コード例 #1
0
  public static void main(String[] args) {
    File envisionFile = new File("./resources/envision-example 1.xls");
    Sheet sheet = StringTable.openWorkSheet(envisionFile).getSheetAt(0);

    Point bckndTablePos = StringTable.findNextPlatePosition(sheet, new Point(1, 1));
    Point corTablePos =
        StringTable.findNextPlatePosition(
            sheet, new Point((int) bckndTablePos.getX(), (int) (bckndTablePos.getY() + 1)));

    Rectangle tableBounds = StringTable.guessPlateBounds(sheet, corTablePos);
    StringTable table = StringTable.readStringGridFromExcel(tableBounds, sheet);

    System.err.println("starting point is" + corTablePos);
    System.err.println("table-bounds are" + tableBounds);
    System.err.println("the table is " + table);
    //        envisionFile  = StringTable.readStringGridFromCsv(envisionFile, ",", new Point(2, 4),
    // new Point(25, 19))
  }
コード例 #2
0
  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);
        }
      }
    }
  }