DynamicTimeWarp (empty) → 0.1.0.0

raw patch · 6 files changed

+341/−0 lines, 6 filesdep +QuickCheckdep +arraydep +basesetup-changed

Dependencies added: QuickCheck, array, base, criterion, random, vector

Files

• DynamicTimeWarp.cabal +81/−0
• LICENSE +165/−0
• Setup.hs +2/−0
• src/Benchmark.hs +33/−0
• src/Data/Vector/DynamicTimeWarping.hs +39/−0
• src/Test.hs +21/−0

@@ -0,0 +1,81 @@+-- Initial DynamicTimeWarp.cabal generated by cabal init.  For further +-- documentation, see http://haskell.org/cabal/users-guide/++-- The name of the package.+name:                DynamicTimeWarp++-- The package version.  See the Haskell package versioning policy (PVP) +-- for standards guiding when and how versions should be incremented.+-- http://www.haskell.org/haskellwiki/Package_versioning_policy+-- PVP summary:      +-+------- breaking API changes+--                   | | +----- non-breaking API additions+--                   | | | +--- code changes with no API change+version:             0.1.0.0++-- A short (one-line) description of the package.+synopsis:            Dynamic time warping of sequences.++-- A longer description of the package.+-- description:         ++-- URL for the project homepage or repository.+homepage:            https://github.com/zombiecalypse/DynamicTimeWarp++-- The license under which the package is released.+license:             LGPL-3++-- The file containing the license text.+license-file:        LICENSE++-- The package author(s).+author:              Aaron Karper++-- An email address to which users can send suggestions, bug reports, and +-- patches.+maintainer:          maergil@gmail.com++-- A copyright notice.+-- copyright:           ++category:            Data++build-type:          Simple++-- Extra files to be distributed with the package, such as examples or a +-- README.+-- extra-source-files:  ++-- Constraint on the version of Cabal needed to build this package.+cabal-version:       >=1.10+++library+  -- Modules exported by the library.+  exposed-modules:     Data.Vector.DynamicTimeWarping+  +  -- Modules included in this library but not exported.+  -- other-modules:       +  +  -- LANGUAGE extensions used by modules in this package.+  -- other-extensions:    +  +  -- Other library packages from which modules are imported.+  build-depends:       base >=4.6 && <4.7, vector, array+  +  -- Directories containing source files.+  hs-source-dirs:      src+  +  -- Base language which the package is written in.+  default-language:    Haskell2010+  +executable benchmark+  main-is: Benchmark.hs+  hs-source-dirs:      src+  build-depends:       base >=4.6 && <4.7, vector, array, criterion == 1.0.*, random == 1.0.*+  default-language:    Haskell2010+  +executable test+  main-is: Test.hs+  hs-source-dirs:      src+  build-depends:       base >=4.6 && <4.7, vector, array, QuickCheck == 2.7.*+  default-language:    Haskell2010

@@ -0,0 +1,165 @@+                  GNU LESSER GENERAL PUBLIC LICENSE+                       Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.+++  This version of the GNU Lesser General Public License incorporates+the terms and conditions of version 3 of the GNU General Public+License, supplemented by the additional permissions listed below.++  0. Additional Definitions.++  As used herein, "this License" refers to version 3 of the GNU Lesser+General Public License, and the "GNU GPL" refers to version 3 of the GNU+General Public License.++  "The Library" refers to a covered work governed by this License,+other than an Application or a Combined Work as defined below.++  An "Application" is any work that makes use of an interface provided+by the Library, but which is not otherwise based on the Library.+Defining a subclass of a class defined by the Library is deemed a mode+of using an interface provided by the Library.++  A "Combined Work" is a work produced by combining or linking an+Application with the Library.  The particular version of the Library+with which the Combined Work was made is also called the "Linked+Version".++  The "Minimal Corresponding Source" for a Combined Work means the+Corresponding Source for the Combined Work, excluding any source code+for portions of the Combined Work that, considered in isolation, are+based on the Application, and not on the Linked Version.++  The "Corresponding Application Code" for a Combined Work means the+object code and/or source code for the Application, including any data+and utility programs needed for reproducing the Combined Work from the+Application, but excluding the System Libraries of the Combined Work.++  1. Exception to Section 3 of the GNU GPL.++  You may convey a covered work under sections 3 and 4 of this License+without being bound by section 3 of the GNU GPL.++  2. 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You may convey such object+code under terms of your choice, provided that, if the incorporated+material is not limited to numerical parameters, data structure+layouts and accessors, or small macros, inline functions and templates+(ten or fewer lines in length), you do both of the following:++   a) Give prominent notice with each copy of the object code that the+   Library is used in it and that the Library and its use are+   covered by this License.++   b) Accompany the object code with a copy of the GNU GPL and this license+   document.++  4. 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Combined Libraries.++  You may place library facilities that are a work based on the+Library side by side in a single library together with other library+facilities that are not Applications and are not covered by this+License, and convey such a combined library under terms of your+choice, if you do both of the following:++   a) Accompany the combined library with a copy of the same work based+   on the Library, uncombined with any other library facilities,+   conveyed under the terms of this License.++   b) Give prominent notice with the combined library that part of it+   is a work based on the Library, and explaining where to find the+   accompanying uncombined form of the same work.++  6. Revised Versions of the GNU Lesser General Public License.++  The Free Software Foundation may publish revised and/or new versions+of the GNU Lesser General Public License from time to time. Such new+versions will be similar in spirit to the present version, but may+differ in detail to address new problems or concerns.++  Each version is given a distinguishing version number. If the+Library as you received it specifies that a certain numbered version+of the GNU Lesser General Public License "or any later version"+applies to it, you have the option of following the terms and+conditions either of that published version or of any later version+published by the Free Software Foundation. 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@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

@@ -0,0 +1,33 @@+import Control.Monad+import Control.Arrow (first, second)+import Control.Applicative+import Data.Vector.DynamicTimeWarping+import Data.Vector.Unboxed (fromList, Vector, postscanl)+import System.Random+import Text.Printf++import Criterion+import Criterion.Main++genSeq :: Int -> IO (Int, Vector (Float, Float))+genSeq n = do+  let genTuple = (,) <$> randomRIO (0,100) <*> randomRIO (0,100)+  (,) n <$> postscanl (\(x,y) (z,w) -> (x+z,y+w)) (0,0) . fromList <$> replicateM n genTuple++genSeqs (l, r) = do+  left <- genSeq l+  right <- genSeq r+  return (left, right)++setupEnv = do+  let sizes = [(l, r) | l <- [5,10,100, 1000, 10000], r <- [5,10,100, 1000, 10000], l <= r] :: [(Int, Int)]+  mapM genSeqs sizes++dist (l, r) = distanceBy (\(x1,x2) (y1,y2) -> (x1-y1)^2 + (x2-y2)^2) l r++main = defaultMain [+  env setupEnv $ \ ~l ->+    bgroup "dtw" [+      bench (printf "dtw(%03d, %03d)" l r) $ nf dist (ll,rr) | ((l, ll), (r, rr)) <- l+    ]+  ]

@@ -0,0 +1,39 @@+module Data.Vector.DynamicTimeWarping where+import Control.Monad (forM_)+import qualified Data.Vector.Generic as V+import qualified Data.Array.ST as ST+import qualified Data.Array.MArray as MArray+import qualified Data.Array.Base as Arr++-- | Calculate the modification distance of two vectors.+--+-- The sequences don't need to be of equal length, multiple points of one+-- sequence can be matched to the same point of the other sequence. The matches+-- must be in order though.+distanceBy :: V.Vector v a => (a -> a -> Float) -> v a -> v a -> Float+distanceBy d left right+  | V.null left || V.null right = 1/0+  | otherwise =+    -- The algorithm is extremely simple in an imperative framework unless we+    -- carefully craft the memoization. Even then the mutable array is way+    -- faster.+    let lenl = V.length left+        lenr = V.length right+        def = 1/0+        tabl = ST.runSTUArray $ do+          table <- MArray.newArray_ ((0,0), (lenl, lenr))+          let write = MArray.writeArray table+              read_ = MArray.readArray table+          write (0,0) 0+          forM_ [1..lenl] $ \i -> write (i, 0) def+          forM_ [1..lenr] $ \j -> write (0, j) def+          forM_ [1..lenl] $ \i ->+            forM_ [1..lenr] $ \j -> do+              ins <- read_ (i-1,j)+              del <- read_ (i,j-1)+              mat <- read_ (i-1,j-1)+              let cost = d (left V.! (i-1)) (right V.! (j-1))+                  rec = ins `min` del `min` mat+              write (i,j) $ cost + rec+          return table+    in tabl Arr.! (lenl, lenr)

@@ -0,0 +1,21 @@+{-# LANGUAGE TemplateHaskell #-}+import Data.Vector.DynamicTimeWarping+import Data.Vector.Unboxed (fromList)+import Test.QuickCheck++dist l r = distanceBy (\x y -> (x-y)^2) l r++prop_Reflexivity :: [Float] -> [Float] -> Bool+prop_Reflexivity l r =+  let l' = fromList l+      r' = fromList r+  in abs (dist l' r' - dist r' l') <= 1e-10 ||+        (dist l' r' == 1/0 && dist r' l' == 1/0)++prop_NonNegative :: [Float] -> [Float] -> Bool+prop_NonNegative l r =+  let l' = fromList l+      r' = fromList r+  in dist l' r' >= 0++main = $quickCheckAll