private NXobject getNexusObjectForMetadataType(NXentry entry, MetadataType type) {
if (type == null) {
return entry;
}
switch (type) {
case ENTRY:
return entry;
case INSTRUMENT:
return entry.getInstrument();
case SAMPLE:
return entry.getSample();
case USER:
return entry.getUser();
default:
throw new IllegalArgumentException("Unknown metadata type " + type);
}
}
/** Validate group 'entry' of type NXentry. */
private void validateGroup_entry(final NXentry group) throws Exception {
// validate that the group is not null
validateGroupNotNull("entry", NXentry.class, group);
// validate field 'title' of unknown type.
final IDataset title = group.getTitle();
validateFieldNotNull("title)", title);
// validate field 'start_time' of type NX_DATE_TIME.
final IDataset start_time = group.getStart_time();
validateFieldNotNull("start_time)", start_time);
validateFieldType("start_time)", start_time, NX_DATE_TIME);
// validate field 'end_time' of type NX_DATE_TIME.
final IDataset end_time = group.getEnd_time();
validateFieldNotNull("end_time)", end_time);
validateFieldType("end_time)", end_time, NX_DATE_TIME);
// validate field 'definition' of unknown type.
final IDataset definition = group.getDefinition();
validateFieldNotNull("definition)", definition);
validateFieldEnumeration("definition", definition, "NXrefscan");
// validate child group 'instrument' of type NXinstrument
// $groupNameInBaseClass = instrument
validateGroup_entry_instrument(group.getInstrument());
// validate child group 'sample' of type NXsample
// $groupNameInBaseClass = sample
validateGroup_entry_sample(group.getSample());
// validate child group 'control' of type NXmonitor
// $groupNameInBaseClass = monitor
validateGroup_entry_control(group.getMonitor());
// validate child group 'data' of type NXdata
// $groupNameInBaseClass = data
validateGroup_entry_data(group.getData());
}
private void checkNexusFile(
IRunnableDevice<ScanModel> scanner, List<ScanMetadata> scanMetadata, int... sizes)
throws Exception {
final ScanModel scanModel = ((AbstractRunnableDevice<ScanModel>) scanner).getModel();
assertEquals(DeviceState.READY, scanner.getDeviceState());
NXroot rootNode = getNexusRoot(scanner);
NXentry entry = rootNode.getEntry();
checkMetadata(entry, scanMetadata);
// check that the scan points have been written correctly
assertScanPointsGroup(entry, sizes);
NXinstrument instrument = entry.getInstrument();
LinkedHashMap<String, List<String>> signalFieldAxes = new LinkedHashMap<>();
// axis for additional dimensions of a datafield, e.g. image
signalFieldAxes.put(NXdetector.NX_DATA, Arrays.asList("real", "imaginary"));
signalFieldAxes.put("spectrum", Arrays.asList("spectrum_axis"));
signalFieldAxes.put("value", Collections.emptyList());
String detectorName = scanModel.getDetectors().get(0).getName();
NXdetector detector = instrument.getDetector(detectorName);
// map of detector data field to name of nxData group where that field
// is the @signal field
Map<String, String> expectedDataGroupNames =
signalFieldAxes
.keySet()
.stream()
.collect(
Collectors.toMap(
Function.identity(),
x -> detectorName + (x.equals(NXdetector.NX_DATA) ? "" : "_" + x)));
// validate the main NXdata generated by the NexusDataBuilder
Map<String, NXdata> nxDataGroups = entry.getChildren(NXdata.class);
assertEquals(signalFieldAxes.size(), nxDataGroups.size());
assertTrue(nxDataGroups.keySet().containsAll(expectedDataGroupNames.values()));
for (String nxDataGroupName : nxDataGroups.keySet()) {
NXdata nxData = entry.getData(nxDataGroupName);
String sourceFieldName =
nxDataGroupName.equals(detectorName)
? NXdetector.NX_DATA
: nxDataGroupName.substring(nxDataGroupName.indexOf('_') + 1);
assertSignal(nxData, sourceFieldName);
// check the nxData's signal field is a link to the appropriate source data node of the
// detector
DataNode dataNode = detector.getDataNode(sourceFieldName);
IDataset dataset = dataNode.getDataset().getSlice();
assertSame(dataNode, nxData.getDataNode(sourceFieldName));
assertTarget(
nxData,
sourceFieldName,
rootNode,
"/entry/instrument/" + detectorName + "/" + sourceFieldName);
// check that the other primary data fields of the detector haven't been added to this NXdata
for (String primaryDataFieldName : signalFieldAxes.keySet()) {
if (!primaryDataFieldName.equals(sourceFieldName)) {
assertNull(nxData.getDataNode(primaryDataFieldName));
}
}
int[] shape = dataset.getShape();
for (int i = 0; i < sizes.length; i++) assertEquals(sizes[i], shape[i]);
// Make sure none of the numbers are NaNs. The detector
// is expected to fill this scan with non-nulls.
final PositionIterator it = new PositionIterator(shape);
while (it.hasNext()) {
int[] next = it.getPos();
assertFalse(Double.isNaN(dataset.getDouble(next)));
}
// Check axes
final IPosition pos = scanModel.getPositionIterable().iterator().next();
final Collection<String> scannableNames = pos.getNames();
// Append _value_demand to each name in list, then add detector axis fields to result
List<String> expectedAxesNames =
Stream.concat(
scannableNames.stream().map(x -> x + "_value_set"),
signalFieldAxes.get(sourceFieldName).stream())
.collect(Collectors.toList());
assertAxes(nxData, expectedAxesNames.toArray(new String[expectedAxesNames.size()]));
int[] defaultDimensionMappings = IntStream.range(0, sizes.length).toArray();
int i = -1;
for (String scannableName : scannableNames) {
i++;
NXpositioner positioner = instrument.getPositioner(scannableName);
assertNotNull(positioner);
dataNode = positioner.getDataNode("value_set");
dataset = dataNode.getDataset().getSlice();
shape = dataset.getShape();
assertEquals(1, shape.length);
assertEquals(sizes[i], shape[0]);
String nxDataFieldName = scannableName + "_value_set";
assertSame(dataNode, nxData.getDataNode(nxDataFieldName));
assertIndices(nxData, nxDataFieldName, i);
assertTarget(
nxData, nxDataFieldName, rootNode, "/entry/instrument/" + scannableName + "/value_set");
// Actual values should be scanD
dataNode = positioner.getDataNode(NXpositioner.NX_VALUE);
dataset = dataNode.getDataset().getSlice();
shape = dataset.getShape();
assertArrayEquals(sizes, shape);
nxDataFieldName = scannableName + "_" + NXpositioner.NX_VALUE;
assertSame(dataNode, nxData.getDataNode(nxDataFieldName));
assertIndices(nxData, nxDataFieldName, defaultDimensionMappings);
assertTarget(
nxData,
nxDataFieldName,
rootNode,
"/entry/instrument/" + scannableName + "/" + NXpositioner.NX_VALUE);
}
}
}