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

Example 11 with TMACoreObject

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

the class TMADataIO method importDearrayedTMAData.

/**
 * Import a TMA grid from an exported TMA analysis file, i.e. with extension ".qptma"
 *
 * @param file
 * @return
 */
public static TMAGrid importDearrayedTMAData(final File file) {
    try (Scanner scanner = new Scanner(file)) {
        int gridWidth = -1;
        int gridHeight = -1;
        String line = null;
        while (scanner.hasNextLine()) {
            line = scanner.nextLine();
            if (line.startsWith("TMA grid width:"))
                gridWidth = Integer.parseInt(line.replace("TMA grid width:", "").trim());
            else if (line.startsWith("TMA grid height:"))
                gridHeight = Integer.parseInt(line.replace("TMA grid height:", "").trim());
            if (gridWidth >= 0 && gridHeight >= 0)
                break;
        }
        if (gridWidth <= 0 || gridHeight <= 0) {
            logger.error("No grid dimensions available!");
            return null;
        }
        Map<String, List<String>> csvData = TMAScoreImporter.readCSV(scanner);
        List<String> colNames = csvData.get("Core name");
        List<String> colX = csvData.get("X");
        List<String> colY = csvData.get("Y");
        List<String> colWidth = csvData.get("Width");
        List<String> colHeight = csvData.get("Height");
        List<String> colPresent = csvData.get("Present");
        List<String> colID = csvData.get(TMACoreObject.KEY_UNIQUE_ID);
        if (colX == null || colY == null || colWidth == null || colHeight == null) {
            logger.error("No core locations available!");
            return null;
        }
        // int count = 0;
        List<TMACoreObject> cores = new ArrayList<>();
        for (int i = 0; i < colX.size(); i++) {
            double x = Double.parseDouble(colX.get(i));
            double y = Double.parseDouble(colY.get(i));
            double w = Double.parseDouble(colWidth.get(i));
            double h = Double.parseDouble(colHeight.get(i));
            boolean present = colPresent == null ? true : Boolean.parseBoolean(colPresent.get(i));
            String name = colNames == null ? null : colNames.get(i);
            String id = colID == null ? null : colID.get(i);
            TMACoreObject core = PathObjects.createTMACoreObject(x, y, w, h, !present);
            if (name != null)
                core.setName(name);
            if (id != null && !id.isEmpty())
                core.setUniqueID(id);
            cores.add(core);
        }
        return DefaultTMAGrid.create(cores, gridWidth);
    } catch (FileNotFoundException e) {
        logger.error("Cannot find file: {}", file);
        return null;
    }
}

Example 12 with TMACoreObject

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

the class TMASummaryViewer method getEntriesForTMAData.

private static List<TMAEntry> getEntriesForTMAData(final ImageData<BufferedImage> imageData) {
    List<TMAEntry> entriesNew = new ArrayList<>();
    if (imageData.getHierarchy().getTMAGrid() == null)
        return entriesNew;
    ObservableMeasurementTableData data = new ObservableMeasurementTableData();
    data.setImageData(imageData, imageData.getHierarchy().getTMAGrid().getTMACoreList());
    for (TMACoreObject core : imageData.getHierarchy().getTMAGrid().getTMACoreList()) {
        entriesNew.add(TMAEntries.createTMAObjectEntry(imageData, data, core));
    }
    return entriesNew;
}

Example 13 with TMACoreObject

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

the class TMAScoreImporter method importFromCSV.

private static int importFromCSV(final Map<String, List<String>> map, final PathObjectHierarchy hierarchy) {
    TMAGrid tmaGrid = hierarchy.getTMAGrid();
    if (tmaGrid == null || tmaGrid.nCores() == 0) {
        logger.error("No TMA grid found!");
        return 0;
    }
    // Try to get a 'core' column
    String coreKey = null;
    for (String key : map.keySet()) {
        if (key.trim().toLowerCase().equals("core")) {
            coreKey = key;
            break;
        }
    }
    List<String> coreNames = coreKey == null ? null : map.remove(coreKey);
    // Try to get a unique ID column
    List<String> coreIDs = map.remove(TMACoreObject.KEY_UNIQUE_ID);
    // If we don't have a core column OR a unique ID column, we can't do anything
    if (coreNames == null && coreIDs == null) {
        logger.error("No column with header 'core' or '" + TMACoreObject.KEY_UNIQUE_ID + "' found");
        return 0;
    }
    // int n = coreNames == null ? coreIDs.size() : coreNames.size();
    // Get a list of cores ordered by whatever info we have
    Map<Integer, List<TMACoreObject>> cores = new HashMap<>();
    boolean coresFound = false;
    // If we have any unique IDs, use these and change names accordingly - if possible, and necessary
    if (coreIDs != null) {
        int i = 0;
        for (String id : coreIDs) {
            List<TMACoreObject> coresByID = new ArrayList<>();
            for (TMACoreObject coreTemp : tmaGrid.getTMACoreList()) if (id != null && id.equals(coreTemp.getUniqueID()))
                coresByID.add(coreTemp);
            if (!coresByID.isEmpty()) {
                cores.put(i, coresByID);
                coresFound = true;
                if (coreNames != null && coresByID.size() == 1) {
                    String currentName = coresByID.get(0).getName();
                    String newName = coreNames.get(i);
                    if (!newName.equals(currentName)) {
                        coresByID.get(0).setName(newName);
                        if (currentName != null)
                            logger.warn("Core name changed from {} to {}", currentName, newName);
                    }
                }
            }
            i++;
        }
    }
    // If we didn't have any unique IDs, we need to work with core names instead
    if (!coresFound && coreNames != null) {
        int i = 0;
        for (String name : coreNames) {
            TMACoreObject core = tmaGrid.getTMACore(name);
            if (core != null) {
                cores.put(i, Collections.singletonList(core));
                coresFound = true;
                if (coreIDs != null) {
                    String currentID = core.getUniqueID();
                    String newID = coreIDs.get(i);
                    if (newID != null && !newID.equals(currentID)) {
                        core.setUniqueID(newID);
                        // It shouldn't occur that an existing ID is changed... although it's possible if there are duplicates
                        if (currentID != null)
                            logger.warn("Core unique ID changed from {} to {}", currentID, newID);
                    }
                }
            }
            i++;
        }
    }
    // Add extra columns from the map, either as metadata or measurements
    for (Entry<String, List<String>> entry : map.entrySet()) {
        // Skip columns without headers
        if (entry.getKey() == null || entry.getKey().trim().length() == 0)
            continue;
        // If we have survival data, or else can't parse numeric values, add as metadata
        boolean isOverallSurvival = entry.getKey().equalsIgnoreCase(TMACoreObject.KEY_OVERALL_SURVIVAL);
        boolean isRecurrenceFreeSurvival = entry.getKey().equalsIgnoreCase(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL);
        boolean isOSCensored = entry.getKey().equalsIgnoreCase(TMACoreObject.KEY_OS_CENSORED);
        boolean isRFSCensored = entry.getKey().equalsIgnoreCase(TMACoreObject.KEY_RFS_CENSORED);
        // Try to parse numeric data, if we can
        boolean isSurvivalRelated = isOverallSurvival || isRecurrenceFreeSurvival || isOSCensored || isRFSCensored;
        double[] vals = parseNumeric(entry.getValue(), !isSurvivalRelated);
        if (isSurvivalRelated || vals == null || vals.length == GeneralTools.numNaNs(vals)) {
            for (int i : cores.keySet()) {
                for (TMACoreObject core : cores.get(i)) {
                    if (core == null)
                        continue;
                    if (isOverallSurvival)
                        core.getMeasurementList().putMeasurement(TMACoreObject.KEY_OVERALL_SURVIVAL, vals[i]);
                    else if (isRecurrenceFreeSurvival)
                        core.getMeasurementList().putMeasurement(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL, vals[i]);
                    else if (isOSCensored)
                        core.getMeasurementList().putMeasurement(TMACoreObject.KEY_OS_CENSORED, vals[i] > 0 ? 1 : 0);
                    else if (isRFSCensored)
                        core.getMeasurementList().putMeasurement(TMACoreObject.KEY_RFS_CENSORED, vals[i] > 0 ? 1 : 0);
                    else
                        core.putMetadataValue(entry.getKey(), entry.getValue().get(i));
                }
            }
        } else {
            // If we have a numeric column, add to measurement list
            for (int i : cores.keySet()) {
                for (TMACoreObject core : cores.get(i)) {
                    core.getMeasurementList().addMeasurement(entry.getKey(), vals[i]);
                }
            }
        }
    }
    // Loop through and close any measurement lists, recording anywhere changes were made
    Set<PathObject> changed = new HashSet<>();
    for (List<TMACoreObject> coreList : cores.values()) {
        for (TMACoreObject core : coreList) {
            if (core == null)
                continue;
            core.getMeasurementList().close();
            changed.add(core);
        }
    }
    hierarchy.fireObjectsChangedEvent(null, changed);
    return changed.size();
}

Example 14 with TMACoreObject

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

the class GuiTools method promptToClearAllSelectedObjects.

/**
 * Prompt user to select all currently-selected objects (except TMA core objects).
 *
 * @param imageData
 * @return
 */
public static boolean promptToClearAllSelectedObjects(final ImageData<?> imageData) {
    // Get all non-TMA core objects
    PathObjectHierarchy hierarchy = imageData.getHierarchy();
    Collection<PathObject> selectedRaw = hierarchy.getSelectionModel().getSelectedObjects();
    List<PathObject> selected = selectedRaw.stream().filter(p -> !(p instanceof TMACoreObject)).collect(Collectors.toList());
    if (selected.isEmpty()) {
        if (selectedRaw.size() > selected.size())
            Dialogs.showErrorMessage("Delete selected objects", "No valid objects selected! \n\nNote: Individual TMA cores cannot be deleted with this method.");
        else
            Dialogs.showErrorMessage("Delete selected objects", "No objects selected!");
        return false;
    }
    int n = selected.size();
    String message;
    if (n == 1)
        message = "Delete selected object?";
    else
        message = "Delete " + n + " selected objects?";
    if (Dialogs.showYesNoDialog("Delete objects", message)) {
        // Check for descendants
        List<PathObject> children = new ArrayList<>();
        for (PathObject temp : selected) {
            children.addAll(temp.getChildObjects());
        }
        children.removeAll(selected);
        boolean keepChildren = true;
        if (!children.isEmpty()) {
            Dialogs.DialogButton response = Dialogs.showYesNoCancelDialog("Delete objects", "Keep descendant objects?");
            if (response == Dialogs.DialogButton.CANCEL)
                return false;
            keepChildren = response == Dialogs.DialogButton.YES;
        }
        hierarchy.removeObjects(selected, keepChildren);
        hierarchy.getSelectionModel().clearSelection();
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Delete selected objects", "clearSelectedObjects(" + keepChildren + ");"));
        if (keepChildren)
            logger.info(selected.size() + " object(s) deleted");
        else
            logger.info(selected.size() + " object(s) deleted with descendants");
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Delete selected objects", "clearSelectedObjects();"));
        logger.info(selected.size() + " object(s) deleted");
        return true;
    } else
        return false;
}

Example 15 with TMACoreObject

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

the class QuPathViewer method getImageLocationString.

/**
 * Get a string representing the image coordinates for a particular x & y location.
 * @param xx x-coordinate in the image space (not the component/viewer space)
 * @param yy y-coordinate in the image space (not the component/viewer space)
 * @param useCalibratedUnits
 * @return
 */
private String getImageLocationString(double xx, double yy, boolean useCalibratedUnits) {
    ImageServer<BufferedImage> server = getServer();
    if (server == null)
        return "";
    String units;
    if (xx < 0 || yy < 0 || xx > server.getWidth() - 1 || yy > server.getHeight() - 1)
        return "";
    double xDisplay = xx;
    double yDisplay = yy;
    PixelCalibration cal = server.getPixelCalibration();
    if (useCalibratedUnits && cal.hasPixelSizeMicrons()) {
        units = GeneralTools.micrometerSymbol();
        xDisplay *= cal.getPixelWidthMicrons();
        yDisplay *= cal.getPixelHeightMicrons();
    } else {
        units = "px";
    }
    // See if we're on top of a TMA core
    String prefix = "";
    TMAGrid tmaGrid = getHierarchy().getTMAGrid();
    if (tmaGrid != null) {
        TMACoreObject core = PathObjectTools.getTMACoreForPixel(tmaGrid, xx, yy);
        if (core != null && core.getName() != null)
            prefix = "Core: " + core.getName() + "\n";
    }
    String s = null;
    RegionRequest request = ImageRegionStoreHelpers.getTileRequest(server, xx, yy, downsampleFactor.get(), getZPosition(), getTPosition());
    if (request != null) {
        BufferedImage img = regionStore.getCachedTile(server, request);
        int xi = 0, yi = 0;
        if (img == null) {
            // Try getting a value from the thumbnail for the whole image
            BufferedImage imgThumbnail = regionStore.getCachedThumbnail(server, getZPosition(), getTPosition());
            if (imgThumbnail != null) {
                img = imgThumbnail;
                double downsample = (double) server.getWidth() / imgThumbnail.getWidth();
                xi = (int) (xx / downsample + .5);
                yi = (int) (yy / downsample + .5);
            }
        } else {
            xi = (int) ((xx - request.getX()) / request.getDownsample());
            yi = (int) ((yy - request.getY()) / request.getDownsample());
        }
        if (img != null) {
            // Make sure we are within range
            xi = Math.min(xi, img.getWidth() - 1);
            yi = Math.min(yi, img.getHeight() - 1);
            // Get the value, having applied any required color transforms
            if (imageDisplay != null)
                s = imageDisplay.getTransformedValueAsString(img, xi, yi);
        }
    }
    // Append z, t position if required
    String zString = null;
    if (server.nZSlices() > 1) {
        double zSpacing = server.getPixelCalibration().getZSpacingMicrons();
        if (!useCalibratedUnits || Double.isNaN(zSpacing))
            zString = "z = " + getZPosition();
        else
            zString = String.format("z = %.2f %s", getZPosition() * zSpacing, GeneralTools.micrometerSymbol());
    }
    String tString = null;
    if (server.nTimepoints() > 1) {
        // TODO: Consider use of TimeUnit
        // TimeUnit timeUnit = server.getTimeUnit();
        // if (!useMicrons || timeUnit == null)
        tString = "t = " + getTPosition();
    // else
    // tString = String.format("z = %.2f %s", getTPosition(), timeUnit.toString());
    }
    String dimensionString;
    if (tString == null && zString == null)
        dimensionString = "";
    else {
        dimensionString = "\n";
        if (zString != null) {
            dimensionString += zString;
            if (tString != null)
                dimensionString += ", " + tString;
        } else
            dimensionString += tString;
    }
    if (s != null)
        return String.format("%s%.2f, %.2f %s\n%s%s", prefix, xDisplay, yDisplay, units, s, dimensionString);
    else
        return String.format("%s%.2f, %.2f %s%s", prefix, xDisplay, yDisplay, units, dimensionString);
// if (s != null)
// return String.format("<html><center>%.2f, %.2f %s<br>%s", xDisplay, yDisplay, units, s);
// else
// return String.format("<html><center>%.2f, %.2f %s", xDisplay, yDisplay, units);
}