Examples with ParameterList qupath.lib.plugins.parameters.ParameterList used on opensource projects

Example 51 with ParameterList

use of qupath.lib.plugins.parameters.ParameterList in project qupath by qupath.

the class NeuralNetworksClassifier method createAndTrainClassifier.

@Override
protected void createAndTrainClassifier() {
    // Create the required Mats
    int nMeasurements = measurements.size();
    Mat matTraining = new Mat(arrayTraining.length / nMeasurements, nMeasurements, CV_32FC1);
    ((FloatBuffer) matTraining.createBuffer()).put(arrayTraining);
    // Parse parameters
    ParameterList params = getParameterList();
    int nHidden = Math.max(2, params.getIntParameterValue("nHidden"));
    int termIterations = params.getIntParameterValue("termCritMaxIterations");
    double termEPS = params.getDoubleParameterValue("termCritEPS");
    TermCriteria crit = createTerminationCriteria(termIterations, termEPS);
    // Create & train the classifier
    classifier = createClassifier();
    ANN_MLP nnet = (ANN_MLP) classifier;
    System.out.println(nnet.getLayerSizes());
    Mat layers = new Mat(3, 1, CV_32F);
    int n = arrayTraining.length / nMeasurements;
    // layers.put(0, 0, new float[]{nMeasurements, nHidden, pathClasses.size()});
    FloatBuffer bufLayers = layers.createBuffer();
    bufLayers.clear();
    bufLayers.put(nMeasurements);
    // Number of hidden layers
    bufLayers.put(nHidden);
    bufLayers.put(pathClasses.size());
    if (crit != null)
        nnet.setTermCriteria(crit);
    else
        crit = nnet.getTermCriteria();
    nnet.setLayerSizes(layers);
    // matResponses.convertTo(matResponses, CV_32F);
    Mat matResponses = new Mat(n, pathClasses.size(), CV_32F, Scalar.ZERO);
    FloatIndexer indexerResponses = matResponses.createIndexer();
    for (int i = 0; i < n; i++) {
        indexerResponses.put(i, arrayResponses[i], 1);
        indexerResponses.release();
    // matResponses.put(i, arrayResponses[i], 1);
    }
    nnet.setActivationFunction(ANN_MLP.SIGMOID_SYM, 1, 1);
    nnet.train(matTraining, opencv_ml.ROW_SAMPLE, matResponses);
// lastDescription = getName() + "\n\nMain parameters:\n  " + DefaultPluginWorkflowStep.getParameterListJSON(params, "\n  ") + "\n\nTermination criteria:\n  " + crit.toString();
}

Example 52 with ParameterList

use of qupath.lib.plugins.parameters.ParameterList in project qupath by qupath.

the class SVMClassifier method createClassifier.

@Override
protected SVM createClassifier() {
    SVM svm = SVM.create();
    ParameterList params = getParameterList();
    if (params != null) {
        String kernel = (String) params.getChoiceParameterValue("kernel");
        kernel = kernel.toLowerCase();
        if (kernel.equals("linear"))
            svm.setKernel(SVM.LINEAR);
        else if (kernel.equals("polynomial"))
            svm.setKernel(SVM.POLY);
        else if (kernel.equals("rbf"))
            svm.setKernel(SVM.RBF);
        else if (kernel.equals("sigmoid"))
            svm.setKernel(SVM.SIGMOID);
        else if (kernel.equals("chi2"))
            svm.setKernel(SVM.CHI2);
        else if (kernel.equals("histogram intersection"))
            svm.setKernel(SVM.INTER);
        double c = params.getDoubleParameterValue("c");
        if (c > 0)
            svm.setC(c);
        svm.setGamma(params.getDoubleParameterValue("gamma"));
        svm.setDegree(params.getIntParameterValue("degree"));
    }
    return svm;
}

Example 53 with ParameterList

use of qupath.lib.plugins.parameters.ParameterList in project qupath by qupath.

the class GuiTools method promptForParentObjects.

/**
 * Get the parent objects to use when running the plugin, or null if no suitable parent objects are found.
 * This involves prompting the user if multiple options are possible, and logging an appropriate command
 * in the workflow history of the {@link ImageData} if possible.
 *
 * @param name command name, to include in dialog messages
 * @param imageData imageData containing potential parent objects
 * @param includeSelected if true, provide 'selected objects' as an option
 * @param supportedParents collection of valid parent objects
 * @return
 */
public static <T> boolean promptForParentObjects(final String name, final ImageData<T> imageData, final boolean includeSelected, final Collection<Class<? extends PathObject>> supportedParents) {
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null)
        return false;
    // Check what possible parent types are available
    Collection<PathObject> possibleParents = null;
    int nParents = 0;
    List<Class<? extends PathObject>> availableTypes = new ArrayList<>();
    for (Class<? extends PathObject> cls : supportedParents) {
        if (cls.equals(PathRootObject.class))
            continue;
        possibleParents = hierarchy.getObjects(possibleParents, cls);
        if (possibleParents.size() > nParents)
            availableTypes.add(cls);
        nParents = possibleParents.size();
    }
    // Create a map of potential choices
    LinkedHashMap<String, Class<? extends PathObject>> choices = new LinkedHashMap<>();
    for (Class<? extends PathObject> cls : availableTypes) choices.put(PathObjectTools.getSuitableName(cls, true), cls);
    if (supportedParents.contains(PathRootObject.class))
        choices.put("Entire image", PathRootObject.class);
    ArrayList<String> choiceList = new ArrayList<>(choices.keySet());
    // Add selected objects option, if required
    if (includeSelected)
        choiceList.add(0, "Selected objects");
    // Determine the currently-selected object
    PathObject pathObjectSelected = hierarchy.getSelectionModel().getSelectedObject();
    // If the currently-selected object is supported, use it as the parent
    if (!includeSelected && pathObjectSelected != null && !pathObjectSelected.isRootObject()) {
        if (supportedParents.contains(pathObjectSelected.getClass()))
            return true;
    // else {
    // String message = name + " does not support parent objects of type " + pathObjectSelected.getClass().getSimpleName();
    // DisplayHelpers.showErrorMessage(name + " error", message);
    // return false;
    // }
    }
    // If the root object is supported, and we don't have any of the other types, just run for the root object
    if (!includeSelected && availableTypes.isEmpty()) {
        if (supportedParents.contains(PathRootObject.class))
            return true;
        else {
            String message = name + " requires parent objects of one of the following types:";
            for (Class<? extends PathObject> cls : supportedParents) message += ("\n" + PathObjectTools.getSuitableName(cls, false));
            Dialogs.showErrorMessage(name + " error", message);
            return false;
        }
    }
    // Prepare to prompt
    ParameterList paramsParents = new ParameterList();
    paramsParents.addChoiceParameter(KEY_REGIONS, "Process all", choiceList.get(0), choiceList);
    if (!Dialogs.showParameterDialog("Process regions", paramsParents))
        return false;
    String choiceString = (String) paramsParents.getChoiceParameterValue(KEY_REGIONS);
    if (!"Selected objects".equals(choiceString))
        Commands.selectObjectsByClass(imageData, choices.get(choiceString));
    // Success!  Probably...
    return !hierarchy.getSelectionModel().noSelection();
}