/**
* @param x
* @param rootName
* @return
*/
public static String getName(IDataset x, String rootName) {
if (x == null) return null;
try {
return rootName != null ? x.getName().substring(rootName.length()) : x.getName();
} catch (StringIndexOutOfBoundsException ne) {
return x.getName();
}
}
public void setYs(List<IDataset> ys) {
this.min = Double.MAX_VALUE;
this.max = -Double.MAX_VALUE;
for (IDataset y : ys) {
this.min = Math.min(min, y.min().doubleValue());
this.max = Math.max(max, y.max().doubleValue());
}
}
@Test
public void testMerlinDataLoaderU32() throws Exception {
final String path = testFileFolder + "I13-20150210-101459-1.mib";
IDataHolder dataHolder = LoaderFactory.getData(path, null);
IDataset data = dataHolder.getDataset(0);
int[] shape = data.getShape();
assertEquals(515, shape[0], 0.0);
assertEquals(515, shape[1], 0.0);
}
@Test
public void testMerlinDataLoader() throws Exception {
final String path = testFileFolder + "default1.mib";
IDataHolder dataHolder = LoaderFactory.getData(path, null);
IDataset data = dataHolder.getDataset(0);
int[] shape = data.getShape();
assertEquals(512, shape[0], 0.0);
assertEquals(512, shape[1], 0.0);
assertEquals(4095, data.max().intValue(), 0.0);
}
@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 List<IDataset> getSelectionData(GalleryItem[] items) {
final List<IDataset> ys = new ArrayList<IDataset>(11);
for (GalleryItem item : items) {
final ImageItem ii = new ImageItem();
ii.setIndex(item.getItemCount());
ii.setItem(item);
try {
IDataset slice = info.getData(true, ii);
slice.setName(selectionDataLabel + " " + info.getItemName(item.getItemCount(), false));
ys.add(slice);
} catch (Exception e) {
logger.error("Cannot slice ", e);
continue;
}
}
return ys;
}
@SuppressWarnings("unchecked")
public static String getTitle(
final IDataset xIn,
final List<? extends IDataset> ysIn,
final boolean isFileName,
final String rootName) {
final IDataset x;
final List<IDataset> ys;
if (ysIn == null) {
ys = new ArrayList<IDataset>(1);
ys.add(xIn);
x = DatasetFactory.createRange(DoubleDataset.class, ys.get(0).getSize());
x.setName("Index of " + xIn.getName());
} else {
x = xIn;
ys = (List<IDataset>) ysIn;
}
final StringBuilder buf = new StringBuilder();
buf.append("Plot of ");
final Set<String> used = new HashSet<String>(7);
int i = 0;
int dataSetSize = ys.size();
for (IDataset dataSet : ys) {
String name = getName(dataSet, rootName);
if (isFileName && name != null) {
// Strip off file name
final Matcher matcher = Pattern.compile("(.*) \\(.*\\)").matcher(name);
if (matcher.matches()) name = matcher.group(1);
}
if (used.contains(name)) continue;
if (i == 0) buf.append(name);
if (ys.size() < 2) break;
if (i == 1 && 1 == dataSetSize - 1) buf.append("," + name);
if (i == dataSetSize - 1 && dataSetSize - 1 != 1) buf.append("..." + name);
i++;
}
buf.append(" against ");
buf.append(x.getName());
return buf.toString();
}
/**
* Perform a two-dimensional interpolation
*
* @param oldx an IDataset containing a 1D array of X-values, sorted in increasing order,
* corresponding to the first dimension of <code>oldxy</code>
* @param oldy an IDataset containing a 1D array of Y-values, sorted in increasing order,
* corresponding to the second dimension of <code>oldxy</code>
* @param oldxy an IDataset containing a 2D grid of interpolation points
* @param newx an IDataset containing a 1D array of X-values that will be sent to the
* interpolating function
* @param newy an IDataset containing a 1D array of Y-values that will be sent to the
* interpolating function
* @param interpolator an instance of {@link
* org.apache.commons.math3.analysis.interpolation.BivariateGridInterpolator}
* @param output_type an {@link BicubicInterpolationOutput} that will determine how <code>newx
* </code> and <code>newy</code> will be interpreted, and therefore whether a 1D or 2D Dataset
* will be returned.
* @return rank 1 or 2 Dataset, depending on <code>output_type}</code>
* @throws NonMonotonicSequenceException
* @throws NumberIsTooSmallException
*/
public static Dataset interpolate(
IDataset oldx,
IDataset oldy,
IDataset oldxy,
IDataset newx,
IDataset newy,
BivariateGridInterpolator interpolator,
BicubicInterpolationOutput output_type)
throws NonMonotonicSequenceException, NumberIsTooSmallException {
// check shapes
if (oldx.getRank() != 1) throw new IllegalArgumentException("oldx Shape must be 1D");
if (oldy.getRank() != 1) throw new IllegalArgumentException("oldy Shape must be 1D");
if (oldxy.getRank() != 2) throw new IllegalArgumentException("oldxy Shape must be 2D");
if (oldx.getShape()[0] != oldxy.getShape()[0])
throw new IllegalArgumentException("oldx Shape must match oldxy Shape[0]");
if (oldy.getShape()[0] != oldxy.getShape()[1])
throw new IllegalArgumentException("oldy Shape must match oldxy Shape[1]");
if (newx.getRank() != 1) throw new IllegalArgumentException("newx Shape must be 1D");
if (newy.getRank() != 1) throw new IllegalArgumentException("newx Shape must be 1D");
if (output_type == BicubicInterpolationOutput.ONED && newy.getSize() != newx.getSize())
throw new IllegalArgumentException(
"newx and newy Size must be identical when expecting a rank 1 dataset result");
DoubleDataset oldx_dd = (DoubleDataset) DatasetUtils.cast(oldx, Dataset.FLOAT64);
DoubleDataset oldy_dd = (DoubleDataset) DatasetUtils.cast(oldy, Dataset.FLOAT64);
DoubleDataset oldxy_dd = (DoubleDataset) DatasetUtils.cast(oldxy, Dataset.FLOAT64);
// unlike in Interpolation1D, we will not be sorting here, as it just too complicated
// the user will be responsible for ensuring the arrays are properly sorted
// oldxy_dd needs to be transformed into a double[][] array
// this call may throw an exception that needs handling by the calling method
BivariateFunction func =
interpolator.interpolate(
oldx_dd.getData(), oldy_dd.getData(), convertDoubleDataset2DtoPrimitive(oldxy_dd));
Dataset rv = null;
if (output_type == BicubicInterpolationOutput.ONED) {
rv = DatasetFactory.zeros(new int[] {newx.getSize()}, Dataset.FLOAT64);
for (int i = 0; i < newx.getSize(); i++) {
double val = 0.0;
try {
val = func.value(newx.getDouble(i), newy.getDouble(i));
rv.set(val, i);
} catch (OutOfRangeException e) {
rv.set(0.0, i);
}
}
} else if (output_type == BicubicInterpolationOutput.TWOD) {
rv = DatasetFactory.zeros(new int[] {newx.getSize(), newy.getSize()}, Dataset.FLOAT64);
for (int i = 0; i < newx.getSize(); i++) {
for (int j = 0; j < newy.getSize(); j++) {
double val = 0.0;
try {
val = func.value(newx.getDouble(i), newy.getDouble(j));
rv.set(val, i, j);
} catch (OutOfRangeException e) {
rv.set(0.0, i, j);
}
}
}
}
rv.setName(oldxy.getName() + "_interpolated");
return rv;
}
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);
}
}
}
public static void handleException(
final ScanFileHolderException e,
final IDataHolder dh,
final String fileName,
final double maxVal,
final boolean unsigned,
final int numBits)
throws ScanFileHolderException, UnsupportedOperationException, IllegalArgumentException {
/*
* Need massive error handling here, since we get same type of
* exception with different messages.
* The exception throwing might change as time passes, the
* current handling is determined on 2014-03-04.
* "Unable" means we can not recover, the image could not be
* created. Currently this can not happen, instead we get an
* exception with "Error" in its message. See below.
* "ScaledSaver" means not allowed parameters, that is use either 32 bits or float,
* or <=16 bits with big enough max and not unsigned if there is any negative value.
* "No writer" means the writer could not write the image (for
* example bmp writer can save only RGBDataset), in this case
* converting the dataset might help.
* "Error" means other kind of problem, probably not recoverable.
*/
do {
if (StringUtils.matchStringWithPattern(e.getMessage(), ".*Unable.*", true)) break;
final StringBuffer sb = new StringBuffer();
if (StringUtils.matchStringWithPattern(e.getMessage(), ".*No writer.*", true)) {
sb.append(e.getLocalizedMessage());
sb.append("\n\nSuggestion: ");
sb.append(
"To save the image as "
+ FileUtils.getFileExtension(fileName)
+ " type, you can try to ");
if (dh.getDataset(0) instanceof RGBDataset)
sb.append("convert the RGB dataset to integer dataset.");
else sb.append("convert the dataset to RGB dataset.");
throw new IllegalArgumentException(sb.toString(), e.getCause());
}
if (StringUtils.matchStringWithPattern(e.getMessage(), ".*ScaledSaver.*", true)) {
if (numBits > 16) // Currently impossible case
break;
sb.append(e.getLocalizedMessage());
sb.append("\n\nSuggestion: ");
sb.append(
"To save the image as "
+ FileUtils.getFileExtension(fileName)
+ " type, you can try to any of these possibilites:\n");
sb.append("- Choose 32 bits or float type.\n");
double maxTotalValue = maxVal;
boolean addedSignedHint = !unsigned;
for (int i = 0; i < dh.size() && !addedSignedHint && maxVal > 0; i++) {
final IDataset data = dh.getDataset(i);
if (maxVal > 0) maxTotalValue = Math.max(data.max().doubleValue(), maxTotalValue);
if (!addedSignedHint && (unsigned && data.min().doubleValue() < 0)) {
sb.append("- Choose signed values.\n");
addedSignedHint = true;
}
}
if (maxTotalValue > maxVal)
sb.append("- Choose max value >= max value of image (" + maxTotalValue + ").\n");
sb.append("- Choose autoscale option.");
throw new IllegalArgumentException(sb.toString(), e.getCause());
}
if (StringUtils.matchStringWithPattern(e.getMessage(), ".*Error.*", true)) break;
throw new UnsupportedOperationException(
"Unexpected error: " + e.getLocalizedMessage(), e.getCause());
} while (false);
throw e;
}