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Axis out of bounds when reading trigger #447

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oesteban opened this issue May 3, 2023 · 0 comments
Open

Axis out of bounds when reading trigger #447

oesteban opened this issue May 3, 2023 · 0 comments
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Bug Something isn't working

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@oesteban
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oesteban commented May 3, 2023

Expected Behavior

Actual Behavior

/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/physio_obj.py:649: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
  channel_ts = np.array(self.timeseries[1:])
Traceback (most recent call last):
  File "/home/oesteban/.miniconda/bin/phys2bids", line 8, in <module>
    sys.exit(_main())
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/phys2bids.py", line 544, in _main
    phys2bids(**vars(options))
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/phys2bids.py", line 250, in phys2bids
    phys_in = load_acq(infile, chtrig)
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/io.py", line 376, in load_acq
    return BlueprintInput(timeseries, freq, names, units, chtrig)
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/physio_obj.py", line 254, in __init__
    self.auto_trigger_selection()
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/phys2bids/physio_obj.py", line 652, in auto_trigger_selection
    min_ts = np.min(channel_ts, axis=1)[:, None]
  File "<__array_function__ internals>", line 180, in amin
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2918, in amin
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
  File "/home/oesteban/.miniconda/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
numpy.AxisError: axis 1 is out of bounds for array of dimension 1
@oesteban oesteban added the Bug Something isn't working label May 3, 2023
@rgbayrak rgbayrak moved this to To Do in phys2bids Jan 18, 2024
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