Re: [Matplotlib-users] 16bit tiff support?

[Philipp L. <phi...@tu...>]

Jeff Whitaker wrote:
> Philipp Lies wrote:
>> On 02/12/2010 07:49 PM, Eric Firing wrote:
>>  
>>> Philipp Lies wrote:
>>>    
>>>> Hi,
>>>>
>>>> is there a backend that supports 16bit tiff images?
>>>>       
> 
> The macosx backend supports tiff.
Thanks, but I need a linux backend :-/


>>> Can you just use png, and use the netpbm utilities or ImageMagick
>>> convert program to go to and from tiff?
>>>     
>> Would be 'dirty' but acceptable if matplotlib would support saving
>> uncompressed grayscale uint16 png files. But saving  nxm uint16 arrays
>> leads to nxmx3 float arrays which do not even closely resemble my
>> original data.
>> Example:
>> A
>> array([[47705, 11865,   739, 16941, 37700],
>>         [64321, 26860, 49945, 63556, 13498],
>>         [ 2676,  7720,  5995, 22399, 32735],
>>         [56577, 34443,  6636, 23409, 61331],
>>         [ 1020, 26013, 34677, 37262, 36136]], dtype=uint16)
>> imsave('t.png',A)
>> B = imread('t.png')
>> B[:,:,0]
>>
>> array([[ 1.,  0.,  0.,  0.,  0.74117649],
>>         [ 0.49803922,  0.19607843,  1.,  0.5529412 ,  0. ],
>>         [ 0.,  0.,  0.,  0.,  0.48627451],
>>         [ 1.,  0.57647061,  0.,  0.01960784,  0.71372551],
>>         [ 0.,  0.14509805,  0.58823532,  0.72941178,  0.66666669]],
>> dtype=float32)
>>
>>
>>  
>>>> According to the website GDK supports tiff but that's wrong:
>>>>
>>>>      
>>>>>>> import matplotlib
>>>>>>> matplotlib.use('GDK')
>>>>>>> import matplotlib.pyplot as pyplot
>>>>>>> pyplot.imsave(arr=X, fname='test.tif')
>>>>>>>             
>>>> Traceback (most recent call last):
>>>> File "<stdin>", line 1, in <module>
>>>> File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 1425,
>>>> in imsave
>>>> return _imsave(*args, **kwargs)
>>>> File "/usr/lib/pymodules/python2.6/matplotlib/image.py", line 813, in
>>>> imsave
>>>> fig.savefig(fname, dpi=1, format=format)
>>>> File "/usr/lib/pymodules/python2.6/matplotlib/figure.py", line 1033,
>>>> in savefig
>>>> self.canvas.print_figure(*args, **kwargs)
>>>> File "/usr/lib/pymodules/python2.6/matplotlib/backend_bases.py", line
>>>> 1420, in print_figure
>>>> '%s.' % (format, ', '.join(formats)))
>>>> ValueError: Format "tif" is not supported.
>>>> Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz.
>>>>      
>>>>>>> matplotlib.backends.backend
>>>>>>>             
>>>> 'gdk'
>>>>
>>>> matplotlib 0.99.0 python 2.6.4 ubuntu karmic x64
>>>>
>>>> If matplotlib cannot provide tiff support, does someone know an
>>>> alternative? PIL doesn't work either, at least not intuitively.