Cannot open Img as CellImg if underlying type is ND2

[bnorthan]

Hi all

I'm having an issue reading an ND2 file as a CellImg. I have plugins that take an ImagePlus as input and re-opens it as a CellImg. This is done, instead of just converting it to an Img becasue the underlyhing ImagePlus can be very large, and is often a virtual image. Up until very recently this process was working fine. However now it fails with ND2 images, but not with .tifs. Below is the error that occurs and a Command that can be used to repeat the problem. An example image is in dropbox here

at net.imglib2.cache.util.CacheAsUncheckedCacheAdapter.get(CacheAsUncheckedCacheAdapter.java:32)
at net.imglib2.img.cell.LazyCellImg$LazyCells.get(LazyCellImg.java:104)
at net.imglib2.img.list.AbstractLongListImg$LongListCursor.get(AbstractLongListImg.java:98)
at net.imglib2.img.cell.CellCursor.getCell(CellCursor.java:94)
at net.imglib2.img.cell.CellCursor.moveToNextCell(CellCursor.java:182)
at net.imglib2.img.cell.CellCursor.reset(CellCursor.java:152)
at net.imglib2.img.cell.CellCursor.(CellCursor.java:88)
at net.imglib2.img.cell.AbstractCellImg.cursor(AbstractCellImg.java:92)
at net.imglib2.img.cell.AbstractCellImg.cursor(AbstractCellImg.java:51)
at net.imglib2.img.AbstractImg.firstElement(AbstractImg.java:81)
at net.imagej.ImgPlus.firstElement(ImgPlus.java:276)
at net.imagej.DefaultDataset.getType(DefaultDataset.java:220)
at net.imagej.DefaultDataset.isSigned(DefaultDataset.java:225)
at net.imagej.DefaultDataset.mergedColorCompatible(DefaultDataset.java:704)
at net.imagej.DefaultDataset.(DefaultDataset.java:101)
at net.imagej.DefaultDatasetService.create(DefaultDatasetService.java:200)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:128)
at com.doublehelixoptics.testcommands.TestImgOpenerCommandSimple.run(TestImgOpenerCommandSimple.java:51)
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$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

import java.io.File;
import java.io.IOException;

import org.scijava.command.Command;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;

import ij.ImagePlus;
import io.scif.config.SCIFIOConfig;
import io.scif.config.SCIFIOConfig.ImgMode;
import io.scif.services.DatasetIOService;
import net.imagej.Dataset;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;

@Plugin(type = Command.class, headless = true, menuPath = "Plugins>Test Cell Image Opener Simple")
public class TestImgOpenerCommandSimple<T extends RealType<T> & NativeType<T>> implements Command {

	@Parameter
	DatasetIOService io;

	@Parameter
	ImagePlus image;

	public void run() {

		// create the SCIFIOConfig. This gives us configuration control over
		// how the ImgOpener will open its datasets.
		final SCIFIOConfig config = new SCIFIOConfig();

		// Use CellImg mode to load the image. CellImgs dynamically load
		// image regions
		// and are useful when an image won't fit in memory
		config.imgOpenerSetImgModes(ImgMode.CELL);

		File imageFile = new File(image.getOriginalFileInfo().directory + image.getOriginalFileInfo().fileName);
		Dataset data = null;
		try {
			// open with DatasetIOService
			data = io.open(imageFile.getAbsolutePath(), config);

			for (int d = 0; d < data.numDimensions(); d++) {
				System.out.println(data.axis(d).type());
			}

		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}
}