Allow custom labels in field2bytes

[birm]

Fixes #399

Take custom labels into account in encoding, should they exist by temporarily creating a larger version of ann_label_table including custom labels.

[cx1111]

This looks good, thank you.

Could you please add a test case?

[cx1111]

Also, I'm curious to know: why do you want to write WFDB annotation files?

Trying to get a gauge of what's useful and where to focus future efforts, thanks.

[nanli-emory]

Also, I'm curious to know: why do you want to write WFDB annotation files?

Trying to get a gauge of what's useful and where to focus future efforts, thanks.

We were trying to write the custom beat labels into WFDB annotation format.

import wfdb
import numpy as np
import pandas as pd
ann_idx = np.array([0, 1000, 2000, 3000, 4000, 5000, 6000, 7000])
ann_label_store = np.array([ 4, 4, 1, 2, 2, 3, 2, 3])
ann_chan = np.array([3, 1, 2, 3, 4, 5, 6, 7])
ann_custom_labels = {'label_store': [1, 2, 3, 4], 'symbol': ['v', 'l', 'r', 'z'], 'description': ['pvc', 'lbbb', 'rbbb', 'pac']}
ann_custom_labels = pd.DataFrame(data=ann_custom_labels)
wfdb.wrann('A0001', 'atr', ann_idx, chan=ann_chan, label_store=ann_label_store,custom_labels=ann_custom_labels)

However, there is an error as follows.

Traceback (most recent call last):
  File "test.py", line 10, in <module>
    wfdb.wrann('A0001', 'atr', ann_idx, chan=ann_chan, label_store=ann_label_store,custom_labels=ann_custom_labels)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/wfdb/io/annotation.py", line 1525, in wrann
    annotation.wrann(write_fs=True, write_dir=write_dir)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/wfdb/io/annotation.py", line 292, in wrann
    self.wr_ann_file(write_fs=write_fs, write_dir=write_dir)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/wfdb/io/annotation.py", line 798, in wr_ann_file
    core_bytes = self.calc_core_bytes()
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/wfdb/io/annotation.py", line 937, in calc_core_bytes
    data_bytes.append(field2bytes('samptype', [sampdiff[i], self.symbol[i]]))
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/wfdb/io/annotation.py", line 1369, in field2bytes
    typecode = ann_label_table.loc[ann_label_table['symbol']==value[1], 'label_store'].values[0]
IndexError: index 0 is out of bounds for axis 0 with size 0

After we checked the code and found out the python code never use custom_labels to store the symbol/labels.

So my colleague tries to fix the bug that allows storing custom labels in WFDB annotation format.

The test code that we use:

import wfdb
import numpy as np
import pandas as pd

ann_idx = np.array([1, 1000, 2000, 3000, 4000, 5000, 6000, 7000])
ann_chan = np.array([3, 1, 2, 3, 4, 5, 6, 7])
# write custom labels
ann_label_store = np.array([ 4, 4, 1, 2, 2, 3, 2, 3])
ann_custom_labels = {'label_store': [1, 2, 3, 4], 'symbol': ['v','l','r','z'], 'description':['pvc','lbbb','rbbb','pac']}
ann_custom_labels = pd.DataFrame(data=ann_custom_labels)
wfdb.wrann('A0001', 'atr', ann_idx, chan=ann_chan, custom_labels=ann_custom_labels, label_store=ann_label_store)

# read
ann = wfdb.rdann('A0001', 'atr')
print(ann.sample)
print(ann.custom_labels)
print(ann.symbol)
print(ann.label_store)
print(ann.chan)

After fixed the result:

[   1 1000 2000 3000 4000 5000 6000 7000]
   label_store symbol description
1            1      v         pvc
2            2      l        lbbb
3            3      r        rbbb
4            4      z         pac
['z', 'z', 'v', 'l', 'l', 'r', 'l', 'r']
None
[3 1 2 3 4 5 6 7]

[birm]

Thank you. I've added a test case to the pytest suite in f01a151. Please let me know if this needs some code style changes, or anything else.

[cx1111]

Great, thanks!