[ImageJ-devel] ImageOpener always giving me three channels when these is only one.

[Curtis Rueden]

Hi Grant,

FYI, ImageJ has a "feature" where if the LUT is totally grayscale, ImageJ
ignores it and declares the file to be a regular 8-bit image, rather than
"RGB color." Unfortunately, this makes it difficult to tell if the image has
a "hidden" color table. Still, you could probably eliminate the LUT by
resaving as TIFF again from ImageJ.

-Curtis

On Sun, Dec 12, 2010 at 9:49 PM, Grant B. Harris <gharris at mbl.edu> wrote:

>  Not intending to use ImageJFunctions.displayAsVirtualStack... just was
> seeing if I got the same result.
> I finally found another tiff image that loads with one channel...
> Thanks.
> - GBH
>
>
> On 12/12/2010 4:58 PM, Curtis Rueden wrote:
>
> Hi Grant,
>
> The image has an 8-bit LUT, which is why it's being read as 3 channels.
> Currently ImageOpener expands such lookup tables, since ImgLib does not
> explicitly support indexed color. So the behavior is expected.
>
> Also, it's fine to use ImageJFunctions.displayAsVirtualStack(inImg).show()
> for testing, but presumably you are not using it in IJX for production? The
> work Barry has been doing in ij1bridge is the direction we want to go.
>
> -Curtis
>
> On Sun, Dec 12, 2010 at 1:22 PM, Grant B. Harris <gharris at mbl.edu> wrote:
>
>> I'm having a problem with opening an imglib.Image...
>>
>> I'm testing with an image: Cells.tif is an unsigned 8-bit image.
>> The Image created by ImageOpener.openImage(file) has 3 channels when it
>> should have only one.
>> (http://dev.imagejdev.org/svn/imagej/trunk/ijx/Cells.tif)
>>
>> The code I am using is:
>>
>>        String filename = "Cells.tif";
>>        final ImageOpener imageOpener = new ImageOpener();
>>        Image<T> inImg = imageOpener.openImage(filename);
>>        reportInformation(inImg);
>>
>> This outputs:
>>
>>        Image 'Cells.tif [X Y Channel]', dim=(617, 460, 3)
>>        Type = mpicbg.imglib.type.numeric.integer.UnsignedByteType
>>        Container = mpicbg.imglib.container.planar.PlanarContainer
>>
>> And when I do ImageJFunctions.displayAsVirtualStack(inImg).show()
>> I get an ImageWindow with a slider for 3 channels...
>>
>> Is this a bug?  Or am I doing something wrong?
>>
>> -- Grant
>>
>> _______________________________________________
>> ImageJ-devel mailing list
>> ImageJ-devel at imagejdev.org
>> http://imagejdev.org/mailman/listinfo/imagej-devel
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20101212/bb2d046b/attachment.html>