Hi Anonymous,
maybe this is a problem with one of the new Mac operating systems; on
venerable OS X 10.6.8 I could successfully open ImageJ with a .tiff
image with essentially the same command (just replaced the path):
java -Xmx512m -jar
/Applications/ImageJ/ImageJ64.app/Contents/Resources/Java/ij.jar -ijpath
/Applications/ImageJ ~/Downloads/testfile.tif
Did you try whether you can open your tiff file from ImageJ? There are
seemingly endless possibilities for encoding and compressing tiff files,
ImageJ cannot open all of them.
Further thoughts:
- ijpath should point to the directory containing ImageJ.app (one level
further up than in your example). If you need a plugin to open the tiff,
this would explain your problem.
You can add a -debug switch, it will tell you more both on the command
line and in the ImageJ 'Log' window.
HTH,
Michael
________________________________________________________________
On 2016-11-22 05:41, rfor10 wrote:
> Hi - I do image analysis in python, but haven't found a great 3D image viewer
> for my images. I really like ImageJ for that, but I have had some trouble
> figuring out how to open some images in ImageJ programmatically.
>
> I thought I would be able to temp save an image and issue a system call from
> python along the lines of
>
> java -Xmx512m -jar ~/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar
> -ijpath /ImageJ/ImageJ.app/ ~/Image/acq_4/img_000000000_581_000.tif
>
> When I do this ImageJ loads, but throws an error "File is not in a supported
> format, a reader plugin is not available, or it was not found."
>
> Any suggestions? Or alternate approach for opening an image in ImageJ from
> python?
>
> Thanks!
>
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