Hi Grant,<br><br>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.<br>
<br>-Curtis<br><br><div class="gmail_quote">On Sun, Dec 12, 2010 at 9:49 PM, Grant B. Harris <span dir="ltr"><<a href="mailto:gharris@mbl.edu">gharris@mbl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
Not intending to use ImageJFunctions.displayAsVirtualStack... just
was seeing if I got the same result.<br>
I finally found another tiff image that loads with one channel... <br>
Thanks.<br><font color="#888888">
- GBH</font><div><div></div><div class="h5"><br>
<br>
On 12/12/2010 4:58 PM, Curtis Rueden wrote:
<blockquote type="cite">Hi Grant,<br>
<br>
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.<br>
<br>
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.<br>
<br>
-Curtis<br>
<br>
On Sun, Dec 12, 2010 at 1:22 PM, Grant B. Harris <span dir="ltr"><<a href="mailto:gharris@mbl.edu" target="_blank">gharris@mbl.edu</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I'm having a problem with opening an imglib.Image...<br>
<br>
I'm testing with an image: Cells.tif is an unsigned 8-bit
image.<br>
The Image created by ImageOpener.openImage(file) has 3
channels when it should have only one.<br>
(<a href="http://dev.imagejdev.org/svn/imagej/trunk/ijx/Cells.tif" target="_blank">http://dev.imagejdev.org/svn/imagej/trunk/ijx/Cells.tif</a>)<br>
<br>
The code I am using is:<br>
<br>
String filename = "Cells.tif";<br>
final ImageOpener imageOpener = new ImageOpener();<br>
Image<T> inImg = imageOpener.openImage(filename);<br>
reportInformation(inImg);<br>
<br>
This outputs:<br>
<br>
Image 'Cells.tif [X Y Channel]', dim=(617, 460, 3)<br>
Type =
mpicbg.imglib.type.numeric.integer.UnsignedByteType<br>
Container =
mpicbg.imglib.container.planar.PlanarContainer<br>
<br>
And when I do
ImageJFunctions.displayAsVirtualStack(inImg).show()<br>
I get an ImageWindow with a slider for 3 channels...<br>
<br>
Is this a bug? Or am I doing something wrong?<br>
<br>
-- Grant<br>
<br>
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</blockquote>
</div>
<br>
</blockquote>
</div></div></div>
</blockquote></div><br>