Examples with WorkflowStep qupath.lib.plugins.workflow.WorkflowStep used on opensource projects

Example 11 with WorkflowStep

use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.

the class MeasurementManager method promptToRemoveMeasurements.

private boolean promptToRemoveMeasurements() {
    var selectedItems = new ArrayList<>(listView.getSelectionModel().getSelectedItems());
    if (selectedItems.isEmpty()) {
        Dialogs.showErrorMessage("Remove measurements", "No measurements selected!");
        return false;
    }
    String number = selectedItems.size() == 1 ? String.format("'%s'", selectedItems.iterator().next()) : selectedItems.size() + " measurements";
    if (!Dialogs.showConfirmDialog("Remove measurements", "Are you sure you want to permanently remove " + number + "?"))
        return false;
    String removeString = selectedItems.stream().map(m -> "\"" + m + "\"").collect(Collectors.joining(", "));
    logger.info("Removing measurements: {}", removeString);
    Class<? extends PathObject> cls = comboBox.getSelectionModel().getSelectedItem();
    QP.removeMeasurements(imageData.getHierarchy(), cls, selectedItems.toArray(String[]::new));
    // Keep for scripting
    WorkflowStep step = new DefaultScriptableWorkflowStep("Remove measurements", String.format("removeMeasurements(%s, %s);", cls.getName(), removeString));
    imageData.getHistoryWorkflow().addStep(step);
    // Update
    refreshMeasurements();
    updateCurrentList();
    filterText.set("");
    return true;
}

Example 12 with WorkflowStep

use of qupath.lib.plugins.workflow.WorkflowStep 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);
}

Example 13 with WorkflowStep

use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.

the class ImageDetailsPane method promptToSetPixelSize.

static boolean promptToSetPixelSize(ImageData<BufferedImage> imageData, boolean requestZSpacing) {
    var server = imageData.getServer();
    var hierarchy = imageData.getHierarchy();
    var selected = hierarchy.getSelectionModel().getSelectedObject();
    var roi = selected == null ? null : selected.getROI();
    PixelCalibration cal = server.getPixelCalibration();
    double pixelWidthMicrons = cal.getPixelWidthMicrons();
    double pixelHeightMicrons = cal.getPixelHeightMicrons();
    double zSpacingMicrons = cal.getZSpacingMicrons();
    // Use line or area ROI if possible
    if (!requestZSpacing && roi != null && !roi.isEmpty() && (roi.isArea() || roi.isLine())) {
        boolean setPixelHeight = true;
        boolean setPixelWidth = true;
        String message;
        String units = GeneralTools.micrometerSymbol();
        double pixelWidth = cal.getPixelWidthMicrons();
        double pixelHeight = cal.getPixelHeightMicrons();
        if (!Double.isFinite(pixelWidth))
            pixelWidth = 1;
        if (!Double.isFinite(pixelHeight))
            pixelHeight = 1;
        Double defaultValue = null;
        if (roi.isLine()) {
            setPixelHeight = roi.getBoundsHeight() != 0;
            setPixelWidth = roi.getBoundsWidth() != 0;
            message = "Enter selected line length";
            defaultValue = roi.getScaledLength(pixelWidth, pixelHeight);
        } else {
            message = "Enter selected ROI area";
            units = units + "^2";
            defaultValue = roi.getScaledArea(pixelWidth, pixelHeight);
        }
        // }
        if (Double.isNaN(defaultValue))
            defaultValue = 1.0;
        var params = new ParameterList().addDoubleParameter("inputValue", message, defaultValue, units, "Enter calibrated value in " + units + " for the selected ROI to calculate the pixel size").addBooleanParameter("squarePixels", "Assume square pixels", true, "Set the pixel width to match the pixel height");
        params.setHiddenParameters(setPixelHeight && setPixelWidth, "squarePixels");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        Double result = params.getDoubleParameterValue("inputValue");
        setPixelHeight = setPixelHeight || params.getBooleanParameterValue("squarePixels");
        setPixelWidth = setPixelWidth || params.getBooleanParameterValue("squarePixels");
        // Double result = Dialogs.showInputDialog("Set pixel size", message, defaultValue);
        // if (result == null)
        // return false;
        double sizeMicrons;
        if (roi.isLine())
            sizeMicrons = result.doubleValue() / roi.getLength();
        else
            sizeMicrons = Math.sqrt(result.doubleValue() / roi.getArea());
        if (setPixelHeight)
            pixelHeightMicrons = sizeMicrons;
        if (setPixelWidth)
            pixelWidthMicrons = sizeMicrons;
    } else {
        // Prompt for all required values
        ParameterList params = new ParameterList().addDoubleParameter("pixelWidth", "Pixel width", pixelWidthMicrons, GeneralTools.micrometerSymbol(), "Enter the pixel width").addDoubleParameter("pixelHeight", "Pixel height", pixelHeightMicrons, GeneralTools.micrometerSymbol(), "Entry the pixel height").addDoubleParameter("zSpacing", "Z-spacing", zSpacingMicrons, GeneralTools.micrometerSymbol(), "Enter the spacing between slices of a z-stack");
        params.setHiddenParameters(server.nZSlices() == 1, "zSpacing");
        if (!Dialogs.showParameterDialog("Set pixel size", params))
            return false;
        if (server.nZSlices() != 1) {
            zSpacingMicrons = params.getDoubleParameterValue("zSpacing");
        }
        pixelWidthMicrons = params.getDoubleParameterValue("pixelWidth");
        pixelHeightMicrons = params.getDoubleParameterValue("pixelHeight");
    }
    if ((pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) || (server.nZSlices() > 1 && zSpacingMicrons <= 0)) {
        if (!Dialogs.showConfirmDialog("Set pixel size", "You entered values <= 0, do you really want to remove this pixel calibration information?")) {
            return false;
        }
        zSpacingMicrons = server.nZSlices() > 1 && zSpacingMicrons > 0 ? zSpacingMicrons : Double.NaN;
        if (pixelWidthMicrons <= 0 || pixelHeightMicrons <= 0) {
            pixelWidthMicrons = Double.NaN;
            pixelHeightMicrons = Double.NaN;
        }
    }
    if (QP.setPixelSizeMicrons(imageData, pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons)) {
        // Log for scripts
        WorkflowStep step;
        if (server.nZSlices() == 1) {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f)", pixelWidthMicrons, pixelHeightMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        } else {
            var map = Map.of("pixelWidthMicrons", pixelWidthMicrons, "pixelHeightMicrons", pixelHeightMicrons, "zSpacingMicrons", zSpacingMicrons);
            String script = String.format("setPixelSizeMicrons(%f, %f, %f)", pixelWidthMicrons, pixelHeightMicrons, zSpacingMicrons);
            step = new DefaultScriptableWorkflowStep("Set pixel size " + GeneralTools.micrometerSymbol(), map, script);
        }
        imageData.getHistoryWorkflow().addStep(step);
        return true;
    } else
        return false;
}

Example 14 with WorkflowStep

use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.

the class Commands method selectObjectsByClass.

/**
 * Select objects that are instances of a specified class, logging an appropriate method in the workflow.
 *
 * @param imageData
 * @param cls
 */
public static void selectObjectsByClass(final ImageData<?> imageData, final Class<? extends PathObject> cls) {
    if (cls == TMACoreObject.class)
        QP.selectTMACores(imageData.getHierarchy());
    else
        QP.selectObjectsByClass(imageData.getHierarchy(), cls);
    Map<String, String> params = Collections.singletonMap("Type", PathObjectTools.getSuitableName(cls, false));
    String method;
    if (cls == PathAnnotationObject.class)
        method = "selectAnnotations();";
    else if (cls == PathDetectionObject.class)
        method = "selectDetections();";
    else if (cls == TMACoreObject.class)
        method = "selectTMACores();";
    else if (cls == PathCellObject.class)
        method = "selectCells();";
    else if (cls == PathTileObject.class)
        method = "selectTiles();";
    else
        // TODO: Get a suitable name to disguise Java classes
        method = "selectObjectsByClass(" + cls.getName() + ");";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Select objects by class", params, method);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    if (newStep.equals(lastStep))
        imageData.getHistoryWorkflow().replaceLastStep(newStep);
    else
        imageData.getHistoryWorkflow().addStep(newStep);
}

Example 15 with WorkflowStep

use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.

the class Commands method selectAllObjects.

/**
 * Select all objects (excluding the root object) in the imageData.
 *
 * @param imageData
 */
public static void selectAllObjects(final ImageData<?> imageData) {
    // Select all objects
    QP.selectAllObjects(imageData.getHierarchy(), false);
    // Add this step to the history workflow
    Map<String, String> map = new HashMap<>();
    map.put("includeRootObject", "false");
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Select all objects", map, "selectAllObjects(false)");
    imageData.getHistoryWorkflow().addStep(newStep);
}