/** Validate unnamed group of type NXsample. */
private void validateGroup_entry_NXsample(final NXsample group) throws NexusValidationException {
// validate that the group is not null
validateGroupNotNull(null, NXsample.class, group);
clearLocalGroupDimensionPlaceholderValues();
// validate field 'name' of unknown type.
final IDataset name = group.getName();
validateFieldNotNull("name", name);
// validate field 'nature' of type NX_CHAR. Note: field not defined in base class.
final IDataset nature = group.getDataset("nature");
validateFieldNotNull("nature", nature);
validateFieldType("nature", nature, NX_CHAR);
validateFieldEnumeration("nature", nature, "powder", "liquid", "single crystal");
}
/** Validate group 'sample' of type NXsample. */
private void validateGroup_NXentry_sample(final NXsample group) throws NexusValidationException {
// validate that the group is not null
validateGroupNotNull("sample", NXsample.class, group);
clearLocalGroupDimensionPlaceholderValues();
// validate field 'name' of unknown type.
final IDataset name = group.getName();
validateFieldNotNull("name", name);
// validate field 'aequatorial_angle' of type NX_FLOAT. Note: field not defined in base class.
final IDataset aequatorial_angle = group.getDataset("aequatorial_angle");
validateFieldNotNull("aequatorial_angle", aequatorial_angle);
validateFieldType("aequatorial_angle", aequatorial_angle, NX_FLOAT);
validateFieldUnits("aequatorial_angle", aequatorial_angle, NX_ANGLE);
}
/** Validate group 'sample' of type NXsample. */
private void validateGroup_entry_sample(final NXsample group) throws Exception {
// validate that the group is not null
validateGroupNotNull("sample", NXsample.class, group);
clearLocalGroupDimensionPlaceholderValues();
// validate field 'name' of unknown type.
final IDataset name = group.getName();
validateFieldNotNull("name)", name);
// validate field 'rotation_angle' of type NX_FLOAT.
final IDataset rotation_angle = group.getRotation_angle();
validateFieldNotNull("rotation_angle)", rotation_angle);
validateFieldType("rotation_angle)", rotation_angle, NX_FLOAT);
validateFieldUnits("rotation_angle", rotation_angle, NX_ANGLE);
validateFieldRank("rotation_angle", rotation_angle, 1);
validateFieldDimensions("rotation_angle", rotation_angle, null, "NP");
}
/** Validate unnamed group of type NXsample. */
private void validateGroup_NXentry_NXsample(final NXsample group)
throws NexusValidationException {
// validate that the group is not null
validateGroupNotNull(null, NXsample.class, group);
clearLocalGroupDimensionPlaceholderValues();
// validate field 'rotation_angle' of type NX_NUMBER.
final IDataset rotation_angle = group.getRotation_angle();
validateFieldNotNull("rotation_angle", rotation_angle);
validateFieldType("rotation_angle", rotation_angle, NX_NUMBER);
validateFieldUnits("rotation_angle", rotation_angle, NX_ANGLE);
// validate field 'seblock' of type NX_CHAR. Note: field not defined in base class.
final IDataset seblock = group.getDataset("seblock");
validateFieldNotNull("seblock", seblock);
validateFieldType("seblock", seblock, NX_CHAR);
// validate field 'temperature' of type NX_NUMBER.
final IDataset temperature = group.getTemperature();
validateFieldNotNull("temperature", temperature);
validateFieldType("temperature", temperature, NX_NUMBER);
validateFieldUnits("temperature", temperature, NX_TEMPERATURE);
validateFieldDimensions("temperature", temperature, "NXsample", "n_Temp");
}
@Test
public void testWriteNX() {
String filename = "/tmp/sample.nxs";
NexusFileBuilder builder = new DefaultNexusFileBuilder(filename);
NXsample nxample = sample.getNXsample(builder);
int nCompo = sample.getPhases().size();
assertEquals("NX name incorrect", sample.getName(), nxample.getNameScalar());
assertEquals(
"NX description incorrect",
sample.getName() + ", " + sample.getComposition() + ", " + sample.getShapeName(),
nxample.getDescriptionScalar());
assertEquals(
"NX component names incorrect",
DatasetFactory.createFromList(
sample.getPhases().stream().map(a -> a.getName()).collect(Collectors.toList())),
nxample.getComponent());
assertEquals(
"NX component formulae incorrect",
DatasetFactory.createFromObject(
sample
.getPhases()
.stream()
.map(a -> a.getComposition().getHallNotation(false))
.collect(Collectors.toList()),
nCompo,
1),
nxample.getChemical_formula());
assertEquals(
"NX formula weight incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getComposition().getFormulaMass())
.collect(Collectors.toList())),
nxample.getDataset("chemical_formula_weight"));
// unit cell parameters...
assertEquals(
"NX unit cell volume incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getUnitCellVolume())
.collect(Collectors.toList())),
nxample.getUnit_cell_volume());
assertEquals(
"NX unit cell class incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getCrystalSystem().getName())
.collect(Collectors.toList())),
nxample.getUnit_cell_class());
assertEquals(
"NX unit cell space group incorrect",
DatasetFactory.createFromList(
sample
.getPhases()
.stream()
.map(a -> a.getSpaceGroup().getNumber() + ": " + a.getSpaceGroup().getName())
.collect(Collectors.toList())),
nxample.getUnit_cell_group());
assertEquals(
"NX theoretical densities incorrect",
DatasetFactory.createFromList(
sample.getPhases().stream().map(a -> a.getDensity()).collect(Collectors.toList())),
nxample.getDataset("theoretical_density"));
}
