[Numpy-discussion] import 16-bit tiff - byte-order problem?

Angus McMorland amcmorl@gmail....
Thu Nov 6 21:54:32 CST 2008


Hi all,

I'm trying to import a 16-bit tiff image into a numpy array. I have
found, using google, suggestions to do the following:

After starting with:
i = Image.open('16bitGreyscaleImage.tif')

Stéfan van der Walt suggested:
a = np.array(i.getdata()).reshape(i.size)   # a 1d numpy array

and adapted from Nadav Horesh's suggestion:
a = np.fromstring(i.tostring(), dtype=np.uint16).reshape(256, 256)

Both give me the same answer as:
a = np.array(i, dtype=np.uint16)

In all cases it looks like the resulting byte order is wrong: pixels
with 0 values correctly are 0 in a, in the correct places, but all
non-zero values are wrong compared to the same image opened in ImageJ
(in which the image looks correct).

What's the conversion magic I need to invoke to correctly intepret
this image type?

Thanks,

Angus.
-- 
AJC McMorland
Post-doctoral research fellow
Neurobiology, University of Pittsburgh


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