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

Example 11 with TableData

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

the class DefaultOMEROService method convertOMEROTable.

@Override
public TableData convertOMEROTable(final Table<?, ?> imageJTable) {
    final TableDataColumn[] omeroColumns = new TableDataColumn[imageJTable.getColumnCount()];
    final Object[][] data = new Object[imageJTable.getColumnCount()][];
    for (int c = 0; c < imageJTable.getColumnCount(); c++) {
        omeroColumns[c] = TableUtils.createOMEROColumn(imageJTable.get(c), c);
        data[c] = TableUtils.populateOMEROColumn(imageJTable.get(c), convertService);
    }
    // Create table and attach to image
    final TableData omeroTable = new TableData(omeroColumns, data);
    omeroTable.setNumberOfRows(imageJTable.getRowCount());
    return omeroTable;
}

Example 12 with TableData

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

the class DefaultOMEROService method downloadTable.

@Override
public Table<?, ?> downloadTable(final OMEROCredentials credentials, final long tableID) throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    try (final OMEROSession session = new DefaultOMEROSession(credentials)) {
        final TablesFacility tableService = session.getGateway().getFacility(TablesFacility.class);
        final TableData table = tableService.getTable(session.getSecurityContext(), tableID, 0, Integer.MAX_VALUE - 1);
        final TableDataColumn[] omeroColumns = table.getColumns();
        final Object[][] data = table.getData();
        final Table<?, ?> imageJTable = TableUtils.createImageJTable(omeroColumns);
        imageJTable.setRowCount((int) table.getNumberOfRows());
        boolean colsCreated = false;
        if (!(imageJTable instanceof GenericTable)) {
            imageJTable.appendColumns(omeroColumns.length);
            colsCreated = true;
        }
        for (int i = 0; i < omeroColumns.length; i++) {
            if (!colsCreated) {
                final Column<?> imageJCol = TableUtils.createImageJColumn(omeroColumns[i]);
                TableUtils.populateImageJColumn(omeroColumns[i].getType(), data[omeroColumns[i].getIndex()], imageJCol);
                ((GenericTable) imageJTable).add(omeroColumns[i].getIndex(), imageJCol);
            } else {
                TableUtils.populateImageJColumn(omeroColumns[i].getType(), data[omeroColumns[i].getIndex()], imageJTable.get(i));
                imageJTable.get(i).setHeader(omeroColumns[i].getName());
            }
        }
        return imageJTable;
    }
}

Example 13 with TableData

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

the class ModuleAdapter method attachTablesToImages.

/**
 * Attaches the tables to the input images. This also adds the Table ids to
 * the omero client.
 */
private void attachTablesToImages(final List<ImageData> images, final HashMap<String, TableData> tables, final SecurityContext ctx, final DataManagerFacility dm) throws DSOutOfServiceException, DSAccessException, ExecutionException, ServerError {
    final TablesFacility tablesFacility = gateway.getFacility(TablesFacility.class);
    for (final String name : tables.keySet()) {
        final TableData t = tablesFacility.addTable(ctx, images.get(0), name, tables.get(name));
        client.setOutput(name, omero.rtypes.rlong(t.getOriginalFileId()));
    }
    // Adding tables again would create new tables on the server
    for (int i = 1; i < images.size(); i++) {
        for (final String name : tables.keySet()) {
            final OriginalFile file = new OriginalFileI(tables.get(name).getOriginalFileId(), false);
            final FileAnnotation anno = new FileAnnotationI();
            anno.setFile(file);
            FileAnnotationData annotation = new FileAnnotationData(anno);
            annotation.setDescription(name);
            annotation = (FileAnnotationData) dm.saveAndReturnObject(ctx, annotation);
            dm.attachAnnotation(ctx, annotation, images.get(i));
        }
    }
}

Example 14 with TableData

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

the class UploadTableTest method setUpMethodCalls.

// -- Helper methods --
private void setUpMethodCalls() throws ServerError, PermissionDeniedException, CannotCreateSessionException, DSOutOfServiceException, ExecutionException, DSAccessException {
    new Expectations() {

        {
            new DefaultOMEROSession(credentials);
            gateway.getFacility(BrowseFacility.class);
            result = browseFacility;
            browseFacility.getImage((SecurityContext) any, anyLong);
            result = new ImageData();
            gateway.getFacility(TablesFacility.class);
            result = tablesFacility;
            tablesFacility.addTable((SecurityContext) any, (ImageData) any, anyString, (TableData) any);
            result = new TableData((TableDataColumn[]) any, (Object[][]) any);
        }
    };
}

Example 15 with TableData

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

the class UploadTableTest method testBoolTable.

@Test
public void testBoolTable() throws ServerError, PermissionDeniedException, CannotCreateSessionException, ExecutionException, DSOutOfServiceException, DSAccessException {
    final BoolTable table = new DefaultBoolTable(2, 4);
    table.get(0).fill(new boolean[] { true, true, false, false });
    table.get(1).fill(new boolean[] { true, false, true, false });
    // 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, Boolean.class);
        }
    };
}