linear algebra moved

10 files changed, 162 insertions, 134 deletions

diff --git a/packages/base/hmatrix-base.cabal b/packages/base/hmatrix-base.cabal
index 9a84b7e..3f12dad 100644
--- a/packages/base/hmatrix-base.cabal
+++ b/packages/base/hmatrix-base.cabal
@@ -38,11 +38,11 @@ library
                         Numeric.Conversion
                         Numeric.LinearAlgebra.LAPACK
                         Numeric.LinearAlgebra.Algorithms
-                        Data.Packed.Numeric
-                        Numeric.Vectorized
-                        Numeric.Vector
-                        Numeric.Matrix
                         Numeric.Container
+                        Numeric.LinearAlgebra
+                        Numeric.LinearAlgebra.Util
+                        Numeric.LinearAlgebra.Util.Convolution
+                        Data.Packed.IO
                         
     other-modules:      Data.Packed.Internal,
                         Data.Packed.Internal.Common,
@@ -50,6 +50,11 @@ library
                         Data.Packed.Internal.Vector,
                         Data.Packed.Internal.Matrix
                         Numeric.Chain
+                        Numeric.Vectorized
+                        Numeric.Vector
+                        Numeric.Matrix
+                        Data.Packed.Numeric
+
 
     C-sources:          src/C/lapack-aux.c
                         src/C/vector-aux.c
diff --git a/packages/base/src/Data/Packed/IO.hs b/packages/base/src/Data/Packed/IO.hs
new file mode 100644
index 0000000..dbb2943
--- /dev/null
+++ b/packages/base/src/Data/Packed/IO.hs
@@ -0,0 +1,141 @@
+-----------------------------------------------------------------------------
+-- |
+-- Module      :  Data.Packed.IO
+-- Copyright   :  (c) Alberto Ruiz 2010
+-- License     :  BSD3
+--
+-- Maintainer  :  Alberto Ruiz
+-- Stability   :  provisional
+--
+-- Display, formatting and IO functions for numeric 'Vector' and 'Matrix'
+--
+-----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
+
+module Data.Packed.IO (
+    dispf, disps, dispcf, vecdisp, latexFormat, format,
+    readMatrix, fromArray2D
+) where
+
+import Data.Packed
+import Data.Packed.Development
+import Text.Printf(printf)
+import Data.List(intersperse)
+import Data.Complex
+
+{- | Creates a string from a matrix given a separator and a function to show each entry. Using
+this function the user can easily define any desired display function:
+
+@import Text.Printf(printf)@
+
+@disp = putStr . format \"  \" (printf \"%.2f\")@
+
+-}
+format :: (Element t) => String -> (t -> String) -> Matrix t -> String
+format sep f m = table sep . map (map f) . toLists $ m
+
+{- | Show a matrix with \"autoscaling\" and a given number of decimal places.
+
+>>> putStr . disps 2 $ 120 * (3><4) [1..]
+3x4  E3
+ 0.12  0.24  0.36  0.48
+ 0.60  0.72  0.84  0.96
+ 1.08  1.20  1.32  1.44
+
+-}
+disps :: Int -> Matrix Double -> String
+disps d x = sdims x ++ "  " ++ formatScaled d x
+
+{- | Show a matrix with a given number of decimal places.
+
+>>> dispf 2 (1/3 + ident 3)
+"3x3\n1.33  0.33  0.33\n0.33  1.33  0.33\n0.33  0.33  1.33\n"
+
+>>> putStr . dispf 2 $ (3><4)[1,1.5..]
+3x4
+1.00  1.50  2.00  2.50
+3.00  3.50  4.00  4.50
+5.00  5.50  6.00  6.50
+
+>>> putStr . unlines . tail . lines . dispf 2 . asRow $ linspace 10 (0,1)
+0.00  0.11  0.22  0.33  0.44  0.56  0.67  0.78  0.89  1.00
+
+-}
+dispf :: Int -> Matrix Double -> String
+dispf d x = sdims x ++ "\n" ++ formatFixed (if isInt x then 0 else d) x
+
+sdims x = show (rows x) ++ "x" ++ show (cols x)
+
+formatFixed d x = format "  " (printf ("%."++show d++"f")) $ x
+
+isInt = all lookslikeInt . toList . flatten
+
+formatScaled dec t = "E"++show o++"\n" ++ ss
+    where ss = format " " (printf fmt. g) t
+          g x | o >= 0    = x/10^(o::Int)
+              | otherwise = x*10^(-o)
+          o | rows t == 0 || cols t == 0 = 0
+            | otherwise = floor $ maximum $ map (logBase 10 . abs) $ toList $ flatten t
+          fmt = '%':show (dec+3) ++ '.':show dec ++"f"
+
+{- | Show a vector using a function for showing matrices.
+
+>>> putStr . vecdisp (dispf 2) $ linspace 10 (0,1)
+10 |> 0.00  0.11  0.22  0.33  0.44  0.56  0.67  0.78  0.89  1.00
+
+-}
+vecdisp :: (Element t) => (Matrix t -> String) -> Vector t -> String
+vecdisp f v
+    = ((show (dim v) ++ " |> ") ++) . (++"\n")
+    . unwords . lines .  tail . dropWhile (not . (`elem` " \n"))
+    . f . trans . reshape 1
+    $ v
+
+{- | Tool to display matrices with latex syntax.
+
+>>>  latexFormat "bmatrix" (dispf 2 $ ident 2)
+"\\begin{bmatrix}\n1  &  0\n\\\\\n0  &  1\n\\end{bmatrix}"
+
+-}
+latexFormat :: String -- ^ type of braces: \"matrix\", \"bmatrix\", \"pmatrix\", etc.
+            -> String -- ^ Formatted matrix, with elements separated by spaces and newlines
+            -> String
+latexFormat del tab = "\\begin{"++del++"}\n" ++ f tab ++ "\\end{"++del++"}"
+    where f = unlines . intersperse "\\\\" . map unwords . map (intersperse " & " . words) . tail . lines
+
+-- | Pretty print a complex number with at most n decimal digits.
+showComplex :: Int -> Complex Double -> String
+showComplex d (a:+b)
+    | isZero a && isZero b = "0"
+    | isZero b = sa
+    | isZero a && isOne b = s2++"i"
+    | isZero a = sb++"i"
+    | isOne b = sa++s3++"i"
+    | otherwise = sa++s1++sb++"i"
+  where
+    sa = shcr d a
+    sb = shcr d b
+    s1 = if b<0 then "" else "+"
+    s2 = if b<0 then "-" else ""
+    s3 = if b<0 then "-" else "+"
+
+shcr d a | lookslikeInt a = printf "%.0f" a
+         | otherwise      = printf ("%."++show d++"f") a
+
+
+lookslikeInt x = show (round x :: Int) ++".0" == shx || "-0.0" == shx
+   where shx = show x
+
+isZero x = show x `elem` ["0.0","-0.0"]
+isOne  x = show x `elem` ["1.0","-1.0"]
+
+-- | Pretty print a complex matrix with at most n decimal digits.
+dispcf :: Int -> Matrix (Complex Double) -> String
+dispcf d m = sdims m ++ "\n" ++ format "  " (showComplex d) m
+
+--------------------------------------------------------------------
+
+-- | reads a matrix from a string containing a table of numbers.
+readMatrix :: String -> Matrix Double
+readMatrix = fromLists . map (map read). map words . filter (not.null) . lines
+
diff --git a/packages/hmatrix/src/Numeric/LinearAlgebra.hs b/packages/base/src/Numeric/LinearAlgebra.hs
index 1db860c..1db860c 100644
--- a/packages/hmatrix/src/Numeric/LinearAlgebra.hs
+++ b/packages/base/src/Numeric/LinearAlgebra.hs
diff --git a/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs b/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
index af0c744..9cb67d4 100644
--- a/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/LAPACK.hs
@@ -10,6 +10,8 @@
 -- Functional interface to selected LAPACK functions (<http://www.netlib.org/lapack>).
 --
 -----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
+
 
 module Numeric.LinearAlgebra.LAPACK (
     -- * Matrix product
diff --git a/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs b/packages/base/src/Numeric/LinearAlgebra/Util.hs
index e4f21b0..533c54b 100644
--- a/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Util.hs
@@ -47,22 +47,23 @@ module Numeric.LinearAlgebra.Util(
     vech,
     dup,
     vtrans,
-    -- * Plot
+{-    -- * Plot
     mplot,
     plot, parametricPlot,
     splot, mesh, meshdom,
     matrixToPGM, imshow,
     gnuplotX, gnuplotpdf, gnuplotWin
+-}
 ) where
 
 import Numeric.Container
-import Numeric.IO
+import Data.Packed.IO
 import Numeric.LinearAlgebra.Algorithms hiding (i)
 import Numeric.Matrix()
 import Numeric.Vector()
 
 import Numeric.LinearAlgebra.Util.Convolution
-import Graphics.Plot
+--import Graphics.Plot
 
 
 {- | print a real matrix with given number of digits after the decimal point
diff --git a/packages/hmatrix/src/Numeric/LinearAlgebra/Util/Convolution.hs b/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs
index 82de476..d04c46b 100644
--- a/packages/hmatrix/src/Numeric/LinearAlgebra/Util/Convolution.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Util/Convolution.hs
@@ -10,6 +10,7 @@ Stability   :  provisional
 
 -}
 -----------------------------------------------------------------------------
+{-# OPTIONS_HADDOCK hide #-}
 
 module Numeric.LinearAlgebra.Util.Convolution(
    corr, conv, corrMin,
diff --git a/packages/hmatrix/hmatrix.cabal b/packages/hmatrix/hmatrix.cabal
index 9719c96..c79da8a 100644
--- a/packages/hmatrix/hmatrix.cabal
+++ b/packages/hmatrix/hmatrix.cabal
@@ -90,8 +90,6 @@ library
                         Numeric.GSL.Fitting,
                         Numeric.GSL.ODE,
                         Numeric.GSL,
-                        Numeric.LinearAlgebra,
-                        Numeric.LinearAlgebra.Util,
                         Graphics.Plot,
                         Numeric.HMatrix,
                         Numeric.HMatrix.Data,
@@ -99,8 +97,7 @@ library
     other-modules:      Numeric.Random,
                         Numeric.GSL.Internal,
                         Numeric.GSL.Vector,
-                        Numeric.IO,
-                        Numeric.LinearAlgebra.Util.Convolution
+                        Numeric.IO
                         
 
     C-sources:          src/Numeric/GSL/gsl-aux.c
diff --git a/packages/hmatrix/src/Numeric/HMatrix.hs b/packages/hmatrix/src/Numeric/HMatrix.hs
index 36fcf70..fcd3e02 100644
--- a/packages/hmatrix/src/Numeric/HMatrix.hs
+++ b/packages/hmatrix/src/Numeric/HMatrix.hs
@@ -129,8 +129,8 @@ module Numeric.HMatrix (
 
 import Numeric.HMatrix.Data
 
-import Numeric.Matrix()
-import Numeric.Vector()
+--import Numeric.Matrix()
+--import Numeric.Vector()
 import Numeric.Container
 import Numeric.LinearAlgebra.Algorithms
 import Numeric.LinearAlgebra.Util
diff --git a/packages/hmatrix/src/Numeric/IO.hs b/packages/hmatrix/src/Numeric/IO.hs
index 58fa2b4..08d812b 100644
--- a/packages/hmatrix/src/Numeric/IO.hs
+++ b/packages/hmatrix/src/Numeric/IO.hs
@@ -20,128 +20,10 @@ module Numeric.IO (
 ) where
 
 import Data.Packed
-import Data.Packed.Development
+import Data.Packed.IO
 import System.Process(readProcess)
-import Text.Printf(printf)
-import Data.List(intersperse)
-import Data.Complex
 import Numeric.GSL.Vector
 
-{- | Creates a string from a matrix given a separator and a function to show each entry. Using
-this function the user can easily define any desired display function:
-
-@import Text.Printf(printf)@
-
-@disp = putStr . format \"  \" (printf \"%.2f\")@
-
--}
-format :: (Element t) => String -> (t -> String) -> Matrix t -> String
-format sep f m = table sep . map (map f) . toLists $ m
-
-{- | Show a matrix with \"autoscaling\" and a given number of decimal places.
-
->>> putStr . disps 2 $ 120 * (3><4) [1..]
-3x4  E3
- 0.12  0.24  0.36  0.48
- 0.60  0.72  0.84  0.96
- 1.08  1.20  1.32  1.44
-
--}
-disps :: Int -> Matrix Double -> String
-disps d x = sdims x ++ "  " ++ formatScaled d x
-
-{- | Show a matrix with a given number of decimal places.
-
->>> dispf 2 (1/3 + ident 3)
-"3x3\n1.33  0.33  0.33\n0.33  1.33  0.33\n0.33  0.33  1.33\n"
-
->>> putStr . dispf 2 $ (3><4)[1,1.5..]
-3x4
-1.00  1.50  2.00  2.50
-3.00  3.50  4.00  4.50
-5.00  5.50  6.00  6.50
-
->>> putStr . unlines . tail . lines . dispf 2 . asRow $ linspace 10 (0,1)
-0.00  0.11  0.22  0.33  0.44  0.56  0.67  0.78  0.89  1.00
-
--}
-dispf :: Int -> Matrix Double -> String
-dispf d x = sdims x ++ "\n" ++ formatFixed (if isInt x then 0 else d) x
-
-sdims x = show (rows x) ++ "x" ++ show (cols x)
-
-formatFixed d x = format "  " (printf ("%."++show d++"f")) $ x
-
-isInt = all lookslikeInt . toList . flatten
-
-formatScaled dec t = "E"++show o++"\n" ++ ss
-    where ss = format " " (printf fmt. g) t
-          g x | o >= 0    = x/10^(o::Int)
-              | otherwise = x*10^(-o)
-          o | rows t == 0 || cols t == 0 = 0
-            | otherwise = floor $ maximum $ map (logBase 10 . abs) $ toList $ flatten t
-          fmt = '%':show (dec+3) ++ '.':show dec ++"f"
-
-{- | Show a vector using a function for showing matrices.
-
->>> putStr . vecdisp (dispf 2) $ linspace 10 (0,1)
-10 |> 0.00  0.11  0.22  0.33  0.44  0.56  0.67  0.78  0.89  1.00
-
--}
-vecdisp :: (Element t) => (Matrix t -> String) -> Vector t -> String
-vecdisp f v
-    = ((show (dim v) ++ " |> ") ++) . (++"\n")
-    . unwords . lines .  tail . dropWhile (not . (`elem` " \n"))
-    . f . trans . reshape 1
-    $ v
-
-{- | Tool to display matrices with latex syntax.
-
->>>  latexFormat "bmatrix" (dispf 2 $ ident 2)
-"\\begin{bmatrix}\n1  &  0\n\\\\\n0  &  1\n\\end{bmatrix}"
-
--}
-latexFormat :: String -- ^ type of braces: \"matrix\", \"bmatrix\", \"pmatrix\", etc.
-            -> String -- ^ Formatted matrix, with elements separated by spaces and newlines
-            -> String
-latexFormat del tab = "\\begin{"++del++"}\n" ++ f tab ++ "\\end{"++del++"}"
-    where f = unlines . intersperse "\\\\" . map unwords . map (intersperse " & " . words) . tail . lines
-
--- | Pretty print a complex number with at most n decimal digits.
-showComplex :: Int -> Complex Double -> String
-showComplex d (a:+b)
-    | isZero a && isZero b = "0"
-    | isZero b = sa
-    | isZero a && isOne b = s2++"i"
-    | isZero a = sb++"i"
-    | isOne b = sa++s3++"i"
-    | otherwise = sa++s1++sb++"i"
-  where
-    sa = shcr d a
-    sb = shcr d b
-    s1 = if b<0 then "" else "+"
-    s2 = if b<0 then "-" else ""
-    s3 = if b<0 then "-" else "+"
-
-shcr d a | lookslikeInt a = printf "%.0f" a
-         | otherwise      = printf ("%."++show d++"f") a
-
-
-lookslikeInt x = show (round x :: Int) ++".0" == shx || "-0.0" == shx
-   where shx = show x
-
-isZero x = show x `elem` ["0.0","-0.0"]
-isOne  x = show x `elem` ["1.0","-1.0"]
-
--- | Pretty print a complex matrix with at most n decimal digits.
-dispcf :: Int -> Matrix (Complex Double) -> String
-dispcf d m = sdims m ++ "\n" ++ format "  " (showComplex d) m
-
---------------------------------------------------------------------
-
--- | reads a matrix from a string containing a table of numbers.
-readMatrix :: String -> Matrix Double
-readMatrix = fromLists . map (map read). map words . filter (not.null) . lines
 
 {- |  obtains the number of rows and columns in an ASCII data file
       (provisionally using unix's wc).
diff --git a/packages/hmatrix/src/Numeric/Random.hs b/packages/hmatrix/src/Numeric/Random.hs
index 7bf9e8b..0e722fd 100644
--- a/packages/hmatrix/src/Numeric/Random.hs
+++ b/packages/hmatrix/src/Numeric/Random.hs
@@ -21,8 +21,7 @@ module Numeric.Random (
 ) where
 
 import Numeric.GSL.Vector
-import Data.Packed
-import Data.Packed.Numeric
+import Numeric.Container
 import Numeric.LinearAlgebra.Algorithms
 import System.Random(randomIO)