Chronological Thread 

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---

CellML Automated Notifications wrote:
> Author: aree035
> Date: 2009-01-08 16:29:51 +1300 (Thu, 08 Jan 2009)
> New Revision: 2991
>
> Added:
> CellML_DOM_API/trunk/CCGS/tests/CellML2Matlab.cpp
> Modified:
> CellML_DOM_API/trunk/
> CellML_DOM_API/trunk/CCGS/tests/build.mk
> Log:
> Added CellML2Matlab program. This does not use simulation metadata like the
> export from PCEnv does.
>
I think the CellML2* programs are getting out of hand - CellML2C is
intended to be part of the tests of the CCGS to ensure that it works
properly. It is unclear what having CellML2Python and CellML2Matlab
really achieves in the way of testing - they invoke almost exactly the
same code paths as CellML2C anyway, just with different strings. There
may well be demand for a command line user interface for CellML - if so,
these should really be separate from the API implementation, which is
intended for programmatic use.

See https://tracker.physiomeproject.org/show_bug.cgi?id=1514#c16, and
also https://tracker.physiomeproject.org/show_bug.cgi?id=1279 about the
command line tools.

I will put a note about this on tracker item 1279, and I might also put
a note in build.mk and CellML2C requesting that people not add any more
programs like this unless they are useful for testing purposes.

Best wishes,
Andrew

>
> Property changes on: CellML_DOM_API/trunk
> ___________________________________________________________________
> Name: svn:ignore
> - Makefile.in
> Makefile
> aclocal.m4
> cda_config.h
> config.log
> config.status
> configure.scan
> configure
> autom4te.cache
> stamp-h1
> libtool
> .deps
> .libs
> cellml_corba_server
> CellML2C
> CellML2Python
> CCGSService
> CISService
> RunCellML
> ValidateCellML
> a.exe.manifest
> vc80.pdb
>
> + Makefile.in
> Makefile
> aclocal.m4
> cda_config.h
> config.log
> config.status
> configure.scan
> configure
> autom4te.cache
> stamp-h1
> libtool
> .deps
> .libs
> cellml_corba_server
> CellML2C
> CellML2Python
> CellML2Matlab
> CCGSService
> CISService
> RunCellML
> ValidateCellML
> a.exe.manifest
> vc80.pdb
>
>
> Added: CellML_DOM_API/trunk/CCGS/tests/CellML2Matlab.cpp
> ===================================================================
> --- CellML_DOM_API/trunk/CCGS/tests/CellML2Matlab.cpp
> (rev 0)
> +++ CellML_DOM_API/trunk/CCGS/tests/CellML2Matlab.cpp 2009-01-08 03:29:51
> UTC (rev 2991)
> @@ -0,0 +1,801 @@
> +#include "cda_config.h"
> +#ifdef HAVE_INTTYPES_H
> +#include <inttypes.h>
> +#endif
> +#include <exception>
> +#include "cda_compiler_support.h"
> +#include "IfaceCellML_APISPEC.hxx"
> +#include "IfaceCCGS.hxx"
> +#include "IfaceMaLaES.hxx"
> +#include "IfaceAnnoTools.hxx"
> +#include "CCGSBootstrap.hpp"
> +#include "MaLaESBootstrap.hpp"
> +#include "CellMLBootstrap.hpp"
> +#include "AnnoToolsBootstrap.hpp"
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <string.h>
> +#include <wchar.h>
> +#include <vector>
> +#include <algorithm>
> +#include <string>
> +#include "Utilities.hxx"
> +
> +#ifdef _WIN32
> +#define swprintf _snwprintf
> +#endif
> +
> +wchar_t*
> +TypeToString(iface::cellml_services::VariableEvaluationType vet)
> +{
> + switch (vet)
> + {
> + case iface::cellml_services::VARIABLE_OF_INTEGRATION:
> + return L"variable of integration";
> + case iface::cellml_services::CONSTANT:
> + return L"constant";
> + case iface::cellml_services::STATE_VARIABLE:
> + return L"state variable";
> + case iface::cellml_services::ALGEBRAIC:
> + return L"algebraic variable";
> + case iface::cellml_services::FLOATING:
> + return L"uncomputed";
> + }
> +
> + return L"invalid type";
> +}
> +
> +void
> +WriteCode(iface::cellml_services::CodeInformation* cci)
> +{
> + // Scoped locale change.
> + CNumericLocale locobj;
> +
> + iface::cellml_services::ModelConstraintLevel mcl =
> + cci->constraintLevel();
> + if (mcl == iface::cellml_services::UNDERCONSTRAINED)
> + {
> + printf("Model is underconstrained.\n"
> + "List of undefined targets follows...\n");
> + iface::cellml_services::ComputationTargetIterator* cti =
> cci->iterateTargets();
> + iface::cellml_services::ComputationTarget* ct;
> + std::vector<std::wstring> messages;
> + while (true)
> + {
> + ct = cti->nextComputationTarget();
> + if (ct == NULL)
> + break;
> + if (ct->type() != iface::cellml_services::FLOATING)
> + {
> + ct->release_ref();
> + continue;
> + }
> + iface::cellml_api::CellMLVariable* v = ct->variable();
> + wchar_t* n = v->name();
> + wchar_t* c = v->componentName();
> + std::wstring str = L" ";
> + uint32_t deg = ct->degree();
> + if (deg != 0)
> + {
> + str += L"d^";
> + wchar_t buf[20];
> + swprintf(buf, 20, L"%u", deg);
> + str += buf;
> + str += L"/dt^";
> + str += buf;
> + str += L" ";
> + }
> + str += n;
> + str += L" (in ";
> + str += c;
> + str += L")\n";
> + free(n);
> + free(c);
> + messages.push_back(str);
> + v->release_ref();
> + ct->release_ref();
> + }
> + cti->release_ref();
> + // Sort the messages...
> + std::sort(messages.begin(), messages.end());
> + std::vector<std::wstring>::iterator msgi;
> + for (msgi = messages.begin(); msgi != messages.end(); msgi++)
> + printf("%S", (*msgi).c_str());
> + return;
> + }
> + else if (mcl == iface::cellml_services::OVERCONSTRAINED)
> + {
> + printf("Model is overconstrained.\n"
> + "List variables defined at time of error follows...\n");
> + iface::cellml_services::ComputationTargetIterator* cti =
> cci->iterateTargets();
> + iface::cellml_services::ComputationTarget* ct;
> + std::vector<std::wstring> messages;
> + while (true)
> + {
> + ct = cti->nextComputationTarget();
> + if (ct == NULL)
> + break;
> + if (ct->type() == iface::cellml_services::FLOATING)
> + {
> + ct->release_ref();
> + continue;
> + }
> + iface::cellml_api::CellMLVariable* v = ct->variable();
> + wchar_t* n = v->name();
> + std::wstring str = L" ";
> + uint32_t deg = ct->degree();
> + if (deg != 0)
> + {
> + str += L"d^";
> + wchar_t buf[20];
> + swprintf(buf, 20, L"%u", deg);
> + str += buf;
> + str += L"/dt^";
> + str += buf;
> + str += L" ";
> + }
> + str += n;
> + free(n);
> + str += L"\n";
> + messages.push_back(str);
> + v->release_ref();
> + ct->release_ref();
> + }
> + cti->release_ref();
> +
> + // Sort the messages...
> + std::sort(messages.begin(), messages.end());
> + std::vector<std::wstring>::iterator msgi;
> + for (msgi = messages.begin(); msgi != messages.end(); msgi++)
> + printf("%S", (*msgi).c_str());
> +
> + // Get flagged equations...
> + iface::mathml_dom::MathMLNodeList* mnl = cci->flaggedEquations();
> + printf("Extraneous equation was:\n");
> + iface::dom::Node* n = mnl->item(0);
> + mnl->release_ref();
> + iface::dom::Element* el =
> +
> reinterpret_cast<iface::dom::Element*>(n->query_interface("dom::Element"));
> + n->release_ref();
> +
> + wchar_t* cmeta =
> el->getAttributeNS(L"http://www.cellml.org/metadata/1.0#";,
> + L"id");
> + if (!wcscmp(cmeta, L""))
> + printf(" <equation with no cmeta ID>\n");
> + else
> + printf(" %S\n", cmeta);
> + free(cmeta);
> +
> + n = el->parentNode();
> + el->release_ref();
> +
> + el = reinterpret_cast<iface::dom::Element*>
> + (n->query_interface("dom::Element"));
> + n->release_ref();
> +
> + cmeta = el->getAttributeNS(L"http://www.cellml.org/metadata/1.0#";,
> L"id");
> + if (!wcscmp(cmeta, L""))
> + printf(" in <math with no cmeta ID>\n");
> + else
> + printf(" in math with cmeta:id %S\n", cmeta);
> + free(cmeta);
> + el->release_ref();
> +
> + return;
> + }
> + else if (mcl == iface::cellml_services::UNSUITABLY_CONSTRAINED)
> + {
> + printf("Model is unsuitably constrained (i.e. would need capabilities"
> + "beyond those of the CCGS to solve).\n"
> + "The status of variables at time of error follows...\n");
> + iface::cellml_services::ComputationTargetIterator* cti =
> cci->iterateTargets();
> + iface::cellml_services::ComputationTarget* ct;
> + std::vector<std::wstring> messages;
> + while (true)
> + {
> + ct = cti->nextComputationTarget();
> + if (ct == NULL)
> + break;
> + std::wstring str = L" ";
> + if (ct->type() == iface::cellml_services::FLOATING)
> + str += L" Undefined: ";
> + else
> + str += L" Defined: ";
> +
> + uint32_t deg = ct->degree();
> + if (deg != 0)
> + {
> + str += L"d^";
> + wchar_t buf[20];
> + swprintf(buf, 20, L"%u", deg);
> + str += buf;
> + str += L"/dt^";
> + str += buf;
> + str += L" ";
> + }
> + iface::cellml_api::CellMLVariable* v = ct->variable();
> + wchar_t* n = v->name();
> + str += n;
> + free(n);
> + str += L"\n";
> + messages.push_back(str);
> + v->release_ref();
> + ct->release_ref();
> + }
> + cti->release_ref();
> +
> + // Sort the messages...
> + std::sort(messages.begin(), messages.end());
> + std::vector<std::wstring>::iterator msgi;
> + for (msgi = messages.begin(); msgi != messages.end(); msgi++)
> + printf("%S", (*msgi).c_str());
> +
> + return;
> + }
> +
> + printf("%% Model is correctly constrained.\n");
> + iface::mathml_dom::MathMLNodeList* mnl = cci->flaggedEquations();
> + uint32_t i, l = mnl->length();
> + if (l == 0)
> + printf("%% No equations needed Newton-Raphson evaluation.\n");
> + else
> + printf("%% The following equations needed Newton-Raphson
> evaluation:\n");
> +
> + std::vector<std::wstring> messages;
> + for (i = 0; i < l; i++)
> + {
> + iface::dom::Node* n = mnl->item(i);
> + iface::dom::Element* el =
> +
> reinterpret_cast<iface::dom::Element*>(n->query_interface("dom::Element"));
> + n->release_ref();
> +
> + wchar_t* cmeta =
> el->getAttributeNS(L"http://www.cellml.org/metadata/1.0#";,
> + L"id");
> + std::wstring str;
> + if (!wcscmp(cmeta, L""))
> + str += L"% <equation with no cmeta ID>\n";
> + else
> + {
> + str += L"% ";
> + str += cmeta;
> + str += L"\n";
> + }
> + free(cmeta);
> +
> + n = el->parentNode();
> + el->release_ref();
> +
> + el = reinterpret_cast<iface::dom::Element*>
> + (n->query_interface("dom::Element"));
> + n->release_ref();
> +
> + cmeta = el->getAttributeNS(L"http://www.cellml.org/metadata/1.0#";,
> L"id");
> + if (!wcscmp(cmeta, L""))
> + str += L"% in <math with no cmeta ID>\n";
> + else
> + {
> + str += L"% in math with cmeta:id ";
> + str += cmeta;
> + str += L"\n";
> + }
> + free(cmeta);
> + el->release_ref();
> +
> + messages.push_back(str);
> + }
> + mnl->release_ref();
> +
> + // Sort the messages...
> + std::sort(messages.begin(), messages.end());
> + std::vector<std::wstring>::iterator msgi;
> + for (msgi = messages.begin(); msgi != messages.end(); msgi++)
> + printf("%S", (*msgi).c_str());
> +
> + printf("%%\r\n%% There are a total of %u entries in the algebraic
> variable array.\n", cci->algebraicIndexCount());
> + printf("%% There are a total of %u entries in each of the rates & state
> variable arrays.\n", cci->rateIndexCount());
> + printf("%% There are a total of %u entries in the constant variable
> array.\n%%\r\n", cci->constantIndexCount());
> +
> + messages.clear();
> + iface::cellml_services::ComputationTargetIterator* cti =
> cci->iterateTargets();
> + while (true)
> + {
> + iface::cellml_services::ComputationTarget* ct =
> cti->nextComputationTarget();
> + if (ct == NULL)
> + break;
> + iface::cellml_api::CellMLVariable* v = ct->variable();
> + iface::cellml_api::CellMLElement* el = v->parentElement();
> + iface::cellml_api::CellMLComponent* c =
> + reinterpret_cast<iface::cellml_api::CellMLComponent*>
> + (el->query_interface("cellml_api::CellMLComponent"));
> + el->release_ref();
> +
> + std::wstring str;
> + wchar_t* vn = v->name(), * cn = c->name();
> +
> + str += L" LEGEND_";
> + wchar_t * vsn;
> + vsn = ct->name();
> + str += vsn;
> + free(vsn);
> +
> + str += L" = strpad('";
> + uint32_t deg = ct->degree();
> + if (deg != 0)
> + {
> + str += L"d^";
> + wchar_t buf[20];
> + swprintf(buf, 20, L"%u", deg);
> + str += buf;
> + str += L"/dt^";
> + str += buf;
> + str += L" ";
> + }
> + str += vn;
> + str += L" in component ";
> + str += cn;
> + str += L"');\n";
> + free(vn);
> + free(cn);
> +
> + c->release_ref();
> + v->release_ref();
> + ct->release_ref();
> +
> + messages.push_back(str);
> + }
> + cti->release_ref();
> +
> + // Now start the code...
> +
> + printf("\r\n"
> + "function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()\r\n"
> + " %% Initialise constants and state variables\r\n"
> + " [INIT_STATES, CONSTANTS] = initConsts;\r\n\r\n"
> + " %% Set timespan to solve over\r\n"
> + " tspan = [0,10];\r\n"
> + " %% Set numerical accuracy options for ODE solver\r\n"
> + " options = odeset('RelTol', 1E-6, 'AbsTol', 1E-6, 'MaxStep',
> 0.1);\r\n\r\n"
> + " %% Solve model with ODE solver\r\n"
> + " [VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI,
> STATES, CONSTANTS), tspan, INIT_STATES, options);\r\n\r\n"
> + " %% Compute algebraic variables\r\n"
> + " ALGEBRAIC = computeAlgebraic(CONSTANTS, STATES,
> VOI);\r\n\r\n"
> + " %% Plot state variables against variable of integration\r\n"
> + " [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI,
> LEGEND_CONSTANTS] = createLegends();\r\n"
> + " figure();\r\n"
> + " plot(VOI, STATES);\r\n"
> + " xlabel(LEGEND_VOI);\r\n"
> + " l = legend(LEGEND_STATES);\r\n"
> + " set(l,'Interpreter','none');\r\n"
> + "end\r\n\r\n");
> +
> + // Sort and print the list of variables
> + std::sort(messages.begin(), messages.end());
> + printf("function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI,
> LEGEND_CONSTANTS] = createLegends()\r\n"
> + " LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = '';
> LEGEND_CONSTANTS = '';\r\n");
> + for (msgi = messages.begin(); msgi != messages.end(); msgi++)
> + printf("%S", (*msgi).c_str());
> + printf(" LEGEND_STATES = LEGEND_STATES';\r\n"
> + " LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';\r\n"
> + " LEGEND_RATES = LEGEND_RATES';\r\n"
> + " LEGEND_CONSTANTS = LEGEND_CONSTANTS';\r\n"
> + "end\r\n\r\n");
> +
> + wchar_t* frag = cci->initConstsString();
> + printf("function [STATES, CONSTANTS] = initConsts()\r\n CONSTANTS =
> []; STATES = [];\r\n");
> + printf("%S", frag);
> + printf(" if (isempty(STATES)), warning('Initial values for states not
> set');, end\r\nend\r\n\r\n");
> + free(frag);
> +
> + frag = cci->ratesString();
> + printf("function RATES = computeRates(VOI, STATES, CONSTANTS)\r\n"
> + " STATES = STATES'; RATES = []; ALGEBRAIC = [0];\r\n");
> + printf("%S", frag);
> + printf(" RATES = RATES';\r\nend\r\n\r\n");
> + free(frag);
> +
> + printf("%% Calculate algebraic variables\r\n"
> + "function ALGEBRAIC = computeAlgebraic(CONSTANTS, STATES,
> VOI)\r\n"
> + " ALGEBRAIC = zeros(length(VOI),1);\r\n");
> +
> + // Copy algebraic variable calculations from rate calculations
> + // Use lines beginning with 'A'
> + frag = cci->ratesString();
> + i = 0;
> + bool algebraic = false, newline = true;
> +
> + while(frag[i] != '\0') {
> + if(frag[i] == ' ' || frag[i] == '\t') {
> + i++;
> + continue;
> + }
> + if(newline && frag[i] == 'A') {
> + algebraic = true;
> + newline = false;
> + printf(" ");
> + }
> + else if (newline) {
> + newline = false;
> + }
> + if(algebraic) {
> + printf("%C", frag[i]);
> + }
> + if(frag[i] == '\n') {
> + newline = true;
> + algebraic = false;
> + }
> + i++;
> + }
> + free(frag);
> +
> + frag = cci->variablesString();
> + printf("%S",frag);
> + free(frag);
> + printf("end\r\n\r\n"
> + "%% Compute result of a piecewise function\r\n"
> + "function x = piecewise(cases, default)\r\n"
> + " set = [0];\r\n"
> + " for i = 1:2:length(cases)\r\n"
> + " if (length(cases{i+1}) == 1)\r\n"
> + " x(cases{i} & ~set,:) = cases{i+1};\r\n"
> + " else\r\n"
> + " x(cases{i} & ~set,:) = cases{i+1}(cases{i} &
> ~set);\r\n"
> + " end\r\n"
> + " set = set | cases{i};\r\n"
> + " if(set), break, end\r\n"
> + " end\r\n"
> + " if (length(default) == 1)\r\n"
> + " x(~set,:) = default;\r\n"
> + " else\r\n"
> + " x(~set,:) = default(~set);\r\n"
> + " end\r\n"
> + "end\r\n"
> + "%% Pad out or shorten strings to a set length\r\n"
> + "function strout = strpad(strin)\r\n"
> + " req_length = 50;\r\n"
> + " insize = size(strin,2);\r\n"
> + " if insize > req_length\r\n"
> + " strout = strin(1:req_length);\r\n"
> + " else\r\n"
> + " strout = [strin, blanks(req_length - insize)];\r\n"
> + " end\r\n"
> + "end\r\n"
> + "%% Compute a logarithm to any base\r\n"
> + "function x = arbitrary_log(a, base)\r\n"
> + " x = log(a) ./ log(base);\r\n"
> + "end\r\n"
> + "%% Least common multiple\r\n"
> + "function m = lcm_multi(x)\r\n"
> + " m = x(1);\r\n"
> + " for (i = 1:size(x,2))\r\n"
> + " if(x(i) ~= 0), m = m./gcd(m,x(i)).*x(i);, end\r\n"
> + " end\r\n"
> + "end\r\n"
> + "%% Greatest common divisor\r\n"
> + "function d = gcd_multi(x)\r\n"
> + " d = 0;\r\n"
> + " for (i = 1:size(x,2)), d = gcd(d, x(:,i));, end\r\n"
> + "end\r\n\r\n");
> +
> + frag = cci->functionsString();
> + printf("%S\n", frag);
> + free(frag);
> +}
> +
> +void
> +doNameAnnotations(iface::cellml_api::Model* aModel,
> + iface::cellml_services::CodeGenerator* aCG)
> +{
> + // Make an annotation set...
> + iface::cellml_services::AnnotationToolService* ats
> + (CreateAnnotationToolService());
> + iface::cellml_services::AnnotationSet* as(ats->createAnnotationSet());
> + ats->release_ref();
> +
> + aCG->useAnnoSet(as);
> +
> + // Now we go through all variables in the model and set their
> annotations...
> + iface::cellml_api::CellMLComponentSet* ccs = aModel->allComponents();
> +
> + iface::cellml_api::CellMLComponentIterator* cci =
> ccs->iterateComponents();
> + ccs->release_ref();
> +
> + iface::cellml_api::CellMLComponent* comp;
> + while ((comp = cci->nextComponent()) != NULL)
> + {
> + iface::cellml_api::CellMLVariableSet* vs(comp->variables());
> + wchar_t* compname = comp->name();
> + comp->release_ref();
> + iface::cellml_api::CellMLVariableIterator* vi(vs->iterateVariables());
> + vs->release_ref();
> +
> + iface::cellml_api::CellMLVariable* v;
> + while ((v = vi->nextVariable()) != NULL)
> + {
> + wchar_t* name = v->name();
> + std::wstring varn = compname;
> + varn += L"_";
> + varn += name;
> + free(name);
> + std::wstring raten = L"rate_";
> + raten += varn;
> + as->setStringAnnotation(v, L"expression", varn.c_str());
> + as->setStringAnnotation(v, L"expression_d1", raten.c_str());
> + v->release_ref();
> + }
> +
> + vi->release_ref();
> +
> + free(compname);
> + }
> +
> + cci->release_ref();
> +
> + as->release_ref();
> +}
> +
> +int
> +main(int argc, char** argv)
> +{
> + // Get the URL from which to load the model...
> + if (argc < 2)
> + {
> + printf("Usage: CellML2Matlab modelURL\n");
> + return -1;
> + }
> +
> + uint32_t usenames = 0;
> +
> + if (argc > 2)
> + {
> + if (!strcmp(argv[2], "usenames"))
> + usenames = 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;
> +
> + iface::cellml_services::CodeGeneratorBootstrap* cgb =
> + CreateCodeGeneratorBootstrap();
> + iface::cellml_services::CodeGenerator* cg =
> + cgb->createCodeGenerator();
> + cgb->release_ref();
> +
> + // The code generator is designed to generate C code by default, so
> + // we need to customise it to generate Matlab code instead
> +
> + cg->constantPattern(L"CONSTANTS(:,%)");
> + cg->stateVariableNamePattern(L"STATES(:,%)");
> + cg->algebraicVariableNamePattern(L"ALGEBRAIC(:,%)");
> + cg->rateNamePattern(L"RATES(:,%)");
> + cg->voiPattern(L"VOI");
> + cg->assignPattern(L" <LHS> = <RHS>;\r\n");
> + cg->arrayOffset(1);
> + cg->solvePattern(L"ALGEBRAIC = rootfind_<ID>(VOI, CONSTANTS, STATES,
> ALGEBRAIC);\r\n"
> + L"<SUP>"
> + L"% Functions required for solving differential algebraic equation\r\n"
> + L"function ALGEBRAIC = rootfind_<ID>(VOI, CONSTANTS, STATES,
> ALGEBRAIC_IN)\r\n"
> + L" ALGEBRAIC = ALGEBRAIC_IN;\r\n"
> + L" global initialGuess;\r\n"
> + L" if (length(initialGuess) ~= 1), initialGuess = getInitialGuess"
> + L" options = optimset('Display', 'off', 'TolX', 1E-6);\r\n"
> + L" if length(VOI) == 1\r\n"
> + L" residualfn =
> @(algebraicCandidate)residualSN_<ID>(algebraicCandidate, ALGEBRAIC, VOI,
> CONSTANTS, STATES);\r\n"
> + L" <VAR> = fsolve(residualfn, initialGuess, options);\r\n"
> + L" initialGuess = <VAR>;\r\n"
> + L" else\r\n"
> + L" SET_<VAR> = logical(1);\r\n"
> + L" for i=1:length(VOI)\r\n"
> + L" residualfn =
> @(algebraicCandidate)residualSN_<ID>(algebraicCandidate, ALGEBRAIC(i,:),
> VOI(i), CONSTANTS, STATES(i,:));\r\n"
> + L" TEMP_<VAR> = fsolve(residualfn, initialGuess,
> options);\r\n"
> + L" ALGEBRAIC(i,SET_ALGEBRAIC) =
> TEMP_ALGEBRAIC(SET_ALGEBRAIC);\r\n"
> + L" initialGuess = TEMP_<VAR>;\r\n"
> + L" end\r\n"
> + L" end\r\n"
> + L"end\r\n"
> + L"function resid = residualSN_<ID>(algebraicCandidate, ALGEBRAIC, VOI,
> CONSTANTS, STATES)\r\n"
> + L" <VAR> = algebraicCandidate;\r\n"
> + L" resid = fixnans((<LHS>) - (<RHS>));\r\n"
> + L"end\r\n"
> + L"function algebraicGuess = getInitialGuess(count)\r\n"
> + L" algebraicGuess = ones(count,1) * 0.1;\r\n"
> + L"end\r\n"
> + L"function xfixed = fixnans(x)\r\n"
> + L" xfixed = x;\r\n"
> + L" xfixed(isnan(x)) = 1.0;\r\n"
> + L" xfixed(isinf(x)) = 1E1000;\r\n"
> + L"end\r\n");
> + cg->solveNLSystemPattern(L"ALGEBRAIC = rootfind_<ID>(VOI, CONSTANTS,
> STATES, ALGEBRAIC);\r\n"
> + L"<SUP>"
> + L"% Functions required for solving differential algebraic equation\r\n"
> + L"function ALGEBRAIC = rootfind_<ID>(VOI, CONSTANTS, STATES,
> ALGEBRAIC_IN)\r\n"
> + L" ALGEBRAIC = ALGEBRAIC_IN;\r\n"
> + L" global initialGuess;\r\n"
> + L" if (length(initialGuess) ~= <COUNT>), initialGuess =
> getInitialGuess(<COUNT>);, end\r\n"
> + L" options = optimset('Display', 'off', 'TolX', 1E-6);\r\n"
> + L" if length(VOI) == 1\r\n"
> + L" residualfn =
> @(algebraicCandidate)residualSN_<ID>(algebraicCandidate, ALGEBRAIC, VOI,
> CONSTANTS, STATES);\r\n"
> + L" soln = fsolve(residualfn, initialGuess, options);\r\n"
> + L" initialGuess = soln;\r\n"
> + L" <EQUATIONS><VAR> = soln(<INDEX>);<JOIN>\r\n"
> + L" </EQUATIONS>\r\n"
> + L" else\r\n"
> + L" <EQUATIONS>SET_<VAR> = logical(1);<JOIN>\r\n"
> + L" </EQUATIONS>\r\n"
> + L" for i=1:length(VOI)\r\n"
> + L" residualfn =
> @(algebraicCandidate)residualSN_<ID>(algebraicCandidate, ALGEBRAIC(i,:),
> VOI(i), CONSTANTS, STATES(i,:));\r\n"
> + L" soln = fsolve(residualfn, initialGuess, options);\r\n"
> + L" initialGuess = soln;\r\n"
> + L" <EQUATIONS>TEMP_<VAR> = soln(<INDEX>);<JOIN>\r\n"
> + L" </EQUATIONS>\r\n"
> + L" ALGEBRAIC(i,SET_ALGEBRAIC) =
> TEMP_ALGEBRAIC(SET_ALGEBRAIC);\r\n"
> + L" end\r\n"
> + L" end\r\n"
> + L"end\r\n"
> + L"function resid = residualSN_<ID>(algebraicCandidate, ALGEBRAIC, VOI,
> CONSTANTS, STATES)\r\n"
> + L" <EQUATIONS><VAR> = algebraicCandidate(<INDEX>);<JOIN>\r\n"
> + L" </EQUATIONS>\r\n"
> + L" <EQUATIONS>resid(<INDEX>) = fixnans((<LHS>) - (<RHS>));<JOIN>\r\n"
> + L" </EQUATIONS>\r\n"
> + L"end\r\n"
> + L"function algebraicGuess = getInitialGuess(count)\r\n"
> + L" algebraicGuess = ones(count,1) * 0.1;\r\n"
> + L"end\r\n"
> + L"function xfixed = fixnans(x)\r\n"
> + L" xfixed = x;\r\n"
> + L" xfixed(isnan(x)) = 1.0;\r\n"
> + L" xfixed(isinf(x)) = 1E1000;\r\n"
> + L"end\r\n");
> +
> + iface::cellml_services::MaLaESBootstrap* mb = CreateMaLaESBootstrap();
> +
> + iface::cellml_services::MaLaESTransform* mt =
> + mb->compileTransformer
> + (
> + L"opengroup: (\r\n"
> + L"closegroup: )\r\n"
> + L"abs: #prec[H]abs(#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[H]acot(#expr1)\r\n"
> + L"arccoth: #prec[H]acoth(#expr1)\r\n"
> + L"arccsc: #prec[H]acsc(#expr1)\r\n"
> + L"arccsch: #prec[H]acsch(#expr1)\r\n"
> + L"arcsec: #prec[H]asec(#expr1)\r\n"
> + L"arcsech: #prec[H]asech(#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[H]cot(#expr1)\r\n"
> + L"coth: #prec[H]coth(#expr1)\r\n"
> + L"csc: #prec[H]csc(#expr1)\r\n"
> + L"csch: #prec[H]csch(#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)]mod(#expr1, #expr2) == 0\r\n"
> + L"floor: #prec[H]floor(#expr1)\r\n"
> + L"gcd: #prec[H]gcd_multi([#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)#supplement double func#unique1(double* BOUND, "
> + L"double* CONSTANTS, double* RATES, double* VARIABLES) { return #expr1;
> }\r\n"
> + L"lcm: #prec[H]lcm_multi([#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]max([#exprs[, ]],[],2)\r\n"
> + L"min: #prec[H]min([#exprs[, ]],[],2)\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]#expr1 .^ #expr2\r\n"
> + L"quotient: #prec[900(0)] floor(#expr1 ./ #expr2)\r\n"
> + L"rem: #prec[900(0)] rem(#expr1, #expr2)\r\n"
> + L"root: #prec[1000(900)] #expr1 .^ (1.0 / #degree)\r\n"
> + L"sec: #prec[H]sec(#expr1)\r\n"
> + L"sech: #prec[H]sech(#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)]xor(#expr1 , #expr2)\r\n"
> + L"piecewise_first_case: #prec[5]piecewise({#expr1, #expr2 \r\n"
> + L"piecewise_extra_case: #prec[5], #expr1, #expr2 \r\n"
> + L"piecewise_otherwise: #prec[5]}, #expr1)\r\n"
> + L"piecewise_no_otherwise: #prec[5]}, NaN)\r\n"
> + L"pi: #prec[999] pi\r\n"
> + L"eulergamma: #prec[999]0.577215664901533\r\n"
> + L"infinity: #prec[900] Inf\r\n"
> + );
> +
> + cg->transform(mt);
> +
> + mt->release_ref();
> + mb->release_ref();
> +
> + if (usenames)
> + doNameAnnotations(mod, cg);
> +
> + iface::cellml_services::CodeInformation* cci = NULL;
> + try
> + {
> + cci = cg->generateCode(mod);
> + }
> + catch (iface::cellml_api::CellMLException& ce)
> + {
> + 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();
> +
> + wchar_t* m = cci->errorMessage();
> + if (wcscmp(m, L""))
> + {
> + printf("Error generating code: %S\n", m);
> + cci->release_ref();
> + free(m);
> + return -1;
> + }
> + free(m);
> +
> + // We now have the code information...
> + WriteCode(cci);
> + cci->release_ref();
> +
> + return 0;
> +}
>
> Modified: CellML_DOM_API/trunk/CCGS/tests/build.mk
> ===================================================================
> --- CellML_DOM_API/trunk/CCGS/tests/build.mk 2009-01-07 01:57:04 UTC (rev
> 2990)
> +++ CellML_DOM_API/trunk/CCGS/tests/build.mk 2009-01-08 03:29:51 UTC (rev
> 2991)
> @@ -1,4 +1,4 @@
> -bin_PROGRAMS += CellML2C CellML2Python
> +bin_PROGRAMS += CellML2C CellML2Python CellML2Matlab
> CellML2C_SOURCES=$(top_srcdir)/CCGS/tests/CellML2C.cpp
> CellML2C_LDADD=\
> $(top_builddir)/libcellml.la \
> @@ -11,3 +11,9 @@
> $(top_builddir)/libccgs.la -lxml2
> CellML2Python_LDFLAGS=-O0
> CellML2Python_CXXFLAGS=-I$(top_srcdir)/sources -I$(top_srcdir)/sources/dom
> -I$(top_srcdir)/sources/mathml -I$(top_srcdir)/sources/cellml
> -I$(top_srcdir)/AnnoTools/sources -I$(top_builddir)/interfaces
> -I$(top_srcdir)/CCGS/sources -I$(top_srcdir)/MaLaES/sources -Wall -O0
> $(AM_CXXFLAGS)
> +CellML2Matlab_SOURCES=$(top_srcdir)/CCGS/tests/CellML2Matlab.cpp
> +CellML2Matlab_LDADD=\
> + $(top_builddir)/libcellml.la \
> + $(top_builddir)/libccgs.la -lxml2
> +CellML2Matlab_LDFLAGS=-O0
> +CellML2Matlab_CXXFLAGS=-I$(top_srcdir)/sources -I$(top_srcdir)/sources/dom
> -I$(top_srcdir)/sources/mathml -I$(top_srcdir)/sources/cellml
> -I$(top_srcdir)/AnnoTools/sources -I$(top_builddir)/interfaces
> -I$(top_srcdir)/CCGS/sources -I$(top_srcdir)/MaLaES/sources -Wall -O0
> $(AM_CXXFLAGS)
>
> _______________________________________________
> automated-notifications mailing list
> automated-notifications at cellml.org
> http://www.cellml.org/mailman/listinfo/automated-notifications
>

---

• [cellml-dev] r2991 - in CellML_DOM_API/trunk: . CCGS/tests, Andrew Miller, 01/08/2009
  • [cellml-dev] r2991 - in CellML_DOM_API/trunk: . CCGS/tests, Randall Britten, 01/08/2009
    • [cellml-dev] r2991 - in CellML_DOM_API/trunk: . CCGS/tests, Alan Garny, 01/08/2009

---

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