void CellmlFileRuntime::retrieveDaeCodeInformation(iface::cellml_api::Model *pModel)
{
// Get a code generator bootstrap and create a DAE code generator
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> codeGeneratorBootstrap = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::IDACodeGenerator> codeGenerator = codeGeneratorBootstrap->createIDACodeGenerator();
// Generate some code for the model
try {
mDaeCodeInformation = codeGenerator->generateIDACode(pModel);
// Check that the code generation went fine
checkCodeInformation(mDaeCodeInformation);
} catch (iface::cellml_api::CellMLException &exception) {
couldNotGenerateModelCodeIssue(Core::formatMessage(QString::fromStdWString(exception.explanation)));
} catch (...) {
unknownProblemDuringModelCodeGenerationIssue();
}
// Check the outcome of the DAE code generation
if (mIssues.count())
resetDaeCodeInformation();
}
CellMLModelDefinition::CellMLModelDefinition(const char* url) :
mURL(url)
{
//mCompileCommand = "gcc -fPIC -O3 -shared -x c -o";
mCompileCommand = "gcc -fPIC -g -shared -x c -o";
mTmpDirExists = false;
mCodeFileExists = false;
mDsoFileExists = false;
mSaveTempFiles = false;
mInstantiated = false;
nBound = -1;
nRates = -1;
nAlgebraic = -1;
nConstants = -1;
mNumberOfWantedVariables = 0;
mNumberOfKnownVariables = 0;
mNumberOfIndependentVariables = 0;
mStateCounter = 0;
mIntermediateCounter = 0;
mParameterCounter = 0;
mModel = NULL;
mCodeInformation = NULL;
mAnnotations = NULL;
std::cout << "Creating CellMLModelDefinition from the URL: "
<< url << std::endl;
if (! mURL.empty())
{
//std::cout << "Have a valid simulation description." << std::endl;
//std::cout << " CellML model URI: " << mURL.c_str() << std::endl;
RETURN_INTO_WSTRING(URL,string2wstring(mURL.c_str()));
RETURN_INTO_OBJREF(cb,iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml,iface::cellml_api::ModelLoader,cb->modelLoader());
iface::cellml_api::Model* model = (iface::cellml_api::Model*)NULL;
try
{
model = ml->loadFromURL(URL.c_str());
model->fullyInstantiateImports();
mModel = static_cast<void*>(model);
// create the annotation set
RETURN_INTO_OBJREF(ats,iface::cellml_services::AnnotationToolService,CreateAnnotationToolService());
iface::cellml_services::AnnotationSet* as = ats->createAnnotationSet();
mAnnotations = static_cast<void*>(as);
// make sure we can generate code and get the initial code information
RETURN_INTO_OBJREF(cgb,iface::cellml_services::CodeGeneratorBootstrap,
CreateCodeGeneratorBootstrap());
RETURN_INTO_OBJREF(cg,iface::cellml_services::CodeGenerator,
cgb->createCodeGenerator());
try
{
RETURN_INTO_OBJREF(cci,iface::cellml_services::CodeInformation,
cg->generateCode(model));
// need to keep a handle on the code information
cci->add_ref();
mCodeInformation = static_cast<void*>(cci);
// and add all state variables as wanted and the variable of integration as known
RETURN_INTO_OBJREF(cti,iface::cellml_services::ComputationTargetIterator,cci->iterateTargets());
while(1)
{
RETURN_INTO_OBJREF(ct,iface::cellml_services::ComputationTarget,cti->nextComputationTarget());
if (ct == NULL) break;
if (ct->type() == iface::cellml_services::STATE_VARIABLE)
{
as->setStringAnnotation(ct->variable(),L"flag",L"STATE");
as->setStringAnnotation(ct->variable(),L"array",L"OC_STATE");
as->setStringAnnotation(ct->variable(),L"array_index",formatNumber(mStateCounter).c_str());
mStateCounter++;
}
else if (ct->type() == iface::cellml_services::VARIABLE_OF_INTEGRATION)
{
as->setStringAnnotation(ct->variable(),L"flag",L"INDEPENDENT");
mNumberOfIndependentVariables++;
}
else if (ct->degree() > 0)
{
//as->setStringAnnotation(ct->variable(),L"flag-degree",L"WANTED");
//mNumberOfWantedVariables++;
}
}
}
catch (...)
{
std::wcerr << L"Error generating the code information for the model" << std::endl;
mCodeInformation = static_cast<void*>(NULL);
}
}
catch (...)
{
std::wcerr << L"Error loading model URL: " << URL.c_str() << std::endl;
mModel = static_cast<void*>(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;
}
int
main(int argc, char** argv)
{
// Get the URL from which to load the model...
if (argc < 2)
{
printf("Usage: CellML2C modelURL\n");
return -1;
}
uint32_t usenames = 0, useida = 0;
for (int32_t i = 2; i < argc; i++)
{
if (!strcmp(argv[i], "usenames"))
usenames = 1;
else if (!strcmp(argv[i], "useida"))
useida = 1;
}
wchar_t* URL;
size_t l = strlen(argv[1]);
URL = new wchar_t[l + 1];
memset(URL, 0, (l + 1) * sizeof(wchar_t));
const char* mbrurl = argv[1];
mbsrtowcs(URL, &mbrurl, l, NULL);
iface::cellml_api::CellMLBootstrap* cb =
CreateCellMLBootstrap();
iface::cellml_api::ModelLoader* ml =
cb->modelLoader();
cb->release_ref();
iface::cellml_api::Model* mod;
try
{
mod = ml->loadFromURL(URL);
}
catch (...)
{
printf("Error loading model URL.\n");
// Well, a leak on exit wouldn't be so bad, but someone might reuse this
// code, so...
delete [] URL;
ml->release_ref();
return -1;
}
ml->release_ref();
delete [] URL;
mod->fullyInstantiateImports();
iface::cellml_services::CodeGeneratorBootstrap* cgb =
CreateCodeGeneratorBootstrap();
iface::cellml_services::CodeGenerator* cg;
iface::cellml_services::IDACodeGenerator* icg;
if (useida)
cg = icg = cgb->createIDACodeGenerator();
else
cg = cgb->createCodeGenerator();
cgb->release_ref();
if (usenames)
doNameAnnotations(mod, cg);
iface::cellml_services::CodeInformation* cci = NULL;
try
{
cci = cg->generateCode(mod);
}
catch (iface::cellml_api::CellMLException&)
{
printf("Caught a CellMLException while generating code.\n");
cg->release_ref();
mod->release_ref();
return -1;
}
catch (...)
{
printf("Unexpected exception calling generateCode!\n");
// this is a leak, but it should also never happen :)
return -1;
}
mod->release_ref();
cg->release_ref();
std::wstring m = cci->errorMessage();
if (m != L"")
{
printf("Error generating code: %S\n", m.c_str());
cci->release_ref();
return -1;
}
// We now have the code information...
WriteCode(cci, useida);
cci->release_ref();
return 0;
}
int
main(int argc, char** argv)
{
if (argc < 5)
{
printf("Usage: CustomGen modelURL wanted known unwanted\n"
"Each of wanted, known, and unwanted is a comma separated list.\n"
"Use a single comma to specify an empty list.\n"
"Each entry in the list should be in the form:\n"
" component/variable:degreeOfDerivative\n");
return -1;
}
std::wstring URL(MakeWideString(argv[1]));
std::set<std::pair<std::pair<std::wstring, std::wstring>, uint32_t> > wanted, known, unwanted;
TargetDescriptionToSet(argv[2], wanted);
TargetDescriptionToSet(argv[3], known);
TargetDescriptionToSet(argv[4], unwanted);
RETURN_INTO_OBJREF(cb, iface::cellml_api::CellMLBootstrap,
CreateCellMLBootstrap());
RETURN_INTO_OBJREF(ml, iface::cellml_api::ModelLoader,
cb->modelLoader());
// These assignments to NULL are only here in the test code to help look for
// memory errors by freeing things early... in production code, they wouldn't
// be necessary.
cb = NULL;
ObjRef<iface::cellml_api::Model> mod;
try
{
mod = already_AddRefd<iface::cellml_api::Model>(ml->loadFromURL(URL.c_str()));
}
catch (...)
{
printf("Error loading model URL.\n");
return -1;
}
RETURN_INTO_OBJREF(cgb, iface::cellml_services::CodeGeneratorBootstrap,
CreateCodeGeneratorBootstrap()
);
RETURN_INTO_OBJREF(cg, iface::cellml_services::CodeGenerator,
cgb->createCodeGenerator());
cgb = NULL;
cg->stateVariableNamePattern(L"VARS[%]");
RETURN_INTO_OBJREF(ccg, iface::cellml_services::CustomGenerator,
cg->createCustomGenerator(mod));
cg = NULL;
mod = NULL;
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_OBJREF(cv, iface::cellml_api::CellMLVariable, ct->variable());
RETURN_INTO_WSTRING(compname, cv->componentName());
RETURN_INTO_WSTRING(varname, cv->name());
std::pair<std::pair<std::wstring, std::wstring>, uint32_t> p
(std::pair<std::wstring, std::wstring>(compname, varname), ct->degree());
if (wanted.count(p))
ccg->requestComputation(ct);
else if (known.count(p))
ccg->markAsKnown(ct);
else if (unwanted.count(p))
ccg->markAsUnwanted(ct);
}
cti = NULL;
RETURN_INTO_OBJREF(cci, iface::cellml_services::CustomCodeInformation,
ccg->generateCode());
ccg = NULL;
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(code, cci->generatedCode());
printf("Code: %S\n", code.c_str());
}
std::string generateCodeForModel(CellmlApiObjects* capi,
std::map<std::string, unsigned char>& variableTypes,
std::map<std::string, std::map<unsigned char, int> >& variableIndices,
int numberOfInputs, int numberOfStates)
{
std::stringstream code;
std::string codeString;
if (! (capi && capi->codeInformation))
{
std::cerr << "CellML Model Definition::generateCodeForModel: missing model implementation?" << std::endl;
return "";
}
// We need to regenerate the code information to make use of the flagged variables.
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> cgb = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::CodeGenerator> cg = cgb->createCodeGenerator();
// catch any exceptions from the CellML API
try
{
// annotate the source variables in the model with the code-names based on existing annotations
for (unsigned int i=0; i < capi->cevas->length(); i++)
{
ObjRef<iface::cellml_services::ConnectedVariableSet> cvs = capi->cevas->getVariableSet(i);
ObjRef<iface::cellml_api::CellMLVariable> sv = cvs->sourceVariable();
std::string currentId = getVariableUniqueId(sv);
std::map<std::string, unsigned char>::iterator typeit(variableTypes.find(currentId));
if (typeit != variableTypes.end())
{
std::wstringstream ename;
// here we assign an array and index based on the "primary" purpose of the variable. Later
// we will add in secondary purposes.
unsigned char vType = typeit->second;
if (vType & csim::StateType)
{
ename << L"CSIM_STATE[" << variableIndices[currentId][csim::StateType] << L"]";
}
else if (vType & csim::IndependentType)
{
// do nothing, but stop input and output annotations
}
else if (vType & csim::InputType)
{
ename << L"CSIM_INPUT[" << variableIndices[currentId][csim::InputType] << L"]";
}
else if (vType & csim::OutputType)
{
ename << L"CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType] << L"]";
}
capi->annotations->setStringAnnotation(sv, L"expression", ename.str());
if (vType & csim::StateType)
{
ename.str(L"");
ename.clear();
ename << L"CSIM_RATE[" << variableIndices[currentId][csim::StateType] << L"]";
capi->annotations->setStringAnnotation(sv, L"expression_d1", ename.str());
}
}
}
cg->useCeVAS(capi->cevas);
cg->useAnnoSet(capi->annotations);
ObjRef<iface::cellml_services::CodeInformation> cci = cg->generateCode(capi->model);
std::wstring m = cci->errorMessage();
if (m != L"")
{
std::cerr << "CellML Model Definition::generateCodeForModel: error generating code?" << std::endl;
return "";
}
iface::cellml_services::ModelConstraintLevel mcl = cci->constraintLevel();
if (mcl == iface::cellml_services::UNDERCONSTRAINED)
{
std::cerr << "Model is underconstrained" << std::endl;
return "";
}
else if (mcl == iface::cellml_services::OVERCONSTRAINED)
{
std::cerr << "Model is overconstrained" << std::endl;
return "";
}
else if (mcl == iface::cellml_services::UNSUITABLY_CONSTRAINED)
{
std::cerr << "Model is unsuitably constrained" << std::endl;
return "";
}
std::cout << "Model is correctly constrained" << std::endl;
// create the code in the format we know how to handle
code << "//#include <math.h>\n"
/* required functions */
<< "double fabs(double x);\n"
<< "double acos(double x);\n"
<< "double acosh(double x);\n"
<< "double atan(double x);\n"
<< "double atanh(double x);\n"
<< "double asin(double x);\n"
<< "double asinh(double x);\n"
<< "double acos(double x);\n"
<< "double acosh(double x);\n"
<< "double asin(double x);\n"
<< "double asinh(double x);\n"
<< "double atan(double x);\n"
<< "double atanh(double x);\n"
<< "double ceil(double x);\n"
<< "double cos(double x);\n"
<< "double cosh(double x);\n"
<< "double tan(double x);\n"
<< "double tanh(double x);\n"
<< "double sin(double x);\n"
<< "double sinh(double x);\n"
<< "double exp(double x);\n"
<< "double floor(double x);\n"
<< "double pow(double x, double y);\n"
<< "double factorial(double x);\n"
<< "double log(double x);\n"
<< "double arbitrary_log(double x, double base);\n"
<< "double gcd_pair(double a, double b);\n"
<< "double lcm_pair(double a, double b);\n"
<< "double gcd_multi(unsigned int size, ...);\n"
<< "double lcm_multi(unsigned int size, ...);\n"
<< "double multi_min(unsigned int size, ...);\n"
<< "double multi_max(unsigned int size, ...);\n"
<< "void NR_MINIMISE(double(*func)"
"(double VOI, double *C, double *R, double *S, double *A),"
"double VOI, double *C, double *R, double *S, double *A, "
"double *V);\n";
std::wstring frag = cci->functionsString();
code << ws2s(frag);
int nAlgebraic = cci->algebraicIndexCount();
int nConstants = cci->constantIndexCount();
code << "\n\nvoid csim_rhs_routine(double VOI, double* CSIM_STATE, double* CSIM_RATE, double* CSIM_OUTPUT, "
<< "double* CSIM_INPUT)\n{\n\n"
<< "double DUMMY_ASSIGNMENT;\n"
<< "double CONSTANTS["
<< nConstants
<< "], ALGEBRAIC["
<< nAlgebraic
<< "];\n\n";
/* initConsts - all variables which aren't state variables but have
* an initial_value attribute, and any variables & rates
* which follow.
*/
code << ws2s(cci->initConstsString());
/* rates - All rates which are not static.
*/
code << ws2s(cci->ratesString());
/* 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)
*/
code << ws2s(cci->variablesString());
// add in the setting of any outputs that are not already defined
for (unsigned int i=0; i < capi->cevas->length(); i++)
{
ObjRef<iface::cellml_services::ConnectedVariableSet> cvs = capi->cevas->getVariableSet(i);
ObjRef<iface::cellml_api::CellMLVariable> sv = cvs->sourceVariable();
std::string currentId = getVariableUniqueId(sv);
std::map<std::string, unsigned char>::iterator typeit(variableTypes.find(currentId));
if (typeit != variableTypes.end())
{
unsigned char vType = typeit->second;
if (vType & csim::OutputType)
{
if (vType & csim::StateType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = CSIM_STATE[" << variableIndices[currentId][csim::StateType]
<< "];\n";
else if (vType & csim::InputType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = CSIM_INPUT[" << variableIndices[currentId][csim::InputType]
<< "];\n";
else if (vType & csim::IndependentType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = VOI;\n";
}
}
}
// close the subroutine
code << "\n\n}//csim_rhs_routine()\n\n";
// and now clear out initialisation of state variables and known variables from
// the RHS routine.
codeString = clearCodeAssignments(code.str(), "CSIM_STATE", numberOfStates);
codeString = clearCodeAssignments(codeString, "CSIM_INPUT", numberOfInputs);
// and finally create the initialisation routine
std::stringstream initRoutine;
initRoutine << "\nvoid csim_initialise_routine(double* CSIM_STATE, double* CSIM_OUTPUT, double* CSIM_INPUT)\n{\n";
// FIXME: this doesn't need to be in the interface?
initRoutine << "double CSIM_RATES[" << numberOfStates << "];\n";
initRoutine << "double CONSTANTS[" << nConstants << "];\n";
initRoutine << ws2s(cci->initConstsString());
initRoutine << "\n}\n";
codeString += initRoutine.str();
}
catch (...)
{
std::cerr << "CellML Model Definition::generateCodeForModel: something went wrong generating code?" << std::endl;
return "";
}
return codeString;
}
int CellmlModelDefinition::instantiateCellmlApiObjects()
{
try
{
// create an annotation set to manage our variable usages
ObjRef<iface::cellml_services::AnnotationToolService> ats = CreateAnnotationToolService();
ObjRef<iface::cellml_services::AnnotationSet> as = ats->createAnnotationSet();
mCapi->annotations = as;
// mapping the connections between variables is a very expensive operation, so we want to
// only do it once and keep hold of the mapping (tracker item 3294)
ObjRef<iface::cellml_services::CeVASBootstrap> cvbs = CreateCeVASBootstrap();
ObjRef<iface::cellml_services::CeVAS> cevas = cvbs->createCeVASForModel(mCapi->model);
std::wstring msg = cevas->modelError();
if (msg != L"")
{
std::cerr << "loadModel: Error creating CellML Variable Association Service: "
<< ws2s(msg) << std::endl;
return -2;
}
mCapi->cevas = cevas;
// now check we can generate code and grab hold of the initial code information
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> cgb = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::CodeGenerator> cg = cgb->createCodeGenerator();
try
{
cg->useCeVAS(cevas);
ObjRef<iface::cellml_services::CodeInformation> cci = cg->generateCode(mCapi->model);
msg = cci->errorMessage();
if (msg != L"")
{
std::cerr << "CellmlModelDefintion::loadModel: Error generating code: "
<< ws2s(msg) << std::endl;
return -4;
}
// TODO: we are only interested in models we can work with?
if (cci->constraintLevel() != iface::cellml_services::CORRECTLY_CONSTRAINED)
{
std::cerr << "CellmlModelDefintion::loadModel: Model is not correctly constrained: "
<< std::endl;
return -5;
}
mCapi->codeInformation = cci;
// always flag all state variables and the variable of integration
ObjRef<iface::cellml_services::ComputationTargetIterator> cti = cci->iterateTargets();
while (true)
{
ObjRef<iface::cellml_services::ComputationTarget> ct = cti->nextComputationTarget();
if (ct == NULL) break;
if (ct->degree() > 0) break; // only want to initialise the base variables not the differential
ObjRef<iface::cellml_api::CellMLVariable> v(ct->variable());
if (ct->type() == iface::cellml_services::STATE_VARIABLE)
{
mVariableTypes[getVariableUniqueId(v)] = csim::StateType;
mVariableIndices[getVariableUniqueId(v)][csim::StateType] = mStateCounter;
mStateCounter++;
}
else if (ct->type() == iface::cellml_services::VARIABLE_OF_INTEGRATION)
{
mVariableTypes[getVariableUniqueId(v)] = csim::IndependentType;
mNumberOfIndependentVariables++;
}
else
{
// need to initialise the variable type
mVariableTypes[getVariableUniqueId(v)] = csim::UndefinedType;
}
}
}
catch (...)
{
std::cerr << "loadModel: Error generating the code information for the model" << std::endl;
return -3;
}
// if we get to here, everything worked.
mModelLoaded = true;
}
catch (...)
{
std::wcerr << L"Error instantiating CellML API objects." << std::endl;
return -1;
}
return csim::CSIM_OK;
}
