Align Image by line ROI without rescaling

[Michel Teussink]

Dear List,

I would like to run the "Align image by line ROI" plugin to register 2 images, but without image rescaling. Would this be possible and if so, which lines from the plugin script would need to be modified?

Best,
Michel



Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.


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[Michel Teussink]

Dear List,

This problem has been solved. A modified version of the "Align image by line ROI" is attached. The plugin will now only adjust the angle and position of the line ROI of a source image to that of a target image.

Special thanks to Louis Wolf (Dep. Microscopical Imaging of the Cell, Radboud University Nijmegen Medical Ctr.) for his help with modifying this plugin.

Best regards,
Michel

AlignImageByLine_.jar

[dscho]

Hi Michel,

On Mon, 14 Jan 2013, Michel Teussink wrote:

> This problem has been solved. A modified version of the "Align image by
> line ROI" is attached. The plugin will now only adjust the angle and
> position of the line ROI of a source image to that of a target image.
>
> Special thanks to Louis Wolf (Dep. Microscopical Imaging of the Cell,
> Radboud University Nijmegen Medical Ctr.) for his help with modifying
> this plugin.

Thank you for the contribution.

I am a bit sad, though, that I have to point out that Align image by line
ROI, by virtue of being part of the Virtual Insect Brain plugins, is under
the GNU Public License. That license requires you to provide the source
code upon request if you distribute derivative plugins, which I hereby
request.

I am sad because I would have hoped that it would not be necessary to
dangle the GPL around to get the source code for the improved version of
my plugin.

I am also sad because clearly, my strategy to encourage Open Source by
example did not work at least in this particular case.

Finally, I am sad because in my humble opinion, it should not be necessary
to point out why exactly Open Source is vital to science. But it is vital,
please see e.g. http://developer.imagej.net/faq#t21n236.

Ciao,
Johannes

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[dscho]

Hi Michel,

On Tue, 15 Jan 2013, [hidden email] wrote:

> Because the plugin is Open Source, I thought it would be sufficient to
> make our modified version of the plugin available to the public as a
> .jar file.

Said .jar file contains only .class files. The .java files were not
included. You can verify this by opening the .jar file with your favorite
Zip Archiver (a .jar file is just a .zip file adhering to a certain form).

> I have 2 questions regarding this:
>
> 1. Is it required to firstly send this modified version to the original
> author (you)?

It is not required to send the modified version anywhere ;-) But if you
send it, you should provide the source files, too (the GPL actually
requires you, but I'd prefer it if every scientist had the urge to do so
anyway).

> 2. Could you explain me in what form exactly (a file type, or simply the
> lines of the code?), the source code should be provided? And to whom/
> where (I assume the ImageJ community via the List)?

The .java file should be sufficient (from the contents of the .jar file,
it looks as if there was only an Align_Image.java, no other .java file or
resource file needed), if you want to be nice, you could provide the
build.xml file, too (I assume you made it into an Ant project, as claimed
by the .jar file's manifest).

Since you sent the modified binary to the list, it would make sense to
make the source file(s) available via the same distribution channel.

Ciao,
Johannes

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[Michel Teussink]

Hi Johannes,

Attached is the source code of the modified plugin 'align image by line ROI' (in .java).

Best regards,
Michel

Align_Image_by_line_ROI_without_rescaling.java

[dscho]

Hi Michel,

On Mon, 21 Jan 2013, [hidden email] wrote:

> Attached is the source code of the modified plugin 'align image by line
> ROI' (in .java).

Thank you!

I made your changes conditional upon unchecking the newly-introduced
checkbox "scale". The result can be seen in
https://github.com/fiji/fiji/blob/master/src-plugins/VIB_/src/main/java/Align_Image.java

Since you made that change, it is properly attributed to you, too:
https://github.com/fiji/fiji/commit/d89aaa3f0966e9b274e720db7aa64e3aefbeeaf3

It is also properly uploaded, as a new version of plugins/VIB_.jar and
Align Image by line ROI now also supports two-dimensional color images.

Ciao,
Johannes

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