/**
* Returns the selection array or vector.
*
* <p>The selSizes array contains sizes of the selectors (number of elements that will be
* returned by it). The idx array contains the indices returned by the selectors (that is the
* indices used to compute the source offset).
*
* <p>The selIdx array contains the position in the selector (when this is equal to the selector
* size the selector has overflown).
*/
public Object execute(RArray source, boolean drop, int exact) throws UnexpectedResultException {
int[] sourceDim = source.dimensions();
boolean mayHaveNA = Selector.initialize(offsets, selectorVals, sourceDim, selSizes, ast);
int[] destDim = Selector.calculateDestinationDimensions(selSizes, !subset || drop);
int destSize = Selector.calculateSizeFromSelectorSizes(selSizes);
RArray dest = Utils.createArray(source, destSize, destDim, null, null); // drop attributes
if (destSize == 0) {
return dest;
}
int offset = 0;
for (; ; ) {
int sourceOffset = offsets[0];
if (sourceOffset == RInt.NA) {
Utils.setNA(dest, offset);
} else {
dest.set(offset, source.getRef(sourceOffset));
}
offset++;
if (offset < destSize) {
if (!mayHaveNA) {
Selector.advanceNoNA(offsets, sourceDim, selectorVals, ast);
} else {
Selector.advance(offsets, sourceDim, selectorVals, ast);
}
} else {
break;
}
}
return dest;
}
@Override
protected <N extends RNode> N replaceChild(RNode oldNode, N newNode) {
assert oldNode != null;
if (callNode == oldNode) {
callNode = newNode;
return adoptInternal(newNode);
}
assert Utils.check(oldNode != callableProvider); // this not must not be rewritten
assert Utils.check(oldNode != xArgProvider);
assert Utils.check(oldNode != yArgProvider);
return super.replaceChild(oldNode, newNode);
}
public static <T extends RArray> T trace(RArray orig) {
if (VIEW_TRACING) {
RArray res;
if (orig instanceof RList) {
res = new RListTracingView((RList) orig);
} else if (orig instanceof RString) {
res = new RStringTracingView((RString) orig);
} else if (orig instanceof RComplex) {
res = new RComplexTracingView((RComplex) orig);
} else if (orig instanceof RDouble) {
res = new RDoubleTracingView((RDouble) orig);
} else if (orig instanceof RInt) {
res = new RIntTracingView((RInt) orig);
} else if (orig instanceof RLogical) {
res = new RLogicalTracingView((RLogical) orig);
} else if (orig instanceof RRaw) {
res = new RRawTracingView((RRaw) orig);
} else {
assert Utils.check(false, "missed view type");
res = orig;
}
return (T) res;
} else {
return (T) orig;
}
}
@Override
public Object execute(Frame frame) {
RAny lhsVal = (RAny) lhs.execute(frame);
RAny rowVal = (RAny) rowExpr.execute(frame);
boolean dropVal =
dropExpr.executeLogical(frame)
!= RLogical.FALSE; // FIXME: what is the correct execution order of these args?
int exactVal = exactExpr.executeLogical(frame);
if (!(lhsVal instanceof RArray)) {
throw RError.getObjectNotSubsettable(ast, lhsVal.typeOf());
}
RArray array = (RArray) lhsVal;
int[] dim = array.dimensions();
if (dim == null || dim.length != 2) {
throw RError.getIncorrectDimensions(getAST());
}
int m = dim[0];
int n = dim[1];
try {
int row;
if (rowVal instanceof ScalarIntImpl) {
row = ((ScalarIntImpl) rowVal).getInt();
} else if (rowVal instanceof ScalarDoubleImpl) {
row = Convert.double2int(((ScalarDoubleImpl) rowVal).getDouble());
} else {
throw new UnexpectedResultException(null);
}
if (row > n || row <= 0) {
throw new UnexpectedResultException(null);
}
int[] ndim;
if (dropVal) {
ndim = null;
} else {
ndim = new int[] {1, n};
}
// note: also could be lazy here
RArray res = Utils.createArray(array, n, ndim, null, null); // drop attributes
int offset = row - 1;
for (int i = 0; i < n; i++) {
res.set(i, array.getRef(offset));
offset += m;
}
return res;
} catch (UnexpectedResultException e) {
SelectorNode selIExpr = Selector.createSelectorNode(ast, true, rowExpr);
SelectorNode selJExpr = Selector.createSelectorNode(ast, true, null);
MatrixRead nn = new MatrixRead(ast, true, lhs, selIExpr, selJExpr, dropExpr, exactExpr);
replace(nn, "install MatrixRead from MatrixRowSubset");
Selector selI = selIExpr.executeSelector(rowVal);
Selector selJ = selJExpr.executeSelector(frame);
return nn.executeLoop(array, selI, selJ, dropVal, exactVal);
}
}
private static Field[] getAllFields(Class cls) {
ArrayList<Field> res = new ArrayList<>();
Class c = cls;
while (c != View.class) {
assert Utils.check(c != null);
res.addAll(Arrays.asList(c.getDeclaredFields()));
c = c.getSuperclass();
}
return res.toArray(new Field[res.size()]);
}
public Site(StackTraceElement[] site) {
this.site = site;
int i = 0;
while (!THIS_FILE_NAME.equals(site[i].getFileName())) {
i++;
}
while (THIS_FILE_NAME.equals(site[i].getFileName())) {
i++;
}
assert Utils.check(i < site.length - 1);
this.offset = i;
}
public static RArray expandXVector(RArray x, int xsize, int count) {
int nsize = xsize * count;
RArray res = Utils.createArray(x, nsize);
int offset = 0;
for (int rep = 0; rep < count; rep++) {
for (int i = 0; i < xsize; i++) {
res.set(offset + i, x.get(i));
}
offset += xsize;
}
return res;
}
public static RArray expandYVector(RArray y, int ysize, int count) {
int size = ysize;
int nsize = size * count;
RArray res = Utils.createArray(y, nsize);
int offset = 0;
for (int elem = 0; elem < size; elem++) {
Object v = y.get(elem);
for (int i = 0; i < count; i++) {
res.set(offset + i, v);
}
offset += count;
}
return res;
}
@Override
public Object execute(
RArray base, Selector selectorI, Selector selectorJ, boolean drop, int exact)
throws UnexpectedResultException {
int[] ndim = base.dimensions();
int m = ndim[0];
int n = ndim[1];
selectorI.start(m, ast);
selectorJ.start(n, ast);
int i = selectorI.nextIndex(ast);
int j = selectorJ.nextIndex(ast);
assert Utils.check(i != RInt.NA && j != RInt.NA); // ensured by subscript selectors
int offset = j * m + i;
if (!(base instanceof RList)) {
return base.boxedGet(offset);
} else {
return ((RList) base).getRAny(offset);
}
}
private static void linkChildren(RArray parentRealView, ViewTrace parentTrace) {
Class viewClass = parentRealView.getClass();
Field[] fields = getAllFields(viewClass);
for (Field f : fields) {
if (f.isSynthetic()) {
continue;
}
Class fieldClass = f.getType();
if (RArray.class.isAssignableFrom(fieldClass)) {
try {
f.setAccessible(true);
Object o = f.get(parentRealView);
if (o instanceof TracingView) {
((TracingView) o).getTrace().parentView = parentTrace;
}
} catch (IllegalAccessException e) {
assert Utils.check(false, "can't read a view field " + e);
}
}
}
}
public static ASTNode create(boolean isSuper, ASTNode lhs, ASTNode rhs) {
if (lhs instanceof SimpleAccessVariable) {
return writeVariable(isSuper, ((SimpleAccessVariable) lhs).symbol, rhs);
} else if (lhs instanceof AccessVector) {
return writeVector(isSuper, (AccessVector) lhs, rhs);
} else if (lhs instanceof FieldAccess) {
return writeField(isSuper, (FieldAccess) lhs, rhs);
} else if (lhs instanceof FunctionCall) {
return writeFunction(isSuper, (FunctionCall) lhs, rhs);
} else if (lhs instanceof Constant) { // TODO: move this to the parser?
RAny value = ((Constant) lhs).getValue();
if (value instanceof RString) {
RString svalue = (RString) value;
if (svalue.size() == 1) {
String name = svalue.getString(0);
return writeVariable(isSuper, RSymbol.getSymbol(name), rhs);
}
}
throw RError.getUnknownObject(rhs); // TODO it's own exception
}
Utils.nyi();
return null;
}
public class RContext {
public static final boolean DEBUG = Utils.getProperty("RConsole.debug.gui", false);
private static boolean debuggingFormat = false;
private static boolean usesTruffleOptimizer =
Truffle.getRuntime().equals("Default Truffle Runtime");
private static ManageError errorManager = new ManageError(System.err);
private static Truffleize truffleize = new Truffleize();
private static final int NCONNECTIONS = 128;
private static final Connection[] connections = new Connection[NCONNECTIONS];
static {
Arrays.fill(connections, null);
}
public static boolean usesTruffleOptimizer() {
return usesTruffleOptimizer;
}
public static boolean debuggingFormat() {
return debuggingFormat;
}
public static boolean debuggingFormat(boolean useDebuggingFormat) {
boolean previous = debuggingFormat;
debuggingFormat = useDebuggingFormat;
return previous;
}
public static RAny eval(ASTNode expr, boolean useDebuggingFormat) {
debuggingFormat(useDebuggingFormat);
return eval(expr);
// NOTE: cannot reset to the original value of debuggingFormat here, because usually the pretty
// printer is
// invoked on the results afterwards by the caller of eval; the pretty printer still depends on
// the correct
// setting of debugging format
}
public static RAny eval(ASTNode expr) {
try {
return (RAny) truffleize.createLazyRootTree(expr).execute(null); // null means top-level
} catch (RError e) {
if (DEBUG) {
e.printStackTrace();
}
error(e); // throws an error
}
throw new Error("Never reached");
}
public static RNode createNode(ASTNode expr) {
return truffleize.createTree(expr);
}
public static RNode createRootNode(ASTNode expr, final RFunction rootEnclosingFunction) {
return new BaseR(expr) {
@Child RNode node = adoptChild(truffleize.createTree(ast, rootEnclosingFunction));
@Override
public Object execute(Frame frame) {
return node.execute(frame);
}
};
}
public static void warning(ASTNode expr, String msg, Object... args) {
errorManager.warning(expr, String.format(msg, args));
}
public static void warning(ASTNode expr, String msg) {
errorManager.warning(expr, msg);
}
public static void warning(RError err) {
errorManager.warning(err);
}
public static void error(ASTNode expr, String msg) {
errorManager.error(expr, msg);
}
public static void error(RError err) {
errorManager.error(err);
}
public static int allocateConnection(Connection connection) {
for (int i = 0; i < NCONNECTIONS; i++) {
if (connections[i] == null) {
connections[i] = connection;
return i;
}
}
return -1;
}
/** Release a connection currently in use. */
public static void freeConnection(int i) {
assert Utils.check(connections[i] != null);
connections[i] = null;
}
/** Return a connection or null. */
public static Connection getConnection(int i) {
return i >= 0 && i < NCONNECTIONS ? connections[i] : null;
}
// note: GNUR currently means not only the GNU-R library, but also some other native code, under
// licenses compatible with GPL
private static int hasGNUR = -1;
public static boolean hasGNUR() {
if (hasGNUR == -1) {
try {
System.loadLibrary("gnurglue");
hasGNUR = 1;
} catch (Throwable t) {
hasGNUR = 0;
}
}
return hasGNUR == 1;
}
public static ASTNode parseFile(ANTLRStringStream inputStream) {
CommonTokenStream tokens = new CommonTokenStream();
RLexer lexer = new RLexer(inputStream);
tokens.setTokenSource(lexer);
RParser parser = new RParser(tokens);
try {
return parser.script();
} catch (RecognitionException e) {
Console.parseError(parser, e);
return null;
}
}
}
/** Release a connection currently in use. */
public static void freeConnection(int i) {
assert Utils.check(connections[i] != null);
connections[i] = null;
}
private static void dumpView(int depth, ViewTrace trace) {
printedIndividualViews.add(trace);
ps.println(trace.realView + " size = " + trace.realView.size());
if (TRACE_ALLOCATION_SITE) {
indent(depth);
ps.print(" allocationSite =");
Site.printSite(trace.allocationSite);
ps.println();
}
int unused = trace.unusedElements();
int redundant = trace.redundantGets();
boolean singleUse;
Site[] useSites;
if (TRACE_USE_SITES) {
useSites = trace.useSites.toArray(new Site[trace.useSites.size()]);
singleUse = (useSites.length == 1);
} else if (TRACE_SINGLE_USE_SITE) {
useSites = null;
singleUse = !trace.multipleUseSites;
} else {
useSites = null;
singleUse = false;
}
if (singleUse) {
indent(depth);
ps.print(" singleUseSite = US");
Site.printSite(useSites != null ? useSites[0] : trace.singleUseSite);
if (trace.getCount > 0) {
ps.println(" (get)");
} else if (trace.sumCount > 0) {
ps.println(" (sum)");
} else {
ps.println(" (materialize)");
}
} else if (trace.getCount > 0) {
if (TRACE_FIRST_GET_SITE) {
indent(depth);
ps.print(" firstGetSite =");
Site.printSite(trace.firstGetSite);
ps.println();
}
if (trace.materializeCount == 0 && trace.sumCount == 0) {
if (unused > 0) {
indent(depth);
ps.println(" unusedElements = " + unused);
}
if (redundant > 0) {
indent(depth);
ps.println(" redundantGets = " + redundant + " (no materialize, sum)");
}
}
} else {
if (trace.materializeCount == 0 && trace.sumCount == 0) {
indent(depth);
ps.println(" UNUSED");
} else {
indent(depth);
ps.println(
" materializeCount = "
+ trace.materializeCount
+ " sumCount = "
+ trace.sumCount
+ " getCount = "
+ trace.getCount);
}
}
if (TRACE_FIRST_MATERIALIZE_SITE && trace.materializeCount > 0 && !singleUse) {
indent(depth);
ps.print(" firstMaterializeSite =");
Site.printSite(trace.firstMaterializeSite);
ps.println();
}
if (TRACE_FIRST_SUM_SITE && trace.sumCount > 0 && !singleUse) {
indent(depth);
ps.print(" firstSumSite =");
Site.printSite(trace.firstSumSite);
ps.println();
}
if (TRACE_USE_SITES) {
if (useSites.length != 1) {
indent(depth);
ps.println(" useSites (" + useSites.length + "):");
for (Site s : useSites) {
indent(depth);
ps.print(" US");
Site.printSite(s);
ps.println();
}
}
}
ps.println();
RArray view = trace.realView;
Class viewClass = view.getClass();
Field[] fields = getAllFields(viewClass);
boolean printedField = false;
for (Field f : fields) {
if (f.isSynthetic()) {
continue;
}
Class fieldClass = f.getType();
if (RArray.class.isAssignableFrom(fieldClass)) {
continue; // these later
}
indent(depth);
ps.print(" " + f.getName() + " ");
try {
f.setAccessible(true);
ps.println(f.get(view));
printedField = true;
} catch (IllegalAccessException e) {
assert Utils.check(false, "can't read a view field " + e);
}
}
boolean printNewline = printedField;
for (Field f : fields) {
if (f.isSynthetic()) {
continue;
}
Class fieldClass = f.getType();
if (!RArray.class.isAssignableFrom(fieldClass)) {
continue;
}
if (printNewline) {
ps.println();
printNewline = false;
}
indent(depth);
ps.print(" " + f.getName() + " ");
try {
f.setAccessible(true);
Object o = f.get(view);
if (o instanceof TracingView) {
ps.print("VIEW ");
TracingView child = (TracingView) o;
dumpView(depth + 2, child.getTrace());
} else {
ps.print("ARRAY " + o + " size = " + ((RArray) o).size());
if (o instanceof View) {
ps.println("MISSED VIEW " + o);
}
}
ps.println();
} catch (IllegalAccessException e) {
assert Utils.check(false, "can't read a view field " + e);
}
}
}
private static void extractViewPattern(int depth, ViewTrace trace, StringBuilder p) {
if (!processedViewsForPatterns.add(trace)) {
p.append("(ALIASED) ");
}
p.append(trace.realView.getClass() + " size = " + trace.realView.size() + "\n");
indent(depth, p);
p.append(" use:");
if (trace.materializeCount == 0 && trace.sumCount == 0 && trace.getCount == 0) {
p.append(" UNUSED");
} else {
if (trace.getCount > 0) {
p.append(" get");
}
if (trace.materializeCount > 0) {
p.append(" materialize");
}
if (trace.sumCount > 0) {
p.append(" sum");
}
}
p.append("\n");
if (false) {
p.append(" allocationSite =");
Site.printSite(trace.allocationSite, p);
p.append("\n");
indent(depth, p);
}
RArray view = trace.realView;
Class viewClass = view.getClass();
Field[] fields = getAllFields(viewClass);
boolean printedField = false;
for (Field f : fields) {
if (f.isSynthetic()) {
continue;
}
Class fieldClass = f.getType();
if (RArray.class.isAssignableFrom(fieldClass)) {
continue; // these later
}
indent(depth, p);
p.append(" " + f.getName() + " ");
try {
f.setAccessible(true);
Object o = f.get(view);
p.append(o == null ? "null (" + fieldClass + ")" : o.getClass());
p.append("\n");
printedField = true;
} catch (IllegalAccessException e) {
assert Utils.check(false, "can't read a view field " + e);
}
}
boolean printNewline = printedField;
for (Field f : fields) {
if (f.isSynthetic()) {
continue;
}
Class fieldClass = f.getType();
if (!RArray.class.isAssignableFrom(fieldClass)) {
continue;
}
if (printNewline) {
p.append("\n");
printNewline = false;
}
indent(depth, p);
p.append(" " + f.getName() + " ");
try {
f.setAccessible(true);
Object o = f.get(view);
if (o instanceof TracingView) {
p.append("VIEW ");
TracingView child = (TracingView) o;
extractViewPattern(depth + 2, child.getTrace(), p);
} else {
p.append("ARRAY " + o.getClass() + " size = " + ((RArray) o).size());
if (o instanceof View) {
ps.println("MISSED VIEW " + o);
}
}
p.append("\n");
} catch (IllegalAccessException e) {
assert Utils.check(false, "can't read a view field " + e);
}
}
}
public RAny outer(Frame frame, RAny xarg, RAny yarg, RAny farg) {
// LICENSE: transcribed code from GNU R, which is licensed under GPL
if (!(xarg instanceof RArray && yarg instanceof RArray)) {
Utils.nyi("unsupported type");
return null;
}
RArray x = (RArray) xarg;
RArray y = (RArray) yarg;
int xsize = x.size();
int ysize = y.size();
RArray expy;
RArray expx;
if (EAGER) {
x = x.materialize(); // FIXME: probably unnecessary (both x and y), could be done on-the-fly in the expansion methods
y = y.materialize();
if (y instanceof DoubleImpl) {
expy = expandYVector((DoubleImpl) y, ysize, xsize);
} else if (y instanceof IntImpl) {
expy = expandYVector((IntImpl) y, ysize, xsize);
} else {
expy = expandYVector(y, ysize, xsize);
}
if (xsize > 0) {
if (x instanceof DoubleImpl) {
expx = expandXVector((DoubleImpl) x, xsize, ysize);
} else if (x instanceof IntImpl) {
expx = expandXVector((IntImpl) x, xsize, ysize);
} else {
expx = expandXVector(x, xsize, ysize);
}
} else {
expx = x;
}
} else {
if (y instanceof RInt) {
expy = lazyExpandYVector((RInt) y, ysize, xsize);
} else {
throw Utils.nyi();
}
if (xsize > 0) {
if (x instanceof RInt) {
expx = lazyExpandXVector((RInt) x, xsize, ysize);
} else {
throw Utils.nyi();
}
} else {
expx = x;
}
}
xArgProvider.setValue(expx);
yArgProvider.setValue(expy);
callableProvider.matchAndSet(frame, farg);
RArray res = (RArray) callNode.execute(frame);
int[] dimx = x.dimensions();
int[] dimy = y.dimensions();
int[] dim;
if (dimx == null) {
if (dimy == null) {
dim = new int[]{xsize, ysize};
} else {
dim = new int[1 + dimy.length];
dim[0] = xsize;
System.arraycopy(dimy, 0, dim, 1, dimy.length);
}
} else {
if (dimy == null) {
dim = new int[dimx.length + 1];
System.arraycopy(dimx, 0, dim, 0, dimx.length);
dim[dimx.length] = ysize;
} else {
dim = new int[dimx.length + dimy.length];
System.arraycopy(dimx, 0, dim, 0, dimx.length);
System.arraycopy(dimy, 0, dim, dimx.length, dimy.length);
}
}
return res.setDimensions(dim); // triggers materialization of the result
}
@Override public RNode create(ASTNode call, RSymbol[] names, RNode[] exprs) {
/*ArgumentInfo ia = */
check(call, names, exprs);
if (names.length == 1) {
return new Builtin.Builtin1(call, names, exprs) {
@Override public RAny doBuiltIn(Frame frame, RAny xarg) {
// x must be matrix-like
// method is pearson
// use is everything
RDouble xd;
if (xarg instanceof RDouble || xarg instanceof RInt || xarg instanceof RLogical) {
xd = xarg.asDouble().materialize();
} else {
if (xarg instanceof RArray) {
throw RError.getXNumeric(ast);
} else {
throw RError.getSupplyXYMatrix(ast);
}
}
int[] dim = xd.dimensions();
if (dim == null || dim.length != 2) {
throw RError.getSupplyXYMatrix(ast);
}
int nrow = dim[0];
int ncol = dim[1];
double[] res = new double[ncol * ncol];
double[] x = xd.getContent();
boolean[] hasNA = new boolean[ncol];
boolean anyNA = columnsNAMap(x, nrow, ncol, hasNA);
int n1 = nrow - 1;
boolean sdZero = false;
if (!anyNA) {
double[] colMeans = columnMeansNoNA(x, nrow, ncol);
for (int i = 0; i < ncol ; i++) {
double imean = colMeans[i];
int ioffset = i * nrow;
for (int j = 0; j <= i; j++) {
double jmean = colMeans[j];
int joffset = j * nrow;
double sum = 0;
for (int k = 0; k < nrow; k++) {
sum += (x[ioffset + k] - imean) * (x[joffset + k] - jmean);
}
double tmp = sum / n1;
res[j * ncol + i] = tmp;
res[i * ncol + j] = tmp;
}
}
double[] srcov = colMeans; // colMeans no longer needed
for (int i = 0; i < ncol; i++) {
srcov[i] = Math.sqrt(res[i * ncol + i]);
}
for (int i = 0; i < ncol; i++) {
for (int j = 0; j < i; j++) {
if (srcov[i] == 0 || srcov[j] == 0) {
sdZero = true;
res[j * ncol + i] = RDouble.NA;
res[i * ncol + j] = RDouble.NA;
} else {
double tmp = res[i * ncol + j] / (srcov[i] * srcov[j]);
if (tmp > 1) {
tmp = 1;
}
res[j * ncol + i] = tmp;
res[i * ncol + j] = tmp;
}
}
res[i * ncol + i] = 1;
}
} else {
double[] colMeans = columnMeans(x, nrow, ncol, hasNA);
for (int i = 0; i < ncol ; i++) {
if (hasNA[i]) {
for (int j = 0; j <= i; j++ ) {
res[j * ncol + i] = RDouble.NA; // FIXME: break this into two loops?
res[i * ncol + j] = RDouble.NA;
}
continue;
}
double imean = colMeans[i];
int ioffset = i * nrow;
for (int j = 0; j <= i; j++) {
if (hasNA[j]) {
res[j * ncol + i] = RDouble.NA;
res[i * ncol + j] = RDouble.NA;
continue;
}
double jmean = colMeans[j];
int joffset = j * nrow;
double sum = 0;
for (int k = 0; k < nrow; k++) {
sum += (x[ioffset + k] - imean) * (x[joffset + k] - jmean);
}
double tmp = sum / n1;
res[j * ncol + i] = tmp;
res[i * ncol + j] = tmp;
}
}
double[] srcov = colMeans; // colMeans no longer needed
for (int i = 0; i < ncol; i++) {
if (!hasNA[i]) {
srcov[i] = Math.sqrt(res[i * ncol + i]);
}
}
for (int i = 0; i < ncol; i++) {
if (!hasNA[i]) {
for (int j = 0; j < i; j++) {
if (srcov[i] == 0 || srcov[j] == 0) {
sdZero = true;
res[j * ncol + i] = RDouble.NA;
res[i * ncol + j] = RDouble.NA;
} else {
double tmp = res[i * ncol + j] / (srcov[i] * srcov[j]);
if (tmp > 1) {
tmp = 1;
}
res[j * ncol + i] = tmp;
res[i * ncol + j] = tmp;
}
}
}
res[i * ncol + i] = 1;
}
}
if (sdZero) {
RContext.warning(ast, RError.SD_ZERO);
}
return RDouble.RDoubleFactory.getFor(res, new int[] {ncol, ncol}, null);
}
};
}
// final int xPosition = ia.position("x");
// final int yPosition = ia.position("y");
// final int usePosition = ia.position("use");
// final int methodPosition = ia.position("method");
Utils.nyi("finish cor");
return null;
}
@Override
public Object execute(Frame frame) {
RAny lhsVal = (RAny) lhs.execute(frame);
Object rowFromVal = rowFromExpr.execute(frame);
Object rowToVal = rowToExpr.execute(frame);
Object colFromVal = colFromExpr.execute(frame);
Object colToVal = colToExpr.execute(frame);
boolean dropVal =
dropExpr.executeLogical(frame)
!= RLogical.FALSE; // FIXME: what is the correct execution order of these args?
int exactVal = exactExpr.executeLogical(frame);
if (!(lhsVal instanceof RArray)) {
throw RError.getObjectNotSubsettable(ast, lhsVal.typeOf());
}
RArray array = (RArray) lhsVal;
try {
int rowFrom = extractLimit(rowFromVal); // zero-based
int rowTo = extractLimit(rowToVal);
int colFrom = extractLimit(colFromVal);
int colTo = extractLimit(colToVal);
int[] dim = array.dimensions();
if (dim == null || dim.length != 2) {
throw RError.getIncorrectDimensions(getAST());
}
int m = dim[0];
int n = dim[1];
int rowStep;
int rowSize;
if (rowFrom <= rowTo) {
rowStep = 1;
if (rowTo > m) {
throw new UnexpectedResultException(null);
}
rowSize = rowTo - rowFrom + 1;
} else {
rowStep = -1;
if (rowFrom > m) {
throw new UnexpectedResultException(null);
}
rowSize = rowFrom - rowTo + 1;
}
int colStep;
int colSize;
if (colFrom <= colTo) {
colStep = 1;
if (colTo > n) {
throw new UnexpectedResultException(null);
}
colSize = colTo - colFrom + 1;
} else {
colStep = -1;
if (colFrom > n) {
throw new UnexpectedResultException(null);
}
colSize = colFrom - colTo + 1;
}
int[] ndim;
if (!dropVal || (rowSize > 1 && colSize > 1)) {
ndim = new int[] {rowSize, colSize};
} else {
ndim = null;
}
int size = rowSize * colSize;
RArray res = Utils.createArray(array, size, ndim, null, null); // drop attributes
if (colStep == 1 && rowStep == 1) {
int j = colFrom * m + rowFrom; // j - index to source matrix
int jmax = j + rowSize;
int jadvance = m - rowSize;
for (int i = 0; i < size; i++) {
res.set(i, array.getRef(j++)); // i - index to target matrix
if (j == jmax) {
j += jadvance;
jmax += m;
}
}
} else {
int i = 0;
// NOTE: here we know that colFrom != colTo and rowFrom != rowTo
for (int col = colFrom; col != colTo + colStep; col += colStep) {
for (int row = rowFrom; row != rowTo + rowStep; row += rowStep) {
res.set(i++, array.getRef(col * m + row));
}
}
}
return res;
} catch (UnexpectedResultException e) {
// FIXME: clean this up; does Colon need to be package-private?
ASTNode rowAST = rowFromExpr.getAST().getParent();
Builtin rowColon =
(Builtin)
Primitives.getCallFactory(RSymbol.getSymbol(":"), null)
.create(rowAST, rowFromExpr, rowToExpr);
SelectorNode selIExpr = Selector.createSelectorNode(rowAST, true, rowColon);
ASTNode colAST = colFromExpr.getAST().getParent();
Builtin colColon =
(Builtin)
Primitives.getCallFactory(RSymbol.getSymbol(":"), null)
.create(colAST, colFromExpr, colToExpr);
SelectorNode selJExpr = Selector.createSelectorNode(ast, true, colColon);
MatrixRead nn = new MatrixRead(ast, true, lhs, selIExpr, selJExpr, dropExpr, exactExpr);
replace(nn, "install MatrixRead from MatrixSequenceSubset");
Selector selI =
selIExpr.executeSelector(
rowColon.doBuiltIn(frame, new RAny[] {(RAny) rowFromVal, (RAny) rowToVal}));
Selector selJ =
selJExpr.executeSelector(
colColon.doBuiltIn(frame, new RAny[] {(RAny) colFromVal, (RAny) colToVal}));
return nn.executeLoop(array, selI, selJ, dropVal, exactVal);
}
}
@Override
public Object execute(Frame frame) {
RAny lhsVal = (RAny) lhs.execute(frame);
RAny colVal = (RAny) columnExpr.execute(frame);
boolean dropVal =
dropExpr.executeLogical(frame)
!= RLogical.FALSE; // FIXME: what is the correct execution order of these args?
int exactVal = exactExpr.executeLogical(frame);
// TODO: GNU-R has different behavior when selecting from arrays that have some dimension zero
if (!(lhsVal instanceof RArray)) {
throw RError.getObjectNotSubsettable(ast, lhsVal.typeOf());
}
RArray array = (RArray) lhsVal;
int[] dim = array.dimensions();
if (dim == null || dim.length != nSelectors) {
throw RError.getIncorrectDimensions(getAST());
}
int n = dim[nSelectors - 1]; // limit for the column (last dimension)
try {
int col;
if (colVal instanceof ScalarIntImpl) {
col = ((ScalarIntImpl) colVal).getInt();
} else if (colVal instanceof ScalarDoubleImpl) {
col = Convert.double2int(((ScalarDoubleImpl) colVal).getDouble());
} else {
throw new UnexpectedResultException(null);
}
if (col > n || col <= 0) {
throw new UnexpectedResultException(null);
}
int[] ndim;
int m; // size of the result
if (dropVal) {
boolean hasNonTrivialDimension = false;
boolean resultIsVector = true;
m = 1;
for (int i = 0; i < nSelectors - 1; i++) {
int d = dim[i];
if (d != 1) {
if (hasNonTrivialDimension) {
resultIsVector = false;
} else {
hasNonTrivialDimension = true;
}
}
m *= d;
}
if (resultIsVector) {
ndim = null;
} else {
ndim = new int[nSelectors - 1];
System.arraycopy(dim, 0, ndim, 0, ndim.length);
}
} else {
ndim = new int[nSelectors];
ndim[nSelectors - 1] = 1;
m = 1;
for (int i = 0; i < ndim.length - 1; i++) {
int d = dim[i];
ndim[i] = d;
m *= d;
}
}
// note: also could be lazy here
RArray res = Utils.createArray(array, m, ndim, null, null); // drop attributes
int offset = (col - 1) * m; // note: col is 1-based
for (int i = 0; i < m; i++) {
res.set(i, array.getRef(offset + i));
}
return res;
} catch (UnexpectedResultException e) {
SelectorNode[] selectorExprs = new SelectorNode[nSelectors];
for (int i = 0; i < nSelectors - 1; i++) {
selectorExprs[i] = Selector.createSelectorNode(ast, true, null);
}
selectorExprs[nSelectors - 1] = Selector.createSelectorNode(ast, true, columnExpr);
GenericRead gr = new GenericRead(ast, true, lhs, selectorExprs, dropExpr, exactExpr);
replace(gr, "install GenericRead from ArrayColumnSubset");
for (int i = 0; i < nSelectors - 1; i++) {
gr.selectorVals[i] = selectorExprs[i].executeSelector(frame);
}
gr.selectorVals[nSelectors - 1] = selectorExprs[nSelectors - 1].executeSelector(colVal);
return gr.executeLoop(array, dropVal, exactVal);
}
}
public Object execute(
RArray source, Selector selectorI, Selector selectorJ, boolean drop, int exact)
throws UnexpectedResultException {
assert Utils.check(subset);
int[] ndim = source.dimensions();
int m = ndim[0];
int n = ndim[1];
selectorI.start(m, ast);
selectorJ.start(n, ast);
int nm = selectorI.size();
int nn = selectorJ.size();
boolean mayHaveNA = selectorI.mayHaveNA() || selectorJ.mayHaveNA();
int nsize = nm * nn;
if ((nm != 1 && nn != 1) || !drop) {
ndim = new int[] {nm, nn};
} else {
ndim = null;
}
RArray res = Utils.createArray(source, nsize, ndim, null, null); // drop attributes
if (!mayHaveNA) {
int resoffset = 0;
for (int nj = 0; nj < nn; nj++) {
int j = selectorJ.nextIndex(ast);
int srcoffset = j * m;
for (int ni = 0; ni < nm; ni++) {
int i = selectorI.nextIndex(ast);
Object value =
source.getRef(
srcoffset
+ i); // FIXME: check overflow? (the same is at many locations, whenever
// indexing a matrix)
res.set(resoffset++, value);
}
selectorI.restart();
}
} else {
for (int nj = 0; nj < nn; nj++) {
int j = selectorJ.nextIndex(ast);
if (j != RInt.NA) {
selectorI.restart();
for (int ni = 0; ni < nm; ni++) {
int offset = nj * nm + ni;
int i = selectorI.nextIndex(ast);
if (i != RInt.NA) {
Object value;
value =
source.getRef(
j * m
+ i); // FIXME: check overflow? (the same is at many locations, whenever
// indexing a matrix)
res.set(offset, value);
} else {
Utils.setNA(res, offset);
}
}
} else {
for (int ni = 0; ni < nm; ni++) {
Utils.setNA(res, nj * nm + ni);
}
}
}
}
return res;
}