Coloc_2.java
No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Mon, May 20, 14:08

Coloc_2.java
View Options

	import algorithms.Algorithm;
	import algorithms.AutoThresholdRegression;
	import algorithms.AutoThresholdRegression.Implementation;
	import algorithms.CostesSignificanceTest;
	import algorithms.Histogram2D;
	import algorithms.InputCheck;
	import algorithms.KendallTauRankCorrelation;
	import algorithms.LiHistogram2D;
	import algorithms.LiICQ;
	import algorithms.MandersColocalization;
	import algorithms.MissingPreconditionException;
	import algorithms.PearsonsCorrelation;
	import algorithms.SpearmanRankCorrelation;
	import fiji.Debug;
	import gadgets.DataContainer;
	import ij.IJ;
	import ij.ImagePlus;
	import ij.Prefs;
	import ij.WindowManager;
	import ij.gui.GenericDialog;
	import ij.gui.Roi;
	import ij.gui.ShapeRoi;
	import ij.plugin.PlugIn;
	import ij.plugin.frame.RoiManager;
	import ij.process.Blitter;
	import ij.process.ImageProcessor;

	import java.awt.Checkbox;
	import java.awt.Frame;
	import java.awt.Rectangle;
	import java.awt.event.ItemEvent;
	import java.awt.event.ItemListener;
	import java.awt.event.WindowAdapter;
	import java.awt.event.WindowEvent;
	import java.util.ArrayList;
	import java.util.Arrays;
	import java.util.List;

	import net.imglib2.Cursor;
	import net.imglib2.RandomAccess;
	import net.imglib2.RandomAccessibleInterval;
	import net.imglib2.TwinCursor;
	import net.imglib2.img.ImagePlusAdapter;
	import net.imglib2.img.Img;
	import net.imglib2.img.ImgFactory;
	import net.imglib2.img.array.ArrayImgFactory;
	import net.imglib2.type.NativeType;
	import net.imglib2.type.logic.BitType;
	import net.imglib2.type.numeric.RealType;
	import net.imglib2.view.Views;
	import results.PDFWriter;
	import results.ResultHandler;
	import results.SingleWindowDisplay;
	import results.Warning;

	/**
	Copyright 2010-2015, Daniel J. White, Tom Kazimiers, Johannes Schindelin
	and the Fiji project. Fiji is just imageJ - batteries included.

	This program is free software: you can redistribute it and/or modify
	it under the terms of the GNU General Public License as published by
	the Free Software Foundation, either version 3 of the License, or
	(at your option) any later version.

	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of
	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	GNU General Public License for more details.

	You should have received a copy of the GNU General Public License
	along with this program. If not, see http://www.gnu.org/licenses/ .
	*/

	/**
	* An ImageJ plugin which does pixel intensity correlation based
	* colocalisation analysis on a pair of images,
	* with optional Mask or ROI.
	*
	* @param <T>
	* @author Daniel J. White
	* @author Tom Kazimiers
	* @author Johannes Schindelin
	*/
	public class Coloc_2<T extends RealType< T > & NativeType< T >> implements PlugIn {

	// a small bounding box container
	protected class BoundingBox {
	public long[] offset;
	public long[] size;
	public BoundingBox(long [] offset, long[] size) {
	this.offset = offset.clone();
	this.size = size.clone();
	}
	}

	// a storage class for ROI information
	protected class MaskInfo {
	BoundingBox roi;
	public Img<T> mask;

	// constructors
	public MaskInfo(BoundingBox roi, Img<T> mask) {
	this.roi = roi;
	this.mask = mask;
	}

	public MaskInfo() { }
	}

	// the storage key for Fiji preferences
	protected final static String PREF_KEY = "Coloc_2.";

	// Allowed types of ROI configuration
	protected enum RoiConfiguration {
	None,
	Img1,
	Img2,
	Mask,
	RoiManager
	};

	// the ROI configuration to use
	protected RoiConfiguration roiConfig = RoiConfiguration.Img1;

	// A list of all ROIs/masks found
	protected ArrayList<MaskInfo> masks = new ArrayList<MaskInfo>();

	// A list of auto threshold implementations
	protected String[] regressions = new String[
	AutoThresholdRegression.Implementation.values().length];

	// default indices of image, mask, ROI and regression choices
	protected static int index1 = 0;
	protected static int index2 = 1;
	protected static int indexMask = 0;
	protected static int indexRoi = 0;
	protected static int indexRegr = 0;

	// the images to work on
	protected Img<T> img1, img2;

	// names of the images working on
	protected String Ch1Name = "";
	protected String Ch2Name = "";

	// the channels of the images to use
	protected int img1Channel = 1, img2Channel = 1;

	/* The different algorithms this plug-in provides.
	* If a reference is null it will not get run.
	*/
	protected PearsonsCorrelation<T> pearsonsCorrelation;
	protected LiHistogram2D<T> liHistogramCh1;
	protected LiHistogram2D<T> liHistogramCh2;
	protected LiICQ<T> liICQ;
	protected SpearmanRankCorrelation<T> SpearmanRankCorrelation;
	protected MandersColocalization<T> mandersCorrelation;
	protected KendallTauRankCorrelation<T> kendallTau;
	protected Histogram2D<T> histogram2D;
	protected CostesSignificanceTest<T> costesSignificance;
	// indicates if images should be printed in result
	protected boolean displayImages;

	// indicates if a PDF should be saved automatically
	protected boolean autoSavePdf;

	@Override
	public void run(String arg0) {
	if (showDialog()) {
	try {
	for (MaskInfo mi : masks) {
	colocalise(img1, img2, mi.roi, mi.mask);
	}
	} catch (MissingPreconditionException e) {
	IJ.handleException(e);
	IJ.showMessage("An error occured, could not colocalize!");
	return;
	}
	}
	}

	public boolean showDialog() {
	// get IDs of open windows
	int[] windowList = WindowManager.getIDList();
	// if there are less than 2 windows open, cancel
	if (windowList == null \|\| windowList.length < 2) {
	IJ.showMessage("At least 2 images must be open!");
	return false;
	}

	/* create a new generic dialog for the
	* display of various options.
	*/
	final GenericDialog gd
	= new GenericDialog("Coloc 2");

	String[] titles = new String[windowList.length];
	/* the masks and ROIs array needs three more entries than
	* windows to contain "none", "ROI ch 1" and "ROI ch 2"
	*/
	String[] roisAndMasks= new String[windowList.length + 4];
	roisAndMasks[0]="<None>";
	roisAndMasks[1]="ROI(s) in channel 1";
	roisAndMasks[2]="ROI(s) in channel 2";
	roisAndMasks[3]="ROI Manager";

	// go through all open images and add them to GUI
	for (int i=0; i < windowList.length; i++) {
	ImagePlus imp = WindowManager.getImage(windowList[i]);
	if (imp != null) {
	titles[i] = imp.getTitle();
	roisAndMasks[i + 4] =imp.getTitle();
	} else {
	titles[i] = "";
	}
	}

	// find all available regression strategies
	Implementation[] regressionImplementations =
	AutoThresholdRegression.Implementation.values();
	for (int i=0; i<regressionImplementations.length; ++i) {
	regressions[i] = regressionImplementations[i].toString();
	}

	// set up the users preferences
	displayImages = Prefs.get(PREF_KEY+"displayImages", false);
	autoSavePdf = Prefs.get(PREF_KEY+"autoSavePdf", true);
	boolean displayShuffledCostes = Prefs.get(PREF_KEY+"displayShuffledCostes", false);
	boolean useLiCh1 = Prefs.get(PREF_KEY+"useLiCh1", true);
	boolean useLiCh2 = Prefs.get(PREF_KEY+"useLiCh2", true);
	boolean useLiICQ = Prefs.get(PREF_KEY+"useLiICQ", true);
	boolean useSpearmanRank = Prefs.get(PREF_KEY+"useSpearmanRank", true);
	boolean useManders = Prefs.get(PREF_KEY+"useManders", true);
	boolean useKendallTau = Prefs.get(PREF_KEY+"useKendallTau", true);
	boolean useScatterplot = Prefs.get(PREF_KEY+"useScatterplot", true);
	boolean useCostes = Prefs.get(PREF_KEY+"useCostes", true);
	int psf = (int) Prefs.get(PREF_KEY+"psf", 3);
	int nrCostesRandomisations = (int) Prefs.get(PREF_KEY+"nrCostesRandomisations", 10);
	indexRegr = (int) Prefs.get(PREF_KEY+"regressionImplementation", 0);

	/* make sure the default indices are no bigger
	* than the amount of images we have
	*/
	index1 = clip( index1, 0, titles.length );
	index2 = clip( index2, 0, titles.length );
	indexMask = clip( indexMask, 0, roisAndMasks.length - 1);

	gd.addChoice("Channel_1", titles, titles[index1]);
	gd.addChoice("Channel_2", titles, titles[index2]);
	gd.addChoice("ROI_or_mask", roisAndMasks, roisAndMasks[indexMask]);
	//gd.addChoice("Use ROI", roiLabels, roiLabels[indexRoi]);

	gd.addChoice("Threshold_regression", regressions,
	regressions[indexRegr]);

	gd.addCheckbox("Show_Save_PDF_Dialog", autoSavePdf);
	gd.addCheckbox("Display_Images_in_Result", displayImages);
	gd.addCheckbox("Display_Shuffled_Images", displayShuffledCostes);
	final Checkbox shuffleCb = (Checkbox) gd.getCheckboxes().lastElement();
	// Add algorithm options
	gd.addMessage("Algorithms:");
	gd.addCheckbox("Li_Histogram_Channel_1", useLiCh1);
	gd.addCheckbox("Li_Histogram_Channel_2", useLiCh2);
	gd.addCheckbox("Li_ICQ", useLiICQ);
	gd.addCheckbox("Spearman's_Rank_Correlation", useSpearmanRank);
	gd.addCheckbox("Manders'_Correlation", useManders);
	gd.addCheckbox("Kendall's_Tau_Rank_Correlation", useKendallTau);
	gd.addCheckbox("2D_Instensity_Histogram", useScatterplot);
	gd.addCheckbox("Costes'_Significance_Test", useCostes);
	final Checkbox costesCb = (Checkbox) gd.getCheckboxes().lastElement();
	gd.addNumericField("PSF", psf, 1);
	gd.addNumericField("Costes_randomisations", nrCostesRandomisations, 0);

	// disable shuffle checkbox if costes checkbox is set to "off"
	shuffleCb.setEnabled(useCostes);
	costesCb.addItemListener(new ItemListener() {
	@Override
	public void itemStateChanged(ItemEvent e) {
	shuffleCb.setEnabled(costesCb.getState());
	}
	});

	// show the dialog, finally
	gd.showDialog();
	// do nothing if dialog has been canceled
	if (gd.wasCanceled())
	return false;

	ImagePlus imp1 = WindowManager.getImage(gd.getNextChoiceIndex() + 1);
	ImagePlus imp2 = WindowManager.getImage(gd.getNextChoiceIndex() + 1);

	// get image names for output
	Ch1Name = imp1.getTitle();
	Ch2Name = imp2.getTitle();

	// make sure both images have the same bit-depth
	if (imp1.getBitDepth() != imp2.getBitDepth()) {
	IJ.showMessage("Both images must have the same bit-depth.");
	return false;
	}

	// get information about the mask/ROI to use
	indexMask = gd.getNextChoiceIndex();
	if (indexMask == 0)
	roiConfig = RoiConfiguration.None;
	else if (indexMask == 1)
	roiConfig = RoiConfiguration.Img1;
	else if (indexMask == 2)
	roiConfig = RoiConfiguration.Img2;
	else if (indexMask == 3)
	roiConfig = RoiConfiguration.RoiManager;
	else {
	roiConfig = RoiConfiguration.Mask;
	/* Make indexMask the reference to the mask image to use.
	* To do this we reduce it by three for the first three
	* entries in the combo box.
	*/
	indexMask = indexMask - 4;
	}

	// save the ImgLib wrapped images as members
	img1 = ImagePlusAdapter.wrap(imp1);
	img2 = ImagePlusAdapter.wrap(imp2);

	/* check if we have a valid ROI for the selected configuration
	* and if so, get the ROI's bounds. Alternatively, a mask can
	* be selected (that is basically all, but a rectangle).
	*/
	if (roiConfig == RoiConfiguration.Img1 && hasValidRoi(imp1)) {
	createMasksFromImage(imp1);
	} else if (roiConfig == RoiConfiguration.Img2 && hasValidRoi(imp2)) {
	createMasksFromImage(imp2);
	} else if (roiConfig == RoiConfiguration.RoiManager) {
	if (!createMasksFromRoiManager(imp1.getWidth(), imp1.getHeight()))
	return false;
	} else if (roiConfig == RoiConfiguration.Mask) {
	// get the image to be used as mask
	ImagePlus maskImp = WindowManager.getImage(windowList[indexMask]);
	Img<T> maskImg = ImagePlusAdapter.<T>wrap( maskImp );
	// get a valid mask info for the image
	MaskInfo mi = getBoundingBoxOfMask(maskImg);
	masks.add( mi ) ;
	} else {
	/* if no ROI/mask is selected, just add an empty MaskInfo
	* to colocalise both images without constraints.
	*/
	masks.add(new MaskInfo(null, null));
	}

	// get information about the mask/ROI to use
	indexRegr = gd.getNextChoiceIndex();

	// read out GUI data
	autoSavePdf = gd.getNextBoolean();
	displayImages = gd.getNextBoolean();
	displayShuffledCostes = gd.getNextBoolean();
	useLiCh1 = gd.getNextBoolean();
	useLiCh2 = gd.getNextBoolean();
	useLiICQ = gd.getNextBoolean();
	useSpearmanRank = gd.getNextBoolean();
	useManders = gd.getNextBoolean();
	useKendallTau = gd.getNextBoolean();
	useScatterplot = gd.getNextBoolean();
	useCostes = gd.getNextBoolean();
	psf = (int) gd.getNextNumber();
	nrCostesRandomisations = (int) gd.getNextNumber();

	// save user preferences
	Prefs.set(PREF_KEY+"regressionImplementation", indexRegr);
	Prefs.set(PREF_KEY+"autoSavePdf", autoSavePdf);
	Prefs.set(PREF_KEY+"displayImages", displayImages);
	Prefs.set(PREF_KEY+"displayShuffledCostes", displayShuffledCostes);
	Prefs.set(PREF_KEY+"useLiCh1", useLiCh1);
	Prefs.set(PREF_KEY+"useLiCh2", useLiCh2);
	Prefs.set(PREF_KEY+"useLiICQ", useLiICQ);
	Prefs.set(PREF_KEY+"useSpearmanRank", useSpearmanRank);
	Prefs.set(PREF_KEY+"useManders", useManders);
	Prefs.set(PREF_KEY+"useKendallTau", useKendallTau);
	Prefs.set(PREF_KEY+"useScatterplot", useScatterplot);
	Prefs.set(PREF_KEY+"useCostes", useCostes);
	Prefs.set(PREF_KEY+"psf", psf);
	Prefs.set(PREF_KEY+"nrCostesRandomisations", nrCostesRandomisations);

	// Parse algorithm options
	pearsonsCorrelation = new PearsonsCorrelation<T>(PearsonsCorrelation.Implementation.Fast);

	if (useLiCh1)
	liHistogramCh1 = new LiHistogram2D<T>("Li - Ch1", true);
	if (useLiCh2)
	liHistogramCh2 = new LiHistogram2D<T>("Li - Ch2", false);
	if (useLiICQ)
	liICQ = new LiICQ<T>();
	if (useSpearmanRank)
	SpearmanRankCorrelation = new SpearmanRankCorrelation<T>();
	if (useManders)
	mandersCorrelation = new MandersColocalization<T>();
	if (useKendallTau)
	kendallTau = new KendallTauRankCorrelation<T>();
	if (useScatterplot)
	histogram2D = new Histogram2D<T>("2D intensity histogram");
	if (useCostes) {
	costesSignificance = new CostesSignificanceTest<T>(pearsonsCorrelation,
	psf, nrCostesRandomisations, displayShuffledCostes);
	}

	return true;
	}

	/**
	* Call this method to run a whole colocalisation configuration,
	* all selected algorithms get run on the supplied images. You
	* can specify the data further by supplying appropriate
	* information in the mask structure.
	*
	* @param img1
	* @param img2
	* @param roi
	* @param mask
	* @param maskBB
	* @throws MissingPreconditionException
	*/
	public void colocalise(Img<T> img1, Img<T> img2, BoundingBox roi,
	Img<T> mask) throws MissingPreconditionException {
	// create a new container for the selected images and channels
	DataContainer<T> container;
	if (mask != null) {
	container = new DataContainer<T>(img1, img2,
	img1Channel, img2Channel, Ch1Name, Ch2Name, mask, roi.offset, roi.size);
	} else if (roi != null) {
	// we have no mask, but a regular ROI in use
	container = new DataContainer<T>(img1, img2,
	img1Channel, img2Channel, Ch1Name, Ch2Name, roi.offset, roi.size);
	} else {
	// no mask and no ROI is present
	container = new DataContainer<T>(img1, img2,
	img1Channel, img2Channel, Ch1Name, Ch2Name);
	}

	// create a results handler
	final List<ResultHandler<T>> listOfResultHandlers = new ArrayList<ResultHandler<T>>();
	final PDFWriter<T> pdfWriter = new PDFWriter<T>(container);
	final SingleWindowDisplay<T> swDisplay = new SingleWindowDisplay<T>(container, pdfWriter);
	listOfResultHandlers.add(swDisplay);
	listOfResultHandlers.add(pdfWriter);
	//ResultHandler<T> resultHandler = new EasyDisplay<T>(container);

	// this list contains the algorithms that will be run when the user clicks ok
	List<Algorithm<T>> userSelectedJobs = new ArrayList<Algorithm<T>>();

	// add some pre-processing jobs:
	userSelectedJobs.add( container.setInputCheck(
	new InputCheck<T>()) );
	userSelectedJobs.add( container.setAutoThreshold(
	new AutoThresholdRegression<T>(pearsonsCorrelation,
	AutoThresholdRegression.Implementation.values()[indexRegr])));

	// add user selected algorithms
	addIfValid(pearsonsCorrelation, userSelectedJobs);
	addIfValid(liHistogramCh1, userSelectedJobs);
	addIfValid(liHistogramCh2, userSelectedJobs);
	addIfValid(liICQ, userSelectedJobs);
	addIfValid(SpearmanRankCorrelation, userSelectedJobs);
	addIfValid(mandersCorrelation, userSelectedJobs);
	addIfValid(kendallTau, userSelectedJobs);
	addIfValid(histogram2D, userSelectedJobs);
	addIfValid(costesSignificance, userSelectedJobs);

	// execute all algorithms
	int count = 0;
	int jobs = userSelectedJobs.size();
	for (Algorithm<T> a : userSelectedJobs){
	try {
	count++;
	IJ.showStatus(count + "/" + jobs + ": Running " + a.getName());
	a.execute(container);
	}
	catch (MissingPreconditionException e){
	for (ResultHandler<T> r : listOfResultHandlers){
	r.handleWarning(
	new Warning( "Probem with input data", a.getName() + ": " + e.getMessage() ) );
	}
	}
	}
	// clear status
	IJ.showStatus("");

	// let the algorithms feed their results to the handler
	for (Algorithm<T> a : userSelectedJobs){
	for (ResultHandler<T> r : listOfResultHandlers)
	a.processResults(r);
	}
	// if we have ROIs/masks, add them to results
	if (displayImages) {
	RandomAccessibleInterval<T> channel1, channel2;
	if (mask != null \|\| roi != null) {
	long[] offset = container.getMaskBBOffset();
	long[] size = container.getMaskBBSize();
	channel1 = createMaskImage( container.getSourceImage1(),
	container.getMask(), offset, size );
	channel2 = createMaskImage( container.getSourceImage2(),
	container.getMask(), offset, size );
	} else {
	channel1 = container.getSourceImage1();
	channel2 = container.getSourceImage2();
	}
	for (ResultHandler<T> r : listOfResultHandlers) {
	r.handleImage (channel1, "Channel 1");
	r.handleImage (channel2, "Channel 2");
	}
	}
	// do the actual results processing
	swDisplay.process();
	// add window to the IJ window manager
	swDisplay.addWindowListener(new WindowAdapter() {
	@Override
	public void windowClosed(WindowEvent e) {
	WindowManager.removeWindow((Frame) swDisplay);
	}
	});
	WindowManager.addWindow(swDisplay);
	// show PDF saving dialog if requested
	if (autoSavePdf)
	pdfWriter.process();
	}

	/**
	* A method to get the bounding box from the data in the given
	* image that is above zero. Those values are interpreted as a
	* mask. It will return null if no mask information was found.
	*
	* @param mask The image to look for "on" values in
	* @return a new MaskInfo object or null
	*/
	protected MaskInfo getBoundingBoxOfMask(Img<T> mask) {
	Cursor<T> cursor = mask.localizingCursor();

	int numMaskDims = mask.numDimensions();
	// the "off type" of the mask
	T offType = mask.firstElement().createVariable();
	offType.setZero();
	// the corners of the bounding box
	long[] min = null;
	long[] max = null;
	// indicates if mask data has been found
	boolean maskFound = false;
	// a container for temporary position information
	long[] pos = new long[numMaskDims];
	// walk over the mask
	while (cursor.hasNext() ) {
	cursor.fwd();
	T data = cursor.get();
	// test if the current mask data represents on or off
	if (data.compareTo(offType) > 0) {
	// get current position
	cursor.localize(pos);
	if (!maskFound) {
	// we found mask data, first time
	maskFound = true;
	// init min and max with the current position
	min = Arrays.copyOf(pos, numMaskDims);
	max = Arrays.copyOf(pos, numMaskDims);
	} else {
	/* Is is at least second hit, compare if it
	* has new "extreme" positions, i.e. does
	* is make the BB bigger?
	*/
	for (int d=0; d<numMaskDims; d++) {
	if (pos[d] < min[d]) {
	// is it smaller than min
	min[d] = pos[d];
	} else if (pos[d] > max[d]) {
	// is it larger than max
	max[d] = pos[d];
	}
	}
	}
	}
	}

	if (!maskFound) {
	return null;
	} else {
	// calculate size
	long[] size = new long[numMaskDims];
	for (int d=0; d<numMaskDims; d++)
	size[d] = max[d] - min[d] + 1;
	// create and add bounding box
	BoundingBox bb = new BoundingBox(min, size);
	return new MaskInfo(bb, mask);
	}
	}

	/**
	* Adds the provided Algorithm to the list if it is not null.
	*/
	protected void addIfValid(Algorithm<T> a, List<Algorithm<T>> list) {
	if (a != null)
	list.add(a);
	}

	/**
	* Returns true if a custom ROI has been selected, i.e if the current
	* ROI does not have the extent of the whole image.
	* @return true if custom ROI selected, false otherwise
	*/
	protected boolean hasValidRoi(ImagePlus imp) {
	Roi roi = imp.getRoi();
	if (roi == null)
	return false;

	Rectangle theROI = roi.getBounds();

	// if the ROI is the same size as the image (default ROI), return false
	return (theROI.height != imp.getHeight()
	\|\| theROI.width != imp.getWidth());
	}

	/**
	* Clips a value to the specified bounds.
	*/
	protected static int clip(int val, int min, int max) {
	return Math.max( Math.min( val, max ), min );
	}

	/**
	* This method checks if the given ImagePlus contains any
	* masks or ROIs. If so, the appropriate date structures
	* are created and filled.
	*/
	protected void createMasksFromImage(ImagePlus imp) {
	// get ROIs from current image in Fiji
	Roi[] impRois = split(imp.getRoi());
	// create the ROIs
	createMasksAndRois(impRois, imp.getWidth(), imp.getHeight());
	}

	/**
	* A method to fill the masks array with data based on the ROI manager.
	*/
	protected boolean createMasksFromRoiManager(int width, int height) {
	RoiManager roiManager = RoiManager.getInstance();
	if (roiManager == null) {
	IJ.error("Could not get ROI Manager instance.");
	return false;
	}
	Roi[] selectedRois = roiManager.getSelectedRoisAsArray();
	// create the ROIs
	createMasksAndRois(selectedRois, width, height);
	return true;
	}

	/**
	* Creates appropriate data structures from the ROI information
	* passed. If an irregular ROI is found, it will be put into a
	* frame of its bounding box size and put into an Image<T>.
	*
	* In the end the members ROIs, masks and maskBBs will be
	* filled if ROIs or masks were found. They will be null
	* otherwise.
	*/
	protected void createMasksAndRois(Roi[] rois, int width, int height) {
	// create empty list
	masks.clear();

	for (Roi r : rois ){
	MaskInfo mi = new MaskInfo();
	// add it to the list of masks/ROIs
	masks.add(mi);
	// get the ROIs/masks bounding box
	Rectangle rect = r.getBounds();
	mi.roi = new BoundingBox(
	new long[] {rect.x, rect.y} ,
	new long[] {rect.width, rect.height});
	ImageProcessor ipMask = r.getMask();
	// check if we got a regular ROI and return if so
	if (ipMask == null) {
	continue;
	}

	// create a mask processor of the same size as a slice
	ImageProcessor ipSlice = ipMask.createProcessor(width, height);
	// fill the new slice with black
	ipSlice.setValue(0.0);
	ipSlice.fill();
	// position the mask on the new mask processor
	ipSlice.copyBits(ipMask, (int)mi.roi.offset[0], (int)mi.roi.offset[1], Blitter.COPY);
	// create an Image<T> out of it
	ImagePlus maskImp = new ImagePlus("Mask", ipSlice);
	// and remember it and the masks bounding box
	mi.mask = ImagePlusAdapter.<T>wrap( maskImp );
	}
	}

	/**
	* This method duplicates the given images, but respects
	* ROIs if present. Meaning, a sub-picture will be created when
	* source images are ROI/MaskImages.
	* @throws MissingPreconditionException
	*/
	protected RandomAccessibleInterval<T> createMaskImage(
	RandomAccessibleInterval<T> image, RandomAccessibleInterval<BitType> mask,
	long[] offset, long[] size) throws MissingPreconditionException {
	long[] pos = new long[ image.numDimensions() ];
	// sanity check
	if (pos.length != offset.length \|\| pos.length != size.length) {
	throw new MissingPreconditionException("Mask offset and size must be of same dimensionality like image.");
	}
	// use twin cursor for only one image
	TwinCursor<T> cursor = new TwinCursor<T>(
	image.randomAccess(),
	image.randomAccess(),
	Views.iterable(mask).localizingCursor());
	// prepare output image
	ImgFactory<T> maskFactory = new ArrayImgFactory<T>();
	//Img<T> maskImage = maskFactory.create( size, name );
	RandomAccessibleInterval<T> maskImage = maskFactory.create( size,
	image.randomAccess().get().createVariable() );
	RandomAccess<T> maskCursor = maskImage.randomAccess();
	// go through the visible data and copy it to the output
	while (cursor.hasNext()) {
	cursor.fwd();
	cursor.localize(pos);
	// shift coordinates by offset
	for (int i=0; i < pos.length; ++i) {
	pos[i] = pos[i] - offset[i];
	}
	// write out to correct position
	maskCursor.setPosition( pos );
	maskCursor.get().set( cursor.getFirst() );
	}

	return maskImage;
	}

	/**
	* Splits a non overlapping composite ROI into its sub ROIs.
	*
	* @param roi The ROI to split
	* @return A list of one or more ROIs
	*/
	public static Roi[] split(Roi roi) {
	if (roi instanceof ShapeRoi)
	return ((ShapeRoi)roi).getRois();
	return new Roi[] { roi };
	}

	/**
	* Main method for easier development. To run this plugin with Maven, use:
	* mvn exec:java -Dexec.mainClass="Coloc_2"
	*/
	public static void main(String[] args) {
	Debug.run(null, null);
	}
	}

Coloc_2.javaNo OneTemporaryActions

File Metadata

Coloc_2.javaView Options

Event Timeline

Coloc_2.java
No OneTemporary
Actions

Coloc_2.java
View Options