@Test
public void testSaveFile() throws ScanFileHolderException {
Dataset a = DatasetFactory.createRange(128 * 128, Dataset.FLOAT32).reshape(128, 128);
DataHolder d = new DataHolder();
a.idivide(10000);
d.addDataset("a", a);
String oname = testScratchDirectoryName + "a.tif";
TIFFImageSaver s;
DataHolder in;
s = new TIFFImageSaver(oname, true);
s.saveFile(d);
in = new TIFFImageLoader(oname).loadFile();
checkDataset(a, in.getDataset(0));
s = new TIFFImageSaver(oname);
s.saveFile(d);
in = new TIFFImageLoader(oname).loadFile();
checkDataset(a.cast(Dataset.INT32), in.getDataset(0));
}
public static Dataset convert1DDataset(
Dataset axisData, XAxis inAxisType, XAxis outAxisType, double lambda) throws Exception {
int[] shape = axisData.getShape();
int rank = shape.length;
if (rank > 1) {
throw new Exception("Cannot convert dataset with more than one dimension.");
}
Dataset result = DatasetFactory.zeros(shape, Dataset.FLOAT64);
// TODO FIXME Change the names given to the axis labels to use the ones in the enum.
if (outAxisType.equals(XAxis.ANGLE)) {
for (int i = 0; i < axisData.getSize(); i++) {
Double xAxisVal = axisData.getDouble(i);
result.set(inAxisType.convertToANGLE(xAxisVal, lambda), i);
}
result.setName("2theta");
} else if (outAxisType.equals(XAxis.Q)) {
for (int i = 0; i < axisData.getSize(); i++) {
Double xAxisVal = axisData.getDouble(i);
result.set(inAxisType.convertToQ(xAxisVal, lambda), i);
}
result.setName("Q");
} else if (outAxisType.equals(XAxis.RESOLUTION)) {
for (int i = 0; i < axisData.getSize(); i++) {
Double xAxisVal = axisData.getDouble(i);
result.set(inAxisType.convertToRESOLUTION(xAxisVal, lambda), i);
}
result.setName("d-spacing");
} else {
throw new Exception("Unknown axis type conversion requested.");
}
return result;
}
@SuppressWarnings("unchecked")
public DataHolder loadFile(boolean loadData) {
DataHolder dataHolder = new DataHolder();
NexusFile file;
try {
file = new NexusFile(fileName, NexusFile.NXACC_READ);
if (loadMetadata) {
metadata = new Metadata();
metadata.setFilePath(fileName);
}
// file.opengroup("entry1", "NXentry");
// Look for an NXentry...
Enumeration<String> topKeys = file.groupdir().keys();
while (topKeys.hasMoreElements()) {
String topName = topKeys.nextElement();
String topClass = (String) file.groupdir().get(topName);
if (topClass.compareTo("NXentry") == 0) {
// Specify class explicitly to make sure we are opening the correct one. Otherwise it will
// throw an
// exception.
file.opengroup(topName, "NXentry");
Enumeration<String> keys = file.groupdir().keys();
while (keys.hasMoreElements()) {
String name = keys.nextElement();
String className = (String) file.groupdir().get(name);
if (className.compareTo("NXdata") == 0) {
file.opengroup(name, "NXdata");
// Now lets get a list of the data items
Enumeration<String> dataKeys = file.groupdir().keys();
while (dataKeys.hasMoreElements()) {
// Hashtable h = file.attrdir();
// Enumeration e = h.keys();
// while (e.hasMoreElements()) {
// String attname = (String)e.nextElement();
// AttributeEntry atten = (AttributeEntry)h.get(attname);
// JythonServerFacade.getInstance().print("Found SDS attribute: " + attname +
// " type: "+ atten.type + " ,length: " + atten.length);
//
// }
String dataName = dataKeys.nextElement();
file.opendata(dataName);
int[] iDim = new int[20];
int[] iStart = new int[2];
file.getinfo(iDim, iStart);
// JythonServerFacade.getInstance().print(
// "Found " + dataName + " with: rank = " + iStart[0] + " type = " + iStart[1]
// + " dims = " + iDim[0] + ", " + iDim[1]);
// h = file.attrdir();
// e = h.keys();
// while (e.hasMoreElements()) {
// String attname = (String)e.nextElement();
// AttributeEntry atten = (AttributeEntry)h.get(attname);
// JythonServerFacade.getInstance().print("Found SDS attribute: " + attname +
// " type: "+ atten.type + " ,length: " + atten.length);
//
// }
// Now lets create an array of the dimensions for creating the dataset.
final int rank = iStart[0];
int[] shape = Arrays.copyOf(iDim, rank);
if (loadData) {
final int dtype = Nexus.getDType(iStart[1]);
Dataset ds = DatasetFactory.zeros(shape, dtype);
file.getdata(ds.getBuffer());
ds.setName(dataName);
dataHolder.addDataset(dataName, ds);
}
if (loadMetadata) {
metadata.addDataInfo(dataName, shape);
}
file.closedata();
}
// Close NXdata
file.closegroup();
}
}
// Close the NXentry
file.closegroup();
}
}
// for (Iterator iterator = file.groupdir().values().iterator(); iterator.hasNext();) {
// String type = (String) iterator.next();
// JythonServerFacade.getInstance().print(type);
// }
file.close();
if (loadMetadata) {
dataHolder.setMetadata(metadata);
}
return dataHolder;
} catch (NexusException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} finally {
// TODO Empty clause
}
return null;
}