public void parseFile(Plate plate, String attributeName, File envisionFile) {
Sheet sheet = StringTable.openWorkSheet(envisionFile).getSheetAt(0);
Point tableTopLeftPos = StringTable.findNextPlatePosition(sheet, new Point(1, 1));
int numSkipTables = propTableIndex.getIntValue() - 1;
while (tableTopLeftPos != null && numSkipTables > 0) {
tableTopLeftPos =
StringTable.findNextPlatePosition(
sheet, new Point((int) tableTopLeftPos.getX(), (int) (tableTopLeftPos.getY() + 1)));
numSkipTables--;
}
if (tableTopLeftPos == null) {
throw new RuntimeException("Could not find readout-table in file " + envisionFile);
}
Rectangle tableBounds = StringTable.guessPlateBounds(sheet, tableTopLeftPos);
StringTable envisionTable = StringTable.readStringGridFromExcel(tableBounds, sheet);
// either set the plate dimensions or validate them
if (plate.getNumRows() < 0) {
plate.setNumColumns(envisionTable.getWidth() - 1);
plate.setNumRows(envisionTable.getHeight() - 1);
} else {
assert envisionTable.getWidth() - 1 == plate.getNumColumns();
assert envisionTable.getHeight() - 1 == plate.getNumRows();
}
for (int colIndex = 0; colIndex < plate.getNumColumns(); colIndex++) {
for (int rowIndex = 0; rowIndex < plate.getNumRows(); rowIndex++) {
int plateRow = rowIndex + 1; // this inversion looks weired but it is correct
int plateColumn = colIndex + 1;
Well well = plate.getWell(plateColumn, plateRow);
if (well == null) {
well = new Well();
well.setPlateRow(plateRow);
well.setPlateColumn(plateColumn);
well.setPlate(plate);
plate.addWell(well);
}
Double readout = ScreenImportUtils.parseDouble(envisionTable.get(plateRow, plateColumn));
if (readout != null) {
well.getWellStatistics().put(attributeName, readout);
}
}
}
}
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());
}
}
public AvgerageZStack(List<Plate> curPlateSelection) {
this.curPlateSelection = curPlateSelection;
Plate avgZStack = new Plate();
avgZStack.setBarcode("avgz-stack");
for (Well well : curPlateSelection.get(0).getWells()) {
Well zStackWell = new Well();
zStackWell.setPlateColumn(well.getPlateColumn());
zStackWell.setPlateRow(well.getPlateRow());
populateWell(well.getPlateColumn(), well.getPlateRow(), zStackWell);
avgZStack.getWells().add(zStackWell);
}
PlatePanel.createPanelDialog(avgZStack, null, null);
}
@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()};
}