Examples with TMACoreObject qupath.lib.objects.TMACoreObject used on opensource projects

Example 31 with TMACoreObject

use of qupath.lib.objects.TMACoreObject in project qupath by qupath.

the class FindConvexHullDetectionsPlugin method getParentObjects.

@Override
protected Collection<? extends PathObject> getParentObjects(PluginRunner<T> runner) {
    PathObjectHierarchy hierarchy = getHierarchy(runner);
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    if (selected instanceof TMACoreObject)
        return Collections.singleton(selected);
    if (hierarchy.getTMAGrid() != null)
        return hierarchy.getTMAGrid().getTMACoreList();
    else
        return Collections.emptyList();
}

Example 32 with TMACoreObject

use of qupath.lib.objects.TMACoreObject 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);
}

Example 33 with TMACoreObject

use of qupath.lib.objects.TMACoreObject in project qupath by qupath.

the class TMACommands method promptToAddTMARowOrColumn.

/**
 * Add a new row or column to a TMA grid.
 *
 * @param imageData
 * @param type
 * @return
 */
private static boolean promptToAddTMARowOrColumn(final ImageData<?> imageData, final TMAAddType type) {
    String NAME = type.commandName();
    if (imageData == null) {
        Dialogs.showNoImageError(NAME);
        return false;
    }
    if (imageData.getHierarchy().getTMAGrid() == null) {
        Dialogs.showErrorMessage(NAME, "No image with dearrayed TMA cores selected!");
        return false;
    }
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
    TMACoreObject selectedCore = null;
    if (selected != null)
        selectedCore = PathObjectTools.getAncestorTMACore(selected);
    TMAGrid gridNew = createAugmentedTMAGrid(hierarchy, selectedCore, type);
    double w = imageData.getServer().getWidth();
    double h = imageData.getServer().getHeight();
    // Check if the core centroids all fall within the image or not
    int outsideCores = 0;
    for (TMACoreObject core : gridNew.getTMACoreList()) {
        // Shouldn't happen...
        if (!core.hasROI())
            continue;
        // Check if the centroid for any *new* core falls within the image
        // (don't fail if an existing core is outside)
        double x = core.getROI().getCentroidX();
        double y = core.getROI().getCentroidY();
        if (x < 0 || x >= w || y < 0 || y >= h) {
            if (!hierarchy.getTMAGrid().getTMACoreList().contains(core)) {
                outsideCores++;
            }
        // throw new IllegalArgumentException("Cannot update TMA grid - not enough space within image");
        }
    }
    if (outsideCores > 0) {
        String label = outsideCores == 1 ? "core" : "cores";
        if (!Dialogs.showConfirmDialog("Add to TMA Grid", "Not enough space within image to store " + outsideCores + " new " + label + " - proceed anyway?"))
            return false;
    }
    // If we got this far, update the grid
    hierarchy.setTMAGrid(gridNew);
    // Prompt for relabelling
    TMACommands.promptToRelabelTMAGrid(imageData);
    return true;
}

Example 34 with TMACoreObject

use of qupath.lib.objects.TMACoreObject in project qupath by qupath.

the class ColorToolsFX method getDisplayedColorARGB.

/**
 * Get the color with which an object should be displayed, as a packaged ARGB integer.
 *
 * This could be stored internally, or obtained from its PathClass.
 *
 * If neither of these produces a result, a default color will be returned based on PathPrefs
 * for the specific (Java) class of the PathObject.
 *
 * Assuming PathPrefs does not contain any nulls, this will therefore not return nulls either.
 *
 * @param pathObject
 * @return
 */
public static Integer getDisplayedColorARGB(final PathObject pathObject) {
    // Check if any color has been set - if so, return it
    Integer color = pathObject.getColorRGB();
    if (color != null)
        return color;
    // Check if any class has been set, if so then use its color
    PathClass pathClass = pathObject.getPathClass();
    if (pathClass != null)
        color = pathClass.getColor();
    if (color != null)
        return color;
    if (pathObject instanceof PathTileObject)
        return PathPrefs.colorTileProperty().getValue();
    if (pathObject instanceof TMACoreObject) {
        if (((TMACoreObject) pathObject).isMissing())
            return PathPrefs.colorTMAMissingProperty().getValue();
        else
            return PathPrefs.colorTMAProperty().getValue();
    }
    return PathPrefs.colorDefaultObjectsProperty().getValue();
}

Example 35 with TMACoreObject

use of qupath.lib.objects.TMACoreObject in project qupath by qupath.

the class TMAExplorer method createAndShowStage.

private void createAndShowStage() {
    Project<BufferedImage> project = qupath.getProject();
    entries.clear();
    if (project != null) {
        // Create an output directory for the images
        File dirBaseImageOutput = Projects.getBaseDirectory(project);
        dirBaseImageOutput = new File(dirBaseImageOutput, "TMA");
        dirBaseImageOutput = new File(dirBaseImageOutput, "images");
        if (!dirBaseImageOutput.exists())
            dirBaseImageOutput.mkdirs();
        Map<String, RunningStatistics> statsMap = new HashMap<>();
        for (ProjectImageEntry<BufferedImage> imageEntry : project.getImageList()) {
            // Look for data file
            if (!imageEntry.hasImageData())
                continue;
            File dirImageOutput = new File(dirBaseImageOutput, imageEntry.getImageName());
            if (!dirImageOutput.exists())
                dirImageOutput.mkdirs();
            // Read data
            ImageData<BufferedImage> imageData;
            try {
                imageData = imageEntry.readImageData();
            } catch (IOException e) {
                logger.error("Error reading ImageData for " + imageEntry.getImageName(), e);
                continue;
            }
            TMAGrid tmaGrid = imageData.getHierarchy().getTMAGrid();
            if (tmaGrid == null) {
                logger.warn("No TMA data for {}", imageEntry.getImageName());
                continue;
            }
            // Figure out downsample value
            ImageServer<BufferedImage> server = imageData.getServer();
            double downsample = Math.round(5 / server.getPixelCalibration().getAveragedPixelSizeMicrons());
            // Read the TMA entries
            int counter = 0;
            for (TMACoreObject core : tmaGrid.getTMACoreList()) {
                counter++;
                String name = core.getName();
                if (name == null)
                    name = Integer.toString(counter);
                File fileOutput = new File(dirImageOutput, name + ".jpg");
                if (!fileOutput.exists()) {
                    try {
                        RegionRequest request = RegionRequest.createInstance(server.getPath(), downsample, core.getROI());
                        BufferedImage img = server.readBufferedImage(request);
                        ImageIO.write(img, "jpg", fileOutput);
                    } catch (Exception e) {
                        logger.error("Unable to write {}", fileOutput.getAbsolutePath());
                    }
                }
                var entry = TMAEntries.createDefaultTMAEntry(imageEntry.getImageName(), fileOutput.getAbsolutePath(), null, core.getName(), core.isMissing());
                MeasurementList ml = core.getMeasurementList();
                for (int i = 0; i < ml.size(); i++) {
                    String measurement = ml.getMeasurementName(i);
                    double val = ml.getMeasurementValue(i);
                    entry.putMeasurement(measurement, val);
                    if (!Double.isNaN(val)) {
                        RunningStatistics stats = statsMap.get(measurement);
                        if (stats == null) {
                            stats = new RunningStatistics();
                            statsMap.put(measurement, stats);
                        }
                        stats.addValue(val);
                    }
                }
                entries.add(entry);
            }
            try {
                server.close();
            } catch (Exception e) {
                logger.warn("Problem closing server", e);
            }
        }
        // Loop through all entries and perform outlier count
        double k = 3;
        for (TMAEntry entry : entries) {
            int outlierCount = 0;
            for (Entry<String, RunningStatistics> statsEntry : statsMap.entrySet()) {
                RunningStatistics stats = statsEntry.getValue();
                double val = entry.getMeasurementAsDouble(statsEntry.getKey());
                if (!(val >= stats.getMean() - stats.getStdDev() * k && val <= stats.getMean() + stats.getStdDev() * k))
                    outlierCount++;
            }
            entry.putMeasurement("Outlier count", outlierCount);
        }
    }
    Stage stage = new Stage();
    stage.initOwner(qupath.getStage());
    TMASummaryViewer summaryViewer = new TMASummaryViewer(stage);
    summaryViewer.setTMAEntries(entries);
    summaryViewer.getStage().show();
}