imagej / imagej-modelzoo Goto Github PK

View Code? Open in Web Editor NEW

6.0 12.0 4.0 48.48 MB

License: BSD 2-Clause "Simplified" License

Java 100.00%

imagej-modelzoo's Introduction

imagej-modelzoo

This is an ImageJ consumer for models from the bioimage model zoo.

imagej-modelzoo's People

Contributors

Stargazers

Watchers

Forkers

esgomezm jdeschamps tomburke-rse seanpm2001

imagej-modelzoo's Issues

Empty Metadata fields in new model throw exception

When editing the Metadata information of a new trained model, if the Description and Authors fields are left empty, it will throw the following error into the console (see below).

It only happens in a new trained model. If the same thing is done in a model that already had metadata in it, no error is shown.

[ERROR] Module threw exception
java.lang.NullPointerException
        at net.imagej.modelzoo.consumer.command.ModelArchiveEditMetaDataCommand.stringToList(ModelArchiveEditMetaDataCommand.java:102)
        at net.imagej.modelzoo.consumer.command.ModelArchiveEditMetaDataCommand.run(ModelArchiveEditMetaDataCommand.java:70)
        at org.scijava.command.CommandModule.run(CommandModule.java:196)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
        at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
java.util.concurrent.ExecutionException: java.lang.NullPointerException
        at java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.util.concurrent.FutureTask.get(FutureTask.java:192)
        at net.imagej.modelzoo.display.SwingModelArchiveDisplayViewer.editMetaData(SwingModelArchiveDisplayViewer.java:458)
        at net.imagej.modelzoo.display.SwingModelArchiveDisplayViewer.access$100(SwingModelArchiveDisplayViewer.java:104)
        at net.imagej.modelzoo.display.SwingModelArchiveDisplayViewer$3.lambda$actionPerformed$0(SwingModelArchiveDisplayViewer.java:227)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
        at net.imagej.modelzoo.consumer.command.ModelArchiveEditMetaDataCommand.stringToList(ModelArchiveEditMetaDataCommand.java:102)
        at net.imagej.modelzoo.consumer.command.ModelArchiveEditMetaDataCommand.run(ModelArchiveEditMetaDataCommand.java:70)
        at org.scijava.command.CommandModule.run(CommandModule.java:196)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
        at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        ... 1 more

Modelzoo exporter command

We need a command & API to export trained models into modelzoo format.

Use cases

Export SavedModelBundle method

input: SavedModelBundle directory (including variables, saved_model.pb)
input: additional needed parameters (inputs, outputs, data type etc.)

Add missing information to existing YAML specification

input: A ZIP file with a SavedModelBundle and a model.yaml file

Goal

The exporter should be able to write the YAML specification and ask the user for missing parameters (like author names, a doi to the training data etc.).

Existing code

Writing the model is already implemented in Noise2Void in Fiji and should move from there to this repository, then N2V and others can use imagej-modelzoo as a library: https://github.com/juglab/N2V_fiji/blob/master/src/main/java/de/csbdresden/n2v/train/ModelSpecification.java

Tagging @esgomezm @ctr26 in case it might be possible to reuse code from DeepImageJ for the UI part (discussion started in this issue). @tibuch

Is TiledView necessary?

@tomburke-rse I am curious, why couldn't you just use a CachedCellImg here?

modelzoo example fails to load configuration

I just created a spec compliant (0.3.2. which is the latest version) modelzoo example of stardist : stardist_test_v0.3.2.zip

Upon loading it in fiji, the following error gets thrown:

(cross referencing juglab/n2v#109)

Updating imglib2-cache (v1.0.0-beta-16) from the Fiji update site causes a NoClassDefFoundError in TiledImageDataReference.createTiledOutputView. Compiling against version 30.0.0 of the scijava-pom made the error disappear (but there are JUnit test failures that I did not investigate).

java.lang.NoClassDefFoundError: net/imglib2/cache/img/DiskCachedCellImgOptions$CacheType
	at net.imagej.modelzoo.consumer.tiling.TiledImageDataReference.createTiledOutputView(TiledImageDataReference.java:204)
	at net.imagej.modelzoo.consumer.tiling.TiledImageDataReference.createTiledOutputView(TiledImageDataReference.java:163)
	at net.imagej.modelzoo.consumer.tiling.DefaultTiling.init(DefaultTiling.java:105)
	at net.imagej.modelzoo.consumer.TiledPredictionExecutor.initTiling(TiledPredictionExecutor.java:188)
	at net.imagej.modelzoo.consumer.TiledPredictionExecutor.run(TiledPredictionExecutor.java:84)
	at net.imagej.modelzoo.consumer.AbstractModelZooPrediction.executePrediction(AbstractModelZooPrediction.java:210)
	at net.imagej.modelzoo.consumer.AbstractModelZooPrediction.run(AbstractModelZooPrediction.java:105)
	at net.imagej.modelzoo.consumer.command.AbstractSingleImagePredictionCommand.run(AbstractSingleImagePredictionCommand.java:101)
	at de.csbdresden.n2v.command.N2VPredictCommand.run(N2VPredictCommand.java:59)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: net.imglib2.cache.img.DiskCachedCellImgOptions$CacheType
	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 18 more

This was reported in a N2V_fiji issue.

Unclear error message for no open images, when loading model

A confusing message pops-up when attempting to load a bioimage.io model without open images.
"A RandomAccessibleInterval is required but none exist."

Happens both through File > Import > bioimage.io.zip and Plugins > bioimage.io > bioimage.io prediction

Hosting models for BioImage.IO

We are changing the way we provide models for BioImage.IO, please take a look at here: https://github.com/bioimage-io/bioimage.io/blob/master/docs/join-partners.md

This is the manifest file for Fiji: https://github.com/bioimage-io/fiji-bioimage-io/blob/master/manifest.bioimage.io.yaml

Since Fiji/ImageJ is a community partner, I think it's better to migrate this repo: https://github.com/bioimage-io/fiji-bioimage-io to the imagej organization, either merge with this repo or keep as is.

We are also thinking if a third-party contributor made a model for your imagej plugin, it make more sense to submit it to your managed model repo rather than BioImage.IO.

Another question I have is, what's the logo and name you would like to use? ImageJ or Fiji? In any case, you can change them yourself here: https://github.com/bioimage-io/fiji-bioimage-io/blob/6034c76cda97fd9db48c8c1d6e2e285d1a80136b/manifest.bioimage.io.yaml#L2-L16