Examples with MemoryPeakResults uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults used on opensource projects

Example 11 with MemoryPeakResults

use of uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults in project GDSC-SMLM by aherbert.

the class PeakFit method showResults.

/**
 * Show results.
 */
protected void showResults() {
    IJ.showProgress(1.0);
    if (time >= 0) {
        if (silent) {
            results.end();
            return;
        }
        // Check if we are sorting
        IJ.showStatus("Finalising results ...");
        for (final PeakResults r : results.toArray()) {
            if (r instanceof MemoryPeakResults) {
                if (((MemoryPeakResults) r).isSortAfterEnd()) {
                    IJ.showStatus("Sorting " + r.size() + " results ...");
                }
                break;
            }
        }
        results.end();
        final String textTime = TextUtils.nanosToString(time);
        final String textRunTime = TextUtils.nanosToString(runTime);
        final int size = getSize();
        final String message = String.format("%s. Total fitting time = %s. Run time = %s", TextUtils.pleural(size, "localisation"), textTime, textRunTime);
        if (resultsSettings.getLogProgress()) {
            IJ.log(LOG_SPACER);
        }
        IJ.log(message);
        IJ.showStatus(message);
    } else {
        IJ.showStatus("");
    }
}

Example 12 with MemoryPeakResults

use of uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults in project GDSC-SMLM by aherbert.

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus localImp = this.imp;
    if (fitMaxima && singleFrame > 0 && source instanceof IJImageSource) {
        final String title = source.getName();
        localImp = WindowManager.getImage(title);
    }
    if (singleFrame > 0 && localImp != null) {
        MemoryPeakResults memoryResults = null;
        for (final PeakResults r : this.results.toArray()) {
            if (r instanceof MemoryPeakResults) {
                memoryResults = (MemoryPeakResults) r;
                break;
            }
        }
        if (memoryResults == null || memoryResults.size() == 0) {
            return;
        }
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed()) {
            return;
        }
        final LUT lut = LutHelper.createLut(LutColour.ICE);
        final Overlay o = new Overlay();
        final int size = memoryResults.size();
        final Counter j = new Counter(size);
        final ImagePlus finalImp = localImp;
        memoryResults.forEach(DistanceUnit.PIXEL, (XyResultProcedure) (x, y) -> {
            final PointRoi roi = new OffsetPointRoi(x, y);
            final Color c = LutHelper.getColour(lut, j.decrementAndGet(), size);
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (finalImp.getStackSize() > 1) {
                roi.setPosition(singleFrame);
            }
            o.add(roi);
        });
        localImp.setOverlay(o);
        localImp.getWindow().toFront();
    }
}

Example 13 with MemoryPeakResults

use of uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults in project GDSC-SMLM by aherbert.

the class PeakFit method setup.

@Override
public int setup(String arg, ImagePlus imp) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    pluginFlags = FLAGS;
    extraOptions = ImageJUtils.isExtraOptions();
    maximaIdentification = StringUtils.contains(arg, "spot");
    fitMaxima = StringUtils.contains(arg, "maxima");
    simpleFit = StringUtils.contains(arg, "simple");
    final boolean runSeries = StringUtils.contains(arg, "series");
    ImageSource imageSource = null;
    if (fitMaxima) {
        // The image source will be found from the peak results.
        if (!showMaximaDialog()) {
            return DONE;
        }
        final MemoryPeakResults localResults = ResultsManager.loadInputResults(settings.inputOption, false, DistanceUnit.PIXEL);
        if (localResults == null || localResults.size() == 0) {
            IJ.error(TITLE, "No results could be loaded");
            return DONE;
        }
        if (settings.fitAcrossAllFrames) {
            // Allow the user to select a different image. The source will be set as per the
            // main fit routine from the image (imp).
            singleFrame = 0;
        } else {
            // Check for single frame
            singleFrame = getSingleFrame(localResults);
            // Forces the maxima to be used with their original source.
            imp = null;
            imageSource = localResults.getSource();
            pluginFlags |= NO_IMAGE_REQUIRED;
        }
    } else if (runSeries) {
        imp = null;
        // Select input folder
        final String inputDirectory = IJ.getDirectory("Select image series ...");
        if (inputDirectory == null) {
            return DONE;
        }
        // Load input series ...
        SeriesOpener series;
        if (extraOptions) {
            final String helpKey = maximaIdentification ? "spot-finder-series" : "peak-fit-series";
            series = SeriesOpener.create(inputDirectory, true, HelpUrls.getUrl(helpKey));
        } else {
            series = new SeriesOpener(inputDirectory);
        }
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory);
            return DONE;
        }
        final SeriesImageSource seriesImageSource = new SeriesImageSource(getName(series.getImageList()), series);
        // TrackProgress logging is very verbose if the series has many images
        // Status is used only when reading TIFF info.
        // seriesImageSource.setTrackProgress(SimpleImageJTrackProgress.getInstance());
        seriesImageSource.setTrackProgress(new TrackProgressAdaptor() {

            @Override
            public void status(String format, Object... args) {
                ImageJUtils.showStatus(() -> String.format(format, args));
            }
        });
        imageSource = seriesImageSource;
        pluginFlags |= NO_IMAGE_REQUIRED;
    }
    // If the image source has not been set then use the input image
    if (imageSource == null) {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }
        // Check it is not a previous result
        if (imp.getTitle().endsWith(ImageJImagePeakResults.IMAGE_SUFFIX)) {
            IJImageSource ijImageSource = null;
            // Check the image to see if it has an image source XML structure in the info property
            final Object o = imp.getProperty("Info");
            final Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL);
            final Matcher match = pattern.matcher((o == null) ? "" : o.toString());
            if (match.find()) {
                final ImageSource tmpSource = ImageSource.fromXml(match.group(1));
                if (tmpSource instanceof IJImageSource) {
                    ijImageSource = (IJImageSource) tmpSource;
                    if (!ijImageSource.open()) {
                        ijImageSource = null;
                    } else {
                        imp = WindowManager.getImage(ijImageSource.getName());
                    }
                }
            }
            if (ijImageSource == null) {
                // Look for a parent using the title
                final String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - ImageJImagePeakResults.IMAGE_SUFFIX.length() - 1);
                final ImagePlus parentImp = WindowManager.getImage(parentTitle);
                if (parentImp != null) {
                    ijImageSource = new IJImageSource(parentImp);
                    imp = parentImp;
                }
            }
            String message = "The selected image may be a previous fit result";
            if (ijImageSource != null) {
                if (!TextUtils.isNullOrEmpty(ijImageSource.getName())) {
                    message += " of: \n \n" + ijImageSource.getName();
                }
                message += " \n \nFit the parent?";
            } else {
                message += " \n \nDo you want to continue?";
            }
            final YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message);
            if (ijImageSource == null) {
                if (!d.yesPressed()) {
                    return DONE;
                }
            } else {
                if (d.yesPressed()) {
                    imageSource = ijImageSource;
                }
                if (d.cancelPressed()) {
                    return DONE;
                }
            }
        }
        if (imageSource == null) {
            try {
                imageSource = new IJImageSource(imp);
            } catch (final IllegalArgumentException ex) {
                // This can happen if the image has an origin not in integer pixels
                // e.g. the plugin is run on a plot
                IJ.error(TITLE, "Error using image: " + imp.getTitle() + "\n \n" + ex.getMessage());
                return DONE;
            }
        }
    }
    time = -1;
    if (!initialiseImage(imageSource, getBounds(imp), false)) {
        IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName());
        return DONE;
    }
    final int flags = showDialog(imp);
    if ((flags & DONE) == 0) {
        initialiseFitting();
    }
    return flags;
}

Example 14 with MemoryPeakResults

use of uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults in project GDSC-SMLM by aherbert.

the class TraceExporter method exportSpotOn.

private void exportSpotOn(MemoryPeakResults results) {
    try (BufferedWriter out = Files.newBufferedWriter(Paths.get(settings.directory, results.getName() + ".csv"))) {
        out.write("frame,t,trajectory,x,y");
        out.newLine();
        final TypeConverter<TimeUnit> converter = UnitConverterUtils.createConverter(TimeUnit.FRAME, TimeUnit.SECOND, results.getCalibrationReader().getExposureTime());
        @SuppressWarnings("resource") final BufferedWriter writer = out;
        results.forEach(DistanceUnit.UM, (XyrResultProcedure) (x, y, result) -> {
            try {
                if (result.hasEndFrame()) {
                    final String sId = Integer.toString(result.getId());
                    final String sx = Float.toString(x);
                    final String sy = Float.toString(y);
                    for (int t = result.getFrame(); t <= result.getEndFrame(); t++) {
                        writer.write(Integer.toString(t));
                        writer.write(",");
                        writer.write(Float.toString(converter.convert(t)));
                        writer.write(",");
                        writer.write(sId);
                        writer.write(",");
                        writer.write(sx);
                        writer.write(",");
                        writer.write(sy);
                        writer.newLine();
                    }
                } else {
                    writer.write(Integer.toString(result.getFrame()));
                    writer.write(",");
                    writer.write(Float.toString(converter.convert(result.getFrame())));
                    writer.write(",");
                    writer.write(Integer.toString(result.getId()));
                    writer.write(",");
                    writer.write(Float.toString(x));
                    writer.write(",");
                    writer.write(Float.toString(y));
                    writer.newLine();
                }
            } catch (final IOException ex) {
                throw new RuntimeException(ex);
            }
        });
    } catch (final IOException | RuntimeException ex) {
        handleException(ex);
    }
}

Example 15 with MemoryPeakResults

use of uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults in project GDSC-SMLM by aherbert.

the class TraceExporter method exportVbSpt.

@SuppressWarnings("resource")
private void exportVbSpt(MemoryPeakResults results) {
    // vbSPT file format:
    // https://sourceforge.net/projects/vbspt/
    // Matlab matrix file (.mat) containing at least one variable that is a cell
    // array where each element, representing a trajectory, is a matrix
    // where the rows define the coordinates in one, two or three dimensions
    // in subsequent timesteps. The number of dimensions to be used for the
    // analysis will be set by the runinputfile.
    // The units are arbitrary but vbSPT starting estimates must be in the same
    // units. Either nm or μm are recommended.
    // 3 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. z coordinate (μm)
    // 
    // Note: An extra column is added containing the frame. This allows results to
    // be uniquely identified using frame,x,y,z
    // Count the IDs. Each new result ID will increment the count.
    final FrameCounter idCounter = new FrameCounter(results.getFirst().getId() - 1);
    results.forEach((PeakResultProcedure) result -> {
        if (idCounter.advance(result.getId())) {
            idCounter.increment();
        }
    });
    // Create the cell array as 1xN
    final Cell out = Mat5.newCell(1, idCounter.getCount());
    // This will reset the counter to zero and ensure the current frame does not match
    // in the event of a single track
    idCounter.advanceAndReset(idCounter.currentFrame() + 1);
    final boolean is3d = results.is3D();
    // Write the tracks
    final LocalList<double[]> list = new LocalList<>();
    results.forEach(DistanceUnit.UM, (XyzrResultProcedure) (x, y, z, result) -> {
        if (idCounter.advance(result.getId())) {
            addTrack(out, idCounter.getCount() - 1, list, is3d);
            idCounter.increment();
            list.clear();
        }
        list.add(new double[] { x, y, z, result.getFrame() });
    });
    addTrack(out, idCounter.getCount() - 1, list, is3d);
    try (MatFile matFile = Mat5.newMatFile()) {
        matFile.addArray("tracks", out);
        Mat5.writeToFile(matFile, Paths.get(settings.directory, results.getName() + ".mat").toFile());
    } catch (final IOException ex) {
        handleException(ex);
    }
}