Examples with ColorDeconvolutionStains qupath.lib.color.ColorDeconvolutionStains used on opensource projects

Example 6 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class ImageData method setColorDeconvolutionStains.

/**
 * Set the color deconvolution stain vectors for the current image type.
 * <p>
 * If the type is not brightfield, an IllegalArgumentException is thrown.
 *
 * @param stains
 */
public void setColorDeconvolutionStains(ColorDeconvolutionStains stains) {
    if (!isBrightfield())
        throw new IllegalArgumentException("Cannot set color deconvolution stains for image type " + type);
    logger.trace("Setting stains to {}", stains);
    ColorDeconvolutionStains stainsOld = stainMap.put(type, stains);
    pcs.firePropertyChange("stains", stainsOld, stains);
    addColorDeconvolutionStainsToWorkflow(this);
    // logger.error("WARNING: Setting color deconvolution stains is not yet scriptable!!!!");
    changes = true;
}

Example 7 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class ImageDetailsPane method editStainVector.

void editStainVector(Object value) {
    if (!(value instanceof StainVector || value instanceof double[]))
        return;
    // JOptionPane.showMessageDialog(null, "Modifying stain vectors not yet implemented...");
    ImageData<BufferedImage> imageData = qupath.getImageData();
    if (imageData == null)
        return;
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    // Default to background values
    int num = -1;
    String name = null;
    String message = null;
    if (value instanceof StainVector) {
        StainVector stainVector = (StainVector) value;
        if (stainVector.isResidual() && imageData.getImageType() != ImageType.BRIGHTFIELD_OTHER) {
            logger.warn("Cannot set residual stain vector - this is computed from the known vectors");
            return;
        }
        num = stains.getStainNumber(stainVector);
        if (num <= 0) {
            logger.error("Could not identify stain vector " + stainVector + " inside " + stains);
            return;
        }
        name = stainVector.getName();
        message = "Set stain vector from ROI?";
    } else
        message = "Set color deconvolution background values from ROI?";
    ROI pathROI = imageData.getHierarchy().getSelectionModel().getSelectedROI();
    boolean wasChanged = false;
    String warningMessage = null;
    boolean editableName = imageData.getImageType() == ImageType.BRIGHTFIELD_OTHER;
    if (pathROI != null) {
        if ((pathROI instanceof RectangleROI) && !pathROI.isEmpty() && ((RectangleROI) pathROI).getArea() < 500 * 500) {
            if (Dialogs.showYesNoDialog("Color deconvolution stains", message)) {
                ImageServer<BufferedImage> server = imageData.getServer();
                BufferedImage img = null;
                try {
                    img = server.readBufferedImage(RegionRequest.createInstance(server.getPath(), 1, pathROI));
                } catch (IOException e) {
                    Dialogs.showErrorMessage("Set stain vector", "Unable to read image region");
                    logger.error("Unable to read region", e);
                }
                int rgb = ColorDeconvolutionHelper.getMedianRGB(img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth()));
                if (num >= 0) {
                    StainVector vectorValue = ColorDeconvolutionHelper.generateMedianStainVectorFromPixels(name, img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth()), stains.getMaxRed(), stains.getMaxGreen(), stains.getMaxBlue());
                    if (!Double.isFinite(vectorValue.getRed() + vectorValue.getGreen() + vectorValue.getBlue())) {
                        Dialogs.showErrorMessage("Set stain vector", "Cannot set stains for the current ROI!\n" + "It might be too close to the background color.");
                        return;
                    }
                    value = vectorValue;
                } else {
                    // Update the background
                    value = new double[] { ColorTools.red(rgb), ColorTools.green(rgb), ColorTools.blue(rgb) };
                }
                wasChanged = true;
            }
        } else {
            warningMessage = "Note: To set stain values from an image region, draw a small, rectangular ROI first";
        }
    }
    // Prompt to set the name / verify stains
    ParameterList params = new ParameterList();
    String title;
    String nameBefore = null;
    String valuesBefore = null;
    String collectiveNameBefore = stains.getName();
    String suggestedName;
    if (collectiveNameBefore.endsWith("default"))
        suggestedName = collectiveNameBefore.substring(0, collectiveNameBefore.lastIndexOf("default")) + "modified";
    else
        suggestedName = collectiveNameBefore;
    params.addStringParameter("collectiveName", "Collective name", suggestedName, "Enter collective name for all 3 stains (e.g. H-DAB Scanner A, H&E Scanner B)");
    if (value instanceof StainVector) {
        nameBefore = ((StainVector) value).getName();
        valuesBefore = ((StainVector) value).arrayAsString(Locale.getDefault(Category.FORMAT));
        params.addStringParameter("name", "Name", nameBefore, "Enter stain name").addStringParameter("values", "Values", valuesBefore, "Enter 3 values (red, green, blue) defining color deconvolution stain vector, separated by spaces");
        title = "Set stain vector";
    } else {
        nameBefore = "Background";
        valuesBefore = GeneralTools.arrayToString(Locale.getDefault(Category.FORMAT), (double[]) value, 2);
        params.addStringParameter("name", "Stain name", nameBefore);
        params.addStringParameter("values", "Stain values", valuesBefore, "Enter 3 values (red, green, blue) defining background, separated by spaces");
        params.setHiddenParameters(true, "name");
        title = "Set background";
    }
    if (warningMessage != null)
        params.addEmptyParameter(warningMessage);
    // Disable editing the name if it should be fixed
    ParameterPanelFX parameterPanel = new ParameterPanelFX(params);
    parameterPanel.setParameterEnabled("name", editableName);
    ;
    if (!Dialogs.showConfirmDialog(title, parameterPanel.getPane()))
        return;
    // Check if anything changed
    String collectiveName = params.getStringParameterValue("collectiveName");
    String nameAfter = params.getStringParameterValue("name");
    String valuesAfter = params.getStringParameterValue("values");
    if (collectiveName.equals(collectiveNameBefore) && nameAfter.equals(nameBefore) && valuesAfter.equals(valuesBefore) && !wasChanged)
        return;
    double[] valuesParsed = ColorDeconvolutionStains.parseStainValues(Locale.getDefault(Category.FORMAT), valuesAfter);
    if (valuesParsed == null) {
        logger.error("Input for setting color deconvolution information invalid! Cannot parse 3 numbers from {}", valuesAfter);
        return;
    }
    if (num >= 0) {
        try {
            stains = stains.changeStain(StainVector.createStainVector(nameAfter, valuesParsed[0], valuesParsed[1], valuesParsed[2]), num);
        } catch (Exception e) {
            logger.error("Error setting stain vectors", e);
            Dialogs.showErrorMessage("Set stain vectors", "Requested stain vectors are not valid!\nAre two stains equal?");
        }
    } else {
        // Update the background
        stains = stains.changeMaxValues(valuesParsed[0], valuesParsed[1], valuesParsed[2]);
    }
    // Set the collective name
    stains = stains.changeName(collectiveName);
    imageData.setColorDeconvolutionStains(stains);
    qupath.getViewer().repaintEntireImage();
}

Example 8 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class PositivePixelCounterIJ method getDefaultParameterList.

@Override
public ParameterList getDefaultParameterList(final ImageData<BufferedImage> imageData) {
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    String stain1Name = stains == null ? "Hematoxylin" : stains.getStain(1).getName();
    String stain2Name = stains == null ? "DAB" : stains.getStain(2).getName();
    ParameterList params = new ParameterList().addIntParameter("downsampleFactor", "Downsample factor", 4, "", 1, 32, "Amount to downsample image prior to detection - higher values lead to smaller images (and faster but less accurate processing)").addDoubleParameter("gaussianSigmaMicrons", "Gaussian sigma", 2, GeneralTools.micrometerSymbol(), "Gaussian filter size - higher values give a smoother (less-detailed) result").addDoubleParameter("thresholdStain1", stain1Name + " threshold ('Negative')", 0.1, "OD units", "Threshold to use for 'Negative' detection").addDoubleParameter("thresholdStain2", stain2Name + " threshold ('Positive')", 0.3, "OD units", "Threshold to use for 'Positive' stain detection").addBooleanParameter("addSummaryMeasurements", "Add summary measurements to parent", true, "Add summary measurements to parent objects").addBooleanParameter("clearParentMeasurements", "Clear existing parent measurements", true, "Remove any existing measurements from parent objects").addBooleanParameter("appendDetectionParameters", "Add parameters to measurement names", false, "Append the detection parameters to any measurement names").addBooleanParameter("legacyMeasurements0.1.2", "Use legacy measurements (v0.1.2)", false, "Generate measurements compatible with QuPath v0.1.2");
    return params;
}

Example 9 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class EstimateStainVectors method estimateStains.

/**
 * Check colors only currently applies to H&E.
 *
 * @param rgbPacked
 * @param redOD
 * @param greenOD
 * @param blueOD
 * @param stainsOriginal
 * @param minStain
 * @param maxStain
 * @param ignorePercentage
 * @param checkColors
 * @return
 */
public static ColorDeconvolutionStains estimateStains(final int[] rgbPacked, final float[] redOD, final float[] greenOD, final float[] blueOD, final ColorDeconvolutionStains stainsOriginal, final double minStain, final double maxStain, final double ignorePercentage, final boolean checkColors) {
    double alpha = ignorePercentage / 100;
    int n = rgbPacked.length;
    if (redOD.length != n || greenOD.length != n || blueOD.length != n)
        throw new IllegalArgumentException("All pixel arrays must be the same length!");
    int[] rgb = Arrays.copyOf(rgbPacked, n);
    float[] red = Arrays.copyOf(redOD, n);
    float[] green = Arrays.copyOf(greenOD, n);
    float[] blue = Arrays.copyOf(blueOD, n);
    // Check if we do color sanity test
    boolean doColorTestForHE = checkColors && stainsOriginal.isH_E();
    // boolean doColorTestForHDAB = checkColors && stainsOriginal.isH_DAB();
    boolean doGrayTest = checkColors && (stainsOriginal.isH_E() || stainsOriginal.isH_DAB());
    double sqrt3 = 1 / Math.sqrt(3);
    double grayThreshold = Math.cos(0.15);
    // Loop through and discard pixels that are too faintly or densely stained
    int keepCount = 0;
    double maxStainSq = maxStain * maxStain;
    for (int i = 0; i < rgb.length; i++) {
        float r = red[i];
        float g = green[i];
        float b = blue[i];
        double magSquared = r * r + g * g + b * b;
        if (magSquared > maxStainSq || r < minStain || g < minStain || b < minStain || magSquared <= 0)
            continue;
        // Check for consistency with H&E staining, if required (i.e. only keep red/pink/purple/blue pixels and the like)
        if (doColorTestForHE && (r > g || b > g)) {
            continue;
        }
        // Exclude very 'gray' pixels
        if (doGrayTest && (r * sqrt3 + g * sqrt3 + b * sqrt3) / Math.sqrt(magSquared) >= grayThreshold) {
            continue;
        }
        // Update the arrays
        red[keepCount] = r;
        green[keepCount] = g;
        blue[keepCount] = b;
        rgb[keepCount] = rgb[i];
        keepCount++;
    }
    if (keepCount <= 1)
        throw new IllegalArgumentException("Not enough pixels remain after applying stain thresholds!");
    // Trim the arrays
    if (keepCount < rgb.length) {
        red = Arrays.copyOf(red, keepCount);
        green = Arrays.copyOf(green, keepCount);
        blue = Arrays.copyOf(blue, keepCount);
        rgb = Arrays.copyOf(rgb, keepCount);
    }
    double[][] cov = new double[3][3];
    cov[0][0] = covariance(red, red);
    cov[1][1] = covariance(green, green);
    cov[2][2] = covariance(blue, blue);
    cov[0][1] = covariance(red, green);
    cov[0][2] = covariance(red, blue);
    cov[1][2] = covariance(green, blue);
    cov[2][1] = cov[1][2];
    cov[2][0] = cov[0][2];
    cov[1][0] = cov[0][1];
    RealMatrix mat = MatrixUtils.createRealMatrix(cov);
    logger.debug("Covariance matrix:\n {}", getMatrixAsString(mat.getData()));
    EigenDecomposition eigen = new EigenDecomposition(mat);
    double[] eigenValues = eigen.getRealEigenvalues();
    int[] eigenOrder = rank(eigenValues);
    double[] eigen1 = eigen.getEigenvector(eigenOrder[2]).toArray();
    double[] eigen2 = eigen.getEigenvector(eigenOrder[1]).toArray();
    logger.debug("First eigenvector: " + getVectorAsString(eigen1));
    logger.debug("Second eigenvector: " + getVectorAsString(eigen2));
    double[] phi = new double[keepCount];
    for (int i = 0; i < keepCount; i++) {
        double r = red[i];
        double g = green[i];
        double b = blue[i];
        phi[i] = Math.atan2(r * eigen1[0] + g * eigen1[1] + b * eigen1[2], r * eigen2[0] + g * eigen2[1] + b * eigen2[2]);
    }
    /*
		 * Rather than projecting onto the plane (which might be a bit wrong),
		 * select the vectors directly from the data.
		 * This is effectively like a region selection, but where the region has
		 * been chosen automatically.
		 */
    int[] inds = rank(phi);
    int ind1 = inds[Math.max(0, (int) (alpha * keepCount + .5))];
    int ind2 = inds[Math.min(inds.length - 1, (int) ((1 - alpha) * keepCount + .5))];
    // Create new stain vectors
    StainVector s1 = StainVector.createStainVector(stainsOriginal.getStain(1).getName(), red[ind1], green[ind1], blue[ind1]);
    StainVector s2 = StainVector.createStainVector(stainsOriginal.getStain(2).getName(), red[ind2], green[ind2], blue[ind2]);
    // If working with H&E, we can use the simple heuristic of comparing the red values
    if (stainsOriginal.isH_E()) {
        // Need to check within the stain vectors (*not* original indexed values) because normalisation is important (I think... there were errors before)
        if (s1.getRed() < s2.getRed()) {
            s1 = StainVector.createStainVector(stainsOriginal.getStain(1).getName(), red[ind2], green[ind2], blue[ind2]);
            s2 = StainVector.createStainVector(stainsOriginal.getStain(2).getName(), red[ind1], green[ind1], blue[ind1]);
        }
    } else {
        // Check we've got the closest match - if not, switch the order
        double angle11 = StainVector.computeAngle(s1, stainsOriginal.getStain(1));
        double angle12 = StainVector.computeAngle(s1, stainsOriginal.getStain(2));
        double angle21 = StainVector.computeAngle(s2, stainsOriginal.getStain(1));
        double angle22 = StainVector.computeAngle(s2, stainsOriginal.getStain(2));
        if (Math.min(angle12, angle21) < Math.min(angle11, angle22)) {
            s1 = StainVector.createStainVector(stainsOriginal.getStain(1).getName(), red[ind2], green[ind2], blue[ind2]);
            s2 = StainVector.createStainVector(stainsOriginal.getStain(2).getName(), red[ind1], green[ind1], blue[ind1]);
        }
    }
    ColorDeconvolutionStains stains = new ColorDeconvolutionStains(stainsOriginal.getName(), s1, s2, stainsOriginal.getMaxRed(), stainsOriginal.getMaxGreen(), stainsOriginal.getMaxBlue());
    return stains;
}

Example 10 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class ImageData method addColorDeconvolutionStainsToWorkflow.

// TODO: REINTRODUCE LOGGING!
private static void addColorDeconvolutionStainsToWorkflow(ImageData<?> imageData) {
    // logger.warn("Color deconvolution stain logging not currently enabled!");
    ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
    if (stains == null) {
        return;
    }
    String arg = ColorDeconvolutionStains.getColorDeconvolutionStainsAsString(imageData.getColorDeconvolutionStains(), 5);
    Map<String, String> map = GeneralTools.parseArgStringValues(arg);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    String commandName = "Set color deconvolution stains";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep(commandName, map, "setColorDeconvolutionStains(\'" + arg + "');");
    // else
    if (!Objects.equals(newStep, lastStep))
        imageData.getHistoryWorkflow().addStep(newStep);
// ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
// if (stains == null)
// return;
// 
// String arg = ColorDeconvolutionStains.getColorDeconvolutionStainsAsString(imageData.getColorDeconvolutionStains(), 5);
// Map<String, String> map = GeneralTools.parseArgStringValues(arg);
// WorkflowStep lastStep = imageData.getWorkflow().getLastStep();
// String commandName = "Set color deconvolution stains";
// WorkflowStep newStep = new DefaultScriptableWorkflowStep(commandName,
// map,
// QP.class.getSimpleName() + ".setColorDeconvolutionStains(\'" + arg + "');");
// 
// if (lastStep != null && commandName.equals(lastStep.getName()))
// imageData.getWorkflow().replaceLastStep(newStep);
// else
// imageData.getWorkflow().addStep(newStep);
}