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