@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()};
}
@Override
protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
throws Exception {
BufferedDataTable input = inData[0];
// Get the condition attribute
Attribute treatmentAttribute =
new InputTableAttribute(this.treatmentAttribute.getStringValue(), input);
// Get the library and reference condition names
String libraryName = AbstractScreenTrafoModel.getAndValidateTreatment(reference);
String referenceName = AbstractScreenTrafoModel.getAndValidateTreatment(library);
// Get the parameter and make sure there all double value columns
List<Attribute> parameters = getParameterList(input);
// Split the columns according to groups contained in the condition column
Map<String, List<DataRow>> groupedRows = AttributeUtils.splitRows(input, treatmentAttribute);
List<DataRow> libraryRows = groupedRows.get(libraryName);
List<DataRow> referenceRows = groupedRows.get(referenceName);
int progress = parameters.size();
BufTableUtils.updateProgress(exec, progress / 2, progress);
// Initialize
BufferedDataContainer container = exec.createDataContainer(new DataTableSpec(getListSpec()));
MutualInformation mutualinfo = new MutualInformation();
mutualinfo.set_base(logbase.getDoubleValue());
mutualinfo.set_method(method.getStringValue());
mutualinfo.set_axeslinking(linkaxes.getBooleanValue());
DataCell[] cells = new DataCell[container.getTableSpec().getNumColumns()];
int p = 0;
// Calculate mutual information
for (Attribute parameter : parameters) {
Double[] x = getDataVec(libraryRows, parameter);
Double[] y = getDataVec(referenceRows, parameter);
mutualinfo.set_vectors(x, y);
if (binning.getIntValue() == 0) {
mutualinfo.set_binning();
} else {
mutualinfo.set_binning(binning.getIntValue());
}
int[] bins = mutualinfo.get_binning();
Double[] res = mutualinfo.calculate();
cells[0] = new StringCell(parameter.getName());
cells[1] = new DoubleCell(res[0]);
cells[2] = new DoubleCell(res[1]);
cells[3] = new DoubleCell(res[2]);
cells[4] = new IntCell(bins[0]);
cells[5] = new IntCell(bins[1]);
cells[6] = new DoubleCell(mutualinfo.get_logbase());
cells[7] = new StringCell(mutualinfo.get_method());
container.addRowToTable(new DefaultRow("row" + p, cells));
BufTableUtils.updateProgress(exec, (progress + p++) / 2, progress);
exec.checkCanceled();
}
container.close();
return new BufferedDataTable[] {container.getTable()};
}
