8000 pad in arraypad.py changed behavior in an undocumented fashion · Issue #7353 · numpy/numpy · GitHub
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chiffa opened this issue Feb 27, 2016 · 3 comments
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pad in arraypad.py changed behavior in an undocumented fashion #7353

chiffa opened this issue Feb 27, 2016 · 3 comments

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@chiffa
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chiffa commented Feb 27, 2016

Previously this command worked:

a = [[1, 2], [3, 4]]
np.lib.pad(a, ((3, 2), (2, 3)), 'constant',
                 constant_values=((np.nan, np.nan), (np.nan, np.nan)))

However in the 1.10.4 it now returns the following stack trace:

Traceback (most recent call last):
  File "C:/Users/Andrei/PycharmProjects/Pharmacosensitivity_growth_assays/src/post_processing.py", line 477, in <module>
    all_cell_lines_arr, means_accumulator, errs_accumulator, names_accumulator = stack_data_in_range_of_interest(concs_effective_range)
  File "C:/Users/Andrei/PycharmProjects/Pharmacosensitivity_growth_assays/src/post_processing.py", line 129, in stack_data_in_range_of_interest
    mode='constant', constant_values=((np.nan, np.nan), (np.nan, np.nan)))
  File "C:\Anaconda\lib\site-packages\numpy\lib\arraypad.py", line 1358, in pad
    cast_to_int=False)
  File "C:\Anaconda\lib\site-packages\numpy\lib\arraypad.py", line 1070, in _normalize_shape
    return tuple(tuple(axis) for axis in arr.tolist())
AttributeError: 'tuple' object has no attribute 'tolist'

This is now the way of implementing the padding:

a = [[1, 2], [3, 4]]
nan_pad = np.array(((np.nan, np.nan), (np.nan, np.nan)))

np.lib.pad(a, ((3, 2), (2, 3)), 'constant',
                 constant_values=nan_pad)

Could you please add relevant documentation to the pad function in the arraypad.py?

An additional issue is that it looks like np.nan gets converted to -2147483648 which seems to be overflowing 32-bit signed integer. It does not affect my code that much, but this is an issue you might need to be aware of.
@chiffa chiffa mentioned this issue Feb 27, 2016
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@njsmith
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njsmith commented Feb 27, 2016

This comment is relevant to this bug: #7354 (comment)

chiffa added a commit to chiffa/numpy that referenced this issue Feb 27, 2016
@chiffa
corrected the execution path that led to the issue numpy#7353
615ce3f
chiffa added a commit to chiffa/numpy that referenced this issue Feb 27, 2016
@chiffa
added the test case that exposes issue numpy#7353
ad5e1d4
@chiffa chiffa mentioned this issue Feb 28, 2016
Merged
chiffa added a commit to chiffa/numpy that referenced this issue Feb 28, 2016
@chiffa
TST: added a test for constant padding on 4 sides of a 2d array
8f64328 
This test exposes padding bug described in the issue numpy#7353
chiffa added a commit to chiffa/numpy that referenced this issue Feb 28, 2016
@chiffa
BUG: constant padding expected wrong type in constant_values
3db32cb 
Constant padding on 4 sides of a 2d array expected a numpy ndarray, and not a ndarray like (tuple, list, ...)
Detailed description is in the issue  numpy#7353
njsmith added a commit that referenced this issue Feb 28, 2016
@njsmith
Merge pull request #7358 from chiffa/master
e90e254 
BUG: pull request related to the issue #7353
jaimefrio pushed a commit to jaimefrio/numpy that referenced this issue Mar 22, 2016
@chiffa @jaimefrio
TST: added a test for constant padding on 4 sides of a 2d array
e7d1d99 
This test exposes padding bug described in the issue numpy#7353
jaimefrio pushed a commit to jaimefrio/numpy that referenced this issue Mar 22, 2016
@chiffa @jaimefrio
BUG: constant padding expected wrong type in constant_values
7567169 
Constant padding on 4 sides of a 2d array expected a numpy ndarray, and not a ndarray like (tuple, list, ...)
Detailed description is in the issue  numpy#7353
charris pushed a commit to charris/numpy that referenced this issue Apr 18, 2016
@chiffa @charris
TST: added a test for constant padding on 4 sides of a 2d array
77d911f 
This test exposes padding bug described in the issue numpy#7353
charris pushed a commit to charris/numpy that referenced this issue Apr 18, 2016
@chiffa @charris
BUG: constant padding expected wrong type in constant_values
32f8393 
Constant padding on 4 sides of a 2d array expected a numpy ndarray, and not a ndarray like (tuple, list, ...)
Detailed description is in the issue  numpy#7353
@charris charris mentioned this issue Apr 18, 2016
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@jakirkham
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Retested with NumPy 1.14.3 and this appears to be fixed.

@jakirkham jakirkham mentioned this issue Jun 8, 2018
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@charris charris closed this as completed Jun 8, 2018
@charris
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charris commented Jun 8, 2018

@jakirkham Thanks for the heads up.

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