Examples with TableData omero.gateway.model.TableData used on opensource projects

Example 1 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class DefaultOMEROService method uploadTable.

@Override
public long uploadTable(final OMEROCredentials credentials, final String name, final Table<?, ?> imageJTable, final long imageID) throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final TableData omeroTable = convertOMEROTable(imageJTable);
    long id = -1;
    try (final OMEROSession session = new DefaultOMEROSession(credentials)) {
        // Get image
        final BrowseFacility browseFacility = session.getGateway().getFacility(BrowseFacility.class);
        final ImageData image = browseFacility.getImage(session.getSecurityContext(), imageID);
        // attach table to image
        final TablesFacility tablesFacility = session.getGateway().getFacility(TablesFacility.class);
        final TableData stored = tablesFacility.addTable(session.getSecurityContext(), image, name, omeroTable);
        id = stored.getOriginalFileId();
    }
    return id;
}

Example 2 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class ModuleAdapter method launch.

/**
 * Executes the associated ImageJ module as an OMERO script.
 *
 * @throws IOException
 * @throws ServerError
 * @throws ExecutionException
 * @throws CannotCreateSessionException
 * @throws PermissionDeniedException
 * @throws DSAccessException
 * @throws DSOutOfServiceException
 */
public void launch() throws ServerError, IOException, ExecutionException, PermissionDeniedException, CannotCreateSessionException, DSOutOfServiceException, DSAccessException {
    // populate inputs
    log.debug(info.getTitle() + ": populating inputs");
    final HashMap<String, Object> inputMap = new HashMap<>();
    for (final String name : client.getInputKeys()) {
        final ModuleItem<?> input = getInput(name);
        final Class<?> type = input.getType();
        final Object value = omeroService.toImageJ(client, client.getInput(name), type);
        inputMap.put(input.getName(), value);
    }
    // execute ImageJ module
    log.debug(info.getTitle() + ": executing module");
    final Future<Module> future = moduleService.run(info, true, inputMap);
    final Module module = moduleService.waitFor(future);
    final HashMap<String, TableData> tables = new HashMap<>();
    // populate outputs, except tables
    log.debug(info.getTitle() + ": populating outputs");
    for (final ModuleItem<?> item : module.getInfo().outputs()) {
        final Object value = omeroService.toOMERO(client, item.getValue(module));
        final String name = getOutputName(item);
        if (value == null) {
            log.warn(info.getTitle() + ": output '" + name + "' is null");
        }
        if (value instanceof omero.RType)
            client.setOutput(name, (omero.RType) value);
        if (value instanceof TableData)
            tables.put(name, (TableData) value);
    }
    createOutputLinks(inputMap, tables);
    gateway.disconnect();
    log.debug(info.getTitle() + ": completed execution");
}

Example 3 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class UploadTableTest method testFloatTable.

@Test
public void testFloatTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final FloatTable table = new DefaultFloatTable(4, 2);
    table.get(0).fill(new float[] { -380129.125f, 0.25f });
    table.get(1).fill(new float[] { 9871234.0f, -12.5f });
    table.get(2).fill(new float[] { 0.0625f, 13208.03125f });
    table.get(3).fill(new float[] { -0.0625f, 1908471790.5f });
    final String[] headers = new String[] { "H1", "H2", "H3", "H4" };
    for (int i = 0; i < table.getColumnCount(); i++) {
        table.get(i).setHeader(headers[i]);
    }
    // Create expectations
    setUpMethodCalls();
    final long id = service.uploadTable(credentials, "table", table, 0);
    assertEquals(id, -1);
    // NB: Can only capture in a Verifications block
    new Verifications() {

        {
            TableData td;
            tablesFacility.addTable((SecurityContext) any, (ImageData) any, anyString, td = withCapture());
            tableEquals(table, td, Double.class);
        }
    };
}

Example 4 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class UploadTableTest method testByteArrayTable.

@Test
public void testByteArrayTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final GenericTable table = new DefaultGenericTable();
    final DefaultColumn<ByteArray> ij0 = new DefaultColumn<>(ByteArray.class);
    final DefaultColumn<ByteArray> ij1 = new DefaultColumn<>(ByteArray.class);
    ij0.add(new ByteArray(new byte[] { -128, 127 }));
    ij0.add(new ByteArray(new byte[] { 0, 10 }));
    ij1.add(new ByteArray(new byte[] { 112, 42 }));
    ij1.add(new ByteArray(new byte[] { -13, -84 }));
    table.add(ij0);
    table.add(ij1);
    // Create expectations
    setUpMethodCalls();
    final long id = service.uploadTable(credentials, "table", table, 0);
    assertEquals(id, -1);
    // NB: Can only capture in a Verifications block
    new Verifications() {

        {
            TableData td;
            tablesFacility.addTable((SecurityContext) any, (ImageData) any, anyString, td = withCapture());
            tableEquals(table, td, Long[].class);
        }
    };
}

Example 5 with TableData

use of omero.gateway.model.TableData in project imagej-omero by imagej.

the class UploadTableTest method testCharTable.

@Test
public void testCharTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final CharTable table = new DefaultCharTable(5, 2);
    table.get(0).fill(new char[] { 'q', 'V' });
    table.get(1).fill(new char[] { '2', '$' });
    table.get(2).fill(new char[] { 'b', 'a' });
    table.get(3).fill(new char[] { '\t', '\n' });
    table.get(4).fill(new char[] { '.', ' ' });
    // Create expectations
    setUpMethodCalls();
    final long id = service.uploadTable(credentials, "table", table, 0);
    assertEquals(id, -1);
    // NB: Can only capture in a Verifications block
    new Verifications() {

        {
            TableData td;
            tablesFacility.addTable((SecurityContext) any, (ImageData) any, anyString, td = withCapture());
            tableEquals(table, td, String.class);
        }
    };
}