[Numpy-discussion] load of custom .npy file fails with numpy 2.0.0

Robert Kern robert.kern@gmail....
Thu Aug 2 17:13:37 CDT 2012


On Thu, Aug 2, 2012 at 11:41 PM, Geoffrey Irving <irving@naml.us> wrote:
> On Thu, Aug 2, 2012 at 1:26 PM, Robert Kern <robert.kern@gmail.com> wrote:
>> On Thu, Aug 2, 2012 at 8:46 PM, Geoffrey Irving <irving@naml.us> wrote:
>>> Hello,
>>>
>>> The attached .npy file was written from custom C++ code.  It loads
>>> fine in Numpy 1.6.2 with Python 2.6 installed through MacPorts, but
>>> fails on a different machine with Numpy 2.0.0 installed via Superpack:
>>>
>>> box:array% which python
>>> /usr/bin/python
>>> box:array% which python
>>> box:array% python
>>> Python 2.6.1 (r261:67515, Aug  2 2010, 20:10:18)
>>> [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> import numpy
>>>>>> numpy.load('blah.npy')
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File "/Library/Python/2.6/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy/lib/npyio.py",
>>> line 351, in load
>>>     return format.read_array(fid)
>>>   File "/Library/Python/2.6/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy/lib/format.py",
>>> line 440, in read_array
>>>     shape, fortran_order, dtype = read_array_header_1_0(fp)
>>>   File "/Library/Python/2.6/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy/lib/format.py",
>>> line 361, in read_array_header_1_0
>>>     raise ValueError(msg % (d['descr'],))
>>> ValueError: descr is not a valid dtype descriptor: 'd8'
>>>>>> numpy.__version__
>>> '2.0.0.dev-b5cdaee'
>>>>>> numpy.__file__
>>> '/Library/Python/2.6/site-packages/numpy-2.0.0.dev_b5cdaee_20110710-py2.6-macosx-10.6-universal.egg/numpy/__init__.pyc'
>>>
>>> It seems Numpy 2.0.0 no longer accepts dtype('d8'):
>>>
>>>>>> dtype('d8')
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>> TypeError: data type "d8" not understood
>>>
>>> Was that intentional?  An API change isn't too much of a problem, but
>>> it's unfortunate if old data files are no longer easily readable.
>>
>> As far as I can tell, numpy has never described an array using 'd8'.
>> That would be a really old compatibility typecode from Numeric, if I
>> remember correctly. The intention of the NPY format standard was that
>> it would accept what numpy spits out for the descr, not that it would
>> accept absolutely anything that numpy.dtype() can consume, even
>> deprecated aliases (though I will admit that that is almost what the
>> NEP says). In particular, endianness really should be included or else
>> your files will be misread on big-endian machines.
>>
>> My suspicion is that only your code has ever made .npy files with this
>> descr. I feel your pain, Geoff, and I apologize that my lax
>> specification led you down this path, but I think you need to fix your
>> code anyways.
>
> Sounds good.  Both 1.6.2 and 2.0.0 write out '<f8' for the dtype.
> I'll certainly add the '<' bit to signify endianness, but how should I
> go about determining the letter?  My current code looks like
>
>   // Get dtype info
>   int bits;char letter;
>   switch(type_num){
>       #define CASE(T) case
> NPY_##T:bits=NPY_BITSOF_##T;letter=NPY_##T##LTR;break;
>       #define NPY_BITSOF_BYTE 8
>       #define NPY_BITSOF_UBYTE 8
>       #define NPY_BITSOF_USHORT NPY_BITSOF_SHORT
>       #define NPY_BITSOF_UINT NPY_BITSOF_INT
>       #define NPY_BITSOF_ULONG NPY_BITSOF_LONG
>       #define NPY_BITSOF_ULONGLONG NPY_BITSOF_LONGLONG
>       CASE(BOOL)
>       CASE(BYTE)
>       CASE(UBYTE)
>       CASE(SHORT)
>       CASE(USHORT)
>       CASE(INT)
>       CASE(UINT)
>       CASE(LONG)
>       CASE(ULONG)
>       CASE(LONGLONG)
>       CASE(ULONGLONG)
>       CASE(FLOAT)
>       CASE(DOUBLE)
>       CASE(LONGDOUBLE)
>       #undef CASE
>       default: throw ValueError("Unknown dtype");}
>   int bytes = bits/8;
>   ...
>   len += sprintf(base+len,"{'descr': '%c%d', 'fortran_order': False,
> 'shape': (",letter,bytes);
>
> The code incorrectly assumes that the ...LTR constants are safe ways
> to describe dtypes.  Is there a clean, correct way to do this that
> doesn't require special casing for each type?  I can use numpy headers
> but can't call any numpy functions, since Python might not be
> initialized (e.g., if I'm writing out files through MPI IO collectives
> on a Cray).

These characters plus the byte-size and endian-ness:

        /*
         * These are for dtype 'kinds', not dtype 'typecodes'
         * as the above are for.
         */
        NPY_GENBOOLLTR ='b',
        NPY_SIGNEDLTR = 'i',
        NPY_UNSIGNEDLTR = 'u',
        NPY_FLOATINGLTR = 'f',
        NPY_COMPLEXLTR = 'c'

Less amenable to macro magic, certainly, but workable. To
double-check, see what numpy outputs for each of these cases.

-- 
Robert Kern


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