request #250 from MIT-LCP/fix_ann_249
517d708 
Fixes downsample error #249
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Fixes downsample error #249 MIT-LCP/wfdb-python
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@Yosafat1997 @Lucas-Mc