Class absdiag

: by intern

Member AddKnownsToLinearSystemAlgo::run (MatrixHandle a_in, MatrixHandle b_in, MatrixHandle x, SparseRowMatrixHandle &a_out, MatrixHandle &b_out, bool convert_matrix_types=false)

: if matrix A is sparse (checked and/or converted),

Class AddModule

idea: write addmodule.ShowMesh in python

Member AlgorithmData::get (const Name &name) const

: log incorrect type if present but wrong type

Member AlgorithmData::getList (const Name &name) const

: log incorrect type if present but wrong type

Member AlgorithmData::setTransient (boost::any t)

: lame

Class AlgorithmParameterList

: link this to ModuleState via meeting discussion

Class AlgorithmParameterNotFound

??

Class AlgorithmStatusReporter

: integrate with logger type above

Member AppendMatrixAlgorithm::run (const Inputs &input, const Parameters &params) const

: error

Member Application::controller ()

: these all get configured

: sloppy way to initialize this but similar to v4, oh well

Member Application::version () const

:

Member ArrayMathFunctions::RandomMutex ("Mutex for rand() and random() functions")

:

Member ArrayMathProgram::set_const_variable (size_t j, ArrayMathProgramVariableHandle handle)

: need to remove them at some point

Class ArrayMathProgramSource

replace with boost::variant

Member ASSERTFAIL (string)

: make sure default SCI_ASSERTION_LEVEL is consistent across platforms

Member BasisSimple< T >::interpolate (const VECTOR &, const ElemData &) const

: exceptions being used to avoid virtual inheritance?

: SCIRun 5 porting note: ASSERTFAIL replaced by

Member BBox::center () const

: C assert: assert(is_valid_);

Member BBox::longest_edge () const

: C assert: assert(is_valid_);

Member BBox::shortest_edge () const

: C assert: assert(is_valid_);

Member BinaryPiostream::endianness ()

SCIRUN4_CODE_TO_BE_ENABLED_LATER

Member BinarySwapPiostream::endianness ()

SCIRUN4_CODE_TO_BE_ENABLED_LATER

Member BOOST_PYTHON_MODULE (SCIRunPythonAPI)

Documentation Dataflow/Engine/Python/SCIRunPythonModule.h

Member BuildFEMatrixAlgo::run (FieldHandle input, Datatypes::DenseMatrixHandle ctable, Datatypes::SparseRowMatrixHandle &output) const

: can initialize array using std::fill

Member BuildPointCloudToLatVolMappingMatrix::execute ()

: Better epsilon checking

Class Bundle

:

Member Bundle::getField (const std::string &name) const

: extract into teplate impl, but do it here to avoid including every type in Bundle.h

Member CalculateSignedDistanceFieldAlgoTests::SetUp ()

: needs a surface, I know that much...

Member CollectMatrices::execute ()

: match output matrix type with input type.

Member ColumnMatrixGeneric< T >::operator= (const ColumnMatrixGeneric &)

in C++11–move ctors for all matrix types.

Member ColumnMatrixGeneric< T >::scalar_multiply (T s)

: replace with for_each

Member ColumnMatrixGeneric< T >::set_data (T *d)

: remove

Member Connection::Connection (OutputPortHandle oport, InputPortHandle iport, const ConnectionId &id)

: this is already checked in the controller layer. Do we need a redundant check here?

Member ConnectionInputPort::ConnectionInputPort (ModuleHandle m, size_t index)

: only used in test code

Member ConnectionOutputPort::ConnectionOutputPort (ModuleHandle m, size_t index)

: only used in test code

Member ConvertMeshCoordinateSystemAlgo::run (FieldHandle input, FieldHandle &output)

: check for input field's current coordinate system?

Namespace Core

Documentation Core/Utils/StringContainer.h

Member CreateLatVol::execute ()

: extract algorithm class!!!!!!!!!!!!!!!!!!!!

Member CreateMatrix::execute ()

: quick bug fix, this module is due for rewrite.

Member CreateScalarFieldDataBasic::execute ()

: expand this module and then move it to test module category. then it can be used with python to regression test many combinations of latvol visualization!

Member Datatype::as () const

Member DefinePeriodicBoundariesAlgo::run (FieldHandle &input, MatrixHandle &periodic_nodelink, MatrixHandle &periodic_delemlink)

: add progress reporting

: Need to replace this with searchgrid implementation

Member DenseColMajMatrixGeneric< T >::dense ()

: these will be moved to a separate class to break compilation dependency on the subclasses of Matrix.

Member DenseColMajMatrixGeneric< T >::submatrix (index_type r1, index_type c1, index_type r2, index_type c2)

: Test this.

Member DenseMatrixGeneric< T >::DenseMatrixGeneric (size_t nrows=0, size_t ncols=0)

: don't like this default ctor, since it doesn't act like a vector.

Member DenseMatrixGeneric< T >::invert ()

: this needs to be refactored

Member DesktopExecutionStrategyFactory::createDefault () const

: update this to best working version

Class DimensionMismatch

move these exceptions to new exception header file once it exists

Class DynamicMultithreadedNetworkExecutorImpl

: templatize along with producer/consumer

Member DynamicPortManager::connectionAddedNeedToCloneAPort (const SCIRun::Dataflow::Networks::ConnectionDescription &)

: assumption: dynamic = input

Class EdgeInfo< VirtualMeshType >

: templatize with traits and stuff. for now, a specialized version for edges.

Member EdgeInfo< VirtualMeshType >::EdgeInfo (VirtualMeshType *mesh)

: need to split out that Synchronize enum

Member EigenMatrixFromScirunAsciiFormatConverter::make (const std::string &matFile)

: no access to error(), need alternative for logging this exception

Member ElectrodeCoilSetupModule::setStateDefaults ()

Member EvaluateLinearAlgebraBinaryAlgorithm::EvaluateLinearAlgebraBinaryAlgorithm ()

: idea (type, name)

Member EvaluateLinearAlgebraBinaryAlgorithm::run (const Inputs &inputs, const Parameters &params) const

: absolutely need matrix move semantics here!!!!!!!

Member EvaluateLinearAlgebraUnaryAlgorithm::run (const Inputs &matrix, const Parameters &params) const

: absolutely need matrix move semantics here!!!!!!!

Member EvaluateLinearAlgebraUnaryModule::execute ()

: standardize on camel case!

Member ExceptionBase::typeName () const

very hacky.

Class ExecutableLookup

: hacky duplication...

Member FieldTypeInformation::field_basis_order ()

: an enum would be good for keeping track of basis order...

Member FieldTypeInformation::insert_field_type_information (Field *field)

DAN: use std::replace for strings below.

Class FullFileName

: most of the functionality in this class can be replaced with the

Member GeneratePointSamplesFromField::execute ()

: It looks like the input field is meant to be optional even

Member GenerateROIStatisticsModule::setStateDefaults ()

Member GenericReader< HType, PortTag >::execute ()

: this will be a common pattern for file loading. Perhaps it will be a base class method someday...

Member GenericWriter< HType, PortTag >::execute ()

: this will be a common pattern for file loading. Perhaps it will be a base class method someday...

Member GetDomainBoundaryTests::runTest (bool includeOuterBoundary, bool useRange, int domainValue, int expectedBoundaryNodes, int expectedBoundaryElements)

: this logic matches the wacky module behavior

Member GetMeshNodesAlgo::run (FieldHandle &input, Datatypes::DenseMatrixHandle &output) const

: refactor duplication

Member GlobalCommandBuilderFromCommandLine::build (SCIRun::Core::CommandLine::ApplicationParametersHandle params)

obviously

Member GLWidget::GLWidget (QtGLContext *context)

Implement this intelligently. This function is called everytime there is a new graphics context.

Member HardCodedAlgorithmFactory::HardCodedAlgorithmFactory ()

: add unit test

Member Has2InputPorts< PortTypeTag0, PortTypeTag1 >::inputPortDescription (const std::string &port0Name, const std::string &port1Name)

: use move semantics

Member Has2OutputPorts< PortTypeTag0, PortTypeTag1 >::outputPortDescription (const std::string &port0Name, const std::string &port1Name)

: use move semantics

Class HasId< IdType, IdGenerator >

: split out

Member HexVolMesh< Basis >::get_size (typename Face::index_type idx) const

: This code is incorrect need to create a better call in basis functions

Member HexVolMesh< Basis >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member HexVolMesh< Basis >::insert_node_into_grid (typename Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member HexVolMesh< Basis >::locate_edge (INDEX &edge, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member HexVolMesh< Basis >::locate_elem (INDEX &elem, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member HexVolMesh< Basis >::locate_elem (INDEX &elem, ARRAY &coords, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member HexVolMesh< Basis >::locate_face (INDEX &face, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member IEPluginManager::Initialize ()

: split out into separate file

Class InputPort

: discuss this interface design

Member InsertHexVolSheetAlongSurfaceAlgo::execute (ProgressReporter *reporter, FieldHandle hexfieldh, FieldHandle trifieldh, FieldHandle &side1field, FieldHandle &side2field, bool add_to_side1, bool add_layer)

: Since the algorithm does not copy data

Class IPortDescriber< numPorts, ModuleType >

: make metafunc for Input/Output

Member LinAlgProgram::set_const_variable (size_t j, LinAlgProgramVariableHandle &handle)

: need to remove them at some point

Member LoadFileCommandConsole::execute ()

: real logger

Member Log::get (const std::string &name)

: make thread safe

Member LOG_DEBUG (str)

: log4cpp crashes on Mac more easily, just macro these out on that platform for now.

Member LogImpl::LogImpl (const std::string &name)

Class MapFieldDataOntoNodesRadialbasis

: code cleanup needed

Member MarchingCubesAlgoP< TESSELATOR >::run (AlgoBase *algo, FieldHandle &output, GeomHandle &geometry, MatrixHandle &node_interpolant, MatrixHandle &elem_interpolant)

: FIX MULTI THREADING OF MARCHING CUBES FIELDS ARE NOT PROPORLY LINKED

Class matrix_convert

: move

Class MatrixVisitorGeneric< T >

: use Eigen's Visitor type?

Member MergeFields::execute ()

: Handle falling outside of mesh better. May not be convex.

: We only need to test the edges that are 'close', not all

: Find closest could and will land on degeneracies meaning

Member MergeTriSurfs::execute ()

: Verify that it's a trisurf that we're testing.

Class MeshFactory

: yucky double-singleton to separate registration from construction.

Namespace ModelCreation

Documentation Modules/Legacy/Fields/SplitFieldByConnectingRegion.cc

Member Module::Builder::cloneInputPort (ModuleHandle module, const PortId &id)

: these don't quite belong here, think about extracting

Member Module::defaultStateFactory_

: yuck

Member Module::do_execute ()

: execute signal here.

: status() calls should be logged everywhere, need to change legacy loggers. issue #nnn

: need separate logger per module

: this block is repetitive (logging-wise) if the macros are used to log AND throw an exception with the same message. Figure out a reasonable condition to enable it.

: need separate logger per module

Member Module::hasDynamicPorts () const

: need to examine HasPorts base classes

Member Module::needToExecute () const

: || !oports_cached()

Member ModuleConsumer::operator() () const

: thread pool

Member ModuleDescriptionLookup::lookupDescription (const Dataflow::Networks::ModuleLookupInfo &info) const

: log

Member ModuleDescriptionLookup::ModuleDescriptionLookup ()

: is BUILD_TESTING off when we build releases?

: make EVEN MORE generic...macros? xml?

: at least remove duplication of Name,Package,Category here since we should be able to infer from header somehow.

: possibly use different build setting for these.

Member ModuleExecutor::run ()

: crashes on Mac

Member ModuleInfoProvider::hasOutputPort (const PortId &id) const =0

: kind of ridiculous interface/duplication. Should pull out a subinterface for "PortView" and just return one of those for input/output

Class ModuleInterface

: interface is getting bloated, segregate it.

Member ModuleInterface::getUpdaterFunc () const =0

functions

Member ModuleInterface::needToExecute () const =0

:

Member ModuleInterface::preDestruction ()

: name too clunky. Called before the module is to be destroyed. More importantly, called before the UI widget is to be destroyed.

Member ModuleInterface::set_id (const std::string &id)=0

for deserialization

Member Network::disable_connection (const ConnectionId &)

Member Network::incrementErrorCode (const ModuleId &moduleId)

: store errored modules in a list or something

Class NetworkEditorController

Refactoring: split this class into two classes, NetworkEditorService and Controller.

Member NetworkEditorController::connectNewModule (const SCIRun::Dataflow::Networks::ModuleHandle &moduleToConnectTo, const SCIRun::Dataflow::Networks::PortDescriptionInterface *portToConnect, const std::string &newModuleName)

: see above

duplication

Member NetworkEditorController::duplicateModule (const Networks::ModuleHandle &module)

: probably a pretty poor way to deal with what I think is a race condition with signaling the GUI to place the module widget.

: this will work if we define PortId.id# to be 0..n, unique for each module. But what about gaps?

Member NetworkEditorController::NetworkEditorController (Networks::ModuleFactoryHandle mf, Networks::ModuleStateFactoryHandle sf, ExecutionStrategyFactoryHandle executorFactory, Core::Algorithms::AlgorithmFactoryHandle algoFactory, Networks::ModulePositionEditor *mpg=0)

should this class own the network or just keep a reference?

Member NetworkEditorController::setModulePositionEditor (Networks::ModulePositionEditor *editor)

: eek, getting bloated here. Figure out a better way to wire this one in.

Member NetworkEditorPythonAPI::setExecutionContext (Dataflow::Networks::ExecutableLookup *lookup)

: smelly!

Member NetworkXMLConverter::from_xml_data (const NetworkXML &data)

: need to use NEC here to manage signal/slots for dynamic ports.

Member NodeInfo< VirtualMeshType >::edgeIndices () const

: need to split out that Synchronize enum

Member NOMINMAX

Make this definition specific to windows.

Class NotImplemented

should not need this in production code.

Member ParallelLinearAlgebra::add_matrix (Datatypes::SparseRowMatrixHandle mat, ParallelMatrix &M)

: this should be an invariant of our SparseRowMatrix type.

Member ParallelLinearAlgebra::max (const ParallelVector &a)

: refactor to use algorithm

Member ParallelLinearAlgebra::mult (const ParallelVector &a, const ParallelVector &b, ParallelVector &r)

: refactor duplication

Member ParallelLinearAlgebraSharedData::ParallelLinearAlgebraSharedData (const SolverInputs &inputs, int numProcs)

: use new DimensionMismatch exception type

Member Piostream::io (Persistent *&, const PersistentTypeID &)

ULTRA HACKY CODE

Member PointCloudMesh< Basis >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member Port::detach (Connection *conn)

: use real logger here

Member Port::module_

:

Member PortConnectionDeterminer::canBeConnected (const SCIRun::Dataflow::Networks::PortDescriptionInterface &port1, const SCIRun::Dataflow::Networks::PortDescriptionInterface &port2) const

: unit test

: trying out "wildcard" ports

Member PortId::toString () const

: need smart way to set

Member PortManager< T >::add (const T &item)

: who should manage port indexes?

Member PortManager< T >::operator[] (const PortId &id) const

: need a way to detect and create arbitrary dynamic ports from serialized files.

Member Preferences::showModuleErrorDialogs

: reuse Seg3D state vars

Member PrismVolMesh< Basis >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member PrismVolMesh< Basis >::insert_node_into_grid (typename Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member PrismVolMesh< Basis >::locate_edge (INDEX &edge, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member PrismVolMesh< Basis >::locate_elem (INDEX &elem, ARRAY &coords, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member PrismVolMesh< Basis >::locate_elem (INDEX &elem, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member PrismVolMesh< Basis >::locate_face (INDEX &face, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member PropertyBase::type_id

: should be using Guards here...

Member PropertyManager::copy_properties (const PropertyManager *src)

: currently, field types are passing in pointers

Member PropertyManager::PropertyManager (const PropertyManager &copy)

: this and copy properties share essentially common code.

Member PropertyManager::thaw ()

: since we're using Boost shared pointers, ref_cnt is no longer u sed.

Member QuadSurfMesh< Basis >::has_normals () const

: this is inconsistent with TriSurfMesh - should both surfaces

Member QuadSurfMesh< Basis >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member QuadSurfMesh< Basis >::insert_node_into_grid (typename Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member ReadFieldModule::call_importer (const std::string &filename, FieldHandle &handle) override

: how will this work via python? need more code to set the filetype based on the extension...

Member ReadMatrixModule::execute ()

: unit test. Requires algorithm injection/factory for mocking, to be able to isolate the "optional file argument" part.

: this will be a common pattern for file loading. Perhaps it will be a base class method someday...

Class ReceiveScalarState

Member register

Class RemoveHexVolSheetAlgo

: change vector param to ref

Member REPORT_NOT_IMPLEMENTED (message)

should not need this in production code.

Member ReportFieldInfoModule::execute ()

: requires knowledge of algorithm type

Member ReportMatrixInfoModule::execute ()

: requires knowledge of algorithm type

Member SchedulingWithBoostGraph::setupBasicNetwork ()

: turn this into a convenience network printing function

Class SciBall

Extend this class to include Mouse screen coords -> object space calculations. That way we can rotate around a particular object. May also want to visually represent the sphere when we perform this calculation.

Provide method of setting the default orientation of the object.

Member SciBall::drag (const spire::V2 &mouseScreenCoords)

Perform constraints here.

Namespace SCIRun

MORITZ

DAN

: move

Documentation Core/Application Preferences.h

Documentation Core/Basis/HexSamplingSchemes.h

Documentation Core/Basis/PntSamplingSchemes.h

Documentation Core/Basis/PrismSamplingSchemes.h

Documentation Core/Basis/QuadSamplingSchemes.h

Documentation Core/Basis/TriSamplingSchemes.h

Documentation Core/Command/Command.h

: replace with STL container

Documentation Core/Datatypes/Color.h

Documentation Core/Datatypes/ColorMap.h

Documentation Core/Datatypes/Datatype.h

Documentation Core/Datatypes/DatatypeFwd.h

Documentation Core/Datatypes/Geometry.h

Documentation Core/Datatypes/Legacy/Base/Types.h

Documentation Core/Datatypes/Legacy/Color/ColorMap.cc

Documentation Core/Datatypes/Legacy/Color/Material.cc

Documentation Core/Datatypes/Legacy/Color/Material.h

Documentation Core/Datatypes/Legacy/Field/CastFData.h

Documentation Core/Datatypes/Legacy/Field/cd_templates_fields_1_itk.cc

Documentation Core/Datatypes/Legacy/Field/FieldFwd.h

Documentation Core/Datatypes/Legacy/Field/FieldInformation.h

Documentation Core/Datatypes/Legacy/Field/FieldRNG.cc

Documentation Core/Datatypes/Legacy/Field/FieldRNG.h

Documentation Core/Datatypes/Legacy/Field/VFDataT_0.cc

Documentation Core/Datatypes/Legacy/Field/VFDataT_1.cc

Documentation Core/Datatypes/Legacy/Field/VFDataT_2.cc

Documentation Core/Datatypes/Legacy/Matrix/DenseMatrix.cc

Documentation Core/Datatypes/Legacy/Matrix/DenseMatrixFunctions.cc

Documentation Core/Datatypes/Legacy/Matrix/MatrixAlgorithms.cc

Documentation Core/Datatypes/Legacy/Matrix/MatrixAlgorithms.h

Documentation Core/Datatypes/Legacy/Matrix/MatrixFwd.h

Documentation Core/Datatypes/Legacy/Matrix/MatrixTypeConverter.cc

Documentation Core/Datatypes/Legacy/Matrix/MatrixTypeConverter.h

Documentation Core/Datatypes/Legacy/Other/FieldArray.cc

Documentation Core/Datatypes/Legacy/Other/FieldArray.h

Documentation Core/Datatypes/Matrix.h

Documentation Core/Datatypes/MatrixComparison.h

Documentation Core/Datatypes/MatrixFwd.h

Documentation Core/Datatypes/MatrixIO.h

Documentation Core/Datatypes/MatrixTypeConversion.h

Documentation Core/Datatypes/Mesh/FieldFwd.h

Documentation Core/Datatypes/Mesh/LatticeVolumeMeshRegister.h

Documentation Core/Datatypes/Mesh/MeshFacade.h

Documentation Core/Datatypes/Mesh/MeshFacadeIterators.h

Documentation Core/Datatypes/Mesh/MeshFactory.h

Documentation Core/Datatypes/Mesh/MeshTraits.h

Documentation Core/Datatypes/Mesh/TriSurfMeshRegister.h

Documentation Core/Datatypes/Mesh/VirtualMeshFacade.h

Documentation Core/Datatypes/Mesh/VirtualMeshFactory.h

Documentation Core/Datatypes/PropertyManagerExtensions.h

Documentation Core/Datatypes/Scalar.h

Documentation Core/Datatypes/SparceRowMatrixFromMap.h

Documentation Core/Datatypes/String.h

Documentation Core/GeometryPrimitives/BBox.h

replace asserts in this code with warnings or other reporting mechanism that doesn't abort the program

Documentation Core/GeometryPrimitives/GeomFwd.h

Documentation Core/GeometryPrimitives/Plane.h

Documentation Core/GeometryPrimitives/PointVectorOperators.h

Documentation Core/GeometryPrimitives/SearchGridT.h

Documentation Core/GeometryPrimitives/Transform.h

Documentation Core/GeometryPrimitives/Vector.h

Documentation Core/Logging/ConsoleLogger.h

Documentation Core/Logging/DirectLogger.h

Documentation Core/Logging/Log.h

Documentation Core/Logging/LoggerFwd.h

Documentation Core/Logging/LoggerInterface.h

Documentation Core/Logging/ScopedTimeRemarker.h

Documentation Core/PersistentFwd.h

pimpl?

: pimpl?

Documentation Core/Thread/Legacy/ UsedWithLockingHandle.h

pimpl?

Documentation Core/Utils/Exception.h

Documentation Core/Utils/FileUtil.h

Documentation Core/Utils/Legacy/CheckSum.h

Documentation Core/Utils/Legacy/Debug.h

Documentation Core/Utils/Legacy/Endian.cc

Documentation Core/Utils/Legacy/Environment_Defaults.cc

Documentation Core/Util/Legacy/FullFileName.h

Documentation Core/Utils/Legacy/MemoryUtil.h

Documentation Core/Utils/Legacy/StringUtil.cc

Documentation Core/Utils/Legacy/StringUtil.h

Documentation Core/Utils/Lockable.h

Documentation Core/Utils/StringUtil.h

Documentation Core/Utils/TypeIDTable.h

Documentation Dataflow/Engine/Controller/ControllerInterfaces.h

Documentation Dataflow/Engine/Controller/DynamicPortManager.h

Documentation Dataflow/Engine/Controller/NetworkCommands.h

Documentation Dataflow/Engine/Controller/NetworkEditorController.h

: split out connectionmakerservice

Documentation Dataflow/Engine/Controller/ProvenanceItem.h

Documentation Dataflow/Engine/Controller/ProvenanceItemFactory.h

Documentation Dataflow/Engine/Controller/ProvenanceItemImpl.h

Documentation Dataflow/Engine/Controller/ProvenanceManager.h

Documentation Dataflow/Engine/Python/NetworkEditorPythonAPI.cc

Documentation Dataflow/Engine/Python/NetworkEditorPythonInterface.cc

Documentation Dataflow/Engine/Scheduler/BasicMultithreadedNetworkExecutor.h/

Documentation Dataflow/Engine/Scheduler/BasicParallelExecutionStrategy.h

Documentation Dataflow/Engine/Scheduler/BoostGraphParallelScheduler.h

Documentation Dataflow/Engine/Scheduler/BoostGraphSerialScheduler.h

Documentation Dataflow/Engine/Scheduler/DynamicMultithreadedNetworkExecutor.h

Documentation Dataflow/Network/Connection.h

Documentation Dataflow/Network/ConnectionId.h

Documentation Dataflow/Network/DataflowInterfaces.h

Documentation Dataflow/Network/ExecutableObject.h

Documentation Dataflow/Network/Module.h

Documentation Dataflow/Network/ModuleDescription.h

Documentation Dataflow/Network/ModuleFactory.h

Documentation Dataflow/Network/ModuleInterface.h

Documentation Dataflow/Network/ModuleStateInterface.h

Documentation Dataflow/Network/Network.h

Documentation Dataflow/Network/NetworkFwd.h

Documentation Dataflow/Network/NetworkInterface.h

Documentation Dataflow/Network/NetworkSettings.h

Documentation Dataflow/Network/NullModuleState.h

Documentation Dataflow/Network/Port.h

Documentation Dataflow/Network/PortInterface.h

Documentation Dataflow/Network/PortManager.h

Documentation Dataflow/Network/SimpleSourceSink.h

Documentation Dataflow/Serialization/Network/ModuleDescriptionSerialization.h

Documentation Dataflow/Serialization/Network/ModulePositionGetter.h

Documentation Dataflow/Serialization/Network/NetworkDescriptionSerialization.h

Documentation Dataflow/Serialization/Network/NetworkXMLSerializer.h

Documentation Dataflow/Serialization/Network/StateSerialization.h

Documentation Dataflow/Serialization/Network/XMLSerializer.h

Documentation Dataflow/State/SimpleModuleState.h

Documentation Modules/Basic/DynamicPortTester.h

Documentation Modules/Basic/PrintDatatype.h

Documentation Modules/Basic/ReceiveScalar.h

Documentation Modules/Basic/ReceiveScalarModuleState.h

Documentation Modules/Basic/ReceiveTestMatrix.h

Documentation Modules/Basic/SendScalar.h

Documentation Modules/Basic/SendTestMatrix.h

MORITZ

Documentation Module/DataIO/ReadField.h

Documentation Modules/DataIO/ReadMatrix.h

Documentation Modules/DataIO/WriteField.h

Documentation Modules/DataIO/WriteMatrix.h

Documentation Modules/Factory/HardCodedModuleFactory.h

Documentation Modules/Fields CreateSclarFieldDataBasic.h

Documentation Modules/Fields/ReportFieldInfo.h

Documentation Modules/FiniteElements/TDSSimulator.h

Documentation Modules/Legacy/DataIO/ReadFieldArray.cc

Documentation Modules/Legacy/DataIO/StreamACQFileFromDisk.cc

Documentation Modules/Legacy/DataIO/StreamMatrixFromDisk.cc

Documentation Modules/Legacy/DataIO/WriteFieldArray.cc

Documentation Modules/Legacy/Fields/CalculateMeshCenter.cc

Documentation Modules/Legacy/Fields/GenerateMedialAxisPoints.cc

Documentation Modules/Legacy/Fields/GetAllSegmentationBoundaries.cc

Documentation Modules/Legacy/Fields/GetFieldDomainStructure.cc

Documentation Modules/Legacy/Fields/GetFieldNodes.h

Documentation Modules/Legacy/Fields/GetMeshQualityField.cc

Documentation Modules/Legacy/Fields/MatchDomainLabels.cc

Documentation Modules/Legacy/Fields/PadRegularMesh.cc

Documentation Modules/Legacy/Fields/RefineMesh.cc

Documentation Modules/Legacy/Fields/RemoveUnusedNodes.cc

Documentation Modules/Legacy/Fields/SetFieldNodes.h

Documentation Modules/Legacy/Fields/SplitNodesByDomain.cc

Documentation Modules/Legacy/FiniteElements/BuildFEGridMapping.cc

Documentation Modules/Legacy/FiniteElements/BuildFEGridMappingByDomain.cc

Documentation Modules/Legacy/FiniteElements/BuildFEMatrix.h

Documentation Modules/Legacy/FiniteElements/BuildFESurfRHS.cc

Documentation Modules/Legacy/FiniteElements/BuildFEVolRHS.cc

Documentation Modules/Legacy/FiniteElements/BuildTDCSMatrix.h

Documentation Modules/Legacy/FiniteElements/DefinePeriodicBoundaries.cc

Documentation Modules/Legacy/Math/AddKnownsToLinearSystem.h

Documentation Modules/Legacy/Math/AddLinkedNodesToLinearSystem.cc

Documentation Modules/Legacy/Math/RemoveZeroRowsAndColumns.cc

Documentation Modules/Legacy/Math/RemoveZerosFromMatrix.cc

Documentation Modules/Legacy/Math/SortMatrix.cc

Documentation Modules/Legacy/String/GetNetworkFileName.cc

Documentation Modules/Math/CreateMatrix.h

Documentation Modules/Math/EvaluateLinearAlgebraBinary.h

Documentation Modules/Math/EvaluateLinearAlgebraBinaryState.h

Documentation Modules/Math/EvaluateLinearAlgebraUnary.h

Documentation Modules/Math/ReportMatrixInfo.h

Documentation Modules/Math/SolveLinearSystem.h

Documentation Modules/String/CreatString.h

Documentation Modules/Visualization/CreateBasicColorMap.h

Documentation Modules/Visualization/MatrixAsVectorField.h

Documentation Modules/Visualization/MeshConstruction.h

Documentation Modules/Visualization/ShowField.h

Documentation Modules/Visualization/ShowString.h

Member SCIRun::Add (double, DenseMatrix &, const DenseMatrix &)

: This code does not look OK

Member SCIRun::copyDir (std::string src, std::string dest)

: re-implement with boost

Member SCIRun::Core::DoubleOutOfRangeInfo

make macro for various types

Member SCIRun::Core::Geometry::Min (const T &t1, const T &t2, const T &t3)

move to math header

Member SCIRun::Core::LinearAlgebraErrorMessage

discuss location/type

Member SCIRun::Core::replaceDelimitersWithWhitespace (std::string &line)

this code doesn't work under VS2010 - check with VS2012

Member SCIRun::Dataflow::Engine::executeWithCycleCheck (Scheduler< OrderType > &scheduler, NetworkExecutor< OrderType > &executor, const Networks::NetworkInterface &network, const Networks::ExecutableLookup &lookup, const ExecutionBounds &bounds)

: use real logger here–or just let this exception bubble up–needs testing.

Member SCIRun::Dataflow::Networks::any_cast_or_default_ (const boost::any &x)

split

: use real logger here

Member SCIRun::Dataflow::Networks::operator< (const ConnectionDescriptionXML &lhs, const ConnectionDescriptionXML &rhs)

: assumes only input ports can be dynamic.

Member SCIRun::Gui::buildNormalRenderingForVBO (std::shared_ptr< std::vector< uint8_t >> vboData, size_t stride, float normalLength, std::vector< uint8_t > &out_vboData, std::vector< uint8_t > &out_iboData, size_t posOffset, size_t normOffset)

Possibly parameterize uint16_t output type for ibo using templates.

Member SCIRun::inv (MatrixHandle A)

: does not check if invert operation was successful or not

Member SCIRun::operator>> (const PyPort &from, const PyPort &to)

: bizarre reason for this return type and casting. but it works.

Member SCIRun::Point_get_h_file_path ()

: This one is obsolete when last part dynamic compilation is gone

Member SCIRun::Vector_get_h_file_path ()

: This one is obsolete when dynamic compilation will be abandoned

Namespace SCIRunAlgo

: this was used by the TracePoints module, which

Class SendScalarState

Member SetFieldDataToConstantValueAlgo::SetFieldDataToConstantValueAlgo ()

Member SetMeshNodesAlgo::run (FieldHandle input, Datatypes::DenseMatrixHandle matrix, FieldHandle &output) const

: worth separating out into factory call for mocking purposes? probably not, just keep the concrete dependence

Member SetupRHSforTDCSandTMSModule::setStateDefaults ()

Member SimpleMapModuleState::fireTransientStateChangeSignal ()

: ???

Member SimpleMapModuleState::operator= (const SimpleMapModuleState &rhs)

: I think this is wrong, transient shouldn't be copied

??

Class SmartMeshIterator< VirtualMeshType, MeshComponent >

: Being conservative with mesh synchronization flags until more

Member SmartMeshIterator< VirtualMeshType, MeshComponent >::SmartMeshIterator (VirtualMeshType *vmesh=0, bool isEnd=false)

: need to look up pattern for creating "end" iterators.

: need to split out that Synchronize enum

Class SolveLinearSystemAlgorithm

: this will be the base class of all the solvers. for now it will just contain the Eigen CG impl.

Member SolveLinearSystemAlgorithm::run (const Inputs &input, const Parameters &params) const

: move ctor

Member SolveLinearSystemModule::execute ()

: why aren't these checks in the algo class?

Class SparseRowMatrixFromMap

: refactor with some OO, please...

Member SparseRowMatrixGeneric< T >::castForPrinting () const

!

Member SparseRowMatrixGeneric< T >::dynamic_type_name () const

: lame...figure out a better way

Member SparseRowMatrixGeneric< T >::scalar_multiply (T s)

: replace with for_each

Member SparseRowMatrixGeneric< T >::SparseRowMatrixGeneric ()

: need C++11

Member SRCamera::doAutoView (const Core::Geometry::BBox &bbox)

Use real FOV-Y when we allow the user to change the FOV.

Class SRCommonAttributes

Look into the ability to rename these uniforms in the future. This is so that Spire can adapt to other code bases.

Class SRCommonUniforms

Look into the ability to rename these uniforms in the future. This is so that Spire can adapt to other code bases.

Member SRInterface::eventResize (size_t width, size_t height)

Ensure perspective matrix is rebuilt with correct aspect ratio.

Member SRInterface::getScreenWidthPixels () const

Selecting objects...

Obtaining data from mesh objects in order to spatially partition them and provide quick object feedback.

Member SRInterface::MouseButton

Specify what buttons are pressed.

Member StackWalker::ShowCallstack (HANDLE hThread=GetCurrentThread(), const CONTEXT *context=NULL, PReadProcessMemoryRoutine readMemoryFunction=NULL, LPVOID pUserData=NULL)

: Mache dies sicher...!

Member StreamLineIntegrators::FindAdamsMoulton ()

: Implement AdamsMoulton

Member StructHexVolMesh< Basis >::find_closest_elem (double &pdist, Core::Geometry::Point &result, ARRAY &coords, INDEX &elem, const Core::Geometry::Point &p, double maxdist) const

: Generate bounding boxes for elements and integrate this into the

Member StructHexVolMesh< Basis >::locate_elem (INDEX &elem, ARRAY &coords, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member StructHexVolMesh< Basis >::locate_elem (INDEX &elem, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member StructQuadSurfMesh< Basis >::insert_elem_into_grid (typename ImageMesh< Basis >::Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member StructQuadSurfMesh< Basis >::insert_node_into_grid (typename ImageMesh< Basis >::Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member StructQuadSurfMesh< Basis >::inside3_p (typename ImageMesh< Basis >::Face::index_type i, const Core::Geometry::Point &p) const

: How small is small ???

Member TDCSInputData::contactimpedance ()

: MORITZ insert values as above.

Member TDCSInputData::ElectrodeElementDefinition ()

: MORITZ insert values as above.

Member TDCSInputData::ElectrodeElements ()

: MORITZ insert values as above.

Member TDCSInputData::ElectrodeElementType ()

: MORITZ insert values as above.

Member TDCSInputData::expectedOutput ()

: MORITZ insert values as above.

Member TDCSInputData::stiff ()

: MORITZ fill in values up to 5x5

Member TDCSSimulatorModule::setStateDefaults ()

Member TEST (ParallelArithmeticTests, CanMultiplyVectorsComponentWiseMulti)

: by intern

Member TEST (SolveLinearSystemTests, CanSolveDarrell_Jacobi)

: doesn't converge for this system. Problem?

Member TEST (ColorTests, CanParseString)

DAN

Member TEST (SparseRowMatrixBinaryOperationTests, WhatHappensWhenYouAddDifferentSizes)

: compare to v4.

Member TEST (ParallelArithmeticTests, CanMultiplyMatrixByVector)

: by intern

Member TEST (SolveLinearSystemTests, CanSolveDarrell_CG)

: investigate this significant difference

Member TEST (SolveLinearSystemTests, CanSolveDarrell_MINRES)

: converges but not as accurate.

Member TEST (DenseMatrixBinaryOperationTests, WhatHappensWhenYouAddDifferentSizes)

: compare to v4.

Member TEST (ParallelArithmeticTests, CanInvertElementsOfVectorWithAbsoluteValueThresholdMulti)

: by intern

Member TEST (AppendMatrixAlgorithmTests, ReturnsNullWithSizeMismatch)

: should return with error.

Member TEST (ReadMatrixAlgorithmTest, DISABLED_ThrowsForMatlabFilesICantThemReadYet)

: will hook up Matlab readers soon.

Member TEST (BuildTDCSMatrixAlgorithmTests, ThrowsForNullMesh)

: consider throwing an exception instead of returning false

Member TEST (MatrixCalculatorFunctionalTest, ManualExecutionOfMultiNodeNetwork)

: turn this into a convenience network printing function

Member TEST (SparseMatrixReadTest, RegexOfScirun4Format)

: remove these Eigen tests if they are duplicates of existing SLS tests. Other tests below need to live in separate files.

Member TEST (BuildTDCSMatrixAlgorithmTests, ThrowsForNullElectrodeElements)

: consider throwing an exception instead of returning false

Member TEST (ParallelLinearAlgebraTests, CanFillVectorWithOnes)

: by intern

Member TEST (ParallelArithmeticTests, CanMultiplyVectorsComponentWise)

: by intern

Member TEST (ReadMatrixAlgorithmTest, DISABLED_NonMatrixTextFile)

: will hook-up Importers soon.

Member TEST (ParallelArithmeticTests, CanTakeAbsoluteValueOfDiagonal)

FIX_UNIT_TESTS–Intern.

: by intern

Member TEST (ParallelArithmeticTests, CanSubtractVectors)

: by intern

Member TEST (BuildFEMatrixAlgorithmTests, ThrowsForNullMesh)

: consider throwing an exception instead of returning false

Member TEST (ParallelArithmeticTests, CanComputeDotProduct)

: by intern

Member TEST (ParallelArithmeticTests, CanComputeMaxOfVectorMulti)

: multi thread

Member TEST_F (JoinFieldsModuleTests, DISABLED_ThrowsForNullInput)

: this doesn't work with dynamic ports beyond 1

Member TEST_F (NetworkTests, DISABLED_ConnectionsMustHaveMatchingPortTypes)

: this verification pushed up to higher layer.

Member TEST_F (ProvenanceManagerTests, CanUndoAll)

: need test case (no situation for it yet) for "undo all does not completely clear the network"

Member TEST_F (SchedulingWithBoostGraph, NetworkFromMatrixCalculator)

: let executor thread finish. should be an event generated or something.

Member TEST_F (SchedulingWithBoostGraph, NetworkFromMatrixCalculatorMultiThreaded)

: let executor thread finish. should be an event generated or something.

Member TEST_F (CalculateSignedDistanceToFieldModuleTests, MakesAlgoDecisionBasedOnValuePortConnection)

: must remove this line. Getting strange leaking behavior without, haven't tracked it down yet.

Member TEST_F (SolveMinNormLeastSqSystemTests, BasicTest)

: when algo is extracted, this test needs the real factory:

: waiting on getData() to enable

Member TEST_F (NetworkTests, CanAddAndRemoveConnections)

: yucky, yucky test code now. needs refactoring for readability!

Member TEST_F (PortTests, DISABLED_CannotConnectPortsWithDifferentDatatypes)

: this verification pushed up to higher layer.

Member TEST_F (EvaluateLinearAlgebraUnaryModuleTests, CanCreateWithMockAlgorithm)

: mock module state for passing to algorithm

: algorithm factory to provide mock algorithm

: need algorithm parameters set up from algo ctor. Partial mock?

Member TESTRANGE (c, l, h)

Documentation Core/Datatypes/Legacy/Field/VFDataT.h

Member TetVolMesh< Basis >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member TetVolMesh< Basis >::insert_node_into_grid (typename Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member TetVolMesh< Basis >::locate_edge (INDEX &edge, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member TetVolMesh< Basis >::locate_elem (INDEX &elem, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member TetVolMesh< Basis >::locate_elem (INDEX &elem, ARRAY &coords, const Core::Geometry::Point &p) const

: Generate bounding boxes for elements and integrate this into the

Member TetVolMesh< Basis >::locate_face (INDEX &face, const Core::Geometry::Point &p) const

: Fix this function, needs to use search grid

Member TextToTriSurfFieldAlgorithm::run (const std::string &filename)

: change to FieldHandle when available...

: other exceptions?

Member ThreadingPrototype::WaitingList

: will need to be thread-safe

Member TriSurfMesh< MESH >::has_normals () const

: this is inconsistent with QuadSurfMesh - should both surfaces

Member TriSurfMesh< MESH >::insert_elem_into_grid (typename Elem::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member TriSurfMesh< MESH >::insert_node_into_grid (typename Node::index_type ci)

: This can crash if you insert a new cell outside of the grid.

Member TypeIDTable< CtorInfo >::registerConstructorInfo (const std::string &key, const CtorInfo &info)

: improve for testing

: use real logger here

Member TypeNameGenerator::make_template_id (const std::string &templateName, const std::string &templateParam)

: callers of these can be compressed using macros. worth it?

Member Variable::Value

: expand this

Member ViewSceneDialog::ViewSceneDialog (const std::string &name, SCIRun::Dataflow::Networks::ModuleStateHandle state, QWidget *parent=0)

Display dialog.

Member VirtualMeshFacade< VirtualMeshType >::numEdges () const

: need to split out that Synchronize enum

Member VirtualMeshFacade< VirtualMeshType >::VirtualMeshFacade (boost::shared_ptr< VirtualMeshType > vmesh)

: necessary? interface to vmesh

Member VMesh::copy_nodes (VMesh *imesh, Node::index_type i, Node::index_type o, Node::size_type size)

: Add regular meshes to the mix

Member VMesh::find_closest_elems (double &dist, Core::Geometry::Point &result, VMesh::Elem::array_type &i, const Core::Geometry::Point &point) const

: Need to reformulate this one, closest element can have multiple

Member VMesh::get_constant_weights (coords_type &, std::vector< double > &weights)

: These should go: we have get_weights and get_derivate_weights with basis_order call Direct access to get weights functions in basis functions These four are for interpolation

Member WriteFieldModule::call_exporter (const std::string &filename) override

: how will this work via python? need more code to set the filetype based on the extension...

Member WriteMatrixModule::execute ()

: unit test. Requires algorithm injection/factory for mocking, to be able to isolate the "optional file argument" part.