Examples with ImageData qupath.lib.images.ImageData used on opensource projects

Example 16 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class SummaryMeasurementTableCommand method showTable.

/**
 * Show a measurement table for the specified image data.
 * @param imageData the image data
 * @param type the object type to show
 */
public void showTable(ImageData<BufferedImage> imageData, Class<? extends PathObject> type) {
    if (imageData == null) {
        Dialogs.showNoImageError("Show measurement table");
        return;
    }
    final PathObjectHierarchy hierarchy = imageData.getHierarchy();
    ObservableMeasurementTableData model = new ObservableMeasurementTableData();
    model.setImageData(imageData, imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type));
    SplitPane splitPane = new SplitPane();
    HistogramDisplay histogramDisplay = new HistogramDisplay(model, true);
    // table.setTableMenuButtonVisible(true);
    TableView<PathObject> table = new TableView<>();
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    table.getSelectionModel().getSelectedItems().addListener(new ListChangeListener<PathObject>() {

        @Override
        public void onChanged(ListChangeListener.Change<? extends PathObject> c) {
            synchronizeSelectionModelToTable(hierarchy, c, table);
        }
    });
    StringProperty displayedName = new SimpleStringProperty(ServerTools.getDisplayableImageName(imageData.getServer()));
    var title = Bindings.createStringBinding(() -> {
        if (type == null)
            return "Results " + displayedName.get();
        else
            return PathObjectTools.getSuitableName(type, false) + " results - " + displayedName.get();
    }, displayedName);
    // Handle double-click as a way to center on a ROI
    // var enter = new KeyCodeCombination(KeyCode.ENTER);
    table.setRowFactory(params -> {
        var row = new TableRow<PathObject>();
        row.setOnMouseClicked(e -> {
            if (e.getClickCount() == 2) {
                maybeCenterROI(row.getItem());
            }
        });
        // });
        return row;
    });
    // Create columns according to the table model
    // for (int i = 0; i < model.getColumnCount(); i++) {
    // // Add string column
    // if (model.getColumnClass(i).equals(String.class)) {
    // TableColumn<PathObject, String> col = null;
    // col = new TableColumn<>(model.getColumnName(i));
    // col.setCellValueFactory(new Callback<CellDataFeatures<PathObject, String>, ObservableValue<String>>() {
    // public ObservableValue<String> call(CellDataFeatures<PathObject, String> val) {
    // return new SimpleStringProperty(val.getValue().getDisplayedName());
    // }
    // });
    // col.setCellFactory(column -> new BasicTableCell<String>());
    // table.getColumns().add(col);
    // }
    // }
    boolean tmaCoreList = TMACoreObject.class.isAssignableFrom(type);
    // Add TMA core columns, if suitable
    if (tmaCoreList) {
        TableColumn<PathObject, ROI> col = new TableColumn<>("Image");
        col.setCellValueFactory(val -> new SimpleObjectProperty<>(val.getValue().getROI()));
        double maxWidth = maxDimForTMACore;
        double padding = 10;
        col.setCellFactory(column -> new TMACoreTableCell(table, imageData.getServer(), maxWidth, padding));
        col.widthProperty().addListener((v, o, n) -> table.refresh());
        col.setMaxWidth(maxWidth + padding * 2);
        table.getColumns().add(col);
        // While here, make sure we have fewer bins - don't usually have all that many cores
        histogramDisplay.setNumBins(10);
    }
    // Create numeric columns
    for (String columnName : model.getAllNames()) {
        // Add column
        if (model.isStringMeasurement(columnName)) {
            TableColumn<PathObject, String> col = new TableColumn<>(columnName);
            col.setCellValueFactory(column -> model.createStringMeasurement(column.getValue(), column.getTableColumn().getText()));
            col.setCellFactory(column -> new BasicTableCell<>());
            table.getColumns().add(col);
        } else {
            TableColumn<PathObject, Number> col = new TableColumn<>(columnName);
            col.setCellValueFactory(column -> model.createNumericMeasurement(column.getValue(), column.getTableColumn().getText()));
            col.setCellFactory(column -> new NumericTableCell<PathObject>(histogramDisplay));
            table.getColumns().add(col);
        }
    }
    // Set the PathObjects - need to deal with sorting, since a FilteredList won't handle it directly
    SortedList<PathObject> items = new SortedList<>(model.getItems());
    items.comparatorProperty().bind(table.comparatorProperty());
    table.setItems(items);
    List<ButtonBase> buttons = new ArrayList<>();
    ToggleButton btnHistogram = new ToggleButton("Show histograms");
    btnHistogram.selectedProperty().addListener((v, o, n) -> {
        if (n) {
            Pane paneHistograms = histogramDisplay.getPane();
            splitPane.getItems().add(paneHistograms);
        } else if (histogramDisplay != null)
            splitPane.getItems().remove(histogramDisplay.getPane());
    });
    buttons.add(btnHistogram);
    // Button btnScatterplot = new Button("Show scatterplots");
    // btnScatterplot.setOnAction(e -> {
    // SwingUtilities.invokeLater(() -> {
    // JDialog dialog = new ScatterplotDisplay(null, "Scatterplots: " + displayedName, model).getDialog();
    // dialog.setLocationRelativeTo(null);
    // dialog.setVisible(true);
    // });
    // });
    // buttons.add(btnScatterplot);
    Button btnCopy = new Button("Copy to clipboard");
    btnCopy.setOnAction(e -> {
        // TODO: Deal with repetition immediately below...
        Set<String> excludeColumns = new HashSet<>();
        for (TableColumn<?, ?> col : table.getColumns()) {
            if (!col.isVisible())
                excludeColumns.add(col.getText());
        }
        copyTableContentsToClipboard(model, excludeColumns);
    });
    buttons.add(btnCopy);
    Button btnSave = new Button("Save");
    btnSave.setOnAction(e -> {
        Set<String> excludeColumns = new HashSet<>();
        for (TableColumn<?, ?> col : table.getColumns()) {
            if (!col.isVisible())
                excludeColumns.add(col.getText());
        }
        File fileOutput = promptForOutputFile();
        if (fileOutput == null)
            return;
        if (saveTableModel(model, fileOutput, excludeColumns)) {
            WorkflowStep step;
            String includeColumns;
            if (excludeColumns.isEmpty())
                includeColumns = "";
            else {
                List<String> includeColumnList = new ArrayList<>(model.getAllNames());
                includeColumnList.removeAll(excludeColumns);
                includeColumns = ", " + includeColumnList.stream().map(s -> "'" + s + "'").collect(Collectors.joining(", "));
            }
            String path = qupath.getProject() == null ? fileOutput.toURI().getPath() : fileOutput.getParentFile().toURI().getPath();
            if (type == TMACoreObject.class) {
                step = new DefaultScriptableWorkflowStep("Save TMA measurements", String.format("saveTMAMeasurements('%s'%s)", path, includeColumns));
            } else if (type == PathAnnotationObject.class) {
                step = new DefaultScriptableWorkflowStep("Save annotation measurements", String.format("saveAnnotationMeasurements('%s\'%s)", path, includeColumns));
            } else if (type == PathDetectionObject.class) {
                step = new DefaultScriptableWorkflowStep("Save detection measurements", String.format("saveDetectionMeasurements('%s'%s)", path, includeColumns));
            } else {
                step = new DefaultScriptableWorkflowStep("Save measurements", String.format("saveMeasurements('%s', %s%s)", path, type == null ? null : type.getName(), includeColumns));
            }
            imageData.getHistoryWorkflow().addStep(step);
        }
    });
    buttons.add(btnSave);
    Stage frame = new Stage();
    frame.initOwner(qupath.getStage());
    frame.titleProperty().bind(title);
    BorderPane paneTable = new BorderPane();
    paneTable.setCenter(table);
    // Add text field to filter visible columns
    TextField tfColumnFilter = new TextField();
    GridPane paneFilter = new GridPane();
    paneFilter.add(new Label("Column filter"), 0, 0);
    paneFilter.add(tfColumnFilter, 1, 0);
    GridPane.setHgrow(tfColumnFilter, Priority.ALWAYS);
    paneFilter.setHgap(5);
    if (tmaCoreList) {
        CheckBox cbHideMissing = new CheckBox("Hide missing cores");
        paneFilter.add(cbHideMissing, 2, 0);
        cbHideMissing.selectedProperty().addListener((v, o, n) -> {
            if (n) {
                model.setPredicate(p -> (!(p instanceof TMACoreObject)) || !((TMACoreObject) p).isMissing());
            } else
                model.setPredicate(null);
        });
        cbHideMissing.setSelected(true);
    }
    paneFilter.setPadding(new Insets(2, 5, 2, 5));
    paneTable.setBottom(paneFilter);
    StringProperty columnFilter = tfColumnFilter.textProperty();
    columnFilter.addListener((v, o, n) -> {
        String val = n.toLowerCase().trim();
        if (val.isEmpty()) {
            for (TableColumn<?, ?> col : table.getColumns()) {
                if (!col.isVisible())
                    col.setVisible(true);
            }
            return;
        }
        for (TableColumn<?, ?> col : table.getColumns()) {
            col.setVisible(col.getText().toLowerCase().contains(val));
        }
    });
    BorderPane pane = new BorderPane();
    // pane.setCenter(table);
    splitPane.getItems().add(paneTable);
    pane.setCenter(splitPane);
    GridPane panelButtons = PaneTools.createColumnGridControls(buttons.toArray(new ButtonBase[0]));
    pane.setBottom(panelButtons);
    PathObjectHierarchyListener listener = new PathObjectHierarchyListener() {

        @Override
        public void hierarchyChanged(PathObjectHierarchyEvent event) {
            if (event.isChanging())
                return;
            if (!Platform.isFxApplicationThread()) {
                Platform.runLater(() -> hierarchyChanged(event));
                return;
            }
            if (imageData != null)
                displayedName.set(ServerTools.getDisplayableImageName(imageData.getServer()));
            model.refreshEntries();
            table.refresh();
            if (histogramDisplay != null)
                histogramDisplay.refreshHistogram();
        }
    };
    QuPathViewer viewer = qupath.getViewer();
    TableViewerListener tableViewerListener = new TableViewerListener(viewer, table);
    frame.setOnShowing(e -> {
        hierarchy.addPathObjectListener(listener);
        viewer.addViewerListener(tableViewerListener);
    });
    frame.setOnHiding(e -> {
        hierarchy.removePathObjectListener(listener);
        viewer.removeViewerListener(tableViewerListener);
    });
    Scene scene = new Scene(pane, 600, 500);
    frame.setScene(scene);
    frame.show();
    // Add ability to remove entries from table
    ContextMenu menu = new ContextMenu();
    Menu menuLimitClasses = new Menu("Show classes");
    menu.setOnShowing(e -> {
        Set<PathClass> representedClasses = model.getBackingListEntries().stream().map(p -> p.getPathClass() == null ? null : p.getPathClass().getBaseClass()).collect(Collectors.toCollection(() -> new HashSet<>()));
        representedClasses.remove(null);
        if (representedClasses.isEmpty()) {
            menuLimitClasses.setVisible(false);
        } else {
            menuLimitClasses.setVisible(true);
        }
        menuLimitClasses.getItems().clear();
        List<PathClass> sortedClasses = new ArrayList<>(representedClasses);
        Collections.sort(sortedClasses);
        MenuItem miClass = new MenuItem("All");
        miClass.setOnAction(e2 -> {
            model.setPredicate(null);
            histogramDisplay.refreshHistogram();
        });
        menuLimitClasses.getItems().add(miClass);
        for (PathClass pathClass : sortedClasses) {
            miClass = new MenuItem(pathClass.getName());
            miClass.setOnAction(e2 -> {
                model.setPredicate(p -> pathClass.isAncestorOf(p.getPathClass()));
                histogramDisplay.refreshHistogram();
            });
            menuLimitClasses.getItems().add(miClass);
        }
    });
    if (type != TMACoreObject.class) {
        menu.getItems().add(menuLimitClasses);
        table.setContextMenu(menu);
    }
}

Example 17 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class ScriptCommand method run.

@Override
public void run() {
    try {
        if (projectPath != null && !projectPath.toLowerCase().endsWith(ProjectIO.getProjectExtension()))
            throw new IOException("Project file must end with '.qpproj'");
        if (scriptCommand == null) {
            if (scriptFile == null || scriptFile.equals("") || !scriptFile.endsWith(".groovy"))
                throw new IOException("File must be a valid script file (.groovy): " + scriptFile);
        } else if (scriptFile != null) {
            throw new IllegalArgumentException("Either a script file or a script command may be provided, but not both!");
        }
        // Ensure we have a tile cache set
        createTileCache();
        // Set classloader to include any available extensions
        var extensionClassLoader = new ExtensionClassLoader();
        extensionClassLoader.refresh();
        ImageServerProvider.setServiceLoader(ServiceLoader.load(ImageServerBuilder.class, extensionClassLoader));
        Thread.currentThread().setContextClassLoader(extensionClassLoader);
        // Unfortunately necessary to force initialization (including GsonTools registration of some classes)
        QP.getCoreClasses();
        ImageData<BufferedImage> imageData;
        if (projectPath != null && !projectPath.equals("")) {
            String path = QuPath.getEncodedPath(projectPath);
            Project<BufferedImage> project = ProjectIO.loadProject(new File(path), BufferedImage.class);
            for (var entry : project.getImageList()) {
                if (imagePath != null && !imagePath.equals("") && !imagePath.equals(entry.getImageName()))
                    continue;
                logger.info("Running script for {}", entry.getImageName());
                imageData = entry.readImageData();
                try {
                    Object result = runScript(project, imageData);
                    if (result != null)
                        logger.info("Script result: {}", result);
                    if (save)
                        entry.saveImageData(imageData);
                } catch (Exception e) {
                    logger.error("Error running script for image: " + entry.getImageName(), e);
                    // Otherwise, try to recover and continue processing images
                    if (imagePath != null && imagePath.equals(entry.getImageName()))
                        throw new RuntimeException(e);
                } finally {
                    imageData.getServer().close();
                }
            }
        } else if (imagePath != null && !imagePath.equals("")) {
            String path = QuPath.getEncodedPath(imagePath);
            URI uri = GeneralTools.toURI(path);
            ImageServer<BufferedImage> server = ImageServers.buildServer(uri, parseArgs(serverArgs));
            imageData = new ImageData<>(server);
            Object result = runScript(null, imageData);
            if (result != null)
                logger.info("Script result: {}", result);
            server.close();
        } else {
            Object result = runScript(null, null);
            if (result != null)
                logger.info("Script result: {}", result);
        }
    } catch (Exception e) {
        logger.error(e.getLocalizedMessage(), e);
        throw new RuntimeException(e);
    }
}

Example 18 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class PathClassifierPane method runClassifier.

void runClassifier() {
    QuPathViewer viewer = viewerValue.getValue();
    if (viewer == null)
        return;
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (classifier == null || imageData == null || !classifier.isValid())
        return;
    Collection<PathObject> pathObjects = imageData.getHierarchy().getDetectionObjects();
    var availableFeatures = PathClassifierTools.getAvailableFeatures(pathObjects);
    var requiredFeatures = classifier.getRequiredMeasurements();
    String missingFeatures = requiredFeatures.stream().filter(p -> !availableFeatures.contains(p)).collect(Collectors.joining("\n\t"));
    if (!missingFeatures.isEmpty())
        logger.warn("Detection objects are missing the following feature(s):\n\t" + missingFeatures + "\nWill proceed with classification anyway..");
    // SwingUtilities.getRoot(viewer).setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    try {
        PathClassifierTools.runClassifier(imageData.getHierarchy(), classifier);
        // Log the classifier
        if (pathClassifier != null) {
            imageData.getHistoryWorkflow().addStep(new RunSavedClassifierWorkflowStep(pathClassifier));
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        // SwingUtilities.getRoot(viewer).setCursor(cursor);
        // Update displayed list - names may have changed - and classifier summary
        updateClassifierSummary();
    }
}

Example 19 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class DensityMapDataOp method apply.

@Override
public Mat apply(ImageData<BufferedImage> imageData, RegionRequest request) throws IOException {
    ensureInitialized();
    logger.trace("Applying density map op for {}", request);
    // Calculate how much padding we need
    var padding = op.getPadding();
    if (!padding.isEmpty()) {
        // Add padding to the request
        double downsample = request.getDownsample();
        var padding2 = Padding.getPadding((int) Math.round(padding.getX1() * downsample), (int) Math.round(padding.getX2() * downsample), (int) Math.round(padding.getY1() * downsample), (int) Math.round(padding.getY2() * downsample));
        request = request.pad2D(padding2);
    }
    // Get all objects within the padded region
    var allPathObjects = imageData.getHierarchy().getObjectsForRegion(null, request, null).stream().filter(allObjects).collect(Collectors.toList());
    if (allPathObjects.size() == 1)
        logger.trace("Generating counts tile for 1 object");
    else
        logger.trace("Generating counts tile for {} objects", allPathObjects.size());
    // Create an output mat
    int nChannels = getChannelCount();
    int width = (int) Math.round(request.getWidth() / request.getDownsample());
    int height = (int) Math.round(request.getHeight() / request.getDownsample());
    var mat = new Mat(height, width, opencv_core.CV_64FC(nChannels), Scalar.ZERO);
    DoubleIndexer idx = mat.createIndexer();
    // Get points representing all the centroids of each subpopulation of object
    // Use these to increment pixel values in a counts image
    int c = 0;
    for (var entry : primaryObjects.entrySet()) {
        var predicate = entry.getValue();
        var primaryROIs = allPathObjects.stream().filter(predicate).map(p -> PathObjectTools.getROI(p, true)).collect(Collectors.toList());
        var points = objectsToPoints(primaryROIs);
        incrementCounts(idx, points, request, width, height, c);
        c++;
    }
    // Get points for all objects, if we need them
    if (c < getChannelCount()) {
        var allObjectROIs = allPathObjects.stream().map(p -> PathObjectTools.getROI(p, true)).collect(Collectors.toList());
        var points = objectsToPoints(allObjectROIs);
        incrementCounts(idx, points, request, width, height, c);
        c++;
    }
    idx.close();
    // Now apply the op
    var output = this.op.apply(mat);
    return output;
}

Example 20 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class OMEPyramidWriterCommand method run.

@Override
public void run() {
    if (currentTask != null && !currentTask.isDone()) {
        if (!Dialogs.showConfirmDialog("OME Pyramid writer", "Do you want to stop the current export?"))
            // TODO: Delete exporting file?
            return;
        else {
            currentTask.cancel(true);
        }
    }
    QuPathViewer viewer = qupath.getViewer();
    int zPos = viewer.getZPosition();
    int tPos = viewer.getTPosition();
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (imageData == null) {
        Dialogs.showNoImageError("OME Pyramid writer");
        return;
    }
    ImageServer<BufferedImage> server = imageData.getServer();
    // Region
    PathObject selected = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ImageRegion region = null;
    int width, height;
    if (selected == null || !selected.hasROI() || !selected.getROI().isArea()) {
        width = server.getWidth();
        height = server.getHeight();
    } else {
        region = ImageRegion.createInstance(selected.getROI());
        width = region.getWidth();
        height = region.getHeight();
    }
    // Set compression - with a sanity check for validity, defaulting to another comparable method if necessary
    CompressionType compression = getDefaultPyramidCompression();
    List<String> compatibleCompression = Arrays.stream(CompressionType.values()).filter(c -> c.supportsImage(server)).map(c -> c.toFriendlyString()).collect(Collectors.toList());
    if (!compatibleCompression.contains(compression.toFriendlyString()))
        compression = CompressionType.DEFAULT;
    var params = new ParameterList().addChoiceParameter("compression", "Compression type", compression.toFriendlyString(), compatibleCompression).addIntParameter("scaledDownsample", "Pyramidal downsample", scaledDownsample.get(), "", 1, 8, "Amount to downsample each consecutive pyramidal level; use 1 to indicate the image should not be pyramidal").addIntParameter("tileSize", "Tile size", getDefaultTileSize(), "px", "Tile size for export (should be between 128 and 8192)").addBooleanParameter("parallelize", "Parallelize export", parallelizeTiling.get(), "Export image tiles in parallel - " + "this should be faster, best keep it on unless you encounter export problems").addBooleanParameter("allZ", "All z-slices", allZ.get(), "Include all z-slices in the stack").addBooleanParameter("allT", "All timepoints", allT.get(), "Include all timepoints in the time-series");
    boolean singleTile = server.getTileRequestManager().getTileRequests(RegionRequest.createInstance(server)).size() == 1;
    params.setHiddenParameters(server.nZSlices() == 1, "allZ");
    params.setHiddenParameters(server.nTimepoints() == 1, "allT");
    params.setHiddenParameters(singleTile, "tileSize", "parallelize");
    if (!Dialogs.showParameterDialog("Export OME-TIFF", params))
        return;
    compression = CompressionType.fromFriendlyString((String) params.getChoiceParameterValue("compression"));
    defaultPyramidCompression.set(compression);
    int downsampleScale = params.getIntParameterValue("scaledDownsample");
    scaledDownsample.set(downsampleScale);
    int tileSize = params.getIntParameterValue("tileSize");
    boolean parallelize = params.getBooleanParameterValue("parallelize");
    if (!singleTile) {
        tileSize = GeneralTools.clipValue(tileSize, 128, 8192);
        defaultTileSize.set(tileSize);
        parallelizeTiling.set(parallelize);
    }
    boolean doAllZ = false;
    boolean doAllT = false;
    if (server.nZSlices() > 1) {
        doAllZ = params.getBooleanParameterValue("allZ");
        allZ.set(doAllZ);
    }
    if (server.nTimepoints() > 1) {
        doAllT = params.getBooleanParameterValue("allT");
        allT.set(doAllT);
    }
    OMEPyramidWriter.Builder builder = new OMEPyramidWriter.Builder(server);
    if (region != null) {
        builder = builder.region(region);
    } else {
        if (server.nZSlices() > 1 && !doAllZ)
            builder.zSlice(zPos);
        if (server.nTimepoints() > 1 && !doAllT)
            builder.timePoint(tPos);
    }
    builder.compression(compression);
    if (downsampleScale <= 1 || Math.max(width, height) / server.getDownsampleForResolution(0) < minSizeForTiling.get())
        builder.downsamples(server.getDownsampleForResolution(0));
    else
        builder.scaledDownsampling(server.getDownsampleForResolution(0), downsampleScale);
    // Set tile size; if we just have one tile, use the image width & height
    if (singleTile)
        builder = builder.tileSize(width, height);
    else
        builder = builder.tileSize(tileSize).parallelize(parallelize);
    if (server.nZSlices() > 1 && doAllZ)
        builder.allZSlices();
    if (server.nTimepoints() > 1 && doAllT)
        builder.allTimePoints();
    // Prompt for file
    File fileOutput = Dialogs.promptToSaveFile("Write pyramid", null, null, "OME TIFF pyramid", ".ome.tif");
    if (fileOutput == null)
        return;
    String name = fileOutput.getName();
    // We can have trouble with only the '.tif' part of the name being included
    if (name.endsWith(".tif") && !name.endsWith(".ome.tif"))
        fileOutput = new File(fileOutput.getParentFile(), name.substring(0, name.length() - 4) + ".ome.tif");
    OMEPyramidSeries writer = builder.build();
    if (pool == null) {
        pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("ome-pyramid-export", false));
    }
    currentTask = pool.submit(new WriterTask(OMEPyramidWriter.createWriter(writer), fileOutput.getAbsolutePath()));
}