trakem2_exportAreaLists-asMasks.bsh

trakem2_exportAreaLists-asMasks.bsh

import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.awt.geom.AffineTransform;
import java.awt.geom.Area;
import java.awt.image.BufferedImage;
import java.awt.image.DataBufferByte;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;

import amira.AmiraMeshEncoder;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.Roi;
import ij.io.FileSaver;
import ij.measure.Calibration;
import ij.process.ByteProcessor;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.process.ShortProcessor;
import ini.trakem2.Project;
import ini.trakem2.display.*;
import ini.trakem2.display.paint.USHORTPaint;
import ini.trakem2.tree.ProjectThing;
import ini.trakem2.utils.Utils;

/*
 * See:
 * http://forum.imagej.net/t/trakem2-scripting-export-arealists-as-tiffs-with-template-architecture/9461
 */

destdir="/home/john/tmp/tem2/";

public static void writeArealists( String destdir, ProjectThing root, String prefix, 
		LayerSet layer_set,
		Roi roi, float scale, int first, int last )
{
	// put a check here to be sure root is okay
	if( root == null )
		return;

	// add this object's title to the file name
	String thisprefix = prefix + "_" + root.getTitle();

	// get this project's object and see if it's an AreaList
	Object obj = root.getObject();
	if( obj instanceof AreaList )
	{	
		// if so, write a tif
		ImagePlus imp = exportAsMask( (AreaList)obj, layer_set, roi, scale, first, last );
		System.out.println( "the imp mask : " + imp );
		System.out.println( "writing: " + thisprefix );
		IJ.save( imp, destdir + thisprefix + ".tif" );
	}

	// recurse
	children = root.getChildren();
	if( children != null )
	{
		for( int i = 0; i < children.size(); i++ )
		{
			ProjectThing c = children.get( i );
			writeArealists( destdir, c, thisprefix, layer_set, roi, scale, first, last );
		}
	}
}

static public ImagePlus exportAsMask( AreaList al, LayerSet layer_set, ij.gui.Roi roi, float scale, int first_layer, int last_layer )
{
	
	list = new ArrayList();
	list.add( al );

	// Compute highest label value, which affects of course the stack image type
	label_values = new TreeSet();
	for (Displayable d : list) {
		String label = d.getProperty("label");
		if (null != label) label_values.add(Integer.parseInt(label));
	}
	int lowest=0, highest=0;
	if (label_values.size() > 0) {
		lowest = label_values.first();
		highest = label_values.last();
	}
	int n_non_labeled = list.size() - label_values.size();
	int max_label_value = highest + n_non_labeled;

	int type_ = ImagePlus.GRAY8;
	if (max_label_value > 255) {
		type_ = ImagePlus.GRAY16;
		if (max_label_value > 65535) {
			type_ = ImagePlus.GRAY32;
		}
	}
	int type = type_;

	int width,height;
	Rectangle broi;
	if (null == roi) {
		broi = null;
		width = (int)(layer_set.getLayerWidth() * scale);
		height = (int)(layer_set.getLayerHeight() * scale);
	} else {
		broi = roi.getBounds();
		width = (int)(broi.width * scale);
		height = (int)(broi.height * scale);
	}
	

	ImageStack stack = new ImageStack(width, height);
	Calibration cal = layer_set.getCalibration();

	float len = last_layer - first_layer + 1;
	layers = layer_set.getLayers().subList(first_layer, last_layer+1);

	slices = Collections.synchronizedMap(new TreeMap());

	for (int k = 0; k < layers.size(); k++) {
		Layer la = layers.get(k);
		int slice = k;
				Utils.showProgress(slice / len);

				ImageProcessor ip;

				if (ImagePlus.GRAY8 == type) {
					BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_GRAY);
					Graphics2D g = bi.createGraphics();

					for (AreaList ali : list) {
						Area area = ali.getArea(la);
						if (null == area || area.isEmpty()) continue;
						// Transform: the scale and the roi
						AffineTransform aff = new AffineTransform();
						// reverse order of transformations:
						/* 3 - To scale: */ if (1 != scale) aff.scale(scale, scale);
						/* 2 - To roi coordinates: */ if (null != broi) aff.translate(-broi.x, -broi.y);
						/* 1 - To world coordinates: */ aff.concatenate(ali.getAffineTransform());
						g.setTransform(aff);
						int label = 255;
						g.setColor(new Color(label, label, label));
						g.fill(area);
					}
					g.dispose();
					ip = new ByteProcessor(bi);
					bi.flush();

				} else if (ImagePlus.GRAY16 == type) {
					USHORTPaint paint = new USHORTPaint((short)0);
					BufferedImage bi = new BufferedImage(paint.getComponentColorModel(), paint.getComponentColorModel().createCompatibleWritableRaster(width, height), false, null);
					Graphics2D g = bi.createGraphics();
					//ColorSpace ugray = ColorSpace.getInstance(ColorSpace.CS_GRAY);

					int painted = 0;

					for (AreaList ali : list) {
						Area area = ali.getArea(la);
						if (null == area || area.isEmpty()) continue;
						// Transform: the scale and the roi
						AffineTransform aff = new AffineTransform();
						// reverse order of transformations:
						/* 3 - To scale: */ if (1 != scale) aff.scale(scale, scale);
						/* 2 - To roi coordinates: */ if (null != broi) aff.translate(-broi.x, -broi.y);
						/* 1 - To world coordinates: */ aff.concatenate(ali.at);
						// Fill
						g.setTransform(aff);

						// The color doesn't work: paints in a stretched 8-bit mode
						//g.setColor(new Color(ugray, new float[]{((float)labels.get(d)) / range}, 1));

						short ls = (short)255;
						paint.setValue(ls);
						g.setPaint(paint);

						g.fill(area); //.createTransformedArea(aff));

						painted += 1;
					}
					g.dispose();
					ip = new ShortProcessor(bi);
					bi.flush();

					Utils.log2("painted: " + painted);

				} else {
					// Option 1: could use the same as above, but shifted by 65536, so that 65537 is 1, 65538 is 2, etc.
					//           and keep doing it until no more need to be shifted.
					//           The PROBLEM: cannot keep the order without complicated gymnastics to remember
					//           which label in which image has to be merged to the final image, which prevent
					//           a simple one-pass blitter.
					//
					// Option 2: paint each arealist, extract the image, use it as a mask for filling:

					FloatProcessor fp = new FloatProcessor(width, height);
					float[] fpix = (float[]) fp.getPixels();
					ip = fp;

					BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_GRAY);
					Graphics2D gbi = bi.createGraphics();

					for (AreaList ali : list) {
						Area area = ali.getArea(la);
						if (null == area || area.isEmpty()) {
							continue;
						}
						// Transform: the scale and the roi
						// reverse order of transformations:
						AffineTransform aff = new AffineTransform();
						/* 3 - To scale: */ if (1 != scale) aff.scale(scale, scale);
						/* 2 - To ROI coordinates: */ if (null != broi) aff.translate(-broi.x, -broi.y);
						/* 1 - To world coordinates: */ aff.concatenate(ali.at);
						Area s = area.createTransformedArea(aff);
						Rectangle sBounds = s.getBounds();
						// Need to paint at all?
						if (0 == sBounds.width || 0 == sBounds.height || !sBounds.intersects(0, 0, width, height)) continue;
						// Paint shape
						gbi.setColor(Color.white);
						gbi.fill(s);
						// Read out painted region
						int x0 = Math.max(0, sBounds.x);
						int y0 = Math.max(0, sBounds.y);
						int xN = Math.min(width, sBounds.x + sBounds.width);
						int yN = Math.min(height, sBounds.y + sBounds.height);
						// Get the array
						byte[] bpix = ((DataBufferByte)bi.getRaster().getDataBuffer()).getData();
						float value = 255f;
						// For every non-black pixel, set a 'value' pixel in the FloatProcessor
						for (int y = y0; y < yN; ++y) {
							for (int x = x0; x < xN; ++x) {
								int pos = y * width + x;
								if (0 == bpix[pos]) continue; // black
								fpix[pos] = value;
							}
						}
						// Clear image region
						gbi.setColor(Color.black);
						gbi.fill(s);
					}
					gbi.dispose();
					bi.flush();
				}

				slices.put(slice, ip);
	}


	for ( e : slices.entrySet()) {
		Layer la = layers.get(e.getKey());
		stack.addSlice(la.getZ() * cal.pixelWidth + "", e.getValue());
		if (ImagePlus.GRAY8 != type) {
			e.getValue().setMinAndMax(lowest, highest);
		}
	}

	Utils.showProgress(1);
	// Save via file dialog:
	ImagePlus imp = new ImagePlus("Labels", stack);
	imp.setCalibration(layer_set.getCalibrationCopy());

	return imp;
}


// get the root ProjectThing
project = Project.getProjects().get(0);
root = project.getRootProjectThing();
layer_set = project.getRootLayerSet();

first = 0;
last  = layer_set.size() - 1;
scale = 1.0f;

prefix = "";

// call the function
writeArealists( destdir, root, prefix,
		layer_set, null, scale, first, last );