refactored Data.Packed.Vector to remove any numerics

9 files changed, 65 insertions, 54 deletions

diff --git a/hmatrix.cabal b/hmatrix.cabal
index 009219c..04c3581 100644
--- a/hmatrix.cabal
+++ b/hmatrix.cabal
@@ -97,6 +97,7 @@ library
                         Numeric.LinearAlgebra,
                         Numeric.LinearAlgebra.LAPACK,
                         Numeric.LinearAlgebra.Interface,
+                        Numeric.LinearAlgebra.Linear,
                         Numeric.LinearAlgebra.Algorithms,
                         Graphics.Plot,
                      -- Data.Packed.Convert,
@@ -108,7 +109,6 @@ library
                         Data.Packed.Internal.Signatures,
                         Data.Packed.Internal.Vector,
                         Data.Packed.Internal.Matrix,
-                        Numeric.LinearAlgebra.Linear,
                         Numeric.LinearAlgebra.Instances,
                         Numeric.GSL.Internal
 
diff --git a/lib/Data/Packed/Matrix.hs b/lib/Data/Packed/Matrix.hs
index 438dabc..d5a287d 100644
--- a/lib/Data/Packed/Matrix.hs
+++ b/lib/Data/Packed/Matrix.hs
@@ -30,7 +30,7 @@ module Data.Packed.Matrix (
     extractRows,
     ident, diag, diagRect, takeDiag,
     liftMatrix, liftMatrix2, liftMatrix2Auto,
-    dispf, disps, dispcf, latexFormat, format,
+    dispf, disps, dispcf, vecdisp, latexFormat, format,
     loadMatrix, saveMatrix, fromFile, fileDimensions,
     readMatrix, fromArray2D
 ) where
@@ -314,6 +314,21 @@ formatScaled dec t = "E"++show o++"\n" ++ ss
           o = 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.
+
+@disp = putStr . vecdisp ('dispf' 2)
+
+\> disp ('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 :: String -- ^ type of braces: \"matrix\", \"bmatrix\", \"pmatrix\", etc.
             -> String -- ^ Formatted matrix, with elements separated by spaces and newlines
diff --git a/lib/Data/Packed/Random.hs b/lib/Data/Packed/Random.hs
index e57ba6e..3b02225 100644
--- a/lib/Data/Packed/Random.hs
+++ b/lib/Data/Packed/Random.hs
@@ -24,6 +24,7 @@ import Data.Packed.Matrix
 import Data.Packed.Vector
 import Numeric.LinearAlgebra.Algorithms
 import Numeric.LinearAlgebra.Interface
+import Numeric.LinearAlgebra.Linear
 
 -- | Obtains a matrix whose rows are pseudorandom samples from a multivariate
 -- Gaussian distribution.
diff --git a/lib/Data/Packed/Vector.hs b/lib/Data/Packed/Vector.hs
index 40dd6b5..81dfa37 100644
--- a/lib/Data/Packed/Vector.hs
+++ b/lib/Data/Packed/Vector.hs
@@ -18,9 +18,11 @@ module Data.Packed.Vector (
     fromList, (|>), toList, buildVector,
     dim, (@>),
     subVector, takesV, join,
-    constant, linspace,
-    vecdisp,
---    moved to Numeric.LinearAlgebra.Interface typeclass
+--    moved to Numeric.LinearAlgebra.Linear
+--    constant, linspace, 
+--    moved to Data.Packed.Matrix  
+--    vecdisp,
+--    moved to Numeric.LinearAlgebra.Linear typeclass
 --    vectorFMax, vectorFMin, vectorFMaxIndex, vectorFMinIndex,
 --    vectorMax, vectorMin,
     vectorMaxIndex, vectorMinIndex,
@@ -30,10 +32,9 @@ module Data.Packed.Vector (
     foldLoop, foldVector, foldVectorG
 ) where
 
-import Data.Packed.Internal
+import Data.Packed.Internal.Vector
 import Numeric.GSL.Vector
 -- import Data.Packed.ST
-import Numeric.LinearAlgebra.Linear
 
 import Data.Binary
 import Foreign.Storable
@@ -72,19 +73,6 @@ instance (Binary a, Storable a) => Binary (Vector a) where
 -------------------------------------------------------------------
 
 
-{- | Creates a real vector containing a range of values:
-
-@\> linspace 5 (-3,7)
-5 |> [-3.0,-0.5,2.0,4.5,7.0]@
-
-Logarithmic spacing can be defined as follows:
-
-@logspace n (a,b) = 10 ** linspace n (a,b)@
--}
-linspace :: (Enum e, Linear Vector e, Element e) => Int -> (e, e) -> Vector e
-linspace n (a,b) = addConstant a $ scale s $ fromList [0 .. fromIntegral n-1]
-    where s = (b-a)/fromIntegral (n-1)
-
 {-
 vectorFMax :: Vector Float -> Float
 vectorFMax = toScalarF Max
@@ -114,15 +102,6 @@ vectorMinIndex :: Vector Double -> Int
 vectorMinIndex = round . toScalarR MinIdx
 
 
-{- | creates a vector with a given number of equal components:
-
-@> constant 2 7
-7 |> [2.0,2.0,2.0,2.0,2.0,2.0,2.0]@
--}
-constant :: Element a => a -> Int -> Vector a
--- constant x n = runSTVector (newVector x n)
-constant = constantD -- about 2x faster
-
 {- | creates a Vector of the specified length using the supplied function to
      to map the index to the value at that index.
 
@@ -130,26 +109,11 @@ constant = constantD -- about 2x faster
 4 |> [0.0,1.0,2.0,3.0]@
 
 -}
-buildVector :: Element a => Int -> (Int -> a) -> Vector a
+buildVector :: Storable a => Int -> (Int -> a) -> Vector a
 buildVector len f =
     fromList $ map f [0 .. (len - 1)]
 
 
-{- | Show a vector using a function for showing matrices.
-
-@disp = putStr . vecdisp ('dispf' 2)
-
-\> disp ('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
-
 -- | unzip for Vectors
 unzipVector :: (Storable a, Storable b, Storable (a,b)) => Vector (a,b) -> (Vector a,Vector b)
 unzipVector = unzipVectorWith id
diff --git a/lib/Graphics/Plot.hs b/lib/Graphics/Plot.hs
index 02b0c4c..b2acc15 100644
--- a/lib/Graphics/Plot.hs
+++ b/lib/Graphics/Plot.hs
@@ -30,7 +30,7 @@ module Graphics.Plot(
 
 import Data.Packed
 import Numeric.LinearAlgebra(outer)
-import Numeric.LinearAlgebra.Linear(Vectors(..))
+import Numeric.LinearAlgebra.Linear
 import Data.List(intersperse)
 import System.Process (system)
 
@@ -153,10 +153,10 @@ matrixToPGM m = header ++ unlines (map unwords ll) where
     maxgray = 255.0
     maxval = vectorMax $ flatten $ m
     minval = vectorMin $ flatten $ m
-    scale = if (maxval == minval) 
+    scale' = if (maxval == minval) 
         then 0.0
         else maxgray / (maxval - minval)
-    f x = show ( round ( scale *(x - minval) ) :: Int )
+    f x = show ( round ( scale' *(x - minval) ) :: Int )
     ll = map (map f) (toLists m)
 
 -- | imshow shows a representation of a matrix as a gray level image using ImageMagick's display.
diff --git a/lib/Numeric/LinearAlgebra.hs b/lib/Numeric/LinearAlgebra.hs
index 7664a9f..e8a14d6 100644
--- a/lib/Numeric/LinearAlgebra.hs
+++ b/lib/Numeric/LinearAlgebra.hs
@@ -15,9 +15,11 @@ This module reexports all normally required functions for Linear Algebra applica
 module Numeric.LinearAlgebra (
     module Data.Packed,
     module Numeric.LinearAlgebra.Algorithms,
-    module Numeric.LinearAlgebra.Interface
+    module Numeric.LinearAlgebra.Interface,
+    module Numeric.LinearAlgebra.Linear
 ) where
 
 import Data.Packed
 import Numeric.LinearAlgebra.Algorithms
 import Numeric.LinearAlgebra.Interface
+import Numeric.LinearAlgebra.Linear
diff --git a/lib/Numeric/LinearAlgebra/Algorithms.hs b/lib/Numeric/LinearAlgebra/Algorithms.hs
index 5191480..1109296 100644
--- a/lib/Numeric/LinearAlgebra/Algorithms.hs
+++ b/lib/Numeric/LinearAlgebra/Algorithms.hs
@@ -21,7 +21,6 @@ imported from "Numeric.LinearAlgebra.LAPACK".
 module Numeric.LinearAlgebra.Algorithms (
 -- * Supported types
     Field(),
-    Vectors(..),
 -- * Products
     multiply, -- dot, moved dot to typeclass
     outer, kronecker,
@@ -67,7 +66,6 @@ module Numeric.LinearAlgebra.Algorithms (
 -- * Misc
     ctrans,
     eps, i,
-    Linear(..),
 -- * Util
     haussholder,
     unpackQR, unpackHess,
@@ -78,7 +76,7 @@ module Numeric.LinearAlgebra.Algorithms (
 
 
 import Data.Packed.Internal hiding ((//))
-import Data.Packed.Vector
+--import Data.Packed.Vector
 import Data.Packed.Matrix
 import Data.Complex
 import Numeric.GSL.Vector
diff --git a/lib/Numeric/LinearAlgebra/Interface.hs b/lib/Numeric/LinearAlgebra/Interface.hs
index 8d2b52a..f8917a0 100644
--- a/lib/Numeric/LinearAlgebra/Interface.hs
+++ b/lib/Numeric/LinearAlgebra/Interface.hs
@@ -28,7 +28,7 @@ import Numeric.LinearAlgebra.Instances()
 import Data.Packed.Vector
 import Data.Packed.Matrix
 import Numeric.LinearAlgebra.Algorithms
-import Numeric.LinearAlgebra.Linear()
+import Numeric.LinearAlgebra.Linear
 
 --import Numeric.GSL.Vector
 
diff --git a/lib/Numeric/LinearAlgebra/Linear.hs b/lib/Numeric/LinearAlgebra/Linear.hs
index 8922e51..9a7e65f 100644
--- a/lib/Numeric/LinearAlgebra/Linear.hs
+++ b/lib/Numeric/LinearAlgebra/Linear.hs
@@ -16,11 +16,15 @@ Basic optimized operations on vectors and matrices.
 -----------------------------------------------------------------------------
 
 module Numeric.LinearAlgebra.Linear (
+    -- * Linear Algebra Typeclasses
     Vectors(..),                                    
-    Linear(..)
+    Linear(..),
+    -- * Creation of numeric vectors
+    constant, linspace
 ) where
 
 import Data.Packed.Internal.Vector
+import Data.Packed.Internal.Matrix
 import Data.Packed.Matrix
 import Data.Complex
 import Numeric.GSL.Vector
@@ -29,6 +33,7 @@ import Control.Monad(ap)
 
 -- | basic Vector functions
 class Num e => Vectors a e where
+    -- the C functions sumX are twice as fast as using foldVector
     vectorSum :: a e -> e
     euclidean :: a e -> e
     absSum    :: a e -> e
@@ -153,3 +158,29 @@ instance (Linear Vector a, Container Matrix a) => (Linear Matrix a) where
     divide = liftMatrix2 divide
     equal a b = cols a == cols b && flatten a `equal` flatten b
     scalar x = (1><1) [x]
+
+
+----------------------------------------------------
+
+{- | creates a vector with a given number of equal components:
+
+@> constant 2 7
+7 |> [2.0,2.0,2.0,2.0,2.0,2.0,2.0]@
+-}
+constant :: Element a => a -> Int -> Vector a
+-- constant x n = runSTVector (newVector x n)
+constant = constantD -- about 2x faster
+
+{- | Creates a real vector containing a range of values:
+
+@\> linspace 5 (-3,7)
+5 |> [-3.0,-0.5,2.0,4.5,7.0]@
+
+Logarithmic spacing can be defined as follows:
+
+@logspace n (a,b) = 10 ** linspace n (a,b)@
+-}
+linspace :: (Enum e, Linear Vector e) => Int -> (e, e) -> Vector e
+linspace n (a,b) = addConstant a $ scale s $ fromList [0 .. fromIntegral n-1]
+    where s = (b-a)/fromIntegral (n-1)
+