Exception in thread "main" java.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [B

Question

I tried to read an image from loci tools and save it to FileSaver from imagej but, I got this error when running it

ImagePlus[] imps = BF.openImagePlus("path/to/my/file");
for (ImagePlus imp : imps)new FileSaver(imp).saveAsRaw("E:/test.raw");

when I run the code, it shows

Exception in thread "main" java.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [B
at ij.io.ImageWriter.write(ImageWriter.java:272)
at ij.io.FileSaver.saveAsRaw(FileSaver.java:494)
at Skripsi.dcmtoraw.main(dcmtoraw.java:16)

Answer 1

This is a bug, although it's not trivial to say whether the bug is in ImageJ 1.x, or in the Bio-Formats plugins.

In the ImageJ 1.x code, the ImageWriter assumes (unchecked) that the pixels array is an Object[] when the image is a stack, and a byte[] when it's a single image plane. However, it seems that Bio-Formats produces ImagePlus objects whose pixels are Object[] even for single planes. (Is your image a single plane?)

You could probably work around the issue by using the Bio-Formats Exporter plugin to save your data.

Or you could use the ImageJ2 API, which will use SCIFIO under the hood:

/**
 * Adapted from the
 * <a href="https://github.com/imagej/imagej-tutorials">ImageJ Tutorials</a>
 * {@code LoadAndDisplayDataset} tutorial.
 */
@Plugin(type = Command.class, menuPath = "Plugins>My Useful Command")
public class UsefulCommand implements Command {

  @Parameter
  private DatasetIOService datasetIOService;

  @Parameter
  private LogService log;

  @Parameter
  private File destination;

  @Parameter
  private Dataset image;

  @Override
  public void run() {
    try {
      image = datasetIOService.save(image, destination.getAbsolutePath());
    }
    catch (final IOException exc) {
      log.error(exc);
    }
  }

}