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ImageFunction Class Reference

A function for extracting data from an image or stack of images. More...

#include <ImageFunction.h>

Inheritance diagram for ImageFunction:
[legend]

Public Member Functions

 ImageFunction (const InputParameters &parameters)
 Class constructor. More...
 
virtual ~ImageFunction ()
 Class destructor. More...
 
virtual void initialSetup () override
 Initialize the ImageSampler. More...
 
virtual Real value (Real t, const Point &p) override
 Return the pixel value for the given point. More...
 
virtual Real sample (const Point &p)
 Return the pixel value for the given point. More...
 
virtual void setupImageSampler (MooseMesh &mesh)
 Perform initialization of image data. More...
 
std::string fileSuffix ()
 
const std::vector< std::string > & filenames ()
 
virtual RealVectorValue vectorValue (Real t, const Point &p)
 Override this to evaluate the vector function at a point (t,x,y,z), by default this returns a zero vector, you must override it. More...
 
virtual RealGradient gradient (Real t, const Point &p)
 Function objects can optionally provide a gradient at a point. More...
 
virtual Real timeDerivative (Real t, const Point &p)
 Get the time derivative of the function. More...
 
virtual Real integral ()
 
virtual Real average ()
 
const std::string & name () const
 Get the name of the object. More...
 
const InputParametersparameters () const
 Get the parameters of the object. More...
 
template<typename T >
const T & getParam (const std::string &name) const
 Retrieve a parameter for the object. More...
 
bool isParamValid (const std::string &name) const
 Test if the supplied parameter is valid. More...
 
MooseAppgetMooseApp ()
 Get the MooseApp this object is associated with. More...
 
virtual bool enabled ()
 Return the enabled status of the object. More...
 
template<typename... Args>
void mooseError (Args &&...args) const
 
template<typename... Args>
void mooseWarning (Args &&...args) const
 
template<typename... Args>
void mooseDeprecated (Args &&...args) const
 
template<typename... Args>
void mooseInfo (Args &&...args) const
 
virtual void timestepSetup ()
 Gets called at the beginning of the timestep before this object is asked to do its job. More...
 
virtual void jacobianSetup ()
 Gets called just before the Jacobian is computed and before this object is asked to do its job. More...
 
virtual void residualSetup ()
 Gets called just before the residual is computed and before this object is asked to do its job. More...
 
virtual void subdomainSetup ()
 Gets called when the subdomain changes (i.e. More...
 
virtual const std::vector< ExecFlagType > & execFlags () const
 Get the execution flag for the object. More...
 
ExecFlagType execBitFlags () const
 Build and return the execution flags as a bitfield. More...
 
bool isImplicit ()
 
bool hasPostprocessor (const std::string &name) const
 Determine if the Postprocessor exists. More...
 
bool hasPostprocessorByName (const PostprocessorName &name)
 Determine if the Postprocessor exists. More...
 
template<class T >
const T & getUserObject (const std::string &name)
 Get an user object with a given parameter name. More...
 
template<class T >
const T & getUserObjectByName (const std::string &name)
 Get an user object with a given name. More...
 
const UserObjectgetUserObjectBase (const std::string &name)
 Get an user object with a given parameter name. More...
 
const UserObjectgetUserObjectBaseByName (const std::string &name)
 Get an user object with a given name. More...
 
virtual void meshChanged ()
 Called on this object when the mesh changes. More...
 
const std::vector< MooseVariableScalar * > & getCoupledMooseScalarVars ()
 Get the list of coupled scalar variables. More...
 
const PostprocessorValuegetPostprocessorValue (const std::string &name)
 Retrieve the value of a Postprocessor or one of it's old or older values. More...
 
const PostprocessorValuegetPostprocessorValueOld (const std::string &name)
 
const PostprocessorValuegetPostprocessorValueOlder (const std::string &name)
 
const PostprocessorValuegetPostprocessorValueByName (const PostprocessorName &name)
 Retrieve the value of the Postprocessor. More...
 
const PostprocessorValuegetPostprocessorValueOldByName (const PostprocessorName &name)
 
const PostprocessorValuegetPostprocessorValueOlderByName (const PostprocessorName &name)
 
const PostprocessorValuegetDefaultPostprocessorValue (const std::string &name)
 Return the default postprocessor value. More...
 

Static Public Member Functions

static MultiMooseEnum getExecuteOptions ()
 Returns the available options for the 'execute_on' input parameters. More...
 

Public Attributes

const ConsoleStream _console
 An instance of helper class to write streams to the Console objects. More...
 

Protected Member Functions

void vtkShiftAndScale ()
 Apply image re-scaling using the vtkImageShiftAndRescale object. More...
 
void vtkThreshold ()
 Perform thresholding. More...
 
void vtkMagnitude ()
 Convert the image to greyscale. More...
 
void vtkFlip ()
 Perform image flipping. More...
 
void errorCheck ()
 
template<typename T >
T & declareRestartableData (std::string data_name)
 Declare a piece of data as "restartable". More...
 
template<typename T >
T & declareRestartableData (std::string data_name, const T &init_value)
 Declare a piece of data as "restartable" and initialize it. More...
 
template<typename T >
T & declareRestartableDataWithContext (std::string data_name, void *context)
 Declare a piece of data as "restartable". More...
 
template<typename T >
T & declareRestartableDataWithContext (std::string data_name, const T &init_value, void *context)
 Declare a piece of data as "restartable" and initialize it. More...
 
virtual bool isCoupledScalar (const std::string &var_name, unsigned int i=0)
 Returns true if a variables has been coupled_as name. More...
 
virtual unsigned int coupledScalarComponents (const std::string &var_name)
 Return the number of components to the coupled scalar variable. More...
 
virtual unsigned int coupledScalar (const std::string &var_name, unsigned int comp=0)
 Returns the index for a scalar coupled variable by name. More...
 
virtual Order coupledScalarOrder (const std::string &var_name, unsigned int comp=0)
 Returns the order for a scalar coupled variable by name. More...
 
virtual VariableValuecoupledScalarValue (const std::string &var_name, unsigned int comp=0)
 Returns value of a scalar coupled variable. More...
 
virtual VariableValuecoupledScalarValueOld (const std::string &var_name, unsigned int comp=0)
 Returns the old (previous time step) value of a scalar coupled variable. More...
 
virtual VariableValuecoupledScalarValueOlder (const std::string &var_name, unsigned int comp=0)
 Returns the older (two time steps previous) value of a scalar coupled variable. More...
 
virtual VariableValuecoupledScalarDot (const std::string &var_name, unsigned int comp=0)
 Returns the time derivative of a scalar coupled variable. More...
 
virtual VariableValuecoupledScalarDotDu (const std::string &var_name, unsigned int comp=0)
 Time derivative of a scalar coupled variable with respect to the coefficients. More...
 
VariableValuegetDefaultValue (const std::string &var_name)
 Helper method to return (and insert if necessary) the default value for an uncoupled variable. More...
 
MooseVariableScalargetScalarVar (const std::string &var_name, unsigned int comp)
 Extract pointer to a scalar coupled variable. More...
 

Protected Attributes

int _status
 
std::string _file_suffix
 
std::vector< std::string > _filenames
 
MooseApp_app
 The MooseApp this object is associated with. More...
 
const InputParameters_pars
 Parameters of this object, references the InputParameters stored in the InputParametersWarehouse. More...
 
const std::string & _name
 The name of this object, reference to value stored in InputParameters. More...
 
const bool & _enabled
 Reference to the "enable" InputParaemters, used by Controls for toggling on/off MooseObjects. More...
 
std::vector< ExecFlagType_exec_flags
 execution flag (when is the object executed/evaluated) More...
 
const ExecFlagType_current_execute_flag
 Reference to FEProblemBase. More...
 
const InputParameters_ti_params
 
FEProblemBase_ti_feproblem
 
bool _is_implicit
 If the object is using implicit or explicit form. More...
 
Real & _t
 Time. More...
 
int & _t_step
 The number of the time step. More...
 
Real & _dt
 Time step size. More...
 
Real & _dt_old
 Size of the old time step. More...
 
bool _is_transient
 
FEProblemBase_mci_feproblem
 Reference to FEProblemBase instance. More...
 
const InputParameters_sc_parameters
 
FEProblemBase_sc_fe_problem
 
std::map< std::string, std::vector< MooseVariableScalar * > > _coupled_scalar_vars
 Coupled vars whose values we provide. More...
 
std::map< std::string, VariableValue * > _default_value
 Will hold the default value for optional coupled scalar variables. More...
 
std::vector< MooseVariableScalar * > _coupled_moose_scalar_vars
 Vector of coupled variables. More...
 
bool _sc_is_implicit
 True if implicit value is required. More...
 
const InputParameters_coupleable_params
 Local InputParameters. More...
 

Detailed Description

A function for extracting data from an image or stack of images.

Definition at line 31 of file ImageFunction.h.

Constructor & Destructor Documentation

ImageFunction::ImageFunction ( const InputParameters parameters)

Class constructor.

Parameters
parametersThe parameters object holding data for the class to use.

Definition at line 29 of file ImageFunction.C.

30  : ImageSampler(parameters), Function(parameters)
31 {
32 }
Function(const InputParameters &parameters)
Class constructor.
Definition: Function.C:28
ImageSampler(const InputParameters &parameters)
Constructor.
Definition: ImageSampler.C:62
ImageFunction::~ImageFunction ( )
virtual

Class destructor.

Definition at line 34 of file ImageFunction.C.

34 {}

Member Function Documentation

Real Function::average ( )
virtualinherited

Reimplemented in PiecewiseConstant, and PiecewiseLinear.

Definition at line 75 of file Function.C.

76 {
77  mooseError("Average method not defined for function ", name());
78  return 0;
79 }
const std::string & name() const
Get the name of the object.
Definition: MooseObject.h:47
void mooseError(Args &&...args) const
Definition: MooseObject.h:80
unsigned int ScalarCoupleable::coupledScalar ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns the index for a scalar coupled variable by name.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Index of coupled variable

Definition at line 99 of file ScalarCoupleable.C.

Referenced by ParsedODEKernel::ParsedODEKernel().

100 {
101  return getScalarVar(var_name, comp)->number();
102 }
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
unsigned int number() const
Get variable number coming from libMesh.
unsigned int ScalarCoupleable::coupledScalarComponents ( const std::string &  var_name)
protectedvirtualinherited

Return the number of components to the coupled scalar variable.

Parameters
var_nameThe of the coupled variable

Definition at line 189 of file ScalarCoupleable.C.

190 {
191  return _coupled_scalar_vars[var_name].size();
192 }
std::map< std::string, std::vector< MooseVariableScalar * > > _coupled_scalar_vars
Coupled vars whose values we provide.
VariableValue & ScalarCoupleable::coupledScalarDot ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns the time derivative of a scalar coupled variable.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Reference to a time derivative VariableValue for the coupled variable

Definition at line 161 of file ScalarCoupleable.C.

162 {
163  MooseVariableScalar * var = getScalarVar(var_name, comp);
164  return var->uDot();
165 }
VariableValue & uDot()
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
Class for scalar variables (they are different).
VariableValue & ScalarCoupleable::coupledScalarDotDu ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Time derivative of a scalar coupled variable with respect to the coefficients.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Reference to a VariableValue containing the time derivative of the coupled variable with respect to the coefficients

Definition at line 168 of file ScalarCoupleable.C.

169 {
170  MooseVariableScalar * var = getScalarVar(var_name, comp);
171  return var->duDotDu();
172 }
VariableValue & duDotDu()
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
Class for scalar variables (they are different).
Order ScalarCoupleable::coupledScalarOrder ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns the order for a scalar coupled variable by name.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Order of coupled variable

Definition at line 105 of file ScalarCoupleable.C.

106 {
107  if (!isCoupledScalar(var_name, comp))
109 
110  return getScalarVar(var_name, comp)->order();
111 }
virtual bool isCoupledScalar(const std::string &var_name, unsigned int i=0)
Returns true if a variables has been coupled_as name.
FEProblemBase & _sc_fe_problem
Order getMaxScalarOrder() const
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
Order order() const
Get the order of this variable Note: Order enum can be implicitly converted to unsigned int...
VariableValue & ScalarCoupleable::coupledScalarValue ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns value of a scalar coupled variable.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Reference to a VariableValue for the coupled variable

Definition at line 128 of file ScalarCoupleable.C.

Referenced by ParsedODEKernel::ParsedODEKernel().

129 {
130  if (!isCoupledScalar(var_name, comp))
131  return *getDefaultValue(var_name);
132 
133  MooseVariableScalar * var = getScalarVar(var_name, comp);
134  return (_sc_is_implicit) ? var->sln() : var->slnOld();
135 }
VariableValue & sln()
virtual bool isCoupledScalar(const std::string &var_name, unsigned int i=0)
Returns true if a variables has been coupled_as name.
VariableValue * getDefaultValue(const std::string &var_name)
Helper method to return (and insert if necessary) the default value for an uncoupled variable...
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
bool _sc_is_implicit
True if implicit value is required.
Class for scalar variables (they are different).
VariableValue & slnOld()
VariableValue & ScalarCoupleable::coupledScalarValueOld ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns the old (previous time step) value of a scalar coupled variable.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Reference to a old VariableValue for the coupled variable

Definition at line 138 of file ScalarCoupleable.C.

139 {
140  if (!isCoupledScalar(var_name, comp))
141  return *getDefaultValue(var_name);
142 
143  MooseVariableScalar * var = getScalarVar(var_name, comp);
144  return (_sc_is_implicit) ? var->slnOld() : var->slnOlder();
145 }
virtual bool isCoupledScalar(const std::string &var_name, unsigned int i=0)
Returns true if a variables has been coupled_as name.
VariableValue * getDefaultValue(const std::string &var_name)
Helper method to return (and insert if necessary) the default value for an uncoupled variable...
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
bool _sc_is_implicit
True if implicit value is required.
Class for scalar variables (they are different).
VariableValue & slnOlder()
VariableValue & slnOld()
VariableValue & ScalarCoupleable::coupledScalarValueOlder ( const std::string &  var_name,
unsigned int  comp = 0 
)
protectedvirtualinherited

Returns the older (two time steps previous) value of a scalar coupled variable.

Parameters
var_nameName of coupled variable
compComponent number for vector of coupled variables
Returns
Reference to a older VariableValue for the coupled variable

Definition at line 148 of file ScalarCoupleable.C.

149 {
150  if (!isCoupledScalar(var_name, comp))
151  return *getDefaultValue(var_name);
152 
153  MooseVariableScalar * var = getScalarVar(var_name, comp);
154  if (_sc_is_implicit)
155  return var->slnOlder();
156  else
157  mooseError("Older values not available for explicit schemes");
158 }
virtual bool isCoupledScalar(const std::string &var_name, unsigned int i=0)
Returns true if a variables has been coupled_as name.
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
VariableValue * getDefaultValue(const std::string &var_name)
Helper method to return (and insert if necessary) the default value for an uncoupled variable...
MooseVariableScalar * getScalarVar(const std::string &var_name, unsigned int comp)
Extract pointer to a scalar coupled variable.
bool _sc_is_implicit
True if implicit value is required.
Class for scalar variables (they are different).
VariableValue & slnOlder()
template<typename T >
T & Restartable::declareRestartableData ( std::string  data_name)
protectedinherited

Declare a piece of data as "restartable".

This means that in the event of a restart this piece of data will be restored back to its previous value.

NOTE: This returns a reference! Make sure you store it in a reference!

Parameters
data_nameThe name of the data (usually just use the same name as the member variable)

Definition at line 224 of file Restartable.h.

225 {
226  return declareRestartableDataWithContext<T>(data_name, NULL);
227 }
template<typename T >
T & Restartable::declareRestartableData ( std::string  data_name,
const T &  init_value 
)
protectedinherited

Declare a piece of data as "restartable" and initialize it.

This means that in the event of a restart this piece of data will be restored back to its previous value.

NOTE: This returns a reference! Make sure you store it in a reference!

Parameters
data_nameThe name of the data (usually just use the same name as the member variable)
init_valueThe initial value of the data

Definition at line 231 of file Restartable.h.

232 {
233  return declareRestartableDataWithContext<T>(data_name, init_value, NULL);
234 }
template<typename T >
T & Restartable::declareRestartableDataWithContext ( std::string  data_name,
void *  context 
)
protectedinherited

Declare a piece of data as "restartable".

This means that in the event of a restart this piece of data will be restored back to its previous value.

NOTE: This returns a reference! Make sure you store it in a reference!

Parameters
data_nameThe name of the data (usually just use the same name as the member variable)
contextContext pointer that will be passed to the load and store functions

Definition at line 238 of file Restartable.h.

239 {
241  mooseError("No valid SubProblem found for ", _restartable_system_name, "/", _restartable_name);
242 
243  std::string full_name = _restartable_system_name + "/" + _restartable_name + "/" + data_name;
244  RestartableData<T> * data_ptr = new RestartableData<T>(full_name, context);
245 
247 
248  return data_ptr->get();
249 }
std::string _restartable_system_name
The system name this object is in.
Definition: Restartable.h:202
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
std::string _restartable_name
The name of the object.
Definition: Restartable.h:196
void registerRestartableDataOnSubProblem(std::string name, RestartableDataValue *data, THREAD_ID tid)
Helper function so we don&#39;t have to include SubProblem in the header.
Definition: Restartable.C:49
Concrete definition of a parameter value for a specified type.
SubProblem * _restartable_subproblem
Pointer to the SubProblem class.
Definition: Restartable.h:208
THREAD_ID _restartable_tid
The thread ID for this object.
Definition: Restartable.h:205
template<typename T >
T & Restartable::declareRestartableDataWithContext ( std::string  data_name,
const T &  init_value,
void *  context 
)
protectedinherited

Declare a piece of data as "restartable" and initialize it.

This means that in the event of a restart this piece of data will be restored back to its previous value.

NOTE: This returns a reference! Make sure you store it in a reference!

Parameters
data_nameThe name of the data (usually just use the same name as the member variable)
init_valueThe initial value of the data
contextContext pointer that will be passed to the load and store functions

Definition at line 253 of file Restartable.h.

256 {
258  mooseError("No valid SubProblem found for ", _restartable_system_name, "/", _restartable_name);
259 
260  std::string full_name = _restartable_system_name + "/" + _restartable_name + "/" + data_name;
261  RestartableData<T> * data_ptr = new RestartableData<T>(full_name, context);
262 
263  data_ptr->set() = init_value;
264 
266 
267  return data_ptr->get();
268 }
std::string _restartable_system_name
The system name this object is in.
Definition: Restartable.h:202
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
std::string _restartable_name
The name of the object.
Definition: Restartable.h:196
void registerRestartableDataOnSubProblem(std::string name, RestartableDataValue *data, THREAD_ID tid)
Helper function so we don&#39;t have to include SubProblem in the header.
Definition: Restartable.C:49
Concrete definition of a parameter value for a specified type.
SubProblem * _restartable_subproblem
Pointer to the SubProblem class.
Definition: Restartable.h:208
THREAD_ID _restartable_tid
The thread ID for this object.
Definition: Restartable.h:205
virtual bool MooseObject::enabled ( )
inlinevirtualinherited

Return the enabled status of the object.

Reimplemented in EigenKernel.

Definition at line 77 of file MooseObject.h.

Referenced by EigenKernel::enabled().

77 { return _enabled; }
const bool & _enabled
Reference to the "enable" InputParaemters, used by Controls for toggling on/off MooseObjects.
Definition: MooseObject.h:117
void FileRangeBuilder::errorCheck ( )
protectedinherited

Definition at line 156 of file FileRangeBuilder.C.

Referenced by FileRangeBuilder::filenames(), and ImageMesh::ImageMesh().

157 {
158  switch (_status)
159  {
160  case 0:
161  return;
162  case 1:
163  mooseError("Cannot provide both file and file_base parameters");
164  break;
165  case 2:
166  mooseError("You must provide a valid value for either the 'file' parameter or the "
167  "'file_base' parameter.");
168  break;
169  case 3:
170  mooseError(
171  "If you provide a 'file_base', you must also provide a valid 'file_suffix', e.g. 'png'.");
172  break;
173  default:
174  mooseError("Unknown error code!");
175  }
176 }
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
ExecFlagType SetupInterface::execBitFlags ( ) const
inherited

Build and return the execution flags as a bitfield.

Definition at line 100 of file SetupInterface.C.

Referenced by EigenExecutionerBase::init().

101 {
102  unsigned int exec_bit_field = EXEC_NONE;
103  for (unsigned int i = 0; i < _exec_flags.size(); ++i)
104  exec_bit_field |= _exec_flags[i];
105 
106  return static_cast<ExecFlagType>(exec_bit_field);
107 }
std::vector< ExecFlagType > _exec_flags
execution flag (when is the object executed/evaluated)
ExecFlagType
Execution flags - when is the object executed/evaluated.
Definition: MooseTypes.h:90
const std::vector< ExecFlagType > & SetupInterface::execFlags ( ) const
virtualinherited

Get the execution flag for the object.

Reimplemented in MultiAppTransfer.

Definition at line 94 of file SetupInterface.C.

Referenced by ExecuteMooseObjectWarehouse< T >::addObjectMask(), and MultiAppTransfer::execFlags().

95 {
96  return _exec_flags;
97 }
std::vector< ExecFlagType > _exec_flags
execution flag (when is the object executed/evaluated)
const std::vector<std::string>& FileRangeBuilder::filenames ( )
inlineinherited

Definition at line 44 of file FileRangeBuilder.h.

Referenced by ImageSampler::setupImageSampler().

44 { return _filenames; }
std::vector< std::string > _filenames
std::string FileRangeBuilder::fileSuffix ( )
inlineinherited

Definition at line 43 of file FileRangeBuilder.h.

Referenced by ImageSampler::setupImageSampler().

43 { return _file_suffix; }
std::string _file_suffix
const std::vector< MooseVariableScalar * > & ScalarCoupleable::getCoupledMooseScalarVars ( )
inherited

Get the list of coupled scalar variables.

Returns
The list of coupled variables

Definition at line 72 of file ScalarCoupleable.C.

Referenced by AuxScalarKernel::AuxScalarKernel(), and ScalarInitialCondition::ScalarInitialCondition().

73 {
75 }
std::vector< MooseVariableScalar * > _coupled_moose_scalar_vars
Vector of coupled variables.
const PostprocessorValue & PostprocessorInterface::getDefaultPostprocessorValue ( const std::string &  name)
inherited

Return the default postprocessor value.

Parameters
nameThe name of the postprocessor parameter
Returns
A const reference to the default value

Definition at line 92 of file PostprocessorInterface.C.

Referenced by EigenKernel::EigenKernel().

93 {
95 }
const PostprocessorValue & getDefaultPostprocessorValue(const std::string &name, bool suppress_error=false) const
Get the default value for a postprocessor added with addPostprocessor.
const InputParameters & _ppi_params
PostprocessorInterface Parameters.
VariableValue * ScalarCoupleable::getDefaultValue ( const std::string &  var_name)
protectedinherited

Helper method to return (and insert if necessary) the default value for an uncoupled variable.

Parameters
var_namethe name of the variable for which to retrieve a default value
Returns
VariableValue * a pointer to the associated VarirableValue.

Definition at line 114 of file ScalarCoupleable.C.

Referenced by ScalarCoupleable::coupledScalarValue(), ScalarCoupleable::coupledScalarValueOld(), and ScalarCoupleable::coupledScalarValueOlder().

115 {
116  std::map<std::string, VariableValue *>::iterator default_value_it = _default_value.find(var_name);
117  if (default_value_it == _default_value.end())
118  {
121  default_value_it = _default_value.insert(std::make_pair(var_name, value)).first;
122  }
123 
124  return default_value_it->second;
125 }
MooseArray< Real > VariableValue
FEProblemBase & _sc_fe_problem
Order getMaxScalarOrder() const
const InputParameters & _coupleable_params
Local InputParameters.
std::map< std::string, VariableValue * > _default_value
Will hold the default value for optional coupled scalar variables.
Real defaultCoupledValue(const std::string &coupling_name) const
Get the default value for an optionally coupled variable.
MultiMooseEnum SetupInterface::getExecuteOptions ( )
staticinherited

Returns the available options for the 'execute_on' input parameters.

Returns
A MooseEnum with the available 'execute_on' options, the default is 'residual'

Definition at line 110 of file SetupInterface.C.

Referenced by AddNodalNormalsAction::act(), AdvancedOutput::addValidParams(), AdvancedOutput::initExecutionTypes(), OutputOnWarehouse::OutputOnWarehouse(), validParams< CommonOutputAction >(), validParams< Output >(), and validParams< SetupInterface >().

111 {
112  return MultiMooseEnum("none=0x00 initial=0x01 linear=0x02 nonlinear=0x04 timestep_end=0x08 "
113  "timestep_begin=0x10 final=0x20 custom=0x100",
114  "linear");
115 }
This is a "smart" enum class intended to replace many of the shortcomings in the C++ enum type It sho...
MooseApp& MooseObject::getMooseApp ( )
inlineinherited

Get the MooseApp this object is associated with.

Definition at line 72 of file MooseObject.h.

Referenced by RestartableDataIO::createBackup(), RestartableDataIO::deserializeRestartableData(), Resurrector::restartRestartableData(), and RestartableDataIO::restoreBackup().

72 { return _app; }
MooseApp & _app
The MooseApp this object is associated with.
Definition: MooseObject.h:108
template<typename T >
const T & MooseObject::getParam ( const std::string &  name) const
inherited

Retrieve a parameter for the object.

Parameters
nameThe name of the parameter
Returns
The value of the parameter

Definition at line 122 of file MooseObject.h.

Referenced by FEProblemBase::addMaterial(), ConstraintWarehouse::addObject(), BicubicSplineFunction::BicubicSplineFunction(), Piecewise::buildFromXandY(), EigenKernel::EigenKernel(), FieldSplitPreconditioner::FieldSplitPreconditioner(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), GenericConstantRankTwoTensor::GenericConstantRankTwoTensor(), TimeSequenceStepper::init(), BlockRestrictable::initializeBlockRestrictable(), BoundaryRestrictable::initializeBoundaryRestrictable(), Console::initialSetup(), AdvancedOutput::initialSetup(), SideSetsBetweenSubdomains::modify(), MeshExtruder::modify(), AddExtraNodeset::modify(), SideSetsAroundSubdomain::modify(), RenameBlock::modify(), MooseObject::parameters(), ParsedAddSideset::ParsedAddSideset(), ParsedAux::ParsedAux(), ParsedODEKernel::ParsedODEKernel(), ParsedSubdomainMeshModifier::ParsedSubdomainMeshModifier(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), TimePeriod::TimePeriod(), and VectorOfPostprocessors::VectorOfPostprocessors().

123 {
124  return InputParameters::getParamHelper(name, _pars, static_cast<T *>(0));
125 }
const std::string & name() const
Get the name of the object.
Definition: MooseObject.h:47
static const T & getParamHelper(const std::string &name, const InputParameters &pars, const T *the_type)
const InputParameters & _pars
Parameters of this object, references the InputParameters stored in the InputParametersWarehouse.
Definition: MooseObject.h:111
const PostprocessorValue & PostprocessorInterface::getPostprocessorValue ( const std::string &  name)
inherited

Retrieve the value of a Postprocessor or one of it's old or older values.

Parameters
nameThe name of the Postprocessor parameter (see below)
Returns
A reference to the desired value

The name required by this method is the name that is hard-coded into your source code. For example, if you have a Kernel that requires a Postprocessor you may have an input file with "pp = my_pp", this function requires the "pp" name as input (see .../moose_test/functions/PostprocessorFunction.C)

see getPostprocessorValueByName getPostprocessorValueOldByName getPostprocessorValueOlderByName

Definition at line 29 of file PostprocessorInterface.C.

Referenced by GeneralUserObject::getPostprocessorValue(), and AuxKernel::getPostprocessorValue().

30 {
31  // Return the default if the Postprocessor does not exist and a default does, otherwise
32  // continue as usual
35  else
36  return _pi_feproblem.getPostprocessorValue(_ppi_params.get<PostprocessorName>(name));
37 }
bool hasPostprocessor(const std::string &name) const
Determine if the Postprocessor exists.
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
bool hasDefaultPostprocessorValue(const std::string &name) const
Returns true if a default PostprocessorValue is defined.
const PostprocessorValue & getDefaultPostprocessorValue(const std::string &name, bool suppress_error=false) const
Get the default value for a postprocessor added with addPostprocessor.
PostprocessorValue & getPostprocessorValue(const PostprocessorName &name)
Get a reference to the value associated with the postprocessor.
const InputParameters & _ppi_params
PostprocessorInterface Parameters.
const PostprocessorValue & PostprocessorInterface::getPostprocessorValueByName ( const PostprocessorName &  name)
inherited

Retrieve the value of the Postprocessor.

Parameters
namePostprocessor name (see below)
Returns
A reference to the desired value

The name required by this method is the name defined in the input file. For example, if you have a Kernel that requires a Postprocessor you may have an input file with "pp = my_pp", this method requires the "my_pp" name as input (see .../moose_test/functions/PostprocessorFunction.C)

see getPostprocessorValue getPostprocessorValueOld getPostprocessorValueOlder

Definition at line 62 of file PostprocessorInterface.C.

Referenced by EigenKernel::EigenKernel(), GeneralUserObject::getPostprocessorValueByName(), AuxKernel::getPostprocessorValueByName(), and EigenExecutionerBase::inversePowerIteration().

63 {
65 }
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
PostprocessorValue & getPostprocessorValue(const PostprocessorName &name)
Get a reference to the value associated with the postprocessor.
const PostprocessorValue & PostprocessorInterface::getPostprocessorValueOld ( const std::string &  name)
inherited

Definition at line 40 of file PostprocessorInterface.C.

41 {
42  // Return the default if the Postprocessor does not exist and a default does, otherwise
43  // continue as usual
46  else
47  return _pi_feproblem.getPostprocessorValueOld(_ppi_params.get<PostprocessorName>(name));
48 }
PostprocessorValue & getPostprocessorValueOld(const std::string &name)
Get the reference to the old value of a post-processor.
bool hasPostprocessor(const std::string &name) const
Determine if the Postprocessor exists.
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
bool hasDefaultPostprocessorValue(const std::string &name) const
Returns true if a default PostprocessorValue is defined.
const PostprocessorValue & getDefaultPostprocessorValue(const std::string &name, bool suppress_error=false) const
Get the default value for a postprocessor added with addPostprocessor.
const InputParameters & _ppi_params
PostprocessorInterface Parameters.
const PostprocessorValue & PostprocessorInterface::getPostprocessorValueOldByName ( const PostprocessorName &  name)
inherited

Definition at line 68 of file PostprocessorInterface.C.

Referenced by EigenKernel::EigenKernel().

69 {
71 }
PostprocessorValue & getPostprocessorValueOld(const std::string &name)
Get the reference to the old value of a post-processor.
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
const PostprocessorValue & PostprocessorInterface::getPostprocessorValueOlder ( const std::string &  name)
inherited

Definition at line 51 of file PostprocessorInterface.C.

52 {
53  // Return the default if the Postprocessor does not exist and a default does, otherwise
54  // continue as usual
57  else
58  return _pi_feproblem.getPostprocessorValueOlder(_ppi_params.get<PostprocessorName>(name));
59 }
bool hasPostprocessor(const std::string &name) const
Determine if the Postprocessor exists.
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
PostprocessorValue & getPostprocessorValueOlder(const std::string &name)
Get the reference to the older value of a post-processor.
bool hasDefaultPostprocessorValue(const std::string &name) const
Returns true if a default PostprocessorValue is defined.
const PostprocessorValue & getDefaultPostprocessorValue(const std::string &name, bool suppress_error=false) const
Get the default value for a postprocessor added with addPostprocessor.
const InputParameters & _ppi_params
PostprocessorInterface Parameters.
const PostprocessorValue & PostprocessorInterface::getPostprocessorValueOlderByName ( const PostprocessorName &  name)
inherited

Definition at line 74 of file PostprocessorInterface.C.

75 {
77 }
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
PostprocessorValue & getPostprocessorValueOlder(const std::string &name)
Get the reference to the older value of a post-processor.
MooseVariableScalar * ScalarCoupleable::getScalarVar ( const std::string &  var_name,
unsigned int  comp 
)
protectedinherited

Extract pointer to a scalar coupled variable.

Parameters
var_nameName of parameter desired
compComponent number of multiple coupled variables
Returns
Pointer to the desired variable

Definition at line 175 of file ScalarCoupleable.C.

Referenced by ScalarCoupleable::coupledScalar(), ScalarCoupleable::coupledScalarDot(), ScalarCoupleable::coupledScalarDotDu(), ScalarCoupleable::coupledScalarOrder(), ScalarCoupleable::coupledScalarValue(), ScalarCoupleable::coupledScalarValueOld(), ScalarCoupleable::coupledScalarValueOlder(), and ParsedODEKernel::ParsedODEKernel().

176 {
177  if (_coupled_scalar_vars.find(var_name) != _coupled_scalar_vars.end())
178  {
179  if (comp < _coupled_scalar_vars[var_name].size())
180  return _coupled_scalar_vars[var_name][comp];
181  else
182  mooseError("Trying to get a non-existent component of variable '" + var_name + "'");
183  }
184  else
185  mooseError("Trying to get a non-existent variable '" + var_name + "'");
186 }
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
std::map< std::string, std::vector< MooseVariableScalar * > > _coupled_scalar_vars
Coupled vars whose values we provide.
template<class T >
const T & UserObjectInterface::getUserObject ( const std::string &  name)
inherited

Get an user object with a given parameter name.

Parameters
nameThe name of the parameter key of the user object to retrieve
Returns
The user object with name associated with the parameter 'name'

Definition at line 85 of file UserObjectInterface.h.

86 {
87  unsigned int tid = isDiscreteUserObject(getUserObjectBase(name)) ? _uoi_tid : 0;
88  return _uoi_feproblem.getUserObject<T>(_uoi_params.get<UserObjectName>(name), tid);
89 }
bool isDiscreteUserObject(const UserObject &uo) const
Check if the user object is a DiscreteElementUserObject.
const InputParameters & _uoi_params
Parameters of the object with this interface.
FEProblemBase & _uoi_feproblem
Reference to the FEProblemBase instance.
THREAD_ID _uoi_tid
Thread ID.
const T & getUserObject(const std::string &name, unsigned int tid=0)
Get the user object by its name.
const UserObject & getUserObjectBase(const std::string &name)
Get an user object with a given parameter name.
const UserObject & UserObjectInterface::getUserObjectBase ( const std::string &  name)
inherited

Get an user object with a given parameter name.

Parameters
nameThe name of the parameter key of the user object to retrieve
Returns
The user object with name associated with the parameter 'name'

Definition at line 28 of file UserObjectInterface.C.

Referenced by UserObjectInterface::getUserObject(), InitialCondition::getUserObjectBase(), and AuxKernel::getUserObjectBase().

29 {
30  return _uoi_feproblem.getUserObjectBase(_uoi_params.get<UserObjectName>(name));
31 }
const InputParameters & _uoi_params
Parameters of the object with this interface.
FEProblemBase & _uoi_feproblem
Reference to the FEProblemBase instance.
const UserObject & getUserObjectBase(const std::string &name)
Get the user object by its name.
const UserObject & UserObjectInterface::getUserObjectBaseByName ( const std::string &  name)
inherited

Get an user object with a given name.

Parameters
nameThe name of the user object to retrieve
Returns
The user object with the name

Definition at line 34 of file UserObjectInterface.C.

Referenced by UserObjectInterface::getUserObjectByName().

35 {
36  return _uoi_feproblem.getUserObjectBase(name);
37 }
FEProblemBase & _uoi_feproblem
Reference to the FEProblemBase instance.
const UserObject & getUserObjectBase(const std::string &name)
Get the user object by its name.
template<class T >
const T & UserObjectInterface::getUserObjectByName ( const std::string &  name)
inherited

Get an user object with a given name.

Parameters
nameThe name of the user object to retrieve
Returns
The user object with the name

Definition at line 93 of file UserObjectInterface.h.

94 {
95  unsigned int tid = isDiscreteUserObject(getUserObjectBaseByName(name)) ? _uoi_tid : 0;
96  return _uoi_feproblem.getUserObject<T>(name, tid);
97 }
bool isDiscreteUserObject(const UserObject &uo) const
Check if the user object is a DiscreteElementUserObject.
const UserObject & getUserObjectBaseByName(const std::string &name)
Get an user object with a given name.
FEProblemBase & _uoi_feproblem
Reference to the FEProblemBase instance.
THREAD_ID _uoi_tid
Thread ID.
const T & getUserObject(const std::string &name, unsigned int tid=0)
Get the user object by its name.
RealGradient Function::gradient ( Real  t,
const Point &  p 
)
virtualinherited

Function objects can optionally provide a gradient at a point.

By default this returns 0, you must override it.

Parameters
tThe time
pThe Point in space (x,y,z)
Returns
A gradient of the function evaluated at the time and location

Reimplemented in MooseParsedGradFunction, MooseParsedFunction, SolutionFunction, MooseParsedVectorFunction, BicubicSplineFunction, LinearCombinationFunction, and SplineFunction.

Definition at line 49 of file Function.C.

Referenced by ElementH1SemiError::computeQpIntegral(), ElementW1pError::computeQpIntegral(), ElementH1ErrorFunctionAux::computeValue(), and FunctionIC::gradient().

50 {
51  return RealGradient(0, 0, 0);
52 }
RealVectorValue RealGradient
Definition: Assembly.h:43
bool PostprocessorInterface::hasPostprocessor ( const std::string &  name) const
inherited

Determine if the Postprocessor exists.

Parameters
nameThe name of the Postprocessor parameter
Returns
True if the Postprocessor exists
See also
hasPostprocessorByName getPostprocessorValue

Definition at line 80 of file PostprocessorInterface.C.

Referenced by EigenKernel::EigenKernel(), PostprocessorInterface::getPostprocessorValue(), PostprocessorInterface::getPostprocessorValueOld(), PostprocessorInterface::getPostprocessorValueOlder(), and TestSetupPostprocessorDataActionFunction::TestSetupPostprocessorDataActionFunction().

81 {
82  return _pi_feproblem.hasPostprocessor(_ppi_params.get<PostprocessorName>(name));
83 }
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
bool hasPostprocessor(const std::string &name)
Check existence of the postprocessor.
const InputParameters & _ppi_params
PostprocessorInterface Parameters.
bool PostprocessorInterface::hasPostprocessorByName ( const PostprocessorName &  name)
inherited

Determine if the Postprocessor exists.

Parameters
nameThe name of the Postprocessor
Returns
True if the Postprocessor exists
See also
hasPostprocessor getPostprocessorValueByName

Definition at line 86 of file PostprocessorInterface.C.

Referenced by VectorOfPostprocessors::VectorOfPostprocessors().

87 {
88  return _pi_feproblem.hasPostprocessor(name);
89 }
FEProblemBase & _pi_feproblem
Reference the the FEProblemBase class.
bool hasPostprocessor(const std::string &name)
Check existence of the postprocessor.
void ImageFunction::initialSetup ( )
overridevirtual

Initialize the ImageSampler.

Reimplemented from SetupInterface.

Definition at line 37 of file ImageFunction.C.

38 {
39  FEProblemBase * fe_problem = this->getParam<FEProblemBase *>("_fe_problem_base");
40  MooseMesh & mesh = fe_problem->mesh();
41  setupImageSampler(mesh);
42 }
virtual void setupImageSampler(MooseMesh &mesh)
Perform initialization of image data.
Definition: ImageSampler.C:80
Specialization of SubProblem for solving nonlinear equations plus auxiliary equations.
MooseMesh wraps a libMesh::Mesh object and enhances its capabilities by caching additional data and s...
Definition: MooseMesh.h:74
virtual MooseMesh & mesh() override
Real Function::integral ( )
virtualinherited

Reimplemented in PiecewiseConstant, and PiecewiseLinear.

Definition at line 68 of file Function.C.

69 {
70  mooseError("Integral method not defined for function ", name());
71  return 0;
72 }
const std::string & name() const
Get the name of the object.
Definition: MooseObject.h:47
void mooseError(Args &&...args) const
Definition: MooseObject.h:80
bool ScalarCoupleable::isCoupledScalar ( const std::string &  var_name,
unsigned int  i = 0 
)
protectedvirtualinherited

Returns true if a variables has been coupled_as name.

Parameters
var_nameThe of the coupled variable
iBy default 0, in general the index to test in a vector of MooseVariable pointers.

Definition at line 78 of file ScalarCoupleable.C.

Referenced by ScalarCoupleable::coupledScalarOrder(), ScalarCoupleable::coupledScalarValue(), ScalarCoupleable::coupledScalarValueOld(), and ScalarCoupleable::coupledScalarValueOlder().

79 {
80  std::map<std::string, std::vector<MooseVariableScalar *>>::iterator it =
81  _coupled_scalar_vars.find(var_name);
82  if (it != _coupled_scalar_vars.end())
83  return (i < it->second.size());
84  else
85  {
86  // Make sure the user originally requested this value in the InputParameter syntax
87  if (!_coupleable_params.hasCoupledValue(var_name))
88  mooseError("The coupled scalar variable \"",
89  var_name,
90  "\" was never added to this objects's "
91  "InputParameters, please double-check "
92  "your spelling");
93 
94  return false;
95  }
96 }
bool hasCoupledValue(const std::string &coupling_name) const
Return whether or not the coupled variable exists.
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
const InputParameters & _coupleable_params
Local InputParameters.
std::map< std::string, std::vector< MooseVariableScalar * > > _coupled_scalar_vars
Coupled vars whose values we provide.
bool TransientInterface::isImplicit ( )
inlineinherited

Definition at line 41 of file TransientInterface.h.

41 { return _is_implicit; }
bool _is_implicit
If the object is using implicit or explicit form.
bool MooseObject::isParamValid ( const std::string &  name) const
inlineinherited

Test if the supplied parameter is valid.

Parameters
nameThe name of the parameter to test

Definition at line 67 of file MooseObject.h.

Referenced by BicubicSplineFunction::BicubicSplineFunction(), Piecewise::buildFromFile(), Piecewise::buildFromXandY(), GeneratedMesh::buildMesh(), LibmeshPartitioner::clone(), OversampleOutput::cloneMesh(), CSVReader::CSVReader(), MultiAppNearestNodeTransfer::execute(), FileOutput::FileOutput(), MultiApp::fillPositions(), MultiAppNearestNodeTransfer::getLocalNodes(), MultiAppNearestNodeTransfer::getNearestNode(), IterationAdaptiveDT::init(), EigenExecutionerBase::init(), MooseMesh::init(), AdvancedOutput::initExecutionTypes(), BlockRestrictable::initializeBlockRestrictable(), BoundaryRestrictable::initializeBoundaryRestrictable(), SolutionAux::initialSetup(), MooseParsedVectorFunction::initialSetup(), Console::initialSetup(), Receiver::initialSetup(), SolutionFunction::initialSetup(), MooseParsedGradFunction::initialSetup(), MooseParsedFunction::initialSetup(), AdvancedOutput::initialSetup(), AdvancedOutput::initPostprocessorOrVectorPostprocessorLists(), IterationAdaptiveDT::IterationAdaptiveDT(), LeastSquaresFit::LeastSquaresFit(), LibmeshPartitioner::LibmeshPartitioner(), BreakBoundaryOnSubdomain::modify(), MeshExtruder::modify(), MeshSideSet::modify(), AssignElementSubdomainID::modify(), ParsedSubdomainMeshModifier::modify(), RenameBlock::modify(), SubdomainBoundingBox::modify(), EigenExecutionerBase::normalizeSolution(), Output::Output(), Exodus::outputSetup(), PetscOutput::PetscOutput(), Piecewise::Piecewise(), SolutionUserObject::readExodusII(), RenameBlock::RenameBlock(), Piecewise::setData(), SolutionUserObject::SolutionUserObject(), and TimePeriod::TimePeriod().

67 { return _pars.isParamValid(name); }
const std::string & name() const
Get the name of the object.
Definition: MooseObject.h:47
bool isParamValid(const std::string &name) const
This method returns parameters that have been initialized in one fashion or another, i.e.
const InputParameters & _pars
Parameters of this object, references the InputParameters stored in the InputParametersWarehouse.
Definition: MooseObject.h:111
void SetupInterface::jacobianSetup ( )
virtualinherited

Gets called just before the Jacobian is computed and before this object is asked to do its job.

Definition at line 79 of file SetupInterface.C.

80 {
81 }
virtual void MeshChangedInterface::meshChanged ( )
inlinevirtualinherited

Called on this object when the mesh changes.

Reimplemented in DiracKernel, Console, OversampleOutput, Exodus, Nemesis, GeometryBase, and EqualValueBoundaryConstraint.

Definition at line 43 of file MeshChangedInterface.h.

43 {}
template<typename... Args>
void MooseObject::mooseDeprecated ( Args &&...  args) const
inlineinherited
template<typename... Args>
void MooseObject::mooseError ( Args &&...  args) const
inlineinherited

Definition at line 80 of file MooseObject.h.

Referenced by FEProblemBase::addInitialCondition(), DiracKernel::addPointWithValidId(), FEProblemBase::addPostprocessor(), MooseMesh::addQuadratureNode(), FEProblemBase::addVectorPostprocessor(), Output::advancedExecuteOn(), AnnularMesh::AnnularMesh(), MultiApp::appPostprocessorValue(), MultiApp::appProblem(), MultiApp::appProblemBase(), MultiApp::appUserObjectBase(), Function::average(), Axisymmetric2D3DSolutionFunction::Axisymmetric2D3DSolutionFunction(), BicubicSplineFunction::BicubicSplineFunction(), BoundingValueElementDamper::BoundingValueElementDamper(), BoundingValueNodalDamper::BoundingValueNodalDamper(), BoundsAux::BoundsAux(), MooseMesh::buildCoarseningMap(), Piecewise::buildFromFile(), Piecewise::buildFromXandY(), Piecewise::buildFromXY(), TiledMesh::buildMesh(), GeneratedMesh::buildMesh(), ImageMesh::buildMesh3D(), MooseMesh::buildRefinementMap(), EigenExecutionerBase::chebyshev(), FEProblemBase::checkCoordinateSystems(), FEProblemBase::checkDependMaterialsHelper(), FEProblemBase::checkDisplacementOrders(), Material::checkExecutionStage(), Steady::checkIntegrity(), EigenExecutionerBase::checkIntegrity(), SubProblem::checkMatProps(), FEProblemBase::checkProblemIntegrity(), Material::checkStatefulSanity(), FEProblemBase::checkUserObjects(), LibmeshPartitioner::clone(), CompositeFunction::CompositeFunction(), ElementLpNormAux::compute(), ElementH1ErrorFunctionAux::compute(), TimeSequenceStepperBase::computeFailedDT(), IterationAdaptiveDT::computeFailedDT(), TimeStepper::computeFailedDT(), FEProblemBase::computeResidual(), Material::computeSubdomainProperties(), PenetrationAux::computeValue(), TimeStepper::constrainStep(), AuxKernel::coupledDot(), AuxKernel::coupledDotDu(), DebugResidualAux::DebugResidualAux(), BicubicSplineFunction::derivative(), DGKernel::DGKernel(), SolutionUserObject::discontinuousPointValue(), SolutionUserObject::discontinuousPointValueGradient(), FEProblemBase::duplicateVariableCheck(), EigenProblem::EigenProblem(), Eigenvalues::Eigenvalues(), ElementalVariableValue::ElementalVariableValue(), MooseMesh::errorIfDistributedMesh(), SolutionUserObject::evalMeshFunction(), SolutionUserObject::evalMeshFunctionGradient(), SolutionUserObject::evalMultiValuedMeshFunction(), SolutionUserObject::evalMultiValuedMeshFunctionGradient(), PerflogDumper::execute(), NodalValueSampler::execute(), MultiAppPostprocessorTransfer::execute(), DiscreteElementUserObject::execute(), MultiAppPostprocessorInterpolationTransfer::execute(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), MultiAppNearestNodeTransfer::execute(), PointValue::execute(), MultiAppPostprocessorToAuxScalarTransfer::execute(), MultiAppScalarToAuxScalarTransfer::execute(), MultiAppVariableValueSampleTransfer::execute(), FindValueOnLine::execute(), MultiAppInterpolationTransfer::execute(), TimeExtremeValue::execute(), LeastSquaresFit::execute(), FEProblemBase::executeControls(), FileOutput::FileOutput(), MultiApp::fillPositions(), VerifyElementUniqueID::finalize(), VerifyNodalUniqueID::finalize(), DiscreteElementUserObject::finalize(), MemoryUsage::finalize(), PointSamplerBase::finalize(), Transfer::find_sys(), FiniteDifferencePreconditioner::FiniteDifferencePreconditioner(), FunctionDT::FunctionDT(), FunctionScalarAux::FunctionScalarAux(), FunctionScalarIC::FunctionScalarIC(), GapValueAux::GapValueAux(), GeneratedMesh::GeneratedMesh(), GenericConstantMaterial::GenericConstantMaterial(), GenericFunctionMaterial::GenericFunctionMaterial(), MooseMesh::getBoundaryID(), MultiApp::getBoundingBox(), MooseMesh::getCoarseningMap(), FEProblemBase::getCoordSystem(), PiecewiseConstant::getDirection(), FEProblemBase::getDistribution(), MultiApp::getExecutioner(), FEProblemBase::getFunction(), SolutionUserObject::getLocalVarIndex(), AuxKernel::getMaterialProperty(), AuxKernel::getMaterialPropertyOld(), AuxKernel::getMaterialPropertyOlder(), GeneratedMesh::getMaxInDimension(), AnnularMesh::getMaxInDimension(), FEProblemBase::getMaxQps(), FEProblemBase::getMaxShapeFunctions(), GeneratedMesh::getMinInDimension(), AnnularMesh::getMinInDimension(), MooseMesh::getMortarInterface(), MooseMesh::getMortarInterfaceByName(), MooseMesh::getNodeBlockIds(), MooseMesh::getNodeList(), FEProblemBase::getNonlinearSystem(), MooseMesh::getPairedBoundaryMapping(), ImageMesh::GetPixelInfo(), MaterialStdVectorAux::getRealValue(), MooseMesh::getRefinementMap(), FEProblemBase::getSampler(), DisplacedProblem::getScalarVariable(), FEProblemBase::getScalarVariable(), MooseMesh::getSubdomainBoundaryIds(), MooseMesh::getSubdomainID(), DisplacedProblem::getSystem(), FEProblemBase::getSystem(), FEProblemBase::getUserObjectBase(), NumVars::getValue(), PerformanceData::getValue(), Residual::getValue(), FindValueOnLine::getValueAtPoint(), DisplacedProblem::getVariable(), FEProblemBase::getVariable(), MultiApp::globalAppToLocal(), MooseParsedVectorFunction::gradient(), AdvancedOutput::hasOutputHelper(), CSVTimeSequenceStepper::init(), IterationAdaptiveDT::init(), EigenExecutionerBase::init(), MooseMesh::init(), FEProblemBase::init(), NumPicardIterations::initialize(), FullSolveMultiApp::initialSetup(), SolutionAux::initialSetup(), Axisymmetric2D3DSolutionFunction::initialSetup(), Exodus::initialSetup(), SolutionFunction::initialSetup(), SolutionUserObject::initialSetup(), FEProblemBase::initialSetup(), AdvancedOutput::initOutputList(), AdvancedOutput::initShowHideLists(), Material::initStatefulProperties(), Function::integral(), IntegratedBC::IntegratedBC(), InterfaceKernel::InterfaceKernel(), EigenExecutionerBase::inversePowerIteration(), InversePowerMethod::InversePowerMethod(), IterationAdaptiveDT::IterationAdaptiveDT(), KernelBase::KernelBase(), LeastSquaresFit::LeastSquaresFit(), LibmeshPartitioner::LibmeshPartitioner(), LinearCombinationFunction::LinearCombinationFunction(), LinearCombinationPostprocessor::LinearCombinationPostprocessor(), LinearNodalConstraint::LinearNodalConstraint(), LineMaterialSamplerBase< T >::LineMaterialSamplerBase(), MaterialRealTensorValueAux::MaterialRealTensorValueAux(), MaterialRealVectorValueAux::MaterialRealVectorValueAux(), MaterialStdVectorRealGradientAux::MaterialStdVectorRealGradientAux(), MaterialVectorPostprocessor::MaterialVectorPostprocessor(), SubProblem::meshChanged(), MeshExtruder::MeshExtruder(), SideSetsFromPoints::modify(), SideSetsFromNormals::modify(), AddExtraNodeset::modify(), MeshExtruder::modify(), AssignElementSubdomainID::modify(), AddAllSideSetsByNormals::modify(), ElementDeleterBase::modify(), ParsedSubdomainMeshModifier::modify(), RenameBlock::modify(), ImageSubdomain::modify(), BoundingBoxNodeSet::modify(), OrientedSubdomainBoundingBox::modify(), AddSideSetsFromBoundingBox::modify(), SubdomainBoundingBox::modify(), MultiAppMeshFunctionTransfer::MultiAppMeshFunctionTransfer(), MultiAppPostprocessorTransfer::MultiAppPostprocessorTransfer(), NearestNodeDistanceAux::NearestNodeDistanceAux(), NearestNodeValueAux::NearestNodeValueAux(), NodalBC::NodalBC(), NodalConstraint::NodalConstraint(), NodalEqualValueConstraint::NodalEqualValueConstraint(), NodalKernel::NodalKernel(), NodalVariableValue::NodalVariableValue(), NumDOFs::NumDOFs(), NumNonlinearIterations::NumNonlinearIterations(), XDA::output(), VTKOutput::output(), AdvancedOutput::outputElementalVariables(), AdvancedOutput::outputInput(), AdvancedOutput::outputNodalVariables(), AdvancedOutput::outputPostprocessors(), AdvancedOutput::outputScalarVariables(), AdvancedOutput::outputSystemInformation(), Console::outputVectorPostprocessors(), AdvancedOutput::outputVectorPostprocessors(), PiecewiseBilinear::parse(), ParsedAddSideset::ParsedAddSideset(), ParsedAux::ParsedAux(), ParsedODEKernel::ParsedODEKernel(), ParsedSubdomainMeshModifier::ParsedSubdomainMeshModifier(), PatternedMesh::PatternedMesh(), PhysicsBasedPreconditioner::PhysicsBasedPreconditioner(), Piecewise::Piecewise(), PiecewiseBilinear::PiecewiseBilinear(), PiecewiseLinearInterpolationMaterial::PiecewiseLinearInterpolationMaterial(), PiecewiseMultilinear::PiecewiseMultilinear(), SolutionUserObject::pointValueGradientWrapper(), SolutionUserObject::pointValueWrapper(), LStableDirk2::postStep(), LStableDirk3::postStep(), ImplicitMidpoint::postStep(), ExplicitTVDRK2::postStep(), AStableDirk4::postStep(), LStableDirk4::postStep(), ExplicitRK2::postStep(), Predictor::Predictor(), SolutionUserObject::readExodusII(), SolutionUserObject::readXda(), RelativeSolutionDifferenceNorm::RelativeSolutionDifferenceNorm(), RenameBlock::RenameBlock(), ScalarComponentIC::ScalarComponentIC(), BicubicSplineFunction::secondDerivative(), FEProblemBase::setCoordSystem(), Piecewise::setData(), EigenProblem::setEigenproblemType(), Sampler::setNumberOfRequiedRandomSeeds(), Split::setup(), TransientMultiApp::setupApp(), TimeSequenceStepperBase::setupSequence(), Transient::setupTimeIntegrator(), SideSetsFromNormals::SideSetsFromNormals(), SideSetsFromPoints::SideSetsFromPoints(), SolutionUserObject::SolutionUserObject(), FullSolveMultiApp::solveStep(), UserObject::spatialValue(), SphericalAverage::SphericalAverage(), StitchedMesh::StitchedMesh(), NodalUserObject::subdomainSetup(), GeneralUserObject::subdomainSetup(), Constraint::subdomainSetup(), Console::systemInfoFlags(), Terminator::Terminator(), TestSetupPostprocessorDataActionFunction::TestSetupPostprocessorDataActionFunction(), DiscreteElementUserObject::threadJoin(), GeneralUserObject::threadJoin(), Function::timeDerivative(), TimeExtremeValue::TimeExtremeValue(), TimePeriod::TimePeriod(), MultiAppCopyTransfer::transfer(), MultiAppMeshFunctionTransfer::transferVariable(), Transient::Transient(), TransientMultiApp::TransientMultiApp(), EqualValueBoundaryConstraint::updateConstrainedNodes(), SolutionUserObject::updateExodusBracketingTimeIndices(), Axisymmetric2D3DSolutionFunction::value(), ValueRangeMarker::ValueRangeMarker(), ValueThresholdMarker::ValueThresholdMarker(), MultiAppTransfer::variableIntegrityCheck(), VariableResidual::VariableResidual(), VariableTimeIntegrationAux::VariableTimeIntegrationAux(), VectorOfPostprocessors::VectorOfPostprocessors(), VectorPostprocessorFunction::VectorPostprocessorFunction(), MooseParsedGradFunction::vectorValue(), MooseParsedFunction::vectorValue(), and VolumeHistogram::VolumeHistogram().

81  {
82  std::ostringstream oss;
83  moose::internal::mooseStreamAll(oss, std::forward<Args>(args)...);
84  std::string msg = oss.str();
85  callMooseErrorRaw(msg, &_app);
86  }
void mooseStreamAll(std::ostringstream &ss)
Definition: MooseError.C:78
void callMooseErrorRaw(std::string &msg, MooseApp *app)
Definition: MooseObject.C:45
MooseApp & _app
The MooseApp this object is associated with.
Definition: MooseObject.h:108
template<typename... Args>
void MooseObject::mooseInfo ( Args &&...  args) const
inlineinherited

Definition at line 101 of file MooseObject.h.

102  {
103  moose::internal::mooseInfoStream(_console, std::forward<Args>(args)...);
104  }
void mooseInfoStream(S &oss, Args &&...args)
Definition: MooseError.h:145
const ConsoleStream _console
An instance of helper class to write streams to the Console objects.
template<typename... Args>
void MooseObject::mooseWarning ( Args &&...  args) const
inlineinherited
const std::string& MooseObject::name ( ) const
inlineinherited

Get the name of the object.

Returns
The name of the object

Definition at line 47 of file MooseObject.h.

Referenced by FEProblemBase::addDistribution(), FEProblemBase::addFunction(), FEProblemBase::addIndicator(), FEProblemBase::addInitialCondition(), FEProblemBase::addMarker(), FEProblemBase::addMaterial(), MooseMesh::addMortarInterface(), FEProblemBase::addMultiApp(), FEProblemBase::addPredictor(), FEProblemBase::addSampler(), FEProblemBase::addTransfer(), FEProblemBase::addUserObject(), Output::advancedExecuteOn(), MultiApp::appPostprocessorValue(), MultiApp::appProblem(), MultiApp::appProblemBase(), MultiApp::appUserObjectBase(), AStableDirk4::AStableDirk4(), Function::average(), FEProblemBase::checkDependMaterialsHelper(), Damper::checkMinDamping(), Material::checkStatefulSanity(), CompositeFunction::CompositeFunction(), Material::computeSubdomainProperties(), AuxKernel::coupledCallback(), AuxKernel::coupledDot(), AuxKernel::coupledDotDu(), MultiApp::createApp(), DGKernel::DGKernel(), AB2PredictorCorrector::estimateTimeError(), SolutionUserObject::evalMeshFunction(), SolutionUserObject::evalMeshFunctionGradient(), SolutionUserObject::evalMultiValuedMeshFunction(), SolutionUserObject::evalMultiValuedMeshFunctionGradient(), MultiAppPostprocessorTransfer::execute(), MultiAppPostprocessorInterpolationTransfer::execute(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), MultiAppNearestNodeTransfer::execute(), PointValue::execute(), MultiAppPostprocessorToAuxScalarTransfer::execute(), MultiAppScalarToAuxScalarTransfer::execute(), MultiAppVariableValueSampleTransfer::execute(), MultiAppMeshFunctionTransfer::execute(), MultiAppInterpolationTransfer::execute(), MultiAppUserObjectTransfer::execute(), MultiAppProjectionTransfer::execute(), MultiAppCopyTransfer::execute(), FileOutput::FileOutput(), MultiApp::fillPositions(), PointSamplerBase::finalize(), GeneralUserObject::GeneralUserObject(), MultiApp::getBoundingBox(), Control::getControllableParameterHelper(), Control::getControllableValue(), AuxKernel::getDependObjects(), MultiApp::getExecutioner(), OutputWarehouse::getFileNumbers(), SolutionUserObject::getLocalVarIndex(), AuxKernel::getMaterialProperty(), SubProblem::getMaterialPropertyBlockNames(), SubProblem::getMaterialPropertyBoundaryNames(), AuxKernel::getMaterialPropertyOld(), AuxKernel::getMaterialPropertyOlder(), OutputWarehouse::getOutput(), Transient::getTimeStepperName(), InitialCondition::getUserObject(), AuxKernel::getUserObject(), InitialCondition::getUserObjectByName(), AuxKernel::getUserObjectByName(), AdvancedOutput::hasOutputHelper(), FEProblemBase::init(), CSVReader::initialize(), MultiAppProjectionTransfer::initialSetup(), InitialCondition::initialSetup(), SolutionUserObject::initialSetup(), AdvancedOutput::initOutputList(), AdvancedOutput::initPostprocessorOrVectorPostprocessorLists(), Material::initStatefulProperties(), Function::integral(), IntegratedBC::IntegratedBC(), InterfaceKernel::InterfaceKernel(), KernelBase::KernelBase(), LinearCombinationFunction::LinearCombinationFunction(), Marker::Marker(), MaterialDerivativeTestKernelBase< T >::MaterialDerivativeTestKernelBase(), MaterialVectorPostprocessor::MaterialVectorPostprocessor(), ElementDeleterBase::modify(), NodalBC::NodalBC(), NodalEqualValueConstraint::NodalEqualValueConstraint(), NodalKernel::NodalKernel(), NodalValueSampler::NodalValueSampler(), NodalVariableValue::NodalVariableValue(), DOFMapOutput::output(), AdvancedOutput::outputElementalVariables(), AdvancedOutput::outputInput(), AdvancedOutput::outputNodalVariables(), ConsoleUtils::outputOutputInformation(), Nemesis::outputPostprocessors(), Exodus::outputPostprocessors(), AdvancedOutput::outputPostprocessors(), AdvancedOutput::outputScalarVariables(), AdvancedOutput::outputSystemInformation(), AdvancedOutput::outputVectorPostprocessors(), MooseObject::parameters(), Executioner::parentOutputPositionChanged(), ParsedAddSideset::ParsedAddSideset(), ParsedAux::ParsedAux(), ParsedODEKernel::ParsedODEKernel(), ParsedSubdomainMeshModifier::ParsedSubdomainMeshModifier(), PointSamplerBase::PointSamplerBase(), SubProblem::registerRecoverableData(), SubProblem::registerRestartableData(), Material::resetQpProperties(), Sampler::Sampler(), ScalarComponentIC::ScalarComponentIC(), MooseMesh::setBoundaryName(), Control::setControllableValue(), OutputWarehouse::setFileNumbers(), MooseMesh::setSubdomainName(), Split::setup(), TransientMultiApp::setupApp(), SideValueSampler::SideValueSampler(), TransientMultiApp::solveStep(), UserObject::spatialValue(), SphericalAverage::SphericalAverage(), StitchedMesh::StitchedMesh(), Function::timeDerivative(), TransientMultiApp::TransientMultiApp(), MultiAppTransfer::variableIntegrityCheck(), VariableResidual::VariableResidual(), and AdvancedOutput::wantOutput().

47 { return _name; }
const std::string & _name
The name of this object, reference to value stored in InputParameters.
Definition: MooseObject.h:114
const InputParameters& MooseObject::parameters ( ) const
inlineinherited
void SetupInterface::residualSetup ( )
virtualinherited

Gets called just before the residual is computed and before this object is asked to do its job.

Definition at line 84 of file SetupInterface.C.

85 {
86 }
Real ImageSampler::sample ( const Point &  p)
virtualinherited

Return the pixel value for the given point.

Parameters
pThe point at which to extract pixel data

Definition at line 219 of file ImageSampler.C.

Referenced by ImageSubdomain::modify(), and value().

220 {
221 #ifdef LIBMESH_HAVE_VTK
222 
223  // Do nothing if the point is outside of the image domain
224  if (!_bounding_box.contains_point(p))
225  return 0.0;
226 
227  // Determine pixel coordinates
228  std::vector<int> x(3, 0);
229  for (int i = 0; i < LIBMESH_DIM; ++i)
230  {
231  // Compute position, only if voxel size is greater than zero
232  if (_voxel[i] == 0)
233  x[i] = 0;
234 
235  else
236  {
237  x[i] = std::floor((p(i) - _origin(i)) / _voxel[i]);
238 
239  // If the point falls on the mesh extents the index needs to be decreased by one
240  if (x[i] == _dims[i])
241  x[i]--;
242  }
243  }
244 
245  // Return the image data at the given point
246  return _data->GetScalarComponentAsDouble(x[0], x[1], x[2], _component);
247 
248 #else
249  libmesh_ignore(p); // avoid un-used parameter warnings
250  return 0.0;
251 #endif
252 }
unsigned int _component
Component to extract.
Definition: ImageSampler.h:157
static PetscErrorCode Vec x
BoundingBox _bounding_box
Bounding box for testing points.
Definition: ImageSampler.h:161
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
std::vector< double > _voxel
Physical pixel size.
Definition: ImageSampler.h:153
Point _origin
Origin of image.
Definition: ImageSampler.h:144
std::vector< int > _dims
Pixel dimension of image.
Definition: ImageSampler.h:147
void ImageSampler::setupImageSampler ( MooseMesh mesh)
virtualinherited

Perform initialization of image data.

Definition at line 80 of file ImageSampler.C.

Referenced by initialSetup(), and ImageSubdomain::modify().

81 {
82  // Don't warn that mesh or _is_pars are unused when VTK is not enabled.
83  libmesh_ignore(mesh);
84  libmesh_ignore(_is_pars);
85 
86 #ifdef LIBMESH_HAVE_VTK
87  // Get access to the Mesh object
88  BoundingBox bbox = MeshTools::create_bounding_box(mesh.getMesh());
89 
90  // Set the dimensions from the Mesh if not set by the User
91  if (_is_pars.isParamValid("dimensions"))
92  _physical_dims = _is_pars.get<Point>("dimensions");
93 
94  else
95  {
96  _physical_dims(0) = bbox.max()(0) - bbox.min()(0);
97 #if LIBMESH_DIM > 1
98  _physical_dims(1) = bbox.max()(1) - bbox.min()(1);
99 #endif
100 #if LIBMESH_DIM > 2
101  _physical_dims(2) = bbox.max()(2) - bbox.min()(2);
102 #endif
103  }
104 
105  // Set the origin from the Mesh if not set in the input file
106  if (_is_pars.isParamValid("origin"))
107  _origin = _is_pars.get<Point>("origin");
108  else
109  {
110  _origin(0) = bbox.min()(0);
111 #if LIBMESH_DIM > 1
112  _origin(1) = bbox.min()(1);
113 #endif
114 #if LIBMESH_DIM > 2
115  _origin(2) = bbox.min()(2);
116 #endif
117  }
118 
119  // An array of filenames, to be filled in
120  std::vector<std::string> filenames;
121 
122  // The file suffix, to be determined
123  std::string file_suffix;
124 
125  // Try to parse our own file range parameters. If that fails, then
126  // see if the associated Mesh is an ImageMesh and use its. If that
127  // also fails, then we have to throw an error...
128  //
129  // The parseFileRange method sets parameters, thus a writable reference to the InputParameters
130  // object must be obtained from the warehouse. Generally, this should be avoided, but
131  // this is a special case.
132  if (_status != 0)
133  {
134  // We don't have parameters, so see if we can get them from ImageMesh
135  ImageMesh * image_mesh = dynamic_cast<ImageMesh *>(&mesh);
136  if (!image_mesh)
137  mooseError("No file range parameters were provided and the Mesh is not an ImageMesh.");
138 
139  // Get the ImageMesh's parameters. This should work, otherwise
140  // errors would already have been thrown...
141  filenames = image_mesh->filenames();
142  file_suffix = image_mesh->fileSuffix();
143  }
144  else
145  {
146  // Use our own parameters (using 'this' b/c of conflicts with filenames the local variable)
147  filenames = this->filenames();
148  file_suffix = fileSuffix();
149  }
150 
151  // Storage for the file names
152  _files = vtkSmartPointer<vtkStringArray>::New();
153 
154  for (const auto & filename : filenames)
155  _files->InsertNextValue(filename);
156 
157  // Error if no files where located
158  if (_files->GetNumberOfValues() == 0)
159  mooseError("No image file(s) located");
160 
161  // Read the image stack. Hurray for VTK not using polymorphism in a
162  // smart way... we actually have to explicitly create the type of
163  // reader based on the file extension, using an if-statement...
164  if (file_suffix == "png")
165  _image = vtkSmartPointer<vtkPNGReader>::New();
166  else if (file_suffix == "tiff" || file_suffix == "tif")
167  _image = vtkSmartPointer<vtkTIFFReader>::New();
168  else
169  mooseError("Un-supported file type '", file_suffix, "'");
170 
171  // Now that _image is set up, actually read the images
172  // Indicate that data read has started
173  _is_console << "Reading image(s)..." << std::endl;
174 
175  // Extract the data
176  _image->SetFileNames(_files);
177  _image->Update();
178  _data = _image->GetOutput();
179  _algorithm = _image->GetOutputPort();
180 
181  // Set the image dimensions and voxel size member variable
182  int * dims = _data->GetDimensions();
183  for (unsigned int i = 0; i < 3; ++i)
184  {
185  _dims.push_back(dims[i]);
186  _voxel.push_back(_physical_dims(i) / _dims[i]);
187  }
188 
189  // Set the dimensions of the image and bounding box
190  _data->SetSpacing(_voxel[0], _voxel[1], _voxel[2]);
191  _data->SetOrigin(_origin(0), _origin(1), _origin(2));
192  _bounding_box.min() = _origin;
194 
195  // Indicate data read is completed
196  _is_console << " ...image read finished" << std::endl;
197 
198  // Set the component parameter
199  // If the parameter is not set then vtkMagnitude() will applied
200  if (_is_pars.isParamValid("component"))
201  {
202  unsigned int n = _data->GetNumberOfScalarComponents();
203  _component = _is_pars.get<unsigned int>("component");
204  if (_component >= n)
205  mooseError("'component' parameter must be empty or have a value of 0 to ", n - 1);
206  }
207  else
208  _component = 0;
209 
210  // Apply filters, the toggling on and off of each filter is handled internally
211  vtkMagnitude();
213  vtkThreshold();
214  vtkFlip();
215 #endif
216 }
unsigned int _component
Component to extract.
Definition: ImageSampler.h:157
vtkAlgorithmOutput * _algorithm
VTK-6 seems to work better in terms of "algorithm outputs" rather than vtkImageData pointers...
Definition: ImageSampler.h:116
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
const std::vector< std::string > & filenames()
vtkSmartPointer< vtkImageReader2 > _image
Complete image data.
Definition: ImageSampler.h:119
ConsoleStream _is_console
Create a console stream object for this helper class.
Definition: ImageSampler.h:167
BoundingBox _bounding_box
Bounding box for testing points.
Definition: ImageSampler.h:161
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
std::vector< double > _voxel
Physical pixel size.
Definition: ImageSampler.h:153
std::string fileSuffix()
bool isParamValid(const std::string &name) const
This method returns parameters that have been initialized in one fashion or another, i.e.
MeshBase & getMesh()
Accessor for the underlying libMesh Mesh object.
Definition: MooseMesh.C:2355
void vtkShiftAndScale()
Apply image re-scaling using the vtkImageShiftAndRescale object.
Definition: ImageSampler.C:274
Point _origin
Origin of image.
Definition: ImageSampler.h:144
const InputParameters & _is_pars
Parameters for interface.
Definition: ImageSampler.h:164
void vtkThreshold()
Perform thresholding.
Definition: ImageSampler.C:301
vtkSmartPointer< vtkStringArray > _files
List of file names to extract data.
Definition: ImageSampler.h:110
Point _physical_dims
Physical dimensions of image.
Definition: ImageSampler.h:150
std::vector< int > _dims
Pixel dimension of image.
Definition: ImageSampler.h:147
void vtkFlip()
Perform image flipping.
Definition: ImageSampler.C:337
PetscInt n
void vtkMagnitude()
Convert the image to greyscale.
Definition: ImageSampler.C:255
A 2D GeneratedMesh where xmin, xmax, etc.
Definition: ImageMesh.h:29
void SetupInterface::subdomainSetup ( )
virtualinherited

Gets called when the subdomain changes (i.e.

in a Jacobian or residual loop) and before this object is asked to do its job

Reimplemented in Material, Constraint, GeneralUserObject, and NodalUserObject.

Definition at line 89 of file SetupInterface.C.

90 {
91 }
Real Function::timeDerivative ( Real  t,
const Point &  p 
)
virtualinherited

Get the time derivative of the function.

Parameters
tThe time
pThe point in space (x,y,z)
Returns
The time derivative of the function at the specified time and location

Reimplemented in MooseParsedFunction, PiecewiseConstant, and PiecewiseLinear.

Definition at line 55 of file Function.C.

56 {
57  mooseError("timeDerivative method not defined for function ", name());
58  return 0;
59 }
const std::string & name() const
Get the name of the object.
Definition: MooseObject.h:47
void mooseError(Args &&...args) const
Definition: MooseObject.h:80
void SetupInterface::timestepSetup ( )
virtualinherited

Gets called at the beginning of the timestep before this object is asked to do its job.

Reimplemented in SolutionUserObject, NumNonlinearIterations, and MemoryUsage.

Definition at line 74 of file SetupInterface.C.

75 {
76 }
Real ImageFunction::value ( Real  t,
const Point &  p 
)
overridevirtual

Return the pixel value for the given point.

Parameters
tTime (unused)
pThe point at which to extract pixel data

Reimplemented from Function.

Definition at line 45 of file ImageFunction.C.

46 {
47  return sample(p);
48 }
virtual Real sample(const Point &p)
Return the pixel value for the given point.
Definition: ImageSampler.C:219
RealVectorValue Function::vectorValue ( Real  t,
const Point &  p 
)
virtualinherited

Override this to evaluate the vector function at a point (t,x,y,z), by default this returns a zero vector, you must override it.

Parameters
tThe time
pThe Point in space (x,y,z)
Returns
A vector of the function evaluated at the time and location

Reimplemented in MooseParsedFunction, MooseParsedGradFunction, MooseParsedVectorFunction, and LinearCombinationFunction.

Definition at line 62 of file Function.C.

63 {
64  return RealVectorValue(0, 0, 0);
65 }
VectorValue< Real > RealVectorValue
Definition: Assembly.h:40
void ImageSampler::vtkFlip ( )
protectedinherited

Perform image flipping.

Flip the image along the x, y, and/or z axis. If multiple flips occur, they happen in order.

Definition at line 337 of file ImageSampler.C.

Referenced by ImageSampler::setupImageSampler().

338 {
339 #ifdef LIBMESH_HAVE_VTK
340  // Convert boolean values into an integer array, then loop over it
341  int mask[3] = {
342  _is_pars.get<bool>("flip_x"), _is_pars.get<bool>("flip_y"), _is_pars.get<bool>("flip_z")};
343 
344  for (int dim = 0; dim < 3; ++dim)
345  {
346  if (mask[dim])
347  {
348  _flip_filter = imageFlip(dim);
349 
350  // Update pointers
351  _data = _flip_filter->GetOutput();
352  _algorithm = _flip_filter->GetOutputPort();
353  }
354  }
355 #endif
356 }
vtkAlgorithmOutput * _algorithm
VTK-6 seems to work better in terms of "algorithm outputs" rather than vtkImageData pointers...
Definition: ImageSampler.h:116
vtkSmartPointer< vtkImageFlip > _flip_filter
Pointers to image flipping filter. May be used for x, y, or z.
Definition: ImageSampler.h:131
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
const InputParameters & _is_pars
Parameters for interface.
Definition: ImageSampler.h:164
vtkSmartPointer< vtkImageFlip > imageFlip(const int &axis)
Helper method for flipping image.
Definition: ImageSampler.C:360
void ImageSampler::vtkMagnitude ( )
protectedinherited

Convert the image to greyscale.

By leaving the 'component' input parameter empty, this is called automatically.

Definition at line 255 of file ImageSampler.C.

Referenced by ImageSampler::setupImageSampler().

256 {
257 #ifdef LIBMESH_HAVE_VTK
258  // Do nothing if 'component' is set
259  if (_is_pars.isParamValid("component"))
260  return;
261 
262  // Apply the greyscale filtering
263  _magnitude_filter = vtkSmartPointer<vtkImageMagnitude>::New();
264  _magnitude_filter->SetInputConnection(_algorithm);
265  _magnitude_filter->Update();
266 
267  // Update the pointers
268  _data = _magnitude_filter->GetOutput();
269  _algorithm = _magnitude_filter->GetOutputPort();
270 #endif
271 }
vtkAlgorithmOutput * _algorithm
VTK-6 seems to work better in terms of "algorithm outputs" rather than vtkImageData pointers...
Definition: ImageSampler.h:116
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
bool isParamValid(const std::string &name) const
This method returns parameters that have been initialized in one fashion or another, i.e.
vtkSmartPointer< vtkImageMagnitude > _magnitude_filter
Pointer to the magnitude filter.
Definition: ImageSampler.h:128
const InputParameters & _is_pars
Parameters for interface.
Definition: ImageSampler.h:164
void ImageSampler::vtkShiftAndScale ( )
protectedinherited

Apply image re-scaling using the vtkImageShiftAndRescale object.

Definition at line 274 of file ImageSampler.C.

Referenced by ImageSampler::setupImageSampler().

275 {
276 #ifdef LIBMESH_HAVE_VTK
277  // Capture the parameters
278  double shift = _is_pars.get<double>("shift");
279  double scale = _is_pars.get<double>("scale");
280 
281  // Do nothing if shift and scale are not set
282  if (shift == 0 && scale == 1)
283  return;
284 
285  // Perform the scaling and offset actions
286  _shift_scale_filter = vtkSmartPointer<vtkImageShiftScale>::New();
287  _shift_scale_filter->SetOutputScalarTypeToDouble();
288 
289  _shift_scale_filter->SetInputConnection(_algorithm);
290  _shift_scale_filter->SetShift(shift);
291  _shift_scale_filter->SetScale(scale);
292  _shift_scale_filter->Update();
293 
294  // Update the pointers
295  _data = _shift_scale_filter->GetOutput();
296  _algorithm = _shift_scale_filter->GetOutputPort();
297 #endif
298 }
vtkAlgorithmOutput * _algorithm
VTK-6 seems to work better in terms of "algorithm outputs" rather than vtkImageData pointers...
Definition: ImageSampler.h:116
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
vtkSmartPointer< vtkImageShiftScale > _shift_scale_filter
Pointer to the shift and scaling filter.
Definition: ImageSampler.h:125
const InputParameters & _is_pars
Parameters for interface.
Definition: ImageSampler.h:164
void ImageSampler::vtkThreshold ( )
protectedinherited

Perform thresholding.

Definition at line 301 of file ImageSampler.C.

Referenced by ImageSampler::setupImageSampler().

302 {
303 #ifdef LIBMESH_HAVE_VTK
304  // Do nothing if threshold not set
305  if (!_is_pars.isParamValid("threshold"))
306  return;
307 
308  // Error if both upper and lower are not set
309  if (!_is_pars.isParamValid("upper_value") || !_is_pars.isParamValid("lower_value"))
310  mooseError("When thresholding is applied, both the upper_value and lower_value parameters must "
311  "be set");
312 
313  // Create the thresholding object
314  _image_threshold = vtkSmartPointer<vtkImageThreshold>::New();
315 
316  // Set the data source
317  _image_threshold->SetInputConnection(_algorithm);
318 
319  // Setup the thresholding options
320  _image_threshold->ThresholdByUpper(_is_pars.get<Real>("threshold"));
321  _image_threshold->ReplaceInOn();
322  _image_threshold->SetInValue(_is_pars.get<Real>("upper_value"));
323  _image_threshold->ReplaceOutOn();
324  _image_threshold->SetOutValue(_is_pars.get<Real>("lower_value"));
325  _image_threshold->SetOutputScalarTypeToDouble();
326 
327  // Perform the thresholding
328  _image_threshold->Update();
329 
330  // Update the pointers
331  _data = _image_threshold->GetOutput();
332  _algorithm = _image_threshold->GetOutputPort();
333 #endif
334 }
vtkAlgorithmOutput * _algorithm
VTK-6 seems to work better in terms of "algorithm outputs" rather than vtkImageData pointers...
Definition: ImageSampler.h:116
void mooseError(Args &&...args)
Emit an error message with the given stringified, concatenated args and terminate the application...
Definition: MooseError.h:182
vtkImageData * _data
Complete image data.
Definition: ImageSampler.h:113
bool isParamValid(const std::string &name) const
This method returns parameters that have been initialized in one fashion or another, i.e.
const InputParameters & _is_pars
Parameters for interface.
Definition: ImageSampler.h:164
vtkSmartPointer< vtkImageThreshold > _image_threshold
Pointer to thresholding filter.
Definition: ImageSampler.h:122

Member Data Documentation

MooseApp& MooseObject::_app
protectedinherited

The MooseApp this object is associated with.

Definition at line 108 of file MooseObject.h.

Referenced by AB2PredictorCorrector::AB2PredictorCorrector(), Executioner::addAttributeReporter(), FEProblemBase::addMaterial(), FEProblemBase::addMultiApp(), FEProblemBase::allowOutput(), AStableDirk4::AStableDirk4(), FileMesh::buildMesh(), FEProblemBase::checkNonlinearConvergence(), OversampleOutput::cloneMesh(), FEProblemBase::computeJacobian(), FEProblemBase::computeResidualType(), Console::Console(), TimeStepper::constrainStep(), MultiApp::createApp(), EigenExecutionerBase::EigenExecutionerBase(), EigenKernel::EigenKernel(), InversePowerMethod::execute(), NonlinearEigen::execute(), Transient::execute(), Steady::execute(), FileOutput::FileOutput(), FEProblemBase::forceOutput(), MooseObject::getMooseApp(), InversePowerMethod::init(), NonlinearEigen::init(), Transient::init(), Steady::init(), MooseMesh::init(), NumPicardIterations::initialize(), TimePeriod::initialSetup(), Console::initialSetup(), MultiApp::initialSetup(), FEProblemBase::initialSetup(), AdvancedOutput::initOutputList(), FEProblemBase::initPetscOutput(), AdvancedOutput::initPostprocessorOrVectorPostprocessorLists(), InversePowerMethod::InversePowerMethod(), MooseObject::mooseError(), MooseMesh::MooseMesh(), NonlinearEigen::NonlinearEigen(), Tecplot::output(), Exodus::output(), Nemesis::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Exodus::outputEmptyTimestep(), Console::outputInput(), Exodus::outputInput(), Exodus::outputNodalVariables(), OversampleOutput::outputStep(), Output::outputStep(), FEProblemBase::outputStep(), Console::outputSystemInformation(), MultiApp::parentOutputPositionChanged(), PerformanceData::PerformanceData(), PetscOutput::petscLinearOutput(), PetscOutput::petscNonlinearOutput(), SubProblem::registerRecoverableData(), SubProblem::registerRestartableData(), FEProblemBase::setRestartFile(), TransientMultiApp::setupApp(), TimeSequenceStepperBase::setupSequence(), Transient::setupTimeIntegrator(), TransientMultiApp::solveStep(), FEProblemBase::subdomainSetup(), TimeExtremeValue::TimeExtremeValue(), TimePeriod::TimePeriod(), FEProblemBase::timestepSetup(), Transient::Transient(), and Console::write().

const ConsoleStream ConsoleStreamInterface::_console
inherited

An instance of helper class to write streams to the Console objects.

Definition at line 37 of file ConsoleStreamInterface.h.

Referenced by IterationAdaptiveDT::acceptStep(), CreateProblemAction::act(), SetupRecoverFileBaseAction::act(), Adaptivity::adaptMesh(), FEProblemBase::adaptMesh(), FEProblemBase::advanceMultiApps(), SimplePredictor::apply(), FEProblemBase::backupMultiApps(), FEProblemBase::checkProblemIntegrity(), IterationAdaptiveDT::computeAdaptiveDT(), Transient::computeConstrainedDT(), NonlinearSystemBase::computeDamping(), IterationAdaptiveDT::computeDT(), IterationAdaptiveDT::computeFailedDT(), IterationAdaptiveDT::computeInterpolationDT(), FEProblemBase::computeResidualType(), IterationAdaptiveDT::constrainStep(), TimeStepper::constrainStep(), AB2PredictorCorrector::converged(), FEProblemBase::execMultiApps(), FEProblemBase::execMultiAppTransfers(), MultiAppPostprocessorTransfer::execute(), MultiAppPostprocessorInterpolationTransfer::execute(), MultiAppVariableValueSamplePostprocessorTransfer::execute(), MultiAppNearestNodeTransfer::execute(), MultiAppPostprocessorToAuxScalarTransfer::execute(), MultiAppScalarToAuxScalarTransfer::execute(), MultiAppVariableValueSampleTransfer::execute(), MultiAppUserObjectTransfer::execute(), MultiAppInterpolationTransfer::execute(), MultiAppMeshFunctionTransfer::execute(), MultiAppProjectionTransfer::execute(), MultiAppCopyTransfer::execute(), Steady::execute(), MultiAppDTKUserObjectTransfer::execute(), ActionWarehouse::executeActionsWithAction(), ActionWarehouse::executeAllActions(), MultiApp::globalAppToLocal(), InversePowerMethod::init(), NonlinearEigen::init(), Steady::init(), FEProblemBase::initialAdaptMesh(), FEProblemBase::initialSetup(), EigenExecutionerBase::inversePowerIteration(), Transient::keepGoing(), IterationAdaptiveDT::limitDTByFunction(), IterationAdaptiveDT::limitDTToPostprocessorValue(), EigenExecutionerBase::makeBXConsistent(), Console::meshChanged(), MooseObject::mooseDeprecated(), MooseObject::mooseInfo(), MooseObject::mooseWarning(), DOFMapOutput::output(), VariableResidualNormsDebugOutput::output(), Console::output(), ControlOutput::outputActiveObjects(), ControlOutput::outputChangedControls(), ControlOutput::outputControls(), Console::outputInput(), Console::outputPostprocessors(), Console::outputScalarVariables(), Console::outputSystemInformation(), FEProblemBase::possiblyRebuildGeomSearchPatches(), EigenExecutionerBase::postExecute(), ActionWarehouse::printActionDependencySets(), EigenExecutionerBase::printEigenvalue(), MaterialPropertyDebugOutput::printMaterialMap(), SolutionTimeAdaptiveDT::rejectStep(), DT2::rejectStep(), FEProblemBase::restoreMultiApps(), SimplePredictor::shouldApply(), NonlinearSystem::solve(), LStableDirk2::solve(), LStableDirk3::solve(), ImplicitMidpoint::solve(), ExplicitTVDRK2::solve(), AStableDirk4::solve(), LStableDirk4::solve(), ExplicitRK2::solve(), TransientMultiApp::solveStep(), Transient::solveStep(), DT2::step(), AB2PredictorCorrector::step(), NonlinearEigen::takeStep(), FEProblemBase::useFECache(), Console::writeTimestepInformation(), Console::writeVariableNorms(), and FEProblemBase::~FEProblemBase().

const InputParameters& ScalarCoupleable::_coupleable_params
protectedinherited
std::vector<MooseVariableScalar *> ScalarCoupleable::_coupled_moose_scalar_vars
protectedinherited

Vector of coupled variables.

Definition at line 144 of file ScalarCoupleable.h.

Referenced by ScalarCoupleable::getCoupledMooseScalarVars(), and ScalarCoupleable::ScalarCoupleable().

std::map<std::string, std::vector<MooseVariableScalar *> > ScalarCoupleable::_coupled_scalar_vars
protectedinherited
const ExecFlagType& SetupInterface::_current_execute_flag
protectedinherited

Reference to FEProblemBase.

Definition at line 85 of file SetupInterface.h.

std::map<std::string, VariableValue *> ScalarCoupleable::_default_value
protectedinherited

Will hold the default value for optional coupled scalar variables.

Definition at line 141 of file ScalarCoupleable.h.

Referenced by ScalarCoupleable::getDefaultValue(), and ScalarCoupleable::~ScalarCoupleable().

Real& TransientInterface::_dt
protectedinherited

Time step size.

Definition at line 63 of file TransientInterface.h.

Referenced by TotalVariableValue::execute(), and VariableTimeIntegrationAux::getIntegralValue().

Real& TransientInterface::_dt_old
protectedinherited

Size of the old time step.

Definition at line 66 of file TransientInterface.h.

Referenced by VariableTimeIntegrationAux::getIntegralValue().

const bool& MooseObject::_enabled
protectedinherited

Reference to the "enable" InputParaemters, used by Controls for toggling on/off MooseObjects.

Definition at line 117 of file MooseObject.h.

Referenced by MooseObject::enabled().

std::vector<ExecFlagType> SetupInterface::_exec_flags
protectedinherited

execution flag (when is the object executed/evaluated)

Definition at line 82 of file SetupInterface.h.

Referenced by SetupInterface::execBitFlags(), SetupInterface::execFlags(), and SetupInterface::SetupInterface().

std::string FileRangeBuilder::_file_suffix
protectedinherited
std::vector<std::string> FileRangeBuilder::_filenames
protectedinherited
bool TransientInterface::_is_implicit
protectedinherited

If the object is using implicit or explicit form.

This does NOT mean time scheme, but which values are going to be used in the object - either from current time or old time. Note that even explicit schemes have implicit form (it is the time derivative "kernel")

Definition at line 54 of file TransientInterface.h.

Referenced by EigenKernel::computeJacobian(), EigenKernel::computeOffDiagJacobian(), EigenKernel::EigenKernel(), EigenKernel::enabled(), and TransientInterface::isImplicit().

bool TransientInterface::_is_transient
protectedinherited

Definition at line 69 of file TransientInterface.h.

FEProblemBase& MeshChangedInterface::_mci_feproblem
protectedinherited

Reference to FEProblemBase instance.

Definition at line 47 of file MeshChangedInterface.h.

Referenced by MeshChangedInterface::MeshChangedInterface().

const std::string& MooseObject::_name
protectedinherited
const InputParameters& MooseObject::_pars
protectedinherited
FEProblemBase& ScalarCoupleable::_sc_fe_problem
protectedinherited
bool ScalarCoupleable::_sc_is_implicit
protectedinherited
const InputParameters& ScalarCoupleable::_sc_parameters
protectedinherited

Definition at line 60 of file ScalarCoupleable.h.

Referenced by ScalarCoupleable::ScalarCoupleable().

int FileRangeBuilder::_status
protectedinherited
Real& TransientInterface::_t
protectedinherited
int& TransientInterface::_t_step
protectedinherited

The number of the time step.

Definition at line 60 of file TransientInterface.h.

FEProblemBase& TransientInterface::_ti_feproblem
protectedinherited

Definition at line 46 of file TransientInterface.h.

Referenced by SolutionFunction::SolutionFunction().

const InputParameters& TransientInterface::_ti_params
protectedinherited

Definition at line 44 of file TransientInterface.h.


The documentation for this class was generated from the following files: