Examples with TMAObjectEntry qupath.lib.gui.tma.TMAEntries.TMAObjectEntry used on opensource projects

Example 1 with TMAObjectEntry

use of qupath.lib.gui.tma.TMAEntries.TMAObjectEntry in project qupath by qupath.

the class TMASummaryViewer method importScores.

private int importScores(final String text) {
    Map<String, List<String>> data = TMAScoreImporter.readCSV(text);
    List<String> idColumn = data.remove(TMACoreObject.KEY_UNIQUE_ID);
    if (idColumn == null) {
        Dialogs.showErrorMessage("Import TMA data", "No '" + TMACoreObject.KEY_UNIQUE_ID + "' column found!");
        return 0;
    }
    // Nothing left to import...
    if (data.isEmpty())
        return 0;
    // Get the numeric columns, if possible
    Map<String, double[]> dataNumeric = new HashMap<>();
    for (String key : data.keySet().toArray(new String[0])) {
        double[] vals = TMAScoreImporter.parseNumeric(data.get(key), true);
        if (vals != null && GeneralTools.numNaNs(vals) != vals.length) {
            dataNumeric.put(key, vals);
            data.remove(key);
        }
    }
    // Loop through IDs, adding values where needed
    int counter = 0;
    for (int i = 0; i < idColumn.size(); i++) {
        boolean matched = false;
        String id = idColumn.get(i);
        if (id == null) {
            logger.debug("Skipping missing ID");
            continue;
        }
        for (TMAEntry entry : entriesBase) {
            if (id.equals(entry.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID))) {
                matched = true;
                for (Entry<String, double[]> dataEntry : dataNumeric.entrySet()) {
                    entry.putMeasurement(dataEntry.getKey(), dataEntry.getValue()[i]);
                }
                for (Entry<String, List<String>> dataEntry : data.entrySet()) {
                    entry.putMetadata(dataEntry.getKey(), dataEntry.getValue().get(i));
                }
                counter++;
            }
        }
        if (!matched)
            logger.warn("No match for ID: " + id);
    }
    Optional<TMAEntry> objectEntry = entriesBase.stream().filter(t -> t instanceof TMAObjectEntry).findAny();
    if (objectEntry.isPresent()) {
        Dialogs.showInfoNotification("TMA data update", "TMA cores updated!");
    }
    return counter;
}