/** * Creates a default plate * * @param numberOfPlates The total number of plates. * @param index The index of the plate. * @param numberOfPlateAcquisition The number of plate acquisition to add. * @return See above. */ public Plate createPlate(int numberOfPlates, int index, int numberOfPlateAcquisition) { return createPlate(numberOfPlates, index, ROWS, COLUMNS, FIELDS, numberOfPlateAcquisition); }
/** * Creates a populated plate with images. * * @param numberOfPlates The total number of plates. * @param index The index of the plate. * @param rows The number of rows. * @param columns The number of columns. * @param fields The number of fields. * @param numberOfPlateAcquisition The number of plate acquisition to add. * @return See above. */ public Plate createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition) { return createPlate(numberOfPlates, index, rows, columns, fields, numberOfPlateAcquisition, true); }
/** * Creates a populated plate with images. * * @param numberOfScreens The total number of screens. * @param screenIndex The index of the screen. * @param numberOfPlates The total number of plates. * @param plateIndex The index of the plate. * @param rows The number of rows. * @param columns The number of columns. * @param fields The number of fields. * @param numberOfPlateAcquisition The number of plate acquisition to add. * @return See above. */ public Plate createPlate(int numberOfScreens, int screenIndex, int numberOfPlates, int plateIndex, int rows, int columns, int fields, int numberOfPlateAcquisition) { return createPlate(numberOfScreens, screenIndex, numberOfPlates, plateIndex, rows, columns, fields, numberOfPlateAcquisition, true); } /**
/** * Creates a populated plate with images. * * @param numberOfPlates The total number of plates. * @param index The index of the plate. * @param rows The number of rows. * @param columns The number of columns. * @param fields The number of fields. * @param numberOfPlateAcquisition The number of plate acquisition to add. * @param withMicrobeam Whether the experiment should contain a microbeam * @return See above. */ public Plate createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition, boolean withMicrobeam) { return createPlate(1, 0, numberOfPlates, index, rows, columns, fields, numberOfPlateAcquisition, withMicrobeam); }
/** * Creates several plates but no containing screen. * * @param plates The number of plates to create. * @param rows The number of rows for plate. * @param cols The number of columns for plate. * @param fields The number of fields. * @param acqs The number of plate acquisitions. * @param withMicrobeam Whether the experiment should contain a microbeam * @return See above. */ public OME createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam) { Plate plate; for (int p = 0; p < plates; p++) { plate = createPlate(plates, p, rows, cols, fields, acqs, withMicrobeam); ome.addPlate(plate); } return ome; }
/** * Creates a plate with <code>1</code> row, <code>1</code> column * and <code>1</code>field. * The plate will have images with acquisition data but no plate acquisition * data if the passed value is <code>0</code> otherwise will have * <code>n</code> plate acquisitions. * * @param n The number of plate acquisition. * @return See above */ public OME createPopulatedPlate(int n) { populateInstrument(); ome.addPlate(createPlate(1, 0, 1, 1, 1, n)); return ome; }
/** * Creates a plate with {@link #ROWS} rows, {@link #COLUMNS} columns * and {@link #FIELDS} field. * The plate will have images with acquisition data but no plate acquisition * data. * * @param n The number of plate acquisition. * @return See above */ public OME createFullPopulatedPlate(int n) { populateInstrument(); ome.addPlate(createPlate(1, 0, n)); return ome; }
/** * Creates a plate with <code>1</code> row, <code>1</code> column * and <code>fields</code>field. * The plate will have images with acquisition data but no plate acquisition * data if the passed value is <code>0</code> otherwise will have * <code>n</code> plate acquisitions. * * @param n The number of plate acquisition. * @param fields The number of fields. * @return See above */ public OME createPopulatedPlate(int n, int fields) { if (fields < 1) fields = 1; populateInstrument(); ome.addPlate(createPlate(1, 0, 1, 1, fields, n)); return ome; }
/** * Creates several screens each with several plates. * * @param screens The number of screens to create. * @param plates The number of plates to create. * @param rows The number of rows for plate. * @param cols The number of columns for plate. * @param fields The number of fields. * @param acqs The number of plate acquisitions. * @param withMicrobeam Whether the experiment should contain a microbeam * @return See above. */ public OME createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam) { Screen screen; Plate plate; for (int s = 0; s < screens; s++) { screen = createScreen(s); for (int p = 0; p < plates; p++) { plate = createPlate(screens, s, plates, p, rows, cols, fields, acqs, withMicrobeam); screen.linkPlate(plate); ome.addPlate(plate); } ome.addScreen(screen); } return ome; }
/** * Creates a plate with <code>1</code> row, <code>1</code> column * and <code>1</code> field. This plate will be added to a screen * and the well linked to a reagent. * * @return See above */ public OME createBasicPlateWithReagent() { populateInstrument(); Plate plate = createPlate(1, 0, 1, 1, 1, 0); Reagent r = createReagent(0); plate.getWell(0).linkReagent(r); Screen screen = createScreen(0); screen.addReagent(r); screen.linkPlate(plate); ome.addPlate(plate); ome.addScreen(screen); return ome; }