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bigdataviewer / bigdataviewer-playground

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BigWarp, get transformations back into BDV #93

Open martinschorb opened 4 years ago

martinschorb commented 4 years ago

Hi,

is there a way to get the transformations that I create with bigwarp associated to my selected sources and then back into "our" bdv?

NicoKiaru commented 4 years ago

Not yet, but that's doable. I'll give it a shot

martinschorb commented 4 years ago

I do see a xxxx_xfm when I launch BigWarp appearing in my sources list. Is that it?

martinschorb commented 4 years ago

Also, I noticed that BigWarp's "Export as ImgPlus" does produce entirely empty images. Before it crashed (see https://github.com/saalfeldlab/bigwarp/issues/88) but I got a new snapshot that fixed at least this...

bogovicj commented 4 years ago

Also, I noticed that BigWarp's "Export as ImgPlus" does produce entirely empty images.

Can you elaborate? Obviously, it's not supposed to do that. What's your setup like?

bogovicj commented 4 years ago

@NicoKiaru Regarding getting bigwarp transformed images into bdv, can you give this a try

LandmarkTableModel ltm = new LandmarkTableModel( src.getSource(0, 0).numDimensions() );
try {
    ltm.load(landmarks);
} catch (IOException e) {
    e.printStackTrace();
}

WarpedSource<T> srcOut = new WarpedSource<>( src, src.getName() + "_transformed");
srcOut.updateTransform( new ThinplateSplineTransform( ltm.getTransform() ));
srcOut.setIsTransformed( true );

BdvFunctions.show( srcOut );
martinschorb commented 4 years ago

Minimum working example: https://oc.embl.de/index.php/s/fFxYlIqFmULJspK

BdvHandlePostprocessor:BdvHandle found.
BdvHandlePostprocessor:BdvHandle found.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
    at bigwarp.BigWarpExporter.<init>(BigWarpExporter.java:98)
    at bigwarp.BigWarpRealExporter.<init>(BigWarpRealExporter.java:58)
    at bigwarp.BigWarpRealExporter.<init>(BigWarpRealExporter.java:70)
    at bigwarp.BigWarpExporter.getExporter(BigWarpExporter.java:639)
    at bdv.ij.ApplyBigwarpPlugin.runExport(ApplyBigwarpPlugin.java:740)
    at bigwarp.BigWarp.exportAsImagePlus(BigWarp.java:1071)
    at bigwarp.BigWarp.exportAsImagePlus(BigWarp.java:818)
    at bigwarp.BigWarpActions$ExportImagePlusAction.actionPerformed(BigWarpActions.java:1012)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
    at java.awt.Component.processMouseEvent(Component.java:6539)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
    at java.awt.Component.processEvent(Component.java:6304)
    at java.awt.Container.processEvent(Container.java:2239)
    at java.awt.Component.dispatchEventImpl(Component.java:4889)
    at java.awt.Container.dispatchEventImpl(Container.java:2297)
    at java.awt.Component.dispatchEvent(Component.java:4711)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
    at java.awt.Container.dispatchEventImpl(Container.java:2283)
    at java.awt.Window.dispatchEventImpl(Window.java:2746)
    at java.awt.Component.dispatchEvent(Component.java:4711)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
    at java.awt.EventQueue$4.run(EventQueue.java:733)
    at java.awt.EventQueue$4.run(EventQueue.java:731)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

This happens in both moving and target windows.

Tested on Linux & Windows.

bogovicj commented 4 years ago

Thanks - I also get this behavior. I have an idea what this is about, but can you try something to confirm you get the same thing as me:

1) Open the images in the same way as before. 2) Control-click several times in the image (at least 4). (This explicitly creates an identity transformation.) 3) export as ImgPlus (Target,Target), like before.

You'll hopefully not get an error. A resulting image will appear, but it probably will be empty :(

NicoKiaru commented 4 years ago

FYI, if relevant, the pom file has these explicit versions:

<bigdataviewer-core.version>7.0.0</bigdataviewer-core.version>
        <bigdataviewer-vistools.version>1.0.0-beta-15</bigdataviewer-vistools.version>
        <bigwarp_fiji.version>5.0.0</bigwarp_fiji.version>
martinschorb commented 4 years ago 
1. Open the images in the same way as before.

2. Control-click several times in the image (at least 4).  (This explicitly creates an identity transformation.)

3. export as ImgPlus (Target,Target), like before.

You'll hopefully not get an error. A resulting image will appear, but it probably will be empty :(

Exactly. Empty image. The error message appears when I try to export without doing anything.

bogovicj commented 4 years ago

Perfect, I'll get you a patch as soon as I can.

To clarify - you're using this to export an affine-transformed moving image into target space, right? Is that correct?

martinschorb commented 4 years ago

Both images come affine transformed from @NicoKiaru 's multi-source viewer. I use BigWarp to refine this transformation. This works: the resulting transformed moving image is transformed correctly. I just realized that the export to ImagePlus seems to be broken in this case. When I load the pixel data of the two images into BigWarp the "traditional" way, the export works.

NicoKiaru commented 4 years ago

This repo uses a different 'manual transform' than the one from bigdataviewer. There are 2 ways to store a manual transform (append and mutate), and the way the 'storage' is done depends on the original source class (TransformedSource and AbstractSpimSource supported).

All these modes are in the SourceAndConverterUtils class : https://github.com/bigdataviewer/bigdataviewer-playground/blob/add256dd2bbd6c2a6917c89a47bf7dc837204e6b/src/main/java/sc/fiji/bdvpg/sourceandconverter/SourceAndConverterUtils.java#L441-L497

bogovicj commented 4 years ago

Quick update - I'm confident the cause of the error is fixed, but pretty sure there is another problem which causes the image to be empty (for the test above).

I'm looking into it, and will keep you posted.

NicoKiaru commented 4 years ago

@martinschorb , are sources 2d or 3d ?

martinschorb commented 4 years ago

@martinschorb , are sources 2d or 3d ?

these are 2D. I can try with 3D as well but due to Fiji currently not starting with BDV Playground (#98) in all except one remote installation it is a bit tricky to test... Will keep you posted.

martinschorb commented 4 years ago

Hi,

It seems that the new sources that are added somehow are screwed up in terms of ViewSetupID... Wrong Colour. It also does not remember the Projection mode. When I have Views fused in the BigWarp Window, also the fixed source appears (with assigned Colour and Contrast settings for one moving...)

martinschorb commented 4 years ago

Minimum example:

files: https://oc.embl.de/index.php/s/KihC2SEFIsCBYB1

image

Launch BigWarp, fm... moving

image

landmarks.zip

image

now I have: image

[ERROR] Module threw exception
java.lang.NullPointerException
    at sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService.show(SourceAndConverterBdvDisplayService.java:181)
    at sc.fiji.bdvpg.scijava.command.bdv.BdvSourcesAdderCommand.run(BdvSourcesAdderCommand.java:31)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)