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// ***********************************************************************
//
// Tpetra: Templated Linear Algebra Services Package
// Copyright (2008) Sandia Corporation
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#ifndef __Teuchos_MatrixMarket_CoordDataReader_hpp
#define __Teuchos_MatrixMarket_CoordDataReader_hpp
#include "Teuchos_MatrixMarket_generic.hpp"
#include "Teuchos_RCP.hpp"
#include "Teuchos_ScalarTraits.hpp"
#include "Teuchos_Tuple.hpp"
namespace Teuchos {
namespace MatrixMarket {
/// \class CoordDataReaderBase
/// \brief Common functionality of a coordinate-format sparse
/// matrix or graph data reader.
///
/// This class provides common functionality for reading
/// coordinate-format sparse matrix or graph data from a Matrix
/// Market file. In particular, this class does not depend on the
/// type of matrix entries. If you are writing a function to read
/// a sparse matrix, use CoordDataReader. If you are writing a
/// function to read a sparse graph (a "pattern matrix" in Matrix
/// Market terms), use CoordPatternReader. If you just want to
/// read a sparse matrix into raw compressed sparse row (CSR)
/// arrays, use Raw::Reader. This class is mainly for Teuchos
/// developers.
///
/// \tparam Callback The type of a callback (a.k.a. closure) that
/// knows how to add entries to the sparse graph or matrix.
/// \param Ordinal The type of indices of the sparse graph or matrix.
///
/// Instances of Callback must implement an operator() that adds a
/// single entry to the sparse matrix. If the matrix contains
/// values (i.e., is not a "pattern" matrix), the Callback's
/// operator() takes three arguments: the row index, the column
/// index, and the value to add. If the matrix is a "pattern"
/// matrix, then the operator() takes two arguments: the row
/// index, and the column index. In either case, the Callback
/// expects one-based row and column indices, as specified by the
/// Matrix Market standard. The Raw::Adder class provides a model
/// for Callback with the three-argument version of operator().
///
/// The Callback object defines for itself what happens if one
/// attempts to insert two entries at the same location. They
/// must be "merged" in some way. Usually the right thing to do
/// is to add the values of the two entries, but you may want to
/// define different behavior. Your Callback implementation may
/// defer merging entries at the same location for performance
/// reasons. (Raw::Adder does this. Its merge() method merges
/// the entries.)
///
/// Note that this class does not have the notion of the type of
/// entries of the matrix, only the type of the indices in the
/// matrix (Ordinal). The CoordDataReader subclass defines the
/// type of matrix entries as its Scalar template parameter. The
/// CoordPatternReader subclass does not define the type of matrix
/// entries, because it stores a graph (a "pattern matrix" in
/// Matrix Market terms).
template<class Callback, class Ordinal>
class CoordDataReaderBase {
protected:
//! Closure that knows how to add entries to the sparse graph or matrix.
Teuchos::RCP<Callback> adder_;
public:
/// \brief Constructor with "adder" argument.
///
/// This is the favored way to construct an instance of this
/// type. Only use the no-argument constructor if you have a
/// "chicken-and-egg" problem, where in order to create the
/// Callback instance, you need the graph or matrix dimensions.
///
/// \param adder [in/out] Closure (a.k.a. callback) whose
/// operator() adds an entry to the sparse graph or matrix on
/// each invocation.
CoordDataReaderBase (const Teuchos::RCP<Callback>& adder) :
adder_ (adder) {}
/// \brief No-argument constructor.
///
/// We offer this option in case the adder's constructor needs
/// the graph or matrix dimensions, so that it's necessary to
/// call readDimensions() first before constructing the adder.
/// You should call setAdder() with a non-null argument before
/// calling read() or readLine().
CoordDataReaderBase () : adder_ (null) {}
//! Virtual destructor for safety and happy compilers.
virtual ~CoordDataReaderBase () {}
/// \brief Set the Adder object.
///
/// Please don't call this after calling read() or readLine().
/// The right time to call this is right after calling the
/// no-argument constructor, if it's not possible to supply an
/// Adder object before calling readDimensions().
void setAdder (const Teuchos::RCP<Callback>& adder) {
adder_ = adder;
}
protected:
/// \brief Read in the data from a single line of the input stream.
///
/// \param theLine [in] The line read in from the input stream.
/// \param adder [in/out] The callback to invoke for adding an
/// entry to the sparse matrix.
/// \param lineNumber [in] Current line number of the file.
/// We use this for generating informative exception messages.
/// \param tolerant [in] Whether to parse tolerantly.
///
/// \return In tolerant parsing mode (tolerant==true), then this
/// method returns true if parsing the current line succeeded,
/// else false. Otherwise, this method throws an exception
/// (and does not invoke the adder) if parsing the current
/// line did not succeed.
///
/// Subclasses must implement this method in order to read one
/// entry of the sparse graph or matrix. Implementations should
/// use the callback (\c adder_) to add the entry.
///
/// \note To implementers: We defer implementation of this
/// method to subclasses, because the callback for a graph
/// will take different arguments than the callback for a
/// matrix. Abstracting around that using templates isn't
/// worth the trouble. (Remember you're reading from a file
/// and parsing strings. Virtual method call overhead isn't
/// significant by comparison.)
virtual bool
readLine (const std::string& theLine,
const size_t lineNumber,
const bool tolerant) = 0;
public:
/// \brief Read in all the data from the given input stream.
///
/// \param in [in/out] The input stream from which to read
///
/// \param startingLineNumber [in] The line number of the file
/// from which we begin reading. (This is used for
/// informative error output, if an error is detected in the
/// file.)
///
/// \param tolerant [in] If true, parse tolerantly. The
/// resulting read-in data may be incorrect, but the parser
/// won't throw an exception if it can just let bad data
/// through and continue.
///
/// \param debug [in] If true, print verbose debugging output.
///
/// \return If tolerant==false, the returned pair is always true
/// and the empty vector. If tolerant==true, the first entry
/// of the pair is whether all lines of data were read
/// successfully, and the second entry is the list of line
/// numbers containing bad data. The first entry of the pair
/// is false if and only if the vector has nonzero size.
///
/// \note This method is virtual in case derived classes want to
/// override the default behavior. The specific example we
/// have in mind is a "pattern matrix" (i.e., a sparse graph),
/// which we would represent with Scalar=void.
virtual std::pair<bool, std::vector<size_t> >
read (std::istream& in,
const size_t startingLineNumber,
const bool tolerant,
const bool debug = false)
{
(void) debug; // silence unused input argument warning
TEUCHOS_TEST_FOR_EXCEPTION(! in, std::invalid_argument,
"Input stream is invalid.");
std::string line;
size_t lineNumber = startingLineNumber;
bool allSucceeded = true;
std::vector<size_t> badLineNumbers;
size_t validDataLines = 0;
while (getline (in, line)) {
size_t start, size;
if (checkCommentLine (line, start, size, lineNumber, tolerant)) {
++lineNumber;
continue; // it's a comment line
}
const std::string theLine = line.substr (start, size);
const bool localSuccess = readLine (theLine, lineNumber, tolerant);
++lineNumber;
allSucceeded = allSucceeded && localSuccess;
if (! localSuccess) {
badLineNumbers.push_back (lineNumber);
}
else {
++validDataLines;
}
}
return std::make_pair (allSucceeded, badLineNumbers);
}
/// \brief Read (numRows, numCols, numNonzeros).
///
/// Read one line from the given input stream, and parse it into
/// the number of rows, the number of columns, and the number of
/// nonzeros in the sparse matrix. We assume that those data
/// are in whitespace-delimited format and are read from a
/// Matrix Market - format file.
///
/// \param in [in/out] The input stream from which to attempt to
/// read one line.
///
/// \param lineNumber The starting line number from which we
/// begin reading from the input stream. Used for diagnostic
/// error output.
///
/// \param tolerant [in] Whether to read "tolerantly" (setting
/// defaults and returning whether we were successful) or
/// "intolerantly" (throwing an exception on any deviation
/// from the expected format).
///
/// \return ((numRows, numCols, numNonzeros), success). In
/// tolerant mode, success may be false, meaning that the
/// read-in triple may not be valid.
std::pair<Teuchos::Tuple<Ordinal, 3>, bool>
readDimensions (std::istream& in,
size_t& lineNumber,
const bool tolerant = false)
{
Teuchos::Tuple<Ordinal, 3> dims;
// Fill in (numRows, numCols, numNonzeros) with reasonable
// defaults. If we don't succeed in reading all the data
// from the current line of the input stream, the remaining
// values not read will be these default values.
dims[0] = 0;
dims[1] = 0;
dims[2] = 0;
// Keep reading lines from the input stream until we find a
// non-comment line, or until we run out of lines. The latter
// is an error, since every "coordinate" format Matrix Market
// file must have a dimensions line after the banner (even if
// the matrix has zero rows or columns, or zero entries).
std::string line;
bool commentLine = true;
while (commentLine) {
// Is it even valid to read from the input stream?
if (in.eof() || in.fail()) {
if (tolerant) {
return std::make_pair (dims, false);
}
else {
std::ostringstream os;
os << "Unable to get coordinate dimensions line (at all) "
"from (line " << lineNumber << ") of input stream; the "
"input stream claims that it is at \"end-of-file\" or has "
"an otherwise \"fail\"ed state.";
throw std::invalid_argument(os.str());
}
}
// Try to get the next line from the input stream.
if (getline(in, line)) {
lineNumber++; // We did actually read a line
}
else {
if (tolerant) {
return std::make_pair (dims, false);
}
else {
std::ostringstream os;
os << "Failed to read coordinate dimensions line (at all) "
"from (line " << lineNumber << " from input stream. The "
"line should contain the coordinate matrix dimensions in "
<< " the form \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument (os.str());
}
}
// Is the current line a comment line? Ignore start and
// size; they are only useful for reading the actual matrix
// entries. (We could use them here as an optimization, but
// we've chosen not to.)
size_t start = 0, size = 0;
commentLine = checkCommentLine (line, start, size,
lineNumber, tolerant);
}
//
// Read in <numRows> <numCols> <numNonzeros> from input line
//
std::istringstream istr (line);
// Does line contain anything at all? Can we safely read from
// the input stream wrapping the line?
if (istr.eof() || istr.fail()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "Unable to read any data from line " << lineNumber
<< " of input; the line should contain the coordinate matrix "
<< "dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
// Read in <numRows>
{
Ordinal theNumRows = 0;
istr >> theNumRows;
if (istr.fail()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "Failed to get number of rows from line " << lineNumber
<< " of input; the line should contain the coordinate matrix "
<< " dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
else { // Capture the validly read result before checking for eof.
dims[0] = theNumRows;
}
}
// There should be two more things to read.
if (istr.eof()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "No more data after number of rows on line " << lineNumber
<< " of input; the line should contain the coordinate matrix "
<< " dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
// Read in <numCols>
{
Ordinal theNumCols = 0;
istr >> theNumCols;
if (istr.fail()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "Failed to get number of columns from line " << lineNumber
<< " of input; the line should contain the coordinate matrix "
<< " dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
else { // Capture the validly read result before checking for eof.
dims[1] = theNumCols;
}
}
// There should be one more thing to read.
if (istr.eof()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "No more data after number of columns on line " << lineNumber
<< " of input; the line should contain the coordinate matrix "
<< " dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
// Read in <numNonzeros>
{
Ordinal theNumNonzeros = 0;
istr >> theNumNonzeros;
if (istr.fail()) {
if (tolerant) {
return std::make_pair (dims, false);
}
std::ostringstream os;
os << "Failed to get number of (structural) nonzeros from line "
<< lineNumber
<< " of input; the line should contain the coordinate matrix "
<< " dimensions \"<numRows> <numCols> <numNonzeros>\".";
throw std::invalid_argument(os.str());
}
else { // Capture the validly read result
dims[2] = theNumNonzeros;
}
}
// It would be nice to validate the read-in data further. The
// only thing we can do now is test if it's negative. However,
// we don't know syntactically whether Ordinal is a signed or
// unsigned type, so we shouldn't even test for negativity.
return std::make_pair (dims, true);
}
};
/// \class CoordDataReader
/// \brief Coordinate-format sparse matrix data reader.
///
/// Use this class to read in sparse matrix data and add it to the
/// sparse matrix using your Callback implementation (see the
/// documentation of CoordDataReaderBase).
///
/// \tparam Callback Same as in CoordDataReaderBase. Its
/// operator() takes three arguments: the row index, the column
/// index, and the matrix value. The indices are all one-based.
///
/// \tparam Ordinal Same as in CoordDataReaderBase. The type of
/// indices in the sparse matrix.
///
/// \tparam Scalar The type of entries of the sparse matrix. For
/// a real Scalar type (isComplex=false), any type for which a
/// Teuchos::ScalarTraits specialization exists is valid. If
/// Scalar is complex (isComplex=true), then Scalar's operator=
/// must accept an std::complex<typename
/// Teuchos::ScalarTraits<Scalar>::magnitudeType> input.
///
/// \tparam isComplex Whether Scalar is a complex-valued type or a
/// real-valued type. The default value here is fine for most
/// users.
///
/// This class completes the implementation of CoordDataReaderBase
/// for sparse matrices. We provide two partial specializations:
/// one for real-valued data (isComplex=false), and the other for
/// complex-valued data (isComplex=true).
///
/// If you have an existing sparse matrix implementation to which
/// you want to add entries, you'll either have to make it
/// implement Callback's three-argument operator(), or write your
/// own Callback implementation that wraps the sparse matrix.
template<class Callback,
class Ordinal,
class Scalar,
bool isComplex = Teuchos::ScalarTraits<Scalar>::isComplex>
class CoordDataReader : public CoordDataReaderBase<Callback, Ordinal> {
public:
/// \brief Constructor with "adder" argument.
///
/// This is the favored way to construct an instance of this
/// type. Only use the no-argument constructor if you have a
/// "chicken-and-egg" problem, where in order to create the
/// Callback instance, you need the matrix dimensions. This is
/// the case if your Callback wraps Tpetra::CrsMatrix, for
/// example.
///
/// \param adder [in/out] Closure (a.k.a. callback) whose
/// operator() adds an entry to the sparse graph or matrix on
/// each invocation.
CoordDataReader (const Teuchos::RCP<Callback>& adder);
/// \brief No-argument constructor.
///
/// We offer this option in case the adder's constructor needs
/// the matrix dimensions, so that it's necessary to call
/// readDimensions() first before constructing the adder. You
/// should call setAdder() with a non-null argument before
/// calling read() or readLine().
CoordDataReader ();
//! Virtual destructor for safety and happy compilers.
virtual ~CoordDataReader();
protected:
bool
readLine (const std::string& theLine,
const size_t lineNumber,
const bool tolerant);
};
#ifdef HAVE_TEUCHOS_COMPLEX
// Partial specialization for complex Scalar types.
template<class Callback, class Ordinal, class Scalar>
class CoordDataReader<Callback, Ordinal, Scalar, true> :
public CoordDataReaderBase<Callback, Ordinal> {
public:
CoordDataReader (const Teuchos::RCP<Callback>& adder) :
CoordDataReaderBase<Callback, Ordinal> (adder)
{}
CoordDataReader() :
CoordDataReaderBase<Callback, Ordinal> (null)
{}
virtual ~CoordDataReader() {};
protected:
bool
readLine (const std::string& theLine,
const size_t lineNumber,
const bool tolerant)
{
typedef Teuchos::ScalarTraits<Scalar> STS;
typedef typename STS::magnitudeType Real;
Ordinal rowIndex;
Ordinal colIndex;
Scalar value;
Real realPart, imagPart;
const bool localSuccess =
readComplexLine (theLine, rowIndex, colIndex, realPart, imagPart,
lineNumber, tolerant);
if (localSuccess) {
// Assume that assignment from std::complex<Real> to Scalar
// (which itself is complex-valued) is valid. We have to do
// this, since the C++ compiler may not be smart enough to
// assume here (when it instantiates the templates) that
// Scalar is an std::complex<Real> -- even though it has to
// be, if STS::isComplex is true (which as of 31 Jan 2011,
// only holds for std::complex<T>).
value = std::complex<Real> (realPart, imagPart);
// Now that we've read in the (i, j, A_ij) triple
// successfully, we can add the entry to the sparse matrix.
(*(this->adder_)) (rowIndex, colIndex, value);
}
return localSuccess;
}
};
#endif // HAVE_TEUCHOS_COMPLEX
// Partial specialization for real Scalar types.
template<class Callback, class Ordinal, class Scalar>
class CoordDataReader<Callback, Ordinal, Scalar, false> :
public CoordDataReaderBase<Callback, Ordinal> {
public:
CoordDataReader (const Teuchos::RCP<Callback>& adder) :
CoordDataReaderBase<Callback, Ordinal> (adder)
{}
CoordDataReader() :
CoordDataReaderBase<Callback, Ordinal> (null)
{}
virtual ~CoordDataReader() {};
protected:
bool
readLine (const std::string& theLine,
const size_t lineNumber,
const bool tolerant)
{
Ordinal rowIndex;
Ordinal colIndex;
Scalar value;
const bool localSuccess = readRealLine (theLine, rowIndex, colIndex,
value, lineNumber, tolerant);
if (localSuccess) {
// Now that we've read in the (i, j, A_ij) triple
// successfully, we can add the entry to the sparse matrix.
(*(this->adder_)) (rowIndex, colIndex, value);
}
return localSuccess;
}
};
/// \class CoordPatternReader
/// \brief Coordinate-format sparse graph data reader.
///
/// Use this class to read in sparse graph data and add it to the
/// sparse graph using your Callback implementation (see the
/// documentation of CoordDataReaderBase). CoordDataReaderBase is
/// sufficiently general that we can extend it to read in a sparse
/// graph. "Pattern" refers to the Matrix Market keyword
/// "pattern" that indicates a sparse graph.
///
/// \tparam Callback Same as the \c Callback template parameter of
/// \c CoordDataReaderBase. The type of the callback
/// (a.k.a. closure) for adding entries to the sparse graph.
///
/// \tparam Ordinal Same as the \c Ordinal template parameter of
/// \c CoordDataReaderBase. The type of indices of the sparse
/// graph.
///
/// If you have an existing sparse graph implementation to which
/// you want to add entries, you'll either have to make it
/// implement Callback's two-argument operator(), or write your
/// own Callback implementation that wraps the sparse graph.
template<class Callback, class Ordinal>
class CoordPatternReader : public CoordDataReaderBase<Callback, Ordinal> {
public:
/// \brief Constructor with "adder" argument.
///
/// This is the favored way to construct an instance of this
/// type. Only use the no-argument constructor if you have a
/// "chicken-and-egg" problem, where in order to create the
/// Callback instance, you need the graph dimensions. This is
/// the case if your Callback wraps Tpetra::CrsGraph, for
/// example.
///
/// \param adder [in/out] Closure (a.k.a. callback) whose
/// operator() adds an entry to the sparse graph on each
/// invocation.
CoordPatternReader (const Teuchos::RCP<Callback>& adder) :
CoordDataReaderBase<Callback, Ordinal> (adder)
{}
/// \brief No-argument constructor.
///
/// We offer this option in case the adder's constructor needs
/// the graph dimensions, so that it's necessary to call
/// readDimensions() first before constructing the adder. You
/// should call setAdder() with a non-null argument before
/// calling read() or readLine().
CoordPatternReader() :
CoordDataReaderBase<Callback, Ordinal> (null)
{}
//! Virtual destructor for safety and happy compilers.
virtual ~CoordPatternReader() {};
protected:
bool
readLine (const std::string& theLine,
const size_t lineNumber,
const bool tolerant)
{
Ordinal rowIndex;
Ordinal colIndex;
const bool localSuccess =
readPatternLine (theLine, rowIndex, colIndex, lineNumber, tolerant);
if (localSuccess) {
// Now that we've read in the (i, j) pair successfully, we
// can add the entry to the sparse graph.
(*(this->adder_)) (rowIndex, colIndex);
}
return localSuccess;
}
};
} // namespace MatrixMarket
} // namespace Teuchos
#endif // __Teuchos_MatrixMarket_CoordDataReader_hpp
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