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Removed duplicated code in DeterministicSparseTransitionParser while still keeping it readable and the interface intact. 

Next up: Refactor the Nondeterministic*Parser.


Former-commit-id: 108eea60a0
main
masawei 12 years ago
parent
4245b3c4e3
commit
8adee3629b
5 changed files with 166 additions and 202 deletions
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  1. 325
      src/parser/DeterministicSparseTransitionParser.cpp
  2. 36
      src/parser/DeterministicSparseTransitionParser.h
  3. 3
      src/parser/MarkovAutomatonParser.cpp
  4. 2
      src/parser/MarkovAutomatonParser.h
  5. 2
      src/parser/MarkovAutomatonSparseTransitionParser.h

325
src/parser/DeterministicSparseTransitionParser.cpp
View File

@ -28,19 +28,18 @@ namespace storm {
namespace parser {
/*!
* @brief Perform first pass through the file and obtain number of
* non-zero cells and maximum node id.
*
* This method does the first pass through the .tra file and computes
* the number of non-zero elements.
* It also calculates the maximum node id and stores it in maxnode.
*
* @return The number of non-zero elements
* @param buf Data to scan. Is expected to be some char array.
* @param maxnode Is set to highest id of all nodes.
*/
storm::storage::SparseMatrix<double> DeterministicSparseTransitionParser::parseDeterministicTransitions(std::string const& filename, bool insertDiagonalEntriesIfMissing) {
return DeterministicSparseTransitionParser::parse(filename, false, insertDiagonalEntriesIfMissing);
}
storm::storage::SparseMatrix<double> DeterministicSparseTransitionParser::parseDeterministicTransitionRewards(std::string const& filename, RewardMatrixInformationStruct const& rewardMatrixInformation) {
return DeterministicSparseTransitionParser::parse(filename, true, false, rewardMatrixInformation);
}
DeterministicSparseTransitionParser::FirstPassResult DeterministicSparseTransitionParser::firstPass(char* buf, SupportedLineEndingsEnum lineEndings, bool insertDiagonalEntriesIfMissing) {
DeterministicSparseTransitionParser::FirstPassResult result;
// Skip the format hint if it is there.
@ -107,220 +106,156 @@ DeterministicSparseTransitionParser::FirstPassResult DeterministicSparseTransiti
return result;
}
/*!
* Reads a .tra file and produces a sparse matrix representing the described Markov Chain.
*
* Matrices created with this method have to be freed with the delete operator.
* @param filename input .tra file's name.
* @return a pointer to the created sparse matrix.
*/
storm::storage::SparseMatrix<double> DeterministicSparseTransitionParser::parseDeterministicTransitions(std::string const& filename, bool insertDiagonalEntriesIfMissing) {
storm::storage::SparseMatrix<double> DeterministicSparseTransitionParser::parse(std::string const& filename, bool rewardFile, bool insertDiagonalEntriesIfMissing, RewardMatrixInformationStruct const& rewardMatrixInformation) {
// Enforce locale where decimal point is '.'.
setlocale(LC_NUMERIC, "C");
if (!fileExistsAndIsReadable(filename.c_str())) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": File does not exist or is not readable.");
throw storm::exceptions::FileIoException() << "The supplied Transition input file \"" << filename << "\" does not exist or is not readable by this process.";
}
setlocale(LC_NUMERIC, "C");
// Find out about the used line endings.
SupportedLineEndingsEnum lineEndings = findUsedLineEndings(filename, true);
// Open file.
MappedFile file(filename.c_str());
char* buf = file.data;
// Perform first pass, i.e. count entries that are not zero.
DeterministicSparseTransitionParser::FirstPassResult firstPass = DeterministicSparseTransitionParser::firstPass(file.data, lineEndings, insertDiagonalEntriesIfMissing);
LOG4CPLUS_INFO(logger, "First pass on " << filename << " shows " << firstPass.numberOfNonzeroEntries << " NonZeros.");
// If first pass returned zero, the file format was wrong.
if (firstPass.numberOfNonzeroEntries == 0) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": empty or erroneous file format.");
throw storm::exceptions::WrongFormatException();
}
// Perform second pass.
// Skip the format hint if it is there.
buf = trimWhitespaces(buf);
if(buf[0] != '0') {
buf = storm::parser::forwardToNextLine(buf, lineEndings);
}
if (!fileExistsAndIsReadable(filename.c_str())) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": File does not exist or is not readable.");
throw storm::exceptions::FileIoException() << "The supplied Transition input file \"" << filename << "\" does not exist or is not readable by this process.";
}
// Creating matrix builder here.
// The number of non-zero elements is computed by firstPass().
// The contents are inserted during the readout of the file, below.
// The actual matrix will be build once all contents are inserted.
storm::storage::SparseMatrixBuilder<double> resultMatrix(firstPass.highestStateIndex + 1, firstPass.highestStateIndex + 1, firstPass.numberOfNonzeroEntries);
// Find out about the used line endings.
SupportedLineEndingsEnum lineEndings = findUsedLineEndings(filename, true);
uint_fast64_t row, col, lastRow = 0;
double val;
bool fixDeadlocks = storm::settings::Settings::getInstance()->isSet("fixDeadlocks");
bool hadDeadlocks = false;
bool rowHadDiagonalEntry = false;
// Open file.
MappedFile file(filename.c_str());
char* buf = file.data;
// Perform first pass, i.e. count entries that are not zero.
// Read all transitions from file. Note that we assume that the
// transitions are listed in canonical order, otherwise this will not
// work, i.e. the values in the matrix will be at wrong places.
while (buf[0] != '\0') {
DeterministicSparseTransitionParser::FirstPassResult firstPass = DeterministicSparseTransitionParser::firstPass(file.data, lineEndings, insertDiagonalEntriesIfMissing);
// Read next transition.
row = checked_strtol(buf, &buf);
col = checked_strtol(buf, &buf);
val = checked_strtod(buf, &buf);
LOG4CPLUS_INFO(logger, "First pass on " << filename << " shows " << firstPass.numberOfNonzeroEntries << " NonZeros.");
// Read probability of this transition.
// Check, if the value is a probability, i.e. if it is between 0 and 1.
if ((val < 0.0) || (val > 1.0)) {
LOG4CPLUS_ERROR(logger, "Expected a positive probability but got \"" << val << "\".");
// If first pass returned zero, the file format was wrong.
if (firstPass.numberOfNonzeroEntries == 0) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": empty or erroneous file format.");
throw storm::exceptions::WrongFormatException();
}
// Test if we moved to a new row.
// Handle all incomplete or skipped rows.
if (lastRow != row) {
if (!rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(lastRow, lastRow, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << lastRow << " has no transition to itself. Inserted a 0-transition. (1)");
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << lastRow << " has no transition to itself.");
}
// No increment for lastRow.
rowHadDiagonalEntry = true;
}
for (uint_fast64_t skippedRow = lastRow + 1; skippedRow < row; ++skippedRow) {
hadDeadlocks = true;
if (fixDeadlocks) {
resultMatrix.addNextValue(skippedRow, skippedRow, storm::utility::constantOne<double>());
rowHadDiagonalEntry = true;
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << skippedRow << " has no outgoing transitions. A self-loop was inserted.");
} else {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": state " << skippedRow << " has no outgoing transitions.");
// Before throwing the appropriate exception we will give notice of all deadlock states.
}
}
lastRow = row;
rowHadDiagonalEntry = false;
}
// Perform second pass.
if (col == row) {
rowHadDiagonalEntry = true;
// Skip the format hint if it is there.
buf = trimWhitespaces(buf);
if(buf[0] != '0') {
buf = storm::parser::forwardToNextLine(buf, lineEndings);
}
if (col > row && !rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(row, row, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << row << " has no transition to itself. Inserted a 0-transition. (2)");
if(rewardFile) {
// The reward matrix should match the size of the transition matrix.
if (firstPass.highestStateIndex + 1 > rewardMatrixInformation.rowCount || firstPass.highestStateIndex + 1 > rewardMatrixInformation.columnCount) {
LOG4CPLUS_ERROR(logger, "Reward matrix has more rows or columns than transition matrix.");
throw storm::exceptions::WrongFormatException() << "Reward matrix has more rows or columns than transition matrix.";
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << row << " has no transition to itself.");
// If we found the right number of states or less, we set it to the number of states represented by the transition matrix.
firstPass.highestStateIndex = rewardMatrixInformation.rowCount - 1;
}
rowHadDiagonalEntry = true;
}
resultMatrix.addNextValue(row, col, val);
buf = trimWhitespaces(buf);
}
if (!rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(lastRow, lastRow, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << lastRow << " has no transition to itself. Inserted a 0-transition. (3)");
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << lastRow << " has no transition to itself.");
}
}
// If we encountered deadlock and did not fix them, now is the time to throw the exception.
if (!fixDeadlocks && hadDeadlocks) throw storm::exceptions::WrongFormatException() << "Some of the nodes had deadlocks. You can use --fixDeadlocks to insert self-loops on the fly.";
return resultMatrix.build();
}
/*!
* Reads a .tra file and produces a sparse matrix representing the described Markov Chain.
*
* Matrices created with this method have to be freed with the delete operator.
* @param filename input .tra file's name.
* @return a pointer to the created sparse matrix.
*/
storm::storage::SparseMatrix<double> DeterministicSparseTransitionParser::parseDeterministicTransitionRewards(std::string const& filename, RewardMatrixInformationStruct const& rewardMatrixInformation) {
// Enforce locale where decimal point is '.'.
setlocale(LC_NUMERIC, "C");
if (!fileExistsAndIsReadable(filename.c_str())) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": File does not exist or is not readable.");
throw storm::exceptions::FileIoException() << "The supplied Transition input file \"" << filename << "\" does not exist or is not readable by this process.";
}
// Creating matrix builder here.
// The actual matrix will be build once all contents are inserted.
storm::storage::SparseMatrixBuilder<double> resultMatrix(firstPass.highestStateIndex + 1, firstPass.highestStateIndex + 1, firstPass.numberOfNonzeroEntries);
// Find out about the used line endings.
SupportedLineEndingsEnum lineEndings = findUsedLineEndings(filename, true);
uint_fast64_t row, col, lastRow = 0;
double val;
bool fixDeadlocks = storm::settings::Settings::getInstance()->isSet("fixDeadlocks");
bool hadDeadlocks = false;
bool rowHadDiagonalEntry = false;
// Open file.
MappedFile file(filename.c_str());
char* buf = file.data;
// Perform first pass, i.e. count entries that are not zero.
// Read all transitions from file. Note that we assume that the
// transitions are listed in canonical order, otherwise this will not
// work, i.e. the values in the matrix will be at wrong places.
DeterministicSparseTransitionParser::FirstPassResult firstPass = DeterministicSparseTransitionParser::firstPass(file.data, lineEndings, false);
// Different parsing routines for transition systems and transition rewards.
if(rewardFile) {
while (buf[0] != '\0') {
LOG4CPLUS_INFO(logger, "First pass on " << filename << " shows " << firstPass.numberOfNonzeroEntries << " NonZeros.");
// If first pass returned zero, the file format was wrong.
if (firstPass.numberOfNonzeroEntries == 0) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": empty or erroneous file format.");
throw storm::exceptions::WrongFormatException();
}
// Perform second pass.
// Skip the format hint if it is there.
buf = trimWhitespaces(buf);
if(buf[0] != '0') {
buf = storm::parser::forwardToNextLine(buf, lineEndings);
}
// Read next transition.
row = checked_strtol(buf, &buf);
col = checked_strtol(buf, &buf);
val = checked_strtod(buf, &buf);
// The reward matrix should match the size of the transition matrix.
if (firstPass.highestStateIndex + 1 > rewardMatrixInformation.rowCount || firstPass.highestStateIndex + 1 > rewardMatrixInformation.columnCount) {
LOG4CPLUS_ERROR(logger, "Reward matrix has more rows or columns than transition matrix.");
throw storm::exceptions::WrongFormatException() << "Reward matrix has more rows or columns than transition matrix.";
} else {
// If we found the right number of states or less, we set it to the number of states represented by the transition matrix.
firstPass.highestStateIndex = rewardMatrixInformation.rowCount - 1;
}
resultMatrix.addNextValue(row, col, val);
buf = trimWhitespaces(buf);
}
} else {
while (buf[0] != '\0') {
// Read next transition.
row = checked_strtol(buf, &buf);
col = checked_strtol(buf, &buf);
val = checked_strtod(buf, &buf);
// Read probability of this transition.
// Check, if the value is a probability, i.e. if it is between 0 and 1.
if ((val < 0.0) || (val > 1.0)) {
LOG4CPLUS_ERROR(logger, "Expected a positive probability but got \"" << val << "\".");
throw storm::exceptions::WrongFormatException();
}
// Test if we moved to a new row.
// Handle all incomplete or skipped rows.
if (lastRow != row) {
if (!rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(lastRow, lastRow, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << lastRow << " has no transition to itself. Inserted a 0-transition. (1)");
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << lastRow << " has no transition to itself.");
}
// No increment for lastRow.
rowHadDiagonalEntry = true;
}
for (uint_fast64_t skippedRow = lastRow + 1; skippedRow < row; ++skippedRow) {
hadDeadlocks = true;
if (fixDeadlocks) {
resultMatrix.addNextValue(skippedRow, skippedRow, storm::utility::constantOne<double>());
rowHadDiagonalEntry = true;
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << skippedRow << " has no outgoing transitions. A self-loop was inserted.");
} else {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": state " << skippedRow << " has no outgoing transitions.");
// Before throwing the appropriate exception we will give notice of all deadlock states.
}
}
lastRow = row;
rowHadDiagonalEntry = false;
}
// Creating matrix builder here.
// The number of non-zero elements is computed by firstPass().
// The contents are inserted during the readout of the file, below.
// The actual matrix will be build once all contents are inserted.
storm::storage::SparseMatrixBuilder<double> resultMatrix(firstPass.highestStateIndex + 1, firstPass.highestStateIndex + 1, firstPass.numberOfNonzeroEntries);
if (col == row) {
rowHadDiagonalEntry = true;
}
uint_fast64_t row, col;
double val;
if (col > row && !rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(row, row, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << row << " has no transition to itself. Inserted a 0-transition. (2)");
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << row << " has no transition to itself.");
}
rowHadDiagonalEntry = true;
}
// Read all transitions from file. Note that we assume that the
// transitions are listed in canonical order, otherwise this will not
// work, i.e. the values in the matrix will be at wrong places.
while (buf[0] != '\0') {
resultMatrix.addNextValue(row, col, val);
buf = trimWhitespaces(buf);
}
// Read next transition.
row = checked_strtol(buf, &buf);
col = checked_strtol(buf, &buf);
val = checked_strtod(buf, &buf);
if (!rowHadDiagonalEntry) {
if (insertDiagonalEntriesIfMissing) {
resultMatrix.addNextValue(lastRow, lastRow, storm::utility::constantZero<double>());
LOG4CPLUS_DEBUG(logger, "While parsing " << filename << ": state " << lastRow << " has no transition to itself. Inserted a 0-transition. (3)");
} else {
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": state " << lastRow << " has no transition to itself.");
}
}
resultMatrix.addNextValue(row, col, val);
buf = trimWhitespaces(buf);
}
// If we encountered deadlock and did not fix them, now is the time to throw the exception.
if (!fixDeadlocks && hadDeadlocks) throw storm::exceptions::WrongFormatException() << "Some of the nodes had deadlocks. You can use --fixDeadlocks to insert self-loops on the fly.";
}
return resultMatrix.build();
// Finally, build the actual matrix and return it.
return resultMatrix.build();
}
} // namespace parser

36
src/parser/DeterministicSparseTransitionParser.h
View File

@ -27,21 +27,35 @@ public:
};
/*!
* @brief Load a deterministic transition system from file and create a
* sparse adjacency matrix whose entries represent the weights of the edges
* Load a deterministic transition system from file and create a
* sparse adjacency matrix whose entries represent the weights of the edges.
*
* @param filename The path of file to be parsed.
* @param insertDiagonalEntriesIfMissing A flag set iff entries on the primary diagonal of the matrix should be added in case they are missing in the parsed file.
* @return A SparseMatrix containing the parsed transition system.
*/
static storm::storage::SparseMatrix<double> parseDeterministicTransitions(std::string const& filename, bool insertDiagonalEntriesIfMissing = true);
/*!
* @brief Load the transition rewards for a deterministic transition system from file and create a
* sparse adjacency matrix whose entries represent the rewards of the respective transitions.
* Load the transition rewards for a deterministic transition system from file and create a
* sparse adjacency matrix whose entries represent the rewards of the respective transitions.
*/
/*!
* Load the transition rewards for a deterministic transition system from file and create a
* sparse adjacency matrix whose entries represent the rewards of the respective transitions.
*
* @param filename The path of file to be parsed.
* @param rewardMatrixInformation A struct containing information that is used to check if the transition reward matrix fits to the rest of the model.
* @return A SparseMatrix containing the parsed transition rewards.
*/
static storm::storage::SparseMatrix<double> parseDeterministicTransitionRewards(std::string const& filename, RewardMatrixInformationStruct const& rewardMatrixInformation);
private:
/*
* Performs the first pass on the input pointed to by the given buffer.
* Performs the first pass on the input pointed to by the given buffer to obtain the number of
* transitions and the maximum node id.
*
* @param buffer The buffer that cointains the input.
* @param lineEndings The line endings that are to be used while parsing.
@ -50,6 +64,18 @@ private:
*/
static FirstPassResult firstPass(char* buffer, SupportedLineEndingsEnum lineEndings, bool insertDiagonalEntriesIfMissing = true);
/*
* The main parsing routine.
* Opens the given file, calls the first pass and performs the second pass, parsing the content of the file into a SparseMatrix.
*
* @param filename The path of file to be parsed.
* @param rewardFile A flag set iff the file to be parsed contains transition rewards.
* @param insertDiagonalEntriesIfMissing A flag set iff entries on the primary diagonal of the matrix should be added in case they are missing in the parsed file.
* @param rewardMatrixInformation A struct containing information that is used to check if the transition reward matrix fits to the rest of the model.
* @return A SparseMatrix containing the parsed file contents.
*/
static storm::storage::SparseMatrix<double> parse(std::string const& filename, bool rewardFile, bool insertDiagonalEntriesIfMissing = false, RewardMatrixInformationStruct const& rewardMatrixInformation = nullptr);
};
} // namespace parser

3
src/parser/MarkovAutomatonParser.cpp
View File

@ -18,16 +18,19 @@ storm::models::MarkovAutomaton<double> MarkovAutomatonParser::parseMarkovAutomat
// Parse the state labeling.
storm::models::AtomicPropositionsLabeling resultLabeling(storm::parser::AtomicPropositionLabelingParser(transitionMatrix.getColumnCount(), labelingFilename));
// If given, parse the state rewards file.
boost::optional<std::vector<double>> stateRewards;
if (stateRewardFilename != "") {
stateRewards.reset(storm::parser::SparseStateRewardParser::parseSparseStateReward(transitionMatrix.getColumnCount(), stateRewardFilename));
}
// Since Markov Automata do not support transition rewards no path should be given here.
if (transitionRewardFilename != "") {
LOG4CPLUS_ERROR(logger, "Transition rewards are unsupported for Markov automata.");
throw storm::exceptions::WrongFormatException() << "Transition rewards are unsupported for Markov automata.";
}
// Put the pieces together to generate the Markov Automaton.
storm::models::MarkovAutomaton<double> resultingAutomaton(std::move(transitionMatrix), std::move(resultLabeling), std::move(transitionResult.nondeterministicChoiceIndices), std::move(transitionResult.markovianStates), std::move(transitionResult.exitRates), std::move(stateRewards), boost::optional<storm::storage::SparseMatrix<double>>(), boost::optional<std::vector<boost::container::flat_set<uint_fast64_t>>>());
return resultingAutomaton;

2
src/parser/MarkovAutomatonParser.h
View File

@ -20,7 +20,7 @@ public:
* @param transitionsFilename The name of the file containing the transitions of the Markov automaton.
* @param labelingFilename The name of the file containing the labels for the states of the Markov automaton.
* @param stateRewardFilename The name of the file that contains the state reward of the Markov automaton.
* @param transitionRewardFilename The name of the file that contains the transition rewards of the Markov automaton.
* @param transitionRewardFilename The name of the file that contains the transition rewards of the Markov automaton. This should be empty as transition rewards are not supported by Markov Automata.
*/
static storm::models::MarkovAutomaton<double> parseMarkovAutomaton(std::string const& transitionsFilename, std::string const& labelingFilename, std::string const& stateRewardFilename, std::string const& transitionRewardFilename);
};

2
src/parser/MarkovAutomatonSparseTransitionParser.h
View File

@ -30,7 +30,7 @@ public:
// The highest state index that appears in the model.
uint_fast64_t highestStateIndex;
// The total number of choices in the model.
// The total number of nondeterministic choices in the model.
uint_fast64_t numberOfChoices;
};

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