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

Example 1 with Workflow

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

the class PathIO method readImageDataSerialized.

@SuppressWarnings("unchecked")
private static <T> ImageData<T> readImageDataSerialized(final InputStream stream, ImageData<T> imageData, ImageServer<T> server, Class<T> cls) throws IOException {
    long startTime = System.currentTimeMillis();
    Locale locale = Locale.getDefault(Category.FORMAT);
    boolean localeChanged = false;
    try (ObjectInputStream inStream = new ObjectInputStream(new BufferedInputStream(stream))) {
        ServerBuilder<T> serverBuilder = null;
        PathObjectHierarchy hierarchy = null;
        ImageData.ImageType imageType = null;
        ColorDeconvolutionStains stains = null;
        Workflow workflow = null;
        Map<String, Object> propertyMap = null;
        String firstLine = inStream.readUTF();
        // int versionNumber = -1;
        if (!firstLine.startsWith("Data file version")) {
            logger.error("Input stream does not contain valid QuPath data!");
        }
        // else {
        // // Could try to parse version number... although frankly, at this time, we don't really care...
        // try {
        // versionNumber = NumberFormat.getInstance(Locale.US).parse(firstLine.substring("Data file version".length()).trim()).intValue();
        // } catch (Exception e) {
        // logger.warn("Unable to parse version number from {}", firstLine);
        // }
        // }
        String serverString = (String) inStream.readObject();
        // Don't log warnings if we are provided with a server
        serverBuilder = extractServerBuilder(serverString, server == null);
        while (true) {
            // logger.debug("Starting read: " + inStream.available());
            try {
                // Try to read a relevant object from the stream
                Object input = inStream.readObject();
                logger.debug("Read: {}", input);
                // If we have a Locale, then set it
                if (input instanceof Locale) {
                    if (input != locale) {
                        Locale.setDefault(Category.FORMAT, (Locale) input);
                        localeChanged = true;
                    }
                } else if (input instanceof PathObjectHierarchy)
                    hierarchy = (PathObjectHierarchy) input;
                else if (input instanceof ImageData.ImageType)
                    imageType = (ImageData.ImageType) input;
                else if (input instanceof String && "EOF".equals(input)) {
                    // else if ("EOF".equals(input)) {
                    break;
                // }
                } else if (input instanceof ColorDeconvolutionStains)
                    stains = (ColorDeconvolutionStains) input;
                else if (input instanceof Workflow)
                    workflow = (Workflow) input;
                else if (input instanceof Map)
                    propertyMap = (Map<String, Object>) input;
                else if (input == null) {
                    logger.debug("Null object will be skipped");
                } else
                    logger.warn("Unsupported object of class {} will be skipped: {}", input.getClass().getName(), input);
            } catch (ClassNotFoundException e) {
                logger.error("Unable to find class: " + e.getLocalizedMessage(), e);
            } catch (EOFException e) {
                // Try to recover from EOFExceptions - we may already have enough info
                logger.error("Reached end of file...");
                if (hierarchy == null)
                    logger.error(e.getLocalizedMessage(), e);
                break;
            }
        }
        // Create an entirely new ImageData if necessary
        var existingBuilder = imageData == null || imageData.getServer() == null ? null : imageData.getServer().getBuilder();
        if (imageData == null || !Objects.equals(serverBuilder, existingBuilder)) {
            // Create a new server if we need to
            if (server == null) {
                try {
                    server = serverBuilder.build();
                } catch (Exception e) {
                    logger.error(e.getLocalizedMessage());
                }
                ;
                if (server == null) {
                    logger.error("Warning: Unable to build server with " + serverBuilder);
                // throw new RuntimeException("Warning: Unable to create server for path " + serverPath);
                }
            }
            // TODO: Make this less clumsy... but for now we need to ensure we have a fully-initialized hierarchy (which deserialization alone doesn't achieve)
            PathObjectHierarchy hierarchy2 = new PathObjectHierarchy();
            hierarchy2.setHierarchy(hierarchy);
            hierarchy = hierarchy2;
            imageData = new ImageData<>(server, hierarchy, imageType);
        } else {
            if (imageType != null)
                imageData.setImageType(imageType);
            // Set the new hierarchy
            if (hierarchy != null)
                imageData.getHierarchy().setHierarchy(hierarchy);
        }
        // Set the other properties we have just read
        if (workflow != null) {
            imageData.getHistoryWorkflow().clear();
            imageData.getHistoryWorkflow().addSteps(workflow.getSteps());
        }
        if (stains != null) {
            imageData.setColorDeconvolutionStains(stains);
        }
        if (propertyMap != null) {
            for (Entry<String, Object> entry : propertyMap.entrySet()) imageData.setProperty(entry.getKey(), entry.getValue());
        }
        long endTime = System.currentTimeMillis();
        // if (hierarchy == null) {
        // logger.error(String.format("%s does not contain a valid QUPath object hierarchy!", file.getAbsolutePath()));
        // return null;
        // }
        logger.debug(String.format("Hierarchy with %d object(s) read in %.2f seconds", hierarchy.nObjects(), (endTime - startTime) / 1000.));
    } catch (ClassNotFoundException e1) {
        logger.warn("Class not found reading image data", e1);
    } finally {
        if (localeChanged)
            Locale.setDefault(Category.FORMAT, locale);
    }
    return imageData;
}

Example 2 with Workflow

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

the class WorkflowCommandLogView method changed.

@Override
public void changed(ObservableValue<? extends ImageData<BufferedImage>> source, ImageData<BufferedImage> imageDataOld, ImageData<BufferedImage> imageDataNew) {
    if (imageDataOld == imageDataNew)
        return;
    if (imageDataOld != null)
        imageDataOld.getHistoryWorkflow().removeWorkflowListener(this);
    if (imageDataNew != null) {
        imageDataNew.getHistoryWorkflow().addWorkflowListener(this);
        workflowProperty.set(imageDataNew.getHistoryWorkflow());
        list.getSelectionModel().clearSelection();
        Workflow workflow = imageDataNew.getHistoryWorkflow();
        list.getItems().setAll(workflow.getSteps());
        workflowUpdated(workflow);
    } else {
        workflowProperty.set(null);
        list.getItems().clear();
        workflowUpdated(null);
    }
}

Example 3 with Workflow

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

the class WorkflowCommandLogView method createPane.

protected BorderPane createPane() {
    BorderPane pane = new BorderPane();
    TableColumn<KeyValue<Object>, String> col1 = new TableColumn<>("Parameter");
    col1.setCellValueFactory(c -> c.getValue().keyProperty());
    TableColumn<KeyValue<Object>, Object> col2 = new TableColumn<>("Value");
    col2.setCellValueFactory(c -> c.getValue().valueProperty());
    col2.setCellFactory(t -> new ParameterTableCell<>());
    table.getColumns().add(col1);
    table.getColumns().add(col2);
    table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
    SplitPane splitPane = new SplitPane();
    splitPane.setOrientation(Orientation.VERTICAL);
    splitPane.getItems().addAll(list, table);
    // Allow multiple selections for static model
    list.getSelectionModel().setSelectionMode(isStaticWorkflow ? SelectionMode.MULTIPLE : SelectionMode.SINGLE);
    list.getSelectionModel().selectedItemProperty().addListener((e, f, g) -> {
        WorkflowStep step = list.getSelectionModel().getSelectedItem();
        populateList(table.getItems(), step);
    });
    final ContextMenu contextMenu = new ContextMenu();
    MenuItem miCopyCommand = new MenuItem("Copy command" + (isStaticWorkflow ? "s" : ""));
    miCopyCommand.setOnAction(e -> {
        List<Integer> indices = list.getSelectionModel().getSelectedIndices();
        if (indices == null || indices.isEmpty())
            return;
        copyScriptToClipboard(indices);
    });
    miCopyCommand.disableProperty().bind(workflowProperty.isNull());
    contextMenu.getItems().setAll(miCopyCommand);
    if (isStaticWorkflow) {
        MenuItem miRemoveSelected = new MenuItem("Remove selected items");
        miRemoveSelected.setOnAction(e -> {
            var steps = getSelectedIndices();
            if (steps == null || steps.isEmpty())
                return;
            String message = steps.size() == 1 ? "Remove workflow step?" : "Remove " + steps.size() + " workflow steps?";
            if (!Dialogs.showYesNoDialog("Remove workflow steps", message))
                return;
            Collections.sort(steps);
            for (int i = steps.size() - 1; i >= 0; i--) getWorkflow().removeStep(steps.get(i));
        // workflow.removeSteps(steps);
        });
        miRemoveSelected.disableProperty().bind(workflowProperty.isNull());
        MenuItem miMoveUp = new MenuItem("Move up");
        miMoveUp.setOnAction(e -> {
            var indices = getSelectedIndices();
            if (indices == null || indices.isEmpty() || indices.get(0) <= 0)
                return;
            var workflow = getWorkflow();
            List<WorkflowStep> steps = new ArrayList<>(workflow.getSteps());
            WorkflowStep[] stepsRemoved = new WorkflowStep[indices.size()];
            workflow.removeSteps(steps);
            int[] newIndices = new int[indices.size()];
            for (int i = indices.size() - 1; i >= 0; i--) {
                int ind = indices.get(i);
                int indNew = ind - 1;
                newIndices[i] = indNew;
                stepsRemoved[i] = steps.remove(ind);
            }
            for (int i = 0; i < indices.size(); i++) {
                steps.add(newIndices[i], stepsRemoved[i]);
            }
            workflow.addSteps(steps);
            list.getSelectionModel().clearSelection();
            list.getSelectionModel().selectIndices(newIndices[0], newIndices);
        });
        miMoveUp.disableProperty().bind(workflowProperty.isNull());
        MenuItem miMoveDown = new MenuItem("Move down");
        miMoveDown.setOnAction(e -> {
            var indices = getSelectedIndices();
            var workflow = getWorkflow();
            if (indices == null || indices.isEmpty() || indices.get(indices.size() - 1) >= workflow.size() - 1)
                return;
            list.getSelectionModel().clearSelection();
            Collections.sort(indices);
            List<WorkflowStep> steps = new ArrayList<>(workflow.getSteps());
            WorkflowStep[] stepsRemoved = new WorkflowStep[indices.size()];
            workflow.removeSteps(steps);
            int[] newIndices = new int[indices.size()];
            for (int i = indices.size() - 1; i >= 0; i--) {
                int ind = indices.get(i);
                int indNew = ind + 1;
                newIndices[i] = indNew;
                stepsRemoved[i] = steps.remove(ind);
            }
            for (int i = 0; i < indices.size(); i++) {
                steps.add(newIndices[i], stepsRemoved[i]);
            }
            workflow.addSteps(steps);
            list.getSelectionModel().select(newIndices[0]);
            list.getSelectionModel().selectIndices(newIndices[0], newIndices);
        // int ind = list.getSelectionModel().getSelectedIndex();
        // if (ind < 0 || ind >= workflow.size()-1)
        // return;
        // List<WorkflowStep> steps = new ArrayList<>(workflow.getSteps());
        // WorkflowStep step = steps.remove(ind);
        // steps.add(ind+1, step);
        // workflow.removeSteps(steps);
        // workflow.addSteps(steps);
        // list.getSelectionModel().select(step);
        });
        miMoveDown.disableProperty().bind(workflowProperty.isNull());
        contextMenu.getItems().addAll(new SeparatorMenuItem(), miMoveUp, miMoveDown, new SeparatorMenuItem(), miRemoveSelected);
    }
    list.setCellFactory(new Callback<ListView<WorkflowStep>, ListCell<WorkflowStep>>() {

        @Override
        public ListCell<WorkflowStep> call(ListView<WorkflowStep> p) {
            ListCell<WorkflowStep> cell = new ListCell<>() {

                @Override
                protected void updateItem(WorkflowStep value, boolean bln) {
                    super.updateItem(value, bln);
                    if (value instanceof WorkflowStep)
                        setText(value.getName());
                    else if (value == null)
                        setText(null);
                    else
                        setText(value.toString());
                    setContextMenu(contextMenu);
                    setOnMouseClicked(e -> {
                        // Only handle double clicks
                        if (!e.isPopupTrigger() && e.getClickCount() == 2)
                            runWorkflowStepInteractively(qupath, value);
                    });
                    setOnKeyPressed(e -> {
                        if (copyCombination.match(e)) {
                            copyScriptToClipboard(getSelectedIndices());
                            e.consume();
                        }
                    });
                }
            };
            return cell;
        }
    });
    pane.setCenter(splitPane);
    Button btnCreateScript = new Button("Create script");
    btnCreateScript.setMaxWidth(Double.MAX_VALUE);
    btnCreateScript.setOnAction(e -> showScript());
    btnCreateScript.disableProperty().bind(workflowProperty.isNull());
    Button btnCreateWorkflow = null;
    if (!isStaticWorkflow) {
        btnCreateWorkflow = new Button("Create workflow");
        btnCreateWorkflow.setMaxWidth(Double.MAX_VALUE);
        btnCreateWorkflow.setOnAction(e -> {
            var workflow = getWorkflow();
            if (workflow == null)
                return;
            Stage stage = new Stage();
            stage.initOwner(qupath.getStage());
            stage.setTitle("Workflow");
            Workflow workflowNew = new Workflow();
            workflowNew.addSteps(workflow.getSteps());
            stage.setScene(new Scene(new WorkflowCommandLogView(qupath, workflowNew).getPane(), 400, 600));
            stage.show();
        });
        btnCreateWorkflow.disableProperty().bind(workflowProperty.isNull());
        pane.setBottom(PaneTools.createColumnGridControls(btnCreateWorkflow, btnCreateScript));
    } else
        pane.setBottom(btnCreateScript);
    // pane.setBottom(btnGenerateScript);
    return pane;
}