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

Example 6 with ImageData

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

the class ModuleAdapter method getInputImages.

/**
 * Loops over the input items, and checks for Datasets, and if so gets the
 * corresponding omero ImageData.
 */
private List<ImageData> getInputImages(final HashMap<String, Object> inputMap, final BrowseFacility browse, final SecurityContext ctx) throws ServerError, DSOutOfServiceException, DSAccessException {
    if (imageInput != null) {
        final RLong id = (RLong) client.getInput(IMAGE_NAME);
        return Collections.singletonList(browse.getImage(ctx, id.getValue()));
    }
    final List<ImageData> images = new ArrayList<>();
    for (String key : inputMap.keySet()) {
        if (inputMap.get(key) instanceof Dataset) {
            final RLong id = (RLong) client.getInput(key);
            images.add(browse.getImage(ctx, id.getValue()));
        }
    }
    return images;
}

Example 7 with ImageData

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

the class ModuleAdapter method getOutputImages.

/**
 * Loops over all the orphaned images, and grabs the ones which have IDs that
 * match the omero client outputs.
 */
private List<ImageData> getOutputImages(final long userId, final BrowseFacility browse, final SecurityContext ctx) throws ServerError {
    final Collection<ImageData> orphans = browse.getOrphanedImages(ctx, userId);
    final HashMap<Long, ImageData> mappedOrphans = new HashMap<>();
    for (ImageData i : orphans) mappedOrphans.put(i.getId(), i);
    final List<ImageData> images = new ArrayList<>();
    for (String key : client.getOutputKeys()) {
        final omero.RType type = client.getOutput(key);
        if (type instanceof RLong) {
            if (mappedOrphans.containsKey(((RLong) type).getValue()))
                images.add(mappedOrphans.get(((RLong) type).getValue()));
        }
    }
    return images;
}

Example 8 with ImageData

use of omero.gateway.model.ImageData 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 9 with ImageData

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

the class DownloadTableTest method downloadRefTable.

@Test
public void downloadRefTable() throws PermissionDeniedException, CannotCreateSessionException, ServerError, DSOutOfServiceException, ExecutionException, DSAccessException {
    final TableDataColumn[] tdc = new TableDataColumn[] { new TableDataColumn("Header 1", 0, ImageData.class), new TableDataColumn("Header 2", 1, ImageData.class), new TableDataColumn("Header 3", 2, ImageData.class) };
    final Object[][] data = new Object[3][3];
    final long[][] ids = new long[][] { { 101, 102, 103 }, { 201, 202, 203 }, { 301, 302, 303 } };
    for (int i = 0; i < 3; i++) {
        for (int j = 0; j < 3; j++) {
            data[i][j] = new ImageData(new ImageI(ids[i][j], false));
        }
    }
    final TableData table = new TableData(tdc, data);
    table.setNumberOfRows(3);
    // Create expectations
    setUpMethodCalls(table);
    final Table<?, ?> imageJTable = ((DefaultOMEROService) service).downloadTable(credentials, 0);
    // Tests
    assertTrue(GenericTable.class.isInstance(imageJTable));
    assertEquals(imageJTable.getColumnCount(), 3);
    assertEquals(imageJTable.getRowCount(), 3);
    assertEquals(imageJTable.getColumnHeader(0), "Header 1");
    assertEquals(imageJTable.getColumnHeader(1), "Header 2");
    assertEquals(imageJTable.getColumnHeader(2), "Header 3");
    for (int r = 0; r < imageJTable.getRowCount(); r++) {
        for (int c = 0; c < imageJTable.getColumnCount(); c++) {
            assertTrue(OMERORefColumn.class.isInstance(imageJTable.get(c)));
            assertTrue(imageJTable.get(c).getType() == Long.class);
            assertEquals(((OMERORefColumn) imageJTable.get(c)).getOMERORef(), OMERORef.IMAGE);
            assertEquals(ids[c][r], ((OMERORefColumn) imageJTable.get(c)).get(r).longValue());
        }
    }
}