already_AddRefd<iface::cellml_services::MaLaESTransform>
CDA_DictionaryGenerator::getMalTransform()
throw(std::exception&)
{
RETURN_INTO_OBJREF(malDict, iface::cellml_services::LanguageDictionary,
getDictionary(L"http://www.cellml.org/CeLEDS/MaLaES/1.0#"));
if (malDict == NULL)
return NULL;
uint32_t i;
std::wstring MalString(L"");
RETURN_INTO_OBJREF(entries, iface::dom::NodeList,
malDict->getMappings());
for (i=0; i < entries->length(); i++)
{
RETURN_INTO_OBJREF(currentNode, iface::dom::Node, entries->item(i));
DECLARE_QUERY_INTERFACE_OBJREF(currentEl, currentNode, dom::Element);
if (currentEl == NULL)
continue;
// Get attributes
RETURN_INTO_WSTRING(keyName,
currentEl->getAttribute(L"keyname"));
RETURN_INTO_WSTRING(precedence,
currentEl->getAttribute(L"precedence"));
// Create Mal string
MalString.append(keyName);
MalString.append(L": ");
if (precedence != L"")
{
MalString.append(L"#prec[");
MalString.append(precedence);
MalString.append(L"]");
}
RETURN_INTO_WSTRING(tc, getTextContents(currentNode));
RETURN_INTO_WSTRING(ptc, padMalString(tc.c_str()));
MalString.append(ptc);
MalString.append(L"\r\n");
}
// create transformer
RETURN_INTO_OBJREF(mb, iface::cellml_services::MaLaESBootstrap,
CreateMaLaESBootstrap());
try
{
return mb->compileTransformer(MalString.c_str());
}
catch (...)
{
return NULL;
}
}
std::wstring
CellMLModelDefinition::getModelAsCCode(void* _model,void* _annotations)
{
iface::cellml_api::Model* model = static_cast<iface::cellml_api::Model*>(_model);
iface::cellml_services::AnnotationSet* as = static_cast<iface::cellml_services::AnnotationSet*>(_annotations);
std::wstring code;
RETURN_INTO_OBJREF(cgb,iface::cellml_services::CodeGeneratorBootstrap,
CreateCodeGeneratorBootstrap());
RETURN_INTO_OBJREF(cg,iface::cellml_services::CodeGenerator,
cgb->createCodeGenerator());
#if defined (CUSTOM_CODE_GENERATION)
RETURN_INTO_OBJREF(ccg, iface::cellml_services::CustomGenerator,
cg->createCustomGenerator(model));
RETURN_INTO_OBJREF(cti, iface::cellml_services::ComputationTargetIterator,
ccg->iterateTargets());
while (true)
{
RETURN_INTO_OBJREF(ct, iface::cellml_services::ComputationTarget,
cti->nextComputationTarget());
if (ct == NULL) break;
RETURN_INTO_WSTRING(flag,as->getStringAnnotation(ct->variable(),L"flag"));
if ((flag == L"WANTED") || (ct->degree() > 0))
{
ccg->requestComputation(ct);
}
else if (flag == L"KNOWN")
{
ccg->markAsKnown(ct);
}
}
#endif
/* The trunk MaLaES has been updated since the 1.5 release, so define a
* "custom" MaLaES here
*/
RETURN_INTO_OBJREF(mbs,iface::cellml_services::MaLaESBootstrap,
CreateMaLaESBootstrap());
RETURN_INTO_OBJREF(mt,iface::cellml_services::MaLaESTransform,
mbs->compileTransformer(
L"opengroup: (\r\n"
L"closegroup: )\r\n"
L"abs: #prec[H]fabs(#expr1)\r\n"
L"and: #prec[20]#exprs[&&]\r\n"
L"arccos: #prec[H]acos(#expr1)\r\n"
L"arccosh: #prec[H]acosh(#expr1)\r\n"
L"arccot: #prec[1000(900)]atan(1.0/#expr1)\r\n"
L"arccoth: #prec[1000(900)]atanh(1.0/#expr1)\r\n"
L"arccsc: #prec[1000(900)]asin(1/#expr1)\r\n"
L"arccsch: #prec[1000(900)]asinh(1/#expr1)\r\n"
L"arcsec: #prec[1000(900)]acos(1/#expr1)\r\n"
L"arcsech: #prec[1000(900)]acosh(1/#expr1)\r\n"
L"arcsin: #prec[H]asin(#expr1)\r\n"
L"arcsinh: #prec[H]asinh(#expr1)\r\n"
L"arctan: #prec[H]atan(#expr1)\r\n"
L"arctanh: #prec[H]atanh(#expr1)\r\n"
L"ceiling: #prec[H]ceil(#expr1)\r\n"
L"cos: #prec[H]cos(#expr1)\r\n"
L"cosh: #prec[H]cosh(#expr1)\r\n"
L"cot: #prec[900(0)]1.0/tan(#expr1)\r\n"
L"coth: #prec[900(0)]1.0/tanh(#expr1)\r\n"
L"csc: #prec[900(0)]1.0/sin(#expr1)\r\n"
L"csch: #prec[900(0)]1.0/sinh(#expr1)\r\n"
L"diff: #lookupDiffVariable\r\n"
L"divide: #prec[900]#expr1/#expr2\r\n"
L"eq: #prec[30]#exprs[==]\r\n"
L"exp: #prec[H]exp(#expr1)\r\n"
L"factorial: #prec[H]factorial(#expr1)\r\n"
L"factorof: #prec[30(900)]#expr1 % #expr2 == 0\r\n"
L"floor: #prec[H]floor(#expr1)\r\n"
L"gcd: #prec[H]gcd_multi(#count, #exprs[, ])\r\n"
L"geq: #prec[30]#exprs[>=]\r\n"
L"gt: #prec[30]#exprs[>]\r\n"
L"implies: #prec[10(950)] !#expr1 || #expr2\r\n"
L"int: #prec[H]defint(func#unique1, BOUND, CONSTANTS, RATES, VARIABLES, "
L"#bvarIndex, pret)#supplement double func#unique1(double* BOUND, "
L"double* CONSTANTS, double* RATES, double* VARIABLES, int* pret) { return #expr1; }\r\n"
L"lcm: #prec[H]lcm_multi(#count, #exprs[, ])\r\n"
L"leq: #prec[30]#exprs[<=]\r\n"
L"ln: #prec[H]log(#expr1)\r\n"
L"log: #prec[H]arbitrary_log(#expr1, #logbase)\r\n"
L"lt: #prec[30]#exprs[<]\r\n"
L"max: #prec[H]multi_max(#count, #exprs[, ])\r\n"
L"min: #prec[H]multi_min(#count, #exprs[, ])\r\n"
L"minus: #prec[500]#expr1 - #expr2\r\n"
L"neq: #prec[30]#expr1 != #expr2\r\n"
L"not: #prec[950]!#expr1\r\n"
L"or: #prec[10]#exprs[||]\r\n"
L"plus: #prec[500]#exprs[+]\r\n"
L"power: #prec[H]pow(#expr1, #expr2)\r\n"
L"quotient: #prec[1000(0)] (double)(((int)#expr2) == 0 ? #expr1 / 0.0 : (int)(#expr1) / (int)(#expr2))\r\n"
L"rem: #prec[1000(0)] (double)(((int)#expr2) == 0 ? (#expr1) / 0.0 : (int)(#expr1) % (int)(#expr2))\r\n"
L"root: #prec[1000(900)] pow(#expr1, 1.0 / #degree)\r\n"
L"sec: #prec[900(0)]1.0 / cos(#expr1)\r\n"
L"sech: #prec[900(0)]1.0 / cosh(#expr1)\r\n"
L"sin: #prec[H] sin(#expr1)\r\n"
L"sinh: #prec[H] sinh(#expr1)\r\n"
L"tan: #prec[H] tan(#expr1)\r\n"
L"tanh: #prec[H] tanh(#expr1)\r\n"
L"times: #prec[900] #exprs[*]\r\n"
L"unary_minus: #prec[950]- #expr1\r\n"
L"units_conversion: #prec[500(900)]#expr1*#expr2 + #expr3\r\n"
L"units_conversion_factor: #prec[900]#expr1*#expr2\r\n"
L"units_conversion_offset: #prec[500]#expr1+#expr2\r\n"
L"xor: #prec[25(30)] (#expr1 != 0) ^ (#expr2 != 0)\r\n"
L"piecewise_first_case: #prec[1000(5)](#expr1 ? #expr2 : \r\n"
L"piecewise_extra_case: #prec[1000(5)]#expr1 ? #expr2 : \r\n"
L"piecewise_otherwise: #prec[1000(5)]#expr1)\r\n"
L"piecewise_no_otherwise: #prec[1000(5)]0.0/0.0)\r\n"
L"eulergamma: #prec[999]0.577215664901533\r\n"
L"exponentiale: #prec[999]2.71828182845905\r\n"
L"false: #prec[999]0.0\r\n"
L"infinity: #prec[900]1.0/0.0\r\n"
L"notanumber: #prec[999]0.0/0.0\r\n"
L"pi: #prec[999] 3.14159265358979\r\n"
L"true: #prec[999]1.0\r\n"));
/* now can use the standard transformation?
cg->transform(mt);
*/
try
{
#if defined (CUSTOM_CODE_GENERATION)
RETURN_INTO_OBJREF(cci,iface::cellml_services::CustomCodeInformation,ccg->generateCode());
printf("Constraint level = ");
switch (cci->constraintLevel())
{
case iface::cellml_services::UNDERCONSTRAINED:
printf("UNDERCONSTRAINED\n");
break;
case iface::cellml_services::UNSUITABLY_CONSTRAINED:
printf("UNSUITABLY_CONSTRAINED\n");
break;
case iface::cellml_services::OVERCONSTRAINED:
printf("OVERCONSTRAINED\n");
break;
case iface::cellml_services::CORRECTLY_CONSTRAINED:
printf("CORRECTLY_CONSTRAINED\n");
break;
default:
printf("Unkown value\n");
}
printf("Index count: %u\n", cci->indexCount());
cti = already_AddRefd<iface::cellml_services::ComputationTargetIterator>(cci->iterateTargets());
while (true)
{
RETURN_INTO_OBJREF(ct, iface::cellml_services::ComputationTarget,
cti->nextComputationTarget());
if (ct == NULL)
break;
RETURN_INTO_OBJREF(cv, iface::cellml_api::CellMLVariable, ct->variable());
RETURN_INTO_WSTRING(compname, cv->componentName());
RETURN_INTO_WSTRING(varname, cv->name());
printf("* Computation target %S/%S:%u:\n", compname.c_str(), varname.c_str(),
ct->degree());
printf(" => Type = ");
switch (ct->type())
{
case iface::cellml_services::VARIABLE_OF_INTEGRATION:
printf("VARIABLE_OF_INTEGRATION - was marked as independent.\n");
break;
case iface::cellml_services::CONSTANT:
printf("CONSTANT - this should not happen!\n");
break;
case iface::cellml_services::STATE_VARIABLE:
printf("STATE_VARIABLE - was requested, and is available.\n");
break;
case iface::cellml_services::ALGEBRAIC:
printf("ALGEBRAIC - is used as an intermediate.\n");
break;
case iface::cellml_services::FLOATING:
printf("FLOATING - unused and not requested.\n");
break;
case iface::cellml_services::LOCALLY_BOUND:
printf("LOCALLY_BOUND - locally bound in expressions only.\n");
break;
case iface::cellml_services::PSEUDOSTATE_VARIABLE:
printf("PSEUDOSTATE_VARIABLE - target was requested, but could "
"not be computed from the independent variables and model.\n");
break;
default:
printf("Unknown type!\n");
}
RETURN_INTO_WSTRING(targname, ct->name());
printf(" => Name = %S\n", targname.c_str());
printf(" => Index = %u\n", ct->assignedIndex());
}
// To do: Print output from cci->iterateTargets();
RETURN_INTO_WSTRING(functionsString, cci->functionsString());
printf("Functions: %S\n", functionsString.c_str());
RETURN_INTO_WSTRING(codeS, cci->generatedCode());
printf("Code: %S\n", codeS.c_str());
#else // CUSTOM_CODE_GENERATION
// annotate the source variables in the model with the code-names based on existing annotations
RETURN_INTO_OBJREF(cvbs,iface::cellml_services::CeVASBootstrap,CreateCeVASBootstrap());
RETURN_INTO_OBJREF(cevas,iface::cellml_services::CeVAS,cvbs->createCeVASForModel(model));
for (unsigned int i=0;i<cevas->length();i++)
{
RETURN_INTO_OBJREF(cvs,iface::cellml_services::ConnectedVariableSet,cevas->getVariableSet(i));
RETURN_INTO_OBJREF(sv,iface::cellml_api::CellMLVariable,cvs->sourceVariable());
RETURN_INTO_WSTRING(array,as->getStringAnnotation(sv,L"array"));
RETURN_INTO_WSTRING(index,as->getStringAnnotation(sv,L"array_index"));
if (!array.empty() && !index.empty())
{
std::wstring ename = array;
ename += L"[";
ename += index;
ename += L"]";
as->setStringAnnotation(sv,L"expression",ename.c_str());
if (array == L"OC_STATE")
{
ename = std::wstring(L"OC_RATE");
ename += L"[";
ename += index;
ename += L"]";
as->setStringAnnotation(sv,L"expression_d1",ename.c_str());
}
}
}
cg->useCeVAS(cevas);
cg->useAnnoSet(as);
RETURN_INTO_OBJREF(cci,iface::cellml_services::CodeInformation,cg->generateCode(model));
wchar_t* m = cci->errorMessage();
if (!wcscmp(m,L""))
{
std::cout << "whoo hoo!" << std::endl;
iface::cellml_services::ModelConstraintLevel mcl = cci->constraintLevel();
if (mcl == iface::cellml_services::UNDERCONSTRAINED)
{
std::cerr << "Model is underconstrained" << std::endl;
}
else if (mcl == iface::cellml_services::OVERCONSTRAINED)
{
std::cerr << "Model is overconstrained" << std::endl;
}
else if (mcl == iface::cellml_services::UNSUITABLY_CONSTRAINED)
{
std::cerr << "Model is unsuitably constrained" << std::endl;
}
else
{
std::cout << "Model is correctly constrained" << std::endl;
// create the code in the format we know how to handle
code += L"#include <math.h>\n";
code += L"#include <stdio.h>\n";
/* required functions */
code += L"extern double fabs(double x);\n";
code += L"extern double acos(double x);\n";
code += L"extern double acosh(double x);\n";
code += L"extern double atan(double x);\n";
code += L"extern double atanh(double x);\n";
code += L"extern double asin(double x);\n";
code += L"extern double asinh(double x);\n";
code += L"extern double acos(double x);\n";
code += L"extern double acosh(double x);\n";
code += L"extern double asin(double x);\n";
code += L"extern double asinh(double x);\n";
code += L"extern double atan(double x);\n";
code += L"extern double atanh(double x);\n";
code += L"extern double ceil(double x);\n";
code += L"extern double cos(double x);\n";
code += L"extern double cosh(double x);\n";
code += L"extern double tan(double x);\n";
code += L"extern double tanh(double x);\n";
code += L"extern double sin(double x);\n";
code += L"extern double sinh(double x);\n";
code += L"extern double exp(double x);\n";
code += L"extern double floor(double x);\n";
code += L"extern double pow(double x, double y);\n";
code += L"extern double factorial(double x);\n";
code += L"extern double log(double x);\n";
code += L"extern double arbitrary_log(double x, double base);\n";
code += L"extern double gcd_pair(double a, double b);\n";
code += L"extern double lcm_pair(double a, double b);\n";
code += L"extern double gcd_multi(unsigned int size, ...);\n";
code += L"extern double lcm_multi(unsigned int size, ...);\n";
code += L"extern double multi_min(unsigned int size, ...);\n";
code += L"extern double multi_max(unsigned int size, ...);\n";
code += L"extern void NR_MINIMISE(double(*func)"
L"(double VOI, double *C, double *R, double *S, double *A),"
L"double VOI, double *C, double *R, double *S, double *A, "
L"double *V);\n";
wchar_t* frag = cci->functionsString();
code += frag;
free(frag);
nBound = 1;
nRates = cci->rateIndexCount();
nAlgebraic = cci->algebraicIndexCount();
nConstants = cci->constantIndexCount();
code += L"\n\nvoid OC_CellML_RHS_routine(double VOI, double* OC_STATE, double* OC_RATE, double* OC_WANTED, double* OC_KNOWN)\n{\n\n";
code += L"double DUMMY_ASSIGNMENT;\n";
code += L"double CONSTANTS[";
code += formatNumber(nConstants);
code += L"], ALGEBRAIC[";
code += formatNumber(nAlgebraic);
code += L"];\n\n";
// start the model code...
/* https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/interfaces/CCGS.idl for full description */
/* initConsts - all variables which aren't state variables but have
* an initial_value attribute, and any variables & rates
* which follow.
*/
frag = cci->initConstsString();
//code += L"void SetupFixedConstants(double* CONSTANTS,double* RATES,"
// L"double* STATES)\n{\n";
code += frag;
//code += L"}\n";
free(frag);
/* rates - All rates which are not static.
*/
frag = cci->ratesString();
//code += L"void ComputeRates(double VOI,double* STATES,double* RATES,"
// L"double* CONSTANTS,double* ALGEBRAIC)\n{\n";
code += frag;
//code += L"}\n";
free(frag);
/* variables - All variables not computed by initConsts or rates
* (i.e., these are not required for the integration of the model and
* thus only need to be called for output or presentation or similar
* purposes)
*/
frag = cci->variablesString();
//code += L"void EvaluateVariables(double VOI,double* CONSTANTS,"
// L"double* RATES, double* STATES, double* ALGEBRAIC)\n{\n";
code += frag;
//code += L"}\n";
free(frag);
// and now clear out initialisation of state variables and known variables.
clearCodeAssignments(code,L"OC_STATE",mStateCounter);
clearCodeAssignments(code,L"OC_KNOWN",mParameterCounter);
// close the subroutine
code += L"\n\n}//OC_CellML_RHS_routine()\n\n;";
}
}
else
{
std::wcerr << "Error generating code: " << m << std::endl;
}
free(m);
#endif // CUSTOM_CODE_GENERATION
}
catch (...)
{
std::wcerr << L"Error generating the code information for model"
<< std::endl;
}
return code;
}
void
MaLaESTest::setUp()
{
mMaLaESBootstrap = CreateMaLaESBootstrap();
}
