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());
}
}