[OpenSPIM] ome-tiff output

[HongKee Moon]

Dear Christoph,

We have also faced those problems because the default image opener is trying to get the metadata for every file.
I really recommend you to make own ImageStack class for reading the metadata just once for your whole series.

We had to create our version of VirtualStack class based on https://imagej.nih.gov/ij/plugins/virtual-opener.html <https://imagej.nih.gov/ij/plugins/virtual-opener.html> to avoid redundant metadata reading. The below code is not a perfect version, please, use it as a reference.

Hopefully, it will help you.

Cheers,
HongKee

———————————————————

import ij.ImageStack;
import ij.process.ByteProcessor;
import ij.process.ImageProcessor;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.plugins.util.ImageProcessorReader;

import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;

public class MyImageStack extends ImageStack
{
	private int bitDepth;
	private int width, height;
	ImageProcessorReader imageProcessorReader;
	private int zSize = 1, tSize = 1, cSize = 1;
	private int cEffectiveSize = 1;

	public void addSlice( String path )
	{
		if(path != null)
		{
			if(width == 0)
			{
				// create format reader
				ImageReader reader = getImageReader( path );

				// output dimensional information
				int sizeX = reader.getSizeX();
				this.width = sizeX;

				int sizeY = reader.getSizeY();
				this.height = sizeY;

				// System.out.println("Effective C" + reader.getEffectiveSizeC());
				setcEffectiveSize( reader.getEffectiveSizeC() );

				int sizeC = reader.getSizeC();
				int sizeZ = reader.getSizeZ();
				int sizeT = reader.getSizeT();

				// System.out.println( "C=" + sizeC + " Z=" + sizeZ + " T=" + sizeT );

				setcSize( sizeC );
				setzSize( sizeZ );
				settSize( sizeT );

				this.bitDepth = reader.getBitsPerPixel();
				this.imageProcessorReader = new ImageProcessorReader( reader );
			}
		}
	}

	public ImageProcessor getProcessor(int n) 
	{
		// properly implement to get ImageProcessor based on n
	}

	public static ImageReader getImageReader( String path )
	{
		ImageReader reader = null;

		try
		{
			ServiceFactory factory = new ServiceFactory();
			OMEXMLService service = factory.getInstance(OMEXMLService.class);
			IMetadata meta = service.createOMEXMLMetadata();

			// create format reader
			reader = new ImageReader();
			reader.setMetadataStore(meta);

			// initialize file
//			System.out.println(path);
			reader.setId( path );
		}
		catch ( DependencyException e )
		{
			e.printStackTrace();
		}
		catch ( ServiceException e )
		{
			e.printStackTrace();
		}
		catch ( IOException e )
		{
			e.printStackTrace();
		}
		catch ( FormatException e )
		{
			e.printStackTrace();
		}

		return reader;
	}
}

———————————————


> On Nov 6, 2017, at 10:43 AM, Christoph Sommer <christoph.sommer at ist.ac.at> wrote:
> 
> Dear OpenSpim folks,
> 
> thanks for creating such a great resource!
> 
> We are currently using an OpenSpim setup and the created output is a multi-file ome-tiff. For many applications (e.g. the MVR from Stephan Preibisch et al.) we need to convert the ome-tiff to normal tiff.
> 
> Unfortunately, for long time-lapse the conversion takes forever, since for each conversion step all meta-data is parsed from each single time point. My script uses the Bioformats ImporterOptions class, but I can't see how I can bypass the meta-data parsing. I also tried the 'bvconvert' command line script but also got issues there. Also reading from Python (e.g. with the module 'tifffile' only return always the first angle image-stack...)
> 
> Would you have any idea?
> 
> Cheers,
> 
> Chris
> 
> 
> _______________________________________________
> OpenSPIM mailing list
> OpenSPIM at openspim.org
> http://openspim.org/mailman/listinfo/openspim


--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de

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