From 5158a1717f1d4caee25669a0781602fe64787302 Mon Sep 17 00:00:00 2001
From: Alberto Ruiz <aruiz@um.es>
Date: Thu, 22 May 2014 11:49:23 +0200
Subject: initial support for sparse matrix

---
 packages/base/src/Numeric/Container.hs          | 37 +++++++++++++++----------
 packages/base/src/Numeric/LinearAlgebra.hs      | 14 +++++-----
 packages/base/src/Numeric/LinearAlgebra/Data.hs |  7 ++++-
 3 files changed, 35 insertions(+), 23 deletions(-)

(limited to 'packages/base/src/Numeric')

diff --git a/packages/base/src/Numeric/Container.hs b/packages/base/src/Numeric/Container.hs
index 264a619..0633640 100644
--- a/packages/base/src/Numeric/Container.hs
+++ b/packages/base/src/Numeric/Container.hs
@@ -32,11 +32,11 @@ module Numeric.Container (
     diag, ident,
     ctrans,
     -- * Generic operations
-    Container(..),
+    Container(..), Transposable(..), Linear(..),
     -- * Matrix product
     Product(..), udot, dot, (◇),
     Mul(..),
-    Contraction(..),
+    Contraction(..),(<.>),
     optimiseMult,
     mXm,mXv,vXm,LSDiv(..),
     outer, kronecker,
@@ -55,7 +55,9 @@ module Numeric.Container (
     IndexOf,
     module Data.Complex,
     -- * IO
-    module Data.Packed.IO
+    module Data.Packed.IO,
+    -- * Misc
+    Testable(..)
 ) where
 
 import Data.Packed hiding (stepD, stepF, condD, condF, conjugateC, conjugateQ)
@@ -87,10 +89,9 @@ linspace n (a,b) = addConstant a $ scale s $ fromList $ map fromIntegral [0 .. n
 
 --------------------------------------------------------
 
-class Contraction a b c | a b -> c
-  where
-    infixl 7 <.>
-    {- | Matrix product, matrix - vector product, and dot product
+{- | Matrix product, matrix - vector product, and dot product (equivalent to 'contraction')
+
+(This operator can also be written using the unicode symbol ◇ (25c7).)
 
 Examples:
 
@@ -129,22 +130,28 @@ For complex vectors the first argument is conjugated:
 
 >>> fromList [1,i,1-i] <.> complex a
 fromList [10.0 :+ 4.0,12.0 :+ 4.0,14.0 :+ 4.0,16.0 :+ 4.0]
-
 -}
-    (<.>) :: a -> b -> c
+infixl 7 <.>
+(<.>) :: Contraction a b c => a -> b -> c
+(<.>) = contraction
 
 
+class Contraction a b c | a b -> c
+  where
+    -- | Matrix product, matrix - vector product, and dot product
+    contraction :: a -> b -> c
+
 instance (Product t, Container Vector t) => Contraction (Vector t) (Vector t) t where
-    u <.> v = conj u `udot` v
+    u `contraction` v = conj u `udot` v
 
 instance Product t => Contraction (Matrix t) (Vector t) (Vector t) where
-    (<.>) = mXv
+    contraction = mXv
 
 instance (Container Vector t, Product t) => Contraction (Vector t) (Matrix t) (Vector t) where
-    (<.>) v m = (conj v) `vXm` m
+    contraction v m = (conj v) `vXm` m
 
 instance Product t => Contraction (Matrix t) (Matrix t) (Matrix t) where
-    (<.>) = mXm
+    contraction = mXm
 
 
 --------------------------------------------------------------------------------
@@ -229,10 +236,10 @@ instance Container Matrix e => Build (Int,Int) (e -> e -> e) Matrix e
 
 --------------------------------------------------------------------------------
 
--- | alternative unicode symbol (25c7) for the contraction operator '(\<.\>)'
+-- | alternative unicode symbol (25c7) for 'contraction'
 (◇) :: Contraction a b c => a -> b -> c
 infixl 7 ◇
-(◇) = (<.>)
+(◇) = contraction
 
 -- | dot product: @cdot u v = 'udot' ('conj' u) v@
 dot :: (Container Vector t, Product t) => Vector t -> Vector t -> t
diff --git a/packages/base/src/Numeric/LinearAlgebra.hs b/packages/base/src/Numeric/LinearAlgebra.hs
index 96bf29f..549ebd0 100644
--- a/packages/base/src/Numeric/LinearAlgebra.hs
+++ b/packages/base/src/Numeric/LinearAlgebra.hs
@@ -37,11 +37,11 @@ module Numeric.LinearAlgebra (
 
     -- * Matrix product
     (<.>),
-    
-    -- | This operator can also be written using the unicode symbol ◇ (25c7).
+
+    -- | The overloaded multiplication operator may need type annotations to remove
+    -- ambiguity. In those cases we can also use the specific functions 'mXm', 'mXv', and 'dot'.
     --
-    
-    -- | The matrix x matrix product is also implemented in the "Data.Monoid" instance, where
+    -- The matrix x matrix product is also implemented in the "Data.Monoid" instance, where
     -- single-element matrices (created from numeric literals or using 'scalar')
     -- are used for scaling.
     --
@@ -52,6 +52,7 @@ module Numeric.LinearAlgebra (
     -- , 4.0, 10.0, 0.0 ]
     --
     -- 'mconcat' uses 'optimiseMult' to get the optimal association order.
+
      
     -- * Other products
     outer, kronecker, cross,
@@ -125,7 +126,7 @@ module Numeric.LinearAlgebra (
     RandDist(..), randomVector, rand, randn, gaussianSample, uniformSample,
     
     -- * Misc
-    meanCov, peps, relativeError, haussholder, optimiseMult, udot, Seed, (◇)
+    meanCov, peps, relativeError, haussholder, optimiseMult, dot, udot, mXm, mXv, smXv, (<>), (◇), Seed, checkT
 ) where
 
 import Numeric.LinearAlgebra.Data
@@ -136,6 +137,5 @@ import Numeric.Container
 import Numeric.LinearAlgebra.Algorithms
 import Numeric.LinearAlgebra.Util
 import Numeric.LinearAlgebra.Random
-
-
+import Data.Packed.Internal.Sparse(smXv)
 
diff --git a/packages/base/src/Numeric/LinearAlgebra/Data.hs b/packages/base/src/Numeric/LinearAlgebra/Data.hs
index 7e8af03..49bc1c0 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Data.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Data.hs
@@ -48,6 +48,10 @@ module Numeric.LinearAlgebra.Data(
     latexFormat,
     dispf, disps, dispcf, format,
 
+    -- * Sparse
+    SMatrix, AssocMatrix, mkCSR, toDense,
+    mkDiag,
+
 -- * Conversion
     Convert(..),
     
@@ -56,7 +60,7 @@ module Numeric.LinearAlgebra.Data(
     rows, cols,
     separable,
 
-    module Data.Complex
+    module Data.Complex,
 
 ) where
 
@@ -65,4 +69,5 @@ import Data.Packed.Matrix
 import Numeric.Container
 import Numeric.LinearAlgebra.Util
 import Data.Complex
+import Data.Packed.Internal.Sparse
 
-- 
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