loci.formats.FormatException Java Examples

@Deprecated
private int getRealResolutionCount(IFormatReader imageReader) throws IOException, FormatException {
    ImageReader ir = new ImageReader();
    ir.setFlattenedResolutions(false);
    ir.setId(imageReader.getCurrentFile());
    ir.setSeries(imageReader.getSeries());
    int numRes = 1;
    for (int lev=imageReader.getResolutionCount()-1; lev>=0; lev--) {
        numRes = lev;
        ir.setResolution(lev);
        int thumbW = ir.getSizeX();
        int thumbH = ir.getSizeY();
        double diff = Math.abs((thumbW/(double)thumbH) - (imageReader.getSizeX()/(double)imageReader.getSizeY()));
        System.out.println("diff: "+diff);
        if (diff<0.001) break;
    }
    ir.close();
    return numRes;
}
 

@Override
public BufferedImage openImage(int no, int x, int y, int w, int h) throws FormatException, IOException {
    int[] zct = getZCTCoords(no);
    int z = zct[0];
    int chan = zct[1];
    int t = zct[2];
    RectZT rect = new RectZT(x,y,w,h,z,t);
    if (currentRect==null || !currentRect.equals(rect)) {
        logger.trace("cache failed - loading");
        openUnmixedImages(no,x,y,w,h); // unmix all channels at once
    }
    return unmixedChannels[chan];
}
 

public static int getNumPagesInZVI(String filename) throws IOException, FormatException {

        ImageProcessorReader r = new ImageProcessorReader(
                new ChannelSeparator(new ZeissZVIReader())); // LociPrefs.makeImageReader()
        r.setId(filename);
        int num = r.getImageCount();
        //int width = r.getSizeX();
        //int height = r.getSizeY();
        // howto color conversion: http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/loci-plugins/utils/Read_Image.java
        r.close();
        return num;
    }
 

public static int getNumPagesInLIF(String filename) throws IOException, FormatException {

        ImageProcessorReader r = new ImageProcessorReader(
                new ChannelSeparator(new LIFReader()));
        r.setId(filename);
        int num = r.getImageCount();
        r.close();
        return num;
    }
 

public static PlanarImage getZVIPage(String filename, int num) throws IOException, FormatException {
    ImageProcessorReader r = new ImageProcessorReader(
            new ChannelSeparator(new ZeissZVIReader())); // LociPrefs.makeImageReader()
    r.setId(filename);
    ImageProcessor ip = r.openProcessors(num)[0]; // (page)[0]
    return PlanarImage.wrapRenderedImage(ip.getBufferedImage());
}
 

public static PlanarImage getLIFPage(String filename, int num) throws IOException, FormatException {
    ImageProcessorReader r = new ImageProcessorReader(
            new ChannelSeparator(new LIFReader()));
    r.setId(filename);
    ImageProcessor ip = r.openProcessors(num)[0]; // (page)[0]
    return PlanarImage.wrapRenderedImage(ip.getBufferedImage());
}
 

public BufferedImage getThumbnail() {
  //  if (true) return new BufferedImage(100,60,BufferedImage.TYPE_INT_RGB);
     long thumbW=1;
     long thumbH=1;

    try {
        IFormatReader ir = getIFormatReader(reader.get().getCurrentFile(),null);
        ir.setId(reader.get().getCurrentFile());
        ir.setSeries(reader.get().getSeries());

        //int lev = numLevels-1;
        for (int lev=numLevels-1; lev>=0; lev--)
        {
            ir.setResolution(lev);
            thumbW = ir.getSizeX();
            thumbH = ir.getSizeY();
            double diff = Math.abs((thumbW/(double)thumbH) - (width/(double)height));
            logger.trace("thumb lev: "+lev+"  diff: "+diff+"  WxH: "+thumbW+"x"+thumbH);
            if (diff< THUMBNAIL_RATIO_DIFF) break; // 0.001
        }

        BufferedImageReader bir = BufferedImageReader.makeBufferedImageReader(ir);
        BufferedImage thumb = bir.openImage(0);
        bir.close();

        if (thumbW>maxThumbWidth) {
            int h = (int)(maxThumbWidth * (thumbH/(double)thumbW));
            BufferedImage img = new BufferedImage(maxThumbWidth,h, BufferedImage.TYPE_INT_RGB);
            Graphics2D g2d = (Graphics2D) img.getGraphics();
            g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
            g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
            g2d.drawImage(thumb,0,0,maxThumbWidth,h, null);
            thumb = img;
        }
        return thumb;
    } catch (IOException | FormatException e) {
        e.printStackTrace();
    }
    return null;
}
 

public BufferedImage[] openUnmixedImages(int no, int x, int y, int w, int h) throws FormatException, IOException {
    int[] zct = getZCTCoords(no);
    int z = zct[0];
    int chan = zct[1];
    int t = zct[2];
    // load all channels for current rect
    BufferedImage[] channels = new BufferedImage[sizeC];
    for (int c=0; c<sizeC; c++) {
        int no2 = getIndex(z,c,t);
        channels[c] = super.openImage(no2,x,y,w,h);
    }

    BufferedImage ori = channels[0];
    BufferedImage[] bi = new BufferedImage[sizeC];
    WritableRaster[] raster = new WritableRaster[sizeC];
    for (int c=0; c<sizeC; c++) {
        if (!channelIndependent[c]) {
            bi[c] = new BufferedImage(ori.getColorModel(), ori.getRaster().createCompatibleWritableRaster(0, 0, w, h), ori.isAlphaPremultiplied(), null);
            raster[c] = bi[c].getRaster();
        } else {
            bi[c] = channels[c];   // original image, independent channel
            raster[c] = bi[c].getRaster();
        }
    }
    double[] measurements = new double[sizeDependend];
    double[] out = new double[sizeDependend];
    for (int ix=ori.getMinX(); ix<ori.getMinX()+ori.getWidth(); ix++)
        for (int iy=ori.getMinY(); iy<ori.getMinY()+ori.getHeight(); iy++) {
            for (int c=0; c<sizeDependend; c++) {
                measurements[c] = channels[channelMap[c]].getRaster().getSampleDouble(ix,iy,0); // only 1 banded rasters allowed here
            }
            fastMultiply(invMatrix,measurements,out);   // here the real unmixing takes place
            for (int c=0; c<sizeDependend; c++) {
                if (out[c]>255) out[c] = 255d;        // TODO: adjust for 16bit!!!
                if (out[c]<0) out[c] = 0d;
                raster[channelMap[c]].setSample(ix, iy, 0, out[c]);
            }
        }
    unmixedChannels = bi;
    currentRect = new RectZT(x,y,w,h,z,t);

    return bi;
}
 

public static void main(String[] args) throws IOException, FormatException {
    NDPISReaderOrbit r = new NDPISReaderOrbit();
    r.setId("D:\\pic\\Hamamatsu\\Scan_Manuel\\Staining-DAPI-Cy5.5-FITC-scan all channels fix.ndpis");
    System.out.println(Arrays.toString(getExposureTimesGain(r)));
    r.close();
}