accessing the ImageStack created by Linear Stack Alignment with SIFT?

[Kenneth Sloan-2]

Context: Java plugin.

Assume that I have an ImageStack

++++++++++++++++++++++++++
   ImageStack enFaceStack;
   ...populate the stack with individual images...
++++++++++++++++++++++++++

I would like to register this stack - probably using SIFT (but I'm open to suggestion).

From the macro recorder, I get:

++++++++++++++++++++++++++
run("Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60 steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024 feature_descriptor_size=4 feature_descriptor_orientation_bins=8 closest/next_closest_ratio=0.92 maximal_alignment_error=25 inlier_ratio=0.05 expected_transformation=Rigid interpolate");
++++++++++++++++++++++++++

Based on the online documentation, I'm guessing I want to code this in Java as something like:

++++++++++++++++++++++++++
ImagePlus ipl = new ImagePlus("enFaceStack", enFaceStack);

run(ipl,"Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60 steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024 feature_descriptor_size=4 feature_descriptor_orientation_bins=8 closest/next_closest_ratio=0.92 maximal_alignment_error=25 inlier_ratio=0.05 expected_transformation=Rigid interpolate", null);
++++++++++++++++++++++++++

My questions are:

a) does the above look correct?

b) How do I get a reference to the resulting ImageStack?

When I do this manually, the original ImageStack (packaged up in a StackWindow) is left untouched, and a new StackWindow is created with the title "Aligned 9 of 9" - there were 9 slices.

But, I want my Java program to (perhaps at the user's option) replace the original slices, in the original ImageStack, with the registered versions.

If it matters, the original StackWindow is actually a MyStackWindow which extends StackWindow.  So, I want to keep the same MyStackWindow but replace the contained ImageStack.  I'd be happy to either replace the entire stack, or remove/add slices to replace the individual slices.  

I'm guessing that one way to do this is to (how?) get a list of all open windows and search for the one with the right title.  Better would be some way to get a reference to the window created by the "run" command.

This is probably very basic - but I haven't done it before, and haven't been able to find anything in the documentation.

At a different level, is it possible to get lower level access to the "Linear Stack Alignment with SIFT" (or something else - but it seems to work just fine) s.t. I can pass an ImageStack and get an aligned ImageStack returned?  It might be convenient to *not* display another StackWindow.  But, that would be a bonus.


--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Kenneth,

The plugin source code is here:
https://github.com/axtimwalde/mpicbg/blob/2f411b380cffb580e35410b6517ffeb2c72489e2/mpicbg_/src/main/java/SIFT_Align.java

The run method does many things; the next level down programmatically is
probably the SIFT class here:
https://github.com/axtimwalde/mpicbg/blob/2f411b380cffb580e35410b6517ffeb2c72489e2/mpicbg/src/main/java/mpicbg/ij/SIFT.java

But it is quite low level. It may be simplest to copy/paste/edit code from
the plugin.

And of course, PRs welcome if you want to improve the modularity.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Mar 5, 2018 at 12:34 PM, Kenneth Sloan <[hidden email]>
wrote:

> Context: Java plugin.
>
> Assume that I have an ImageStack
>
> ++++++++++++++++++++++++++
>    ImageStack enFaceStack;
>    ...populate the stack with individual images...
> ++++++++++++++++++++++++++
>
> I would like to register this stack - probably using SIFT (but I'm open to
> suggestion).
>
> From the macro recorder, I get:
>
> ++++++++++++++++++++++++++
> run("Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60
> steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024
> feature_descriptor_size=4 feature_descriptor_orientation_bins=8
> closest/next_closest_ratio=0.92 maximal_alignment_error=25
> inlier_ratio=0.05 expected_transformation=Rigid interpolate");
> ++++++++++++++++++++++++++
>
> Based on the online documentation, I'm guessing I want to code this in
> Java as something like:
>
> ++++++++++++++++++++++++++
> ImagePlus ipl = new ImagePlus("enFaceStack", enFaceStack);
>
> run(ipl,"Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60
> steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024
> feature_descriptor_size=4 feature_descriptor_orientation_bins=8
> closest/next_closest_ratio=0.92 maximal_alignment_error=25
> inlier_ratio=0.05 expected_transformation=Rigid interpolate", null);
> ++++++++++++++++++++++++++
>
> My questions are:
>
> a) does the above look correct?
>
> b) How do I get a reference to the resulting ImageStack?
>
> When I do this manually, the original ImageStack (packaged up in a
> StackWindow) is left untouched, and a new StackWindow is created with the
> title "Aligned 9 of 9" - there were 9 slices.
>
> But, I want my Java program to (perhaps at the user's option) replace the
> original slices, in the original ImageStack, with the registered versions.
>
> If it matters, the original StackWindow is actually a MyStackWindow which
> extends StackWindow.  So, I want to keep the same MyStackWindow but replace
> the contained ImageStack.  I'd be happy to either replace the entire stack,
> or remove/add slices to replace the individual slices.
>
> I'm guessing that one way to do this is to (how?) get a list of all open
> windows and search for the one with the right title.  Better would be some
> way to get a reference to the window created by the "run" command.
>
> This is probably very basic - but I haven't done it before, and haven't
> been able to find anything in the documentation.
>
> At a different level, is it possible to get lower level access to the
> "Linear Stack Alignment with SIFT" (or something else - but it seems to
> work just fine) s.t. I can pass an ImageStack and get an aligned ImageStack
> returned?  It might be convenient to *not* display another StackWindow.
> But, that would be a bonus.
>
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

Thank you for the prompt response.

Does "run" set the "current image"?  I see that WindowManager offers methods such as:

 getActiveWindow()
 getCurrentImage()


Next on my list would be:

  getImageTitles()

finding one starting with "aligned", and then

  getImage(title)


The best bet seems to be "getActiveWindow()" or "getCurrentImage()" - since I think the top window is the aligned stack, on completion.  This might be confounded by the log window showing progress.

Searching titles has the flaw that a careless user may leave old windows laying about, which would confuse things.

I think I'll experiment with these before trying to modify someone else's plugin.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On 5 Mar 2018, at 13:18 , Curtis Rueden <[hidden email]> wrote:
>
> Hi Kenneth,
>
> The plugin source code is here:
> https://github.com/axtimwalde/mpicbg/blob/2f411b380cffb580e35410b6517ffeb2c72489e2/mpicbg_/src/main/java/SIFT_Align.java
>
> The run method does many things; the next level down programmatically is
> probably the SIFT class here:
> https://github.com/axtimwalde/mpicbg/blob/2f411b380cffb580e35410b6517ffeb2c72489e2/mpicbg/src/main/java/mpicbg/ij/SIFT.java
>
> But it is quite low level. It may be simplest to copy/paste/edit code from
> the plugin.
>
> And of course, PRs welcome if you want to improve the modularity.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

Answering my own question...

This seems to work:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 ImageStack enFaceStack = ....create original stack...

 ImageStack originalEnFaceStack = enFaceStack;
 ImagePlus originalImagePlus = new ImagePlus("original", originalEnFaceStack);
 IJ.run(originalImagePlus,
        "Linear Stack Alignment with SIFT",
        "initial_gaussian_blur=1.60 " +
        "steps_per_scale_octave=3 " +
        "minimum_image_size=64 " +
        "maximum_image_size=1024 " +
        "feature_descriptor_size=4 " +
        "feature_descriptor_orientation_bins=8 " +
        "closest/next_closest_ratio=0.92 " +
        "maximal_alignment_error=25 " +
        "inlier_ratio=0.05 " +
        "expected_transformation=Rigid interpolate"
       );
 ImagePlus alignedImagePlus = WindowManager.getCurrentImage();
 ImageStack alignedImageStack = alignedImagePlus.getImageStack();
 for(int i=1;i<=alignedImageStack.getSize();i++)
     alignedImageStack.setSliceLabel(enFaceStack.getSliceLabel(i)+" aligned",i);
 enFaceStack = alignedImageStack;

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
           

This leaves a "log" window, and the "aligned n of n" window visible.  I'll probably start using the "log" window for my own reporting, and I suppose I can make the "aligned n of n" invisible.

I'm not thrilled with depending on a global "current Image" to get a handle on the result of running a command, but I suppose this is necessary for scripting.

Thanks again for the response.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

 
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html