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

Example 41 with PathObject

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

the class PathHierarchyPaintingHelper method paintObject.

/**
 * Paint an object (or, more precisely, its ROI), optionally along with the ROIs of any child objects.
 *
 * This is subject to the OverlayOptions, and therefore may not actually end up painting anything
 * (if the settings are such that objects of the class provided are not to be displayed)
 *
 * @param pathObject
 * @param paintChildren
 * @param g
 * @param boundsDisplayed
 * @param overlayOptions
 * @param selectionModel
 * @param downsample
 * @return true if anything was painted, false otherwise
 */
public static boolean paintObject(PathObject pathObject, boolean paintChildren, Graphics2D g, Rectangle boundsDisplayed, OverlayOptions overlayOptions, PathObjectSelectionModel selectionModel, double downsample) {
    if (pathObject == null)
        return false;
    // g.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_SPEED);
    // g.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_QUALITY);
    // Always paint the selected object
    // Note: this makes the assumption that child ROIs are completely contained within their parents;
    // this probably should be the case, but isn't guaranteed
    boolean isSelected = (selectionModel != null && selectionModel.isSelected(pathObject)) && (PathPrefs.useSelectedColorProperty().get() || !PathObjectTools.hasPointROI(pathObject));
    boolean isDetectedObject = pathObject.isDetection() || (pathObject.isTile() && pathObject.hasMeasurements());
    // Check if the PathClass isn't being shown
    PathClass pathClass = pathObject.getPathClass();
    if (!isSelected && overlayOptions != null && overlayOptions.isPathClassHidden(pathClass))
        return false;
    boolean painted = false;
    // See if we need to check the children
    ROI pathROI = pathObject.getROI();
    if (pathROI != null) {
        double roiBoundsX = pathROI.getBoundsX();
        double roiBoundsY = pathROI.getBoundsY();
        double roiBoundsWidth = pathROI.getBoundsWidth();
        double roiBoundsHeight = pathROI.getBoundsHeight();
        if (PathObjectTools.hasPointROI(pathObject) || boundsDisplayed == null || pathROI instanceof LineROI || boundsDisplayed.intersects(roiBoundsX, roiBoundsY, Math.max(roiBoundsWidth, 1), Math.max(roiBoundsHeight, 1))) {
            // Paint the ROI, if necessary
            if (isSelected || (overlayOptions.getShowDetections() && isDetectedObject) || (overlayOptions.getShowAnnotations() && pathObject.isAnnotation()) || (overlayOptions.getShowTMAGrid() && pathObject.isTMACore())) {
                boolean doFill = overlayOptions.getFillDetections() || pathObject instanceof ParallelTileObject;
                boolean doOutline = true;
                Color color = null;
                boolean useMapper = false;
                double fillOpacity = .75;
                if (isSelected && PathPrefs.useSelectedColorProperty().get() && PathPrefs.colorSelectedObjectProperty().getValue() != null)
                    color = ColorToolsAwt.getCachedColor(PathPrefs.colorSelectedObjectProperty().get());
                else {
                    MeasurementMapper mapper = overlayOptions.getMeasurementMapper();
                    useMapper = mapper != null && mapper.isValid() && pathObject.isDetection();
                    if (useMapper) {
                        if (pathObject.hasMeasurements()) {
                            Integer rgb = mapper.getColorForObject(pathObject);
                            // If the mapper returns null, the object shouldn't be painted
                            if (rgb == null)
                                return false;
                            // , mapper.getColorMapper().hasAlpha());
                            color = ColorToolsAwt.getCachedColor(rgb);
                        } else
                            color = null;
                        // System.out.println(color + " - " + pathObject.getMeasurementList().getMeasurementValue(mapper.));
                        fillOpacity = 1.0;
                        // Outlines are not so helpful with the measurement mapper
                        if (doFill)
                            doOutline = doOutline && !pathObject.isTile();
                    } else {
                        Integer rgb = ColorToolsFX.getDisplayedColorARGB(pathObject);
                        color = ColorToolsAwt.getCachedColor(rgb);
                    }
                // color = PathObjectHelpers.getDisplayedColor(pathObject);
                }
                // Check if we have only one or two pixels to draw - if so, we can be done quickly
                if (isDetectedObject && downsample > 4 && roiBoundsWidth / downsample < 3 && roiBoundsHeight / downsample < 3) {
                    int x = (int) roiBoundsX;
                    int y = (int) roiBoundsY;
                    // Prefer rounding up, lest we lose a lot of regions unnecessarily
                    int w = (int) (roiBoundsWidth + .9);
                    int h = (int) (roiBoundsHeight + .9);
                    if (w > 0 && h > 0) {
                        g.setColor(color);
                        // g.setColor(DisplayHelpers.getMoreTranslucentColor(color));
                        // g.setStroke(getCachedStroke(overlayOptions.strokeThinThicknessProperty().get()));
                        g.fillRect(x, y, w, h);
                    }
                    painted = true;
                } else {
                    Stroke stroke = null;
                    // Decide whether to fill or not
                    Color colorFill = doFill && (isDetectedObject || PathObjectTools.hasPointROI(pathObject)) ? color : null;
                    if (colorFill != null && fillOpacity != 1) {
                        if (pathObject instanceof ParallelTileObject)
                            colorFill = ColorToolsAwt.getMoreTranslucentColor(colorFill);
                        else if (pathObject instanceof PathCellObject && overlayOptions.getShowCellBoundaries() && overlayOptions.getShowCellNuclei()) {
                            // if (isSelected)
                            // colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
                            // else
                            colorFill = ColorToolsAwt.getMoreTranslucentColor(colorFill);
                        } else if (pathObject.getParent() instanceof PathDetectionObject) {
                            colorFill = ColorToolsAwt.getTranslucentColor(colorFill);
                        } else if (pathObject instanceof PathTileObject && pathClass == null && color != null && color.getRGB() == PathPrefs.colorTileProperty().get()) {
                            // Don't fill in empty, unclassified tiles
                            // DisplayHelpers.getMoreTranslucentColor(colorFill);
                            colorFill = null;
                        }
                    }
                    // Color colorStroke = doOutline ? (colorFill == null ? color : (downsample > overlayOptions.strokeThinThicknessProperty().get() ? null : DisplayHelpers.darkenColor(color))) : null;
                    Color colorStroke = doOutline ? (colorFill == null ? color : ColorToolsAwt.darkenColor(color)) : null;
                    // For thick lines, antialiasing is very noticeable... less so for thin lines (of which there may be a huge number)
                    if (isDetectedObject) {
                        // Detections inside detections get half the line width
                        if (pathObject.getParent() instanceof PathDetectionObject)
                            stroke = getCachedStroke(PathPrefs.detectionStrokeThicknessProperty().get() / 2.0);
                        else
                            stroke = getCachedStroke(PathPrefs.detectionStrokeThicknessProperty().get());
                    } else {
                        double thicknessScale = downsample * (isSelected && !PathPrefs.useSelectedColorProperty().get() ? 1.6 : 1);
                        float thickness = (float) (PathPrefs.annotationStrokeThicknessProperty().get() * thicknessScale);
                        if (isSelected && pathObject.getParent() == null && PathPrefs.selectionModeProperty().get()) {
                            stroke = getCachedStrokeDashed(thickness);
                        } else {
                            stroke = getCachedStroke(thickness);
                        }
                    }
                    g.setStroke(stroke);
                    boolean paintSymbols = overlayOptions.getDetectionDisplayMode() == DetectionDisplayMode.CENTROIDS && pathObject.isDetection() && !pathObject.isTile();
                    if (paintSymbols) {
                        pathROI = PathObjectTools.getROI(pathObject, true);
                        double x = pathROI.getCentroidX();
                        double y = pathROI.getCentroidY();
                        double radius = PathPrefs.detectionStrokeThicknessProperty().get() * 2.0;
                        if (pathObject.getParent() instanceof PathDetectionObject)
                            radius /= 2.0;
                        Shape shape;
                        int nSubclasses = 0;
                        if (pathClass != null) {
                            nSubclasses = PathClassTools.splitNames(pathClass).size();
                        }
                        switch(nSubclasses) {
                            case 0:
                                var ellipse = localEllipse2D.get();
                                ellipse.setFrame(x - radius, y - radius, radius * 2, radius * 2);
                                shape = ellipse;
                                break;
                            case 1:
                                var rect = localRect2D.get();
                                rect.setFrame(x - radius, y - radius, radius * 2, radius * 2);
                                shape = rect;
                                break;
                            case 2:
                                var triangle = localPath2D.get();
                                double sqrt3 = Math.sqrt(3.0);
                                triangle.reset();
                                triangle.moveTo(x, y - radius * 2.0 / sqrt3);
                                triangle.lineTo(x - radius, y + radius / sqrt3);
                                triangle.lineTo(x + radius, y + radius / sqrt3);
                                triangle.closePath();
                                shape = triangle;
                                break;
                            case 3:
                                var plus = localPath2D.get();
                                plus.reset();
                                plus.moveTo(x, y - radius);
                                plus.lineTo(x, y + radius);
                                plus.moveTo(x - radius, y);
                                plus.lineTo(x + radius, y);
                                shape = plus;
                                break;
                            default:
                                var cross = localPath2D.get();
                                cross.reset();
                                radius /= Math.sqrt(2);
                                cross.moveTo(x - radius, y - radius);
                                cross.lineTo(x + radius, y + radius);
                                cross.moveTo(x + radius, y - radius);
                                cross.lineTo(x - radius, y + radius);
                                shape = cross;
                                break;
                        }
                        paintShape(shape, g, colorStroke, stroke, colorFill);
                    } else if (pathObject instanceof PathCellObject) {
                        PathCellObject cell = (PathCellObject) pathObject;
                        if (overlayOptions.getShowCellBoundaries())
                            paintROI(pathROI, g, colorStroke, stroke, colorFill, downsample);
                        if (overlayOptions.getShowCellNuclei())
                            paintROI(cell.getNucleusROI(), g, colorStroke, stroke, colorFill, downsample);
                        painted = true;
                    } else {
                        if ((overlayOptions.getFillAnnotations() && pathObject.isAnnotation() && pathObject.getPathClass() != PathClassFactory.getPathClass(StandardPathClasses.REGION) && (pathObject.getPathClass() != null || !pathObject.hasChildren())) || (pathObject.isTMACore() && overlayOptions.getShowTMACoreLabels()))
                            paintROI(pathROI, g, colorStroke, stroke, ColorToolsAwt.getMoreTranslucentColor(colorStroke), downsample);
                        else
                            paintROI(pathROI, g, colorStroke, stroke, colorFill, downsample);
                        painted = true;
                    }
                }
            }
        }
    }
    // Paint the children, if necessary
    if (paintChildren) {
        for (PathObject childObject : pathObject.getChildObjectsAsArray()) {
            // Only call the painting method if required
            ROI childROI = childObject.getROI();
            if ((childROI != null && boundsDisplayed.intersects(childROI.getBoundsX(), childROI.getBoundsY(), childROI.getBoundsWidth(), childROI.getBoundsHeight())) || childObject.hasChildren())
                painted = paintObject(childObject, paintChildren, g, boundsDisplayed, overlayOptions, selectionModel, downsample) | painted;
        }
    }
    return painted;
}

Example 42 with PathObject

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

the class PathHierarchyPaintingHelper method paintConnections.

/**
 * Paint connections between objects (e.g. from Delaunay triangulation).
 *
 * @param connections
 * @param hierarchy
 * @param g2d
 * @param color
 * @param downsampleFactor
 */
public static void paintConnections(final PathObjectConnections connections, final PathObjectHierarchy hierarchy, Graphics2D g2d, final Color color, final double downsampleFactor) {
    if (hierarchy == null || connections == null || connections.isEmpty())
        return;
    float alpha = (float) (1f - downsampleFactor / 5);
    alpha = Math.min(alpha, 0.25f);
    float thickness = PathPrefs.detectionStrokeThicknessProperty().get();
    if (alpha < .1f || thickness / downsampleFactor <= 0.5)
        return;
    g2d = (Graphics2D) g2d.create();
    // Shape clipShape = g2d.getClip();
    g2d.setStroke(getCachedStroke(thickness));
    // g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha * .5f));
    // g2d.setColor(ColorToolsAwt.getColorWithOpacity(getPreferredOverlayColor(), 1));
    g2d.setColor(ColorToolsAwt.getColorWithOpacity(color.getRGB(), alpha));
    // g2d.setColor(Color.BLACK);
    Line2D line = new Line2D.Double();
    // We can have trouble whenever two objects are outside the clip, but their connections would be inside it
    // Here, we just enlarge the region (by quite a lot)
    // It's not guaranteed to work, but it usually does... and avoids much expensive computations
    Rectangle bounds = g2d.getClipBounds();
    int factor = 1;
    Rectangle bounds2 = factor > 0 ? new Rectangle(bounds.x - bounds.width * factor, bounds.y - bounds.height * factor, bounds.width * (factor * 2 + 1), bounds.height * (factor * 2 + 1)) : bounds;
    ImageRegion imageRegion = AwtTools.getImageRegion(bounds2, 0, 0);
    // ImageRegion imageRegion = AwtTools.getImageRegion(bounds, 0, 0);
    g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
    g2d.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED);
    // g2d.draw(g2d.getClipBounds());
    Collection<PathObject> pathObjects = hierarchy.getObjectsForRegion(PathDetectionObject.class, imageRegion, null);
    // double threshold = downsampleFactor*downsampleFactor*4;
    for (PathObject pathObject : pathObjects) {
        ROI roi = PathObjectTools.getROI(pathObject, true);
        double x1 = roi.getCentroidX();
        double y1 = roi.getCentroidY();
        for (PathObjectConnectionGroup dt : connections.getConnectionGroups()) {
            for (PathObject siblingObject : dt.getConnectedObjects(pathObject)) {
                ROI roi2 = PathObjectTools.getROI(siblingObject, true);
                double x2 = roi2.getCentroidX();
                double y2 = roi2.getCentroidY();
                if (bounds.intersectsLine(x1, y1, x2, y2)) {
                    line.setLine(x1, y1, x2, y2);
                    g2d.draw(line);
                }
            }
        }
    }
    g2d.dispose();
}

Example 43 with PathObject

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

the class QuPathViewer method updateRoiEditor.

private void updateRoiEditor() {
    PathObject pathObjectSelected = getSelectedObject();
    ROI previousROI = roiEditor.getROI();
    ROI newROI = pathObjectSelected != null && pathObjectSelected.isEditable() ? pathObjectSelected.getROI() : null;
    if (previousROI == newROI)
        roiEditor.ensureHandlesUpdated();
    else
        roiEditor.setROI(newROI);
    repaint();
}

Example 44 with PathObject

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

the class HierarchyOverlay method paintOverlay.

@Override
public void paintOverlay(final Graphics2D g2d, final ImageRegion imageRegion, final double downsampleFactor, final ImageData<BufferedImage> imageData, final boolean paintCompletely) {
    if (this.imageData != imageData) {
        this.imageData = imageData;
        updateOverlayServer();
    }
    // Get the selection model, which can influence colours (TODO: this might not be the best way to do it!)
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null)
        return;
    if (!isVisible() && hierarchy.getSelectionModel().noSelection())
        return;
    // Default RenderingHints (may be temporarily changed in some places)
    var defaultAntiAlias = RenderingHints.VALUE_ANTIALIAS_ON;
    var defaultStroke = RenderingHints.VALUE_STROKE_PURE;
    // Doesn't seem to help...?
    // boolean fastRendering = true;
    // if (fastRendering) {
    // defaultAntiAlias = RenderingHints.VALUE_ANTIALIAS_OFF;
    // defaultStroke = RenderingHints.VALUE_STROKE_DEFAULT;
    // }
    OverlayOptions overlayOptions = getOverlayOptions();
    long timestamp = overlayOptions.lastChangeTimestamp().get();
    int pointRadius = PathPrefs.pointRadiusProperty().get();
    if (overlayOptionsTimestamp != timestamp || pointRadius != lastPointRadius) {
        lastPointRadius = pointRadius;
        overlayOptionsTimestamp = timestamp;
    }
    int t = imageRegion.getT();
    int z = imageRegion.getZ();
    Rectangle serverBounds = AwtTools.getBounds(imageRegion);
    // Ensure antialias is on...?
    g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, defaultAntiAlias);
    // Get the displayed clip bounds for fast checking if ROIs need to be drawn
    Shape shapeRegion = g2d.getClip();
    if (shapeRegion == null)
        shapeRegion = AwtTools.getBounds(imageRegion);
    var boundsDisplayed = shapeRegion.getBounds();
    // Ensure the bounds do not extend beyond what the server actually contains
    boundsDisplayed = boundsDisplayed.intersection(serverBounds);
    if (boundsDisplayed.width <= 0 || boundsDisplayed.height <= 0)
        return;
    // Get the annotations & selected objects (which must be painted directly)
    Collection<PathObject> selectedObjects = new ArrayList<>(hierarchy.getSelectionModel().getSelectedObjects());
    selectedObjects.removeIf(p -> !p.hasROI() || (p.getROI().getZ() != z || p.getROI().getT() != t));
    ImageRegion region = AwtTools.getImageRegion(boundsDisplayed, z, t);
    // Paint detection objects
    long startTime = System.currentTimeMillis();
    if (overlayOptions.getShowDetections() && !hierarchy.isEmpty()) {
        // If we aren't downsampling by much, or we're upsampling, paint directly - making sure to paint the right number of times, and in the right order
        if (overlayServer == null || regionStore == null || downsampleFactor < 1.0) {
            Collection<PathObject> pathObjects;
            try {
                Set<PathObject> pathObjectsToPaint = new TreeSet<>(comparator);
                pathObjects = hierarchy.getObjectsForRegion(PathDetectionObject.class, region, pathObjectsToPaint);
            } catch (IllegalArgumentException e) {
                // This can happen (rarely) in a multithreaded environment if the level of a detection changes.
                // However, protecting against this fully by caching the level with integer boxing/unboxing would be expensive.
                logger.debug("Exception requesting detections to paint: " + e.getLocalizedMessage(), e);
                pathObjects = hierarchy.getObjectsForRegion(PathDetectionObject.class, region, null);
            }
            g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
            PathHierarchyPaintingHelper.paintSpecifiedObjects(g2d, boundsDisplayed, pathObjects, overlayOptions, hierarchy.getSelectionModel(), downsampleFactor);
            if (overlayOptions.getShowConnections()) {
                Object connections = imageData.getProperty(DefaultPathObjectConnectionGroup.KEY_OBJECT_CONNECTIONS);
                if (connections instanceof PathObjectConnections)
                    PathHierarchyPaintingHelper.paintConnections((PathObjectConnections) connections, hierarchy, g2d, imageData.isFluorescence() ? ColorToolsAwt.TRANSLUCENT_WHITE : ColorToolsAwt.TRANSLUCENT_BLACK, downsampleFactor);
            }
        } else {
            // On the other hand, if a large image has been updated then we may be browsing quickly - better to repaint quickly while tiles may still be loading
            if (paintCompletely) {
                regionStore.paintRegionCompletely(overlayServer, g2d, shapeRegion, z, t, downsampleFactor, null, null, 5000);
            } else {
                regionStore.paintRegion(overlayServer, g2d, shapeRegion, z, t, downsampleFactor, null, null, null);
            }
        }
    }
    long endTime = System.currentTimeMillis();
    if (endTime - startTime > 500)
        logger.debug("Painting time: {} seconds", GeneralTools.formatNumber((endTime - startTime) / 1000.0, 4));
    // The setting below stops some weird 'jiggling' effects during zooming in/out, or poor rendering of shape ROIs
    g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, defaultAntiAlias);
    g2d.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, defaultStroke);
    // Prepare to handle labels, if we need to
    Collection<PathObject> objectsWithNames = new ArrayList<>();
    Collection<PathObject> annotations = hierarchy.getObjectsForRegion(PathAnnotationObject.class, region, null);
    for (var iterator = annotations.iterator(); iterator.hasNext(); ) {
        var next = iterator.next();
        if ((next.getName() != null && !next.getName().isBlank()))
            objectsWithNames.add(next);
        if (selectedObjects.contains(next))
            iterator.remove();
    }
    // Paint the annotations
    List<PathObject> pathObjectList = new ArrayList<>(annotations);
    Collections.sort(pathObjectList, Comparator.comparingInt(PathObject::getLevel).reversed().thenComparing(Comparator.comparingDouble((PathObject p) -> -p.getROI().getArea())));
    PathHierarchyPaintingHelper.paintSpecifiedObjects(g2d, boundsDisplayed, pathObjectList, overlayOptions, null, downsampleFactor);
    // Ensure that selected objects are painted last, to make sure they aren't obscured
    if (!selectedObjects.isEmpty()) {
        Composite previousComposite = g2d.getComposite();
        float opacity = overlayOptions.getOpacity();
        if (opacity < 1) {
            g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
            PathHierarchyPaintingHelper.paintSpecifiedObjects(g2d, boundsDisplayed, selectedObjects, overlayOptions, hierarchy.getSelectionModel(), downsampleFactor);
            g2d.setComposite(previousComposite);
        } else {
            PathHierarchyPaintingHelper.paintSpecifiedObjects(g2d, boundsDisplayed, selectedObjects, overlayOptions, hierarchy.getSelectionModel(), downsampleFactor);
        }
    }
    // Paint labels
    if (overlayOptions.getShowNames() && !objectsWithNames.isEmpty()) {
        double requestedFontSize;
        switch(PathPrefs.viewerFontSizeProperty().get()) {
            case HUGE:
                requestedFontSize = 24;
                break;
            case LARGE:
                requestedFontSize = 18;
                break;
            case SMALL:
                requestedFontSize = 10;
                break;
            case TINY:
                requestedFontSize = 8;
                break;
            case MEDIUM:
            default:
                requestedFontSize = 14;
                break;
        }
        float fontSize = (float) (requestedFontSize * downsampleFactor);
        if (!GeneralTools.almostTheSame(font.getSize2D(), fontSize, 0.001))
            font = font.deriveFont(fontSize);
        g2d.setFont(font);
        var metrics = g2d.getFontMetrics(font);
        var rect = new Rectangle2D.Double();
        g2d.setRenderingHint(RenderingHints.KEY_FRACTIONALMETRICS, RenderingHints.VALUE_FRACTIONALMETRICS_ON);
        g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
        for (var annotation : objectsWithNames) {
            var name = annotation.getName();
            var roi = annotation.getROI();
            if (name != null && !name.isBlank() && roi != null && !overlayOptions.isPathClassHidden(annotation.getPathClass())) {
                g2d.setColor(ColorToolsAwt.TRANSLUCENT_BLACK);
                var bounds = metrics.getStringBounds(name, g2d);
                double pad = 5.0 * downsampleFactor;
                double x = roi.getCentroidX() - bounds.getWidth() / 2.0;
                double y = roi.getCentroidY() + bounds.getY() + metrics.getAscent() + pad;
                rect.setFrame(x + bounds.getX() - pad, y + bounds.getY() - pad, bounds.getWidth() + pad * 2, bounds.getHeight() + pad * 2);
                g2d.fill(rect);
                g2d.setColor(Color.WHITE);
                g2d.drawString(name, (float) x, (float) y);
            }
        }
    }
}

Example 45 with PathObject

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

the class MeasurementExporter method exportMeasurements.

/**
 * Exports the measurements of one or more entries in the project.
 * This function first opens all the images in the project to store
 * all the column names and values of the measurements.
 * Then, it loops through the maps containing the values to write
 * them to the given output stream.
 * @param stream
 */
public void exportMeasurements(OutputStream stream) {
    long startTime = System.currentTimeMillis();
    Map<ProjectImageEntry<?>, String[]> imageCols = new HashMap<>();
    Map<ProjectImageEntry<?>, Integer> nImageEntries = new HashMap<>();
    List<String> allColumns = new ArrayList<>();
    Multimap<String, String> valueMap = LinkedListMultimap.create();
    String pattern = "(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)";
    for (ProjectImageEntry<?> entry : imageList) {
        try {
            ImageData<?> imageData = entry.readImageData();
            ObservableMeasurementTableData model = new ObservableMeasurementTableData();
            Collection<PathObject> pathObjects = imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type);
            if (filter != null)
                pathObjects = pathObjects.stream().filter(filter).collect(Collectors.toList());
            model.setImageData(imageData, pathObjects);
            List<String> data = SummaryMeasurementTableCommand.getTableModelStrings(model, separator, excludeColumns);
            // Get header
            String[] header;
            String headerString = data.get(0);
            if (headerString.chars().filter(e -> e == '"').count() > 1)
                header = headerString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
            else
                header = headerString.split(separator);
            imageCols.put(entry, header);
            nImageEntries.put(entry, data.size() - 1);
            for (String col : header) {
                if (!allColumns.contains(col) && !excludeColumns.contains(col))
                    allColumns.add(col);
            }
            // To keep the same column order, just delete non-relevant columns
            if (!includeOnlyColumns.isEmpty())
                allColumns.removeIf(n -> !includeOnlyColumns.contains(n));
            for (int i = 1; i < data.size(); i++) {
                String[] row;
                String rowString = data.get(i);
                // Check if some values in the row are escaped
                if (rowString.chars().filter(e -> e == '"').count() > 1)
                    row = rowString.split(separator.equals("\t") ? "\\" + separator : separator + pattern, -1);
                else
                    row = rowString.split(separator);
                // Put value in map
                for (int elem = 0; elem < row.length; elem++) {
                    if (allColumns.contains(header[elem]))
                        valueMap.put(header[elem], row[elem]);
                }
            }
        } catch (Exception e) {
            logger.error(e.getLocalizedMessage(), e);
        }
    }
    try (PrintWriter writer = new PrintWriter(new OutputStreamWriter(stream, StandardCharsets.UTF_8))) {
        writer.write(String.join(separator, allColumns));
        writer.write(System.lineSeparator());
        Iterator[] its = new Iterator[allColumns.size()];
        for (int col = 0; col < allColumns.size(); col++) {
            its[col] = valueMap.get(allColumns.get(col)).iterator();
        }
        for (ProjectImageEntry<?> entry : imageList) {
            for (int nObject = 0; nObject < nImageEntries.get(entry); nObject++) {
                for (int nCol = 0; nCol < allColumns.size(); nCol++) {
                    if (Arrays.stream(imageCols.get(entry)).anyMatch(allColumns.get(nCol)::equals)) {
                        String val = (String) its[nCol].next();
                        // NaN values -> blank
                        if (val.equals("NaN"))
                            val = "";
                        writer.write(val);
                    }
                    if (nCol < allColumns.size() - 1)
                        writer.write(separator);
                }
                writer.write(System.lineSeparator());
            }
        }
    } catch (Exception e) {
        logger.error("Error writing to file: " + e.getLocalizedMessage(), e);
    }
    long endTime = System.currentTimeMillis();
    long timeMillis = endTime - startTime;
    String time = null;
    if (timeMillis > 1000 * 60)
        time = String.format("Total processing time: %.2f minutes", timeMillis / (1000.0 * 60.0));
    else if (timeMillis > 1000)
        time = String.format("Total processing time: %.2f seconds", timeMillis / (1000.0));
    else
        time = String.format("Total processing time: %d milliseconds", timeMillis);
    logger.info("Processed {} images", imageList.size());
    logger.info(time);
}