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

Example 16 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid 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 17 with TMAGrid

use of qupath.lib.objects.hierarchy.TMAGrid 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();
}