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Commit fafac04e authored by stepan's avatar stepan
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Covcor: do not use nodes behind Truffle boundary

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com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Covcor.java
+ 77
− 81
View file @ fafac04e
...@@ -16,7 +16,6 @@ import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.toBoolean; ...@@ -16,7 +16,6 @@ import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.toBoolean;
import com.oracle.truffle.api.CompilerDirectives; import com.oracle.truffle.api.CompilerDirectives;
import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary; import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
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.api.profiles.BranchProfile; import com.oracle.truffle.api.profiles.BranchProfile;
import com.oracle.truffle.api.profiles.ConditionProfile; import com.oracle.truffle.api.profiles.ConditionProfile;
...@@ -34,8 +33,7 @@ import com.oracle.truffle.r.runtime.data.RDoubleVector; ...@@ -34,8 +33,7 @@ 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.RNull; import com.oracle.truffle.r.runtime.data.RNull;
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.ReadAccessor; import com.oracle.truffle.r.runtime.data.nodes.GetReadonlyData;
import com.oracle.truffle.r.runtime.data.nodes.VectorReadAccess;
import com.oracle.truffle.r.runtime.nmath.RMath; import com.oracle.truffle.r.runtime.nmath.RMath;
/* /*
...@@ -73,20 +71,20 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -73,20 +71,20 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
/** /**
* Compute Cov(xx[], yy[]) or Cor(.,.) with n = length(xx) * Compute Cov(xx[], yy[]) or Cor(.,.) with n = length(xx)
*/ */
private static void COV_PAIRWISE_BODY(double[] ans, int n, int ncx, int i, int j, ReadAccessor.Double x, ReadAccessor.Double y, int xx, int yy, boolean[] sd_0, boolean cor, boolean kendall) { private static void COV_PAIRWISE_BODY(double[] ans, int n, int ncx, int i, int j, double[] x, double[] y, int xx, int yy, boolean[] sd_0, boolean cor, boolean kendall) {
double xmean = 0, ymean = 0; double xmean = 0, ymean = 0;
int nobs = 0; int nobs = 0;
if (!kendall) { if (!kendall) {
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (!(ISNAN(x.getDataAt(xx + k)) || ISNAN(y.getDataAt(yy + k)))) { if (!(ISNAN(x[xx + k]) || ISNAN(y[yy + k]))) {
nobs++; nobs++;
xmean += x.getDataAt(xx + k); xmean += x[xx + k];
ymean += y.getDataAt(yy + k); ymean += y[yy + k];
} }
} }
} else /* kendall */ } else /* kendall */
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (!(ISNAN(x.getDataAt(xx + k)) || ISNAN(y.getDataAt(yy + k)))) { if (!(ISNAN(x[xx + k]) || ISNAN(y[yy + k]))) {
nobs++; nobs++;
} }
} }
...@@ -100,10 +98,10 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -100,10 +98,10 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
n1 = nobs - 1; n1 = nobs - 1;
} }
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (!(ISNAN(x.getDataAt(xx + k)) || ISNAN(y.getDataAt(yy + k)))) { if (!(ISNAN(x[xx + k]) || ISNAN(y[yy + k]))) {
if (!kendall) { if (!kendall) {
double xm = x.getDataAt(xx + k) - xmean; double xm = x[xx + k] - xmean;
double ym = y.getDataAt(yy + k) - ymean; double ym = y[yy + k] - ymean;
sum += xm * ym; sum += xm * ym;
if (cor) { if (cor) {
...@@ -114,9 +112,9 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -114,9 +112,9 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
else { /* Kendall's tau */ else { /* Kendall's tau */
for (n1 = 0; n1 < k; n1++) { for (n1 = 0; n1 < k; n1++) {
if (!(ISNAN(x.getDataAt(xx + n1)) || ISNAN(y.getDataAt(yy + n1)))) { if (!(ISNAN(x[xx + n1]) || ISNAN(y[yy + n1]))) {
double xm = RMath.sign(x.getDataAt(xx + k) - x.getDataAt(xx + n1)); double xm = RMath.sign(x[xx + k] - x[xx + n1]);
double ym = RMath.sign(y.getDataAt(yy + k) - y.getDataAt(yy + n1)); double ym = RMath.sign(y[yy + k] - y[yy + n1]);
sum += xm * ym; sum += xm * ym;
if (cor) { if (cor) {
...@@ -151,7 +149,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -151,7 +149,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_pairwise1(int n, int ncx, ReadAccessor.Double x, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) { private static void cov_pairwise1(int n, int ncx, double[] x, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) {
for (int i = 0; i < ncx; i++) { for (int i = 0; i < ncx; i++) {
int xx = i * n; int xx = i * n;
for (int j = 0; j <= i; j++) { for (int j = 0; j <= i; j++) {
...@@ -164,7 +162,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -164,7 +162,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_pairwise2(int n, int ncx, int ncy, ReadAccessor.Double x, ReadAccessor.Double y, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) { private static void cov_pairwise2(int n, int ncx, int ncy, double[] x, double[] y, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) {
for (int i = 0; i < ncx; i++) { for (int i = 0; i < ncx; i++) {
int xx = i * n; int xx = i * n;
for (int j = 0; j < ncy; j++) { for (int j = 0; j < ncy; j++) {
...@@ -180,14 +178,14 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -180,14 +178,14 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
*/ */
/* This uses two passes for better accuracy */ /* This uses two passes for better accuracy */
private static void MEAN(int n, int ncx, ReadAccessor.Double x, double[] xm, boolean[] ind, int nobs) { private static void MEAN(int n, int ncx, double[] x, double[] xm, boolean[] ind, int nobs) {
/* variable means */ /* variable means */
for (int i = 0; i < ncx; i++) { for (int i = 0; i < ncx; i++) {
int xx = i * n; int xx = i * n;
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
sum += x.getDataAt(xx + k); sum += x[xx + k];
} }
} }
double tmp = sum / nobs; double tmp = sum / nobs;
...@@ -195,7 +193,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -195,7 +193,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
sum = 0; sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
sum += (x.getDataAt(xx + k) - tmp); sum += (x[xx + k] - tmp);
} }
} }
tmp = tmp + sum / nobs; tmp = tmp + sum / nobs;
...@@ -205,7 +203,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -205,7 +203,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
/* This uses two passes for better accuracy */ /* This uses two passes for better accuracy */
private static void MEAN_(int n, int ncx, ReadAccessor.Double x, double[] xm, boolean[] has_na) { private static void MEAN_(int n, int ncx, double[] x, double[] xm, boolean[] has_na) {
/* variable means (has_na) */ /* variable means (has_na) */
for (int i = 0; i < ncx; i++) { for (int i = 0; i < ncx; i++) {
double tmp; double tmp;
...@@ -215,13 +213,13 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -215,13 +213,13 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
int xx = i * n; int xx = i * n;
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
sum += x.getDataAt(xx + k); sum += x[xx + k];
} }
tmp = sum / n; tmp = sum / n;
if (Double.isFinite(tmp)) { if (Double.isFinite(tmp)) {
sum = 0; sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
sum += (x.getDataAt(xx + k) - tmp); sum += (x[xx + k] - tmp);
} }
tmp = tmp + sum / n; tmp = tmp + sum / n;
} }
...@@ -230,7 +228,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -230,7 +228,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_complete1(int n, int ncx, ReadAccessor.Double x, double[] xm, boolean[] ind, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) { private static void cov_complete1(int n, int ncx, double[] x, double[] xm, boolean[] ind, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) {
int n1 = -1; int n1 = -1;
/* total number of complete observations */ /* total number of complete observations */
...@@ -264,7 +262,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -264,7 +262,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
sum += (x.getDataAt(xx + k) - xxm) * (x.getDataAt(yy + k) - yym); sum += (x[xx + k] - xxm) * (x[yy + k] - yym);
} }
} }
double result = sum / n1; double result = sum / n1;
...@@ -279,7 +277,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -279,7 +277,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
if (ind[k]) { if (ind[k]) {
for (n1 = 0; n1 < n; n1++) { for (n1 = 0; n1 < n; n1++) {
if (ind[n1]) { if (ind[n1]) {
sum += RMath.sign(x.getDataAt(xx + k) - x.getDataAt(xx + n1)) * RMath.sign(x.getDataAt(yy + k) - x.getDataAt(yy + n1)); sum += RMath.sign(x[xx + k] - x[xx + n1]) * RMath.sign(x[yy + k] - x[yy + n1]);
} }
} }
} }
...@@ -316,7 +314,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -316,7 +314,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_na_1(int n, int ncx, ReadAccessor.Double x, double[] xm, boolean[] has_na, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) { private static void cov_na_1(int n, int ncx, double[] x, double[] xm, boolean[] has_na, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) {
int n1 = -1; int n1 = -1;
if (n <= 1) { /* too many missing */ if (n <= 1) { /* too many missing */
for (int i = 0; i < ncx; i++) { for (int i = 0; i < ncx; i++) {
...@@ -351,7 +349,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -351,7 +349,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double yym = xm[j]; double yym = xm[j];
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
sum += (x.getDataAt(xx + k) - xxm) * (x.getDataAt(yy + k) - yym); sum += (x[xx + k] - xxm) * (x[yy + k] - yym);
} }
double result = sum / n1; double result = sum / n1;
ANS(ans, ncx, j, i, result); ANS(ans, ncx, j, i, result);
...@@ -368,7 +366,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -368,7 +366,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
for (n1 = 0; n1 < n; n1++) { for (n1 = 0; n1 < n; n1++) {
sum += RMath.sign(x.getDataAt(xx + k) - x.getDataAt(xx + n1)) * RMath.sign(x.getDataAt(yy + k) - x.getDataAt(yy + n1)); sum += RMath.sign(x[xx + k] - x[xx + n1]) * RMath.sign(x[yy + k] - x[yy + n1]);
} }
} }
ANS(ans, ncx, j, i, sum); ANS(ans, ncx, j, i, sum);
...@@ -409,7 +407,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -409,7 +407,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void COV_SDEV1(int n, int n1, int nc, ReadAccessor.Double array, double[] m, boolean[] ind, boolean kendall) { private static void COV_SDEV1(int n, int n1, int nc, double[] array, double[] m, boolean[] ind, boolean kendall) {
for (int i = 0; i < nc; i++) { /* Var(X[i]) */ for (int i = 0; i < nc; i++) { /* Var(X[i]) */
int xx = i * n; int xx = i * n;
double sum = 0; double sum = 0;
...@@ -417,7 +415,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -417,7 +415,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double xxm = m[i]; double xxm = m[i];
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
sum += (array.getDataAt(xx + k) - xxm) * (array.getDataAt(xx + k) - xxm); sum += (array[xx + k] - xxm) * (array[xx + k] - xxm);
} }
} }
sum /= n1; sum /= n1;
...@@ -425,7 +423,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -425,7 +423,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
for (int n1_ = 0; n1_ < n; n1_++) { for (int n1_ = 0; n1_ < n; n1_++) {
if (ind[n1_] && array.getDataAt(xx + k) != array.getDataAt(xx + n1_)) { if (ind[n1_] && array[xx + k] != array[xx + n1_]) {
sum++; /* = sign(. - .)^2 */ sum++; /* = sign(. - .)^2 */
} }
} }
...@@ -436,8 +434,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -436,8 +434,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_complete2(int n, int ncx, int ncy, ReadAccessor.Double x, ReadAccessor.Double y, double[] xm, double[] ym, boolean[] ind, double[] ans, boolean[] sd_0, boolean cor, private static void cov_complete2(int n, int ncx, int ncy, double[] x, double[] y, double[] xm, double[] ym, boolean[] ind, double[] ans, boolean[] sd_0, boolean cor, boolean kendall) {
boolean kendall) {
int n1 = -1; int n1 = -1;
/* total number of complete observations */ /* total number of complete observations */
...@@ -471,7 +468,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -471,7 +468,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
if (ind[k]) { if (ind[k]) {
sum += (x.getDataAt(xx + k) - xxm) * (y.getDataAt(yy + k) - yym); sum += (x[xx + k] - xxm) * (y[yy + k] - yym);
} }
} }
ANS(ans, ncx, i, j, sum / n1); ANS(ans, ncx, i, j, sum / n1);
...@@ -484,7 +481,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -484,7 +481,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
if (ind[k]) { if (ind[k]) {
for (n1 = 0; n1 < n; n1++) { for (n1 = 0; n1 < n; n1++) {
if (ind[n1]) { if (ind[n1]) {
sum += RMath.sign(x.getDataAt(xx + k) - x.getDataAt(xx + n1)) * RMath.sign(y.getDataAt(yy + k) - y.getDataAt(yy + n1)); sum += RMath.sign(x[xx + k] - x[xx + n1]) * RMath.sign(y[yy + k] - y[yy + n1]);
} }
} }
} }
...@@ -519,7 +516,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -519,7 +516,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void COV_SDEV2(int n, int n1, int nc, ReadAccessor.Double array, double[] m, boolean[] has_na, boolean kendall) { private static void COV_SDEV2(int n, int n1, int nc, double[] array, double[] m, boolean[] has_na, boolean kendall) {
for (int i = 0; i < nc; i++) { for (int i = 0; i < nc; i++) {
if (!has_na[i]) { /* Var(X[j]) */ if (!has_na[i]) { /* Var(X[j]) */
int xx = i * n; int xx = i * n;
...@@ -527,13 +524,13 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -527,13 +524,13 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
if (!kendall) { if (!kendall) {
double xxm = m[i]; double xxm = m[i];
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
sum += (array.getDataAt(xx + k) - xxm) * (array.getDataAt(xx + k) - xxm); sum += (array[xx + k] - xxm) * (array[xx + k] - xxm);
} }
sum /= n1; sum /= n1;
} else { /* Kendall's tau */ } else { /* Kendall's tau */
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
for (int n1_ = 0; n1_ < n; n1_++) { for (int n1_ = 0; n1_ < n; n1_++) {
if (array.getDataAt(xx + k) != array.getDataAt(xx + n1_)) { if (array[xx + k] != array[xx + n1_]) {
sum++; /* = sign(. - .)^2 */ sum++; /* = sign(. - .)^2 */
} }
} }
...@@ -544,8 +541,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -544,8 +541,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void cov_na_2(int n, int ncx, int ncy, ReadAccessor.Double x, ReadAccessor.Double y, double[] xm, double[] ym, boolean[] has_na_x, boolean[] has_na_y, double[] ans, boolean[] sd_0, private static void cov_na_2(int n, int ncx, int ncy, double[] x, double[] y, double[] xm, double[] ym, boolean[] has_na_x, boolean[] has_na_y, double[] ans, boolean[] sd_0, boolean cor,
boolean cor,
boolean kendall) { boolean kendall) {
int n1 = -1; int n1 = -1;
if (n <= 1) {/* too many missing */ if (n <= 1) {/* too many missing */
...@@ -579,7 +575,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -579,7 +575,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double yym = ym[j]; double yym = ym[j];
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
sum += (x.getDataAt(xx + k) - xxm) * (y.getDataAt(yy + k) - yym); sum += (x[xx + k] - xxm) * (y[yy + k] - yym);
} }
ANS(ans, ncx, i, j, sum / n1); ANS(ans, ncx, i, j, sum / n1);
} }
...@@ -593,7 +589,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -593,7 +589,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
double sum = 0; double sum = 0;
for (int k = 0; k < n; k++) { for (int k = 0; k < n; k++) {
for (n1 = 0; n1 < n; n1++) { for (n1 = 0; n1 < n; n1++) {
sum += RMath.sign(x.getDataAt(xx + k) - x.getDataAt(xx + n1)) * RMath.sign(y.getDataAt(yy + k) - y.getDataAt(yy + n1)); sum += RMath.sign(x[xx + k] - x[xx + n1]) * RMath.sign(y[yy + k] - y[yy + n1]);
} }
} }
ANS(ans, ncx, i, j, sum); ANS(ans, ncx, i, j, sum);
...@@ -641,9 +637,9 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -641,9 +637,9 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
* This might look slightly inefficient, but it is designed to optimise paging in virtual memory * This might look slightly inefficient, but it is designed to optimise paging in virtual memory
* systems ... (or at least that's my story, and I'm sticking to it.) * systems ... (or at least that's my story, and I'm sticking to it.)
*/ */
private static void NA_LOOP(int n, int z, ReadAccessor.Double x, boolean[] ind, boolean na_fail) { private static void NA_LOOP(int n, int z, double[] x, boolean[] ind, boolean na_fail) {
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
if (ISNAN(x.getDataAt(z + i))) { if (ISNAN(x[z + i])) {
if (na_fail) { if (na_fail) {
error("missing observations in cov/cor"); error("missing observations in cov/cor");
} else { } else {
...@@ -653,7 +649,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -653,7 +649,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
private static void complete1(int n, int ncx, ReadAccessor.Double x, boolean[] ind, boolean na_fail) { private static void complete1(int n, int ncx, double[] x, boolean[] ind, boolean na_fail) {
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
ind[i] = true; ind[i] = true;
} }
...@@ -663,7 +659,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -663,7 +659,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
static void complete2(int n, int ncx, int ncy, ReadAccessor.Double x, ReadAccessor.Double y, boolean[] ind, boolean na_fail) { static void complete2(int n, int ncx, int ncy, double[] x, double[] y, boolean[] ind, boolean na_fail) {
complete1(n, ncx, x, ind, na_fail); complete1(n, ncx, x, ind, na_fail);
for (int j = 0; j < ncy; j++) { for (int j = 0; j < ncy; j++) {
...@@ -672,12 +668,12 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -672,12 +668,12 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
static void find_na_1(int n, int ncx, ReadAccessor.Double x, boolean[] has_na) { static void find_na_1(int n, int ncx, double[] x, boolean[] has_na) {
for (int j = 0; j < ncx; j++) { for (int j = 0; j < ncx; j++) {
int z = j * n; int z = j * n;
has_na[j] = false; has_na[j] = false;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
if (ISNAN(x.getDataAt(z + i))) { if (ISNAN(x[z + i])) {
has_na[j] = true; has_na[j] = true;
break; break;
} }
...@@ -685,7 +681,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -685,7 +681,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
static void find_na_2(int n, int ncx, int ncy, ReadAccessor.Double x, ReadAccessor.Double y, boolean[] has_na_x, boolean[] has_na_y) { static void find_na_2(int n, int ncx, int ncy, double[] x, double[] y, boolean[] has_na_x, boolean[] has_na_y) {
find_na_1(n, ncx, x, has_na_x); find_na_1(n, ncx, x, has_na_x);
find_na_1(n, ncy, y, has_na_y); find_na_1(n, ncy, y, has_na_y);
} }
...@@ -694,36 +690,36 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -694,36 +690,36 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
* co[vr](x, y, use = { 1, 2, 3, 4, 5 } "all.obs", "complete.obs", "pairwise.complete", * co[vr](x, y, use = { 1, 2, 3, 4, 5 } "all.obs", "complete.obs", "pairwise.complete",
* "everything", "na.or.complete" kendall = TRUE/FALSE) * "everything", "na.or.complete" kendall = TRUE/FALSE)
*/ */
public RDoubleVector corcov(ReadAccessor.Double x, ReadAccessor.Double y, int method, boolean kendall) throws RError { public RDoubleVector corcov(RDoubleVector x, RDoubleVector y, int method, boolean kendall) throws RError {
int n, ncx, ncy; int n, ncx, ncy;
/* Arg.1: x */ /* Arg.1: x */
if (isFactorX.executeIsFactor(x.getVector())) { if (isFactorX.executeIsFactor(x)) {
error("'x' is a factor"); error("'x' is a factor");
// maybe only warning: "Calling var(x) on a factor x is deprecated and will become an // maybe only warning: "Calling var(x) on a factor x is deprecated and will become an
// error.\n Use something like 'all(duplicated(x)[-1L])' to test for a constant vector." // error.\n Use something like 'all(duplicated(x)[-1L])' to test for a constant vector."
} }
/* length check of x -- only if(empty_err) --> below */ /* length check of x -- only if(empty_err) --> below */
int[] xDims = getDimsXNode.getDimensions(x.getVector()); int[] xDims = getDimsXNode.getDimensions(x);
boolean ansmat = matrixProfile.profile(GetDimAttributeNode.isMatrix(xDims)); boolean ansmat = matrixProfile.profile(GetDimAttributeNode.isMatrix(xDims));
if ((ansmat)) { if ((ansmat)) {
n = xDims[0]; n = xDims[0];
ncx = xDims[1]; ncx = xDims[1];
} else { } else {
n = x.getVector().getLength(); n = x.getLength();
ncx = 1; ncx = 1;
} }
/* Arg.2: y */ /* Arg.2: y */
if (y == null) {/* y = x : var() */ if (y == null) {/* y = x : var() */
ncy = ncx; ncy = ncx;
} else { } else {
if (isFactorY.executeIsFactor(y.getVector())) { if (isFactorY.executeIsFactor(y)) {
error("'y' is a factor"); error("'y' is a factor");
// maybe only warning: "Calling var(x) on a factor x is deprecated and will become // maybe only warning: "Calling var(x) on a factor x is deprecated and will become
// an error.\n Use something like 'all(duplicated(x)[-1L])' to test for a constant // an error.\n Use something like 'all(duplicated(x)[-1L])' to test for a constant
// vector." // vector."
} }
int[] yDims = getDimsYNode.getDimensions(y.getVector()); int[] yDims = getDimsYNode.getDimensions(y);
if (GetDimAttributeNode.isMatrix(yDims)) { if (GetDimAttributeNode.isMatrix(yDims)) {
if (yDims[0] != n) { if (yDims[0] != n) {
error("incompatible dimensions"); error("incompatible dimensions");
...@@ -731,7 +727,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -731,7 +727,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
ncy = yDims[1]; ncy = yDims[1];
ansmat = true; ansmat = true;
} else { } else {
if (y.getVector().getLength() != n) { if (y.getLength() != n) {
error("incompatible dimensions"); error("incompatible dimensions");
} }
ncy = 1; ncy = 1;
...@@ -749,7 +745,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -749,7 +745,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
break; break;
case 2: /* complete */ case 2: /* complete */
/* did na.omit in R */ /* did na.omit in R */
if (x.getVector().getLength() == 0) { if (x.getLength() == 0) {
error("no complete element pairs"); error("no complete element pairs");
} }
break; break;
...@@ -766,14 +762,15 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -766,14 +762,15 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
default: default:
error("invalid 'use' (computational method)"); error("invalid 'use' (computational method)");
} }
if (empty_err && x.getVector().getLength() == 0) { if (empty_err && x.getLength() == 0) {
error("'x' is empty"); error("'x' is empty");
} }
double[] xData = getReadonlyDataNode.execute(x);
double[] ans = new double[ncx * ncy]; double[] ans = new double[ncx * ncy];
boolean[] sd_0 = new boolean[1]; boolean[] sd_0 = new boolean[1];
evaluate(y, kendall, isCor, n, ncx, ncy, na_fail, everything, empty_err, pair, x, ans, sd_0); evaluate(y, kendall, isCor, n, ncx, ncy, na_fail, everything, empty_err, pair, xData, ans, sd_0);
if (sd_0[0]) { /* only in cor() */ if (sd_0[0]) { /* only in cor() */
warning(RError.Message.SD_ZERO); warning(RError.Message.SD_ZERO);
...@@ -791,7 +788,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -791,7 +788,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
if (ansmat) { /* set dimnames() when applicable */ if (ansmat) { /* set dimnames() when applicable */
RList newDimNames = null; RList newDimNames = null;
if (y == null) { if (y == null) {
RList dimNames = getDimsNamesXNode.getDimNames(x.getVector()); RList dimNames = getDimsNamesXNode.getDimNames(x);
if (dimNames != null) { if (dimNames != null) {
Object names = dimNames.getDataAt(1); Object names = dimNames.getDataAt(1);
if (names != RNull.instance) { if (names != RNull.instance) {
...@@ -799,8 +796,8 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -799,8 +796,8 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
} else { } else {
RList dimNamesX = getDimsNamesXNode.getDimNames(x.getVector()); RList dimNamesX = getDimsNamesXNode.getDimNames(x);
RList dimNamesY = getDimsNamesYNode.getDimNames(y.getVector()); RList dimNamesY = getDimsNamesYNode.getDimNames(y);
Object namesX = dimNamesX.getLength() >= 2 ? dimNamesX.getDataAt(1) : RNull.instance; Object namesX = dimNamesX.getLength() >= 2 ? dimNamesX.getDataAt(1) : RNull.instance;
Object namesY = dimNamesY.getLength() >= 2 ? dimNamesY.getDataAt(1) : RNull.instance; Object namesY = dimNamesY.getLength() >= 2 ? dimNamesY.getDataAt(1) : RNull.instance;
if (namesX != RNull.instance || namesY != RNull.instance) { if (namesX != RNull.instance || namesY != RNull.instance) {
...@@ -818,19 +815,19 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -818,19 +815,19 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
@TruffleBoundary @TruffleBoundary
private static void evaluate(ReadAccessor.Double y, boolean kendall, boolean cor, int n, int ncx, int ncy, boolean na_fail, boolean everything, boolean empty_err, boolean pair, private static void evaluate(RDoubleVector y, boolean kendall, boolean cor, int n, int ncx, int ncy, boolean na_fail, boolean everything, boolean empty_err, boolean pair, double[] xData,
ReadAccessor.Double x, double[] ans, boolean[] sd_0) { double[] ans, boolean[] sd_0) {
if (y == null) { if (y == null) {
if (everything) { /* NA's are propagated */ if (everything) { /* NA's are propagated */
double[] xm = new double[ncx]; double[] xm = new double[ncx];
boolean[] ind = new boolean[ncx]; boolean[] ind = new boolean[ncx];
find_na_1(n, ncx, x, /* --> has_na[] = */ ind); find_na_1(n, ncx, xData, /* --> has_na[] = */ ind);
cov_na_1(n, ncx, x, xm, ind, ans, sd_0, cor, kendall); cov_na_1(n, ncx, xData, xm, ind, ans, sd_0, cor, kendall);
} else if (!pair) { /* all | complete "var" */ } else if (!pair) { /* all | complete "var" */
double[] xm = new double[ncx]; double[] xm = new double[ncx];
boolean[] ind = new boolean[n]; boolean[] ind = new boolean[n];
complete1(n, ncx, x, ind, na_fail); complete1(n, ncx, xData, ind, na_fail);
cov_complete1(n, ncx, x, xm, ind, ans, sd_0, cor, kendall); cov_complete1(n, ncx, xData, xm, ind, ans, sd_0, cor, kendall);
if (empty_err) { if (empty_err) {
boolean indany = false; boolean indany = false;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
...@@ -844,22 +841,23 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -844,22 +841,23 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
} else { /* pairwise "var" */ } else { /* pairwise "var" */
cov_pairwise1(n, ncx, x, ans, sd_0, cor, kendall); cov_pairwise1(n, ncx, xData, ans, sd_0, cor, kendall);
} }
} else { /* Co[vr] (x, y) */ } else { /* Co[vr] (x, y) */
double[] yData = y.getReadonlyData();
if (everything) { if (everything) {
double[] xm = new double[ncx]; double[] xm = new double[ncx];
double[] ym = new double[ncy]; double[] ym = new double[ncy];
boolean[] ind = new boolean[ncx]; boolean[] ind = new boolean[ncx];
boolean[] has_na_y = new boolean[ncy]; boolean[] has_na_y = new boolean[ncy];
find_na_2(n, ncx, ncy, x, y, ind, has_na_y); find_na_2(n, ncx, ncy, xData, yData, ind, has_na_y);
cov_na_2(n, ncx, ncy, x, y, xm, ym, ind, has_na_y, ans, sd_0, cor, kendall); cov_na_2(n, ncx, ncy, xData, yData, xm, ym, ind, has_na_y, ans, sd_0, cor, kendall);
} else if (!pair) { /* all | complete */ } else if (!pair) { /* all | complete */
double[] xm = new double[ncx]; double[] xm = new double[ncx];
double[] ym = new double[ncy]; double[] ym = new double[ncy];
boolean[] ind = new boolean[n]; boolean[] ind = new boolean[n];
complete2(n, ncx, ncy, x, y, ind, na_fail); complete2(n, ncx, ncy, xData, yData, ind, na_fail);
cov_complete2(n, ncx, ncy, x, y, xm, ym, ind, ans, sd_0, cor, kendall); cov_complete2(n, ncx, ncy, xData, yData, xm, ym, ind, ans, sd_0, cor, kendall);
if (empty_err) { if (empty_err) {
boolean indany = false; boolean indany = false;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
...@@ -873,7 +871,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -873,7 +871,7 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
} }
} else { /* pairwise */ } else { /* pairwise */
cov_pairwise2(n, ncx, ncy, x, y, ans, sd_0, cor, kendall); cov_pairwise2(n, ncx, ncy, xData, yData, ans, sd_0, cor, kendall);
} }
} }
} }
...@@ -893,21 +891,19 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 { ...@@ -893,21 +891,19 @@ public abstract class Covcor extends RExternalBuiltinNode.Arg4 {
} }
@Specialization @Specialization
public Object call(RAbstractDoubleVector x, @SuppressWarnings("unused") RNull y, int method, boolean iskendall, public Object call(RAbstractDoubleVector x, @SuppressWarnings("unused") RNull y, int method, boolean iskendall) {
@Cached("create()") VectorReadAccess.Double vecReadAccess) { return corcov(x.materialize(), null, method, iskendall);
return corcov(new ReadAccessor.Double(x, vecReadAccess), null, method, iskendall);
} }
@Specialization @Specialization
public Object call(RAbstractDoubleVector x, RAbstractDoubleVector y, int method, boolean iskendall, public Object call(RAbstractDoubleVector x, RAbstractDoubleVector y, int method, boolean iskendall) {
@Cached("create()") VectorReadAccess.Double xReadAccess, return corcov(x.materialize(), y.materialize(), method, iskendall);
@Cached("create()") VectorReadAccess.Double yReadAccess) {
return corcov(new ReadAccessor.Double(x, xReadAccess), new ReadAccessor.Double(y, yReadAccess), method, iskendall);
} }
private final BranchProfile naInRes = BranchProfile.create(); private final BranchProfile naInRes = BranchProfile.create();
private final ConditionProfile matrixProfile = ConditionProfile.createBinaryProfile(); private final ConditionProfile matrixProfile = ConditionProfile.createBinaryProfile();
@Child private GetReadonlyData.Double getReadonlyDataNode = GetReadonlyData.Double.create();
@Child private GetDimAttributeNode getDimsXNode = GetDimAttributeNode.create(); @Child private GetDimAttributeNode getDimsXNode = GetDimAttributeNode.create();
@Child private GetDimAttributeNode getDimsYNode = GetDimAttributeNode.create(); @Child private GetDimAttributeNode getDimsYNode = GetDimAttributeNode.create();
@Child private GetDimNamesAttributeNode getDimsNamesXNode = GetDimNamesAttributeNode.create(); @Child private GetDimNamesAttributeNode getDimsNamesXNode = GetDimNamesAttributeNode.create();
......
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