itk::PSMProject Class Reference

This class is a data object that holds information about a Particle Shape Modeling project. More...

#include <itkPSMProject.h>

Inheritance diagram for itk::PSMProject:

Collaboration diagram for itk::PSMProject:

Public Types
typedef PSMProject	Self
typedef Object	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer

Public Member Functions
	itkNewMacro (Self)
	itkTypeMacro (PSMProject, Object)
void	SetDOMNode (PSMDOMNode *p)
PSMDOMNode::Pointer &	GetDOMNode ()
bool	HasDomains () const
const DOMNode *	GetDomainNode (const std::string &name) const
bool	HasDomainDistanceTransform (const std::string &name) const
const std::vector< std::string > &	GetDomainDistanceTransform (const std::string &name) const
bool	HasDomainCuttingPlanes (const std::string &name) const
std::vector< vnl_vector_fixed< double, 3 > >	GetDomainCuttingPlanes (const std::string &name) const
std::vector< std::string >	GetDomainNames () const
const std::vector< std::string > &	GetModel (const std::string &name)
bool	HasModel (const std::string &name) const
const std::vector< std::string > &	GetDistanceTransforms () const
const DOMNode *	GetOptimization () const
unsigned int	GetNumberOfOptimizationScales () const
bool	HasOptimizationAttribute (const std::string &name, unsigned int i=0) const
double	GetOptimizationAttribute (const std::string &name, unsigned int i=0) const
bool	HasProcrustes () const
bool	HasVariables (const std::string &name) const
std::vector< double >	GetVariables (const std::string &name) const
const std::vector< std::string > &	GetVariablesText (const std::string &name) const
void	Stream (std::ostream &os)

Static Public Attributes
static const std::string	data_tag = "data"
static const std::string	distance_transform_tag = "distance_transform"
static const std::string	distance_transforms_tag = "distance_transforms"
static const std::string	domain_tag = "domain"
static const std::string	correspondences_tag = "correspondences"
static const std::string	cutting_plane_tag = "cutting_plane"
static const std::string	model_tag = "model"
static const std::string	name_tag = "name"
static const std::string	optimization_tag = "optimization"
static const std::string	number_of_scales_tag = "number_of_scales"
static const std::string	preprocessing_tag = "preprocessing"
static const std::string	procrustes_tag = "procrustes_registration"
static const std::string	psm_project_tag = "psm_project"
static const std::string	scale_tag = "scale"
static const std::string	scale_number_tag = "number"
static const std::string	variables_tag = "variables"

Protected Member Functions
void	PrintSelf (std::ostream &os, Indent indent) const
void	StreamChildren (PSMDOMNode *, std::ostream &os, Indent indent)
const PSMDOMNode *	GetDataNode () const

Detailed Description

This class is a data object that holds information about a Particle Shape Modeling project.

This class is a data object that holds information about a Particle Shape Modeling project. It contains information such as lists of input and output files, paths, processing parameters, the author of the project, and other metainformation that is useful to keep track of the multiple steps and image files necessary to compute a particle-based shape model.

At its core, this class is a wrapper around a PSMDOMNode object that provides a simplified interface to the data in the DOM node.

Definition at line 47 of file itkPSMProject.h.

Member Typedef Documentation

typedef PSMProject itk::PSMProject::Self

Standard class typedefs

Definition at line 51 of file itkPSMProject.h.

Member Function Documentation

const PSMDOMNode * itk::PSMProject::GetDataNode ( ) const

protected

Return the parent node of the Data section.

Definition at line 444 of file itkPSMProject.cxx.

{
 // Look for the data section
  const PSMDOMNode *data 
    = static_cast<const PSMDOMNode *>(m_DOMNode->GetChild(data_tag));
  
  if (data == 0) // data is not found
    {
      itkExceptionMacro( "PSM Project file does not specify " + data_tag );
    }
  else
    {
      return data;
    }
}

const std::vector< std::string > & itk::PSMProject::GetDistanceTransforms

(

)

const

Get the file names of the distance transforms that are to be used as input to an optimization process. Corresponds to the text found in the XML tag <distance_transforms>

Definition at line 462 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();

  const PSMDOMNode *dt = 0;
  dt = static_cast<const PSMDOMNode *>(data->GetChild(distance_transforms_tag));
  if (dt == 0)
    {
      itkExceptionMacro( "PSM Project file does not specify " + distance_transforms_tag );
    }
  else return dt->GetText();
}

std::vector< vnl_vector_fixed< double, 3 > > itk::PSMProject::GetDomainCuttingPlanes

(

const std::string &

name

)

const

Returns a list of cutting planes for the named domain. Throws an exception if the domain does not contain cutting planes (call HasDomainCuttingPlanes first).

Definition at line 185 of file itkPSMProject.cxx.

{
  const DOMNode *domain = this->GetDomainNode(name);
  
  // Search the domain for nodes called cutting_plane
  DOMNode::ConstChildrenListType p;
  domain->GetChildren(cutting_plane_tag, p);
  
 // Did we find anything called a cutting plane?  If not, this is an
 // error.  Proper way is to check for cutting planes first using
 // HasDomainCuttingPlanes.
  if (p.size() == 0)
    { 
      itkExceptionMacro("Did not find cutting planes in domain " + name + " ");
    }

  std::vector<vnl_vector_fixed<double,3> > planes;

  for (unsigned int i = 0; i < p.size(); i++)
    {
      std::istringstream inputsBuffer;
      std::vector<double> pts;
      double pt;

      std::vector<std::string> txt
     = dynamic_cast<const PSMDOMNode *>(p[i])->GetText();
      for (unsigned int j = 0; j < txt.size(); j++)
     {
       inputsBuffer.str(txt[j]);    

       while (inputsBuffer >> pt)
         {   pts.push_back(pt); }

       inputsBuffer.clear();
     }

      // If we didn't get the right number of points, throw an
      // exception.
      if (pts.size() != 9)
     {
       itkExceptionMacro("Cutting plane data for " + name + " does not consist of three points.");
     }

      vnl_vector_fixed<double,3> x;
      vnl_vector_fixed<double,3> y;
      vnl_vector_fixed<double,3> z;
      x[0] = pts[0]; x[1] = pts[1]; x[2] = pts[2];
      y[0] = pts[3]; y[1] = pts[4]; y[2] = pts[5];
      z[0] = pts[6]; z[1] = pts[7]; z[2] = pts[8];

      planes.push_back(x);
      planes.push_back(y);
      planes.push_back(z);
 
    }

  return planes;
}

const std::vector< std::string > & itk::PSMProject::GetDomainDistanceTransform

(

const std::string &

name

)

const

Returns the name of the distance transform from the given domain

Definition at line 118 of file itkPSMProject.cxx.

{

 const DOMNode *domain = this->GetDomainNode(name);
 const DOMNode *dt = domain->GetChild(distance_transform_tag);

 if (dt == 0)
   {
     itkExceptionMacro("No distance transform filename was found in the domain called " + name + " ");
   }
 
 return ((dynamic_cast<const PSMDOMNode *>(dt))->GetText());  
}

std::vector< std::string > itk::PSMProject::GetDomainNames

(

)

const

Returns a list of the names of all domains present in the project file. Will throw an exception if no domain names are present, so call HasDomains() first to check is the file has domains defined.

Definition at line 133 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();
  
  // Search the data tree for nodes called domain_tag
  DOMNode::ConstChildrenListType domains;
  data->GetChildren(domain_tag, domains);
  
  // Did we find anything called a domain?
  if (domains.size() == 0)
    {
      itkExceptionMacro( "PSM Project file does not specify any elements called " + domain_tag );
    }
  
  std::vector<std::string> s;
  
  // Compile the list of names of the domains
  for (unsigned int i = 0; i < domains.size(); i++)
    {
      if (domains[i]->HasAttribute(name_tag))
     {
       s.push_back(domains[i]->GetAttribute(name_tag));
     }
      else
     {
       itkExceptionMacro( "The name attribute is missing from a PSM Project file"  + model_tag + ".");
     }
    }
  return s;
}

const DOMNode * itk::PSMProject::GetDomainNode

(

const std::string &

name

)

const

Returns the node associated with the given name

Definition at line 74 of file itkPSMProject.cxx.

{
 // Look for the data section
  const DOMNode *data = this->GetDataNode();

  // Compile the list of domains
  DOMNode::ConstChildrenListType domains;
  data->GetChildren(domain_tag, domains);

  for (unsigned int i = 0; i < domains.size(); i++)
    {
      // Look for the name
      if (domains[i]->HasAttribute(name_tag))
        {
       if (domains[i]->GetAttribute(name_tag) == name)
         {
           return domains[i];
         }
        }
    }

  // Didn't find the name!
  itkExceptionMacro( "Could not find a domain called " + name );
  return 0;
}

PSMDOMNode::Pointer& itk::PSMProject::GetDOMNode ( )

inline

Get the DOM Node object, which contains the XML tree of parameter data. This method is only intended for special cases in which the DOM tree needs to be modified or contains nonstandard data objects.

Definition at line 90 of file itkPSMProject.h.

    { return m_DOMNode; }

const std::vector< std::string > & itk::PSMProject::GetModel

(

const std::string &

name

)

The file names of the original segmentations for the project. Corresponds to the text found in the XML tag <segmentations> The file names for the correspondence points for a model, specified by name. If no name is given, this method just returns the first list of names give by a model_tag.

Definition at line 477 of file itkPSMProject.cxx.

{
 const PSMDOMNode *data = this->GetDataNode();

 // Search the data tree for nodes called model_tag
 DOMNode::ConstChildrenListType models;
 data->GetChildren(model_tag, models);

 if (models.size() == 0)
   {
     itkExceptionMacro( "PSM Project file does not specify any elements called " + model_tag );
   }

 // Search the list of models for one with the correct name
 for (unsigned int i = 0; i < models.size(); i++)
   {
     if (models[i]->HasAttribute(name_tag))
       {
         if (models[i]->GetAttribute(name_tag) == name)
           {
             return ((dynamic_cast<const PSMDOMNode *>(models[i]))->GetText());
           }
       }
   }
 itkExceptionMacro( "PSM Project file does not have any " + model_tag + " entries with name = " << name );
}

unsigned int itk::PSMProject::GetNumberOfOptimizationScales

(

)

const

Returns the number of optimization scales.

Definition at line 245 of file itkPSMProject.cxx.

{
  DOMNode *opt = m_DOMNode->GetChild(optimization_tag);
  
  if (opt != 0)
    {
      if (opt->HasAttribute(number_of_scales_tag))
        {
          return static_cast<unsigned int>(atoi(opt->GetAttribute(number_of_scales_tag).c_str()));
        }
      else
        {
          itkExceptionMacro("Number of scales not specified");
        }
    }

  itkExceptionMacro("No " + optimization_tag + " was found.");
}

const DOMNode* itk::PSMProject::GetOptimization ( ) const

inline

Return the DOM node with the optimization_tag. User can query optimization parameters, for example by making calls such as: GetOptimization()->GetAttribute("my_optimization_parameter"). This method returns 0 if no optimization_tag is present in the file. User should check the return value.

Definition at line 146 of file itkPSMProject.h.

  {
    return m_DOMNode->GetChild(optimization_tag);
  }

double itk::PSMProject::GetOptimizationAttribute	(	const std::string &	name,
		unsigned int	i = 0
	)		const

Returns an attribute of the optimization_tag element as a double-precision floating point number. To work with attributes that are text or integer values, you can call GetOptimization->GetAttribute instead, which will return the attribute as text, and convert as needed. This method is a convenience for the most common case. User may optionally provide the scale, if there are multiple scales in the optimization.

Definition at line 308 of file itkPSMProject.cxx.

{
  DOMNode *opt = m_DOMNode->GetChild(optimization_tag);
  if (opt != 0) // found the optimization element
    {
      unsigned int nscales = 1;
      
      // Are there scale elements?
      if (opt->HasAttribute(number_of_scales_tag))
        {
          nscales = static_cast<unsigned int>(atoi(opt->GetAttribute(number_of_scales_tag).c_str()));
        }
      
      // Did the user ask for a scale that isn't specified?
      if (s+1 > nscales)
        { 
          itkExceptionMacro("Requested data for scale that was not specified.");
        }
      
      // If only one scale, then look in element attributes for name
      if (nscales == 1) 
        {
          if (opt->HasAttribute(name)) 
            { 
              return atof(opt->GetAttribute(name).c_str());
            }
        }
      
      // Finally, look for a scale element with name i
      DOMNode::ChildrenListType children;
      opt->GetAllChildren(children);

      for (unsigned i = 0; i < children.size(); i++)
        {
          if ( children[i]->GetName() == scale_tag 
               && 
               static_cast<unsigned int>(atoi(children[i]->GetAttribute(scale_number_tag).c_str())) == s )
            {
              if (children[i]->HasAttribute(name)) 
                { 
                  return atof(children[i]->GetAttribute(name).c_str()); 
                }
              else 
                { 
                  itkExceptionMacro("Found " + scale_tag + " element, but it does not have an attribute named " + name + ".");
                }
            }
        }
    }
  itkExceptionMacro("File has no " + optimization_tag + " element");
}

std::vector< double > itk::PSMProject::GetVariables

(

const std::string &

name

)

const

Returns a vector of doubles for the variable_tag with the specified name. This is a convenience method for the common case. For more complex parsing, the user can call GetVariablesText(name). This method will throw an exception if the variable name does not exist, so User should first check using HasVariables.

Definition at line 405 of file itkPSMProject.cxx.

{
  const std::vector<std::string> &vartext = this->GetVariablesText(name);
 
  std::vector<double> ans;
  for (unsigned int i = 0; i < vartext.size(); i++)
    {
      ans.push_back(atof(vartext[i].c_str()));      
    }
  return ans;
}

const std::vector< std::string > & itk::PSMProject::GetVariablesText

(

const std::string &

name

)

const

Returns the text for the specified variable. This method will throw an exception if the variable does no exist, so User should first check HasVariables.

Definition at line 417 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();
  
  // Search the data tree for nodes called variables_tag
  DOMNode::ConstChildrenListType variables;
  data->GetChildren(variables_tag, variables);
  
  if (variables.size() == 0)
    {
      itkExceptionMacro( "PSM Project file does not have any " + variables_tag + " entries with name = " << name );
    }
  
  // Search the list of variables for one with the correct name
  for (unsigned int i = 0; i < variables.size(); i++)
    {
      if (variables[i]->HasAttribute(name_tag))
        {
          if (variables[i]->GetAttribute(name_tag) == name)
            {
              return ((dynamic_cast<const PSMDOMNode *>(variables[i]))->GetText());
            }
        }
    }
  itkExceptionMacro( "PSM Project file does not have any " + variables_tag + " entries with name = " << name );
}

bool itk::PSMProject::HasDomainCuttingPlanes

(

const std::string &

name

)

const

Returns true if the named domain has cutting planes defined

Definition at line 165 of file itkPSMProject.cxx.

{
  const DOMNode *domain = this->GetDomainNode(name);

  // Search the domain for nodes called cutting_plane
  DOMNode::ConstChildrenListType p;
  domain->GetChildren(cutting_plane_tag, p);
  
 // Did we find anything called a cutting plane?
  if (p.size() > 0)
    { 
      return true;
    }
  else
    {
      return false;
    }
}

bool itk::PSMProject::HasDomainDistanceTransform

(

const std::string &

name

)

const

Returns true if the named domain has distance transforms defined

Definition at line 101 of file itkPSMProject.cxx.

{

 const DOMNode *domain = this->GetDomainNode(name);
 const DOMNode *dt = domain->GetChild(distance_transform_tag);

 if (dt == 0)
   {
     return false;
   }
 else
   {
     return true;
   }
}

bool itk::PSMProject::HasDomains

(

)

const

Returns true if the file has specified at least one "domain" tag.

Definition at line 56 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();
  
  // Search the data tree for nodes called domain_tag
  DOMNode::ConstChildrenListType domains;
  data->GetChildren(domain_tag, domains);
  
  // Did we find anything called a domain?
  if (domains.size() == 0)
    {
      return false;
    }
  else return true;

}

bool itk::PSMProject::HasModel

(

const std::string &

name

)

const

Returns true if the model with the specified name is given.

Definition at line 505 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();
  
  // Search the data tree for nodes called model_tag
  DOMNode::ConstChildrenListType models;
  data->GetChildren(model_tag, models);
  
  if (models.size() == 0)
  {
    return false;
  }
  
  // Search the list of variables for one with the correct name
  for (unsigned int i = 0; i < models.size(); i++)
    {
      if (models[i]->HasAttribute(name_tag))
        {
          if (models[i]->GetAttribute(name_tag) == name)
            {
              return true;
            }
        }
    }
  return false;
}

bool itk::PSMProject::HasOptimizationAttribute	(	const std::string &	name,
		unsigned int	i = 0
	)		const

Returns true if the optimization_tag element includes the given parameter at the given scale (optional). Also returns false if no optimization_tag exists.

Definition at line 265 of file itkPSMProject.cxx.

{
  DOMNode *opt = m_DOMNode->GetChild(optimization_tag);
  if (opt != 0) // found the optimization element
    {
      unsigned int nscales = 1;
      
      // Are there scale elements?
      if (opt->HasAttribute(number_of_scales_tag))
        {
          nscales = static_cast<unsigned int>(atoi(opt->GetAttribute(number_of_scales_tag).c_str()));
          // If the number_of_scales_tag is the one being checked
          if(name == number_of_scales_tag) { return true; }
        }
      
      // Did the user ask for a scale that isn't specified?
      if (s+1 > nscales)  { return false; }
      
      // If only one scale, then look in element attributes for name
      if (nscales == 1) 
        {
          if (opt->HasAttribute(name)) { return true; }
        }
      
      // Finally, look for a scale element with name i
      DOMNode::ChildrenListType children;
      opt->GetAllChildren(children);

      for (unsigned i = 0; i < children.size(); i++)
        {
          if ( children[i]->GetName() == scale_tag 
               && 
               static_cast<unsigned int>(atoi(children[i]->GetAttribute(scale_number_tag).c_str())) == s )
            {
              if (children[i]->HasAttribute(name)) { return true; }
              else { return false; }
            }
        }
    }
  return false;
}

bool itk::PSMProject::HasProcrustes

(

)

const

Returns true if the project has a procrustes tag

Definition at line 360 of file itkPSMProject.cxx.

{
  DOMNode *proc = m_DOMNode->GetChild(procrustes_tag);
  if (proc != 0) // Found the procrustes element
  {
    if (proc->HasAttribute("value"))
    {
      if (atoi(proc->GetAttribute("value").c_str()) == 0)
        return false;
      else
        return true;
    }
  }
  return false;
}

bool itk::PSMProject::HasVariables

(

const std::string &

name

)

const

Returns true if the project has a variables_tag with the specified name.

Definition at line 376 of file itkPSMProject.cxx.

{
  const PSMDOMNode *data = this->GetDataNode();

  // Search the data tree for nodes called variables_tag
  DOMNode::ConstChildrenListType variables;
  data->GetChildren(variables_tag, variables);
  
  if (variables.size() == 0)
    {
      return false;
    }
  
  // Search the list of variables for one with the correct name
  for (unsigned int i = 0; i < variables.size(); i++)
    {
     if (variables[i]->HasAttribute(name_tag))
       {
         if (variables[i]->GetAttribute(name_tag) == name)
           {
             return true;
             //   return ((dynamic_cast<const PSMDOMNode *>(variables[i]))->GetText());
           }
       }
   }
  // itkExceptionMacro( "PSM Project file does not have any " + model_tag + " entries with name = " << name );
  return false;
}

itk::PSMProject::itkNewMacro

(

Self

)

Method for creation through the object factory.

itk::PSMProject::itkTypeMacro	(	PSMProject	,
		Object
	)

Run-time type information (and related methods).

void itk::PSMProject::SetDOMNode

(

PSMDOMNode *

p

)

Set the DOM node object, which contains the XML tree of parameter data. This method will throw an exception if the DOMNode is not a valid PSMProject file.

Definition at line 42 of file itkPSMProject.cxx.

{
  if (dom->GetName() == psm_project_tag)
    { 
      m_DOMNode = dom;
    }
  else
    {
      itkExceptionMacro( "DOM object does not appear to contain a valid PSM Project file." );
    }
}

void itk::PSMProject::Stream

(

std::ostream &

os

)

Stream the XML content of this project to a standard ostream. Note that this method cannot be made const because the necessary accessor methods in itkDOMNode are not defined as const. This method, however, does not modify the content of the PSMProject.

Definition at line 540 of file itkPSMProject.cxx.

{
  Indent indent;

  this->StreamChildren(m_DOMNode,os,indent);
}

void itk::PSMProject::StreamChildren ( PSMDOMNode *  node, std::ostream &  os, Indent  indent  )

protected

Helper function for Stream. Like Stream, this method cannot be const due to nonconst accessor methods in itkDOMNode.

Definition at line 547 of file itkPSMProject.cxx.

{
  // Print this node's name and attributes
  os << indent << "<" << node->GetName();  
  
  DOMNode::AttributesListType attr;
  node->GetAllAttributes(attr);
  
  for (DOMNode::AttributesListType::const_iterator it = attr.begin(); 
       it != attr.end(); it++)
    {
      os << " " << it->first << " = \"" << it->second << "\"";
    }
  
  
  os << ">" << std::endl;
  
  // Now print this node's text, line by line.
  for (unsigned int i = 0; i < node->GetText().size(); i++)
    {
      os << indent.GetNextIndent() << node->GetText()[i] << std::endl;
    }

  DOMNode::ChildrenListType children;
  node->GetAllChildren(children);

  // Now print all of this node's children.
  for (unsigned i = 0; i < children.size(); i++)
    {
      this->StreamChildren(static_cast<PSMDOMNode *>(children[i]),
                           os,indent.GetNextIndent());
    }

  // Print the closing tag for this node.
  os << indent << "<\\" << node->GetName() << ">" << std::endl;
}

Member Data Documentation

const std::string itk::PSMProject::data_tag = "data"

static

Reserved keywords for use in XML parameter files.

Definition at line 63 of file itkPSMProject.h.

---

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

• C:/Users/Brig/Documents/ShapeWorksStudio/src/ParticleShapeworks/include/itkPSMProject.h
• C:/Users/Brig/Documents/ShapeWorksStudio/src/ParticleShapeworks/src/itkPSMProject.cxx