Examples with Well ome.xml.model.Well used on opensource projects

Example 1 with Well

use of ome.xml.model.Well in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidWellSamples.

@Test(dependsOnMethods = { "testValidPlateNode" })
public void testValidWellSamples() {
    Plate plate = ome.getPlate(0);
    Integer wellSampleIndex = 0;
    for (int row = 0; row < plate.getRows().getValue(); row++) {
        for (int col = 0; col < plate.getColumns().getValue(); col++) {
            Well well = plate.getWell(row * plate.getColumns().getValue() + col);
            assertEquals(1, well.sizeOfWellSampleList());
            WellSample sample = well.getWellSample(0);
            assertNotNull(sample);
            assertEquals(String.format("WellSample:%d_%d", row, col), sample.getID());
            assertEquals(wellSampleIndex, sample.getIndex().getValue());
            Image image = sample.getLinkedImage();
            assertNotNull(image);
            assertEquals(IMAGE_ID, image.getID());
            wellSampleIndex++;
        }
    }
}

Example 2 with Well

use of ome.xml.model.Well in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidPlateNode.

@Test(dependsOnMethods = { "testValidOMENode" })
public void testValidPlateNode() {
    Plate plate = ome.getPlate(0);
    assertNotNull(plate);
    assertEquals(PLATE_ID, plate.getID());
    assertEquals(plate.getRows(), WELL_ROWS);
    assertEquals(plate.getColumns(), WELL_COLS);
    assertEquals(plate.getRowNamingConvention(), WELL_ROW);
    assertEquals(plate.getColumnNamingConvention(), WELL_COL);
    assertEquals(plate.sizeOfWellList(), WELL_ROWS.getValue() * WELL_COLS.getValue());
    for (Integer row = 0; row < WELL_ROWS.getValue(); row++) {
        for (Integer col = 0; col < WELL_COLS.getValue(); col++) {
            Well well = plate.getWell(row * WELL_COLS.getValue() + col);
            assertNotNull(well);
            assertEquals(String.format("Well:%d_%d", row, col), well.getID());
            assertEquals(well.getRow(), row);
            assertEquals(well.getColumn(), col);
        }
    }
}

Example 3 with Well

use of ome.xml.model.Well in project bioformats by openmicroscopy.

the class ObjectBasedOMEModelMock method makePlate.

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);
    TimestampAnnotation plateAnnotation = new TimestampAnnotation();
    plateAnnotation.setID(InOutCurrentTest.PLATE_ANNOTATION_ID);
    plateAnnotation.setValue(new Timestamp(InOutCurrentTest.PLATE_ANNOTATION_VALUE));
    plateAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    plate.linkAnnotation(plateAnnotation);
    annotations.addTimestampAnnotation(plateAnnotation);
    int wellSampleIndex = 0;
    for (int row = 0; row < InOutCurrentTest.WELL_ROWS.getValue(); row++) {
        for (int col = 0; col < InOutCurrentTest.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));
            if (row == 0 && col == 0) {
                LongAnnotation annotation = new LongAnnotation();
                annotation.setID(InOutCurrentTest.WELL_ANNOTATION_ID);
                annotation.setValue(InOutCurrentTest.WELL_ANNOTATION_VALUE);
                annotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
                well.linkAnnotation(annotation);
                annotations.addLongAnnotation(annotation);
            }
            WellSample sample = new WellSample();
            sample.setID(String.format("WellSample:%d_%d", row, col));
            sample.setIndex(new NonNegativeInteger(wellSampleIndex));
            sample.linkImage(ome.getImage(0));
            well.addWellSample(sample);
            plate.addWell(well);
            wellSampleIndex++;
        }
    }
    return plate;
}

Example 4 with Well

use of ome.xml.model.Well in project bioformats by openmicroscopy.

the class FileWriteSPW method cleanup.

/**
 * Close the file writer.
 */
public void cleanup() {
    // No of planes expected for each image = 1 if not FLIM
    int validPlanes = 1;
    if (delays != null) {
        validPlanes = sizet;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
    Plate plate = root.getPlate(0);
    StructuredAnnotations anns = root.getStructuredAnnotations();
    ArrayList<Image> invalidImages = new ArrayList<>();
    // if not record those images as being invalid
    for (int i = 0; i < expectedImages.length; i++) {
        if (expectedImages[i] < validPlanes) {
            Image im = root.getImage(i);
            invalidImages.add(im);
            // remove modulo Annotation if FLIM
            if (delays != null) {
                XMLAnnotation ann = (XMLAnnotation) im.getLinkedAnnotation(0);
                anns.removeXMLAnnotation(ann);
            }
        }
    }
    // Now remove all limked wellSnmples and then invalid images
    for (int i = 0; i < invalidImages.size(); i++) {
        Image im = invalidImages.get(i);
        List<WellSample> list = im.copyLinkedWellSampleList();
        if (!list.isEmpty()) {
            WellSample wellSample = im.getLinkedWellSample(0);
            Well well = wellSample.getWell();
            well.removeWellSample(wellSample);
        }
        root.removeImage(im);
    }
    if (writer != null) {
        try {
            writer.close();
        } catch (IOException e) {
            System.err.println("Failed to close file writer.");
        }
    }
}

Example 5 with Well

use of ome.xml.model.Well in project bioformats by openmicroscopy.

the class SPWModelMock method makePlate.

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;
}