public void setWellType(String type, int plateIndex, int wellIndex) { // Parents: {u'Plate': {u'OME': None}} // Type is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); if (o1.sizeOfWellList() == wellIndex) { o1.addWell(new Well()); } Well o2 = o1.getWell(wellIndex); o2.setType(type); }
public void setPlateColumnNamingConvention(NamingConvention columnNamingConvention, int plateIndex) { // Parents: {u'OME': None} // ColumnNamingConvention is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setColumnNamingConvention(columnNamingConvention); }
public void setPlateColumns(PositiveInteger columns, int plateIndex) { // Parents: {u'OME': None} // Columns is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setColumns(columns); }
/** * Creates a basic plate. * * @param index The index of the plate. * @return See above. */ public Plate createBasicPlate(int index) { Plate plate = new Plate(); plate.setID("Plate:"+index); plate.setName("Plate Name "+index); plate.setDescription("Plate Description "+index); return plate; }
public void setPlateRowNamingConvention(NamingConvention rowNamingConvention, int plateIndex) { // Parents: {u'OME': None} // RowNamingConvention is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setRowNamingConvention(rowNamingConvention); }
setStatus(String.valueOf( element.getAttribute("Status"))); setRows(PositiveInteger.valueOf( element.getAttribute("Rows"))); setExternalIdentifier(String.valueOf( element.getAttribute("ExternalIdentifier"))); setRowNamingConvention(NamingConvention.fromString( element.getAttribute("RowNamingConvention"))); setColumnNamingConvention(NamingConvention.fromString( element.getAttribute("ColumnNamingConvention"))); setFieldIndex(NonNegativeInteger.valueOf( element.getAttribute("FieldIndex"))); setColumns(PositiveInteger.valueOf( element.getAttribute("Columns"))); unitSymbol = getWellOriginYUnitXsdDefault(); setWellOriginY(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit)); unitSymbol = getWellOriginXUnitXsdDefault(); setWellOriginX(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit));
numberOfPlateAcquisition = 0; Plate plate = new Plate(); plate.setID("Plate:"+totalPlateIndex); plate.setName("Plate Name "+totalPlateIndex); plate.setDescription(String.format("Plate %d of %d", plateIndex, numberOfPlates)); plate.setExternalIdentifier("External Identifier"); plate.setRows(new PositiveInteger(rows)); plate.setColumns(new PositiveInteger(columns)); plate.setRowNamingConvention(ROW_NAMING_CONVENTION); plate.setColumnNamingConvention(COLUMN_NAMING_CONVENTION); plate.setWellOriginX(new Length(0.0, UNITS.MICROMETER)); plate.setWellOriginY(new Length(1.0, UNITS.MICROMETER)); plate.setStatus("Plate status"); PlateAcquisition pa = null; List<PlateAcquisition> pas = new ArrayList<PlateAcquisition>(); pa.setEndTime(new Timestamp(TIME)); pa.setStartTime(new Timestamp(TIME)); plate.addPlateAcquisition(pa); pas.add(pa); plate.addWell(well);
private Plate makePlate() { Plate plate = new Plate(); plate.setName(PLATE_NAME); plate.setID(PLATE_ID); plate.setRows(WELL_ROWS); plate.setColumns(WELL_COLS); plate.setRowNamingConvention(WELL_ROW); plate.setColumnNamingConvention(WELL_COL); int wellSampleIndex = 0; for (int row=0; row<WELL_ROWS.getValue(); row++) { for (int col=0; col<WELL_COLS.getValue(); col++) { Well well = new Well(); well.setID(String.format("Well:%d_%d", row, col)); well.setRow(new NonNegativeInteger(row)); well.setColumn(new NonNegativeInteger(col)); WellSample sample = new WellSample(); sample.setID(String.format("WellSample:%d_%d", row, col)); sample.setIndex(new NonNegativeInteger(wellSampleIndex)); sample.linkImage(ome.getImage(wellSampleIndex)); well.addWellSample(sample); plate.addWell(well); wellSampleIndex++; } } return plate; }
private Plate makePlate() { Plate plate = new Plate(); plate.setID(InOutCurrentTest.PLATE_ID); plate.setRows(InOutCurrentTest.WELL_ROWS); plate.setColumns(InOutCurrentTest.WELL_COLS); plate.setRowNamingConvention(InOutCurrentTest.WELL_ROW); plate.setColumnNamingConvention(InOutCurrentTest.WELL_COL); plateAnnotation.setValue(new Timestamp(InOutCurrentTest.PLATE_ANNOTATION_VALUE)); plateAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE); plate.linkAnnotation(plateAnnotation); annotations.addTimestampAnnotation(plateAnnotation); sample.linkImage(ome.getImage(0)); well.addWellSample(sample); plate.addWell(well); wellSampleIndex++;
public String getWellExternalIdentifier(int plateIndex, int wellIndex) { // Parents: {u'Plate': {u'OME': None}} // ExternalIdentifier is not a reference return root.getPlate(plateIndex).getWell(wellIndex).getExternalIdentifier(); }
public void setPlateAcquisitionMaximumFieldCount(PositiveInteger maximumFieldCount, int plateIndex, int plateAcquisitionIndex) { // Parents: {u'Plate': {u'OME': None}} // MaximumFieldCount is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); if (o1.sizeOfPlateAcquisitionList() == plateAcquisitionIndex) { o1.addPlateAcquisition(new PlateAcquisition()); } PlateAcquisition o2 = o1.getPlateAcquisition(plateAcquisitionIndex); o2.setMaximumFieldCount(maximumFieldCount); }
public void setPlateDescription(String description, int plateIndex) { // Parents: {u'OME': None} // Description is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setDescription(description); }
public void setPlateWellOriginX(Length wellOriginX, int plateIndex) { // Parents: {u'OME': None} // WellOriginX is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setWellOriginX(wellOriginX); }
public void setPlateWellOriginY(Length wellOriginY, int plateIndex) { // Parents: {u'OME': None} // WellOriginY is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setWellOriginY(wellOriginY); }
public void setPlateExternalIdentifier(String externalIdentifier, int plateIndex) { // Parents: {u'OME': None} // ExternalIdentifier is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setExternalIdentifier(externalIdentifier); }
public void setPlateFieldIndex(NonNegativeInteger fieldIndex, int plateIndex) { // Parents: {u'OME': None} // FieldIndex is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); o1.setFieldIndex(fieldIndex); }