@Test
public void testLazyAlignment() throws Exception {
int[] shape = data.getShape();
ILazyDataset alignedImages = null;
// read from temp file
alignedImages = transform.align(data, null);
assertArrayEquals(shape, alignedImages.getShape());
assertEquals(shape[2], alignedImages.getShape()[2]);
}
@Test
public void testLazyRotation() throws Exception {
int[] shape = data.getShape();
// rotated shape
int[] newShape = new int[] {data.getShape()[0], 724, 724};
String name = "testLazyRotation.h5";
ILazyWriteableDataset lazy = TestUtils.createTempLazyFile(newShape, name);
for (int i = 0; i < shape[0]; i++) {
IDataset slice = data.getSlice(new Slice(i, shape[0], shape[1])).squeeze();
IDataset rotated = DatasetUtils.convertToDataset(transform.rotate(slice, 45, false));
// add rotated image to temp file
TestUtils.appendDataset(lazy, rotated, i, null);
}
assertArrayEquals(newShape, lazy.getShape());
assertEquals(newShape[2], lazy.getShape()[2]);
IDataset rotatedImage = lazy.getSlice(new Slice(10, shape[0], shape[1])).squeeze();
assertEquals(newShape[2], rotatedImage.getShape()[1]);
}
public void removeLargeStacks(ISliceSystem slicingSystem, int maxStack) {
for (DimsData dd : getDimsData()) {
if (dd.getPlotAxis().isStack(slicingSystem)) {
if (dd.getSliceRange(true) == null
|| "".equals(dd.getSliceRange(true))
|| "all".equals(dd.getSliceRange(true))) {
final ILazyDataset lz = slicingSystem.getData().getLazySet();
if (lz != null) {
final int size = lz.getShape()[dd.getDimension()];
if (size >= maxStack) { // We set a default slice
dd.setSliceRange("0:25");
}
}
}
}
}
}
@BeforeClass
public static void buildData() throws Exception {
file = folder.newFile("file1.nxs");
MapNexusFileBuilderUtils.makeGridScanWithSum(file.getAbsolutePath());
IDataHolder data = LoaderFactory.getData(file.getAbsolutePath());
ILazyDataset lazyDataset = data.getLazyDataset(MapNexusFileBuilderUtils.DETECTOR_PATH);
MapScanDimensions msd = new MapScanDimensions(1, 0, 2);
gridScanBlock =
new MappedDataBlock(
MapNexusFileBuilderUtils.DETECTOR_PATH, lazyDataset, file.getAbsolutePath(), msd);
ILazyDataset sum = data.getLazyDataset(MapNexusFileBuilderUtils.SUM_PATH);
gridScanMap =
new MappedData(
MapNexusFileBuilderUtils.SUM_PATH,
sum.getSlice(),
gridScanBlock,
file.getAbsolutePath());
fileRemap = folder.newFile("file2.nxs");
MapNexusFileBuilderUtils.makeDiagLineScanWithSum(fileRemap.getAbsolutePath());
}
/**
* In order to implement a file watcher, we loop forever ensuring requesting to take the next
* item from the file watchers queue.
*/
@Override
public void run() {
final Path path = Paths.get(spath);
try {
// We wait until the file we are told to monitor exists.
while (!Files.exists(path)) {
Thread.sleep(200);
}
// get the first event before looping
WatchKey key = null;
while (session.isOpen() && connected && (key = watcher.take()) != null) {
try {
if (!Files.exists(path)) continue;
for (WatchEvent<?> event : key.pollEvents()) {
if (!Files.exists(path)) continue;
Path epath = (Path) event.context();
if (!Files.isDirectory(path) && !path.endsWith(epath)) continue;
try {
// Data has changed, read its shape and publish the event using a web socket.
final IDataHolder holder =
ServiceHolder.getLoaderService().getData(spath, new IMonitor.Stub());
if (holder == null) continue; // We do not stop if the loader got nothing.
final ILazyDataset lz =
sdataset != null && !"".equals(sdataset)
? holder.getLazyDataset(sdataset)
: holder.getLazyDataset(0);
if (lz == null) continue; // We do not stop if the loader got nothing.
if (lz instanceof IDynamicDataset) {
((IDynamicDataset) lz).refreshShape();
}
if (writing) {
ServiceHolder.getLoaderService().clearSoftReferenceCache(spath);
}
final DataEvent evt = new DataEvent(lz.getName(), lz.getShape());
evt.setFilePath(spath);
// We manually JSON the object because we
// do not want a dependency and object simple
String json = evt.encode();
session.getRemote().sendString(json);
if (diagInfo != null) diagInfo.record("JSON Send", json);
} catch (HDF5FunctionArgumentException h5error) {
// This happens sometimes when the file is not ready to read.
logger.trace("Path might not be ready to read " + path);
continue;
} catch (Exception ne) {
logger.error("Exception getting data from " + path);
continue;
}
break;
}
} finally {
key.reset();
}
}
} catch (Exception e) {
logger.error("Exception monitoring " + path, e);
if (session.isOpen()) session.close(403, e.getMessage());
} finally {
if (diagInfo != null) diagInfo.record("Close Thread", Thread.currentThread().getName());
try {
watcher.close();
} catch (IOException e) {
logger.error("Error closing watcher", e);
}
}
}