@Test
public void lazyLoadLoaderFactory() throws Exception {
IDataHolder dataHolder = LoaderFactory.getData(testFileFolder + file, true, true, true, null);
ILazyDataset lazy = dataHolder.getLazyDataset("Portable Grey Map");
assertArrayEquals(new int[] {1024, 1024}, lazy.getShape());
IDataset data = lazy.getSlice();
// Check the first data point
assertEquals(data.getDouble(0, 0), 0.0, 0.0);
// Check the middle data point
assertEquals(data.getDouble(512, 511), 15104.0, 0.0);
// Check the last data point
assertEquals(data.getDouble(1023, 1023), 0.0, 0.0);
}
private void updateSliceWidget(String path) {
try {
IDataHolder dh = ServiceHolder.getLoaderService().getData(path, new IMonitor.Stub());
ILazyDataset lazy = dh.getLazyDataset(fileManager.getContext().getDatasetNames().get(0));
int[] shape = lazy.getShape();
int[] dd = Slicer.getDataDimensions(shape, fileManager.getContext().getSliceDimensions());
Slice[] slices =
Slicer.getSliceArrayFromSliceDimensions(
fileManager.getContext().getSliceDimensions(), shape);
csw.setDatasetShapeInformation(shape, dd.clone(), slices);
String ss = Slice.createString(csw.getCurrentSlice());
currentSliceLabel.setText("Current slice of data: [" + ss + "]");
currentSliceLabel.getParent().layout(true);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
}
@Test
public void testStackedFile() throws ScanFileHolderException {
ILazyDataset image =
new TIFFImageLoader(TestFileFolder + "untitled1020.TIF").loadFile().getLazyDataset(0);
Assert.assertArrayEquals("Shape not equal", new int[] {3, 2048, 2048}, image.getShape());
IDataset d = image.getSlice(new Slice(1));
Assert.assertArrayEquals("Shape not equal", new int[] {1, 2048, 2048}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
d = image.getSlice(new Slice(1, 3), new Slice(1));
Assert.assertArrayEquals("Shape not equal", new int[] {2, 1, 2048}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
d = image.getSlice(new Slice(1, 3), new Slice(null, null, 4), new Slice(2, 25));
Assert.assertArrayEquals("Shape not equal", new int[] {2, 512, 23}, d.getShape());
Assert.assertEquals("Type is int32", Integer.class, d.elementClass());
}
@Override
protected IStatus run(IProgressMonitor monitor) {
output.setEnabled(false);
EscapableSliceVisitor sliceVisitor = null;
try {
if (path == null) path = context.getFilePaths().get(0);
final IDataHolder dh = ServiceHolder.getLoaderService().getData(path, new IMonitor.Stub());
ILazyDataset lazyDataset = dh.getLazyDataset(context.getDatasetNames().get(0));
if (lazyDataset == null) {
logger.error("Selected dataset not in file!!!!");
return Status.CANCEL_STATUS;
}
// take a local view
lazyDataset = lazyDataset.getSliceView();
Map<Integer, String> axesNames = context.getAxesNames();
if (axesNames != null) {
AxesMetadata am =
ServiceHolder.getLoaderService().getAxesMetadata(lazyDataset, path, axesNames);
lazyDataset.setMetadata(am);
// AxesMetadata axMeta = SlicedDataUtils.createAxisMetadata(path, lazyDataset,
// axesNames);
// if (axMeta != null) lazyDataset.setMetadata(axMeta);
// else lazyDataset.clearMetadata(AxesMetadata.class);
}
int[] dataDims =
Slicer.getDataDimensions(lazyDataset.getShape(), context.getSliceDimensions());
Slice[] s = csw.getCurrentSlice();
// Plot input, probably a bit wasteful to do each time
IDataset firstSlice = null;
if (lazyDataset instanceof IDataset) {
firstSlice = ((IDataset) lazyDataset).getSliceView(s);
} else {
firstSlice = lazyDataset.getSlice(s);
}
eventManager.sendInitialDataUpdate(firstSlice.getSliceView().squeeze());
MetadataPlotUtils.plotDataWithMetadata(firstSlice, input);
IOperation<? extends IOperationModel, ? extends OperationData>[] ops = getOperations();
if (ops == null) {
output.clear();
return Status.OK_STATUS;
}
// Only run what is necessary
if (inputData != null) {
if (inputData.getCurrentOperation() != end) {
int pos = 0;
for (int i = 0; i < ops.length; i++) {
if (ops[i] == end) break;
if (ops[i] == inputData.getCurrentOperation()) {
pos = i;
pos++;
break;
}
}
if (pos != 0) {
firstSlice = inputData.getInputData();
ops = Arrays.copyOfRange(ops, pos - 1, ops.length);
}
} else {
firstSlice = inputData.getInputData();
ops = new IOperation[] {inputData.getCurrentOperation()};
}
}
SourceInformation si =
new SourceInformation(path, context.getDatasetNames().get(0), lazyDataset);
SliceInformation sli = csw.getCurrentSliceInformation();
// TODO replace with check shape
firstSlice.setMetadata(new SliceFromSeriesMetadata(si, sli));
// OriginMetadataImpl om = new OriginMetadataImpl(lazyDataset, viewSlice, dataDims, path,
// context.getDatasetNames().get(0));
// om.setCurrentSlice(csw.getCurrentSlice());
// lazyDataset.setMetadata(om);
sliceVisitor =
getSliceVisitor(
ops,
lazyDataset,
Slicer.getDataDimensions(lazyDataset.getShape(), context.getSliceDimensions()));
sliceVisitor.setEndOperation(end);
long start = System.currentTimeMillis();
sliceVisitor.visit(firstSlice);
inputData = sliceVisitor.getOperationInputData();
eventManager.sendInputDataUpdate(inputData);
logger.debug("Ran in: " + (System.currentTimeMillis() - start) / 1000. + " s");
eventManager.sendErrorUpdate(null);
} catch (OperationException e) {
logger.error(e.getMessage(), e);
eventManager.sendErrorUpdate(e);
return Status.CANCEL_STATUS;
} catch (Exception e) {
logger.error(e.getMessage(), e);
String message = e.getMessage();
if (message == null) message = "Unexpected error!";
eventManager.sendErrorUpdate(new OperationException(null, message));
return Status.CANCEL_STATUS;
} finally {
if (sliceVisitor != null) {
inputData = sliceVisitor.getOperationInputData();
eventManager.sendInputDataUpdate(inputData);
}
output.setEnabled(true);
}
return Status.OK_STATUS;
}