Hello Nick,
I'm using NumPy/SciPy with ImageJ, but I couldn't find any plugin
reading numpy matrices.
I usally save the NumPy Matrices as textfiles and use the ImageJ ->
Import Textfile option.
For better performance I would recommend the WrapITK-package to save
your matrix as a tiff file, which is easy to import to ImageJ.
Greetings
Fred
Nick Rubert wrote:
> Hi listserve,
>
> So scipy/numpy is a great open source package for performing matrix math and
> manipulating images. Currently, my method for getting numpy arrays into
> imageJ is to use the imshow method and save the figure as a PNG. However,
> this adds a white border to my image along with axes to show the image
> dimensions. I've been looking for a way to write the floating point values
> along with some header information to a file that I can open in ImageJ, and
> then perform measurements with. Ideally, ImageJ would automatically read in
> the geometry information from the header. Maybe the header info and the
> numpy array could even be two separate files, as in the .mhd format provided
> by ITK.
>
> So, my question is, is anyone else working with numpy/ImageJ and has written
> a plugin for reading in numpy arrays? If not, can anyone point me to a
> really thorough tutorial on how I'd go about writing such a plugin?
>
> Thanks,
>
> Nicholas Rubert
>
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