@Test
public void testLarge() throws Exception {
final long start = System.currentTimeMillis();
final List<IDataset> images = new ArrayList<IDataset>(10);
final File dir = new File(System.getProperty("GDALargeTestFilesLocation") + "EDFLoaderTest/");
final File[] files = dir.listFiles();
for (int i = 0; i < files.length; i++) {
if (files[i].getName().startsWith("billeA")) {
images.add(LoaderFactory.getData(files[i].getAbsolutePath(), null).getDataset(0));
}
}
final AbstractDataset median = CollectionStats.median(images);
final long end = System.currentTimeMillis();
if (median.getShape()[0] != 2048) throw new Exception("Median has wrong size!");
if (median.getShape()[1] != 2048) throw new Exception("Median has wrong size!");
System.out.println("Did median of ten images 2048x2048 in " + ((end - start) / 1000d) + "s");
final AbstractDataset mean = CollectionStats.median(images);
final long end1 = System.currentTimeMillis();
if (mean.getShape()[0] != 2048) throw new Exception("Mean has wrong size!");
if (mean.getShape()[1] != 2048) throw new Exception("Mean has wrong size!");
System.out.println("Did mean of ten images 2048x2048 in " + ((end1 - end) / 1000d) + "s");
}
@Override
public void setElements(AbstractDataset source, int element) {
if (element < 0) element += isize;
if (element < 0 || element > isize) {
throw new IllegalArgumentException(
String.format("Invalid choice of element: %d/%d", element, isize));
}
if (elementClass() != source.elementClass()) {
throw new IllegalArgumentException(
"Element class of destination does not match this dataset");
}
final IndexIterator it = getIterator(element);
final int[] elements = ((IntegerDataset) source).data; // CLASS_TYPE // PRIM_TYPE
if (source.isContiguous()) {
int n = 0;
while (it.hasNext()) {
data[it.index] = elements[n];
n++;
}
} else {
final IndexIterator sit = source.getIterator();
while (it.hasNext() && sit.hasNext()) {
data[it.index] = elements[sit.index];
}
}
}
/**
* Cast a dataset to this compound type. If repeat is set, the first element of each item in the
* given dataset is repeated across all elements of an item. Otherwise, each item comprises a
* truncated or zero-padded copy of elements from the given dataset.
*
* @param itemSize
* @param repeat repeat first element
* @param dataset
*/
public CompoundIntegerDataset(
final int itemSize, final boolean repeat, final AbstractDataset dataset) {
isize = itemSize;
size = dataset.size;
shape = dataset.shape.clone();
name = new String(dataset.name);
odata = data = createArray(size);
final int os = dataset.getElementsPerItem();
IndexIterator iter = dataset.getIterator();
if (repeat) {
int i = 0;
while (iter.hasNext()) {
final int v =
(int) dataset.getElementLongAbs(iter.index); // PRIM_TYPE // GET_ELEMENT_WITH_CAST
for (int k = 0; k < isize; k++) data[i++] = v;
}
} else {
final int kmax = Math.min(isize, os);
int i = 0;
while (iter.hasNext()) {
for (int k = 0; k < kmax; k++)
data[i + k] = (int) dataset.getElementLongAbs(iter.index + k); // GET_ELEMENT_WITH_CAST
i += isize;
}
}
}
@Override
public CompoundIntegerDataset ipower(final Object b) {
if (b instanceof AbstractDataset) {
final AbstractDataset bds = (AbstractDataset) b;
checkCompatibility(bds);
final IndexIterator it1 = getIterator();
final IndexIterator it2 = bds.getIterator();
final int bis = bds.getElementsPerItem();
if (bis == 1) {
while (it1.hasNext() && it2.hasNext()) {
final int db =
(int) bds.getElementLongAbs(it2.index); // PRIM_TYPE // GET_ELEMENT_WITH_CAST
for (int i = 0; i < isize; i++) {
final double v = Math.pow(data[it1.index + i], db);
if (Double.isInfinite(v) || Double.isNaN(v)) { // INT_ZEROTEST
data[it1.index + i] = 0; // INT_ZEROTEST // CLASS_TYPE
} else { // INT_ZEROTEST
data[it1.index + i] = (int) (long) v; // PRIM_TYPE_LONG // ADD_CAST
} // INT_ZEROTEST
}
}
} else if (bis == isize) {
while (it1.hasNext() && it2.hasNext()) {
for (int i = 0; i < isize; i++) {
final double v = Math.pow(data[it1.index + i], bds.getElementDoubleAbs(it2.index + i));
if (Double.isInfinite(v) || Double.isNaN(v)) { // INT_ZEROTEST
data[it1.index + i] = 0; // INT_ZEROTEST // CLASS_TYPE
} else { // INT_ZEROTEST
data[it1.index + i] = (int) (long) v; // PRIM_TYPE_LONG // ADD_CAST
} // INT_ZEROTEST
}
}
} else {
throw new IllegalArgumentException(
"Argument does not have same number of elements per item or is not a non-compound dataset");
}
} else {
final int[] vr = toIntegerArray(b, isize); // PRIM_TYPE // CLASS_TYPE
final IndexIterator it1 = getIterator();
while (it1.hasNext()) {
for (int i = 0; i < isize; i++) {
final double v = Math.pow(data[it1.index + i], vr[i]);
if (Double.isInfinite(v) || Double.isNaN(v)) { // INT_ZEROTEST
data[it1.index + i] = 0; // INT_ZEROTEST // CLASS_TYPE
} else { // INT_ZEROTEST
data[it1.index + i] = (int) (long) v; // PRIM_TYPE_LONG // ADD_CAST
} // INT_ZEROTEST
}
}
}
setDirty();
return this;
}
@Override
public double residual(final Object b) {
double sum = 0;
if (b instanceof AbstractDataset) {
final AbstractDataset bds = (AbstractDataset) b;
checkCompatibility(bds);
final IndexIterator it1 = getIterator();
final IndexIterator it2 = bds.getIterator();
final int bis = bds.getElementsPerItem();
if (bis == 1) {
double comp = 0;
while (it1.hasNext() && it2.hasNext()) {
final double db = bds.getElementDoubleAbs(it2.index);
for (int i = 0; i < isize; i++) {
final double diff = data[it1.index + i] - db;
final double err = diff * diff - comp;
final double temp = sum + err;
comp = (temp - sum) - err;
sum = temp;
}
}
} else if (bis == isize) {
double comp = 0;
while (it1.hasNext() && it2.hasNext()) {
for (int i = 0; i < isize; i++) {
final double diff = data[it1.index + i] - bds.getElementDoubleAbs(it2.index + i);
final double err = diff * diff - comp;
final double temp = sum + err;
comp = (temp - sum) - err;
sum = temp;
}
}
} else {
throw new IllegalArgumentException(
"Argument does not have same number of elements per item or is not a non-compound dataset");
}
} else {
final double[] vr = toDoubleArray(b, isize);
final IndexIterator it1 = getIterator();
double comp = 0;
while (it1.hasNext()) {
for (int i = 0; i < isize; i++) {
final double diff = data[it1.index + i] - vr[i];
final double err = diff * diff - comp;
final double temp = sum + err;
comp = (temp - sum) - err;
sum = temp;
}
}
}
return sum;
}
@Override
public CompoundIntegerDataset iremainder(final Object b) {
if (b instanceof AbstractDataset) {
final AbstractDataset bds = (AbstractDataset) b;
checkCompatibility(bds);
final IndexIterator it1 = getIterator();
final IndexIterator it2 = bds.getIterator();
final int bis = bds.getElementsPerItem();
if (bis == 1) {
while (it1.hasNext() && it2.hasNext()) {
final int db =
(int) bds.getElementLongAbs(it2.index); // PRIM_TYPE // GET_ELEMENT_WITH_CAST
if (db == 0) { // INT_ZEROTEST
for (int i = 0; i < isize; i++) // INT_ZEROTEST
data[it1.index + i] = 0; // INT_ZEROTEST
} else { // INT_ZEROTEST
for (int i = 0; i < isize; i++) data[it1.index + i] %= db;
} // INT_ZEROTEST
}
} else if (bis == isize) {
while (it1.hasNext() && it2.hasNext()) {
for (int i = 0; i < isize; i++) {
try {
data[it1.index + i] %=
bds.getElementLongAbs(it2.index + i); // GET_ELEMENT // INT_EXCEPTION
} catch (ArithmeticException e) {
data[it1.index + i] = 0;
}
}
}
} else {
throw new IllegalArgumentException(
"Argument does not have same number of elements per item or is not a non-compound dataset");
}
} else {
final double[] vr = toDoubleArray(b, isize);
final IndexIterator it1 = getIterator();
while (it1.hasNext()) {
for (int i = 0; i < isize; i++) {
if (vr[i] == 0) { // INT_ZEROTEST
data[it1.index + i] = 0; // INT_ZEROTEST
} else { // INT_ZEROTEST
data[it1.index + i] %= vr[i];
} // INT_ZEROTEST
}
}
}
setDirty();
return this;
}
@Test
public void test1D() throws Exception {
final AbstractDataset median = CollectionStats.median(SETS1D);
if (median.getDouble(0) != 1) throw new Exception("Median not calculated correctly!");
if (median.getDouble(4) != 5) throw new Exception("Median not calculated correctly!");
final AbstractDataset mean = CollectionStats.mean(SETS1D);
if (!DoubleUtils.equalsWithinTolerance(mean.getDouble(0), 100.8, 0.0001))
throw new Exception("Mean not calculated correctly!");
if (!DoubleUtils.equalsWithinTolerance(mean.getDouble(4), 104, 0.0001))
throw new Exception("Mean not calculated correctly!");
}
@Override
public void fillDataset(AbstractDataset result, IndexIterator iter) {
IndexIterator riter = result.getIterator();
int[] rdata = ((CompoundIntegerDataset) result).data; // PRIM_TYPE
while (riter.hasNext() && iter.hasNext()) {
for (int i = 0; i < isize; i++) rdata[riter.index + i] = data[iter.index + i];
}
}
@Override
public CompoundIntegerDataset imultiply(final Object b) {
if (b instanceof AbstractDataset) {
final AbstractDataset bds = (AbstractDataset) b;
checkCompatibility(bds);
final IndexIterator it1 = getIterator();
final IndexIterator it2 = bds.getIterator();
final int bis = bds.getElementsPerItem();
if (bis == 1) {
while (it1.hasNext() && it2.hasNext()) {
final int db =
(int) bds.getElementLongAbs(it2.index); // PRIM_TYPE // GET_ELEMENT_WITH_CAST
for (int i = 0; i < isize; i++) data[it1.index + i] *= db;
}
} else if (bis == isize) {
while (it1.hasNext() && it2.hasNext()) {
for (int i = 0; i < isize; i++)
data[it1.index + i] *= bds.getElementLongAbs(it2.index + i); // GET_ELEMENT
}
} else {
throw new IllegalArgumentException(
"Argument does not have same number of elements per item or is not a non-compound dataset");
}
} else {
final int[] vr = toIntegerArray(b, isize); // PRIM_TYPE // CLASS_TYPE
final IndexIterator it1 = getIterator();
while (it1.hasNext()) {
for (int i = 0; i < isize; i++) data[it1.index + i] *= vr[i];
}
}
setDirty();
return this;
}
@Override
public void copyItemsFromAxes(final int[] pos, final boolean[] axes, final AbstractDataset dest) {
int[] ddata = (int[]) dest.odata; // PRIM_TYPE
if (dest.getElementsPerItem() != isize) {
throw new IllegalArgumentException(
String.format(
"Destination dataset is incompatible as it has %d elements per item not %d",
dest.getElementsPerItem(), isize));
}
SliceIterator siter = getSliceIteratorFromAxes(pos, axes);
int[] sshape = squeezeShape(siter.getSliceShape(), false);
IndexIterator diter = dest.getSliceIterator(null, sshape, null);
if (ddata.length < calcSize(sshape)) {
throw new IllegalArgumentException("destination array is not large enough");
}
while (siter.hasNext() && diter.hasNext()) {
for (int i = 0; i < isize; i++) ddata[diter.index + i] = data[siter.index + i];
}
}
@Test
public void test2D() throws Exception {
final AbstractDataset median = CollectionStats.median(SETS2D);
if (median.getDouble(0, 0) != 1) throw new Exception("Median not calculated correctly!");
if (median.getDouble(1, 1) != 4) throw new Exception("Median not calculated correctly!");
if (median.getShape()[0] != 2) throw new Exception("Median shape not correct!");
if (median.getShape()[1] != 2) throw new Exception("Median shape not correct!");
final AbstractDataset mean = CollectionStats.mean(SETS2D);
if (!DoubleUtils.equalsWithinTolerance(mean.getDouble(0, 0), 100.8d, 0.01))
throw new Exception("Mean not calculated correctly!");
if (!DoubleUtils.equalsWithinTolerance(mean.getDouble(1, 1), 103.2d, 0.01))
throw new Exception("Mean not calculated correctly!");
}
@Override
public void copyElements(AbstractDataset destination, int element) {
if (element < 0) element += isize;
if (element < 0 || element > isize) {
throw new IllegalArgumentException(
String.format("Invalid choice of element: %d/%d", element, isize));
}
if (elementClass() != destination.elementClass()) {
throw new IllegalArgumentException(
"Element class of destination does not match this dataset");
}
final IndexIterator it = getIterator(element);
final int[] elements = ((IntegerDataset) destination).data; // CLASS_TYPE // PRIM_TYPE
int n = 0;
while (it.hasNext()) {
elements[n] = data[it.index];
n++;
}
}
@Override
public CompoundIntegerDataset setByBoolean(final Object o, BooleanDataset selection) {
if (o instanceof AbstractDataset) {
AbstractDataset ds = (AbstractDataset) o;
final int length = ((Number) selection.sum()).intValue();
if (length != ds.getSize()) {
throw new IllegalArgumentException(
"Number of true items in selection does not match number of items in dataset");
}
IndexIterator iter = ds.getIterator();
BooleanIterator biter = getBooleanIterator(selection);
if (ds instanceof AbstractCompoundDataset) {
if (isize != ds.getElementsPerItem()) {
throw new IllegalArgumentException("Input dataset is not compatible with slice");
}
while (biter.hasNext() && iter.hasNext()) {
for (int i = 0; i < isize; i++)
data[biter.index + i] =
(int) ds.getElementLongAbs(iter.index + i); // GET_ELEMENT_WITH_CAST
}
} else {
while (biter.hasNext() && iter.hasNext()) {
data[biter.index] = (int) ds.getElementLongAbs(iter.index); // GET_ELEMENT_WITH_CAST
for (int i = 1; i < isize; i++) data[biter.index + i] = 0;
}
}
} else {
try {
final int[] vr = toIntegerArray(o, isize); // PRIM_TYPE // CLASS_TYPE
final BooleanIterator biter = getBooleanIterator(selection);
while (biter.hasNext()) {
for (int i = 0; i < isize; i++) data[biter.index + i] = vr[i];
}
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException("Object for setting is not a dataset or number");
}
}
return this;
}
@Override
public CompoundIntegerDataset setSlice(final Object o, final SliceIterator siter) {
if (o instanceof IDataset) {
final IDataset ds = (IDataset) o;
final int[] oshape = ds.getShape();
if (!areShapesCompatible(siter.getSliceShape(), oshape)) {
throw new IllegalArgumentException(
String.format(
"Input dataset is not compatible with slice: %s cf %s",
Arrays.toString(oshape), Arrays.toString(siter.getSliceShape())));
}
if (ds instanceof AbstractDataset) {
final AbstractDataset ads = (AbstractDataset) ds;
IndexIterator oiter = ads.getIterator();
if (ds instanceof AbstractCompoundDataset) {
if (isize != ads.getElementsPerItem()) {
throw new IllegalArgumentException("Input dataset is not compatible with slice");
}
while (siter.hasNext() && oiter.hasNext()) {
for (int i = 0; i < isize; i++)
data[siter.index + i] =
(int) ads.getElementLongAbs(oiter.index + i); // GET_ELEMENT_WITH_CAST
}
} else {
while (siter.hasNext() && oiter.hasNext()) {
data[siter.index] = (int) ads.getElementLongAbs(oiter.index); // GET_ELEMENT_WITH_CAST
for (int i = 1; i < isize; i++) data[siter.index + i] = 0;
}
}
} else {
final IndexIterator oiter = new PositionIterator(oshape);
final int[] pos = oiter.getPos();
if (ds.getElementsPerItem() == 1) {
while (siter.hasNext() && oiter.hasNext()) {
data[siter.index] = ds.getInt(pos); // PRIM_TYPE
for (int i = 1; i < isize; i++) data[siter.index + i] = 0;
}
} else {
while (siter.hasNext() && oiter.hasNext()) {
final int[] val = toIntegerArray(ds.getObject(pos), isize); // PRIM_TYPE // CLASS_TYPE
for (int i = 0; i < isize; i++) data[siter.index + i] = val[i];
}
}
}
} else {
try {
final int[] vr = toIntegerArray(o, isize); // PRIM_TYPE // CLASS_TYPE
while (siter.hasNext()) {
for (int i = 0; i < isize; i++) data[siter.index + i] = vr[i];
}
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException("Object for setting slice is not a dataset or number");
}
}
setDirty();
return this;
}
