Added NumExprCapability to VCell Expressions

vcell-math/src/main/java/cbit/vcell/parser/ASTAndNode.java

@@ -178,6 +178,14 @@ public String infixString(int lang)
 			  buffer.append(jjtGetChild(i).infixString(lang));
 		  }
 		  buffer.append("))");
+	  }else if (lang == LANGUAGE_NUM_EXPR) {
+		  int numChildren = jjtGetNumChildren();
+		  for (int i=0;i<numChildren;i++){
+			  if (i>0) buffer.append(" & ");
+			  buffer.append("(0.0!=");
+			  buffer.append(jjtGetChild(i).infixString(lang));
+			  buffer.append(")");
+		  }
 	  }else{
 		  for (int i=0;i<jjtGetNumChildren();i++){
 			if (i>0) {

vcell-math/src/main/java/cbit/vcell/parser/ASTFloatNode.java

@@ -146,7 +146,11 @@ public String infixString(int lang)
               if (value == Double.POSITIVE_INFINITY) return "float('inf')";
               if (value == Double.NEGATIVE_INFINITY) return "float('-inf')";
               return value.toString();
-          } else {
+          } else if (lang == LANGUAGE_NUM_EXPR) {
+			  if (value == Double.POSITIVE_INFINITY) return "inf";
+			  if (value == Double.NEGATIVE_INFINITY) return "-inf";
+			  return value.toString();
+		  } else {
 		      return value.toString();
 		  }
 	  }

vcell-math/src/main/java/cbit/vcell/parser/ASTFuncNode.java

@@ -134,6 +134,29 @@ public final String getPythonTranslation() {
 				default -> "math." + getName();
 			};
 		}
+
+		public final String getNumExprTranslation() {
+			return switch (this){
+				case USERDEFINED -> throw new IllegalArgumentException("User defined functions have nothing to do with standard python names.");
+				case ABS -> "abs";
+				case MAX -> "maximum";
+				case MIN -> "minimum";
+				case CSC -> "1.0/" + SIN.getNumExprTranslation();
+				case COT -> "1.0/" + TAN.getNumExprTranslation();
+				case SEC -> "1.0/" + COS.getNumExprTranslation();
+				case ASIN -> "arcsin";
+				case ACOS -> "arccos";
+				case ATAN -> "arctan";
+				case ATAN2 -> "arctan2";
+				case CSCH -> "1.0/" + SINH.getNumExprTranslation();
+				case COTH -> "1.0/" + TANH.getNumExprTranslation();
+				case SECH -> "1.0/" + COSH.getNumExprTranslation();
+				case LOGBASE -> "1.0/" + LOG.getNumExprTranslation();
+				case ACSC, ACOT, ASEC, ACSCH, ACOTH, ASECH, FACTORIAL -> throw new UnsupportedOperationException("Python has no equivalent name.");
+				default -> getName();
+			};
+		}
+
 		public final String getHtmlDescription() {
 			return htmlDescription;
 		}
@@ -2389,12 +2412,28 @@ String getMathMLName() {
 }
 
 String getPythonName(){
-	if (funcType == FunctionType.USERDEFINED){
+	return getPythonName(funcType);
+}
+
+// This function is used when we need to "override" `funcType` to get the correct answer
+private String getPythonName(ASTFuncNode.FunctionType functionType){
+	if (functionType == FunctionType.USERDEFINED){
 		return funcName;
 	}
-	return funcType.getPythonTranslation();
+	return functionType.getPythonTranslation();
 }
 
+String getNumExprName(){
+	return getNumExprName(funcType);
+}
+
+// This function is used when we need to "override" `funcType` to get the correct answer
+private String getNumExprName(ASTFuncNode.FunctionType functionType){
+	if (functionType == FunctionType.USERDEFINED){
+		return funcName;
+	}
+	return functionType.getNumExprTranslation();
+}
 
 /**
  * Insert the method's description here.
@@ -2455,7 +2494,7 @@ public String infixString(int lang) {
 				buffer.append(",");
 				buffer.append("((double)(" + jjtGetChild(1).infixString(lang) + "))");
 				buffer.append(")");
-			} else if (lang == LANGUAGE_PYTHON) {
+			} else if (lang == LANGUAGE_PYTHON || lang == LANGUAGE_NUM_EXPR) {
                 buffer.append("((");
                 buffer.append(jjtGetChild(0).infixString(lang));
                 buffer.append(")**(");
@@ -2485,48 +2524,89 @@ public String infixString(int lang) {
 				buffer.append(jjtGetChild(0).infixString(lang));
 				buffer.append("))");
 				break;
+			} else if (lang == LANGUAGE_NUM_EXPR){
+				// Need parenthesis to encapsulate the "1.0/x" operation
+				buffer.append("(");
+				buffer.append(getNumExprName());
+				buffer.append("(");
+				buffer.append(jjtGetChild(0).infixString(lang));
+				buffer.append("))");
+				break;
 			}
 			// DO NOT PUT A "BREAK" HERE! We want to "fall through" to default!
 		}
 		case ACSC:
-		case ACOT:
 		case ASEC:
 		case ACSCH:
 		case ACOTH:
 		case ASECH:{
-			if (lang == LANGUAGE_PYTHON){ // Need parenthesis to encapsulate the "1.0/x" operation
+			if (lang == LANGUAGE_PYTHON){
+				// Need parenthesis to encapsulate the "1.0/x" operation
 				Map<FunctionType, FunctionType> inversionMap = Map.of(
 						FunctionType.ACSC, FunctionType.ASIN,
-						FunctionType.ACOT, FunctionType.ATAN,
 						FunctionType.ASEC, FunctionType.ACOS,
 						FunctionType.ACSCH, FunctionType.ASINH,
 						FunctionType.ACOTH, FunctionType.ATANH,
 						FunctionType.ASECH, FunctionType.ACOSH
 				);
 				FunctionType inversionType = inversionMap.get(funcType);
 				buffer.append("(");
-				buffer.append(getPythonName());
+				buffer.append(getPythonName(inversionType));
+				buffer.append("(1.0/(");
+				buffer.append(jjtGetChild(0).infixString(lang));
+				buffer.append(")))");
+				break;
+			} else if (lang == LANGUAGE_NUM_EXPR){
+				// Need parenthesis to encapsulate the "1.0/x" operation
+				Map<FunctionType, FunctionType> inversionMap = Map.of(
+						FunctionType.ACSC, FunctionType.ASIN,
+						FunctionType.ASEC, FunctionType.ACOS,
+						FunctionType.ACSCH, FunctionType.ASINH,
+						FunctionType.ACOTH, FunctionType.ATANH,
+						FunctionType.ASECH, FunctionType.ACOSH
+				);
+				FunctionType inversionType = inversionMap.get(funcType);
+				buffer.append("(");
+				buffer.append(getNumExprName(inversionType));
 				buffer.append("(1.0/(");
 				buffer.append(jjtGetChild(0).infixString(lang));
 				buffer.append(")))");
 				break;
 			}
 			// DO NOT PUT A "BREAK" HERE! We want to "fall through" to default!
 		}
+		case ACOT:{
+			if (lang == LANGUAGE_PYTHON){
+				buffer.append("(math.pi/2.0 - ");
+				buffer.append(getPythonName(FunctionType.ATAN));
+				buffer.append("(");
+				buffer.append(jjtGetChild(0).infixString(lang));
+				buffer.append("))");
+				break;
+			} else if (lang == LANGUAGE_NUM_EXPR){
+				buffer.append(String.format("((%s/2.0) - ", Math.PI));
+				buffer.append(getNumExprName(FunctionType.ATAN));
+				buffer.append("(");
+				buffer.append(jjtGetChild(0).infixString(lang));
+				buffer.append("))");
+				break;
+			}
+		}
 		case FACTORIAL:
 			if (lang == LANGUAGE_PYTHON){
 				String name = getPythonName();
-				// Since VCell now only accepts integer-values for factorial, integer casting should be safe
-				buffer.append(name).append("(int(");
+				// Since VCell now only accepts integer-values for factorial,
+				// Before we used casting, but there's a chance after math python can generate a different round off error.
+				// Since we know VCell only accepts integer, we're safe using `round` instead of just `int`
+				buffer.append(name).append("(round(");
 				if (1 < this.jjtGetNumChildren()) throw new UnsupportedOperationException("Cannot take factorial of multiple children");
 				buffer.append(jjtGetChild(0).infixString(lang));
 				buffer.append("))");
 				break;
 			}
 			// DO NOT PUT A "BREAK" HERE! We want to "fall through" to default!
 	 	default:{
-		    boolean needPythonicVersionOfName = lang == LANGUAGE_PYTHON && !funcType.equals(FunctionType.USERDEFINED);
-            String name = needPythonicVersionOfName ? getPythonName(): getName();
+            String name = getAppropriateName(lang);
 			buffer.append(name + "(");
 			for (int i=0;i<jjtGetNumChildren();i++){
 				if (i>0) buffer.append(", ");
@@ -2545,6 +2625,15 @@ public String infixString(int lang) {
 
 }
 
+private String getAppropriateName(int language){
+	if (FunctionType.USERDEFINED.equals(funcType)) return getName();
+	return switch (language){
+		case LANGUAGE_PYTHON -> getPythonName();
+		case LANGUAGE_NUM_EXPR -> getNumExprName();
+		default -> getName();
+	};
+}
+
 /**
  * Insert the method's description here.
  * Creation date: (6/20/01 11:04:41 AM)

vcell-math/src/main/java/cbit/vcell/parser/ASTMultNode.java

@@ -416,7 +416,7 @@ public String infixString(int lang){
 
 	buffer.append("(");
 
-	if (bAllBoolean || bNoBoolean || (lang != SimpleNode.LANGUAGE_C && lang != SimpleNode.LANGUAGE_VISIT && lang != SimpleNode.LANGUAGE_PYTHON)) { // old way
+	if (bAllBoolean || bNoBoolean || (lang != SimpleNode.LANGUAGE_C && lang != SimpleNode.LANGUAGE_VISIT && lang != SimpleNode.LANGUAGE_PYTHON&& lang != SimpleNode.LANGUAGE_NUM_EXPR)) { // old way
 		for (int i=0;i<jjtGetNumChildren();i++){
 			if (jjtGetChild(i) instanceof ASTInvertTermNode){
 				// bAllBoolean must be false here!
@@ -430,9 +430,15 @@ public String infixString(int lang){
 				if (i>0){
 					if (lang == SimpleNode.LANGUAGE_MATLAB){
 						buffer.append(" .* ");
-					} else if(lang == SimpleNode.LANGUAGE_PYTHON && bAllBoolean){
-						buffer.append(" and ");
-					} else {
+					} else if (bAllBoolean){
+						if (lang == SimpleNode.LANGUAGE_PYTHON){
+							buffer.append(" and ");
+						} else if (lang == SimpleNode.LANGUAGE_NUM_EXPR) {
+							buffer.append(" & ");
+						} else {
+							buffer.append(" * ");
+						}
+					} else { // mixed or no-boolean, and not matlab
 						buffer.append(" * ");
 					}
 				}
@@ -447,6 +453,8 @@ public String infixString(int lang){
 				if (conditionBuffer.length() > 0) {
 					if (lang == SimpleNode.LANGUAGE_PYTHON){
 						conditionBuffer.append(" and ");
+					} else if (lang == SimpleNode.LANGUAGE_NUM_EXPR) {
+						conditionBuffer.append(" & ");
 					} else {
 						conditionBuffer.append(" && ");
 					}
@@ -476,6 +484,8 @@ public String infixString(int lang){
 			}
 		}else if (lang == SimpleNode.LANGUAGE_PYTHON) {
 			buffer.append("(").append(valueBuffer).append(") if (").append(conditionBuffer).append(") else 0.0");
+		}else if (lang == SimpleNode.LANGUAGE_NUM_EXPR) {
+			buffer.append("where(").append(conditionBuffer).append(", ").append(valueBuffer).append(", 0.0)");
 		}else{
 			buffer.append("((" + conditionBuffer + ") ? (" + valueBuffer + ") : 0.0)");
 		}

vcell-math/src/main/java/cbit/vcell/parser/ASTNotNode.java

@@ -136,19 +136,23 @@ public Node flatten(boolean substituteConstants) throws ExpressionException {
 public String infixString(int language) {
 	StringBuffer buffer = new StringBuffer();
 	boolean parentIsLogical = parent != null && parent.isLogical();
+	boolean childIsLogical = jjtGetChild(0).isLogical();
 	if (language == LANGUAGE_VISIT){
 		buffer.append("not(");
 	}else if(language == LANGUAGE_PYTHON){
 		if (parentIsLogical) buffer.append("not(");
 		else buffer.append("float(not(");
+	}else if(language == LANGUAGE_NUM_EXPR){
+		if (childIsLogical) buffer.append("~(");
+		else buffer.append("(0.0==(");
 	}else if (language == LANGUAGE_ECLiPSe){
 		buffer.append("neg(");
 	}else{
 		buffer.append("!(");
 	}
 	buffer.append(jjtGetChild(0).infixString(language));
 	buffer.append(")");
-	if (language == LANGUAGE_PYTHON && !parentIsLogical) buffer.append(")");
+	if ((language == LANGUAGE_PYTHON && !parentIsLogical) || (language == LANGUAGE_NUM_EXPR && !childIsLogical)) buffer.append(")");
 
 	return buffer.toString();
 }

vcell-math/src/main/java/cbit/vcell/parser/ASTOrNode.java

@@ -180,6 +180,14 @@ public String infixString(int lang)
 			  buffer.append(jjtGetChild(i).infixString(lang));
 		  }
 		  buffer.append("))");
+	  }else if (lang == LANGUAGE_NUM_EXPR) {
+		  int numChildren = jjtGetNumChildren();
+		  for (int i=0;i<numChildren;i++){
+			  if (i>0) buffer.append(" | ");
+			  buffer.append("(0.0!=");
+			  buffer.append(jjtGetChild(i).infixString(lang));
+			  buffer.append(")");
+		  }
 	  }else{
 		  for (int i=0;i<jjtGetNumChildren();i++){
 			if (i>0) {

vcell-math/src/main/java/cbit/vcell/parser/ASTPowerNode.java

@@ -260,7 +260,7 @@ public String infixString(int lang){
 		buffer.append(" ^ ");
 		buffer.append(jjtGetChild(1).infixString(lang));
 		buffer.append(")");
-	} else if (lang == LANGUAGE_PYTHON) {
+	} else if (lang == LANGUAGE_PYTHON || lang == LANGUAGE_NUM_EXPR) {
 		buffer.append("((");
 		buffer.append(jjtGetChild(0).infixString(lang));
 		buffer.append(")**(");

vcell-math/src/main/java/cbit/vcell/parser/Expression.java

@@ -707,6 +707,10 @@ public String infix_Matlab()
    public String infix_Python() {
        return rootNode == null ?  null : rootNode.infixString(SimpleNode.LANGUAGE_PYTHON);
    }
+
+   public String infix_NumExpr() {
+	   return rootNode == null ?  null : rootNode.infixString(SimpleNode.LANGUAGE_NUM_EXPR);
+   }
 /**
  * This method was created by a SmartGuide.
  * @return cbit.vcell.model.Expression

vcell-math/src/main/java/cbit/vcell/parser/SimpleNode.java

@@ -32,6 +32,7 @@ public abstract class SimpleNode implements Node, java.io.Serializable {
   final static int LANGUAGE_UNITS = 6;
   final static int LANGUAGE_BNGL = 7;
   final static int LANGUAGE_PYTHON = 8;
+  final static int LANGUAGE_NUM_EXPR = 9;
 
   public SimpleNode(int i) {
     id = i;

vcell-math/src/test/java/cbit/vcell/parser/ExpressionTest.java

@@ -4,6 +4,7 @@
 import cbit.vcell.parser.SymbolTableFunctionEntry.FunctionArgType;
 import cbit.vcell.units.VCUnitSystem;
 import net.sourceforge.interval.ia_math.RealInterval;
+import org.apache.commons.math4.core.jdkmath.AccurateMath;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.BeforeAll;
@@ -29,7 +30,7 @@
 
 @Tag("Fast")
 public class ExpressionTest {
-	private static final boolean FAIL_ON_FIRST = true;
+	private static final boolean FAIL_ON_FIRST = false;
 	private static final boolean ENSURE_SAME_SEED = true; // change me
 	private static final long SAME_SEED = 1772035787937L;
 	private static File tempDir;
@@ -47,26 +48,29 @@ public class ExpressionTest {
 //	}
 
 	private static Set<String> skipInfixList = new HashSet<>(List.of(
+		"acoth(min(cot( - id_0), floor((0.8708964264563003 * 0.29826500971825554 * 0.6457243719944876))))",
 		"floor((pow(asinh(0.10118387985713251),cos(id_0)) * !(cot(id_0)) * min(csch(0.9837650351250335), coth(id_6))))",
 		" - (min(cot(id_0), csch(0.36737356253208997)) * atan2((0.7233117778683602 >= 0.9759958353333693), (0.1299551891086368 * id_7 * 0.7165699878023953)) / abs(id_1))",
 		"sech( - (coth(0.028177547796530367) ^ cot(id_1)))",
 		"coth(((sinh(0.6449666197606081) ^ (id_4 * id_8 * id_9)) + cot((id_3 < 0.2261011754280382)) + sech(abs(0.8120086721536708))))",
 		"(((cosh(id_3) * log(0.5598410965557573) * asin(0.015550241603964676)) * sin(floor(id_0)) * cosh(max(id_1, 0.585221823072032))) >= cot(floor((id_9 * id_2 * 0.30343841532874716))))",
+		"(cot(!( - id_6)) || ((tan(id_8) * atan2(id_5, id_7) * atan2(id_5, id_2)) * (pow(0.9897201897706811,id_1) * acosh(id_0) * (id_1 * 0.01088401412622797 * 0.8882413207692971)) * acot((0.3322552640871813 + id_9 + id_2))))",
 		"coth(floor(cot(abs(id_0))))",
 		" - factorial(( - id_2 / id_1 * ceil(id_5)))",
 		"csch(exp(csc((id_2 * id_2 * id_9))))",
 		"atan((tan(ceil(0.0)) || (cot(id_0) + asinh(0.5597772404451554) + sec(id_4))))",
 		"cot(factorial( - (0.20783348997951046 && id_5)))",
+		"(sqrt((atan2(0.7218065889622693, id_1) + asech(0.5381259927491784) + atanh(0.78855529690269))) >= asinh((atan2(id_0, id_9) <= cot(id_0))))",
 		" - cos((cos(id_1) ^ cot(id_0)))",
+		"pow(sinh(exp(acot(id_5))),tan(min(cot(id_0), (id_3 ^ id_8))))",
 		"atan(abs(cot(floor(id_5))))",
 		"coth(floor(cot((id_0 * 0.10280284481700341 * 0.3190467590050531))))",
 		" - (( - id_1 * acos(0.9408318720601397) * cot(id_0)) && asinh(min(id_6, 0.130136440506475)))",
 		"coth(factorial(floor(log(id_4))))",
 		"(cot(!(sech(id_3))) ^ min( - atan2(0.7870190039110462, id_2), ((id_7 * id_0 * 0.10143937822636417) * min(id_4, id_2) * sech(0.5569515469432404))))",
 		"cot(exp(coth((0.01722292952879423 ^ 0.7576553654648215))))",
-		"cosh(min(cot((id_7 * id_0 * 0.9871116728260001)),  - !(id_6)))",
-		" - acos(((0.01949787088472099 * id_1 * id_9) ^ cot(id_0)))",
-		"factorial(min(tanh((id_9 ^ id_1)), floor( - 0.5153523376029631)))"
+		"(sec((asinh(0.0) && min(id_5, 0.648784608185188))) * (cot(floor(id_7)) <= (exp(id_7) *  - 0.012384014519015274 * sqrt(0.7079441990714145))) * ceil(acot((0.8546428622959772 + id_0 + id_6))))",
+		"acsch(max(cot((id_0 * id_3 * 0.59541956426409)), (atan2(0.681661337447432, id_6) ^ atan2(0.2719307064055214, id_8))))"
 	));
 
 
@@ -413,6 +417,21 @@ public void testEval() {
 	}
 }
 
+@Test
+public void testNumExprGeneration() throws ExpressionException {
+	Expression expr1 = new Expression("(2.0 && id_2) * 3.3 / acsc(1 + id_1) * pow(2, 3.2 ^ 2)");
+	String numExpr1 = expr1.infix_NumExpr();
+	Assertions.assertEquals("(where(((0.0!=2.0) & (0.0!=id_2)), 3.3 / (arcsin(1.0/((1.0 + id_1)))) * ((2.0)**(((3.2)**(2.0)))), 0.0))", numExpr1);
+
+	Expression expr2 = new Expression("(1.2 * 2.2) * logbase(3.3) * 2.0");
+	String numExpr2 = expr2.infix_NumExpr();
+	Assertions.assertEquals("((1.2 * 2.2) * (1.0/log(3.3)) * 2.0)", numExpr2);
+
+	Expression expr3 = new Expression("(1.2 || 2.2) * (3.3 && !(2.0 && 0.0))");
+	String numExpr3 = expr3.infix_NumExpr();
+	Assertions.assertEquals("(((0.0!=1.2) | (0.0!=2.2)) & ((0.0!=3.3) & (0.0!=~(((0.0!=2.0) & (0.0!=0.0))))))", numExpr3);
+}
+
 
 /**
  * Insert the method's description here.