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16bit tiff support?

Philipp Lies-2
Hi,

is there a backend that supports 16bit tiff images?
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: [hidden email]
http://www.kyb.mpg.de/bethgegroup

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Re: 16bit tiff support?

Eric Firing
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?

Eric

> 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
>


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Re: 16bit tiff support?

Philipp Lies-2
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: [hidden email]
http://www.kyb.mpg.de/bethgegroup

------------------------------------------------------------------------------
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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: 16bit tiff support?

Jeff Whitaker
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.

-Jeff

>> 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
>>>
>>>      
>
>  


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Re: 16bit tiff support?

Philipp Lies-2
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.

------------------------------------------------------------------------------
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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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