export_for_CATMAID.bsh

/**
 * Export tiles for CATMAID.
 *
 * 
 * To use this script, open project in TrakEM2, regenerate mipmaps
 * Open script editor (File/New/Script) Select Beanshell as language, paste this script in. 
 * Select layer range you wish to export (firstLayer and lastLayer)
 * Select appropriate path
 * Click Run
 * 
 */

import ij.Prefs;
Prefs.setThreads(1);
import java.lang.*;
import ij.ImagePlus;
import ij.process.ByteProcessor;
import ij.io.FileSaver;
import ij.IJ;
import ij.process.Blitter;
import ini.trakem2.Project;
import ini.trakem2.display.*;
import mpicbg.trakem2.transform.*;
import mpicbg.ij.util.*;




firstLayer = 31;  // Section number minus one. first section = 0
lastLayer = 31;

path = "/home/witvliet/Desktop/trakem_export_test/"; //remember trailing slash





jpegQuality = 80;

tileWidth = 512;
tileHeight = 512;

front = Display.getFront();
layerSet = front.getLayerSet();
layers = layerSet.getLayers();
emptyImage = new ImagePlus("",new ByteProcessor(tileWidth,tileHeight));
left = 0;
top = 0;
w = layerSet.getLayerWidth();
h = layerSet.getLayerHeight();

ImagePlus openAndDelete(path) {
	file = new File(path);
	if ( file.exists() ) {
		imp = new ImagePlus( path );
		file.delete();
		return imp;
	} else {
		return emptyImage;
    }
}

emptySections = new ArrayList();

for ( int l = firstLayer; l <= lastLayer; ++l )
{
	
	layer = layers.get( l );
	if ( layer.getDisplayables( Patch.class ).size() == 0 ) {
		IJ.log( "Section " + l + " empty" );
		continue;
	}

	print(l);


	dirPath = path + l;
	dir = new File( dirPath );
	if ( !dir.exists() )
		dir.mkdirs();

	/* level 0 tiles */
	for ( y = 0; y < h; y += tileHeight )
	{
		for ( x = 0; x < w; x += tileWidth )
		{
			box = new Rectangle( x + left, y + top, tileWidth, tileHeight );
			
			impTile = layer.getProject().getLoader().getFlatImage(
				layer,
				box,
				1.0,
				-1,
				ImagePlus.GRAY8,
				Patch.class,
				true );

			fileSaver = new FileSaver(impTile);
			fileSaver.setJpegQuality( jpegQuality );
			fileSaver.saveAsJpeg(dirPath + "/" + (y / tileHeight) + "_" + (x / tileWidth) + "_0.jpg");
			fileSaver.saveAsTiff(dirPath + "/" + (y / tileHeight) + "_" + (x / tileWidth) + "_0.tif");
		}
	}

	/* level [1,n] tiles */
	for (
		int w1 = ( int )Math.ceil( w / 2.0 ), h1 = ( int )Math.ceil( h / 2.0 ), s = 1;
		w1 > tileWidth && h1 > tileHeight;
		w1 = ( int )Math.ceil( w1 / 2.0 ), h1 = ( int )Math.ceil( h1 / 2.0 ), ++s )
	{
		IJ.log( w1 + " " + h1 );
		for ( y = 0; y < h1; y += tileHeight )
		{
			yt = y / tileHeight;
			for ( x = 0; x < w1; x += tileWidth )
			{
				xt = x / tileWidth;
				imp1 = openAndDelete(
					dirPath + "/" +
					(2 * yt) + "_" +
					(2 * xt) + "_" +
					(s - 1) + ".tif");
				imp2 = openAndDelete(
					dirPath + "/" +
					(2 * yt) + "_" +
					(2 * xt + 1) + "_" +
					(s - 1) + ".tif");
				imp3 = openAndDelete(
					dirPath + "/" +
					(2 * yt + 1) + "_" +
					(2 * xt) + "_" +
					(s - 1) + ".tif");
				imp4 = openAndDelete(
					dirPath + "/" +
					(2 * yt + 1) + "_" +
					(2 * xt + 1) + "_" +
					(s - 1) + ".tif");

				ip4 = new ByteProcessor(tileWidth * 2, tileHeight * 2);
				ip4.copyBits(imp1.getProcessor(), 0, 0, Blitter.COPY);
				ip4.copyBits(imp2.getProcessor(), tileWidth, 0, Blitter.COPY);
				ip4.copyBits(imp3.getProcessor(), 0, tileHeight, Blitter.COPY);
				ip4.copyBits(imp4.getProcessor(), tileWidth, tileHeight, Blitter.COPY);

				ip = mpicbg.trakem2.util.Downsampler.downsampleImageProcessor(ip4);
				impTile = new ImagePlus("", ip);

				fileSaver = new FileSaver( impTile );
				fileSaver.setJpegQuality( jpegQuality );
				fileSaver.saveAsJpeg( dirPath + "/" + yt + "_" + xt + "_" + s + ".jpg" );
				if ( Math.ceil( w1 / 2.0 ) > tileWidth && Math.ceil( h1 / 2.0 ) > tileHeight )
					fileSaver.saveAsTiff( dirPath + "/" + yt + "_" + xt + "_" + s + ".tif" );
			}
		}
	}
}



print("done");