Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 1 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PSFDrift method createImageList.

public static List<String> createImageList() {
    List<String> titles = new LinkedList<String>();
    int[] ids = WindowManager.getIDList();
    if (ids != null) {
        for (int id : ids) {
            ImagePlus imp = WindowManager.getImage(id);
            if (imp != null) {
                // Image must be greyscale
                if (imp.getType() == ImagePlus.GRAY8 || imp.getType() == ImagePlus.GRAY16 || imp.getType() == ImagePlus.GRAY32) {
                    // Image must be square and a stack of a single channel
                    if (imp.getWidth() == imp.getHeight() && imp.getNChannels() == 1) {
                        // Check if these are PSF images created by the SMLM plugins
                        PSFSettings psfSettings = getPSFSettings(imp);
                        if (psfSettings != null) {
                            if (psfSettings.zCentre <= 0) {
                                Utils.log(TITLE + ": Unknown PSF z-centre setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.nmPerPixel <= 0) {
                                Utils.log(TITLE + ": Unknown PSF nm/pixel setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.nmPerSlice <= 0) {
                                Utils.log(TITLE + ": Unknown PSF nm/slice setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.fwhm <= 0) {
                                Utils.log(TITLE + ": Unknown PSF FWHM setting for image: " + imp.getTitle());
                                continue;
                            }
                            titles.add(imp.getTitle());
                        }
                    }
                }
            }
        }
    }
    return titles;
}

Example 2 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PSFCombiner method createImageList.

public static List<String> createImageList() {
    List<String> titles = new LinkedList<String>();
    int[] ids = WindowManager.getIDList();
    if (ids != null) {
        for (int id : ids) {
            ImagePlus imp = WindowManager.getImage(id);
            if (imp != null) {
                // Image must be greyscale
                if (imp.getType() == ImagePlus.GRAY8 || imp.getType() == ImagePlus.GRAY16 || imp.getType() == ImagePlus.GRAY32) {
                    // Image must be square and a stack of a single channel
                    if (imp.getWidth() == imp.getHeight() && imp.getNChannels() == 1) {
                        // Check if these are PSF images created by the SMLM plugins
                        if (containsPSF(imp))
                            titles.add(imp.getTitle());
                    }
                }
            }
        }
    }
    return titles;
}

Example 3 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class ResultsImageSampler method getSample.

/**
	 * Gets the sample image. The image is a stack of the samples with an overlay of the localisation positions. The
	 * info property is set with details of the localisations and the image is calibrated.
	 *
	 * @param nNo
	 *            the number of samples with no localisations
	 * @param nLow
	 *            the number of samples with low localisations
	 * @param nHigh
	 *            the number of samples with high localisations
	 * @return the sample image (could be null if no samples were made)
	 */
public ImagePlus getSample(int nNo, int nLow, int nHigh) {
    ImageStack out = new ImageStack(size, size);
    if (!isValid())
        return null;
    list.clearf();
    // empty
    for (int i : Random.sample(nNo, no.length, r)) list.add(ResultsSample.createEmpty(no[i]));
    // low
    for (int i : Random.sample(nLow, lower, r)) list.add(data[i]);
    // high
    for (int i : Random.sample(nHigh, upper, r)) list.add(data[i + lower]);
    if (list.isEmpty())
        return null;
    double nmPerPixel = 1;
    if (results.getCalibration() != null) {
        Calibration calibration = results.getCalibration();
        if (calibration.hasNmPerPixel()) {
            nmPerPixel = calibration.getNmPerPixel();
        }
    }
    // Sort descending by number in the frame
    ResultsSample[] sample = list.toArray(new ResultsSample[list.size()]);
    Arrays.sort(sample, rcc);
    int[] xyz = new int[3];
    Rectangle stackBounds = new Rectangle(stack.getWidth(), stack.getHeight());
    Overlay overlay = new Overlay();
    float[] ox = new float[10], oy = new float[10];
    StringBuilder sb = new StringBuilder();
    if (nmPerPixel == 1)
        sb.append("Sample X Y Z Signal\n");
    else
        sb.append("Sample X(nm) Y(nm) Z(nm) Signal\n");
    for (ResultsSample s : sample) {
        getXYZ(s.index, xyz);
        // Construct the region to extract
        Rectangle target = new Rectangle(xyz[0], xyz[1], size, size);
        target = target.intersection(stackBounds);
        if (target.width == 0 || target.height == 0)
            continue;
        // Extract the frame
        int slice = xyz[2];
        ImageProcessor ip = stack.getProcessor(slice);
        // Cut out the desired pixels (some may be blank if the block overruns the source image)
        ImageProcessor ip2 = ip.createProcessor(size, size);
        for (int y = 0; y < target.height; y++) for (int x = 0, i = y * size, index = (y + target.y) * ip.getWidth() + target.x; x < target.width; x++, i++, index++) {
            ip2.setf(i, ip.getf(index));
        }
        int size = s.size();
        if (size > 0) {
            int position = out.getSize() + 1;
            // Create an ROI with the localisations
            for (int i = 0; i < size; i++) {
                PeakResult p = s.list.get(i);
                ox[i] = p.getXPosition() - xyz[0];
                oy[i] = p.getYPosition() - xyz[1];
                sb.append(position).append(' ');
                sb.append(Utils.rounded(ox[i] * nmPerPixel)).append(' ');
                sb.append(Utils.rounded(oy[i] * nmPerPixel)).append(' ');
                // Z can be stored in the error field
                sb.append(Utils.rounded(p.error * nmPerPixel)).append(' ');
                sb.append(Utils.rounded(p.getSignal())).append('\n');
            }
            PointRoi roi = new PointRoi(ox, oy, size);
            roi.setPosition(position);
            overlay.add(roi);
        }
        out.addSlice(String.format("Frame=%d @ %d,%d px (n=%d)", slice, xyz[0], xyz[1], size), ip2.getPixels());
    }
    if (out.getSize() == 0)
        return null;
    ImagePlus imp = new ImagePlus("Sample", out);
    imp.setOverlay(overlay);
    // Note: Only the info property can be saved to a TIFF file
    imp.setProperty("Info", sb.toString());
    if (nmPerPixel != 1) {
        ij.measure.Calibration cal = new ij.measure.Calibration();
        cal.setUnit("nm");
        cal.pixelHeight = cal.pixelWidth = nmPerPixel;
        imp.setCalibration(cal);
    }
    return imp;
}

Example 4 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PCPALMMolecules method getRunMode.

private boolean getRunMode(boolean resultsAvailable) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    // Build a list of all images with a region ROI
    List<String> titles = new LinkedList<String>();
    if (WindowManager.getWindowCount() > 0) {
        for (int imageID : WindowManager.getIDList()) {
            ImagePlus imp = WindowManager.getImage(imageID);
            if (imp != null && imp.getRoi() != null && imp.getRoi().isArea())
                titles.add(imp.getTitle());
        }
    }
    if (!resultsAvailable) {
        runMode = 3;
        gd.addMessage("Simulate molecules for cluster analysis.\nComputes a binary image from localisation data");
        gd.addNumericField("Molecules", nMolecules, 0);
        gd.addNumericField("Simulation_size (um)", simulationSize, 2);
        gd.addNumericField("Blinking_rate", blinkingRate, 2);
        gd.addChoice("Blinking_distribution", BLINKING_DISTRIBUTION, BLINKING_DISTRIBUTION[blinkingDistribution]);
        gd.addNumericField("Average_precision (nm)", sigmaS, 2);
        gd.addCheckbox("Show_histograms", showHistograms);
        gd.addCheckbox("Distance_analysis", distanceAnalysis);
        gd.addChoice("Cluster_simulation", CLUSTER_SIMULATION, CLUSTER_SIMULATION[clusterSimulation]);
        gd.addNumericField("Cluster_number", clusterNumber, 2);
        gd.addNumericField("Cluster_variation (SD)", clusterNumberSD, 2);
        gd.addNumericField("Cluster_radius", clusterRadius, 2);
        gd.addCheckbox("Show_cluster_mask", showClusterMask);
        Recorder.recordOption("Run_mode", RUN_MODE[runMode]);
    } else {
        gd.addMessage("Prepare molecules for cluster analysis.\nComputes a binary image from raw localisation data");
        ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
        if (!titles.isEmpty())
            gd.addCheckbox((titles.size() == 1) ? "Use_ROI" : "Choose_ROI", chooseRoi);
        gd.addChoice("Run_mode", RUN_MODE, RUN_MODE[runMode]);
    }
    gd.addMessage("Select options for low resolution image:");
    gd.addSlider("Image_size (px)", 512, 2048, lowResolutionImageSize);
    gd.addSlider("ROI_size (um)", 1.5, 4, roiSizeInUm);
    gd.addMessage("Select options for high resolution image:");
    gd.addCheckbox("Show_high_res_image", showHighResolutionImage);
    gd.addSlider("nm_per_pixel_limit", 0, 20, nmPerPixelLimit);
    gd.addMessage("Optionally remove all analysis results from memory");
    gd.addCheckbox("Clear_results", clearResults);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    if (!resultsAvailable) {
        nMolecules = (int) Math.abs(gd.getNextNumber());
        simulationSize = Math.abs(gd.getNextNumber());
        blinkingRate = Math.abs(gd.getNextNumber());
        blinkingDistribution = gd.getNextChoiceIndex();
        sigmaS = Math.abs(gd.getNextNumber());
        showHistograms = gd.getNextBoolean();
        distanceAnalysis = gd.getNextBoolean();
        clusterSimulation = gd.getNextChoiceIndex();
        clusterNumber = Math.abs(gd.getNextNumber());
        clusterNumberSD = Math.abs(gd.getNextNumber());
        clusterRadius = Math.abs(gd.getNextNumber());
        showClusterMask = gd.getNextBoolean();
    } else {
        inputOption = ResultsManager.getInputSource(gd);
        if (!titles.isEmpty())
            chooseRoi = gd.getNextBoolean();
        runMode = gd.getNextChoiceIndex();
    }
    lowResolutionImageSize = (int) gd.getNextNumber();
    roiSizeInUm = gd.getNextNumber();
    showHighResolutionImage = gd.getNextBoolean();
    nmPerPixelLimit = Math.abs(gd.getNextNumber());
    clearResults = gd.getNextBoolean();
    // Check arguments
    try {
        if (!resultsAvailable) {
            Parameters.isAboveZero("Molecules", nMolecules);
            Parameters.isAboveZero("Simulation size", simulationSize);
            Parameters.isEqualOrAbove("Blinking rate", blinkingRate, 1);
            Parameters.isEqualOrAbove("Cluster number", clusterNumber, 1);
        }
        Parameters.isAbove("Image scale", lowResolutionImageSize, 1);
        Parameters.isAboveZero("ROI size", roiSizeInUm);
    } catch (IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    if (!titles.isEmpty() && chooseRoi && resultsAvailable) {
        if (titles.size() == 1) {
            roiImage = titles.get(0);
            Recorder.recordOption("Image", roiImage);
        } else {
            String[] items = titles.toArray(new String[titles.size()]);
            gd = new ExtendedGenericDialog(TITLE);
            gd.addMessage("Select the source image for the ROI");
            gd.addChoice("Image", items, roiImage);
            gd.showDialog();
            if (gd.wasCanceled())
                return false;
            roiImage = gd.getNextChoice();
        }
        ImagePlus imp = WindowManager.getImage(roiImage);
        roiBounds = imp.getRoi().getBounds();
        roiImageWidth = imp.getWidth();
        roiImageHeight = imp.getHeight();
    } else {
        roiBounds = null;
    }
    if (!resultsAvailable) {
        if (!getPValue())
            return false;
    }
    if (clearResults) {
        PCPALMAnalysis.results.clear();
        PCPALMFitting.previous_gr = null;
    }
    return true;
}

Example 5 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PCPALMMolecules method displayImage.

static ImagePlus displayImage(String title, ImageProcessor ip, double nmPerPixel) {
    ImagePlus imp = Utils.display(title, ip);
    Calibration cal = new Calibration();
    cal.setUnit("um");
    cal.pixelWidth = cal.pixelHeight = nmPerPixel / 1000;
    imp.setCalibration(cal);
    return imp;
}