io plugin issue (8bits 16bits)

[jip]

Dear all,

I meet some problem to open/display 12bits tif (16 bits) gray images.
I can open an image but I fail to display it:
import skimage
path='/media/Elements__/Science/Biologie/QTeloFISH/myoblastes 
HPS/JPP55_nFF/16/DAPI'
image='/1.tif'
from skimage import io as io

print skimage.io.plugin_info('matplotlib')
#skimage.io.use_plugin('matplotlib', 'read')

#dapi=io.imread(path+image,plugin='matplotlib')
dapi=io.imread(path+image)

print type(dapi)
print type(dapi)
print 'dapi.dtype',dapi.dtype

io.imshow(dapi)
#import pylab
#pylab.imshow(dapi)
#pylab.show()
Then I get the following error:
*<type 'numpy.ndarray'>
<type 'numpy.ndarray'>
dapi.dtype object
Traceback (most recent call last):
  File "/home/claire/.spyder2/.temp.py", line 28, in <module>
    io.imshow(dapi)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", 
line 149, in imshow
    return call_plugin('imshow', arr, plugin=plugin, **plugin_args)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", 
line 88, in call
    return func(*args, **kwargs)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", 
line 108, in imshow
    Image.fromarray(arr).show()
  File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in 
fromarray
    raise TypeError("Cannot handle this data type")
TypeError: Cannot handle this data type
*
The default plugin is PIL.If I try to switch to matplotlib (or freeimage), 
the plugin doesn't seem available:
*Traceback (most recent call last):
  File "/home/claire/.spyder2/.temp.py", line 16, in <module>
    dapi=io.imread(path+image,plugin='matplotlib')
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", 
line 72, in imread
    img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", 
line 86, in call
    (plugin, kind))
RuntimeError: Could not find the plugin "matplotlib" for imread.*
I can open the same image with plugin='pil' but I fail to display it:
*uint16
(1024, 1536)
Traceback (most recent call last):
  File "/home/claire/.spyder2/.temp.py", line 28, in <module>
    io.imshow(dapi0)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_io.py", 
line 149, in imshow
    return call_plugin('imshow', arr, plugin=plugin, **plugin_args)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/plugin.py", 
line 88, in call
    return func(*args, **kwargs)
  File 
"/usr/local/lib/python2.6/dist-packages/skimage-0.4-py2.6-linux-i686.egg/skimage/io/_plugins/pil_plugin.py", 
line 108, in imshow
    Image.fromarray(arr).show()
  File "/usr/lib/python2.6/dist-packages/PIL/Image.py", line 1886, in 
fromarray
    raise TypeError("Cannot handle this data type")
TypeError: Cannot handle this data type*

Does io.imshow() support only 8bits image?

I can open and display the image with readmagick/pylab.

Best regards
Jean-Patrick


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