ImageFileHeader.java

package ini.trakem2.io;

import ij.ImagePlus;
import loci.formats.ChannelSeparator;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;

public class ImageFileHeader {

	public final int width, height, type;
	public final IFormatReader fr;
	
	/** Reads the header of the image file at {@code filepath}
	 * using an {@link IFormatReader} from the bio-formats library,
	 * and then extracts the {link #width}, {@link #height} and {@link #type}
	 * of the image. If the type is not one supported by TrakEM2, the {@link #type}
	 * is set to the value returned by {@link IFormatReader#getPixelType()}.
	 * 
	 * @param filepath
	 * @throws Exception
	 */
	public ImageFileHeader(final String filepath) throws Exception {
		fr = new ChannelSeparator();
		fr.setGroupFiles(false);
		try {
			fr.setId(filepath);
			width = fr.getSizeX();
			height = fr.getSizeY();

			if (fr.isRGB()) {
				type = ImagePlus.COLOR_RGB;
			} else {
				switch (fr.getPixelType()) {
				case FormatTools.INT8:
				case FormatTools.UINT8:
					if (fr.isIndexed() || fr.isFalseColor()) {
						type = ImagePlus.COLOR_256;
					} else {
						type = ImagePlus.GRAY8;
					}
					break;
				case FormatTools.INT16:
				case FormatTools.UINT16:
					type = ImagePlus.GRAY16;
					break;
				case FormatTools.FLOAT:
					type = ImagePlus.GRAY32;
					break;
				default:
					type = fr.getPixelType();
					break;
				}
			}
		} finally {
			fr.close();
		}
	}
	
	/**
	 * @return Whether the {link #type} is supported by ImageJ and TrakEM2.
	 */
	public boolean isSupportedType() {
		switch (type) {
			case ImagePlus.GRAY8:
			case ImagePlus.GRAY16:
			case ImagePlus.GRAY32:
			case ImagePlus.COLOR_256:
			case ImagePlus.COLOR_RGB:
				return true;
			default:
				return false;
		}
	}
}