diff --git a/CHANGELOG.markdown b/CHANGELOG.markdown --- a/CHANGELOG.markdown +++ b/CHANGELOG.markdown @@ -1,3 +1,3 @@ -0.2.0.1 +0.1.0.1 Added MatrixMarket module from `accelerate-examples` SMVM diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -1,3 +1,5 @@ Trevor McDonell (tmcdonell) and the `accelerate` contributors : Data.Matrix.MatrixMarket Peter Simons (peti) + +Gregory Schwartz (GregorySchwartz) diff --git a/matrix-market-attoparsec.cabal b/matrix-market-attoparsec.cabal --- a/matrix-market-attoparsec.cabal +++ b/matrix-market-attoparsec.cabal @@ -1,5 +1,5 @@ name: matrix-market-attoparsec -version: 0.1.0.8 +version: 0.1.0.9 synopsis: Parsing and serialization functions for the NIST Matrix Market format description: Parsing and serialization functions for the NIST Matrix Market format. homepage: https://github.com/ocramz/matrix-market-attoparsec @@ -17,7 +17,7 @@ data-files: fidapm05.mtx fidapm05_rhs1.mtx cabal-version: >=1.10 -tested-with: GHC == 8.0.1 +tested-with: GHC == 8.0.1, GHC == 8.6.5 diff --git a/src/Data/Matrix/MatrixMarket.hs b/src/Data/Matrix/MatrixMarket.hs --- a/src/Data/Matrix/MatrixMarket.hs +++ b/src/Data/Matrix/MatrixMarket.hs @@ -8,14 +8,12 @@ -- Stability : experimental -- Portability : portable -- --- Attoparsec parser and serializer for the NIST MatrixMarket format. The parser logic originally appeared in `accelerate-examples` and it is reused here (courtesy of T.McDonell and the `accelerate` developers) with some amendments. --- --- In this version: +-- @attoparsec@-based parser and serializer for the NIST MatrixMarket format [1]. The parser logic originally appeared in @accelerate-examples@ and it is reused here (courtesy of T.McDonell and the @accelerate@ developers) with some amendments. -- --- *) Numbers are represented with Scientific notation instead of floating point -- --- *) Parsing rules are a bit relaxed to accommodate various whitespace corner cases +-- References : -- +-- 1. https://math.nist.gov/MatrixMarket/ ----------------------------------------------------------------------------- module Data.Matrix.MatrixMarket (-- * Load diff --git a/src/Data/Matrix/MatrixMarket/Internal.hs b/src/Data/Matrix/MatrixMarket/Internal.hs --- a/src/Data/Matrix/MatrixMarket/Internal.hs +++ b/src/Data/Matrix/MatrixMarket/Internal.hs @@ -10,15 +10,15 @@ -- Portability : portable -- -- Attoparsec parser and serializer for the NIST MatrixMarket format. The parser logic originally appeared in `accelerate-examples` and it is reused here (courtesy of T.McDonell and the `accelerate` developers) with some amendments. --- +-- -- In this version: -- * Numbers are represented with Scientific notation instead of floating point -- * Parsing rules are a bit relaxed to accommodate various whitespace corner cases -- ----------------------------------------------------------------------------- module Data.Matrix.MatrixMarket.Internal - (readMatrix, readArray, - writeMatrix, writeArray, + (readMatrix, readMatrix', readArray, + writeMatrix, writeMatrix', writeArray, Matrix(..), Array(..), Format (Coordinate, Array), Structure (General, Symmetric, Hermitian, Skew), nnz, dim, numDat, @@ -61,8 +61,8 @@ -- data Field = R | C | I | P deriving (Eq, Show) - + -- | Specifies any special structure in the matrix. For symmetric and hermitian -- matrices, only the lower-triangular part of the matrix is given. For skew -- matrices, only the entries below the diagonal are stored. @@ -147,7 +147,7 @@ line3 f = (,,) <$> integral <*> integral <*> f - <* endOfLine + <* (endOfLine <|> L.endOfInput) skipSpace' :: Parser String skipSpace' = many' space @@ -164,7 +164,7 @@ if f /= Coordinate then fail "matrix is not in Coordinate format" else - case t of + case t of R -> RMatrix (m,n) l s <$> many1 (line3 floating) C -> CMatrix (m,n) l s <$> many1 (line3 ((:+) <$> floating <*> floating)) I -> IntMatrix (m,n) l s <$> many1 (line3 integral) @@ -185,8 +185,11 @@ -- | Load a matrix (sparse, i.e. in Coordinate format) from file readMatrix :: FilePath -> IO (Matrix S.Scientific) -readMatrix file = do - chunks <- L.readFile file +readMatrix file = L.readFile file >>= readMatrix' + +-- | Load a matrix (sparse, i.e. in Coordinate format) from a bytestring. +readMatrix' :: L.ByteString -> IO (Matrix S.Scientific) +readMatrix' chunks = case L.parse matrix chunks of L.Fail _ _ msg -> throwM (FileParseError "readMatrix" msg) L.Done _ mtx -> return mtx @@ -225,7 +228,7 @@ nl :: L.ByteString -nl = toLBS "\n" +nl = toLBS "\n" showLines :: (a -> String) -> [a] -> L.ByteString showLines showf d = L.concat (L.pack . withNewline . showf <$> d) where @@ -235,13 +238,17 @@ -- | Serialize a sparse matrix in Coordinate format writeMatrix :: Show b => FilePath -> Matrix b -> IO () -writeMatrix file mat = - case mat of (RMatrix d nz s dat) -> - L.writeFile file (matrixByteString d nz R s dat) - (CMatrix d nz s dat) -> - L.writeFile file (matrixByteString d nz C s dat) - (IntMatrix d nz s dat) -> - L.writeFile file (matrixByteString d nz I s dat) +writeMatrix file = L.writeFile file . writeMatrix' + +-- | Serialize a sparse matrix in Coordinate format as a bytestring +writeMatrix' :: Show b => Matrix b -> L.ByteString +writeMatrix' mat = + case mat of (RMatrix d nz s dat) -> + matrixByteString d nz R s dat + (CMatrix d nz s dat) -> + matrixByteString d nz C s dat + (IntMatrix d nz s dat) -> + matrixByteString d nz I s dat _ -> error "writeMatrix : PatternMatrix not implemented yet" where matrixByteString di nz t s d = @@ -252,11 +259,11 @@ showLines sf3 d] where sf3 (i,j,x) = unwords [show i, show j, show x] - headerSzMatrix (m,n) numz = B.pack $ unwords [show m, show n, show numz] + headerSzMatrix (m,n) numz = B.pack $ unwords [show m, show n, show numz] -- | Serialize a dense matrix in Array format -writeArray :: Show a => FilePath -> Array a -> IO () -writeArray file arr = +writeArray :: Show a => FilePath -> Array a -> IO () +writeArray file arr = case arr of (RArray d s dat) -> L.writeFile file (arrayByteString d R s dat) (CArray d s dat) -> L.writeFile file (arrayByteString d C s dat) where @@ -267,14 +274,14 @@ nl, showLines show d] where headerSzArray (m,n) = B.pack $ unwords [show m, show n] - - + + -- | helpers -- | Number of matrix nonzeros @@ -291,7 +298,7 @@ (PatternMatrix d _ _ _) -> d (IntMatrix d _ _ _) -> d --- | Length of data vector internal to the Matrix; this is _not_ necessarily the actual number of matrix entries because symmetric entries are not stored +-- | Length of data vector internal to the Matrix; this is _not_ necessarily the actual number of matrix entries because symmetric entries are not stored numDat :: Matrix t -> Int numDat m = case m of (RMatrix _ _ _ d) -> length d (CMatrix _ _ _ d) -> length d @@ -304,10 +311,10 @@ dimArr a = case a of (RArray d _ _) -> d (CArray d _ _) -> d --- | Length of data vector internal to the Array; this is _not_ necessarily the actual number of matrix entries because symmetric entries are not stored +-- | Length of data vector internal to the Array; this is _not_ necessarily the actual number of matrix entries because symmetric entries are not stored numDatArr :: Array a -> Int -numDatArr a = case a of (RArray _ _ ll) -> length ll - (CArray _ _ ll) -> length ll +numDatArr a = case a of (RArray _ _ ll) -> length ll + (CArray _ _ ll) -> length ll