Lots of optimizations to Lepton, including creating CompiledExpression class.

libraries/lepton/include/Lepton.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "lepton/CompiledExpression.h"
 #include "lepton/CustomFunction.h"
 #include "lepton/ExpressionProgram.h"
 #include "lepton/ExpressionTreeNode.h"

libraries/lepton/include/lepton/CompiledExpression.h

+#ifndef LEPTON_COMPILED_EXPRESSION_H_
+#define LEPTON_COMPILED_EXPRESSION_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <set>
+#include <string>
+#include <vector>
+
+namespace Lepton {
+
+class Operation;
+class ParsedExpression;
+
+/**
+ * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate
+ * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation
+ * is visible.
+ * 
+ * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.
+ */
+
+class LEPTON_EXPORT CompiledExpression {
+public:
+    CompiledExpression();
+    CompiledExpression(const CompiledExpression& expression);
+    ~CompiledExpression();
+    CompiledExpression& operator=(const CompiledExpression& expression);
+    /**
+     * Get the names of all variables used by this expression.
+     */
+    const std::set<std::string>& getVariables() const;
+    /**
+     * Get a reference to the memory location where the value of a particular variable is stored.  This can be used
+     * to set the value of the variable before calling evaluate().
+     */
+    double& getVariableReference(const std::string& name);
+    /**
+     * Evaluate the expression.  The values of all variables should have been set before calling this.
+     */
+    double evaluate() const;
+private:
+    friend class ParsedExpression;
+    CompiledExpression(const ParsedExpression& expression);
+    void compileExpression(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    int findTempIndex(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    std::vector<std::vector<int> > arguments;
+    std::vector<int> target;
+    std::vector<Operation*> operation;
+    std::map<std::string, int> variableIndices;
+    std::set<std::string> variableNames;
+    mutable std::vector<double> workspace;
+    mutable std::vector<double> argValues;
+    std::map<std::string, double> dummyVariables;
+};
+
+} // namespace Lepton
+
+#endif /*LEPTON_COMPILED_EXPRESSION_H_*/

libraries/lepton/include/lepton/ExpressionProgram.h

@@ -48,9 +48,7 @@ class ParsedExpression;
  * evaluated and the result is pushed back onto the stack.  At the end, the stack contains a single value,
  * which is the value of the expression.
  *
- * An ExpressionProgram is created by calling createProgram() on a ParsedExpression.  It can generally be evaluated
- * more quickly than the ParsedExpression itself, so when you need to evaluate an expression many times, it is
- * most efficient to create an ExpressionProgram from it.
+ * An ExpressionProgram is created by calling createProgram() on a ParsedExpression.
  */
 
 class LEPTON_EXPORT ExpressionProgram {

libraries/lepton/include/lepton/Operation.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -965,6 +965,8 @@ private:
 class LEPTON_EXPORT Operation::PowerConstant : public Operation {
 public:
     PowerConstant(double value) : value(value) {
+        intValue = (int) value;
+        isIntPower = (intValue == value);
     }
     std::string getName() const {
         std::stringstream name;
@@ -981,7 +983,26 @@ public:
         return new PowerConstant(value);
     }
     double evaluate(double* args, const std::map<std::string, double>& variables) const {
-        return std::pow(args[0], value);
+        if (isIntPower) {
+            // Integer powers can be computed much more quickly by repeated multiplication.
+            
+            int exponent = intValue;
+            double base = args[0];
+            if (exponent < 0) {
+                exponent = -exponent;
+                base = 1.0/base;
+            }
+            double result = 1.0;
+            while (exponent != 0) {
+                if ((exponent&1) == 1)
+                    result *= base;
+                base *= base;
+                exponent = exponent>>1;
+           }
+           return result;
+        }
+        else
+            return std::pow(args[0], value);
     }
     ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
     double getValue() const {
@@ -996,6 +1017,8 @@ public:
     }
 private:
     double value;
+    int intValue;
+    bool isIntPower;
 };
 
 class LEPTON_EXPORT Operation::Min : public Operation {

libraries/lepton/include/lepton/ParsedExpression.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009=2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,6 +39,7 @@
 
 namespace Lepton {
 
+class CompiledExpression;
 class ExpressionProgram;
 
 /**
@@ -97,6 +98,10 @@ public:
      * Create an ExpressionProgram that represents the same calculation as this expression.
      */
     ExpressionProgram createProgram() const;
+    /**
+     * Create a CompiledExpression that represents the same calculation as this expression.
+     */
+    CompiledExpression createCompiledExpression() const;
     /**
      * Create a new ParsedExpression which is identical to this one, except that the names of some
      * variables have been changed.

libraries/lepton/src/CompiledExpression.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "lepton/CompiledExpression.h"
+#include "lepton/Operation.h"
+#include "lepton/ParsedExpression.h"
+#include <utility>
+
+using namespace Lepton;
+using namespace std;
+
+CompiledExpression::CompiledExpression() {
+}
+
+CompiledExpression::CompiledExpression(const ParsedExpression& expression) {
+    ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized.
+    vector<pair<ExpressionTreeNode, int> > temps;
+    compileExpression(expr.getRootNode(), temps);
+}
+
+CompiledExpression::~CompiledExpression() {
+    for (int i = 0; i < (int) operation.size(); i++)
+        if (operation[i] != NULL)
+            delete operation[i];
+}
+
+CompiledExpression::CompiledExpression(const CompiledExpression& expression) {
+    *this = expression;
+}
+
+CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expression) {
+    arguments = expression.arguments;
+    target = expression.target;
+    variableIndices = expression.variableIndices;
+    variableNames = expression.variableNames;
+    workspace.resize(expression.workspace.size());
+    argValues.resize(expression.argValues.size());
+    operation.resize(expression.operation.size());
+    for (int i = 0; i < (int) operation.size(); i++)
+        operation[i] = expression.operation[i]->clone();
+    return *this;
+}
+
+void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, int> >& temps) {
+    if (findTempIndex(node, temps) != -1)
+        return; // We have already processed a node identical to this one.
+    
+    // Process the child nodes.
+    
+    vector<int> args;
+    for (int i = 0; i < node.getChildren().size(); i++) {
+        compileExpression(node.getChildren()[i], temps);
+        args.push_back(findTempIndex(node.getChildren()[i], temps));
+    }
+    
+    // Process this node.
+    
+    if (node.getOperation().getId() == Operation::VARIABLE) {
+        variableIndices[node.getOperation().getName()] = workspace.size();
+        variableNames.insert(node.getOperation().getName());
+    }
+    else {
+        int stepIndex = arguments.size();
+        arguments.push_back(vector<int>());
+        target.push_back(workspace.size());
+        operation.push_back(node.getOperation().clone());
+        if (args.size() == 0)
+            arguments[stepIndex].push_back(0); // The value won't actually be used.  We just need something there.
+        else {
+            // If the arguments are sequential, we can just pass a pointer to the first one.
+            
+            bool sequential = true;
+            for (int i = 1; i < args.size(); i++)
+                if (args[i] != args[i-1]+1)
+                    sequential = false;
+            if (sequential)
+                arguments[stepIndex].push_back(args[0]);
+            else {
+                arguments[stepIndex] = args;
+                if (args.size() > argValues.size())
+                    argValues.resize(args.size(), 0.0);
+            }
+        }
+    }
+    temps.push_back(make_pair(node, workspace.size()));
+    workspace.push_back(0.0);
+}
+
+int CompiledExpression::findTempIndex(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, int> >& temps) {
+    for (int i = 0; i < (int) temps.size(); i++)
+        if (temps[i].first == node)
+            return i;
+    return -1;
+}
+
+const set<string>& CompiledExpression::getVariables() const {
+    return variableNames;
+}
+
+double& CompiledExpression::getVariableReference(const string& name) {
+    map<string, int>::iterator index = variableIndices.find(name);
+    if (index == variableIndices.end())
+        throw Exception("getVariableReference: Unknown variable '"+name+"'");
+    return workspace[index->second];
+}
+
+double CompiledExpression::evaluate() const {
+    // Loop over the operations and evaluate each one.
+    
+    for (int step = 0; step < operation.size(); step++) {
+        const vector<int>& args = arguments[step];
+        if (args.size() == 1)
+            workspace[target[step]] = operation[step]->evaluate(&workspace[args[0]], dummyVariables);
+        else {
+            for (int i = 0; i < args.size(); i++)
+                argValues[i] = workspace[args[i]];
+            workspace[target[step]] = operation[step]->evaluate(&argValues[0], dummyVariables);
+        }
+    }
+    return workspace[workspace.size()-1];
+}

libraries/lepton/src/ExpressionProgram.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -93,14 +93,13 @@ double ExpressionProgram::evaluate() const {
 }
 
 double ExpressionProgram::evaluate(const std::map<std::string, double>& variables) const {
-    vector<double> args(max(maxArgs, 1));
-    vector<double> stack(stackSize);
-    int stackPointer = 0;
+    vector<double> stack(stackSize+1);
+    int stackPointer = stackSize;
     for (int i = 0; i < (int) operations.size(); i++) {
         int numArgs = operations[i]->getNumArguments();
-        for (int j = 0; j < numArgs; j++)
-            args[j] = stack[--stackPointer];
-        stack[stackPointer++] = operations[i]->evaluate(&args[0], variables);
+        double result = operations[i]->evaluate(&stack[stackPointer], variables);
+        stackPointer += numArgs-1;
+        stack[stackPointer] = result;
     }
-    return stack[0];
+    return stack[stackSize-1];
 }

libraries/lepton/src/ParsedExpression.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "lepton/ParsedExpression.h"
+#include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 #include "lepton/Operation.h"
 #include <limits>
@@ -294,6 +295,10 @@ ExpressionProgram ParsedExpression::createProgram() const {
     return ExpressionProgram(*this);
 }
 
+CompiledExpression ParsedExpression::createCompiledExpression() const {
+    return CompiledExpression(*this);
+}
+
 ParsedExpression ParsedExpression::renameVariables(const map<string, string>& replacements) const {
     return ParsedExpression(renameNodeVariables(getRootNode(), replacements));
 }

tests/TestParser.cpp

@@ -56,6 +56,12 @@ void verifyEvaluation(const string& expression, double expectedValue) {
     ExpressionProgram program = parsed.createProgram();
     value = program.evaluate();
     ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
+
+    // Create a CompiledExpression and see if that also gives the same result.
+
+    CompiledExpression compiled = parsed.createCompiledExpression();
+    value = compiled.evaluate();
+    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
 }
 
 /**
@@ -86,6 +92,16 @@ void verifyEvaluation(const string& expression, double x, double y, double expec
     value = program.evaluate(variables);
     ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
 
+    // Create a CompiledExpression and see if that also gives the same result.
+
+    CompiledExpression compiled = parsed.createCompiledExpression();
+    if (compiled.getVariables().find("x") != compiled.getVariables().end())
+        compiled.getVariableReference("x") = x;
+    if (compiled.getVariables().find("y") != compiled.getVariables().end())
+        compiled.getVariableReference("y") = y;
+    value = compiled.evaluate();
+    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
+
     // Make sure that variable renaming works.
 
     variables.clear();