Examples with PixelTypeEnumHandler ome.xml.model.enums.handlers.PixelTypeEnumHandler used on opensource projects

Example 1 with PixelTypeEnumHandler

use of ome.xml.model.enums.handlers.PixelTypeEnumHandler in project bioformats by openmicroscopy.

the class ImageViewer method save.

/**
 * Saves the current images to the given destination
 * using the current format writer.
 */
public void save(String id) {
    if (images == null)
        return;
    wait(true);
    try {
        if (omeMeta == null) {
            omeMeta = omexmlService.createOMEXMLMetadata();
            omeMeta.setImageID(MetadataTools.createLSID("Image", 0), 0);
            omeMeta.setPixelsID(MetadataTools.createLSID("Pixels", 0), 0);
            omeMeta.setPixelsBigEndian(false, 0);
            String order = "XYCZT";
            if (in != null)
                order = in.getDimensionOrder();
            omeMeta.setPixelsDimensionOrder((DimensionOrder) new DimensionOrderEnumHandler().getEnumeration(order), 0);
            int type = AWTImageTools.getPixelType(images[0]);
            String pixelType = FormatTools.getPixelTypeString(type);
            omeMeta.setPixelsType((PixelType) new PixelTypeEnumHandler().getEnumeration(pixelType), 0);
            int rgbChannelCount = images[0].getRaster().getNumBands();
            int realChannelCount = sizeC / rgbChannelCount;
            for (int i = 0; i < realChannelCount; i++) {
                omeMeta.setChannelID(MetadataTools.createLSID("Channel", i, 0), 0, i);
                omeMeta.setChannelSamplesPerPixel(new PositiveInteger(rgbChannelCount), 0, i);
            }
            omeMeta.setPixelsSizeX(new PositiveInteger(images[0].getWidth()), 0);
            omeMeta.setPixelsSizeY(new PositiveInteger(images[0].getHeight()), 0);
            omeMeta.setPixelsSizeC(new PositiveInteger(sizeC), 0);
            omeMeta.setPixelsSizeZ(new PositiveInteger(sizeZ), 0);
            omeMeta.setPixelsSizeT(new PositiveInteger(sizeT), 0);
        }
        myWriter.setMetadataRetrieve(omexmlService.asRetrieve(omeMeta));
        myWriter.setId(id);
        boolean stack = myWriter.canDoStacks();
        ProgressMonitor progress = new ProgressMonitor(this, "Saving " + id, null, 0, stack ? images.length : 1);
        if (stack) {
            // save entire stack
            for (int i = 0; i < images.length; i++) {
                progress.setProgress(i);
                boolean canceled = progress.isCanceled();
                myWriter.saveImage(i, images[i]);
                if (canceled)
                    break;
            }
            progress.setProgress(images.length);
        } else {
            // save current image only
            myWriter.savePlane(0, getImage());
            progress.setProgress(1);
        }
        myWriter.close();
    } catch (FormatException exc) {
        LOGGER.info("", exc);
    } catch (IOException exc) {
        LOGGER.info("", exc);
    } catch (ServiceException exc) {
        LOGGER.info("", exc);
    } catch (EnumerationException exc) {
        LOGGER.info("", exc);
    }
    wait(false);
}