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Example 26 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method showTemplateInfo.

/**
	 * Show the info from the template.
	 *
	 * @param name
	 *            the name
	 */
private void showTemplateInfo(String name) {
    GlobalSettings settings = getTemplate(name);
    if (settings == null || Utils.isNullOrEmpty(settings.getNotes()))
        return;
    if (infoWindow == null || !infoWindow.isVisible()) {
        infoWindow = new TextWindow(TITLE + " Info", "", "", 450, 250);
        // Put underneath the results window
        if (resultsWindow != null) {
            Point p = resultsWindow.getLocation();
            p.y += resultsWindow.getHeight();
            infoWindow.setLocation(p);
        }
    }
    infoWindow.getTextPanel().clear();
    // Text window cannot show tabs
    infoWindow.append(settings.getNotes().replace('\t', ','));
}
Also used : TextWindow(ij.text.TextWindow) GlobalSettings(gdsc.smlm.ij.settings.GlobalSettings) Point(java.awt.Point)

Example 27 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method updateResults.

/**
	 * Update the results window using the current selected slice from the template image.
	 *
	 * @param slice
	 *            the slice
	 * @return the text window
	 */
public TextWindow updateResults(int slice) {
    if (slice == currentSlice || text == null)
        return resultsWindow;
    currentSlice = slice;
    if (resultsWindow == null || !resultsWindow.isVisible()) {
        resultsWindow = new TextWindow(TITLE + " Results", headings, "", 450, 250);
        // Put next to the image
        ImagePlus imp = WindowManager.getImage(templateId);
        if (imp != null && imp.getWindow() != null) {
            ImageWindow iw = imp.getWindow();
            Point p = iw.getLocation();
            p.x += iw.getWidth();
            resultsWindow.setLocation(p);
        }
    }
    resultsWindow.getTextPanel().clear();
    String data = text.get(slice);
    if (!Utils.isNullOrEmpty(data))
        resultsWindow.append(data);
    return resultsWindow;
}
Also used : ImageWindow(ij.gui.ImageWindow) TextWindow(ij.text.TextWindow) Point(java.awt.Point) ImagePlus(ij.ImagePlus)

Example 28 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method compareCoordinates.

private void compareCoordinates(MemoryPeakResults results1, MemoryPeakResults results2, double dThreshold, int increments, double delta) {
    boolean requirePairs = showPairs || saveClassifications;
    FilePeakResults fileResults = createFilePeakResults(results2);
    List<PointPair> allMatches = new LinkedList<PointPair>();
    List<PointPair> pairs = (requirePairs) ? new LinkedList<PointPair>() : null;
    List<PeakResult> actualPoints = results1.getResults();
    List<PeakResult> predictedPoints = results2.getResults();
    double maxDistance = dThreshold + increments * delta;
    // Old implementation
    //// Process each time point
    //for (Integer t : getTimepoints(actualPoints, predictedPoints))
    //{
    //	Coordinate[] actual = getCoordinates(actualPoints, t);
    //	Coordinate[] predicted = getCoordinates(predictedPoints, t);
    // Divide the results into time points
    TIntObjectHashMap<ArrayList<Coordinate>> actualCoordinates = getCoordinates(actualPoints);
    TIntObjectHashMap<ArrayList<Coordinate>> predictedCoordinates = getCoordinates(predictedPoints);
    int n1 = 0;
    int n2 = 0;
    // Process each time point
    for (Integer t : getTimepoints(actualCoordinates, predictedCoordinates)) {
        Coordinate[] actual = getCoordinates(actualCoordinates, t);
        Coordinate[] predicted = getCoordinates(predictedCoordinates, t);
        List<Coordinate> TP = null;
        List<Coordinate> FP = null;
        List<Coordinate> FN = null;
        List<PointPair> matches = new LinkedList<PointPair>();
        if (requirePairs) {
            FP = new LinkedList<Coordinate>();
            FN = new LinkedList<Coordinate>();
        }
        MatchCalculator.analyseResults2D(actual, predicted, maxDistance, TP, FP, FN, matches);
        // Aggregate
        n1 += actual.length;
        n2 += predicted.length;
        allMatches.addAll(matches);
        if (showPairs) {
            pairs.addAll(matches);
            for (Coordinate c : FN) pairs.add(new PointPair(c, null));
            for (Coordinate c : FP) pairs.add(new PointPair(null, c));
        }
        if (fileResults != null) {
            // Matches are marked in the original value with 1 for true, 0 for false 
            for (PointPair pair : matches) {
                PeakResult p = ((PeakResultPoint) pair.getPoint2()).peakResult;
                fileResults.add(p.getFrame(), p.origX, p.origY, 1, p.error, p.noise, p.params, null);
            }
            for (Coordinate c : FP) {
                PeakResult p = ((PeakResultPoint) c).peakResult;
                fileResults.add(p.getFrame(), p.origX, p.origY, 0, p.error, p.noise, p.params, null);
            }
        }
    }
    if (fileResults != null)
        fileResults.end();
    // XXX : DEBUGGING : Output for signal correlation and fitting analysis
    /*
		 * try
		 * {
		 * OutputStreamWriter o = new OutputStreamWriter(new FileOutputStream("/tmp/ResultsMatchCalculator.txt"));
		 * FilePeakResults r1 = new FilePeakResults("/tmp/" + results1.getName() + ".txt", false);
		 * FilePeakResults r2 = new FilePeakResults("/tmp/" + results2.getName() + ".txt", false);
		 * r1.begin();
		 * r2.begin();
		 * //OutputStreamWriter o2 = new OutputStreamWriter(new FileOutputStream("/tmp/"+results1.getName()+".txt"));
		 * //OutputStreamWriter o3 = new OutputStreamWriter(new FileOutputStream("/tmp/"+results2.getName()+".txt"));
		 * for (PointPair pair : allMatches)
		 * {
		 * PeakResult p1 = ((PeakResultPoint) pair.getPoint1()).peakResult;
		 * PeakResult p2 = ((PeakResultPoint) pair.getPoint2()).peakResult;
		 * r1.add(p1);
		 * r2.add(p2);
		 * o.write(Float.toString(p1.getSignal()));
		 * o.write('\t');
		 * o.write(Float.toString(p2.getSignal()));
		 * o.write('\n');
		 * }
		 * o.close();
		 * r1.end();
		 * r2.end();
		 * }
		 * catch (Exception e)
		 * {
		 * e.printStackTrace();
		 * }
		 */
    boolean doIdAnalysis1 = (idAnalysis) ? haveIds(results1) : false;
    boolean doIdAnalysis2 = (idAnalysis) ? haveIds(results2) : false;
    boolean doIdAnalysis = doIdAnalysis1 || doIdAnalysis2;
    // Create output
    if (!java.awt.GraphicsEnvironment.isHeadless()) {
        String header = createResultsHeader(doIdAnalysis);
        Utils.refreshHeadings(resultsWindow, header, true);
        if (showTable && (resultsWindow == null || !resultsWindow.isShowing())) {
            resultsWindow = new TextWindow(TITLE + " Results", header, "", 900, 300);
        }
        if (showPairs) {
            if (pairsWindow == null || !pairsWindow.isShowing()) {
                pairsWindow = new TextWindow(TITLE + " Pairs", createPairsHeader(pairs), "", 900, 300);
                if (resultsWindow != null) {
                    Point p = resultsWindow.getLocation();
                    p.y += resultsWindow.getHeight();
                    pairsWindow.setLocation(p);
                }
                pairPainter = new ImageROIPainter(pairsWindow.getTextPanel(), "", this);
            }
            pairsWindow.getTextPanel().clear();
            String title = "Results 1";
            if (results1.getSource() != null && results1.getSource().getOriginal().getName().length() > 0)
                title = results1.getSource().getOriginal().getName();
            pairPainter.setTitle(title);
            IJ.showStatus("Writing pairs table");
            IJ.showProgress(0);
            int c = 0;
            final int total = pairs.size();
            final int step = Utils.getProgressInterval(total);
            final ArrayList<String> list = new ArrayList<String>(total);
            boolean flush = true;
            for (PointPair pair : pairs) {
                if (++c % step == 0)
                    IJ.showProgress(c, total);
                list.add(addPairResult(pair));
                if (flush && c == 9) {
                    pairsWindow.getTextPanel().append(list);
                    list.clear();
                    flush = false;
                }
            }
            pairsWindow.getTextPanel().append(list);
            IJ.showProgress(1);
        }
    } else {
        if (writeHeader && showTable) {
            writeHeader = false;
            IJ.log(createResultsHeader(idAnalysis));
        }
    }
    if (!showTable)
        return;
    // We have the results for the largest distance.
    // Now reduce the distance threshold and recalculate the results
    double[] distanceThresholds = getDistances(dThreshold, increments, delta);
    double[] pairDistances = getPairDistances(allMatches);
    // Re-use storage for the ID analysis
    TIntHashSet id1 = null, id2 = null, matchId1 = null, matchId2 = null;
    if (doIdAnalysis) {
        if (doIdAnalysis1) {
            id1 = getIds(results1);
            matchId1 = new TIntHashSet(id1.size());
        }
        if (doIdAnalysis2) {
            id2 = getIds(results2);
            matchId2 = new TIntHashSet(id2.size());
        }
    }
    for (double distanceThreshold : distanceThresholds) {
        double rms = 0;
        int tp2 = 0;
        final double d2 = distanceThreshold * distanceThreshold;
        for (double d : pairDistances) {
            if (d <= d2) {
                rms += d;
                tp2++;
            }
        }
        // All non-true positives must be added to the false totals.
        int fp2 = n2 - tp2;
        int fn2 = n1 - tp2;
        MatchResult result = new MatchResult(tp2, fp2, fn2, (tp2 > 0) ? Math.sqrt(rms / tp2) : 0);
        MatchResult idResult1 = null, idResult2 = null;
        if (doIdAnalysis) {
            if (doIdAnalysis1)
                matchId1.clear();
            if (doIdAnalysis2)
                matchId2.clear();
            int i = 0;
            for (PointPair pair : allMatches) {
                if (pairDistances[i++] <= d2) {
                    if (doIdAnalysis1)
                        matchId1.add(((PeakResultPoint) pair.getPoint1()).peakResult.getId());
                    if (doIdAnalysis2)
                        matchId2.add(((PeakResultPoint) pair.getPoint2()).peakResult.getId());
                }
            }
            // => Only the recall will be valid: tp / (tp + fn)
            if (doIdAnalysis1)
                idResult1 = new MatchResult(matchId1.size(), 0, id1.size() - matchId1.size(), 0);
            if (doIdAnalysis2)
                idResult2 = new MatchResult(matchId2.size(), 0, id2.size() - matchId2.size(), 0);
        }
        addResult(inputOption1, inputOption2, distanceThreshold, result, idResult1, idResult2);
    }
}
Also used : ArrayList(java.util.ArrayList) MatchResult(gdsc.core.match.MatchResult) PeakResult(gdsc.smlm.results.PeakResult) TIntHashSet(gnu.trove.set.hash.TIntHashSet) PointPair(gdsc.core.match.PointPair) ImageROIPainter(gdsc.smlm.ij.utils.ImageROIPainter) Point(java.awt.Point) BasePoint(gdsc.core.match.BasePoint) LinkedList(java.util.LinkedList) Point(java.awt.Point) BasePoint(gdsc.core.match.BasePoint) FilePeakResults(gdsc.smlm.results.FilePeakResults) TextWindow(ij.text.TextWindow) Coordinate(gdsc.core.match.Coordinate)

Example 29 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class IJTablePeakResults method createResultsWindow.

/**
	 * Create the result window (if it is not available)
	 */
private void createResultsWindow() {
    String header = createResultsHeader();
    ImageROIPainter roiPainter = null;
    for (Frame f : WindowManager.getNonImageWindows()) {
        if (f != null && tableTitle.equals(f.getTitle()) && f instanceof TextWindow) {
            resultsWindow = (TextWindow) f;
            // Check if the existing table matches the desired header
            String currentHeader = resultsWindow.getTextPanel().getColumnHeadings();
            if (!currentHeader.startsWith(header)) {
                resultsWindow = null;
                continue;
            }
            roiPainter = map.get(resultsWindow.getTextPanel());
            break;
        }
    }
    if (resultsWindow == null || !resultsWindow.isShowing()) {
        resultsWindow = new TextWindow(tableTitle, header, "", 800, 300);
        roiPainter = new ImageROIPainter(resultsWindow.getTextPanel(), "", this);
        // The ROI painter adds itself to the TextPanel as a mouse listener. However
        // the TextPanel addMouseListener() adds to the private TextCanvas object so it 
        // cannot be retrieved. Store the painter in a global lookup table.
        map.put(resultsWindow.getTextPanel(), roiPainter);
    }
    tp = resultsWindow.getTextPanel();
    if (roiPainter != null && getSource() != null) {
        roiPainter.setTitle(getSource().getOriginal().getName());
        // Update the coordinate provider (avoids memory leaks with old objects lying around)
        roiPainter.setCoordProvider(this);
        // Get the headings for extracting the coordinates 
        String[] headings = tp.getColumnHeadings().split("\t");
        for (int i = 0; i < headings.length; i++) {
            if (headings[i].equals(peakIdColumnName)) {
                indexT = i;
                continue;
            }
            if (headings[i].equals("X")) {
                indexX = i;
                continue;
            }
            if (headings[i].equals("Y")) {
                indexY = i;
                continue;
            }
        }
    }
}
Also used : Frame(java.awt.Frame) TextWindow(ij.text.TextWindow) ImageROIPainter(gdsc.smlm.ij.utils.ImageROIPainter)

Example 30 with TextWindow

use of ij.text.TextWindow in project GDSC-SMLM by aherbert.

the class TraceMatchCalculator method compareCoordinates.

private void compareCoordinates(MemoryPeakResults results1, MemoryPeakResults results2, MemoryPeakResults results3, double dThreshold) {
    Pulse[] p1 = extractPulses(results1);
    Pulse[] p2 = extractPulses(results2);
    Pulse[] p3 = extractPulses(results3);
    List<Pulse> TP = null;
    List<Pulse> FP = null;
    List<Pulse> FN = null;
    List<PointPair> pairs = null;
    List<Pulse> TP2 = null;
    List<Pulse> FP2 = null;
    List<Pulse> FN2 = null;
    List<PointPair> pairs2 = null;
    if (showPairs) {
        pairs = new LinkedList<PointPair>();
        FP = new LinkedList<Pulse>();
        FN = new LinkedList<Pulse>();
        pairs2 = new LinkedList<PointPair>();
        FP2 = new LinkedList<Pulse>();
        FN2 = new LinkedList<Pulse>();
    }
    MatchResult result = MatchCalculator.analyseResults2D(p1, p2, dThreshold, TP, FP, FN, pairs);
    MatchResult result2 = MatchCalculator.analyseResults2D(p1, p3, dThreshold, TP2, FP2, FN2, pairs2);
    // Create output
    if (!java.awt.GraphicsEnvironment.isHeadless()) {
        if (resultsWindow == null || !resultsWindow.isShowing()) {
            resultsWindow = new TextWindow(TITLE + " Results", createResultsHeader(), "", 900, 300);
        }
        if (showPairs) {
            if (p3 == null) {
                // Produce a pairs output
                if (pairsWindow == null || !pairsWindow.isShowing()) {
                    pairsWindow = new TextWindow(TITLE + " Pairs", createPairsHeader(), "", 900, 300);
                    Point p = resultsWindow.getLocation();
                    p.y += resultsWindow.getHeight();
                    pairsWindow.setLocation(p);
                    pairPainter = new ImageROIPainter(pairsWindow.getTextPanel(), results1.getSource().getOriginal().getName(), this);
                }
                pairsWindow.getTextPanel().clear();
                pairPainter.setTitle(results1.getSource().getOriginal().getName());
                // Add the unmatched points
                for (Coordinate c : FN) pairs.add(new PointPair(c, null));
                for (Coordinate c : FP) pairs.add(new PointPair(null, c));
                List<? extends PointPair> sortedPairs = sort(pairs);
                for (PointPair pair : sortedPairs) addPairResult(pair);
            } else {
                // Produce a triple output
                if (triplesWindow == null || !triplesWindow.isShowing()) {
                    triplesWindow = new TextWindow(TITLE + " Triples", createTriplesHeader(), "", 900, 300);
                    Point p = resultsWindow.getLocation();
                    p.y += resultsWindow.getHeight();
                    triplesWindow.setLocation(p);
                    triplePainter = new ImageROIPainter(triplesWindow.getTextPanel(), results1.getSource().getName(), this);
                }
                triplesWindow.getTextPanel().clear();
                triplePainter.setTitle(results1.getSource().getOriginal().getName());
                HashMap<Pulse, Triple> map = new HashMap<Pulse, Triple>();
                ArrayList<Triple> triples = new ArrayList<Triple>(pairs.size());
                for (PointPair pair : pairs) {
                    Pulse p = (Pulse) pair.getPoint1();
                    Triple t = new Triple(p, (Pulse) pair.getPoint2(), null);
                    triples.add(t);
                    map.put(p, t);
                }
                // Complete the reference set of points
                for (Coordinate c : FN) {
                    Pulse p = (Pulse) c;
                    Triple t = new Triple(p, null, null);
                    triples.add(t);
                    map.put(p, t);
                }
                // Add the unmatched points
                for (Coordinate c : FP) triples.add(new Triple(null, (Pulse) c, null));
                for (Coordinate c : FP2) triples.add(new Triple(null, null, (Pulse) c));
                // Add the results from the second match
                for (PointPair pair : pairs2) {
                    Pulse p = (Pulse) pair.getPoint1();
                    Pulse pp = (Pulse) pair.getPoint2();
                    Triple t = map.get(p);
                    if (t != null) {
                        t.p3 = pp;
                    } else {
                        triples.add(new Triple(null, null, pp));
                    }
                }
                List<? extends Triple> sortedTriples = sort(triples);
                for (Triple t : sortedTriples) addTripleResult(t);
            }
        }
    } else {
        if (writeHeader) {
            writeHeader = false;
            IJ.log(createResultsHeader());
        }
    }
    addResult(inputOption1, inputOption2, dThreshold, result);
    if (p3 != null)
        addResult(inputOption1, inputOption3, dThreshold, result2);
}
Also used : HashMap(java.util.HashMap) Pulse(gdsc.core.match.Pulse) ArrayList(java.util.ArrayList) Point(java.awt.Point) MatchResult(gdsc.core.match.MatchResult) TextWindow(ij.text.TextWindow) Coordinate(gdsc.core.match.Coordinate) PointPair(gdsc.core.match.PointPair) ImageROIPainter(gdsc.smlm.ij.utils.ImageROIPainter)

Aggregations

TextWindow (ij.text.TextWindow)61 Point (java.awt.Point)11 BufferedTextWindow (uk.ac.sussex.gdsc.core.ij.BufferedTextWindow)11 BufferedTextWindow (gdsc.core.ij.BufferedTextWindow)7 ArrayList (java.util.ArrayList)6 PointPair (uk.ac.sussex.gdsc.core.match.PointPair)5 IJ (ij.IJ)4 ImagePlus (ij.ImagePlus)4 LinkedList (java.util.LinkedList)4 Coordinate (uk.ac.sussex.gdsc.core.match.Coordinate)4 ImageROIPainter (gdsc.smlm.ij.utils.ImageROIPainter)3 List (java.util.List)3 PeakResultPoint (uk.ac.sussex.gdsc.smlm.results.PeakResultPoint)3 Coordinate (gdsc.core.match.Coordinate)2 MatchResult (gdsc.core.match.MatchResult)2 PointPair (gdsc.core.match.PointPair)2 TIntHashSet (gnu.trove.set.hash.TIntHashSet)2 GenericDialog (ij.gui.GenericDialog)2 ImageWindow (ij.gui.ImageWindow)2 PlotWindow (ij.gui.PlotWindow)2