empty hmatrix-base

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diff --git a/packages/hmatrix/src/Data/Packed/Matrix.hs b/packages/hmatrix/src/Data/Packed/Matrix.hs
new file mode 100644
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+++ b/packages/hmatrix/src/Data/Packed/Matrix.hs
@@ -0,0 +1,490 @@
+{-# LANGUAGE TypeFamilies #-}
+{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE FlexibleInstances #-}
+{-# LANGUAGE MultiParamTypeClasses #-}
+{-# LANGUAGE CPP #-}
+
+-----------------------------------------------------------------------------
+-- |
+-- Module      :  Data.Packed.Matrix
+-- Copyright   :  (c) Alberto Ruiz 2007-10
+-- License     :  GPL
+--
+-- Maintainer  :  Alberto Ruiz <aruiz@um.es>
+-- Stability   :  provisional
+--
+-- A Matrix representation suitable for numerical computations using LAPACK and GSL.
+--
+-- This module provides basic functions for manipulation of structure.
+
+-----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
+
+module Data.Packed.Matrix (
+    Matrix,
+    Element,
+    rows,cols,
+    (><),
+    trans,
+    reshape, flatten,
+    fromLists, toLists, buildMatrix,
+    (@@>),
+    asRow, asColumn,
+    fromRows, toRows, fromColumns, toColumns,
+    fromBlocks, diagBlock, toBlocks, toBlocksEvery,
+    repmat,
+    flipud, fliprl,
+    subMatrix, takeRows, dropRows, takeColumns, dropColumns,
+    extractRows, extractColumns,
+    diagRect, takeDiag,
+    mapMatrix, mapMatrixWithIndex, mapMatrixWithIndexM, mapMatrixWithIndexM_,
+    liftMatrix, liftMatrix2, liftMatrix2Auto,fromArray2D
+) where
+
+import Data.Packed.Internal
+import qualified Data.Packed.ST as ST
+import Data.Array
+
+import Data.List(transpose,intersperse)
+import Foreign.Storable(Storable)
+import Control.Monad(liftM)
+
+-------------------------------------------------------------------
+
+#ifdef BINARY
+
+import Data.Binary
+import Control.Monad(replicateM)
+
+instance (Binary a, Element a, Storable a) => Binary (Matrix a) where
+    put m = do
+            let r = rows m
+            let c = cols m
+            put r
+            put c
+            mapM_ (\i -> mapM_ (\j -> put $ m @@> (i,j)) [0..(c-1)]) [0..(r-1)]
+    get = do
+          r <- get
+          c <- get
+          xs <- replicateM r $ replicateM c get
+          return $ fromLists xs
+
+#endif
+
+-------------------------------------------------------------------
+
+instance (Show a, Element a) => (Show (Matrix a)) where
+    show m | rows m == 0 || cols m == 0 = sizes m ++" []"
+    show m = (sizes m++) . dsp . map (map show) . toLists $ m
+
+sizes m = "("++show (rows m)++"><"++show (cols m)++")\n"
+
+dsp as = (++" ]") . (" ["++) . init . drop 2 . unlines . map (" , "++) . map unwords' $ transpose mtp
+    where
+        mt = transpose as
+        longs = map (maximum . map length) mt
+        mtp = zipWith (\a b -> map (pad a) b) longs mt
+        pad n str = replicate (n - length str) ' ' ++ str
+        unwords' = concat . intersperse ", "
+
+------------------------------------------------------------------
+
+instance (Element a, Read a) => Read (Matrix a) where
+    readsPrec _ s = [((rs><cs) . read $ listnums, rest)]
+        where (thing,rest) = breakAt ']' s
+              (dims,listnums) = breakAt ')' thing
+              cs = read . init . fst. breakAt ')' . snd . breakAt '<' $ dims
+              rs = read . snd . breakAt '(' .init . fst . breakAt '>' $ dims
+
+
+breakAt c l = (a++[c],tail b) where
+    (a,b) = break (==c) l
+
+------------------------------------------------------------------
+
+-- | creates a matrix from a vertical list of matrices
+joinVert :: Element t => [Matrix t] -> Matrix t
+joinVert [] = emptyM 0 0
+joinVert ms = case common cols ms of
+    Nothing -> error "(impossible) joinVert on matrices with different number of columns"
+    Just c  -> matrixFromVector RowMajor (sum (map rows ms)) c $ vjoin (map flatten ms)
+
+-- | creates a matrix from a horizontal list of matrices
+joinHoriz :: Element t => [Matrix t] -> Matrix t
+joinHoriz ms = trans. joinVert . map trans $ ms
+
+{- | Create a matrix from blocks given as a list of lists of matrices.
+
+Single row-column components are automatically expanded to match the
+corresponding common row and column:
+
+@
+disp = putStr . dispf 2
+@
+
+>>> disp $ fromBlocks [[ident 5, 7, row[10,20]], [3, diagl[1,2,3], 0]]
+8x10
+1  0  0  0  0  7  7  7  10  20
+0  1  0  0  0  7  7  7  10  20
+0  0  1  0  0  7  7  7  10  20
+0  0  0  1  0  7  7  7  10  20
+0  0  0  0  1  7  7  7  10  20
+3  3  3  3  3  1  0  0   0   0
+3  3  3  3  3  0  2  0   0   0
+3  3  3  3  3  0  0  3   0   0
+
+-}
+fromBlocks :: Element t => [[Matrix t]] -> Matrix t
+fromBlocks = fromBlocksRaw . adaptBlocks
+
+fromBlocksRaw mms = joinVert . map joinHoriz $ mms
+
+adaptBlocks ms = ms' where
+    bc = case common length ms of
+          Just c -> c
+          Nothing -> error "fromBlocks requires rectangular [[Matrix]]"
+    rs = map (compatdim . map rows) ms
+    cs = map (compatdim . map cols) (transpose ms)
+    szs = sequence [rs,cs]
+    ms' = splitEvery bc $ zipWith g szs (concat ms)
+
+    g [Just nr,Just nc] m
+                | nr == r && nc == c = m
+                | r == 1 && c == 1 = matrixFromVector RowMajor nr nc (constantD x (nr*nc))
+                | r == 1 = fromRows (replicate nr (flatten m))
+                | otherwise = fromColumns (replicate nc (flatten m))
+      where
+        r = rows m
+        c = cols m
+        x = m@@>(0,0)
+    g _ _ = error "inconsistent dimensions in fromBlocks"
+
+
+--------------------------------------------------------------------------------
+
+{- | create a block diagonal matrix
+
+>>>  disp 2 $ diagBlock [konst 1 (2,2), konst 2 (3,5), col [5,7]]
+7x8
+1  1  0  0  0  0  0  0
+1  1  0  0  0  0  0  0
+0  0  2  2  2  2  2  0
+0  0  2  2  2  2  2  0
+0  0  2  2  2  2  2  0
+0  0  0  0  0  0  0  5
+0  0  0  0  0  0  0  7
+
+>>> diagBlock [(0><4)[], konst 2 (2,3)]  :: Matrix Double
+(2><7)
+ [ 0.0, 0.0, 0.0, 0.0, 2.0, 2.0, 2.0
+ , 0.0, 0.0, 0.0, 0.0, 2.0, 2.0, 2.0 ]
+
+-}
+diagBlock :: (Element t, Num t) => [Matrix t] -> Matrix t
+diagBlock ms = fromBlocks $ zipWith f ms [0..]
+  where
+    f m k = take n $ replicate k z ++ m : repeat z
+    n = length ms
+    z = (1><1) [0]
+
+--------------------------------------------------------------------------------
+
+
+-- | Reverse rows
+flipud :: Element t => Matrix t -> Matrix t
+flipud m = extractRows [r-1,r-2 .. 0] $ m
+  where
+    r = rows m
+
+-- | Reverse columns
+fliprl :: Element t => Matrix t -> Matrix t
+fliprl m = extractColumns [c-1,c-2 .. 0] $ m
+  where
+    c = cols m
+
+------------------------------------------------------------
+
+{- | creates a rectangular diagonal matrix:
+
+>>> diagRect 7 (fromList [10,20,30]) 4 5 :: Matrix Double
+(4><5)
+ [ 10.0,  7.0,  7.0, 7.0, 7.0
+ ,  7.0, 20.0,  7.0, 7.0, 7.0
+ ,  7.0,  7.0, 30.0, 7.0, 7.0
+ ,  7.0,  7.0,  7.0, 7.0, 7.0 ]
+
+-}
+diagRect :: (Storable t) => t -> Vector t -> Int -> Int -> Matrix t
+diagRect z v r c = ST.runSTMatrix $ do
+        m <- ST.newMatrix z r c
+        let d = min r c `min` (dim v)
+        mapM_ (\k -> ST.writeMatrix m k k (v@>k)) [0..d-1]
+        return m
+
+-- | extracts the diagonal from a rectangular matrix
+takeDiag :: (Element t) => Matrix t -> Vector t
+takeDiag m = fromList [flatten m `at` (k*cols m+k) | k <- [0 .. min (rows m) (cols m) -1]]
+
+------------------------------------------------------------
+
+{- | An easy way to create a matrix:
+
+>>> (2><3)[2,4,7,-3,11,0]
+(2><3)
+ [  2.0,  4.0, 7.0
+ , -3.0, 11.0, 0.0 ]
+
+This is the format produced by the instances of Show (Matrix a), which
+can also be used for input.
+
+The input list is explicitly truncated, so that it can
+safely be used with lists that are too long (like infinite lists).
+
+>>> (2><3)[1..]
+(2><3)
+ [ 1.0, 2.0, 3.0
+ , 4.0, 5.0, 6.0 ]
+
+
+-}
+(><) :: (Storable a) => Int -> Int -> [a] -> Matrix a
+r >< c = f where
+    f l | dim v == r*c = matrixFromVector RowMajor r c v
+        | otherwise    = error $ "inconsistent list size = "
+                                 ++show (dim v) ++" in ("++show r++"><"++show c++")"
+        where v = fromList $ take (r*c) l
+
+----------------------------------------------------------------
+
+-- | Creates a matrix with the first n rows of another matrix
+takeRows :: Element t => Int -> Matrix t -> Matrix t
+takeRows n mt = subMatrix (0,0) (n, cols mt) mt
+-- | Creates a copy of a matrix without the first n rows
+dropRows :: Element t => Int -> Matrix t -> Matrix t
+dropRows n mt = subMatrix (n,0) (rows mt - n, cols mt) mt
+-- |Creates a matrix with the first n columns of another matrix
+takeColumns :: Element t => Int -> Matrix t -> Matrix t
+takeColumns n mt = subMatrix (0,0) (rows mt, n) mt
+-- | Creates a copy of a matrix without the first n columns
+dropColumns :: Element t => Int -> Matrix t -> Matrix t
+dropColumns n mt = subMatrix (0,n) (rows mt, cols mt - n) mt
+
+----------------------------------------------------------------
+
+{- | Creates a 'Matrix' from a list of lists (considered as rows).
+
+>>> fromLists [[1,2],[3,4],[5,6]]
+(3><2)
+ [ 1.0, 2.0
+ , 3.0, 4.0
+ , 5.0, 6.0 ]
+
+-}
+fromLists :: Element t => [[t]] -> Matrix t
+fromLists = fromRows . map fromList
+
+-- | creates a 1-row matrix from a vector
+--
+-- >>> asRow (fromList [1..5])
+--  (1><5)
+--   [ 1.0, 2.0, 3.0, 4.0, 5.0 ]
+--
+asRow :: Storable a => Vector a -> Matrix a
+asRow v = reshape (dim v) v
+
+-- | creates a 1-column matrix from a vector
+--
+-- >>> asColumn (fromList [1..5])
+-- (5><1)
+--  [ 1.0
+--  , 2.0
+--  , 3.0
+--  , 4.0
+--  , 5.0 ]
+--
+asColumn :: Storable a => Vector a -> Matrix a
+asColumn = trans . asRow
+
+
+
+{- | creates a Matrix of the specified size using the supplied function to
+     to map the row\/column position to the value at that row\/column position.
+
+@> buildMatrix 3 4 (\\(r,c) -> fromIntegral r * fromIntegral c)
+(3><4)
+ [ 0.0, 0.0, 0.0, 0.0, 0.0
+ , 0.0, 1.0, 2.0, 3.0, 4.0
+ , 0.0, 2.0, 4.0, 6.0, 8.0]@
+
+Hilbert matrix of order N:
+
+@hilb n = buildMatrix n n (\\(i,j)->1/(fromIntegral i + fromIntegral j +1))@
+
+-}
+buildMatrix :: Element a => Int -> Int -> ((Int, Int) -> a) -> Matrix a
+buildMatrix rc cc f =
+    fromLists $ map (map f)
+        $ map (\ ri -> map (\ ci -> (ri, ci)) [0 .. (cc - 1)]) [0 .. (rc - 1)]
+
+-----------------------------------------------------
+
+fromArray2D :: (Storable e) => Array (Int, Int) e -> Matrix e
+fromArray2D m = (r><c) (elems m)
+    where ((r0,c0),(r1,c1)) = bounds m
+          r = r1-r0+1
+          c = c1-c0+1
+
+
+-- | rearranges the rows of a matrix according to the order given in a list of integers.
+extractRows :: Element t => [Int] -> Matrix t -> Matrix t
+extractRows [] m = emptyM 0 (cols m)
+extractRows l m = fromRows $ extract (toRows m) l
+  where
+    extract l' is = [l'!!i | i<- map verify is]
+    verify k
+        | k >= 0 && k < rows m = k
+        | otherwise = error $ "can't extract row "
+                           ++show k++" in list " ++ show l ++ " from matrix " ++ shSize m
+
+-- | rearranges the rows of a matrix according to the order given in a list of integers.
+extractColumns :: Element t => [Int] -> Matrix t -> Matrix t
+extractColumns l m = trans . extractRows (map verify l) . trans $ m
+  where
+    verify k
+        | k >= 0 && k < cols m = k
+        | otherwise = error $ "can't extract column "
+                           ++show k++" in list " ++ show l ++ " from matrix " ++ shSize m
+
+
+
+{- | creates matrix by repetition of a matrix a given number of rows and columns
+
+>>> repmat (ident 2) 2 3
+(4><6)
+ [ 1.0, 0.0, 1.0, 0.0, 1.0, 0.0
+ , 0.0, 1.0, 0.0, 1.0, 0.0, 1.0
+ , 1.0, 0.0, 1.0, 0.0, 1.0, 0.0
+ , 0.0, 1.0, 0.0, 1.0, 0.0, 1.0 ]
+
+-}
+repmat :: (Element t) => Matrix t -> Int -> Int -> Matrix t
+repmat m r c
+    | r == 0 || c == 0 = emptyM (r*rows m) (c*cols m)
+    | otherwise = fromBlocks $ replicate r $ replicate c $ m
+
+-- | A version of 'liftMatrix2' which automatically adapt matrices with a single row or column to match the dimensions of the other matrix.
+liftMatrix2Auto :: (Element t, Element a, Element b) => (Vector a -> Vector b -> Vector t) -> Matrix a -> Matrix b -> Matrix t
+liftMatrix2Auto f m1 m2
+    | compat' m1 m2 = lM f m1  m2
+    | ok            = lM f m1' m2'
+    | otherwise = error $ "nonconformable matrices in liftMatrix2Auto: " ++ shSize m1 ++ ", " ++ shSize m2
+  where
+    (r1,c1) = size m1
+    (r2,c2) = size m2
+    r = max r1 r2
+    c = max c1 c2
+    r0 = min r1 r2
+    c0 = min c1 c2
+    ok = r0 == 1 || r1 == r2 && c0 == 1 || c1 == c2
+    m1' = conformMTo (r,c) m1
+    m2' = conformMTo (r,c) m2
+
+-- FIXME do not flatten if equal order
+lM f m1 m2 = matrixFromVector
+                RowMajor
+                (max (rows m1) (rows m2))
+                (max (cols m1) (cols m2))
+                (f (flatten m1) (flatten m2))
+
+compat' :: Matrix a -> Matrix b -> Bool
+compat' m1 m2 = s1 == (1,1) || s2 == (1,1) || s1 == s2
+  where
+    s1 = size m1
+    s2 = size m2
+
+------------------------------------------------------------
+
+toBlockRows [r] m | r == rows m = [m]
+toBlockRows rs m = map (reshape (cols m)) (takesV szs (flatten m))
+    where szs = map (* cols m) rs
+
+toBlockCols [c] m | c == cols m = [m]
+toBlockCols cs m = map trans . toBlockRows cs . trans $ m
+
+-- | Partition a matrix into blocks with the given numbers of rows and columns.
+-- The remaining rows and columns are discarded.
+toBlocks :: (Element t) => [Int] -> [Int] -> Matrix t -> [[Matrix t]]
+toBlocks rs cs m = map (toBlockCols cs) . toBlockRows rs $ m
+
+-- | Fully partition a matrix into blocks of the same size. If the dimensions are not
+-- a multiple of the given size the last blocks will be smaller.
+toBlocksEvery :: (Element t) => Int -> Int -> Matrix t -> [[Matrix t]]
+toBlocksEvery r c m
+    | r < 1 || c < 1 = error $ "toBlocksEvery expects block sizes > 0, given "++show r++" and "++ show c
+    | otherwise = toBlocks rs cs m
+  where
+    (qr,rr) = rows m `divMod` r
+    (qc,rc) = cols m `divMod` c
+    rs = replicate qr r ++ if rr > 0 then [rr] else []
+    cs = replicate qc c ++ if rc > 0 then [rc] else []
+
+-------------------------------------------------------------------
+
+-- Given a column number and a function taking matrix indexes, returns
+-- a function which takes vector indexes (that can be used on the
+-- flattened matrix).
+mk :: Int -> ((Int, Int) -> t) -> (Int -> t)
+mk c g = \k -> g (divMod k c)
+
+{- |
+
+>>> mapMatrixWithIndexM_ (\(i,j) v -> printf "m[%d,%d] = %.f\n" i j v :: IO()) ((2><3)[1 :: Double ..])
+m[0,0] = 1
+m[0,1] = 2
+m[0,2] = 3
+m[1,0] = 4
+m[1,1] = 5
+m[1,2] = 6
+
+-}
+mapMatrixWithIndexM_
+  :: (Element a, Num a, Monad m) =>
+      ((Int, Int) -> a -> m ()) -> Matrix a -> m ()
+mapMatrixWithIndexM_ g m = mapVectorWithIndexM_ (mk c g) . flatten $ m
+  where
+    c = cols m
+
+{- |
+
+>>> mapMatrixWithIndexM (\(i,j) v -> Just $ 100*v + 10*fromIntegral i + fromIntegral j) (ident 3:: Matrix Double)
+Just (3><3)
+ [ 100.0,   1.0,   2.0
+ ,  10.0, 111.0,  12.0
+ ,  20.0,  21.0, 122.0 ]
+
+-}
+mapMatrixWithIndexM
+  :: (Element a, Storable b, Monad m) =>
+      ((Int, Int) -> a -> m b) -> Matrix a -> m (Matrix b)
+mapMatrixWithIndexM g m = liftM (reshape c) . mapVectorWithIndexM (mk c g) . flatten $ m 
+    where
+      c = cols m
+
+{- |
+
+>>> mapMatrixWithIndex (\\(i,j) v -> 100*v + 10*fromIntegral i + fromIntegral j) (ident 3:: Matrix Double)
+(3><3)
+ [ 100.0,   1.0,   2.0
+ ,  10.0, 111.0,  12.0
+ ,  20.0,  21.0, 122.0 ]
+
+ -}
+mapMatrixWithIndex
+  :: (Element a, Storable b) =>
+      ((Int, Int) -> a -> b) -> Matrix a -> Matrix b
+mapMatrixWithIndex g m = reshape c . mapVectorWithIndex (mk c g) . flatten $ m
+    where
+      c = cols m
+
+mapMatrix :: (Storable a, Storable b) => (a -> b) -> Matrix a -> Matrix b
+mapMatrix f = liftMatrix (mapVector f)