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Type error in h5py when data_array index exceeds number of items in data_array #299

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thladnik opened this issue May 23, 2018 · 1 comment
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Type error in h5py when data_array index exceeds number of items in data_array #299

thladnik opened this issue May 23, 2018 · 1 comment
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@achilleas-k

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@thladnik
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traceData = self.bHandle.data_arrays[traceName][int(traceStart*Fs):int(traceEnd*Fs)]
  File "/usr/local/lib/python3.5/dist-packages/nixio/data_array.py", line 137, in __getitem__
    self._read_data(raw, count, offset)
  File "/usr/local/lib/python3.5/dist-packages/nixio/pycore/data_array.py", line 82, in _read_data
    super(DataArray, self)._read_data(data, count, offset)
  File "/usr/local/lib/python3.5/dist-packages/nixio/pycore/data_array.py", line 28, in _read_data
    dataset.read_data(data, count, offset)
  File "/usr/local/lib/python3.5/dist-packages/nixio/pycore/h5dataset.py", line 57, in read_data
    self.dataset.read_direct(data, sl)
  File "/usr/local/lib/python3.5/dist-packages/h5py/_hl/dataset.py", line 656, in read_direct
    for mspace in dest_sel.broadcast(source_sel.mshape):
  File "/usr/local/lib/python3.5/dist-packages/h5py/_hl/selections.py", line 299, in broadcast
    raise TypeError("Can't broadcast %s -> %s" % (target_shape, count))
TypeError: Can't broadcast (97080,) -> (97081,)

Nixpy does not throw an exception when the index in a data_array call exceeds the number of items in the data_array. Instead it causes an error in h5py when the number of items retrieved from file does not match the number of expected items.
Maybe nixpy could instead check if the index is out of range before calling h5py.
@achilleas-k
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Good idea. A nicer error from nixpy would be more informative. Thanks for the suggestion.

@achilleas-k achilleas-k self-assigned this May 23, 2018
@achilleas-k achilleas-k mentioned this issue Jun 14, 2018
Merged
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jul 11, 2018
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
db2dec5 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jul 12, 2018
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
e8e6107 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jul 12, 2018
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
9881bf1 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jul 12, 2018
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
c7256ef 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jul 12, 2018
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
0b1c141 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
achilleas-k added a commit to achilleas-k/nixpy that referenced this issue Jan 18, 2019
@achilleas-k
[h5dataset] Catch H5Py indexing ValueError
6b08c0a 
H5Py throws ValueError for out-of-bounds indexing. We catch it and throw
IndexError instead, reusing the error message from H5Py.

This also makes indexing more flexible. Slices now work the same as in
numpy, so no slice is ever out-of-bounds. The corresponding test has
been updated accordingly.

This is an updated version of PR G-Node#303, which was a fix for G-Node#299.
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