/**
* Creates a basic plate and links the wells to the passed reagent.
*
* @param rows The number of rows.
* @param columns The number of columns.
* @param fields The number of fields.
* @param r The reagent.
* @return See above.
*/
public Plate createPlateWithReagent(int rows, int columns, int fields, Reagent r) {
Plate p = new PlateI();
p.setRows(omero.rtypes.rint(rows));
p.setColumns(omero.rtypes.rint(columns));
p.setName(omero.rtypes.rstring("plate"));
// now make wells
Well well;
WellSample sample;
for (int row = 0; row < rows; row++) {
for (int column = 0; column < columns; column++) {
well = new WellI();
well.setRow(omero.rtypes.rint(row));
well.setColumn(omero.rtypes.rint(column));
well.linkReagent(r);
for (int field = 0; field < fields; field++) {
sample = new WellSampleI();
sample.setImage(simpleImage(0));
well.addWellSample(sample);
}
p.addWell(well);
}
}
return p;
}
/**
* Creates a 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 acquisitions.
* @param fullImage Pass <code>true</code> to add image with pixels, <code>false</code> to create
* a simple image.
* @return See above.
*/
public Plate createPlate(
int rows, int columns, int fields, int numberOfPlateAcquisition, boolean fullImage)
throws Exception {
if (numberOfPlateAcquisition < 0) numberOfPlateAcquisition = 0;
Plate p = new PlateI();
p.setRows(omero.rtypes.rint(rows));
p.setColumns(omero.rtypes.rint(columns));
p.setName(omero.rtypes.rstring("plate name"));
p.setDescription(omero.rtypes.rstring("plate description"));
p.setStatus(omero.rtypes.rstring("plate status"));
p.setExternalIdentifier(omero.rtypes.rstring("external identifier"));
// now make wells
Well well;
WellSample sample;
List<PlateAcquisition> pas = new ArrayList<PlateAcquisition>();
PlateAcquisition pa;
for (int i = 0; i < numberOfPlateAcquisition; i++) {
pa = new PlateAcquisitionI();
pa.setName(omero.rtypes.rstring("plate acquisition"));
pa.setPlate(p);
pas.add(pa);
}
Iterator<PlateAcquisition> i;
for (int row = 0; row < rows; row++) {
for (int column = 0; column < columns; column++) {
well = new WellI();
well.setRow(omero.rtypes.rint(row));
well.setColumn(omero.rtypes.rint(column));
if (pas.size() == 0) {
for (int field = 0; field < fields; field++) {
sample = new WellSampleI();
if (fullImage) sample.setImage(createImage());
else sample.setImage(simpleImage(0));
well.addWellSample(sample);
}
} else {
i = pas.iterator();
while (i.hasNext()) {
pa = i.next();
for (int field = 0; field < fields; field++) {
sample = new WellSampleI();
if (fullImage) sample.setImage(createImage());
else sample.setImage(simpleImage(0));
well.addWellSample(sample);
pa.addWellSample(sample);
}
}
}
p.addWell(well);
}
}
return p;
}
public Object generateThumbnails(ThumbnailGenerationJob tgj) throws Throwable {
List<Long> plateIds = new ArrayList<Long>();
Image image = pixList.get(0).getImage();
if (image.sizeOfWellSamples() > 0) {
Plate plate = image.copyWellSamples().get(0).getWell().getPlate();
plateIds.add(plate.getId().getValue());
}
notifyObservers(new ImportEvent.IMPORT_OVERLAYS(0, null, userSpecifiedTarget, null, 0, null));
importOverlays(pixList, plateIds);
notifyObservers(new ImportEvent.IMPORT_PROCESSING(0, null, userSpecifiedTarget, null, 0, null));
if (doThumbnails) {
store.resetDefaultsAndGenerateThumbnails(plateIds, pixelIds());
} else {
log.warn("Not creating thumbnails at user request!");
}
return null;
}