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

Example 6 with DefaultScriptableWorkflowStep

use of qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep 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 7 with DefaultScriptableWorkflowStep

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

the class TMACommands method promptToExportTMAData.

/**
 * Prompt to export summary TMA data for a specific image to a directory.
 * @param qupath
 * @param imageData
 */
public static void promptToExportTMAData(QuPathGUI qupath, ImageData<BufferedImage> imageData) {
    String title = "Export TMA data";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null || hierarchy.isEmpty() || hierarchy.getTMAGrid() == null || hierarchy.getTMAGrid().nCores() == 0) {
        Dialogs.showErrorMessage(title, "No TMA data available!");
        return;
    }
    var overlayOptions = qupath.getViewers().stream().filter(v -> v.getImageData() == imageData).map(v -> v.getOverlayOptions()).findFirst().orElse(qupath.getOverlayOptions());
    String defaultName = ServerTools.getDisplayableImageName(imageData.getServer());
    File file = Dialogs.promptToSaveFile(null, null, defaultName, "TMA data", ".qptma");
    if (file != null) {
        if (!file.getName().endsWith(".qptma"))
            file = new File(file.getParentFile(), file.getName() + ".qptma");
        double downsample = PathPrefs.tmaExportDownsampleProperty().get();
        TMADataIO.writeTMAData(file, imageData, overlayOptions, downsample);
        WorkflowStep step = new DefaultScriptableWorkflowStep("Export TMA data", "exportTMAData(\"" + GeneralTools.escapeFilePath(file.getParentFile().getAbsolutePath()) + "\", " + downsample + ")");
        imageData.getHistoryWorkflow().addStep(step);
    // PathAwtIO.writeTMAData(file, imageData, viewer.getOverlayOptions(), Double.NaN);
    }
}

Example 8 with DefaultScriptableWorkflowStep

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

the class Commands method resetSelection.

/**
 * Reset the selection for an image.
 * @param imageData
 */
public static void resetSelection(final ImageData<?> imageData) {
    if (imageData == null) {
        logger.warn("No image available!");
        return;
    }
    // Do the action reset
    imageData.getHierarchy().getSelectionModel().clearSelection();
    // Log the appropriate command
    String method = "resetSelection();";
    WorkflowStep newStep = new DefaultScriptableWorkflowStep("Reset selection", method);
    WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
    if (newStep.equals(lastStep))
        imageData.getHistoryWorkflow().replaceLastStep(newStep);
    else
        imageData.getHistoryWorkflow().addStep(newStep);
}

Example 9 with DefaultScriptableWorkflowStep

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

the class Commands method makeInverseAnnotation.

/**
 * Make an inverse annotation for the selected objects, storing the command in the history workflow.
 * @param imageData
 * @see QP#makeInverseAnnotation(ImageData)
 */
public static void makeInverseAnnotation(ImageData<?> imageData) {
    if (imageData == null)
        return;
    logger.debug("Make inverse annotation");
    QP.makeInverseAnnotation(imageData);
    imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Invert selected annotation", "makeInverseAnnotation()"));
}

Example 10 with DefaultScriptableWorkflowStep

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

the class MeasurementManager method promptToRemoveAllMeasurements.

private boolean promptToRemoveAllMeasurements() {
    var selectedClass = comboBox.getSelectionModel().getSelectedItem();
    var selectedItems = new ArrayList<>(measurementList);
    if (selectedClass == null || 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;
    logger.info("Removing all measurements for ", PathObjectTools.getSuitableName(selectedClass, true));
    Class<? extends PathObject> cls = comboBox.getSelectionModel().getSelectedItem();
    String script;
    var hierarchy = imageData.getHierarchy();
    if (cls == PathAnnotationObject.class) {
        script = "clearAnnotationMeasurements()";
        QP.clearAnnotationMeasurements(hierarchy);
    } else if (cls == PathCellObject.class) {
        script = "clearCellMeasurements()";
        QP.clearCellMeasurements(hierarchy);
    } else if (cls == PathTileObject.class) {
        script = "clearTileMeasurements()";
        QP.clearTileMeasurements(hierarchy);
    } else if (cls == PathRootObject.class) {
        script = "clearRootMeasurements()";
        QP.clearRootMeasurements(hierarchy);
    } else if (cls == TMACoreObject.class) {
        script = "clearTMACoreMeasurements()";
        QP.clearTMACoreMeasurements(hierarchy);
    } else {
        script = "clearMeasurements(" + cls.getName() + ")";
        QP.clearMeasurements(hierarchy, cls);
    }
    // Keep for scripting
    WorkflowStep step = new DefaultScriptableWorkflowStep("Clear all measurements", script);
    imageData.getHistoryWorkflow().addStep(step);
    // Update
    refreshMeasurements();
    updateCurrentList();
    filterText.set("");
    return true;
}