Nothing
R/cppDefs_nimbleFunction.R
In nimble: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Defines functions
makeCopyFromRobjectDef
makeSingleCopyCall
updateADproxyModelMethods
modifyForAD_calculate
modifyForAD_eigenBlock
modifyForAD_getSetValues
modifyForAD_recordable
modifyForAD_chainedCall
modifyForAD_nfMethod
modifyForAD_getDerivs_wrapper
modifyForAD_RCfunction
modifyForAD_prependNimDerivs
modifyForAD_AssignEigenMap
modifyForAD_RecyclingRule
modifyForAD_ADbreak
modifyForAD_MAKE_FIXED_VECTOR
modifyForAD_matinverse
modifyForAD_matmult
modifyForAD_issuePowWarning
recurse_modifyForAD
exprClasses_modifyForAD
##
cppVirtualNimbleFunctionClass <- setRefClass('cppVirtualNimbleFunctionClass',
contains = 'cppClassDef',
fields = list(
nfProc = 'ANY'
),
methods = list(
initialize = function(nfProc, ...) {
callSuper(...)
if(!missing(nfProc)) processNFproc(nfProc)
useGenerator <<- FALSE
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(is.null(baseClassObj)) {
addInheritance("NamedObjects")
} else {
if(is.character(baseClassObj)) addInheritance(baseClassObj)
else {
virtual <- environment(baseClassObj)$virtual
if(isTRUE(virtual))
baseClassName <- environment(baseClassObj)$className
else
baseClassName <- environment(baseClassObj)$CclassName
addInheritance(baseClassName)
}
}
},
processNFproc = function(nfp) {
nfProc <<- nfp
assign('cppDef', .self, envir = environment(nfProc$nfGenerator))
for(i in names(nfp$RCfunProcs)) { ## This is what we should do for cppNimbleFunctions too
abstract <- !isFALSE( environment(nfProc$nfGenerator)$methodControl[[i]]$required ) # default required = TRUE. required is a synonym for abstract. If it's abstract, it's required in derived classes.
functionDefs[[i]] <<- RCfunctionDef(virtual = TRUE, abstract = abstract)
functionDefs[[i]]$buildFunction(nfp$RCfunProcs[[i]])
}
}
)
)
## cppNimbleClassClass defines commonalities between cppNimbleFunctionClass and cppNimbleListClass, both of which are classes in nimble
cppNimbleClassClass <- setRefClass('cppNimbleClassClass',
contains = 'cppNamedObjectsClass',
fields = list(
## Inherits a functionDefs list for member functions
## Inherits an objectDefs list for member data
SEXPmemberInterfaceFuns = 'ANY', ## List of SEXP interface functions, one for each member function
nimCompProc = 'ANY', ## nfProcessing or nlProcessing object, needed to get the member data symbol table post-compilation
Rgenerator = 'ANY' , ## function to generate and wrap a new object from an R object
CmultiInterface = 'ANY', ## object for interfacing multiple C instances when a top-level interface is not needed
built = 'ANY',
loaded = 'ANY',
Cwritten = 'ANY',
RCfunDefs = 'ANY'
),
methods = list(
getDefs = function() {
callSuper()
},
getHincludes = function() {
callSuper()
},
getCPPincludes = function() {
callSuper()
},
getCPPusings = function() {
callSuper()
},
genNeededTypes = function(debugCpp = FALSE, fromModel = FALSE) {
for(i in seq_along(nimCompProc$neededTypes)) {
neededType<- nimCompProc$neededTypes[[i]]
if(inherits(neededType, 'nfMethodRC')) {
thisCppDef <- nimbleProject$getRCfunCppDef(neededType, NULLok = TRUE)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$needRCfunCppClass(neededType, genNeededTypes = TRUE, fromModel = fromModel)
neededTypeDefs[[neededType$uniqueName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolModelValues')) {
thisCppDef <- nimbleProject$getModelValuesCppDef(neededType$mvConf, NULLok = TRUE)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$needModelValuesCppClass(neededType$mvConf, fromModel = fromModel)
mvClassName <- environment(neededType$mvConf)$className
neededTypeDefs[[mvClassName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleFunction')) {
generatorName <- environment(neededType$nfProc$nfGenerator)$name
thisCppDef <- nimbleProject$getNimbleFunctionCppDef(generatorName = generatorName)
if(is.null(thisCppDef)) {
className <- names(nimCompProc$neededTypes)[i]
if(neededType$type == 'nimbleFunction')
thisCppDef <- nimbleProject$buildNimbleFunctionCompilationInfo(generatorName = generatorName, fromModel = fromModel)
else if(neededType$type == 'nimbleFunctionVirtual')
thisCppDef <- nimbleProject$buildVirtualNimbleFunctionCompilationInfo(vfun = generatorName)
else stop('symbolNimbleFunction does not have type nimbleFunction or nimbleFunctionVirtual')
neededTypeDefs[[ className ]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleList')) {
CPPincludes <<- c(CPPincludes, nimbleIncludeFile("smartPtrs.h"))
generatorName <- neededType$nlProc$name
if(generatorName == 'NIMBLE_ADCLASS') Hincludes <<- c(Hincludes, nimbleIncludeFile("nimbleCppAD.h"))
thisCppDef <- nimbleProject$getNimbleListCppDef(generatorName = generatorName)
if(is.null(thisCppDef)){
className <- names(nimCompProc$neededTypes)[i]
thisCppDef <- nimbleProject$buildNimbleListCompilationInfo(className = generatorName, fromModel = fromModel)
neededTypeDefs[[ className ]] <<- thisCppDef
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleFunctionList')) {
baseClassName <- environment(neededType$baseClass)$name
thisCppDef <- nimbleProject$getNimbleFunctionCppDef(generatorName = baseClassName)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$buildVirtualNimbleFunctionCompilationInfo(vfun = neededType$baseClass)
neededTypeDefs[[baseClassName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
}
}
},
initialize = function(nimCompProc, debugCpp = FALSE, fromModel = FALSE, ...) {
callSuper(...) ## must call this first because it sets objectDefs to list()
RCfunDefs <<- list()
if(!missing(nimCompProc)) processNimCompProc(nimCompProc, debugCpp = debugCpp, fromModel = fromModel)
built <<- FALSE
loaded <<- FALSE
Cwritten <<- FALSE
},
processNimCompProc = function(ncp, debugCpp = FALSE, fromModel = FALSE) {
ncp$cppDef <- .self
nimCompProc <<- ncp
genNeededTypes(debugCpp = debugCpp, fromModel = fromModel)
objectDefs <<- symbolTable2cppVars(ncp$getSymbolTable())
},
addCopyFromRobject = function() {
## The next line creates the cppCopyTypes exactly the same way as in buildNimbleObjInterface
## and CmultiNimbleObjClass::initialize.
cppCopyTypes <- makeNimbleFxnCppCopyTypes(nimCompProc$getSymbolTable(), objectDefs$getSymbolNames())
buildDerivsInCopier <- FALSE
if(inherits(nimCompProc, 'virtualNFprocessing')) {
buildDerivs <- environment(nimCompProc$nfGenerator)[['buildDerivs']]
buildDerivsInCopier <- (length(buildDerivs) > 0) & (!isFALSE(buildDerivs))
}
copyFromRobjectDefs <- makeCopyFromRobjectDef(cppCopyTypes,
buildDerivs = buildDerivsInCopier)
functionDefs[['copyFromRobject']] <<- copyFromRobjectDefs$copyFromRobjectDef
},
buildAll = function(where = where) {
makeCppNames()
buildConstructorFunctionDef()
buildSEXPgenerator(finalizer = "namedObjects_Finalizer")
buildRgenerator(where = where)
buildCmultiInterface()
},
buildRgenerator = function() {message('whoops, base class version of buildRgenerator')},
buildCmultiInterface = function() {message('whoops, base class version of buildCmultiInterface')},
makeCppNames = function() {
Rnames2CppNames <<- as.list(Rname2CppName(objectDefs$getSymbolNames()))
names(Rnames2CppNames) <<- objectDefs$getSymbolNames()
},
buildConstructorFunctionDef = function() {
newNestedListLines <- list()
flagLine <- list()
pointerLine <- list()
if(!(is.null(nimCompProc[['nimbleListObj']]))){
flagText <- paste0('RCopiedFlag = false')
flagLine[[1]] <- substitute(FLAGTEXT,
list(FLAGTEXT = as.name(flagText)))
pointerText <- paste0('RObjectPointer = NULL')
pointerLine[[1]] <- substitute(POINTERTEXT,
list(POINTERTEXT = as.name(pointerText)))
for(i in seq_along(nimCompProc$neededTypes)){
newListText <- paste0(nimCompProc$neededTypes[[i]]$name, " = new ", as.name(names(nimCompProc$neededTypes)[i]))
newNestedListLines[[i]] <- substitute(NEWLISTTEXT,
list(NEWLISTTEXT = as.name(newListText)))
}
}
code <- putCodeLinesInBrackets(c(flagLine, pointerLine, newNestedListLines,
list(namedObjectsConstructorCodeBlock())))
conFunDef <- cppFunctionDef(name = name,
returnType = emptyTypeInfo(),
code = cppCodeBlock(code = code, skipBrackets = TRUE))
functionDefs[['constructor']] <<- conFunDef
}
),
)
cppNimbleFunctionClass <- setRefClass('cppNimbleFunctionClass',
contains = 'cppNimbleClassClass',
fields = list(
nfProc = 'ANY', ## an nfProcessing class, needed to get the member data symbol table post-compilation
parentsSizeAndDims = 'ANY',
ADconstantsInfo = 'ANY'
),
methods = list(
getDefs = function() {
c(callSuper(), SEXPmemberInterfaceFuns)
},
getHincludes = function() {
c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getHincludes()), recursive = FALSE))
},
getCPPincludes = function() {
c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getCPPincludes()), recursive = FALSE))
},
getCPPusings = function() {
CPPuse <- unique(c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getCPPusings()))))
CPPuse
},
initialize = function(nfProc, isNode, debugCpp = FALSE, fromModel = FALSE, ...) {
callSuper(nfProc, debugCpp, fromModel, ...)
if(!missing(nfProc)) processNFproc(nfProc, debugCpp = debugCpp, fromModel = fromModel)
if(isNode) {
inheritance <<- inheritance[inheritance != 'NamedObjects']
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(is.null(baseClassObj)) {
inheritance <<- c(inheritance, 'nodeFun')
parentsSizeAndDims <<- environment(nfProc$nfGenerator)$parentsSizeAndDims
ADconstantsInfo <<- environment(nfProc$nfGenerator)$ADconstantsInfo
}
}
},
processNFproc = function(nfp, debugCpp = FALSE, fromModel = FALSE) {
nfProc <<- nimCompProc
buildFunctionDefs()
## This is slightly klugey
## The objectDefs here are for the member data
## We need them to be the parentST for each member function
## However the building of the cpp objects is slightly out of order, with the
## member functions already having been built during nfProcessing.
for(i in seq_along(functionDefs)) {
functionDefs[[i]]$args$parentST <<- objectDefs
}
SEXPmemberInterfaceFuns <<- lapply(functionDefs,
function(x)
if(inherits(x$SEXPinterfaceFun, "cppFunctionDef"))
x$SEXPinterfaceFun
else
NULL
)
SEXPmemberInterfaceFuns <<-
SEXPmemberInterfaceFuns[ !unlist(lapply(SEXPmemberInterfaceFuns, is.null)) ]
nimCompProc <<- nfProc
},
buildFunctionDefs = function() {
for(i in seq_along(nfProc$RCfunProcs)) {
RCname <- names(nfProc$RCfunProcs)[i]
functionDefs[[RCname]] <<- RCfunctionDef$new() ## all nodeFunction members are const f
functionDefs[[RCname]]$buildFunction(nfProc$RCfunProcs[[RCname]])
if(!grepl("ADproxyModel", RCname)) ## don't build "CALL_" function for AD functions
functionDefs[[RCname]]$buildSEXPinterfaceFun(className = nfProc$name)
RCfunDefs[[RCname]] <<- functionDefs[[RCname]]
}
},
addTypeTemplateFunction = function(funName,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
useModelInfo <- list()
## if(static) {
## newFunName <- paste0(funName, '_AD_')
## ## We need the template<TYPE_> function and also
## ## whether a calculate was detected and if so its nodeFxnVector_name
## res <- makeTypeTemplateFunction(newName = newFunName,
## .self = regularFun,
## static = TRUE,
## useRecordingInfo = TRUE,
## derivControl = derivControl)
## functionDefs[[newFunName]] <<- res$fun
## useModelInfo$nodeFxnVector_name <- res[['nodeFxnVector_name']]
## } else {
## We need a separate one for the "reconfigure" system that is non-static
## if(isTRUE(nimbleOptions('useADreconfigure'))) {
newFunName <- paste0(funName, '_AD2_')
res <- makeTypeTemplateFunction(newName = newFunName,
.self = regularFun,
##static = FALSE,
useRecordingInfo = TRUE,
derivControl = derivControl)
functionDefs[[newFunName]] <<- res$fun
useModelInfo$nodeFxnVector_name <- res[['nodeFxnVector_name']]
## }
## }
useModelInfo
},
add_deriv_function = function(funName,
independentVarNames,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
## static <- isTRUE(derivControl[['static']])
## if(static) {
## message("add_deriv_function support for static is not written.")
## } else {
if(isTRUE(nimbleOptions("useADreconfigure"))) {
newFunName <- paste0(funName, '_deriv_')
argTransName <- paste0(funName, '_ADargumentTransfer2_')
functionDefs[[newFunName]] <<- make_deriv_function(regularFun,
newFunName,
independentVarNames,
argTransName)
## Add meta-taping type template function of the new function
newMetaFunName <- paste0(funName, '_AD2__deriv_')
argTransName <- paste0(funName, '_ADargumentTransfer2__AD2_')
functionDefs[[newMetaFunName]] <<- make_deriv_function(regularFun,
newMetaFunName,
independentVarNames,
argTransName,
meta = TRUE)
} else {
message("Don't know how to use static=FALSE without nimbleOptions('useADreconfigure')." )
}
## }
},
addADtapingFunction = function( funName,
independentVarNames,
dependentVarNames,
useModelInfo = NULL,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
if(is.null(useModelInfo))
useModelInfo <- list()
## static <- isTRUE(derivControl[['static']])
## if(static) {
## ADfunName <- paste0(funName, '_AD_')
## newFunName <- paste0(funName, '_callForADtaping2_')
## functionDefs[[newFunName]] <<- makeADtapingFunction2(newFunName,
## regularFun,
## ADfunName,
## independentVarNames,
## dependentVarNames,
## nfProc$isNode,
## className = name)
## }
## if(!static) {
## if(isTRUE(nimbleOptions("useADreconfigure"))) {
ADfunName2 <- paste0(funName, '_AD2_')
newFunName2 <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2]] <<- makeADtapingFunction2(newFunName2,
regularFun,
ADfunName2,
independentVarNames,
dependentVarNames,
nfProc$isNode,
className = name,
useModelInfo = useModelInfo)
## }
## }
invisible(NULL)
},
addADargumentTransferFunction = function(funName,
independentVarNames,
funIndex,
useModelInfo = NULL,
derivControl = list()) {
## static <- isTRUE(derivControl[['static']])
regularFun <- RCfunDefs[[funName]]
## funIndex <- which(names(environment(nfProc$nfGenerator)$enableDerivs == funName)) ## needed for correct index for allADtapePtrs_
## if(static) {
## newFunName <- paste0(funName, '_ADargumentTransfer_')
## functionDefs[[newFunName]] <<- makeADargumentTransferFunction(newFunName,
## regularFun,
## independentVarNames,
## funIndex,
## parentsSizeAndDims,
## ADconstantsInfo)
## } else {
## Version 2 is for the "reconfig" version
## if(isTRUE(nimbleOptions("useADreconfigure"))) {
newFunName2 <- paste0(funName, '_ADargumentTransfer2_')
## For now, use same funIndex since this will use the non-static tape vector, but we may want to be more careful
callForTapingName <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2]] <<- makeADargumentTransferFunction2(newFunName2,
regularFun,
callForTapingName,
independentVarNames,
funIndex,
parentsSizeAndDims,
ADconstantsInfo,
useModelInfo,
derivControl)
newFunName2meta <- paste0(funName, '_ADargumentTransfer2__AD2_')
## For now, use same funIndex since this will use the non-static tape vector, but we may want to be more careful
callForTapingName <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2meta]] <<- makeADargumentTransferFunction2(newFunName2meta,
regularFun,
callForTapingName,
independentVarNames,
funIndex,
parentsSizeAndDims,
ADconstantsInfo,
useModelInfo,
derivControl,
metaTape = TRUE)
## }
## }
invisible(NULL)
},
## addStaticInitClass = function(staticMethods) {
## neededTypeDefs[['staticInitClass']] <<- makeStaticInitClass(.self, staticMethods) ##
## invisible(NULL)
## },
addADclassContentOneFun = function(funName,
derivControl,
funIndex) {
##outSym <- nfProc$RCfunProcs[[funName]]$compileInfo$returnSymbol
## TO-DO: revisit checking arguments for deriv compability
## isStatic <- isTRUE(derivControl[['static']])
## if(!isTRUE(derivControl[['meta']]) & isStatic)
## checkADargument(funName, outSym, returnType = TRUE)
RCfunProc <- nfProc$RCfunProcs[[funName]]
nameSubList <- RCfunProc$nameSubList
compileInfo <- nfProc$compileInfos[[funName]]
if(length(nameSubList) == 0)
stop(paste0('Derivatives cannot be built for method ',
funName,
', since this method has no arguments.'))
## if(!nfProc$isNode & !isTRUE(derivControl[['meta']]) & isStatic){
## for(iArg in seq_along(functionDefs[[funName]]$args$symbols)){
## arg <- functionDefs[[funName]]$args$symbols[[iArg]]
## argSym <- nfProc$RCfunProcs[[funName]]$compileInfo$origLocalSymTab$getSymbolObject(arg$name)
## argName <- names(nfProc$RCfunProcs[[funName]]$nameSubList)[iArg]
## checkADargument(funName, argSym, argName = argName)
## }
## }
useModelInfo <- addTypeTemplateFunction(funName,
derivControl = derivControl) ## returns either NULL (if there is no model$calculate) or a nodeFxnVector name (if there is)
## independentVarNames <- names(functionDefs[[funName]]$args$symbols)
independentVarNames <- as.character(nameSubList)
## ivBaseTypes <- unlist(lapply(functionDefs[[funName]]$args$symbols, `[[`, "baseType"))
ivBaseTypes <- lapply(compileInfo$newLocalSymTab$symbols[independentVarNames], `[[`, "type")
## independentVarNames <- names(ivBaseTypes)
includeIV <- ivBaseTypes == "double" ## previously ivBaseTypes != "bool"
ignore <- derivControl[["ignore"]]
if(!is.null(ignore)) {
noDeriv_mangledArgNames <- as.character(unlist(nameSubList[ignore]))
includeIV <- includeIV & !(independentVarNames %in% noDeriv_mangledArgNames)
}
independentVarNames <- as.character(independentVarNames[includeIV])
if(nfProc$isNode) independentVarNames <- independentVarNames[-1] ## remove ARG1_INDEXEDNODEINFO__ from independentVars
if(!isTRUE(derivControl[['meta']])) {
addADtapingFunction(funName,
independentVarNames = independentVarNames,
dependentVarNames = 'ANS_',
useModelInfo,
derivControl = derivControl )
addADargumentTransferFunction(funName,
independentVarNames = independentVarNames,
funIndex = funIndex,
useModelInfo = useModelInfo,
derivControl = derivControl)
add_deriv_function(funName,
independentVarNames,
derivControl)
funIndex + 1 ## function return value increments by one in non-meta case
} else {
funIndex ## but does not increment in meta case
}
},
## addNimDerivsCalculateContentOneFun = function(funName,
## derivControl,
## funIndex) {
## ## We only need to add one line here, which can go at the beginning
## ## set_tape_ptr(ADtapeSetup, myADtapePtrs_[<funIndex>-1], true);
## thisFunctionDef <- functionDefs[[funName]]
## thisCode <- thisFunctionDef$code$code ## lines of code
## newFunIndex <- exprClasses_updateNimDerivsCalculate(thisCode, funIndex)
## newFunIndex
## },
checkADargument = function(funName, argSym, argName = NULL, returnType = FALSE){
argTypeText <- if(returnType) 'returnType' else 'argument'
if(argSym$type != 'double')
stop(paste0('The ', argName, ' ', argTypeText, ' of the ', funName, ' method is not a double, this method cannot have derivatives built.'))
# if(!(argSym$nDim %in% c(0,1)))
# stop(paste0('The ', argName, ' ', argTypeText, ' of the ', funName, ' method must be a double scalar or double vector for derivatives to be enabled.'))
if((argSym$nDim != 0) && is.na(argSym$size))
stop(paste0('To build derivatives, size must be given for the ',
argName, ' ', argTypeText, ' of the ', funName,
' method, e.g. double(1, 3) for a length 3 vector.' ))
},
addADclassContent = function() {
constructorCode <- NULL ## default return object
buildDerivs <- environment(nfProc$nfGenerator)$buildDerivs
buildNames <- names(buildDerivs)
ADinUse <- FALSE
for(iED in seq_along(buildDerivs)) {
if(!isTRUE(buildDerivs[[iED]][['isNode']])) {
ADinUse <- TRUE
if(!isTRUE(buildDerivs[[iED]][['calculate']])) {
addADclassContentOneFun(buildNames[iED],
buildDerivs[[iED]],
funIndex = iED) ## funIndex might be deprecated
}
}
}
if(ADinUse) {
Hincludes <<- c(nimbleIncludeFile("nimbleCppADbaseClass.h"),
Hincludes)
CPPincludes <<- c(nimbleIncludeFile("nimbleCppAD.h"),
nimbleIncludeFile("nimDerivs_dists.h"),
## The ".cpp" extension make it end up linked as a .o
## in cppProjectClass$writeFiles. Prior to that, it is
## copied and locally compiled by cppProjectClass
"nimbleCppADbaseClass.cpp", CPPincludes)
addInheritance("nimbleFunctionCppADbase")
addADinfoObjects(.self)
}
constructorCode
},
buildCmultiInterface = function(dll = NULL) {
sym <- if(!is.null(dll))
getNativeSymbolInfo(SEXPgeneratorFun$name, dll)
else
SEXPgeneratorFun$name
## copyFromRobject_sym <- if(!is.null(dll))
## getNativeSymbolInfo(SEXPmemberInterfaceFuns[['copyFromRobject']]$name, dll)
## else
## SEXPmemberInterfaceFuns[['copyFromRobject']]$name
CmultiInterface <<- CmultiNimbleFunctionClass(compiledNodeFun = .self,
basePtrCall = sym,
##copyFromRobjectCall = copyFromRobject_sym,
project = nimbleProject)
},
buildRgenerator = function(where = globalenv(), dll = NULL) {
sym <- if(!is.null(dll))
getNativeSymbolInfo(SEXPgeneratorFun$name, dll)
else
SEXPgeneratorFun$name
Rgenerator <<- buildNimbleObjInterface(paste0(name,'_refClass') , .self, sym, where = where)
},
promoteCallable = function(R_NimbleFxn, asTopLevel = TRUE){
## see comment in nimbleProjectClass::compileNimbleFunction
oldCobjectInterface <- nf_getRefClassObject(R_NimbleFxn)$.CobjectInterface
if(!is.list(oldCobjectInterface)) return(oldCobjectInterface)
existingExtPtrs <- oldCobjectInterface[[1]]$getExtPtrs(oldCobjectInterface[[2]])
thisDll <- oldCobjectInterface[[1]]$dll
newCobjectInterface <- Rgenerator(R_NimbleFxn, thisDll, project = nimbleProject, existingExtPtrs = existingExtPtrs)
newCobjectInterface
},
buildCallable = function(R_NimbleFxn, dll = NULL, asTopLevel = TRUE){
cppInterfaceObject <- NULL
if(asTopLevel) {
if(!is.null(Rgenerator))
cppInterfaceObject <- Rgenerator(R_NimbleFxn, dll, project = nimbleProject)
} else { ## actually this particular pathway should never be taken. asTopLevel = FALSE will occur only for nimbleProject$instantiateNimbleFunction
if(!is.null(CmultiInterface))
cppInterfaceObject <- CmultiInterface$addInstance(R_NimbleFxn, dll)
}
cppInterfaceObject
},
buildAll = function(where = where) {
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(!is.null(baseClassObj)) {
inheritance <<- inheritance[inheritance != 'NamedObjects']
baseClassName <- environment(baseClassObj)$name
addInheritance(baseClassName)
addAncestors('NamedObjects')
}
handleDerivs <- isTRUE(nimbleOptions("enableDerivs")) &&
length(environment(nfProc$nfGenerator)$buildDerivs) > 0
if(handleDerivs) {
constructorCode <- addADclassContent() ## Might generate code to insert into constructor, which is built later
if('nodeFun' %in% .self$inheritance) {
updateADproxyModelMethods(.self)
}
}
addCopyFromRobject()
callSuper(where)
if(handleDerivs) {
if(!is.null(constructorCode)) { ## insert AD-related code to constructor
conDef <- functionDefs[['constructor']] ## Very hacky way to insert this code.
curlen <- length(conDef$code$code[[2]]$code)
conDef$code$code[[2]]$code[[curlen + 1 ]] <- constructorCode
}
}
}
),
)
## updateNimDerivsCalculateHandlers <- list(nimDerivs_calculate = "updateNimDerivsCalculate_update")
## exprClasses_updateNimDerivsCalculate <- function(code, funIndex) {
## if(code$isName) return(funIndex)
## if(code$isCall) {
## for(i in seq_along(code$args)) {
## if(inherits(code$args[[i]], 'exprClass')) {
## funIndex <- exprClasses_updateNimDerivsCalculate(code$args[[i]], funIndex)
## }
## }
## handler <- updateNimDerivsCalculateHandlers[[code$name]]
## if(!is.null(handler)) funIndex <- eval(call(handler, code, funIndex))
## }
## funIndex
## }
## updateNimDerivsCalculate_update <- function(code, funIndex) {
## ## newExpr <- substitute(set_tape_ptr(ADtapeSetup, myADtapePtrs_[NUM], 1),
## ## list(NUM = funIndex))
## ## newExpr <- RparseTree2ExprClasses(newExpr)
## newArg1 <- RparseTree2ExprClasses(quote(ADtapeSetup))
## newArg2 <- substitute(myADtapePtrs_[NUM],
## list(NUM = funIndex))
## newArg2 <- RparseTree2ExprClasses(newArg2)
## oldArgs <- code$args
## for(i in rev(seq_along(code$args))) {
## setArg(code, i+2, oldArgs[[i]])
## }
## setArg(code, 1, newArg1)
## setArg(code, 2, newArg2)
## rm(oldArgs)
## funIndex + 1
## }
## The next block of code has the initial setup for an AST processing stage
## to make modifications for AD based on context etc.
modifyForAD_handlers <- c(list(
pow = 'modifyForAD_issuePowWarning',
eigenBlock = 'modifyForAD_eigenBlock',
calculate = 'modifyForAD_calculate',
getValues = 'modifyForAD_getSetValues',
setValues = 'modifyForAD_getSetValues',
nfMethod = 'modifyForAD_nfMethod',
chainedCall = 'modifyForAD_chainedCall',
getDerivs_wrapper = 'modifyForAD_getDerivs_wrapper',
AssignEigenMap = 'modifyForAD_AssignEigenMap',
ADbreak = 'modifyForAD_ADbreak',
`*` = 'modifyForAD_matmult',
eigInverse = 'modifyForAD_matinverse',
MAKE_FIXED_VECTOR = 'modifyForAD_MAKE_FIXED_VECTOR'),
makeCallList(recyclingRuleOperatorsAD, 'modifyForAD_RecyclingRule'),
makeCallList(c('EIGEN_FS', 'EIGEN_BS', 'EIGEN_SOLVE', 'EIGEN_CHOL', 'nimNewMatrixD', 'nimCd',
'nimRepd','nimDiagonalD', 'nimNonseqIndexedd'),
'modifyForAD_prependNimDerivs'))
exprClasses_modifyForAD <- function(code, symTab,
workEnv = list2env(list(wrap_in_value = FALSE))) {
if(code$isName) {
if(!isTRUE(workEnv[['wrap_in_value']]))
return(invisible())
else {
symObj <- symTab$getSymbolObject(code$name)
if(!is.null(symObj)) {
if(identical(symObj$baseType, "CppAD::AD")) {
insertExprClassLayer(code$caller, code$callerArgID, 'Value') ## It is ok to leave some fields (type, sizeExpr) unpopulated at this late processing stage
}
}
}
}
if(code$isCall) {
recurse_modifyForAD(code, symTab, workEnv)
handler <- modifyForAD_handlers[[code$name]]
if(!is.null(handler))
eval(call(handler, code, symTab, workEnv))
if(workEnv$RsymTab$symbolExists(code$name, TRUE)) ## Could be a nimbleFunction class method
modifyForAD_recordable(code, symTab, workEnv)
else {
if(!is.null(code$aux)) {
if(isTRUE(code$aux[['buildDerivs']])) ## This is added in sizeRCfunction
modifyForAD_RCfunction(code, symTab, workEnv)
}
}
}
if(is.null(code$caller)) { ## It is the top level `{`
if(identical(code$name, "{")) {
if(isTRUE(workEnv[['hasCalculate']])) {
if(is.null( workEnv[['nodeFxnVector_name']] ) )
stop("While setting up C++ AD code: calculate found but nodeFxnVector_name not set.")
## insert setup_extraInput_step(nfv)
set_model_tape_info_line <- RparseTree2ExprClasses(cppLiteral(
paste0("set_CppAD_tape_info_for_model my_tape_info_RAII_(",
workEnv[['nodeFxnVector_name']],
", recordingInfo_.tape_id(), recordingInfo_.tape_handle());")))
## ", TYPE_::get_tape_id_nimble(), TYPE_::get_tape_handle_nimble());")))
set_atomic_info_line <- RparseTree2ExprClasses(cppLiteral(
paste0("set_CppAD_atomic_info_for_model(",
workEnv[['nodeFxnVector_name']],
", recordingInfo_.atomic_vec_ptr());")))
## ", CppAD::local::atomic_index_info_vec_manager_nimble<double>::manage());")))
## This inserts a single line at the beginning by
## creating a new `{` block.
## If anything more general is needed later, we could use
## the exprClasses_insertAssertions system
newExpr <- newBracketExpr(args = c(list(set_model_tape_info_line,
set_atomic_info_line),
code$args))
code$args <- list()
setArg(code, 1, newExpr)
}
}
}
invisible(NULL)
}
recurse_modifyForAD <- function(code, symTab, workEnv) {
if(is.list(code$aux))
if(isTRUE(code$aux$.avoidAD))
return(invisible(NULL))
for(i in seq_along(code$args)) {
if(inherits(code$args[[i]], 'exprClass')) {
exprClasses_modifyForAD(code$args[[i]], symTab, workEnv)
}
}
invisible(NULL)
}
modifyForAD_issuePowWarning <- function(code, symTab, workEnv) {
message(" [Note] Operator `pow` may cause derivative problems with negative arguments. If the exponent is guaranteed to be an integer, use `pow_int` instead.", call. = FALSE)
invisible(NULL)
}
modifyForAD_matmult <- function(code, symTab, workEnv) {
if(isTRUE(nimbleOptions("useADmatMultAtomic")))
if(length(code$args)==2) ## something is wrong if there are not 2 args
if(!(isEigScalar(code$args[[1]]) || isEigScalar(code$args[[2]]))) ## are both non-scalar?
code$name <- 'nimDerivs_matmult'
invisible(NULL)
}
modifyForAD_matinverse <- function(code, symTab, workEnv) {
if(isTRUE(nimbleOptions("useADmatInverseAtomic")))
code$name <- 'nimDerivs_matinverse'
invisible(NULL)
}
modifyForAD_MAKE_FIXED_VECTOR <- function(code, symTab, workEnv) {
if(length(code$args) >= 5) {
go <- if(length(code$args) >= 6)
isTRUE(code$args[[6]])
else TRUE
if(go)
if(identical(code$args[[5]], "double"))
code$args[[5]] <- "CppAD::AD<double>"
}
}
modifyForAD_ADbreak <- function(code, symTab, workEnv) {
code$name <- 'CppAD::Value'
invisible(NULL)
}
modifyForAD_RecyclingRule <- function(code, symTab, workEnv) {
## The conversion to nimDerivs_really has to do with the C++ return type
## and that should always convert to CppAD::AD<double>, which is achieved
## by the following changes. In other words, there is no need to parse
## through the arguments and see which are AD types and which not.
code$name <- paste0('nimDerivs_', code$name)
code$name <- gsub('::', '::nimDerivs_', code$name)
code$name <- gsub("<MatrixXd>", "<MatrixXd_TYPE_>", code$name)
invisible(NULL)
}
modifyForAD_AssignEigenMap <- function(code, symTab, workEnv) {
EigMapName <- code$args[[1]]$name
## We extract the variable name by undoing the construction of the Eigen Map variable name.
## This would be nicer to do with generic functions that undo the label creation.
## At this time of this writing, hacking the solution here was more practical.
##
## This method of extracting the name of the variable we are making a map into
## attempted to invert the name-generation and name-mangling steps that led to it.
## However, it is not fully general. In addition, it is not clear if this would
## ever really make sense. Although noDerivs_vars can make a variable enter
## a deriv-enabled function with its raw types, we should never really be doing
## any vectorized operation with it. The reason is that the result will be CppAD::AD<double> (or TYPE_),
## since we do not attempt to somehow track AD and non-AD types through the AST processing.
## And Eigen requires same-type operations, I believe, because we manually cast when necessary among
## basic types, but we do not cast between AD and non-AD types.
## However, we try this for cases where it succeeds. Notably it is useful for the results of
## lifting "order = nimC(0, 1)" from nimDerivs, for example.
## The pieces created from that are now protected from AD modification.
go <- TRUE
varSym <- NULL
## We try to look for the relevant base symbol. If we can't find it, by default we do the AD modification
# unpack the getPtr step, which might have an offset added via "+"
ptrExpr <- code$args[[2]]
if(ptrExpr$name == "+")
ptrExpr <- ptrExpr$args[[1]]
if(ptrExpr$name == "getPtr") {
varName <- ptrExpr$args[[1]]$name
varSym <- symTab$getSymbolObject(varName, inherits = TRUE)
}
if(!isTRUE(workEnv$.inModel)) {
if(!is.null(varSym)) {
scalarType <- varSym$templateArgs[[2]]
go <- identical(scalarType, "TYPE_")
}
}
if(go) {
EigMapSym <- symTab$getSymbolObject(EigMapName)
EigMapSym_baseType <- EigMapSym$baseType
if(EigMapSym_baseType == "EigenMapStrd") {
EigMapSym$baseType <- "EigenMapStrd_TYPE_"
#MatrixXd_label <- code$args[[3]]
code$args[[3]]$name <- "MatrixXd_TYPE_"
}
if(EigMapSym_baseType == "Map") {
EigMapSym$templateArgs[[1]] <- "MatrixXd_TYPE_"
code$args[[3]]$name <- "MatrixXd_TYPE_"
}
}
invisible(NULL)
}
modifyForAD_prependNimDerivs <- function(code, symTab, workEnv) {
origName <- code$name
atomic <- TRUE
if(origName == 'EIGEN_FS' | origName == 'EIGEN_BS')
if(!isTRUE(nimbleOptions("useADsolveAtomic")))
atomic <- FALSE
if(origName == "EIGEN_CHOL")
if(!isTRUE(nimbleOptions("useADcholAtomic")))
atomic <- FALSE
if(atomic)
code$name <- paste0("nimDerivs_", origName)
else
code$name <- paste0("nimDerivs_", origName, '_no_atomic')
invisible(NULL)
}
modifyForAD_RCfunction <- function(code, symTab, workEnv) {
code$name <- paste0(code$name, "< CppAD::AD<double> >")
invisible(NULL)
}
modifyForAD_getDerivs_wrapper <- function(code, symTab, workEnv) {
## This really modifies the "argumentTransfer" call in the first argument of getDerivs_wrapper
arg1 <- code$args[[1]]
arg1$name <- paste0(arg1$name, "_AD2_")
code$name <- "getDerivs_wrapper_meta"
nArgs <- length(code$args)
newExpr <- RparseTree2ExprClasses(quote(recordingInfo_))
setArg(code, nArgs + 1, newExpr)
invisible(NULL)
}
modifyForAD_nfMethod <- function(code, symTab, workEnv) {
if(code$args[[1]]$name != "cppPointerDereference")
message(" [Note] In modifyForAD_nfMethod, was expecting cppPointerDereference. There must be another case that needs implementation.")
objName <- code$args[[1]]$args[[1]]$name
NFsymObj <- workEnv$RsymTab$getSymbolObject(objName, TRUE)
methodName <- code$args[[2]]
if(!is.character(methodName))
message(" [Note] In modifyForAD_nfMethod, was expecting method name to be character. There must be another case that needs implementation.")
methodSymObj <- NFsymObj$nfProc$compileInfos[[methodName]]$newLocalSymTab$getSymbolObject(methodName, TRUE)
buildDerivs <- methodSymObj$nfMethodRCobj$buildDerivs
if(!is.null(buildDerivs))
if(!isFALSE(buildDerivs)) {
code$args[[2]] <- paste0( code$args[[2]], "_AD2_")
code$name <- "nfMethodAD" ## This is a tag for modifyForAD_chainedCall
}
invisible(NULL)
}
modifyForAD_chainedCall <- function(code, symTab, workEnv) {
arg1name <- code$args[[1]]$name
if(arg1name == "nfMethodAD") { ## A tag set in modifyForAD_nfMethod
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(recordingInfo_)))
code$args[[1]]$name <- "nfMethod" ## tag is no longer needed. revert to regular nfMethodAD
}
invisible(NULL)
}
modifyForAD_recordable <- function(code, symTab, workEnv) {
symObj <- workEnv$RsymTab$getSymbolObject(code$name, TRUE)
buildDerivs <- symObj$nfMethodRCobj$buildDerivs
if(!is.null(buildDerivs))
if(!isFALSE(buildDerivs)) {
code$name <- paste0(code$name, "_AD2_")
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(recordingInfo_)))
}
invisible(NULL)
}
modifyForAD_getSetValues <- function(code, symTab, workEnv) {
if(code$name == 'setValues') {
code$name <- 'setValues_AD_AD_taping'
}
accessorName <- code$args[[2]]$name
already_AD_name <- grepl("_AD_$", accessorName) ## _AD_ is at the end. I'm not sure it would ever already be there, so this is defensive.
if(!already_AD_name) {
classSymTab <- symTab$getParentST()$getParentST()
newSymbolName <- paste0(accessorName, '_AD_')
if(!classSymTab$symbolExists(newSymbolName)) {
newSymbol <- classSymTab$getSymbolObject(accessorName)$copy()
if(newSymbol$name != accessorName)
warning("Something is wrong with internal processing of names in managing use of values() for nimDerivs.")
newSymbol$name <- newSymbolName
classSymTab$addSymbol(newSymbol)
}
code$args[[2]]$name <- newSymbolName
}
thirdArg <- RparseTree2ExprClasses(as.name(accessorName))
setArg(code, 3, thirdArg)
fourthArg <- RparseTree2ExprClasses(quote(recordingInfo_))
setArg(code, 4, fourthArg)
invisible(NULL)
}
modifyForAD_eigenBlock <- function(code, symTab, workEnv) {
orig_wrap_in_value <- workEnv[['wrap_in_value']]
workEnv[['wrap_in_value']] <- TRUE
recurse_modifyForAD(code, symTab, workEnv)
workEnv[['wrap_in_value']] <- orig_wrap_in_value
invisible(NULL)
}
modifyForAD_calculate <- function(code, symTab, workEnv) {
workEnv$hasCalculate <- TRUE
workEnv$nodeFxnVector_name <- code$args[[1]]$name
recurse_modifyForAD(code, symTab, workEnv)
code$name <- "calculate_ADproxyModel"
code$args[[2]] <- 1 ## this sets includeExtraOutputStep = true
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(cppLiteral("recordingInfo_"))))
invisible(NULL)
}
updateADproxyModelMethods <- function(.self) {
## Update return type and names of functions like dnorm -> nimDerivs_dnorm
functionNames <- names(.self$functionDefs)
ADproxyModel_functionNames <- functionNames[ grepl("_ADproxyModel", functionNames ) ]
if(length(ADproxyModel_functionNames) > 0) {
## The following two headers were added to CPPincludes because nimDerives_dists must
## come before Rmath.h
.self$CPPincludes <- c(nimbleIncludeFile("nimbleCppAD.h"),
nimbleIncludeFile("nimDerivs_dists.h"), .self$CPPincludes)
}
for(fn in ADproxyModel_functionNames) {
thisDef <- .self$functionDefs[[fn]]
thisDef$returnType <- cppVarSym2templateTypeCppVarSym( thisDef$returnType,
replacementBaseType = "CppAD::AD",
replacementTemplateArgs = "double" )
parentST <- thisDef$code$objectDefs$getParentST()
thisDef$code$objectDefs <-
symbolTable2templateTypeSymbolTable(thisDef$code$objectDefs) #,
## replacementBaseType = "CppAD::AD",
## replacementTemplateArgs = "double" )
thisDef$code$objectDefs$setParentST(parentST)
thisDef$code$cppADCode <- 2L
ADtypeDefs <- symbolTable()
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef typename EigenTemplateTypes<CppAD::AD<double> >::typeEigenMapStrd", name = "EigenMapStrd_TYPE_") )
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef Matrix<CppAD::AD<double>, Dynamic, Dynamic>", name = "MatrixXd_TYPE_") )
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef CppAD::AD<double>", name = "TYPE_") )
thisDef$code$typeDefs <- ADtypeDefs
workEnv <- new.env()
workEnv$RsymTab <- thisDef$RCfunProc$compileInfo$newLocalSymTab
workEnv$.inModel <- TRUE
exprClasses_modifyForAD(thisDef$code$code, thisDef$code$objectDefs, workEnv)
}
classST <- .self$objectDefs
classSymNames <- classST$getSymbolNames()
ADproxySymNames <- classSymNames[ grepl("ADproxyModel_", classSymNames ) ]
for(sn in ADproxySymNames) {
newSym <-
cppVarSym2templateTypeCppVarSym(classST$getSymbolObject(sn),
replacementBaseType = "CppAD::AD",
replacementTemplateArgs = "double") ## These end up the header file so they should not use TYPE_ as that is not typedef'd there
classST$addSymbol(newSym, allowReplace = TRUE)
}
NULL
}
makeSingleCopyCall <- function(varName, cppCopyType,
buildDerivs = FALSE) {
switch(cppCopyType,
'nimbleFunction' = {
cppLiteral(paste0("COPY_NIMBLE_FXN_FROM_R_OBJECT(\"", varName, "\");"))
},
'numericVector' = {
cppLiteral(paste0("COPY_NUMERIC_VECTOR_FROM_R_OBJECT(\"", varName, "\");"))
},
'doubleScalar' = {
cppLiteral(paste0("COPY_DOUBLE_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'integerScalar' = {
cppLiteral(paste0("COPY_INTEGER_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'logicalScalar' = {
cppLiteral(paste0("COPY_LOGICAL_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'nodeFxnVec' = {
cppLiteral(paste0("COPY_NODE_FXN_VECTOR_FROM_R_OBJECT(\"", varName, "\");"))
},
'nodeFxnVec_nimDerivs' = {
cppLiteral(paste0("COPY_NODE_FXN_VECTOR_DERIVS_FROM_R_OBJECT(\"", varName, "\");"))
},
'modelVarAccess' = {
cppLiteral(paste0("COPY_VALUE_MAP_ACCESSORS_FROM_NODE_NAMES(\"", varName, "\"",
if(isTRUE(buildDerivs)) ", 1" else ", 0", ");"))
},
NULL)
}
makeCopyFromRobjectDef <- function(cppCopyTypes,
buildDerivs = FALSE) {
## Make method for copying from R object
copyFromRobjectDef <- RCfunctionDef()
copyFromRobjectDef$name <- 'copyFromRobject'
copyFromRobjectDef$returnType <- cppVoid()
copyFromRobjectDef$args <- symbolTable()
localVars <- symbolTable()
RobjectVarSym <- cppSEXP(name = 'Robject')
copyFromRobjectDef$args$addSymbol(RobjectVarSym)
copyCalls <- list()
varNames <- names(cppCopyTypes)
for(i in seq_along(cppCopyTypes)) {
copyCalls[[varNames[i]]] <- makeSingleCopyCall(varNames[i], cppCopyTypes[[i]],
buildDerivs = buildDerivs)
}
if(length(copyCalls) == 0) {
## create an empty function
allRcode <- do.call('call',
list('{'),
quote = TRUE
)
} else {
unprotectCount <- 2 + length(copyCalls) ## 2 from SETUP_S_xData
allRcode <- do.call('call',
c(list('{'),
list(cppLiteral("SETUP_S_xData;")),
copyCalls,
list(cppLiteral(paste0("UNPROTECT(",unprotectCount,");")))),
quote = TRUE
)
}
allCode <- RparseTree2ExprClasses(allRcode)
copyFromRobjectDef$code <- cppCodeBlock(code = allCode,
objectDefs = localVars)
copyFromRobjectInterfaceDef <- NULL
list(copyFromRobjectDef = copyFromRobjectDef,
copyFromRobjectInterfaceDef = copyFromRobjectInterfaceDef)
}
Try the nimble package in your browser
Any scripts or data that you put into this service are public.
nimble documentation built on July 9, 2023, 5:24 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions makeCopyFromRobjectDef makeSingleCopyCall updateADproxyModelMethods modifyForAD_calculate modifyForAD_eigenBlock modifyForAD_getSetValues modifyForAD_recordable modifyForAD_chainedCall modifyForAD_nfMethod modifyForAD_getDerivs_wrapper modifyForAD_RCfunction modifyForAD_prependNimDerivs modifyForAD_AssignEigenMap modifyForAD_RecyclingRule modifyForAD_ADbreak modifyForAD_MAKE_FIXED_VECTOR modifyForAD_matinverse modifyForAD_matmult modifyForAD_issuePowWarning recurse_modifyForAD exprClasses_modifyForAD
##
cppVirtualNimbleFunctionClass <- setRefClass('cppVirtualNimbleFunctionClass',
contains = 'cppClassDef',
fields = list(
nfProc = 'ANY'
),
methods = list(
initialize = function(nfProc, ...) {
callSuper(...)
if(!missing(nfProc)) processNFproc(nfProc)
useGenerator <<- FALSE
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(is.null(baseClassObj)) {
addInheritance("NamedObjects")
} else {
if(is.character(baseClassObj)) addInheritance(baseClassObj)
else {
virtual <- environment(baseClassObj)$virtual
if(isTRUE(virtual))
baseClassName <- environment(baseClassObj)$className
else
baseClassName <- environment(baseClassObj)$CclassName
addInheritance(baseClassName)
}
}
},
processNFproc = function(nfp) {
nfProc <<- nfp
assign('cppDef', .self, envir = environment(nfProc$nfGenerator))
for(i in names(nfp$RCfunProcs)) { ## This is what we should do for cppNimbleFunctions too
abstract <- !isFALSE( environment(nfProc$nfGenerator)$methodControl[[i]]$required ) # default required = TRUE. required is a synonym for abstract. If it's abstract, it's required in derived classes.
functionDefs[[i]] <<- RCfunctionDef(virtual = TRUE, abstract = abstract)
functionDefs[[i]]$buildFunction(nfp$RCfunProcs[[i]])
}
}
)
)
## cppNimbleClassClass defines commonalities between cppNimbleFunctionClass and cppNimbleListClass, both of which are classes in nimble
cppNimbleClassClass <- setRefClass('cppNimbleClassClass',
contains = 'cppNamedObjectsClass',
fields = list(
## Inherits a functionDefs list for member functions
## Inherits an objectDefs list for member data
SEXPmemberInterfaceFuns = 'ANY', ## List of SEXP interface functions, one for each member function
nimCompProc = 'ANY', ## nfProcessing or nlProcessing object, needed to get the member data symbol table post-compilation
Rgenerator = 'ANY' , ## function to generate and wrap a new object from an R object
CmultiInterface = 'ANY', ## object for interfacing multiple C instances when a top-level interface is not needed
built = 'ANY',
loaded = 'ANY',
Cwritten = 'ANY',
RCfunDefs = 'ANY'
),
methods = list(
getDefs = function() {
callSuper()
},
getHincludes = function() {
callSuper()
},
getCPPincludes = function() {
callSuper()
},
getCPPusings = function() {
callSuper()
},
genNeededTypes = function(debugCpp = FALSE, fromModel = FALSE) {
for(i in seq_along(nimCompProc$neededTypes)) {
neededType<- nimCompProc$neededTypes[[i]]
if(inherits(neededType, 'nfMethodRC')) {
thisCppDef <- nimbleProject$getRCfunCppDef(neededType, NULLok = TRUE)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$needRCfunCppClass(neededType, genNeededTypes = TRUE, fromModel = fromModel)
neededTypeDefs[[neededType$uniqueName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolModelValues')) {
thisCppDef <- nimbleProject$getModelValuesCppDef(neededType$mvConf, NULLok = TRUE)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$needModelValuesCppClass(neededType$mvConf, fromModel = fromModel)
mvClassName <- environment(neededType$mvConf)$className
neededTypeDefs[[mvClassName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleFunction')) {
generatorName <- environment(neededType$nfProc$nfGenerator)$name
thisCppDef <- nimbleProject$getNimbleFunctionCppDef(generatorName = generatorName)
if(is.null(thisCppDef)) {
className <- names(nimCompProc$neededTypes)[i]
if(neededType$type == 'nimbleFunction')
thisCppDef <- nimbleProject$buildNimbleFunctionCompilationInfo(generatorName = generatorName, fromModel = fromModel)
else if(neededType$type == 'nimbleFunctionVirtual')
thisCppDef <- nimbleProject$buildVirtualNimbleFunctionCompilationInfo(vfun = generatorName)
else stop('symbolNimbleFunction does not have type nimbleFunction or nimbleFunctionVirtual')
neededTypeDefs[[ className ]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleList')) {
CPPincludes <<- c(CPPincludes, nimbleIncludeFile("smartPtrs.h"))
generatorName <- neededType$nlProc$name
if(generatorName == 'NIMBLE_ADCLASS') Hincludes <<- c(Hincludes, nimbleIncludeFile("nimbleCppAD.h"))
thisCppDef <- nimbleProject$getNimbleListCppDef(generatorName = generatorName)
if(is.null(thisCppDef)){
className <- names(nimCompProc$neededTypes)[i]
thisCppDef <- nimbleProject$buildNimbleListCompilationInfo(className = generatorName, fromModel = fromModel)
neededTypeDefs[[ className ]] <<- thisCppDef
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
next
}
if(inherits(neededType, 'symbolNimbleFunctionList')) {
baseClassName <- environment(neededType$baseClass)$name
thisCppDef <- nimbleProject$getNimbleFunctionCppDef(generatorName = baseClassName)
if(is.null(thisCppDef)) {
thisCppDef <- nimbleProject$buildVirtualNimbleFunctionCompilationInfo(vfun = neededType$baseClass)
neededTypeDefs[[baseClassName]] <<- thisCppDef
} else {
Hincludes <<- c(Hincludes, thisCppDef)
CPPincludes <<- c(CPPincludes, thisCppDef)
}
}
}
},
initialize = function(nimCompProc, debugCpp = FALSE, fromModel = FALSE, ...) {
callSuper(...) ## must call this first because it sets objectDefs to list()
RCfunDefs <<- list()
if(!missing(nimCompProc)) processNimCompProc(nimCompProc, debugCpp = debugCpp, fromModel = fromModel)
built <<- FALSE
loaded <<- FALSE
Cwritten <<- FALSE
},
processNimCompProc = function(ncp, debugCpp = FALSE, fromModel = FALSE) {
ncp$cppDef <- .self
nimCompProc <<- ncp
genNeededTypes(debugCpp = debugCpp, fromModel = fromModel)
objectDefs <<- symbolTable2cppVars(ncp$getSymbolTable())
},
addCopyFromRobject = function() {
## The next line creates the cppCopyTypes exactly the same way as in buildNimbleObjInterface
## and CmultiNimbleObjClass::initialize.
cppCopyTypes <- makeNimbleFxnCppCopyTypes(nimCompProc$getSymbolTable(), objectDefs$getSymbolNames())
buildDerivsInCopier <- FALSE
if(inherits(nimCompProc, 'virtualNFprocessing')) {
buildDerivs <- environment(nimCompProc$nfGenerator)[['buildDerivs']]
buildDerivsInCopier <- (length(buildDerivs) > 0) & (!isFALSE(buildDerivs))
}
copyFromRobjectDefs <- makeCopyFromRobjectDef(cppCopyTypes,
buildDerivs = buildDerivsInCopier)
functionDefs[['copyFromRobject']] <<- copyFromRobjectDefs$copyFromRobjectDef
},
buildAll = function(where = where) {
makeCppNames()
buildConstructorFunctionDef()
buildSEXPgenerator(finalizer = "namedObjects_Finalizer")
buildRgenerator(where = where)
buildCmultiInterface()
},
buildRgenerator = function() {message('whoops, base class version of buildRgenerator')},
buildCmultiInterface = function() {message('whoops, base class version of buildCmultiInterface')},
makeCppNames = function() {
Rnames2CppNames <<- as.list(Rname2CppName(objectDefs$getSymbolNames()))
names(Rnames2CppNames) <<- objectDefs$getSymbolNames()
},
buildConstructorFunctionDef = function() {
newNestedListLines <- list()
flagLine <- list()
pointerLine <- list()
if(!(is.null(nimCompProc[['nimbleListObj']]))){
flagText <- paste0('RCopiedFlag = false')
flagLine[[1]] <- substitute(FLAGTEXT,
list(FLAGTEXT = as.name(flagText)))
pointerText <- paste0('RObjectPointer = NULL')
pointerLine[[1]] <- substitute(POINTERTEXT,
list(POINTERTEXT = as.name(pointerText)))
for(i in seq_along(nimCompProc$neededTypes)){
newListText <- paste0(nimCompProc$neededTypes[[i]]$name, " = new ", as.name(names(nimCompProc$neededTypes)[i]))
newNestedListLines[[i]] <- substitute(NEWLISTTEXT,
list(NEWLISTTEXT = as.name(newListText)))
}
}
code <- putCodeLinesInBrackets(c(flagLine, pointerLine, newNestedListLines,
list(namedObjectsConstructorCodeBlock())))
conFunDef <- cppFunctionDef(name = name,
returnType = emptyTypeInfo(),
code = cppCodeBlock(code = code, skipBrackets = TRUE))
functionDefs[['constructor']] <<- conFunDef
}
),
)
cppNimbleFunctionClass <- setRefClass('cppNimbleFunctionClass',
contains = 'cppNimbleClassClass',
fields = list(
nfProc = 'ANY', ## an nfProcessing class, needed to get the member data symbol table post-compilation
parentsSizeAndDims = 'ANY',
ADconstantsInfo = 'ANY'
),
methods = list(
getDefs = function() {
c(callSuper(), SEXPmemberInterfaceFuns)
},
getHincludes = function() {
c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getHincludes()), recursive = FALSE))
},
getCPPincludes = function() {
c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getCPPincludes()), recursive = FALSE))
},
getCPPusings = function() {
CPPuse <- unique(c(callSuper(), unlist(lapply(SEXPmemberInterfaceFuns, function(x) x$getCPPusings()))))
CPPuse
},
initialize = function(nfProc, isNode, debugCpp = FALSE, fromModel = FALSE, ...) {
callSuper(nfProc, debugCpp, fromModel, ...)
if(!missing(nfProc)) processNFproc(nfProc, debugCpp = debugCpp, fromModel = fromModel)
if(isNode) {
inheritance <<- inheritance[inheritance != 'NamedObjects']
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(is.null(baseClassObj)) {
inheritance <<- c(inheritance, 'nodeFun')
parentsSizeAndDims <<- environment(nfProc$nfGenerator)$parentsSizeAndDims
ADconstantsInfo <<- environment(nfProc$nfGenerator)$ADconstantsInfo
}
}
},
processNFproc = function(nfp, debugCpp = FALSE, fromModel = FALSE) {
nfProc <<- nimCompProc
buildFunctionDefs()
## This is slightly klugey
## The objectDefs here are for the member data
## We need them to be the parentST for each member function
## However the building of the cpp objects is slightly out of order, with the
## member functions already having been built during nfProcessing.
for(i in seq_along(functionDefs)) {
functionDefs[[i]]$args$parentST <<- objectDefs
}
SEXPmemberInterfaceFuns <<- lapply(functionDefs,
function(x)
if(inherits(x$SEXPinterfaceFun, "cppFunctionDef"))
x$SEXPinterfaceFun
else
NULL
)
SEXPmemberInterfaceFuns <<-
SEXPmemberInterfaceFuns[ !unlist(lapply(SEXPmemberInterfaceFuns, is.null)) ]
nimCompProc <<- nfProc
},
buildFunctionDefs = function() {
for(i in seq_along(nfProc$RCfunProcs)) {
RCname <- names(nfProc$RCfunProcs)[i]
functionDefs[[RCname]] <<- RCfunctionDef$new() ## all nodeFunction members are const f
functionDefs[[RCname]]$buildFunction(nfProc$RCfunProcs[[RCname]])
if(!grepl("ADproxyModel", RCname)) ## don't build "CALL_" function for AD functions
functionDefs[[RCname]]$buildSEXPinterfaceFun(className = nfProc$name)
RCfunDefs[[RCname]] <<- functionDefs[[RCname]]
}
},
addTypeTemplateFunction = function(funName,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
useModelInfo <- list()
## if(static) {
## newFunName <- paste0(funName, '_AD_')
## ## We need the template<TYPE_> function and also
## ## whether a calculate was detected and if so its nodeFxnVector_name
## res <- makeTypeTemplateFunction(newName = newFunName,
## .self = regularFun,
## static = TRUE,
## useRecordingInfo = TRUE,
## derivControl = derivControl)
## functionDefs[[newFunName]] <<- res$fun
## useModelInfo$nodeFxnVector_name <- res[['nodeFxnVector_name']]
## } else {
## We need a separate one for the "reconfigure" system that is non-static
## if(isTRUE(nimbleOptions('useADreconfigure'))) {
newFunName <- paste0(funName, '_AD2_')
res <- makeTypeTemplateFunction(newName = newFunName,
.self = regularFun,
##static = FALSE,
useRecordingInfo = TRUE,
derivControl = derivControl)
functionDefs[[newFunName]] <<- res$fun
useModelInfo$nodeFxnVector_name <- res[['nodeFxnVector_name']]
## }
## }
useModelInfo
},
add_deriv_function = function(funName,
independentVarNames,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
## static <- isTRUE(derivControl[['static']])
## if(static) {
## message("add_deriv_function support for static is not written.")
## } else {
if(isTRUE(nimbleOptions("useADreconfigure"))) {
newFunName <- paste0(funName, '_deriv_')
argTransName <- paste0(funName, '_ADargumentTransfer2_')
functionDefs[[newFunName]] <<- make_deriv_function(regularFun,
newFunName,
independentVarNames,
argTransName)
## Add meta-taping type template function of the new function
newMetaFunName <- paste0(funName, '_AD2__deriv_')
argTransName <- paste0(funName, '_ADargumentTransfer2__AD2_')
functionDefs[[newMetaFunName]] <<- make_deriv_function(regularFun,
newMetaFunName,
independentVarNames,
argTransName,
meta = TRUE)
} else {
message("Don't know how to use static=FALSE without nimbleOptions('useADreconfigure')." )
}
## }
},
addADtapingFunction = function( funName,
independentVarNames,
dependentVarNames,
useModelInfo = NULL,
derivControl = list()) {
regularFun <- RCfunDefs[[funName]]
if(is.null(useModelInfo))
useModelInfo <- list()
## static <- isTRUE(derivControl[['static']])
## if(static) {
## ADfunName <- paste0(funName, '_AD_')
## newFunName <- paste0(funName, '_callForADtaping2_')
## functionDefs[[newFunName]] <<- makeADtapingFunction2(newFunName,
## regularFun,
## ADfunName,
## independentVarNames,
## dependentVarNames,
## nfProc$isNode,
## className = name)
## }
## if(!static) {
## if(isTRUE(nimbleOptions("useADreconfigure"))) {
ADfunName2 <- paste0(funName, '_AD2_')
newFunName2 <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2]] <<- makeADtapingFunction2(newFunName2,
regularFun,
ADfunName2,
independentVarNames,
dependentVarNames,
nfProc$isNode,
className = name,
useModelInfo = useModelInfo)
## }
## }
invisible(NULL)
},
addADargumentTransferFunction = function(funName,
independentVarNames,
funIndex,
useModelInfo = NULL,
derivControl = list()) {
## static <- isTRUE(derivControl[['static']])
regularFun <- RCfunDefs[[funName]]
## funIndex <- which(names(environment(nfProc$nfGenerator)$enableDerivs == funName)) ## needed for correct index for allADtapePtrs_
## if(static) {
## newFunName <- paste0(funName, '_ADargumentTransfer_')
## functionDefs[[newFunName]] <<- makeADargumentTransferFunction(newFunName,
## regularFun,
## independentVarNames,
## funIndex,
## parentsSizeAndDims,
## ADconstantsInfo)
## } else {
## Version 2 is for the "reconfig" version
## if(isTRUE(nimbleOptions("useADreconfigure"))) {
newFunName2 <- paste0(funName, '_ADargumentTransfer2_')
## For now, use same funIndex since this will use the non-static tape vector, but we may want to be more careful
callForTapingName <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2]] <<- makeADargumentTransferFunction2(newFunName2,
regularFun,
callForTapingName,
independentVarNames,
funIndex,
parentsSizeAndDims,
ADconstantsInfo,
useModelInfo,
derivControl)
newFunName2meta <- paste0(funName, '_ADargumentTransfer2__AD2_')
## For now, use same funIndex since this will use the non-static tape vector, but we may want to be more careful
callForTapingName <- paste0(funName, '_callForADtaping2_')
functionDefs[[newFunName2meta]] <<- makeADargumentTransferFunction2(newFunName2meta,
regularFun,
callForTapingName,
independentVarNames,
funIndex,
parentsSizeAndDims,
ADconstantsInfo,
useModelInfo,
derivControl,
metaTape = TRUE)
## }
## }
invisible(NULL)
},
## addStaticInitClass = function(staticMethods) {
## neededTypeDefs[['staticInitClass']] <<- makeStaticInitClass(.self, staticMethods) ##
## invisible(NULL)
## },
addADclassContentOneFun = function(funName,
derivControl,
funIndex) {
##outSym <- nfProc$RCfunProcs[[funName]]$compileInfo$returnSymbol
## TO-DO: revisit checking arguments for deriv compability
## isStatic <- isTRUE(derivControl[['static']])
## if(!isTRUE(derivControl[['meta']]) & isStatic)
## checkADargument(funName, outSym, returnType = TRUE)
RCfunProc <- nfProc$RCfunProcs[[funName]]
nameSubList <- RCfunProc$nameSubList
compileInfo <- nfProc$compileInfos[[funName]]
if(length(nameSubList) == 0)
stop(paste0('Derivatives cannot be built for method ',
funName,
', since this method has no arguments.'))
## if(!nfProc$isNode & !isTRUE(derivControl[['meta']]) & isStatic){
## for(iArg in seq_along(functionDefs[[funName]]$args$symbols)){
## arg <- functionDefs[[funName]]$args$symbols[[iArg]]
## argSym <- nfProc$RCfunProcs[[funName]]$compileInfo$origLocalSymTab$getSymbolObject(arg$name)
## argName <- names(nfProc$RCfunProcs[[funName]]$nameSubList)[iArg]
## checkADargument(funName, argSym, argName = argName)
## }
## }
useModelInfo <- addTypeTemplateFunction(funName,
derivControl = derivControl) ## returns either NULL (if there is no model$calculate) or a nodeFxnVector name (if there is)
## independentVarNames <- names(functionDefs[[funName]]$args$symbols)
independentVarNames <- as.character(nameSubList)
## ivBaseTypes <- unlist(lapply(functionDefs[[funName]]$args$symbols, `[[`, "baseType"))
ivBaseTypes <- lapply(compileInfo$newLocalSymTab$symbols[independentVarNames], `[[`, "type")
## independentVarNames <- names(ivBaseTypes)
includeIV <- ivBaseTypes == "double" ## previously ivBaseTypes != "bool"
ignore <- derivControl[["ignore"]]
if(!is.null(ignore)) {
noDeriv_mangledArgNames <- as.character(unlist(nameSubList[ignore]))
includeIV <- includeIV & !(independentVarNames %in% noDeriv_mangledArgNames)
}
independentVarNames <- as.character(independentVarNames[includeIV])
if(nfProc$isNode) independentVarNames <- independentVarNames[-1] ## remove ARG1_INDEXEDNODEINFO__ from independentVars
if(!isTRUE(derivControl[['meta']])) {
addADtapingFunction(funName,
independentVarNames = independentVarNames,
dependentVarNames = 'ANS_',
useModelInfo,
derivControl = derivControl )
addADargumentTransferFunction(funName,
independentVarNames = independentVarNames,
funIndex = funIndex,
useModelInfo = useModelInfo,
derivControl = derivControl)
add_deriv_function(funName,
independentVarNames,
derivControl)
funIndex + 1 ## function return value increments by one in non-meta case
} else {
funIndex ## but does not increment in meta case
}
},
## addNimDerivsCalculateContentOneFun = function(funName,
## derivControl,
## funIndex) {
## ## We only need to add one line here, which can go at the beginning
## ## set_tape_ptr(ADtapeSetup, myADtapePtrs_[<funIndex>-1], true);
## thisFunctionDef <- functionDefs[[funName]]
## thisCode <- thisFunctionDef$code$code ## lines of code
## newFunIndex <- exprClasses_updateNimDerivsCalculate(thisCode, funIndex)
## newFunIndex
## },
checkADargument = function(funName, argSym, argName = NULL, returnType = FALSE){
argTypeText <- if(returnType) 'returnType' else 'argument'
if(argSym$type != 'double')
stop(paste0('The ', argName, ' ', argTypeText, ' of the ', funName, ' method is not a double, this method cannot have derivatives built.'))
# if(!(argSym$nDim %in% c(0,1)))
# stop(paste0('The ', argName, ' ', argTypeText, ' of the ', funName, ' method must be a double scalar or double vector for derivatives to be enabled.'))
if((argSym$nDim != 0) && is.na(argSym$size))
stop(paste0('To build derivatives, size must be given for the ',
argName, ' ', argTypeText, ' of the ', funName,
' method, e.g. double(1, 3) for a length 3 vector.' ))
},
addADclassContent = function() {
constructorCode <- NULL ## default return object
buildDerivs <- environment(nfProc$nfGenerator)$buildDerivs
buildNames <- names(buildDerivs)
ADinUse <- FALSE
for(iED in seq_along(buildDerivs)) {
if(!isTRUE(buildDerivs[[iED]][['isNode']])) {
ADinUse <- TRUE
if(!isTRUE(buildDerivs[[iED]][['calculate']])) {
addADclassContentOneFun(buildNames[iED],
buildDerivs[[iED]],
funIndex = iED) ## funIndex might be deprecated
}
}
}
if(ADinUse) {
Hincludes <<- c(nimbleIncludeFile("nimbleCppADbaseClass.h"),
Hincludes)
CPPincludes <<- c(nimbleIncludeFile("nimbleCppAD.h"),
nimbleIncludeFile("nimDerivs_dists.h"),
## The ".cpp" extension make it end up linked as a .o
## in cppProjectClass$writeFiles. Prior to that, it is
## copied and locally compiled by cppProjectClass
"nimbleCppADbaseClass.cpp", CPPincludes)
addInheritance("nimbleFunctionCppADbase")
addADinfoObjects(.self)
}
constructorCode
},
buildCmultiInterface = function(dll = NULL) {
sym <- if(!is.null(dll))
getNativeSymbolInfo(SEXPgeneratorFun$name, dll)
else
SEXPgeneratorFun$name
## copyFromRobject_sym <- if(!is.null(dll))
## getNativeSymbolInfo(SEXPmemberInterfaceFuns[['copyFromRobject']]$name, dll)
## else
## SEXPmemberInterfaceFuns[['copyFromRobject']]$name
CmultiInterface <<- CmultiNimbleFunctionClass(compiledNodeFun = .self,
basePtrCall = sym,
##copyFromRobjectCall = copyFromRobject_sym,
project = nimbleProject)
},
buildRgenerator = function(where = globalenv(), dll = NULL) {
sym <- if(!is.null(dll))
getNativeSymbolInfo(SEXPgeneratorFun$name, dll)
else
SEXPgeneratorFun$name
Rgenerator <<- buildNimbleObjInterface(paste0(name,'_refClass') , .self, sym, where = where)
},
promoteCallable = function(R_NimbleFxn, asTopLevel = TRUE){
## see comment in nimbleProjectClass::compileNimbleFunction
oldCobjectInterface <- nf_getRefClassObject(R_NimbleFxn)$.CobjectInterface
if(!is.list(oldCobjectInterface)) return(oldCobjectInterface)
existingExtPtrs <- oldCobjectInterface[[1]]$getExtPtrs(oldCobjectInterface[[2]])
thisDll <- oldCobjectInterface[[1]]$dll
newCobjectInterface <- Rgenerator(R_NimbleFxn, thisDll, project = nimbleProject, existingExtPtrs = existingExtPtrs)
newCobjectInterface
},
buildCallable = function(R_NimbleFxn, dll = NULL, asTopLevel = TRUE){
cppInterfaceObject <- NULL
if(asTopLevel) {
if(!is.null(Rgenerator))
cppInterfaceObject <- Rgenerator(R_NimbleFxn, dll, project = nimbleProject)
} else { ## actually this particular pathway should never be taken. asTopLevel = FALSE will occur only for nimbleProject$instantiateNimbleFunction
if(!is.null(CmultiInterface))
cppInterfaceObject <- CmultiInterface$addInstance(R_NimbleFxn, dll)
}
cppInterfaceObject
},
buildAll = function(where = where) {
baseClassObj <- environment(nfProc$nfGenerator)$contains
if(!is.null(baseClassObj)) {
inheritance <<- inheritance[inheritance != 'NamedObjects']
baseClassName <- environment(baseClassObj)$name
addInheritance(baseClassName)
addAncestors('NamedObjects')
}
handleDerivs <- isTRUE(nimbleOptions("enableDerivs")) &&
length(environment(nfProc$nfGenerator)$buildDerivs) > 0
if(handleDerivs) {
constructorCode <- addADclassContent() ## Might generate code to insert into constructor, which is built later
if('nodeFun' %in% .self$inheritance) {
updateADproxyModelMethods(.self)
}
}
addCopyFromRobject()
callSuper(where)
if(handleDerivs) {
if(!is.null(constructorCode)) { ## insert AD-related code to constructor
conDef <- functionDefs[['constructor']] ## Very hacky way to insert this code.
curlen <- length(conDef$code$code[[2]]$code)
conDef$code$code[[2]]$code[[curlen + 1 ]] <- constructorCode
}
}
}
),
)
## updateNimDerivsCalculateHandlers <- list(nimDerivs_calculate = "updateNimDerivsCalculate_update")
## exprClasses_updateNimDerivsCalculate <- function(code, funIndex) {
## if(code$isName) return(funIndex)
## if(code$isCall) {
## for(i in seq_along(code$args)) {
## if(inherits(code$args[[i]], 'exprClass')) {
## funIndex <- exprClasses_updateNimDerivsCalculate(code$args[[i]], funIndex)
## }
## }
## handler <- updateNimDerivsCalculateHandlers[[code$name]]
## if(!is.null(handler)) funIndex <- eval(call(handler, code, funIndex))
## }
## funIndex
## }
## updateNimDerivsCalculate_update <- function(code, funIndex) {
## ## newExpr <- substitute(set_tape_ptr(ADtapeSetup, myADtapePtrs_[NUM], 1),
## ## list(NUM = funIndex))
## ## newExpr <- RparseTree2ExprClasses(newExpr)
## newArg1 <- RparseTree2ExprClasses(quote(ADtapeSetup))
## newArg2 <- substitute(myADtapePtrs_[NUM],
## list(NUM = funIndex))
## newArg2 <- RparseTree2ExprClasses(newArg2)
## oldArgs <- code$args
## for(i in rev(seq_along(code$args))) {
## setArg(code, i+2, oldArgs[[i]])
## }
## setArg(code, 1, newArg1)
## setArg(code, 2, newArg2)
## rm(oldArgs)
## funIndex + 1
## }
## The next block of code has the initial setup for an AST processing stage
## to make modifications for AD based on context etc.
modifyForAD_handlers <- c(list(
pow = 'modifyForAD_issuePowWarning',
eigenBlock = 'modifyForAD_eigenBlock',
calculate = 'modifyForAD_calculate',
getValues = 'modifyForAD_getSetValues',
setValues = 'modifyForAD_getSetValues',
nfMethod = 'modifyForAD_nfMethod',
chainedCall = 'modifyForAD_chainedCall',
getDerivs_wrapper = 'modifyForAD_getDerivs_wrapper',
AssignEigenMap = 'modifyForAD_AssignEigenMap',
ADbreak = 'modifyForAD_ADbreak',
`*` = 'modifyForAD_matmult',
eigInverse = 'modifyForAD_matinverse',
MAKE_FIXED_VECTOR = 'modifyForAD_MAKE_FIXED_VECTOR'),
makeCallList(recyclingRuleOperatorsAD, 'modifyForAD_RecyclingRule'),
makeCallList(c('EIGEN_FS', 'EIGEN_BS', 'EIGEN_SOLVE', 'EIGEN_CHOL', 'nimNewMatrixD', 'nimCd',
'nimRepd','nimDiagonalD', 'nimNonseqIndexedd'),
'modifyForAD_prependNimDerivs'))
exprClasses_modifyForAD <- function(code, symTab,
workEnv = list2env(list(wrap_in_value = FALSE))) {
if(code$isName) {
if(!isTRUE(workEnv[['wrap_in_value']]))
return(invisible())
else {
symObj <- symTab$getSymbolObject(code$name)
if(!is.null(symObj)) {
if(identical(symObj$baseType, "CppAD::AD")) {
insertExprClassLayer(code$caller, code$callerArgID, 'Value') ## It is ok to leave some fields (type, sizeExpr) unpopulated at this late processing stage
}
}
}
}
if(code$isCall) {
recurse_modifyForAD(code, symTab, workEnv)
handler <- modifyForAD_handlers[[code$name]]
if(!is.null(handler))
eval(call(handler, code, symTab, workEnv))
if(workEnv$RsymTab$symbolExists(code$name, TRUE)) ## Could be a nimbleFunction class method
modifyForAD_recordable(code, symTab, workEnv)
else {
if(!is.null(code$aux)) {
if(isTRUE(code$aux[['buildDerivs']])) ## This is added in sizeRCfunction
modifyForAD_RCfunction(code, symTab, workEnv)
}
}
}
if(is.null(code$caller)) { ## It is the top level `{`
if(identical(code$name, "{")) {
if(isTRUE(workEnv[['hasCalculate']])) {
if(is.null( workEnv[['nodeFxnVector_name']] ) )
stop("While setting up C++ AD code: calculate found but nodeFxnVector_name not set.")
## insert setup_extraInput_step(nfv)
set_model_tape_info_line <- RparseTree2ExprClasses(cppLiteral(
paste0("set_CppAD_tape_info_for_model my_tape_info_RAII_(",
workEnv[['nodeFxnVector_name']],
", recordingInfo_.tape_id(), recordingInfo_.tape_handle());")))
## ", TYPE_::get_tape_id_nimble(), TYPE_::get_tape_handle_nimble());")))
set_atomic_info_line <- RparseTree2ExprClasses(cppLiteral(
paste0("set_CppAD_atomic_info_for_model(",
workEnv[['nodeFxnVector_name']],
", recordingInfo_.atomic_vec_ptr());")))
## ", CppAD::local::atomic_index_info_vec_manager_nimble<double>::manage());")))
## This inserts a single line at the beginning by
## creating a new `{` block.
## If anything more general is needed later, we could use
## the exprClasses_insertAssertions system
newExpr <- newBracketExpr(args = c(list(set_model_tape_info_line,
set_atomic_info_line),
code$args))
code$args <- list()
setArg(code, 1, newExpr)
}
}
}
invisible(NULL)
}
recurse_modifyForAD <- function(code, symTab, workEnv) {
if(is.list(code$aux))
if(isTRUE(code$aux$.avoidAD))
return(invisible(NULL))
for(i in seq_along(code$args)) {
if(inherits(code$args[[i]], 'exprClass')) {
exprClasses_modifyForAD(code$args[[i]], symTab, workEnv)
}
}
invisible(NULL)
}
modifyForAD_issuePowWarning <- function(code, symTab, workEnv) {
message(" [Note] Operator `pow` may cause derivative problems with negative arguments. If the exponent is guaranteed to be an integer, use `pow_int` instead.", call. = FALSE)
invisible(NULL)
}
modifyForAD_matmult <- function(code, symTab, workEnv) {
if(isTRUE(nimbleOptions("useADmatMultAtomic")))
if(length(code$args)==2) ## something is wrong if there are not 2 args
if(!(isEigScalar(code$args[[1]]) || isEigScalar(code$args[[2]]))) ## are both non-scalar?
code$name <- 'nimDerivs_matmult'
invisible(NULL)
}
modifyForAD_matinverse <- function(code, symTab, workEnv) {
if(isTRUE(nimbleOptions("useADmatInverseAtomic")))
code$name <- 'nimDerivs_matinverse'
invisible(NULL)
}
modifyForAD_MAKE_FIXED_VECTOR <- function(code, symTab, workEnv) {
if(length(code$args) >= 5) {
go <- if(length(code$args) >= 6)
isTRUE(code$args[[6]])
else TRUE
if(go)
if(identical(code$args[[5]], "double"))
code$args[[5]] <- "CppAD::AD<double>"
}
}
modifyForAD_ADbreak <- function(code, symTab, workEnv) {
code$name <- 'CppAD::Value'
invisible(NULL)
}
modifyForAD_RecyclingRule <- function(code, symTab, workEnv) {
## The conversion to nimDerivs_really has to do with the C++ return type
## and that should always convert to CppAD::AD<double>, which is achieved
## by the following changes. In other words, there is no need to parse
## through the arguments and see which are AD types and which not.
code$name <- paste0('nimDerivs_', code$name)
code$name <- gsub('::', '::nimDerivs_', code$name)
code$name <- gsub("<MatrixXd>", "<MatrixXd_TYPE_>", code$name)
invisible(NULL)
}
modifyForAD_AssignEigenMap <- function(code, symTab, workEnv) {
EigMapName <- code$args[[1]]$name
## We extract the variable name by undoing the construction of the Eigen Map variable name.
## This would be nicer to do with generic functions that undo the label creation.
## At this time of this writing, hacking the solution here was more practical.
##
## This method of extracting the name of the variable we are making a map into
## attempted to invert the name-generation and name-mangling steps that led to it.
## However, it is not fully general. In addition, it is not clear if this would
## ever really make sense. Although noDerivs_vars can make a variable enter
## a deriv-enabled function with its raw types, we should never really be doing
## any vectorized operation with it. The reason is that the result will be CppAD::AD<double> (or TYPE_),
## since we do not attempt to somehow track AD and non-AD types through the AST processing.
## And Eigen requires same-type operations, I believe, because we manually cast when necessary among
## basic types, but we do not cast between AD and non-AD types.
## However, we try this for cases where it succeeds. Notably it is useful for the results of
## lifting "order = nimC(0, 1)" from nimDerivs, for example.
## The pieces created from that are now protected from AD modification.
go <- TRUE
varSym <- NULL
## We try to look for the relevant base symbol. If we can't find it, by default we do the AD modification
# unpack the getPtr step, which might have an offset added via "+"
ptrExpr <- code$args[[2]]
if(ptrExpr$name == "+")
ptrExpr <- ptrExpr$args[[1]]
if(ptrExpr$name == "getPtr") {
varName <- ptrExpr$args[[1]]$name
varSym <- symTab$getSymbolObject(varName, inherits = TRUE)
}
if(!isTRUE(workEnv$.inModel)) {
if(!is.null(varSym)) {
scalarType <- varSym$templateArgs[[2]]
go <- identical(scalarType, "TYPE_")
}
}
if(go) {
EigMapSym <- symTab$getSymbolObject(EigMapName)
EigMapSym_baseType <- EigMapSym$baseType
if(EigMapSym_baseType == "EigenMapStrd") {
EigMapSym$baseType <- "EigenMapStrd_TYPE_"
#MatrixXd_label <- code$args[[3]]
code$args[[3]]$name <- "MatrixXd_TYPE_"
}
if(EigMapSym_baseType == "Map") {
EigMapSym$templateArgs[[1]] <- "MatrixXd_TYPE_"
code$args[[3]]$name <- "MatrixXd_TYPE_"
}
}
invisible(NULL)
}
modifyForAD_prependNimDerivs <- function(code, symTab, workEnv) {
origName <- code$name
atomic <- TRUE
if(origName == 'EIGEN_FS' | origName == 'EIGEN_BS')
if(!isTRUE(nimbleOptions("useADsolveAtomic")))
atomic <- FALSE
if(origName == "EIGEN_CHOL")
if(!isTRUE(nimbleOptions("useADcholAtomic")))
atomic <- FALSE
if(atomic)
code$name <- paste0("nimDerivs_", origName)
else
code$name <- paste0("nimDerivs_", origName, '_no_atomic')
invisible(NULL)
}
modifyForAD_RCfunction <- function(code, symTab, workEnv) {
code$name <- paste0(code$name, "< CppAD::AD<double> >")
invisible(NULL)
}
modifyForAD_getDerivs_wrapper <- function(code, symTab, workEnv) {
## This really modifies the "argumentTransfer" call in the first argument of getDerivs_wrapper
arg1 <- code$args[[1]]
arg1$name <- paste0(arg1$name, "_AD2_")
code$name <- "getDerivs_wrapper_meta"
nArgs <- length(code$args)
newExpr <- RparseTree2ExprClasses(quote(recordingInfo_))
setArg(code, nArgs + 1, newExpr)
invisible(NULL)
}
modifyForAD_nfMethod <- function(code, symTab, workEnv) {
if(code$args[[1]]$name != "cppPointerDereference")
message(" [Note] In modifyForAD_nfMethod, was expecting cppPointerDereference. There must be another case that needs implementation.")
objName <- code$args[[1]]$args[[1]]$name
NFsymObj <- workEnv$RsymTab$getSymbolObject(objName, TRUE)
methodName <- code$args[[2]]
if(!is.character(methodName))
message(" [Note] In modifyForAD_nfMethod, was expecting method name to be character. There must be another case that needs implementation.")
methodSymObj <- NFsymObj$nfProc$compileInfos[[methodName]]$newLocalSymTab$getSymbolObject(methodName, TRUE)
buildDerivs <- methodSymObj$nfMethodRCobj$buildDerivs
if(!is.null(buildDerivs))
if(!isFALSE(buildDerivs)) {
code$args[[2]] <- paste0( code$args[[2]], "_AD2_")
code$name <- "nfMethodAD" ## This is a tag for modifyForAD_chainedCall
}
invisible(NULL)
}
modifyForAD_chainedCall <- function(code, symTab, workEnv) {
arg1name <- code$args[[1]]$name
if(arg1name == "nfMethodAD") { ## A tag set in modifyForAD_nfMethod
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(recordingInfo_)))
code$args[[1]]$name <- "nfMethod" ## tag is no longer needed. revert to regular nfMethodAD
}
invisible(NULL)
}
modifyForAD_recordable <- function(code, symTab, workEnv) {
symObj <- workEnv$RsymTab$getSymbolObject(code$name, TRUE)
buildDerivs <- symObj$nfMethodRCobj$buildDerivs
if(!is.null(buildDerivs))
if(!isFALSE(buildDerivs)) {
code$name <- paste0(code$name, "_AD2_")
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(recordingInfo_)))
}
invisible(NULL)
}
modifyForAD_getSetValues <- function(code, symTab, workEnv) {
if(code$name == 'setValues') {
code$name <- 'setValues_AD_AD_taping'
}
accessorName <- code$args[[2]]$name
already_AD_name <- grepl("_AD_$", accessorName) ## _AD_ is at the end. I'm not sure it would ever already be there, so this is defensive.
if(!already_AD_name) {
classSymTab <- symTab$getParentST()$getParentST()
newSymbolName <- paste0(accessorName, '_AD_')
if(!classSymTab$symbolExists(newSymbolName)) {
newSymbol <- classSymTab$getSymbolObject(accessorName)$copy()
if(newSymbol$name != accessorName)
warning("Something is wrong with internal processing of names in managing use of values() for nimDerivs.")
newSymbol$name <- newSymbolName
classSymTab$addSymbol(newSymbol)
}
code$args[[2]]$name <- newSymbolName
}
thirdArg <- RparseTree2ExprClasses(as.name(accessorName))
setArg(code, 3, thirdArg)
fourthArg <- RparseTree2ExprClasses(quote(recordingInfo_))
setArg(code, 4, fourthArg)
invisible(NULL)
}
modifyForAD_eigenBlock <- function(code, symTab, workEnv) {
orig_wrap_in_value <- workEnv[['wrap_in_value']]
workEnv[['wrap_in_value']] <- TRUE
recurse_modifyForAD(code, symTab, workEnv)
workEnv[['wrap_in_value']] <- orig_wrap_in_value
invisible(NULL)
}
modifyForAD_calculate <- function(code, symTab, workEnv) {
workEnv$hasCalculate <- TRUE
workEnv$nodeFxnVector_name <- code$args[[1]]$name
recurse_modifyForAD(code, symTab, workEnv)
code$name <- "calculate_ADproxyModel"
code$args[[2]] <- 1 ## this sets includeExtraOutputStep = true
setArg(code, length(code$args) + 1, RparseTree2ExprClasses(quote(cppLiteral("recordingInfo_"))))
invisible(NULL)
}
updateADproxyModelMethods <- function(.self) {
## Update return type and names of functions like dnorm -> nimDerivs_dnorm
functionNames <- names(.self$functionDefs)
ADproxyModel_functionNames <- functionNames[ grepl("_ADproxyModel", functionNames ) ]
if(length(ADproxyModel_functionNames) > 0) {
## The following two headers were added to CPPincludes because nimDerives_dists must
## come before Rmath.h
.self$CPPincludes <- c(nimbleIncludeFile("nimbleCppAD.h"),
nimbleIncludeFile("nimDerivs_dists.h"), .self$CPPincludes)
}
for(fn in ADproxyModel_functionNames) {
thisDef <- .self$functionDefs[[fn]]
thisDef$returnType <- cppVarSym2templateTypeCppVarSym( thisDef$returnType,
replacementBaseType = "CppAD::AD",
replacementTemplateArgs = "double" )
parentST <- thisDef$code$objectDefs$getParentST()
thisDef$code$objectDefs <-
symbolTable2templateTypeSymbolTable(thisDef$code$objectDefs) #,
## replacementBaseType = "CppAD::AD",
## replacementTemplateArgs = "double" )
thisDef$code$objectDefs$setParentST(parentST)
thisDef$code$cppADCode <- 2L
ADtypeDefs <- symbolTable()
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef typename EigenTemplateTypes<CppAD::AD<double> >::typeEigenMapStrd", name = "EigenMapStrd_TYPE_") )
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef Matrix<CppAD::AD<double>, Dynamic, Dynamic>", name = "MatrixXd_TYPE_") )
ADtypeDefs$addSymbol(cppVarFull(baseType = "typedef CppAD::AD<double>", name = "TYPE_") )
thisDef$code$typeDefs <- ADtypeDefs
workEnv <- new.env()
workEnv$RsymTab <- thisDef$RCfunProc$compileInfo$newLocalSymTab
workEnv$.inModel <- TRUE
exprClasses_modifyForAD(thisDef$code$code, thisDef$code$objectDefs, workEnv)
}
classST <- .self$objectDefs
classSymNames <- classST$getSymbolNames()
ADproxySymNames <- classSymNames[ grepl("ADproxyModel_", classSymNames ) ]
for(sn in ADproxySymNames) {
newSym <-
cppVarSym2templateTypeCppVarSym(classST$getSymbolObject(sn),
replacementBaseType = "CppAD::AD",
replacementTemplateArgs = "double") ## These end up the header file so they should not use TYPE_ as that is not typedef'd there
classST$addSymbol(newSym, allowReplace = TRUE)
}
NULL
}
makeSingleCopyCall <- function(varName, cppCopyType,
buildDerivs = FALSE) {
switch(cppCopyType,
'nimbleFunction' = {
cppLiteral(paste0("COPY_NIMBLE_FXN_FROM_R_OBJECT(\"", varName, "\");"))
},
'numericVector' = {
cppLiteral(paste0("COPY_NUMERIC_VECTOR_FROM_R_OBJECT(\"", varName, "\");"))
},
'doubleScalar' = {
cppLiteral(paste0("COPY_DOUBLE_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'integerScalar' = {
cppLiteral(paste0("COPY_INTEGER_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'logicalScalar' = {
cppLiteral(paste0("COPY_LOGICAL_SCALAR_FROM_R_OBJECT(\"", varName, "\");"))
},
'nodeFxnVec' = {
cppLiteral(paste0("COPY_NODE_FXN_VECTOR_FROM_R_OBJECT(\"", varName, "\");"))
},
'nodeFxnVec_nimDerivs' = {
cppLiteral(paste0("COPY_NODE_FXN_VECTOR_DERIVS_FROM_R_OBJECT(\"", varName, "\");"))
},
'modelVarAccess' = {
cppLiteral(paste0("COPY_VALUE_MAP_ACCESSORS_FROM_NODE_NAMES(\"", varName, "\"",
if(isTRUE(buildDerivs)) ", 1" else ", 0", ");"))
},
NULL)
}
makeCopyFromRobjectDef <- function(cppCopyTypes,
buildDerivs = FALSE) {
## Make method for copying from R object
copyFromRobjectDef <- RCfunctionDef()
copyFromRobjectDef$name <- 'copyFromRobject'
copyFromRobjectDef$returnType <- cppVoid()
copyFromRobjectDef$args <- symbolTable()
localVars <- symbolTable()
RobjectVarSym <- cppSEXP(name = 'Robject')
copyFromRobjectDef$args$addSymbol(RobjectVarSym)
copyCalls <- list()
varNames <- names(cppCopyTypes)
for(i in seq_along(cppCopyTypes)) {
copyCalls[[varNames[i]]] <- makeSingleCopyCall(varNames[i], cppCopyTypes[[i]],
buildDerivs = buildDerivs)
}
if(length(copyCalls) == 0) {
## create an empty function
allRcode <- do.call('call',
list('{'),
quote = TRUE
)
} else {
unprotectCount <- 2 + length(copyCalls) ## 2 from SETUP_S_xData
allRcode <- do.call('call',
c(list('{'),
list(cppLiteral("SETUP_S_xData;")),
copyCalls,
list(cppLiteral(paste0("UNPROTECT(",unprotectCount,");")))),
quote = TRUE
)
}
allCode <- RparseTree2ExprClasses(allRcode)
copyFromRobjectDef$code <- cppCodeBlock(code = allCode,
objectDefs = localVars)
copyFromRobjectInterfaceDef <- NULL
list(copyFromRobjectDef = copyFromRobjectDef,
copyFromRobjectInterfaceDef = copyFromRobjectInterfaceDef)
}
Try the nimble package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.