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maksteel opened this issue Jun 9, 2020 · 0 comments · Fixed by #232
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units are not parsed correctly #231

maksteel opened this issue Jun 9, 2020 · 0 comments · Fixed by #232
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@maksteel
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maksteel commented Jun 9, 2020

If the units contains a slash '/' they are not parsed correctly.

Bug in the regex:

wfdb-python/wfdb/io/_header.py

Line 110 in c616cb6

"/?(?P<units>[\w\^\-\?%]*)[ \t]*(?P<adc_res>\d*)[ \t]*",

Example:
Traces.hea file

Traces 8 1 31210 20:00:00 21/03/2020
Traces.dat 16x100 10.8692551374(1)/uV 15 0 0 24244 0 Chin
Traces.dat 16x100 10.8692551374(1)/uV 15 0 0 22989 0 Left Leg
Traces.dat 16x100 10.8692551374(1)/uV 15 0 0 -22154 0 Right Leg
Traces.dat 16x200 223.15372252(1)/mcmH2O 15 0 0 -24985 0 CPAP Pressure
Traces.dat 16x200 5948.85369237(1)/l/min 15 0 0 -22447 0 CPAP Flow
Traces.dat 16x200 505.31578574(1)/l/min 15 0 0 10563 0 CPAP Leak
Traces.dat 16x5 45.467096819(1)/m 15 0 0 17314 0 Light_BU
Traces.dat 16x10 4507.25807894(1)/mV/s 15 0 0 -12675 0 XFlow_DR

python code that fails

sig = wfdb.rdheader('Traces')
df = pd.DataFrame({'sig_name':sig.sig_name, 'units':sig.units,\
 'adc_res':sig.adc_res, 'init_value':sig.init_value,\
 'checksum':sig.checksum, 'block_size':sig.block_size})
print(df.to_string())

output contains NaN

                         sig_name   units  adc_res  init_value  checksum  block_size
0                            Chin      uV     15.0         0.0   24244.0         0.0
1                        Left Leg      uV     15.0         0.0   22989.0         0.0
2                       Right Leg      uV     15.0         0.0  -22154.0         0.0
3                   CPAP Pressure  mcmH2O     15.0         0.0  -24985.0         0.0
4  /min 15 0 0 -22447 0 CPAP Flow       l      NaN         NaN       NaN         NaN
5   /min 15 0 0 10563 0 CPAP Leak       l      NaN         NaN       NaN         NaN
6                        Light_BU       m     15.0         0.0   17314.0         0.0
7     /s 15 0 0 -12675 0 XFlow_DR      mV      NaN         NaN       NaN         NaN
maksteel pushed a commit to maksteel/wfdb-python that referenced this issue Jun 9, 2020
fixes MIT-LCP#231
acb6437
@maksteel maksteel mentioned this issue Jun 9, 2020
Merged
@Lucas-Mc Lucas-Mc added the bug label Jun 9, 2020
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updated regex to correctly parse units maksteel/wfdb-python
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@maksteel @Lucas-Mc