IJ 1.41c bug and 16 Bit BW images

[Phase GmbH]

Hi,

today I have updated to IJ 1.41c (Windows). After update some of my Plugins located in subfolders of the plugins folder did not appear in the Plugins Menu. After "down-date" to IJ 1.40g, all available plugins are shown in the Plugins Menu again.


I do not know whether this a bug or may have another reason:

When I transfer a short array with 16 bit BW pixel data to the ImageProcessor by the setPixels method (ImagePlus was created by NewImage.createShortImage), the resulting image is BW  16 bit with the invert LUT. This is surprising, since I thougth LUTs are only applicable to 8 Bit index images. When applying the ImageProcessor method invertLut before displaying that image, this has no effect. However the invert LUT can be sucessfully applied from the IJ Menu to the displayed 16 Bit BW image, finally showing the desired image.

If this is not a bug, how can I get a 16 Bit BW image from a pixel array which is finally normally displayed?  

Regards

Christian Kreutzfeldt

[Wayne Rasband]

> today I have updated to IJ 1.41c (Windows). After update some of my
> Plugins located in subfolders of the plugins folder did not appear in
> the Plugins Menu. After "down-date" to IJ 1.40g, all available plugins
> are shown in the Plugins Menu again.

The missing plugins are either in the "Miscellaneous" submenu of the
Plugins menu or in submenus that correspond to subfolders containing
the plugins.

> I do not know whether this a bug or may have another reason:
>
> When I transfer a short array with 16 bit BW pixel data to the
> ImageProcessor by the setPixels method (ImagePlus was created by
> NewImage.createShortImage), the resulting image is BW  16 bit with the
> invert LUT. This is surprising, since I thougth LUTs are only
> applicable to 8 Bit index images. When applying the ImageProcessor
> method invertLut before displaying that image, this has no effect.
> However the invert LUT can be sucessfully applied from the IJ Menu to
> the displayed 16 Bit BW image, finally showing the desired image.
>
> If this is not a bug, how can I get a 16 Bit BW image from a pixel
> array which is finally normally displayed?

                int w=512, h=512;
                ImagePlus imp = IJ.createImage("Test", "16-bit black", w, h, 1);
                imp.show();
                IJ.wait(2000);
                short[] data = new short[w*h];
                for (int i=0; i<w*h; i++)
                        data[i] = (short)i;
                ImageProcessor ip = imp.getProcessor();
                ip.setPixels(data);
                imp.updateAndDraw();

-wayne

[Joachim Wesner]

Hi Wayne and others,

ImageJ Interest Group <[hidden email]> schrieb am 20.05.2008 17:46:55:

> > today I have updated to IJ 1.41c (Windows). After update some of my
> > Plugins located in subfolders of the plugins folder did not appear in
> > the Plugins Menu. After "down-date" to IJ 1.40g, all available plugins
> > are shown in the Plugins Menu again.
>
> The missing plugins are either in the "Miscellaneous" submenu of the
> Plugins menu or in submenus that correspond to subfolders containing
> the plugins.
>

What is the exact reason and inner logic for this change? I just started
my updated copy of IJ and also noticed "missing plugins" till I found those
plugins under "Miscellaneous".

Is it no longer possible to have own subdirectories under "plugins"?
Apparently
not, it´s still possible, but I do not seem to understand under what
circumstances
the plugin is moved to "Misc" or not. Some of my subdirectories still
appear under
the Plugins menu entry, some no longer.

Sincerely

Joachim


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[Gabriel Landini]

On Friday 06 June 2008 09:55:43 Joachim Wesner wrote:
> > The missing plugins are either in the "Miscellaneous" submenu of the
> > Plugins menu or in submenus that correspond to subfolders containing
> > the plugins.
>
> What is the exact reason and inner logic for this change? I just started
> my updated copy of IJ and also noticed "missing plugins" till I found those
> plugins under "Miscellaneous".
>
> Is it no longer possible to have own subdirectories under "plugins"?

Hi Joachim,

Yes, it is possible. The method now is much more flexible and does not force
one to have 1000 sub entries in the Plugins folder.

One can make their own categories (folders) and the plugins put there will
appear under that category regardless of the plugins.config entries (I think
the limit is up to 4 commands).
Plugins in the Plugin folder (but not subfolders), will use the plugins.config
file for creating their entries.

This thread explains it all
https://list.nih.gov/cgi-bin/wa?A2=ind0805&L=imagej&H=1&O=A&P=197

More specifically the 2nd message (option #1) and 3rd messages of the thread.

and this was the final announcement.

http://rsb.info.nih.gov/ij/notes.html
1.41b, 6 May 2008
To reduce the size of the Plugins menu, JAR files that implement fewer than
four Plugins submenu commands are installed in the submenu corresponding to
the folder containing the JAR file. In addition, single plugins distributed
as ZIP archives are installed in the "Miscellaneous" submenu.

Cheers,
G.