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

Example 6 with ParameterList

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

the class NeuralNetworksClassifier method createParameterList.

@Override
protected ParameterList createParameterList() {
    ParameterList params = new ParameterList();
    params.addIntParameter("nHidden", "Number of hidden layers", 8, null, "Number of hidden layers for neural network (must be >= 2)");
    params.addIntParameter("termCritMaxIterations", "Termination criterion - max iterations", 100, null, "Optional termination criterion based on maximum number of iterations - set <= 0 to disable and use accuracy criterion only");
    params.addDoubleParameter("termCritEPS", "Termination criterion - accuracy", 0.01, null, "Optional termination criterion based on out-of-bag error - set <= 0 to disable and use max trees only");
    return params;
}

Example 7 with ParameterList

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

the class Commands method promptToSetGridLineSpacing.

/**
 * Prompt to input the spacing for the grid lines optionally displayed on viewers.
 * @param options the {@link OverlayOptions} that manage the grid lines.
 */
public static void promptToSetGridLineSpacing(OverlayOptions options) {
    GridLines gridLines = options.getGridLines();
    ParameterList params = new ParameterList().addDoubleParameter("hSpacing", "Horizontal spacing", gridLines.getSpaceX()).addDoubleParameter("vSpacing", "Vertical spacing", gridLines.getSpaceY()).addBooleanParameter("useMicrons", "Use microns", gridLines.useMicrons());
    if (!Dialogs.showParameterDialog("Set grid spacing", params))
        return;
    gridLines = new GridLines();
    gridLines.setSpaceX(params.getDoubleParameterValue("hSpacing"));
    gridLines.setSpaceY(params.getDoubleParameterValue("vSpacing"));
    gridLines.setUseMicrons(params.getBooleanParameterValue("useMicrons"));
    options.gridLinesProperty().set(gridLines);
}

Example 8 with ParameterList

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

the class ExportObjectsCommand method runGeoJsonExport.

/**
 * Run the path object GeoJSON export command.
 * @param qupath
 * @return success
 * @throws IOException
 */
public static boolean runGeoJsonExport(QuPathGUI qupath) throws IOException {
    // Get ImageData
    var imageData = qupath.getImageData();
    if (imageData == null)
        return false;
    // Get hierarchy
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    String allObjects = "All objects";
    String selectedObjects = "Selected objects";
    String defaultObjects = hierarchy.getSelectionModel().noSelection() ? allObjects : selectedObjects;
    // Params
    var parameterList = new ParameterList().addChoiceParameter("exportOptions", "Export ", defaultObjects, Arrays.asList(allObjects, selectedObjects), "Choose which objects to export - run a 'Select annotations/detections' command first if needed").addBooleanParameter("excludeMeasurements", "Exclude measurements", false, "Exclude object measurements during export - for large numbers of detections this can help reduce the file size").addBooleanParameter("doPretty", "Pretty JSON", false, "Pretty GeoJSON is more human-readable but results in larger file sizes").addBooleanParameter("doFeatureCollection", "Export as FeatureCollection", true, "Export as a 'FeatureCollection', which is a standard GeoJSON way to represent multiple objects; if not, a regular JSON object/array will be export").addBooleanParameter("doZip", "Compress data (zip)", false, "Compressed files take less memory");
    if (!Dialogs.showParameterDialog("Export objects", parameterList))
        return false;
    Collection<PathObject> toProcess;
    var comboChoice = parameterList.getChoiceParameterValue("exportOptions");
    if (comboChoice.equals("Selected objects")) {
        if (hierarchy.getSelectionModel().noSelection()) {
            Dialogs.showErrorMessage("No selection", "No selection detected!");
            return false;
        }
        toProcess = hierarchy.getSelectionModel().getSelectedObjects();
    } else
        toProcess = hierarchy.getObjects(null, null);
    // Remove PathRootObject
    toProcess = toProcess.stream().filter(e -> !e.isRootObject()).collect(Collectors.toList());
    // Check if includes ellipse(s), as they will need to be polygonized
    var nEllipses = toProcess.stream().filter(ann -> isEllipse(ann)).count();
    if (nEllipses > 0) {
        String message = nEllipses == 1 ? "1 ellipse will be polygonized, continue?" : String.format("%d ellipses will be polygonized, continue?", nEllipses);
        var response = Dialogs.showYesNoDialog("Ellipse polygonization", message);
        if (!response)
            return false;
    }
    File outFile;
    // Get default name & output directory
    var project = qupath.getProject();
    String defaultName = imageData.getServer().getMetadata().getName();
    if (project != null) {
        var entry = project.getEntry(imageData);
        if (entry != null)
            defaultName = entry.getImageName();
    }
    defaultName = GeneralTools.getNameWithoutExtension(defaultName);
    File defaultDirectory = project == null || project.getPath() == null ? null : project.getPath().toFile();
    while (defaultDirectory != null && !defaultDirectory.isDirectory()) defaultDirectory = defaultDirectory.getParentFile();
    if (parameterList.getBooleanParameterValue("doZip"))
        outFile = Dialogs.promptToSaveFile("Export to file", defaultDirectory, defaultName + ".zip", "ZIP archive", ".zip");
    else
        outFile = Dialogs.promptToSaveFile("Export to file", defaultDirectory, defaultName + ".geojson", "GeoJSON", ".geojson");
    // If user cancels
    if (outFile == null)
        return false;
    List<GeoJsonExportOptions> options = new ArrayList<>();
    if (parameterList.getBooleanParameterValue("excludeMeasurements"))
        options.add(GeoJsonExportOptions.EXCLUDE_MEASUREMENTS);
    if (parameterList.getBooleanParameterValue("doPretty"))
        options.add(GeoJsonExportOptions.PRETTY_JSON);
    if (parameterList.getBooleanParameterValue("doFeatureCollection"))
        options.add(GeoJsonExportOptions.FEATURE_COLLECTION);
    // Export
    QP.exportObjectsToGeoJson(toProcess, outFile.getAbsolutePath(), options.toArray(GeoJsonExportOptions[]::new));
    // Notify user of success
    int nObjects = toProcess.size();
    String message = nObjects == 1 ? "1 object was exported to " + outFile.getAbsolutePath() : String.format("%d objects were exported to %s", nObjects, outFile.getAbsolutePath());
    Dialogs.showInfoNotification("Succesful export", message);
    // Get history workflow
    var historyWorkflow = imageData.getHistoryWorkflow();
    // args for workflow step
    Map<String, String> map = new LinkedHashMap<>();
    map.put("path", outFile.getPath());
    String method = comboChoice.equals(allObjects) ? "exportAllObjectsToGeoJson" : "exportSelectedObjectsToGeoJson";
    String methodTitle = comboChoice.equals(allObjects) ? "Export all objects" : "Export selected objects";
    String optionsString = options.stream().map(o -> "\"" + o.name() + "\"").collect(Collectors.joining(", "));
    map.put("options", optionsString);
    if (!optionsString.isEmpty())
        optionsString = ", " + optionsString;
    String methodString = String.format("%s(%s%s)", method, "\"" + GeneralTools.escapeFilePath(outFile.getPath()) + "\"", optionsString);
    historyWorkflow.addStep(new DefaultScriptableWorkflowStep(methodTitle, map, methodString));
    return true;
}

Example 9 with ParameterList

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

the class TMACommands method promptToRelabelTMAGrid.

/**
 * Prompt to relabel the core names within a TMA grid.
 * @param imageData image containing the TMA grid
 */
public static void promptToRelabelTMAGrid(ImageData<?> imageData) {
    String title = "Relabel TMA grid";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    if (imageData.getHierarchy().getTMAGrid() == null) {
        Dialogs.showErrorMessage(title, "No TMA grid selected!");
        return;
    }
    ParameterList params = new ParameterList();
    params.addStringParameter("labelsHorizontal", "Column labels", columnLabelsProperty.get(), "Enter column labels.\nThis can be a continuous range of letters or numbers (e.g. 1-10 or A-J),\nor a discontinuous list separated by spaces (e.g. A B C E F G).");
    params.addStringParameter("labelsVertical", "Row labels", rowLabelsProperty.get(), "Enter row labels.\nThis can be a continuous range of letters or numbers (e.g. 1-10 or A-J),\nor a discontinuous list separated by spaces (e.g. A B C E F G).");
    params.addChoiceParameter("labelOrder", "Label order", rowFirstProperty.get() ? "Row first" : "Column first", Arrays.asList("Column first", "Row first"), "Create TMA labels either in the form Row-Column or Column-Row");
    if (!Dialogs.showParameterDialog(title, params))
        return;
    // Parse the arguments
    String labelsHorizontal = params.getStringParameterValue("labelsHorizontal");
    String labelsVertical = params.getStringParameterValue("labelsVertical");
    boolean rowFirst = "Row first".equals(params.getChoiceParameterValue("labelOrder"));
    // Figure out if this will work
    TMAGrid grid = imageData.getHierarchy().getTMAGrid();
    String[] columnLabels = PathObjectTools.parseTMALabelString(labelsHorizontal);
    String[] rowLabels = PathObjectTools.parseTMALabelString(labelsVertical);
    if (columnLabels.length < grid.getGridWidth()) {
        Dialogs.showErrorMessage(title, "Not enough column labels specified!");
        return;
    }
    if (rowLabels.length < grid.getGridHeight()) {
        Dialogs.showErrorMessage(title, "Not enough row labels specified!");
        return;
    }
    // Apply the labels
    QP.relabelTMAGrid(imageData.getHierarchy(), labelsHorizontal, labelsVertical, rowFirst);
    // Add to workflow history
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Relabel TMA grid", String.format("relabelTMAGrid(\"%s\", \"%s\", %s)", GeneralTools.escapeFilePath(labelsHorizontal), GeneralTools.escapeFilePath(labelsVertical), Boolean.toString(rowFirst))));
    // Store values
    rowLabelsProperty.set(labelsVertical);
    columnLabelsProperty.set(labelsHorizontal);
    rowFirstProperty.set(rowFirst);
}

Example 10 with ParameterList

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

the class EstimateStainVectorsCommand method showStainEditor.

@SuppressWarnings("unchecked")
public static ColorDeconvolutionStains showStainEditor(final BufferedImage img, final ColorDeconvolutionStains stains) {
    // 
    int[] buf = img.getRGB(0, 0, img.getWidth(), img.getHeight(), null, 0, img.getWidth());
    // int[] rgb = buf;
    int[] rgb = EstimateStainVectors.subsample(buf, 10000);
    float[] red = ColorDeconvolutionHelper.getRedOpticalDensities(rgb, stains.getMaxRed(), null);
    float[] green = ColorDeconvolutionHelper.getGreenOpticalDensities(rgb, stains.getMaxGreen(), null);
    float[] blue = ColorDeconvolutionHelper.getBlueOpticalDensities(rgb, stains.getMaxBlue(), null);
    // panelPlots.setBorder(BorderFactory.createTitledBorder(null, "Stain vector scatterplots", TitledBorder.CENTER, TitledBorder.TOP));
    StainsWrapper stainsWrapper = new StainsWrapper(stains);
    Node panelRedGreen = createScatterPanel(new ScatterPlot(red, green, null, rgb), stainsWrapper, AxisColor.RED, AxisColor.GREEN);
    Node panelRedBlue = createScatterPanel(new ScatterPlot(red, blue, null, rgb), stainsWrapper, AxisColor.RED, AxisColor.BLUE);
    Node panelGreenBlue = createScatterPanel(new ScatterPlot(green, blue, null, rgb), stainsWrapper, AxisColor.GREEN, AxisColor.BLUE);
    // GridPane panelPlots = PanelToolsFX.createColumnGrid(panelRedGreen, panelRedBlue, panelGreenBlue);
    GridPane panelPlots = new GridPane();
    panelPlots.setHgap(10);
    panelPlots.add(panelRedGreen, 0, 0);
    panelPlots.add(panelRedBlue, 1, 0);
    panelPlots.add(panelGreenBlue, 2, 0);
    // panelPlots.getChildren().addAll(panelRedGreen, panelRedBlue, panelGreenBlue);
    panelPlots.setPadding(new Insets(0, 0, 10, 0));
    BorderPane panelSouth = new BorderPane();
    TableView<Integer> table = new TableView<>();
    table.getItems().setAll(1, 2, 3);
    stainsWrapper.addStainListener(new StainChangeListener() {

        @Override
        public void stainChanged(StainsWrapper stainsWrapper) {
            table.refresh();
        }
    });
    TableColumn<Integer, String> colName = new TableColumn<>("Name");
    colName.setCellValueFactory(v -> new SimpleStringProperty(stainsWrapper.getStains().getStain(v.getValue()).getName()));
    TableColumn<Integer, String> colOrig = new TableColumn<>("Original");
    colOrig.setCellValueFactory(v -> new SimpleStringProperty(stainArrayAsString(Locale.getDefault(Category.FORMAT), stainsWrapper.getOriginalStains().getStain(v.getValue()), " | ", 3)));
    TableColumn<Integer, String> colCurrent = new TableColumn<>("Current");
    colCurrent.setCellValueFactory(v -> new SimpleStringProperty(stainArrayAsString(Locale.getDefault(Category.FORMAT), stainsWrapper.getStains().getStain(v.getValue()), " | ", 3)));
    TableColumn<Integer, String> colAngle = new TableColumn<>("Angle");
    colAngle.setCellValueFactory(v -> {
        return new SimpleStringProperty(GeneralTools.formatNumber(StainVector.computeAngle(stainsWrapper.getOriginalStains().getStain(v.getValue()), stainsWrapper.getStains().getStain(v.getValue())), 2));
    });
    // new SimpleStringProperty(stainsWrapper.getStains().getStain(v.getValue()).arrayAsString(", ", 3)));
    table.getColumns().addAll(colName, colOrig, colCurrent, colAngle);
    table.setColumnResizePolicy(TableView.UNCONSTRAINED_RESIZE_POLICY);
    table.setPrefHeight(120);
    // // Fix first & preferred column sizes
    // int widthName = 0, widthStain = 0;
    // for (int row = 0; row < table.getRowCount(); row++) {
    // TableCellRenderer renderer = table.getCellRenderer(row, 0);
    // Component comp = table.prepareRenderer(renderer, row, 0);
    // widthName = Math.max(comp.getPreferredSize().width, widthName);
    // 
    // renderer = table.getCellRenderer(row, 1);
    // comp = table.prepareRenderer(renderer, row, 1);
    // widthStain = Math.max(comp.getPreferredSize().width, widthStain);
    // renderer = table.getCellRenderer(row, 2);
    // comp = table.prepareRenderer(renderer, row, 2);
    // widthStain = Math.max(comp.getPreferredSize().width, widthStain);
    // }
    // table.getColumnModel().getColumn(0).setMaxWidth(widthName + 10);
    // table.getColumnModel().getColumn(0).setPreferredWidth(widthName + 10);
    // table.getColumnModel().getColumn(1).setPreferredWidth(widthStain + 20);
    // table.getColumnModel().getColumn(2).setPreferredWidth(widthStain + 20);
    // Create auto detection parameters
    ParameterList params = new ParameterList().addDoubleParameter("minStainOD", "Min channel OD", 0.05, "", "Minimum staining OD - pixels with a lower OD in any channel (RGB) are ignored (default = 0.05)").addDoubleParameter("maxStainOD", "Max total OD", 1., "", "Maximum staining OD - more densely stained pixels are ignored (default = 1)").addDoubleParameter("ignorePercentage", "Ignore extrema", 1., "%", "Percentage of extreme pixels to ignore, to improve robustness in the presence of noise/other artefacts (default = 1)").addBooleanParameter("checkColors", "Exclude unrecognised colors (H&E only)", false, "Exclude unexpected colors (e.g. green) that are likely to be caused by artefacts and not true staining");
    // .addDoubleParameter("ignorePercentage", "Ignore extrema", 1., "%", 0, 20, "Percentage of extreme pixels to ignore, to improve robustness in the presence of noise/other artefacts");
    Button btnAuto = new Button("Auto");
    btnAuto.setOnAction(e -> {
        double minOD = params.getDoubleParameterValue("minStainOD");
        double maxOD = params.getDoubleParameterValue("maxStainOD");
        double ignore = params.getDoubleParameterValue("ignorePercentage");
        // Only accept if H&E
        boolean checkColors = params.getBooleanParameterValue("checkColors") && stainsWrapper.getOriginalStains().isH_E();
        ignore = Math.max(0, Math.min(ignore, 100));
        // ColorDeconvolutionStains stains = estimateStains(imgFinal, stainsWrapper.getStains(), minOD, maxOD, ignore);
        try {
            ColorDeconvolutionStains stainsNew = EstimateStainVectors.estimateStains(img, stainsWrapper.getStains(), minOD, maxOD, ignore, checkColors);
            stainsWrapper.setStains(stainsNew);
        } catch (Exception e2) {
            Dialogs.showErrorMessage("Estimate stain vectors", e2);
        }
    });
    ParameterPanelFX panelParams = new ParameterPanelFX(params);
    // panelParams.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    BorderPane panelAuto = new BorderPane();
    // panelAuto.setBorder(BorderFactory.createTitledBorder("Auto detect"));
    panelAuto.setCenter(panelParams.getPane());
    panelAuto.setBottom(btnAuto);
    // JScrollPane scrollPane = new JScrollPane(table);
    // JPanel panelTable = new JPanel(new BorderLayout());
    // panelTable.add(scrollPane, BorderLayout.CENTER);
    // //		JTextArea textInstructions = new JTextArea();
    // //		textInstructions.setWrapStyleWord(true);
    // //		textInstructions.setLineWrap(true);
    // //		textInstructions.setText(
    // //				"Viewer for manually and automatically adjusting stain vectors used for stain separation.\n\n" +
    // //				"Each stain vector is 3 values describing the red, green and blue components that define the colour of each " +
    // //				"stain (e.g. hematoxylin, DAB, eosin).  The scatterplots show how these relate to pixel colours for each " +
    // //				"combination of red, green and blue.\n\n" +
    // //				"'Good' stain vectors should point along the edges of the scattered points, ignoring any artefacts resulting from " +
    // //				"pixels that don't belong to normal staining patterns."
    // //				);
    // //		panelTable.add(new JScrollPane(textInstructions), BorderLayout.SOUTH);
    // panelTable.setBorder(BorderFactory.createTitledBorder("Stain vectors"));
    panelSouth.setCenter(new TitledPane("Stain vectors", table));
    panelSouth.setBottom(new TitledPane("Auto detect", panelAuto));
    BorderPane panelMain = new BorderPane();
    panelMain.setCenter(panelPlots);
    panelMain.setBottom(panelSouth);
    if (Dialogs.showConfirmDialog("Visual Stain Editor", panelMain)) {
        return stainsWrapper.getStains();
    } else {
        stainsWrapper.resetStains();
        return stainsWrapper.getStains();
    }
}