aGrUM  0.20.3
a C++ library for (probabilistic) graphical models
Public Member Functions | List of all members
gum::O3prmBNReader< GUM_SCALAR > Class Template Reference

Read an O3PRM and transform the gum::prm::PRMSystem into gum::BayesNet. More...

#include <agrum/PRM/o3prm/O3prmBNReader.h>

+ Inheritance diagram for gum::O3prmBNReader< GUM_SCALAR >:
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Public Member Functions

 O3prmBNReader (BayesNet< GUM_SCALAR > *bn, const std::string &filename, const std::string &entityName="", const std::string &classPath="")
 
 ~O3prmBNReader ()
 
Size proceed ()
 parse the file More...
 
Size errors ()
 publishing Errors API More...
 
Size warnings ()
 

of errors

More...
 
Idx errLine (Idx i)
 publishing Errors API More...
 
Idx errCol (Idx i)
 col of ith error or warning More...
 
bool errIsError (Idx i)
 type of ith error or warning More...
 
std::string errMsg (Idx i)
 message of ith error or warning More...
 
void showElegantErrors (std::ostream &o=std::cerr)
 send on std::cerr the list of errors More...
 
void showElegantErrorsAndWarnings (std::ostream &o=std::cerr)
 send on std::cerr the list of errors or warnings More...
 
void showErrorCounts (std::ostream &o=std::cerr)
 send on std::cerr the number of errors and the number of warnings More...
 

Detailed Description

template<typename GUM_SCALAR>
class gum::O3prmBNReader< GUM_SCALAR >

Read an O3PRM and transform the gum::prm::PRMSystem into gum::BayesNet.

Template Parameters
GUM_SCALARThe scalar type used both for the gum::prm::PRM and the gum::BayesNet.

Definition at line 56 of file O3prmBNReader.h.

Constructor & Destructor Documentation

◆ O3prmBNReader()

template<typename GUM_SCALAR >
gum::O3prmBNReader< GUM_SCALAR >::O3prmBNReader ( BayesNet< GUM_SCALAR > *  bn,
const std::string &  filename,
const std::string &  entityName = "",
const std::string &  classPath = "" 
)

Definition at line 61 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

64  :
65  BNReader< GUM_SCALAR >(bn, filename) {
66  GUM_CONSTRUCTOR(O3prmBNReader);
67  _bn_ = bn;
68  _filename_ = filename;
69  _entityName_ = entityName == "" ? _getEntityName_(filename) : entityName;
70  _classpath_ = classpath;
71  }
gum::O3prmBNReader::_filename_
std::string _filename_
Definition: O3prmBNReader.h:99
gum::O3prmBNReader::O3prmBNReader
O3prmBNReader(BayesNet< GUM_SCALAR > *bn, const std::string &filename, const std::string &entityName="", const std::string &classPath="")
Definition: O3prmBNReader_tpl.h:61
gum::O3prmBNReader::_getEntityName_
static std::string _getEntityName_(const std::string &filename)
Definition: O3prmBNReader_tpl.h:53
gum::O3prmBNReader::_entityName_
std::string _entityName_
Definition: O3prmBNReader.h:102
gum::O3prmBNReader::_bn_
BayesNet< GUM_SCALAR > * _bn_
Definition: O3prmBNReader.h:104
gum::O3prmBNReader::_classpath_
std::string _classpath_
Definition: O3prmBNReader.h:101
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◆ ~O3prmBNReader()

template<typename GUM_SCALAR >
gum::O3prmBNReader< GUM_SCALAR >::~O3prmBNReader ( )

Definition at line 74 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

74  {
75  GUM_DESTRUCTOR(O3prmBNReader);
76  }
gum::O3prmBNReader::O3prmBNReader
O3prmBNReader(BayesNet< GUM_SCALAR > *bn, const std::string &filename, const std::string &entityName="", const std::string &classPath="")
Definition: O3prmBNReader_tpl.h:61
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Member Function Documentation

◆ _generateBN_()

template<typename GUM_SCALAR >
void gum::O3prmBNReader< GUM_SCALAR >::_generateBN_ ( prm::PRMSystem< GUM_SCALAR > &  system)
private

Definition at line 173 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

173  {
174  system.instantiate();
175  BayesNetFactory< GUM_SCALAR > factory(_bn_);
176  system.groundedBN(factory);
177  _bn_->setProperty("name", _entityName_);
178  }
gum::O3prmBNReader::_entityName_
std::string _entityName_
Definition: O3prmBNReader.h:102
gum::O3prmBNReader::_bn_
BayesNet< GUM_SCALAR > * _bn_
Definition: O3prmBNReader.h:104
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◆ _getEntityName_()

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::_getEntityName_ ( const std::string &  filename)
staticprivate

Definition at line 53 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

53  {
54  auto b = filename.find_last_of("/\\");
55  auto e = filename.find_last_of(".") - 1;
56  GUM_ASSERT(e > b); // we are waiting ../../basename.o3prm
57  return filename.substr(b + 1, e - b);
58  }
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◆ _getInstanceName_()

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::_getInstanceName_ ( const std::string &  classname)
staticprivate

Definition at line 46 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

46  {
47  auto res = classname.substr(0, 4);
48  std::transform(res.begin(), res.end(), res.begin(), ::tolower);
49  return res;
50  }
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◆ _getVariableName_()

template<typename GUM_SCALAR >
INLINE std::string gum::O3prmBNReader< GUM_SCALAR >::_getVariableName_ ( const std::string &  path,
const std::string &  type,
const std::string &  name,
const std::string &  toRemove = "" 
)
staticprivate

Definition at line 34 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

37  {
38  auto res = path + name; // path ends up with a "."
39  if (toRemove != "") {
40  if (res.substr(0, toRemove.size()) == toRemove) { res = res.substr(toRemove.size()); }
41  }
42  return res;
43  }
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◆ errCol()

template<typename GUM_SCALAR >
Idx gum::O3prmBNReader< GUM_SCALAR >::errCol ( Idx  i)
inline

col of ith error or warning

Definition at line 80 of file O3prmBNReader.h.

80 { return _errors_.error(i).column; }
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::ErrorsContainer::error
ParseError error(Idx i) const
Returns the i-th error.
gum::ParseError::column
Idx column
The column of this gum::ParseError, default is 0.
Definition: errorsContainer.h:126

◆ errIsError()

template<typename GUM_SCALAR >
bool gum::O3prmBNReader< GUM_SCALAR >::errIsError ( Idx  i)
inline

type of ith error or warning

Definition at line 82 of file O3prmBNReader.h.

82 { return _errors_.error(i).is_error; }
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::ParseError::is_error
bool is_error
If false, this gum::ParseError is a warning.
Definition: errorsContainer.h:120
gum::ErrorsContainer::error
ParseError error(Idx i) const
Returns the i-th error.

◆ errLine()

template<typename GUM_SCALAR >
Idx gum::O3prmBNReader< GUM_SCALAR >::errLine ( Idx  i)
inline

publishing Errors API

of errors

Definition at line 78 of file O3prmBNReader.h.

78 { return _errors_.error(i).line; }
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::ParseError::line
Idx line
The line of this gum::ParseError.
Definition: errorsContainer.h:123
gum::ErrorsContainer::error
ParseError error(Idx i) const
Returns the i-th error.

◆ errMsg()

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::errMsg ( Idx  i)
inline

message of ith error or warning

Definition at line 84 of file O3prmBNReader.h.

84 { return _errors_.error(i).msg; }
gum::ParseError::msg
std::string msg
The gum::ParseError message.
Definition: errorsContainer.h:129
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::ErrorsContainer::error
ParseError error(Idx i) const
Returns the i-th error.

◆ errors()

template<typename GUM_SCALAR >
Size gum::O3prmBNReader< GUM_SCALAR >::errors ( )
inline

publishing Errors API

of errors

Definition at line 74 of file O3prmBNReader.h.

74 { return _errors_.error_count; }
gum::ErrorsContainer::error_count
Size error_count
Number of errors detected.
Definition: errorsContainer.h:166
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105

◆ proceed()

template<typename GUM_SCALAR >
Size gum::O3prmBNReader< GUM_SCALAR >::proceed ( )
virtual

parse the file

parse.

Returns
the number of detected errors and warnings
Exceptions
IOErrorif file not exists
Returns
the number of detected errors
Exceptions
IOErrorif file not exists

Implements gum::BNReader< GUM_SCALAR >.

Definition at line 82 of file O3prmBNReader_tpl.h.

References gum::Set< Key, Alloc >::emplace().

82  {
83  prm::o3prm::O3prmReader< GUM_SCALAR > reader;
84  if (_classpath_ != "") { reader.addClassPath(_classpath_); }
85  reader.readFile(_filename_);
86  gum::prm::PRM< GUM_SCALAR >* prm = reader.prm();
87  _errors_ = reader.errorsContainer();
88 
89 
90  if (errors() == 0) {
91  std::string instanceName = "";
92  if (prm->isSystem(_entityName_)) {
93  _generateBN_(prm->getSystem(_entityName_));
94  } else if (prm->isClass(_entityName_)) {
95  ParseError warn(false,
96  "No system '" + _entityName_
97  + "' found but class found. Generating unnamed instance.",
98  _filename_,
99  0);
100  _errors_.add(warn);
101  gum::prm::PRMSystem< GUM_SCALAR > s("S_" + _entityName_);
102  instanceName = _getInstanceName_(_entityName_);
103  auto i = new gum::prm::PRMInstance< GUM_SCALAR >(instanceName, prm->getClass(_entityName_));
104  s.add(i);
105  _generateBN_(s);
106  instanceName += "."; // to be removed in _getVariableName_
107  } else if (prm->classes().size() == 1) {
108  const std::string& entityName = (*prm->classes().begin())->name();
109  ParseError warn(false,
110  "Unique class '" + entityName + "' found. Generating unnamed instance.",
111  _filename_,
112  0);
113  _errors_.add(warn);
114 
115  gum::prm::PRMSystem< GUM_SCALAR > s("S_" + entityName);
116  instanceName = _getInstanceName_(entityName);
117  auto i = new gum::prm::PRMInstance< GUM_SCALAR >(instanceName, prm->getClass(entityName));
118  s.add(i);
119  _generateBN_(s);
120 
121  // force the name of the BN to be the name of the class instead of the name
122  // of the file
123  _bn_->setProperty("name", entityName);
124  instanceName += "."; // to be removed in _getVariableName_
125  } else {
126  ParseError err(true,
127  "Neither system nor class '" + _entityName_ + "' and more than one class.",
128  _filename_,
129  0);
130  _errors_.add(err);
131  }
132 
133  // renaming variables in th BN
134  gum::Set< std::string > names;
135  for (auto node: _bn_->nodes()) {
136  // keeping the complete name in description
137  const std::string& nn = _bn_->variable(node).name();
138  _bn_->variable(node).setDescription(nn);
139 
140  // trying to simplify the
141  auto start = nn.find_first_of('(');
142  auto end = nn.find_first_of(')');
143  if (0 < start && start < end && end < nn.size()) {
144  auto path = nn.substr(0, start);
145  auto type = nn.substr(start + 1, end - start - 1);
146  auto name = nn.substr(end + 1, std::string::npos);
147 
148  std::string newNameRadical = _getVariableName_(path, type, name, instanceName);
149 
150  std::string newName = newNameRadical;
151  // forcing newName to be unique
152  int num = 0;
153  while (names.contains(newName)) {
154  newName = newNameRadical + std::to_string(++num);
155  }
156 
157  names.insert(newName);
158  _bn_->changeVariableName(node, newName);
159  } else {
160  ParseError warn(false, "Name " + nn + " cannot be simplified.", _filename_, 0);
161  _errors_.add(warn);
162  }
163  }
164  }
165 
166  delete prm;
167 
168  return errors();
169  }
gum::O3prmBNReader::_generateBN_
void _generateBN_(prm::PRMSystem< GUM_SCALAR > &system)
Definition: O3prmBNReader_tpl.h:173
gum::Set::contains
bool contains(const Key &k) const
Indicates whether a given elements belong to the set.
Definition: set_tpl.h:558
gum::O3prmBNReader::_filename_
std::string _filename_
Definition: O3prmBNReader.h:99
gum::prm::PRM::isClass
bool isClass(const std::string &name) const
Definition: PRM_tpl.h:78
gum::prm::PRMInstance::add
void add(NodeId id, PRMInstance< GUM_SCALAR > &instance)
Add an PRMInstance<GUM_SCALAR> to a given PRMReferenceSlot, PRMSlotChain<GUM_SCALAR> or output node...
Definition: PRMInstance_tpl.h:153
gum::O3prmBNReader::_getVariableName_
static std::string _getVariableName_(const std::string &path, const std::string &type, const std::string &name, const std::string &toRemove="")
Definition: O3prmBNReader_tpl.h:34
gum::prm::PRMInstance
An PRMInstance is a Bayesian network fragment defined by a Class and used in a PRMSystem.
Definition: PRMInstance.h:62
gum::prm::PRM::classes
const Set< PRMClass< GUM_SCALAR > *> & classes() const
Returns the Set of all Class<GUM_SCALAR> in this PRM.
Definition: PRM_tpl.h:119
gum::ErrorsContainer::add
void add(ParseError error)
Add an error object to the container.
Definition: errorsContainer_inl.h:50
gum::O3prmBNReader::_getInstanceName_
static std::string _getInstanceName_(const std::string &classname)
Definition: O3prmBNReader_tpl.h:46
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::to_string
std::string to_string(const Formula &f)
Definition: formula_inl.h:474
gum::prm::PRM::isSystem
bool isSystem(const std::string &name) const
Definition: PRM_tpl.h:88
gum::prm::PRM::getSystem
PRMSystem< GUM_SCALAR > & getSystem(const std::string &name)
Returns a constant reference on a PRMSystem<GUM_SCALAR> given it&#39;s name.
Definition: PRM_tpl.h:140
gum::O3prmBNReader::_entityName_
std::string _entityName_
Definition: O3prmBNReader.h:102
gum::prm::PRMSystem
A PRMSystem is a container of PRMInstance and describe a relational skeleton.
Definition: PRMObject.h:234
gum::prm::PRM
This class represents a Probabilistic Relational PRMSystem<GUM_SCALAR>.
Definition: PRM.h:65
gum::O3prmBNReader::_bn_
BayesNet< GUM_SCALAR > * _bn_
Definition: O3prmBNReader.h:104
gum::prm::PRM::getClass
PRMClass< GUM_SCALAR > & getClass(const std::string &name)
Returns a constant reference on a Class<GUM_SCALAR> given it&#39;s name.
Definition: PRM_tpl.h:108
gum::O3prmBNReader::errors
Size errors()
publishing Errors API
Definition: O3prmBNReader.h:74
gum::O3prmBNReader::_classpath_
std::string _classpath_
Definition: O3prmBNReader.h:101
gum::Set::insert
void insert(const Key &k)
Inserts a new element into the set.
Definition: set_tpl.h:606
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◆ showElegantErrors()

template<typename GUM_SCALAR >
void gum::O3prmBNReader< GUM_SCALAR >::showElegantErrors ( std::ostream &  o = std::cerr)
inline

send on std::cerr the list of errors

Definition at line 87 of file O3prmBNReader.h.

87 { _errors_.elegantErrors(o); }
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105
gum::ErrorsContainer::elegantErrors
void elegantErrors(std::ostream &o) const
Print errors on output stream.

◆ showElegantErrorsAndWarnings()

template<typename GUM_SCALAR >
void gum::O3prmBNReader< GUM_SCALAR >::showElegantErrorsAndWarnings ( std::ostream &  o = std::cerr)
inline

send on std::cerr the list of errors or warnings

Definition at line 90 of file O3prmBNReader.h.

90  {
91  _errors_.elegantErrorsAndWarnings(o);
92  }
gum::ErrorsContainer::elegantErrorsAndWarnings
void elegantErrorsAndWarnings(std::ostream &o) const
Print errors on output stream.
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105

◆ showErrorCounts()

template<typename GUM_SCALAR >
void gum::O3prmBNReader< GUM_SCALAR >::showErrorCounts ( std::ostream &  o = std::cerr)
inline

send on std::cerr the number of errors and the number of warnings

Definition at line 95 of file O3prmBNReader.h.

95 { _errors_.syntheticResults(o); }
gum::ErrorsContainer::syntheticResults
void syntheticResults(std::ostream &o) const
Print errors on output stream.
Definition: errorsContainer_inl.h:84
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105

◆ warnings()

template<typename GUM_SCALAR >
Size gum::O3prmBNReader< GUM_SCALAR >::warnings ( )
inline

of errors

Definition at line 76 of file O3prmBNReader.h.

76 { return _errors_.warning_count; }
gum::O3prmBNReader::_errors_
ErrorsContainer _errors_
Definition: O3prmBNReader.h:105

Member Data Documentation

◆ _bn_

template<typename GUM_SCALAR >
BayesNet< GUM_SCALAR >* gum::O3prmBNReader< GUM_SCALAR >::_bn_
private

Definition at line 104 of file O3prmBNReader.h.

◆ _classpath_

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::_classpath_
private

Definition at line 101 of file O3prmBNReader.h.

◆ _entityName_

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::_entityName_
private

Definition at line 102 of file O3prmBNReader.h.

◆ _errors_

template<typename GUM_SCALAR >
ErrorsContainer gum::O3prmBNReader< GUM_SCALAR >::_errors_
private

Definition at line 105 of file O3prmBNReader.h.

◆ _filename_

template<typename GUM_SCALAR >
std::string gum::O3prmBNReader< GUM_SCALAR >::_filename_
private

Definition at line 99 of file O3prmBNReader.h.

The documentation for this class was generated from the following files:
aGrUM 0.20.3
Mon Jun 7 2021 17:34:54
© PHW&CG&others - 2021
DoXyGeN 1.8.13