private void populateWell(Integer plateColumn, Integer plateRow, Well zStackWell) {
List<String> readouts = TdsUtils.flattenReadoutNames(curPlateSelection);
for (String readoutName : readouts) {
DescriptiveStatistics descStats = new DescriptiveStatistics();
for (Plate plate : curPlateSelection) {
Well curWell = plate.getWell(plateColumn, plateRow);
if (curWell == null) continue;
Double readoutValue = curWell.getReadout(readoutName);
if (readoutValue != null) {
descStats.addValue(readoutValue);
}
}
zStackWell.getWellStatistics().put(readoutName, descStats.getMean());
}
}
@Override
protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
throws Exception {
List<File> inputFiles =
FileSelectPanel.getInputFiles(propInputDir.getStringValue(), getAllowedFileExtensions());
if (inputFiles.isEmpty()) {
throw new RuntimeException("No files selected");
}
// first group files into plate-groups
Map<String, List<File>> plateFiles = splitFilesIntoPlates(inputFiles);
if (inputFiles.isEmpty()) {
throw new RuntimeException("No valid envision-files in selection " + inputFiles);
}
// split files
List<String> allAttributes = mergeAttributes(plateFiles);
List<Attribute> colAttributes = compileColumnModel(allAttributes);
DataTableSpec outputSpec = AttributeUtils.compileTableSpecs(colAttributes);
BufferedDataContainer container = exec.createDataContainer(outputSpec);
// populate the table
int fileCounter = 0, rowCounter = 0;
for (String barcode : plateFiles.keySet()) {
logger.info("Processing plate " + barcode);
Plate plate = new Plate();
// invalidate plate-dims as these become fixed in the loop
plate.setNumColumns(-1);
plate.setNumRows(-1);
for (File file : plateFiles.get(barcode)) {
String attributeName = getAttributeNameOfEnvisionFile(file);
parseFile(plate, attributeName, file);
BufTableUtils.updateProgress(exec, fileCounter++, inputFiles.size());
}
// now create the data-rows for this table
for (Well well : plate.getWells()) {
if (well.getReadOutNames().isEmpty()) {
continue;
}
DataCell[] knimeRow = new DataCell[colAttributes.size()];
// first add the barcode-column
knimeRow[0] = new StringCell(barcode);
knimeRow[1] = colAttributes.get(1).createCell(well.getPlateRow());
knimeRow[2] = colAttributes.get(2).createCell(well.getPlateColumn());
for (String attributeName : allAttributes) {
int rowIndex = allAttributes.indexOf(attributeName);
Double value = well.getReadout(attributeName);
if (value != null) {
knimeRow[3 + rowIndex] = new DoubleCell(value);
} else {
knimeRow[3 + rowIndex] = DataType.getMissingCell();
}
}
DataRow tableRow = new DefaultRow(new RowKey("" + rowCounter++), knimeRow);
container.addRowToTable(tableRow);
}
}
container.close();
return new BufferedDataTable[] {container.getTable()};
}
