On 02/12/2010 07:49 PM, Eric Firing wrote:
> Philipp Lies wrote:
>> Hi,
>>
>> is there a backend that supports 16bit tiff images?
>
> 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.
>>
>> Cheers
>>
>> Philipp
>>
>
--
Philipp Lies
Max Planck Institute for Biological Cybernetics
Computational Vision & Neuroscience Group
Spemannstr. 41
D-72076 Tuebingen
Germany
Phone: +49-7071-601-1788
Fax: +49-7071-601-552
E-Mail: philipp.l...@tuebingen.mpg.de
http://www.kyb.mpg.de/bethgegroup
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