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nanli-emory opened this issue Jun 27, 2022 · 0 comments · Fixed by #404
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How to use wfdb.wrann with custom_labels and label_store to write the custom labels? #399

nanli-emory opened this issue Jun 27, 2022 · 0 comments · Fixed by #404

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@nanli-emory
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nanli-emory commented Jun 27, 2022 •
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I was trying to write an annotation as wfdb format annotation.

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 a error.

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

I think probably I used the incorrect way to write the custom labels.
Could you guide me on how to correctly use wfdb.wrann with custom_labels and label_store to write the annotation?
Thanks.
@nanli-emory nanli-emory changed the title How to use wfdb.wrann with custom_labels and label_store? How to use wfdb.wrann with custom_labels and label_store to write the custom labels? Jun 27, 2022
@birm birm mentioned this issue Jun 30, 2022
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Allow custom labels in field2bytes birm/wfdb-python
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