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Commit a97a4e9e authored by Lukas Stadler's avatar Lukas Stadler
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convert Cdist, Cutree and DoubleCentre to VectorAccess

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com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Cdist.java
+ 45
− 33
View file @ a97a4e9e
......@@ -12,9 +12,9 @@
*/
package com.oracle.truffle.r.library.stats;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.nullValue;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.missingValue;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.instanceOf;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.missingValue;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.nullValue;
import static com.oracle.truffle.r.runtime.nmath.MathConstants.DBL_MIN;
import com.oracle.truffle.api.dsl.Cached;
......@@ -25,8 +25,6 @@ import com.oracle.truffle.r.nodes.attributes.SetAttributeNode;
import com.oracle.truffle.r.nodes.attributes.SpecialAttributesFunctions.GetDimAttributeNode;
import com.oracle.truffle.r.nodes.attributes.SpecialAttributesFunctions.SetClassAttributeNode;
import com.oracle.truffle.r.nodes.builtin.RExternalBuiltinNode;
import com.oracle.truffle.r.runtime.data.nodes.ReadAccessor;
import com.oracle.truffle.r.runtime.data.nodes.VectorReadAccess;
import com.oracle.truffle.r.runtime.RError;
import com.oracle.truffle.r.runtime.RRuntime;
import com.oracle.truffle.r.runtime.data.RDataFactory;
......@@ -34,9 +32,12 @@ import com.oracle.truffle.r.runtime.data.RDoubleVector;
import com.oracle.truffle.r.runtime.data.RList;
import com.oracle.truffle.r.runtime.data.RStringVector;
import com.oracle.truffle.r.runtime.data.model.RAbstractDoubleVector;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess.RandomIterator;
import com.oracle.truffle.r.runtime.ops.na.NACheck;
public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
private static final NACheck naCheck = NACheck.create();
@Child private GetFixedAttributeNode getNamesAttrNode = GetFixedAttributeNode.createNames();
......@@ -49,9 +50,10 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
casts.arg(3).asDoubleVector().findFirst();
}
@Specialization(guards = "method == cachedMethod")
protected RDoubleVector cdist(RAbstractDoubleVector x, @SuppressWarnings("unused") int method, RList list, double p, @SuppressWarnings("unused") @Cached("method") int cachedMethod,
@Cached("create()") VectorReadAccess.Double xAccess,
@Specialization(guards = {"method == cachedMethod", "xAccess.supports(x)"})
protected RDoubleVector cdist(RAbstractDoubleVector x, @SuppressWarnings("unused") int method, RList list, double p,
@Cached("method") @SuppressWarnings("unused") int cachedMethod,
@Cached("x.access()") VectorAccess xAccess,
@Cached("getMethod(method)") Method methodObj,
@Cached("create()") SetAttributeNode setAttrNode,
@Cached("create()") SetClassAttributeNode setClassAttrNode,
......@@ -60,8 +62,10 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
int nc = getDimNode.ncols(x);
int n = nr * (nr - 1) / 2; /* avoid int overflow for N ~ 50,000 */
double[] ans = new double[n];
RDoubleVector xm = x.materialize();
rdistance(new ReadAccessor.Double(x, xAccess), nr, nc, ans, false, methodObj, p);
try (RandomIterator xIter = xAccess.randomAccess(x)) {
rdistance(xAccess, xIter, nr, nc, ans, false, methodObj, p);
}
RDoubleVector result = RDataFactory.createDoubleVector(ans, naCheck.neverSeenNA());
DynamicObject resultAttrs = result.initAttributes();
......@@ -81,6 +85,14 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
return result;
}
@Specialization(replaces = "cdist")
protected RDoubleVector cdistGeneric(RAbstractDoubleVector x, int method, RList list, double p,
@Cached("create()") SetAttributeNode setAttrNode,
@Cached("create()") SetClassAttributeNode setClassAttrNode,
@Cached("create()") GetDimAttributeNode getDimNode) {
return cdist(x, method, list, p, method, x.slowPathAccess(), getMethod(method), setAttrNode, setClassAttrNode, getDimNode);
}
private static boolean bothNonNAN(double a, double b) {
return !RRuntime.isNAorNaN(a) && !RRuntime.isNAorNaN(b);
}
......@@ -96,7 +108,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
return Method.values()[method - 1];
}
private void rdistance(ReadAccessor.Double xAccess, int nr, int nc, double[] d, boolean diag, Method method, double p) {
private void rdistance(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, double[] d, boolean diag, Method method, double p) {
int ij; /* can exceed 2^31 - 1, but Java can't handle that */
//
if (method == Method.MINKOWSKI) {
......@@ -109,7 +121,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
naCheck.enable(true);
for (int j = 0; j <= nr; j++) {
for (int i = j + dc; i < nr; i++) {
double r = method.dist(xAccess, nr, nc, i, j, p);
double r = method.dist(xAccess, xIter, nr, nc, i, j, p);
naCheck.check(r);
d[ij++] = r;
}
......@@ -119,7 +131,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
public enum Method {
EUCLIDEAN {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
double dev;
......@@ -130,8 +142,8 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
count = 0;
dist = 0;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
dev = (xAccess.getDataAt(i1) - xAccess.getDataAt(i2));
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
dev = (xAccess.getDouble(xIter, i1) - xAccess.getDouble(xIter, i2));
if (!RRuntime.isNAorNaN(dev)) {
dist += dev * dev;
count++;
......@@ -152,7 +164,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
},
MAXIMUM {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
double dev;
......@@ -163,8 +175,8 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
count = 0;
dist = -Double.MAX_VALUE;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
dev = Math.abs(xAccess.getDataAt(i1) - xAccess.getDataAt(i2));
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
dev = Math.abs(xAccess.getDouble(xIter, i1) - xAccess.getDouble(xIter, i2));
if (!RRuntime.isNAorNaN(dev)) {
if (dev > dist) {
dist = dev;
......@@ -184,7 +196,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
},
MANHATTAN {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
double dev;
......@@ -195,8 +207,8 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
count = 0;
dist = 0;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
dev = Math.abs(xAccess.getDataAt(i1) - xAccess.getDataAt(i2));
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
dev = Math.abs(xAccess.getDouble(xIter, i1) - xAccess.getDouble(xIter, i2));
if (!RRuntime.isNAorNaN(dev)) {
dist += dev;
count++;
......@@ -217,7 +229,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
},
CANBERRA {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
double dev;
......@@ -230,9 +242,9 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
count = 0;
dist = 0;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
sum = Math.abs(xAccess.getDataAt(i1) + xAccess.getDataAt(i2));
diff = Math.abs(xAccess.getDataAt(i1) - xAccess.getDataAt(i2));
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
sum = Math.abs(xAccess.getDouble(xIter, i1) + xAccess.getDouble(xIter, i2));
diff = Math.abs(xAccess.getDouble(xIter, i1) - xAccess.getDouble(xIter, i2));
if (sum > DBL_MIN || diff > DBL_MIN) {
dev = diff / sum;
if (!RRuntime.isNAorNaN(dev) ||
......@@ -258,7 +270,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
},
BINARY {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
int total;
......@@ -271,13 +283,13 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
dist = 0;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
if (!bothFinite(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
if (!bothFinite(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
RError.warning(RError.SHOW_CALLER2, RError.Message.GENERIC, "treating non-finite values as NA");
} else {
if (xAccess.getDataAt(i1) != 0. || xAccess.getDataAt(i2) != 0.) {
if (xAccess.getDouble(xIter, i1) != 0. || xAccess.getDouble(xIter, i2) != 0.) {
count++;
if (!(xAccess.getDataAt(i1) != 0. && xAccess.getDataAt(i2) != 0.)) {
if (!(xAccess.getDouble(xIter, i1) != 0. && xAccess.getDouble(xIter, i2) != 0.)) {
dist++;
}
}
......@@ -300,7 +312,7 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
},
MINKOWSKI {
@Override
public double dist(ReadAccessor.Double xAccess, int nr, int nc, final int i1in, final int i2in, double p) {
public double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, final int i1in, final int i2in, double p) {
int i1 = i1in;
int i2 = i2in;
double dev;
......@@ -311,8 +323,8 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
count = 0;
dist = 0;
for (j = 0; j < nc; j++) {
if (bothNonNAN(xAccess.getDataAt(i1), xAccess.getDataAt(i2))) {
dev = (xAccess.getDataAt(i1) - xAccess.getDataAt(i2));
if (bothNonNAN(xAccess.getDouble(xIter, i1), xAccess.getDouble(xIter, i2))) {
dev = (xAccess.getDouble(xIter, i1) - xAccess.getDouble(xIter, i2));
if (!RRuntime.isNAorNaN(dev)) {
dist += Math.pow(Math.abs(dev), p);
count++;
......@@ -331,6 +343,6 @@ public abstract class Cdist extends RExternalBuiltinNode.Arg4 {
}
};
public abstract double dist(ReadAccessor.Double xAccess, int nr, int nc, int i1, int i2, double p);
public abstract double dist(VectorAccess xAccess, RandomIterator xIter, int nr, int nc, int i1, int i2, double p);
}
}
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Cutree.java
+ 80
− 75
View file @ a97a4e9e
......@@ -20,7 +20,8 @@ import com.oracle.truffle.r.nodes.builtin.RExternalBuiltinNode;
import com.oracle.truffle.r.runtime.data.RDataFactory;
import com.oracle.truffle.r.runtime.data.RIntVector;
import com.oracle.truffle.r.runtime.data.model.RAbstractIntVector;
import com.oracle.truffle.r.runtime.data.nodes.VectorReadAccess;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess.RandomIterator;
// translated from library/stats/src/hclust_utils.c
......@@ -32,10 +33,10 @@ public abstract class Cutree extends RExternalBuiltinNode.Arg2 {
casts.arg(1).mustNotBeMissing().mapIf(nullValue(), emptyIntegerVector()).asIntegerVector();
}
@Specialization
@Specialization(guards = {"mergeAccess.supports(merge)", "whichAccess.supports(which)"})
protected RIntVector cutree(RAbstractIntVector merge, RAbstractIntVector which,
@Cached("create()") VectorReadAccess.Int mergeAccess,
@Cached("create()") VectorReadAccess.Int whichAccess,
@Cached("merge.access()") VectorAccess mergeAccess,
@Cached("which.access()") VectorAccess whichAccess,
@Cached("create()") GetDimAttributeNode getDimNode) {
int whichLen = which.getLength();
......@@ -59,92 +60,96 @@ public abstract class Cutree extends RExternalBuiltinNode.Arg2 {
int[] z = new int[n];
int[] iAns = new int[n * whichLen];
Object mergeStore = mergeAccess.getDataStore(merge);
Object whichStore = whichAccess.getDataStore(which);
try (RandomIterator mergeIter = mergeAccess.randomAccess(merge); RandomIterator whichIter = whichAccess.randomAccess(which)) {
// for (k = 1; k <= n; k++) {
for (k = 0; k < n; k++) {
sing[k] = true; /* is k-th obs. still alone in cluster ? */
mNr[k] = 0; /* containing last merge-step number of k-th obs. */
}
// for (k = 1; k <= n; k++) {
for (k = 0; k < n; k++) {
sing[k] = true; /* is k-th obs. still alone in cluster ? */
mNr[k] = 0; /* containing last merge-step number of k-th obs. */
}
for (k = 1; k <= n - 1; k++) {
/* k-th merge, from n-k+1 to n-k atoms: (m1,m2) = merge[ k , ] */
m1 = mergeAccess.getDataAt(merge, mergeStore, k - 1);
m2 = mergeAccess.getDataAt(merge, mergeStore, n - 1 + k - 1);
if (m1 < 0 && m2 < 0) { /* merging atoms [-m1] and [-m2] */
mNr[adj(-m1)] = mNr[adj(-m2)] = k;
sing[adj(-m1)] = sing[adj(-m2)] = false;
} else if (m1 < 0 || m2 < 0) { /* the other >= 0 */
if (m1 < 0) {
j = -m1;
m1 = m2;
} else {
j = -m2;
}
/* merging atom j & cluster m1 */
for (l = 1; l <= n; l++) {
if (mNr[adj(l)] == m1) {
mNr[adj(l)] = k;
for (k = 1; k <= n - 1; k++) {
/* k-th merge, from n-k+1 to n-k atoms: (m1,m2) = merge[ k , ] */
m1 = mergeAccess.getInt(mergeIter, k - 1);
m2 = mergeAccess.getInt(mergeIter, n - 1 + k - 1);
if (m1 < 0 && m2 < 0) { /* merging atoms [-m1] and [-m2] */
mNr[adj(-m1)] = mNr[adj(-m2)] = k;
sing[adj(-m1)] = sing[adj(-m2)] = false;
} else if (m1 < 0 || m2 < 0) { /* the other >= 0 */
if (m1 < 0) {
j = -m1;
m1 = m2;
} else {
j = -m2;
}
}
mNr[adj(j)] = k;
sing[adj(j)] = false;
} else { /* both m1, m2 >= 0 */
for (l = 1; l <= n; l++) {
if (mNr[adj(l)] == m1 || mNr[adj(l)] == m2) {
mNr[adj(l)] = k;
/* merging atom j & cluster m1 */
for (l = 1; l <= n; l++) {
if (mNr[adj(l)] == m1) {
mNr[adj(l)] = k;
}
}
mNr[adj(j)] = k;
sing[adj(j)] = false;
} else { /* both m1, m2 >= 0 */
for (l = 1; l <= n; l++) {
if (mNr[adj(l)] == m1 || mNr[adj(l)] == m2) {
mNr[adj(l)] = k;
}
}
}
}
/*
* does this k-th merge belong to a desired group size which[j] ? if yes, find j (maybe
* multiple ones):
*/
foundJ = false;
for (j = 0; j < whichLen; j++) {
if (whichAccess.getDataAt(which, whichStore, j) == n - k) {
if (!foundJ) { /* first match (and usually only one) */
foundJ = true;
// for (l = 1; l <= n; l++)
for (l = 0; l < n; l++) {
z[l] = 0;
}
nclust = 0;
mm = j * n; /* may want to copy this column of ans[] */
for (l = 1, m1 = mm; l <= n; l++, m1++) {
if (sing[adj(l)]) {
iAns[m1] = ++nclust;
} else {
if (z[adj(mNr[adj(l)])] == 0) {
z[adj(mNr[adj(l)])] = ++nclust;
/*
* does this k-th merge belong to a desired group size which[j] ? if yes, find j
* (maybe multiple ones):
*/
foundJ = false;
for (j = 0; j < whichLen; j++) {
if (whichAccess.getInt(whichIter, j) == n - k) {
if (!foundJ) { /* first match (and usually only one) */
foundJ = true;
// for (l = 1; l <= n; l++)
for (l = 0; l < n; l++) {
z[l] = 0;
}
nclust = 0;
mm = j * n; /* may want to copy this column of ans[] */
for (l = 1, m1 = mm; l <= n; l++, m1++) {
if (sing[adj(l)]) {
iAns[m1] = ++nclust;
} else {
if (z[adj(mNr[adj(l)])] == 0) {
z[adj(mNr[adj(l)])] = ++nclust;
}
iAns[m1] = z[adj(mNr[adj(l)])];
}
iAns[m1] = z[adj(mNr[adj(l)])];
}
} else { /* found_j: another which[j] == n-k : copy column */
for (l = 1, m1 = j * n, m2 = mm; l <= n; l++, m1++, m2++) {
iAns[m1] = iAns[m2];
}
}
} else { /* found_j: another which[j] == n-k : copy column */
for (l = 1, m1 = j * n, m2 = mm; l <= n; l++, m1++, m2++) {
iAns[m1] = iAns[m2];
}
} /* if ( match ) */
} /* for(j .. which[j] ) */
} /* for(k ..) {merge} */
/* Dealing with trivial case which[] = n : */
for (j = 0; j < whichLen; j++) {
if (whichAccess.getInt(whichIter, j) == n) {
for (l = 1, m1 = j * n; l <= n; l++, m1++) {
iAns[m1] = l;
}
} /* if ( match ) */
} /* for(j .. which[j] ) */
} /* for(k ..) {merge} */
/* Dealing with trivial case which[] = n : */
for (j = 0; j < whichLen; j++) {
if (whichAccess.getDataAt(which, whichStore, j) == n) {
for (l = 1, m1 = j * n; l <= n; l++, m1++) {
iAns[m1] = l;
}
}
}
RIntVector result = RDataFactory.createIntVector(iAns, RDataFactory.COMPLETE_VECTOR, new int[]{n, whichLen});
return result;
return RDataFactory.createIntVector(iAns, RDataFactory.COMPLETE_VECTOR, new int[]{n, whichLen});
}
@Specialization(replaces = "cutree")
protected RIntVector cutreeGeneric(RAbstractIntVector merge, RAbstractIntVector which,
@Cached("create()") GetDimAttributeNode getDimNode) {
return cutree(merge, which, merge.slowPathAccess(), which.slowPathAccess(), getDimNode);
}
private static int adj(int i) {
......
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DoubleCentre.java
+ 42
− 35
View file @ a97a4e9e
......@@ -10,56 +10,63 @@
*/
package com.oracle.truffle.r.library.stats;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.missingValue;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.nullValue;
import com.oracle.truffle.api.dsl.Cached;
import com.oracle.truffle.api.dsl.Specialization;
import com.oracle.truffle.r.nodes.attributes.SpecialAttributesFunctions.GetDimAttributeNode;
import com.oracle.truffle.r.nodes.builtin.RExternalBuiltinNode;
import com.oracle.truffle.r.runtime.RError;
import com.oracle.truffle.r.runtime.data.RDoubleVector;
import com.oracle.truffle.r.runtime.data.model.RAbstractDoubleVector;
import com.oracle.truffle.r.runtime.data.nodes.SetDataAt;
import com.oracle.truffle.r.runtime.data.nodes.VectorReadAccess;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess;
import com.oracle.truffle.r.runtime.data.nodes.VectorAccess.RandomIterator;
import com.oracle.truffle.r.runtime.data.nodes.VectorReuse;
public abstract class DoubleCentre extends RExternalBuiltinNode.Arg1 {
static {
Casts casts = new Casts(DoubleCentre.class);
casts.arg(0).mustBe(missingValue().not()).mustBe(nullValue().not(), RError.Message.MACRO_CAN_BE_APPLIED_TO, "REAL()", "numeric", "NULL").asDoubleVector();
casts.arg(0).mustNotBeNull(RError.Message.MACRO_CAN_BE_APPLIED_TO, "REAL()", "numeric", "NULL").mustNotBeMissing().asDoubleVector();
}
@Specialization
protected RDoubleVector doubleCentre(RAbstractDoubleVector aVecAbs,
@Cached("create()") VectorReadAccess.Double aAccess,
@Cached("create()") SetDataAt.Double aSetter,
@Specialization(guards = {"aAccess.supports(a)", "reuse.supports(a)"})
protected RAbstractDoubleVector doubleCentre(RAbstractDoubleVector a,
@Cached("a.access()") VectorAccess aAccess,
@Cached("createNonShared(a)") VectorReuse reuse,
@Cached("create()") GetDimAttributeNode getDimNode) {
RDoubleVector aVec = aVecAbs.materialize();
int n = getDimNode.nrows(aVec);
Object aStore = aAccess.getDataStore(aVec);
for (int i = 0; i < n; i++) {
double sum = 0;
for (int j = 0; j < n; j++) {
sum += aAccess.getDataAt(aVec, aStore, i + j * n);
}
sum /= n;
for (int j = 0; j < n; j++) {
double val = aAccess.getDataAt(aVec, aStore, i + j * n);
aSetter.setDataAt(aVec, aStore, i + j * n, val - sum);
}
}
for (int j = 0; j < n; j++) {
double sum = 0;
for (int i = 0; i < n; i++) {
sum += aAccess.getDataAt(aVec, aStore, i + j * n);
}
sum /= n;
for (int i = 0; i < n; i++) {
double val = aAccess.getDataAt(aVec, aStore, i + j * n);
aSetter.setDataAt(aVec, aStore, i + j * n, val - sum);
int n = getDimNode.nrows(a);
try (RandomIterator aIter = aAccess.randomAccess(a)) {
RAbstractDoubleVector result = reuse.getResult(a);
VectorAccess resultAccess = reuse.access(result);
try (RandomIterator resultIter = resultAccess.randomAccess(result)) {
for (int i = 0; i < n; i++) {
double sum = 0;
for (int j = 0; j < n; j++) {
sum += aAccess.getDouble(aIter, i + j * n);
}
sum /= n;
for (int j = 0; j < n; j++) {
resultAccess.setDouble(resultIter, i + j * n, aAccess.getDouble(aIter, i + j * n) - sum);
}
}
for (int j = 0; j < n; j++) {
double sum = 0;
for (int i = 0; i < n; i++) {
sum += resultAccess.getDouble(aIter, i + j * n);
}
sum /= n;
for (int i = 0; i < n; i++) {
resultAccess.setDouble(resultIter, i + j * n, resultAccess.getDouble(aIter, i + j * n) - sum);
}
}
}
return result;
}
return aVec;
}
@Specialization(replaces = "doubleCentre")
protected RAbstractDoubleVector doubleCentreGeneric(RAbstractDoubleVector a,
@Cached("createNonSharedGeneric()") VectorReuse reuse,
@Cached("create()") GetDimAttributeNode getDimNode) {
return doubleCentre(a, a.slowPathAccess(), reuse, getDimNode);
}
}
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