Examples with TMAGrid qupath.lib.objects.hierarchy.TMAGrid used on opensource projects

Example 11 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid in project qupath by qupath.

the class TMAGridOverlay method paintOverlay.

@Override
public void paintOverlay(final Graphics2D g, final ImageRegion imageRegion, final double downsampleFactor, final ImageData<BufferedImage> imageData, final boolean paintCompletely) {
    if (!isVisible())
        return;
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null)
        return;
    TMAGrid tmaGrid = hierarchy.getTMAGrid();
    if (tmaGrid == null)
        return;
    Graphics2D g2d = (Graphics2D) g.create();
    // Set alpha composite if needed
    setAlphaComposite(g2d);
    // Rectangle serverBounds = imageRegion.getBounds();
    // Ensure antialias is on...?
    g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    PathHierarchyPaintingHelper.paintTMAGrid(g2d, tmaGrid, getOverlayOptions(), hierarchy.getSelectionModel(), downsampleFactor);
    g2d.dispose();
}

Example 12 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid in project qupath by qupath.

the class TMADearrayerPluginIJ method addRunnableTasks.

@Override
protected void addRunnableTasks(final ImageData<BufferedImage> imageData, final PathObject parentObject, List<Runnable> tasks) {
    if (dearrayer == null)
        dearrayer = new Dearrayer();
    tasks.add(() -> {
        try {
            dearrayer.runDetection(imageData, getParameterList(imageData), null);
            TMAGrid tmaGrid = dearrayer.getTMAGrid();
            if (tmaGrid != null)
                imageData.getHierarchy().setTMAGrid(tmaGrid);
        } catch (Exception e) {
            logger.error("Error running TMA dearrayer", e);
        }
    });
}

Example 13 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid in project qupath by qupath.

the class PathObjectTools method getTMACoreObjects.

/**
 * Extract a list of TMA cores from an object hierarchy.  If no cores are present, an empty list is returned.
 *
 * @param hierarchy
 * @param includeMissingCores
 * @return
 */
public static List<TMACoreObject> getTMACoreObjects(final PathObjectHierarchy hierarchy, final boolean includeMissingCores) {
    TMAGrid tmaGrid = hierarchy.getTMAGrid();
    if (tmaGrid == null || tmaGrid.nCores() == 0)
        return Collections.emptyList();
    // If we have a TMA grid, add all the objects
    if (includeMissingCores)
        return tmaGrid.getTMACoreList();
    List<TMACoreObject> cores = new ArrayList<>();
    for (TMACoreObject core : tmaGrid.getTMACoreList()) {
        if (!core.isMissing())
            cores.add(core);
    }
    return cores;
}

Example 14 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid in project qupath by qupath.

the class TMADataImporter method importTMAData.

public static void importTMAData(ImageData<?> imageData) {
    if (imageData == null) {
        Dialogs.showNoImageError(TITLE);
        return;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    if (hierarchy.getTMAGrid() == null) {
        Dialogs.showErrorMessage(TITLE, "No TMA grid has been set for the selected image!");
        return;
    }
    // Show a GUI with the current TMA grid status
    TMAGrid grid = hierarchy.getTMAGrid();
    CoreInfoGrid infoGrid = new CoreInfoGrid(grid);
    // Create the table
    TableView<CoreInfoRow> table = new TableView<>();
    table.getItems().setAll(infoGrid.getRows());
    for (int c = 0; c < grid.getGridWidth(); c++) {
        final int col = c;
        TableColumn<CoreInfoRow, TMACoreObject> tableColumn = new TableColumn<>();
        tableColumn.setCellValueFactory(column -> new ReadOnlyObjectWrapper<>(column.getValue().get(col)));
        tableColumn.setCellFactory(column -> new CoreInfoTableCell());
        tableColumn.setResizable(false);
        table.getColumns().add(tableColumn);
    }
    table.widthProperty().addListener(c -> {
        Pane headerRow = (Pane) table.lookup("TableHeaderRow");
        headerRow.setMaxHeight(0);
        headerRow.setMinHeight(0);
        headerRow.setPrefHeight(0);
        headerRow.setVisible(false);
    });
    table.getSelectionModel().setCellSelectionEnabled(true);
    BorderPane pane = new BorderPane();
    pane.setCenter(table);
    // table.setPadding(new Insets(5));
    // Label label = new Label("Import TMA map or unique identifiers for TMA cores.");
    // pane.setTop(label);
    Button btnImportData = new Button("Import data");
    btnImportData.setTooltip(new Tooltip("Import TMA core data from a tab-delimited or .csv file"));
    btnImportData.setOnAction(e -> {
        if (handleImportDataFromFile(infoGrid))
            table.refresh();
    });
    Button btnPasteData = new Button("Paste data");
    btnPasteData.setTooltip(new Tooltip("Paste tab-delimited TMA core data from the clipboard"));
    btnPasteData.setOnAction(e -> {
        if (handleImportDataFromClipboard(infoGrid))
            table.refresh();
    });
    Button btnPasteGrid = new Button("Paste grid");
    btnPasteGrid.setTooltip(new Tooltip("Paste a tab-delimited grid containing TMA core names from the clipboard"));
    btnPasteGrid.setOnAction(e -> {
        if (handlePasteGrid(infoGrid)) {
            table.refresh();
        }
    });
    Button btnLoadGrid = new Button("Import grid");
    btnLoadGrid.setTooltip(new Tooltip("Import a grid containing TMA core names from a tab-delimited or .csv file"));
    btnLoadGrid.setOnAction(e -> {
        if (handleLoadGridFromFile(infoGrid))
            table.refresh();
    });
    GridPane buttonPane = PaneTools.createColumnGridControls(btnImportData, btnPasteData, btnLoadGrid, btnPasteGrid);
    buttonPane.setHgap(10);
    buttonPane.setPadding(new Insets(5, 0, 5, 0));
    pane.setBottom(buttonPane);
    if (Dialogs.builder().title(TITLE).content(pane).buttons(ButtonType.APPLY, ButtonType.CANCEL).showAndWait().orElse(ButtonType.CANCEL) == ButtonType.APPLY) {
        infoGrid.synchronizeTMAGridToInfo();
        hierarchy.fireObjectsChangedEvent(infoGrid, new ArrayList<>(grid.getTMACoreList()));
        return;
    }
}

Example 15 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid in project qupath by qupath.

the class TMACommands method createAugmentedTMAGrid.

/**
 * Add a new row or column to a TMA grid.
 *
 * @param hierarchy
 * @param selectedCore
 * @param type
 * @return
 */
private static TMAGrid createAugmentedTMAGrid(final PathObjectHierarchy hierarchy, final TMACoreObject selectedCore, final TMAAddType type) {
    TMAGrid grid = hierarchy.getTMAGrid();
    // Convert to easier form
    boolean addAfter = type == TMAAddType.COLUMN_AFTER || type == TMAAddType.ROW_AFTER;
    boolean addColumn = type == TMAAddType.COLUMN_AFTER || type == TMAAddType.COLUMN_BEFORE;
    // Try to identify the row/column that we want
    int row = -1;
    int col = -1;
    if (selectedCore != null) {
        for (int y = 0; y < grid.getGridHeight(); y++) {
            for (int x = 0; x < grid.getGridWidth(); x++) {
                if (grid.getTMACore(y, x) == selectedCore) {
                    if (addAfter) {
                        row = y + 1;
                        col = x + 1;
                    } else {
                        row = y;
                        col = x;
                    }
                    break;
                }
            }
        }
    }
    // If we don't have a row or column, choose based on the add type
    if (row < 0) {
        switch(type) {
            case COLUMN_AFTER:
                col = grid.getGridWidth();
                break;
            case COLUMN_BEFORE:
                col = 0;
                break;
            case ROW_AFTER:
                row = grid.getGridHeight();
                break;
            case ROW_BEFORE:
                row = 0;
                break;
            default:
                break;
        }
    }
    // Compute the width of the new grid
    int newWidth = addColumn ? grid.getGridWidth() + 1 : grid.getGridWidth();
    int newHeight = addColumn ? grid.getGridHeight() : grid.getGridHeight() + 1;
    // Loop through cores, getting mean widths, heights & displacements
    RunningStatistics statsWidth = new RunningStatistics();
    RunningStatistics statsHeight = new RunningStatistics();
    RunningStatistics statsDx = new RunningStatistics();
    RunningStatistics statsDy = new RunningStatistics();
    for (int r = 0; r < grid.getGridHeight(); r++) {
        TMACoreObject coreColBefore = null;
        for (int c = 0; c < grid.getGridWidth(); c++) {
            TMACoreObject core = grid.getTMACore(r, c);
            if (!core.hasROI())
                continue;
            statsWidth.addValue(core.getROI().getBoundsWidth());
            statsHeight.addValue(core.getROI().getBoundsHeight());
            if (coreColBefore != null && coreColBefore.hasROI()) {
                statsDx.addValue(core.getROI().getCentroidX() - coreColBefore.getROI().getCentroidX());
            }
            if (r > 0) {
                TMACoreObject coreRowBefore = grid.getTMACore(r - 1, c);
                if (coreRowBefore != null && coreRowBefore.hasROI()) {
                    statsDy.addValue(core.getROI().getCentroidY() - coreRowBefore.getROI().getCentroidY());
                }
            }
            coreColBefore = core;
        }
    }
    double meanWidth = statsWidth.getMean();
    double meanHeight = statsHeight.getMean();
    double meanDx = statsDx.getMean();
    double meanDy = statsDy.getMean();
    double diameter = (meanWidth + meanHeight) / 2;
    // Create a new list of cores, adding where necessary
    List<TMACoreObject> coresNew = new ArrayList<>();
    for (int r = 0; r < newHeight; r++) {
        for (int c = 0; c < newWidth; c++) {
            // Copy existing rows & columns, or create new cores if required
            if (addColumn) {
                if (c < col) {
                    coresNew.add(grid.getTMACore(r, c));
                } else if (c > col) {
                    coresNew.add(grid.getTMACore(r, c - 1));
                } else if (c == col) {
                    // Try to get average x & y coordinates between surrounding columns
                    double x1, x2, y;
                    if (col == 0) {
                        x2 = grid.getTMACore(r, c).getROI().getCentroidX();
                        x1 = x2 - meanDx * 2;
                        y = grid.getTMACore(r, c).getROI().getCentroidY();
                    } else if (col == grid.getGridWidth()) {
                        x1 = grid.getTMACore(r, c - 1).getROI().getCentroidX();
                        x2 = x1 + meanDx * 2;
                        y = grid.getTMACore(r, c - 1).getROI().getCentroidY();
                    } else {
                        x1 = grid.getTMACore(r, c - 1).getROI().getCentroidX();
                        x2 = grid.getTMACore(r, c).getROI().getCentroidX();
                        y = (grid.getTMACore(r, c - 1).getROI().getCentroidY() + grid.getTMACore(r, c).getROI().getCentroidY()) / 2;
                    }
                    TMACoreObject coreNew = PathObjects.createTMACoreObject((x1 + x2) / 2, y, diameter, true);
                    coresNew.add(coreNew);
                }
            } else {
                if (r < row) {
                    coresNew.add(grid.getTMACore(r, c));
                } else if (r > row) {
                    coresNew.add(grid.getTMACore(r - 1, c));
                } else if (r == row) {
                    // Try to get average x & y coordinates between surrounding columns
                    double x, y1, y2;
                    if (row == 0) {
                        y2 = grid.getTMACore(r, c).getROI().getCentroidY();
                        y1 = y2 - meanDy * 2;
                        x = grid.getTMACore(r, c).getROI().getCentroidX();
                    } else if (row == grid.getGridHeight()) {
                        y1 = grid.getTMACore(r - 1, c).getROI().getCentroidY();
                        y2 = y1 + meanDy * 2;
                        x = grid.getTMACore(r - 1, c).getROI().getCentroidX();
                    } else {
                        y1 = grid.getTMACore(r - 1, c).getROI().getCentroidY();
                        y2 = grid.getTMACore(r, c).getROI().getCentroidY();
                        x = (grid.getTMACore(r - 1, c).getROI().getCentroidX() + grid.getTMACore(r, c).getROI().getCentroidX()) / 2;
                    }
                    TMACoreObject coreNew = PathObjects.createTMACoreObject(x, (y1 + y2) / 2, diameter, true);
                    coresNew.add(coreNew);
                }
            }
        }
    }
    // Update with a new TMAGrid
    return DefaultTMAGrid.create(coresNew, newWidth);
}