/*!
* TraParser.cpp
*
* Created on: 20.11.2012
* Author: Gereon Kremer
*/
#include "src/parser/NondeterministicSparseTransitionParser.h"
#include <errno.h>
#include <time.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <locale.h>
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <clocale>
#include <iostream>
#include <utility>
#include <string>
#include "src/utility/Settings.h"
#include "src/exceptions/FileIoException.h"
#include "src/exceptions/WrongFileFormatException.h"
#include "boost/integer/integer_mask.hpp"
#include "log4cplus/logger.h"
#include "log4cplus/loggingmacros.h"
extern log4cplus::Logger logger;
namespace storm {
namespace parser {
/*!
* @brief Perform first pass through the file and obtain overall number of
* choices, number of non-zero cells and maximum node id.
*
* This method does the first pass through the transition file.
*
* It computes the overall number of nondeterministic choices, i.e. the
* number of rows in the matrix that should be created.
* It also calculates the overall number of non-zero cells, i.e. the number
* of elements the matrix has to hold, and the maximum node id, i.e. the
* number of columns of the matrix.
*
* @param buf Data to scan. Is expected to be some char array.
* @param choices Overall number of choices.
* @param maxnode Is set to highest id of all nodes.
* @return The number of non-zero elements.
*/
uint_fast64_t NondeterministicSparseTransitionParser::firstPass(char* buf, uint_fast64_t& choices, int_fast64_t& maxnode, RewardMatrixInformationStruct* rewardMatrixInformation) {
bool isRewardFile = rewardMatrixInformation != nullptr;
/*
* Check file header and extract number of transitions.
*/
if (!isRewardFile) {
buf = strchr(buf, '\n') + 1; // skip format hint
}
/*
* Read all transitions.
*/
int_fast64_t source, target, choice, lastchoice = -1;
int_fast64_t lastsource = -1;
uint_fast64_t nonzero = 0;
double val;
choices = 0;
maxnode = 0;
while (buf[0] != '\0') {
/*
* Read source state and choice.
*/
source = checked_strtol(buf, &buf);
// Read the name of the nondeterministic choice.
choice = checked_strtol(buf, &buf);
// Check if we encountered a state index that is bigger than all previously seen.
if (source > maxnode) {
maxnode = source;
}
if (isRewardFile) {
// If we have switched the source state, we possibly need to insert the rows of the last
// last source state.
if (source != lastsource && lastsource != -1) {
choices += lastchoice - ((*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource] - 1);
}
// If we skipped some states, we need to reserve empty rows for all their nondeterministic
// choices.
for (int_fast64_t i = lastsource + 1; i < source; ++i) {
choices += ((*rewardMatrixInformation->nondeterministicChoiceIndices)[i + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[i]);
}
// If we advanced to the next state, but skipped some choices, we have to reserve rows
// for them
if (source != lastsource) {
choices += choice + 1;
} else if (choice != lastchoice) {
choices += choice - lastchoice;
}
} else {
// If we have skipped some states, we need to reserve the space for the self-loop insertion
// in the second pass.
if (source > lastsource + 1) {
nonzero += source - lastsource - 1;
choices += source - lastsource - 1;
} else if (source != lastsource || choice != lastchoice) {
// If we have switched the source state or the nondeterministic choice, we need to
// reserve one row more.
++choices;
}
}
// Read target and check if we encountered a state index that is bigger than all previously
// seen.
target = checked_strtol(buf, &buf);
if (target > maxnode) {
maxnode = target;
}
// Read value and check whether it's positive.
val = checked_strtod(buf, &buf);
if ((val < 0.0) || (val > 1.0)) {
LOG4CPLUS_ERROR(logger, "Expected a positive probability but got \"" << std::string(buf, 0, 16) << "\".");
return 0;
}
lastchoice = choice;
lastsource = source;
/*
* Increase number of non-zero values.
*/
nonzero++;
// The PRISM output format lists the name of the transition in the fourth column,
// but omits the fourth column if it is an internal action. In either case, however, the third column
// is followed by a space. We need to skip over that space first (instead of trimming whitespaces),
// before we can skip to the line end, because trimming the white spaces will proceed to the next line
// in case there is no action label in the fourth column.
if (buf[0] == ' ') {
++buf;
}
/*
* Proceed to beginning of next line.
*/
buf += strcspn(buf, " \t\n\r");
buf = trimWhitespaces(buf);
}
if (isRewardFile) {
// If not all rows were filled for the last state, we need to insert them.
choices += lastchoice - ((*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource] - 1);
// If we skipped some states, we need to reserve empty rows for all their nondeterministic
// choices.
for (uint_fast64_t i = lastsource + 1; i < rewardMatrixInformation->nondeterministicChoiceIndices->size() - 1; ++i) {
choices += ((*rewardMatrixInformation->nondeterministicChoiceIndices)[i + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[i]);
}
}
return nonzero;
}
/*!
* 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.
*/
NondeterministicSparseTransitionParser::NondeterministicSparseTransitionParser(std::string const &filename, RewardMatrixInformationStruct* rewardMatrixInformation)
: matrix(nullptr) {
/*
* Enforce locale where decimal point is '.'.
*/
setlocale(LC_NUMERIC, "C");
bool isRewardFile = rewardMatrixInformation != nullptr;
/*
* Open file.
*/
MappedFile file(filename.c_str());
char* buf = file.data;
/*
* Perform first pass, i.e. obtain number of columns, rows and non-zero elements.
*/
int_fast64_t maxnode;
uint_fast64_t choices;
uint_fast64_t nonzero = this->firstPass(file.data, choices, maxnode, rewardMatrixInformation);
/*
* If first pass returned zero, the file format was wrong.
*/
if (nonzero == 0) {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": erroneous file format.");
throw storm::exceptions::WrongFileFormatException();
}
/*
* Perform second pass.
*
* From here on, we already know that the file header is correct.
*/
/*
* Skip file header.
*/
if (!isRewardFile) {
buf = strchr(buf, '\n') + 1; // skip format hint
}
if (isRewardFile) {
if (choices > rewardMatrixInformation->rowCount || (uint_fast64_t)(maxnode + 1) > rewardMatrixInformation->columnCount) {
LOG4CPLUS_ERROR(logger, "Reward matrix size exceeds transition matrix size.");
throw storm::exceptions::WrongFileFormatException() << "Reward matrix size exceeds transition matrix size.";
} else if (choices != rewardMatrixInformation->rowCount) {
LOG4CPLUS_ERROR(logger, "Reward matrix row count does not match transition matrix row count.");
throw storm::exceptions::WrongFileFormatException() << "Reward matrix row count does not match transition matrix row count.";
} else {
maxnode = rewardMatrixInformation->columnCount - 1;
}
}
/*
* Create and initialize matrix.
* The matrix should have as many columns as we have nodes and as many rows as we have choices.
* Those two values, as well as the number of nonzero elements, was been calculated in the first run.
*/
LOG4CPLUS_INFO(logger, "Attempting to create matrix of size " << choices << " x " << (maxnode+1) << " with " << nonzero << " entries.");
this->matrix = std::shared_ptr<storm::storage::SparseMatrix<double>>(new storm::storage::SparseMatrix<double>(choices, maxnode + 1));
if (this->matrix == nullptr) {
LOG4CPLUS_ERROR(logger, "Could not create matrix of size " << choices << " x " << (maxnode+1) << ".");
throw std::bad_alloc();
}
this->matrix->initialize(nonzero);
/*
* Create row mapping.
*/
this->rowMapping = std::shared_ptr<std::vector<uint_fast64_t>>(new std::vector<uint_fast64_t>(maxnode+2,0));
/*
* Parse file content.
*/
int_fast64_t source, target, lastsource = -1, choice, lastchoice = -1;
uint_fast64_t curRow = -1;
double val;
bool fixDeadlocks = storm::settings::instance()->isSet("fix-deadlocks");
bool hadDeadlocks = false;
/*
* Read all transitions from file.
*/
while (buf[0] != '\0') {
/*
* Read source state and choice.
*/
source = checked_strtol(buf, &buf);
choice = checked_strtol(buf, &buf);
if (isRewardFile) {
// If we have switched the source state, we possibly need to insert the rows of the last
// last source state.
if (source != lastsource && lastsource != -1) {
curRow += lastchoice - ((*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[lastsource] - 1);
}
// If we skipped some states, we need to reserve empty rows for all their nondeterministic
// choices.
for (int_fast64_t i = lastsource + 1; i < source; ++i) {
curRow += ((*rewardMatrixInformation->nondeterministicChoiceIndices)[i + 1] - (*rewardMatrixInformation->nondeterministicChoiceIndices)[i]);
}
// If we advanced to the next state, but skipped some choices, we have to reserve rows
// for them
if (source != lastsource) {
curRow += choice + 1;
} else if (choice != lastchoice) {
curRow += choice - lastchoice;
}
} else {
// Increase line count if we have either finished reading the transitions of a certain state
// or we have finished reading one nondeterministic choice of a state.
if ((source != lastsource || choice != lastchoice)) {
++curRow;
}
/*
* Check if we have skipped any source node, i.e. if any node has no
* outgoing transitions. If so, insert a self-loop.
* Also add self-loops to rowMapping.
*/
for (int_fast64_t node = lastsource + 1; node < source; node++) {
hadDeadlocks = true;
if (fixDeadlocks) {
this->rowMapping->at(node) = curRow;
this->matrix->addNextValue(curRow, node, 1);
++curRow;
LOG4CPLUS_WARN(logger, "Warning while parsing " << filename << ": node " << node << " has no outgoing transitions. A self-loop was inserted.");
} else {
LOG4CPLUS_ERROR(logger, "Error while parsing " << filename << ": node " << node << " has no outgoing transitions.");
}
}
if (source != lastsource) {
/*
* Add this source to rowMapping, if this is the first choice we encounter for this state.
*/
this->rowMapping->at(source) = curRow;
}
}
// Read target and value and write it to the matrix.
target = checked_strtol(buf, &buf);
val = checked_strtod(buf, &buf);
this->matrix->addNextValue(curRow, target, val);
lastsource = source;
lastchoice = choice;
/*
* Proceed to beginning of next line in file and next row in matrix.
*/
if (buf[0] == ' ') {
++buf;
}
buf += strcspn(buf, " \t\n\r");
buf = trimWhitespaces(buf);
}
this->rowMapping->at(maxnode+1) = curRow + 1;
if (!fixDeadlocks && hadDeadlocks && !isRewardFile) throw storm::exceptions::WrongFileFormatException() << "Some of the nodes had deadlocks. You can use --fix-deadlocks to insert self-loops on the fly.";
/*
* Finalize matrix.
*/
this->matrix->finalize();
}
} // namespace parser
} // namespace storm