Examples with MemoryPeakResults gdsc.smlm.results.MemoryPeakResults used on opensource projects

Example 31 with MemoryPeakResults

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

the class RenameResults method renameResults.

private int renameResults() {
    // Start with the original names for the mapping from old to new
    HashMap<String, String> mappedNames = new HashMap<String, String>();
    for (String name : MemoryPeakResults.getResultNames()) mappedNames.put(name, name);
    // Get the new names
    String[] lines = renameText.split("[;\n]");
    for (String line : lines) {
        String[] fields = line.split("[=]");
        if (fields.length == 2) {
            String oldName = fields[0].trim();
            String newName = fields[1].trim();
            if (!mappedNames.containsKey(oldName)) {
                IJ.error(TITLE, "An unknown original name has been specified: " + oldName);
                return 0;
            }
            if (oldName.equals(newName))
                // No update required
                continue;
            mappedNames.put(oldName, newName);
        }
    }
    // Check the new names are unique
    Set<String> newNames = new HashSet<String>();
    for (String newName : mappedNames.values()) {
        if (newNames.contains(newName)) {
            IJ.error(TITLE, "A duplicate new name has been specified: " + newName);
            return 0;
        }
        newNames.add(newName);
    }
    // Rename
    List<MemoryPeakResults> renamedResults = new LinkedList<MemoryPeakResults>();
    for (Entry<String, String> entry : mappedNames.entrySet()) {
        if (entry.getKey().equals(entry.getValue()))
            continue;
        // Remove from memory and store in a list
        MemoryPeakResults results = MemoryPeakResults.removeResults(entry.getKey());
        if (results != null) {
            results.setName(entry.getValue());
            renamedResults.add(results);
        }
    }
    // Add back to memory
    for (MemoryPeakResults results : renamedResults) MemoryPeakResults.addResults(results);
    return renamedResults.size();
}

Example 32 with MemoryPeakResults

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

the class PeakFit method addMemoryResults.

private void addMemoryResults(PeakResultsList resultsList, boolean force) {
    if (resultsSettings.resultsInMemory || force) {
        MemoryPeakResults results = new MemoryPeakResults();
        results.setSortAfterEnd(Prefs.getThreads() > 1);
        resultsList.addOutput(results);
        MemoryPeakResults.addResults(results);
    }
}

Example 33 with MemoryPeakResults

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

the class PeakFit method setup.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
	 */
public int setup(String arg, ImagePlus imp) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    plugin_flags = FLAGS;
    extraOptions = Utils.isExtraOptions();
    maximaIdentification = (arg != null && arg.contains("spot"));
    fitMaxima = (arg != null && arg.contains("maxima"));
    simpleFit = (arg != null && arg.contains("simple"));
    boolean runSeries = (arg != null && arg.contains("series"));
    ImageSource imageSource = null;
    if (fitMaxima) {
        imp = null;
        // The image source will be found from the peak results.
        if (!showMaximaDialog())
            return DONE;
        MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
        if (results == null || results.size() == 0) {
            IJ.error(TITLE, "No results could be loaded");
            return DONE;
        }
        // Check for single frame
        singleFrame = results.getHead().getFrame();
        for (PeakResult result : results.getResults()) {
            if (singleFrame != result.getFrame()) {
                singleFrame = 0;
                break;
            }
        }
        imageSource = results.getSource();
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else if (runSeries) {
        imp = null;
        // Select input folder
        String inputDirectory;
        inputDirectory = IJ.getDirectory("Select image series ...");
        //inputDirectory = getInputDirectory("Select image series ...");
        if (inputDirectory == null)
            return DONE;
        // Load input series ...
        SeriesOpener series;
        if (extraOptions)
            series = new SeriesOpener(inputDirectory, true, numberOfThreads);
        else
            series = new SeriesOpener(inputDirectory);
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory);
            return DONE;
        }
        SeriesImageSource seriesImageSource = new SeriesImageSource(getName(series.getImageList()), series);
        seriesImageSource.setLogProgress(true);
        if (extraOptions) {
            numberOfThreads = Math.max(1, series.getNumberOfThreads());
            seriesImageSource.setNumberOfThreads(numberOfThreads);
        }
        imageSource = seriesImageSource;
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }
        // Check it is not a previous result
        if (imp.getTitle().endsWith(IJImagePeakResults.IMAGE_SUFFIX)) {
            IJImageSource tmpImageSource = null;
            // Check the image to see if it has an image source XML structure in the info property
            Object o = imp.getProperty("Info");
            Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL);
            Matcher match = pattern.matcher((o == null) ? "" : o.toString());
            if (match.find()) {
                ImageSource source = ImageSource.fromXML(match.group(1));
                if (source instanceof IJImageSource) {
                    tmpImageSource = (IJImageSource) source;
                    if (!tmpImageSource.open()) {
                        tmpImageSource = null;
                    } else {
                        imp = WindowManager.getImage(tmpImageSource.getName());
                    }
                }
            }
            if (tmpImageSource == null) {
                // Look for a parent using the title
                String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - IJImagePeakResults.IMAGE_SUFFIX.length() - 1);
                ImagePlus parentImp = WindowManager.getImage(parentTitle);
                if (parentImp != null) {
                    tmpImageSource = new IJImageSource(parentImp);
                    imp = parentImp;
                }
            }
            String message = "The selected image may be a previous fit result";
            if (tmpImageSource != null) {
                // are missing
                if (!Utils.isNullOrEmpty(tmpImageSource.getName()))
                    message += " of: \n \n" + tmpImageSource.getName();
                message += " \n \nFit the parent?";
            } else
                message += " \n \nDo you want to continue?";
            YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message);
            if (tmpImageSource == null) {
                if (!d.yesPressed())
                    return DONE;
            } else {
                if (d.yesPressed())
                    imageSource = tmpImageSource;
                if (d.cancelPressed())
                    return DONE;
            }
        }
        if (imageSource == null)
            imageSource = new IJImageSource(imp);
    }
    time = -1;
    if (!initialiseImage(imageSource, getBounds(imp), false)) {
        IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName());
        return DONE;
    }
    int flags = showDialog(imp);
    if ((flags & DONE) == 0) {
        // Repeat so that we pass in the selected option for ignoring the bounds.
        // This should not be necessary since it is set within the readDialog method.
        //if (ignoreBoundsForNoise)
        //	initialiseImage(imageSource, bounds, ignoreBoundsForNoise);
        initialiseFitting();
    }
    return flags;
}

Example 34 with MemoryPeakResults

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

the class PulseActivationAnalysis method createOutput.

private PeakResultsList createOutput(int c) {
    PeakResultsList output = new PeakResultsList();
    output.copySettings(results);
    if (channels > 1)
        output.setName(results.getName() + " " + TITLE + " C" + c);
    else
        output.setName(results.getName() + " " + TITLE);
    // Store the set in memory
    MemoryPeakResults memoryResults = new MemoryPeakResults(this.results.size());
    output.addOutput(memoryResults);
    MemoryPeakResults.addResults(memoryResults);
    // Draw the super-resolution image
    Rectangle bounds = results.getBounds(true);
    addImageResults(output, results.getName(), bounds, results.getNmPerPixel(), results.getGain());
    output.begin();
    return output;
}

Example 35 with MemoryPeakResults

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

the class ResultsManagerTest method writeTSFMatchesRead.

private void writeTSFMatchesRead(int channels, int slices, int positions, int types) {
    String filename = createFile();
    FileOutputStream out = null;
    try {
        out = new FileOutputStream(filename);
    } catch (Exception e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Write the offsets used in the TSF format
    try {
        DataOutputStream dos = new DataOutputStream(out);
        dos.writeInt(0);
        dos.writeLong(0);
    } catch (IOException e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Generate random spots
    int size = 1000;
    Spot[] spots = new Spot[size];
    for (int i = 1; i <= size; i++) {
        Spot.Builder builder = Spot.newBuilder();
        builder.setChannel(1 + rand.nextInt(channels));
        builder.setSlice(1 + rand.nextInt(slices));
        builder.setPos(1 + rand.nextInt(positions));
        builder.setFluorophoreType(rand.nextInt(1, types));
        // This is a required field but is ignored when reading
        builder.setMolecule(i);
        builder.setCluster(rand.nextInt(10));
        builder.setFrame(rand.nextInt(1, 100));
        builder.setXPosition(rand.nextInt(50));
        builder.setYPosition(rand.nextInt(50));
        builder.setBackground(rand.next());
        builder.setIntensity(rand.next());
        builder.setX(rand.next());
        builder.setY(rand.next());
        builder.setWidth(TSFPeakResultsWriter.SD_TO_FWHM_FACTOR * rand.next());
        Spot spot = builder.build();
        spots[i - 1] = spot;
        try {
            spot.writeDelimitedTo(out);
        } catch (IOException e) {
            closeOutput(out);
            e.printStackTrace();
            Assert.fail(e.getMessage());
        }
    }
    // Write the header
    // Get the offset to the SpotList message
    long offset = 0;
    try {
        // The offset is the amount to skip forward after reading the int 
        // magic number (4 bytes) and long offset (8 bytes)
        //out.flush();
        offset = out.getChannel().position() - 12;
    } catch (IOException e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Record the SpotList message
    SpotList.Builder builder = SpotList.newBuilder();
    builder.setApplicationId(1);
    builder.setNrSpots(size);
    builder.setLocationUnits(LocationUnits.PIXELS);
    builder.setIntensityUnits(IntensityUnits.COUNTS);
    builder.setFitMode(FitMode.ONEAXIS);
    builder.setNrChannels(channels);
    builder.setNrSlices(slices);
    builder.setNrPos(positions);
    for (int type = 1; type <= types; type++) {
        FluorophoreType.Builder typeBuilder = FluorophoreType.newBuilder();
        typeBuilder.setId(type);
        typeBuilder.setDescription("Type " + type);
        typeBuilder.setIsFiducial(rand.next() < 0.5f);
        builder.addFluorophoreTypes(typeBuilder.build());
    }
    SpotList spotList = builder.build();
    try {
        spotList.writeDelimitedTo(out);
    } catch (IOException e) {
        e.printStackTrace();
        Assert.fail(e.getMessage());
    } finally {
        closeOutput(out);
    }
    // Write the offset to the SpotList message into the offset position
    RandomAccessFile f = null;
    try {
        f = new RandomAccessFile(new File(filename), "rw");
        f.seek(4);
        f.writeLong(offset);
    } catch (Exception e) {
        e.printStackTrace();
        Assert.fail(e.getMessage());
    } finally {
        if (f != null) {
            try {
                f.close();
            } catch (IOException e) {
            }
        }
    }
    // Read each combination 
    for (int channel = 1; channel <= channels; channel++) for (int slice = 1; slice <= slices; slice++) for (int position = 1; position <= positions; position++) for (int type = 1; type <= types; type++) {
        StringBuilder sb = new StringBuilder();
        sb.append(" channel=").append(channel);
        sb.append(" slice=").append(slice);
        sb.append(" position=").append(position);
        sb.append(" fluorophore_type=[").append(type).append(":Type ").append(type).append(":fiducial=").append(builder.getFluorophoreTypes(type - 1).getIsFiducial()).append(']');
        // This is needed to trick the Macro class into returning the options 
        // for the thread to the GenericDialog used in the ResultsManager
        Thread.currentThread().setName("Run$_");
        Macro.setOptions(sb.toString());
        ResultsManager.setInputFilename(filename);
        MemoryPeakResults in = ResultsManager.loadInputResults(ResultsManager.INPUT_FILE, false);
        checkEqual(spots, channel, slice, position, type, in);
    }
}