hstatistics 0.1.0.3 → 0.1.0.4

raw patch · 11 files changed

+125/−86 lines, 11 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• CHANGES +6/−2
• configure.hs +7/−1
• hstatistics.cabal +1/−1
• lib/Numeric/GSL/Distribution/Continuous.hs +5/−4
• lib/Numeric/GSL/Distribution/Discrete.hs +5/−4
• lib/Numeric/GSL/Fitting/Linear.hs +56/−25
• lib/Numeric/GSL/Histogram.hs +11/−16
• lib/Numeric/GSL/Histogram2D.hs +13/−14
• lib/Numeric/GSL/Permutation.hs +4/−3
• lib/Numeric/GSL/Statistics.hs +1/−1
• lib/Numeric/GSL/fitting-aux.c +16/−15

@@ -6,5 +6,9 @@ 		updated to reflect exportation of check from Data.Packed.Development 		   in hmatrix-0.9.3.0 -0.1.03:		-		added Numeric.GSL.Regression.Linear+0.1.0.3:		+		added Numeric.GSL.Fitting.Linear++0.1.0.4:+		fixed argument types in Numeric.GSL.Fitting.Linear+		removed redundant imports

@@ -18,7 +18,7 @@ -}  import System-import System.Directory(createDirectoryIfMissing)+import System.Directory(createDirectoryIfMissing,getCurrentDirectory,getDirectoryContents) import Data.List(isPrefixOf, intercalate) import Distribution.Simple.LocalBuildInfo import Distribution.Simple.Configure@@ -96,6 +96,12 @@           cs x   = x  main = do+    dir <- getCurrentDirectory+    putStrLn $ "Current directory: " ++ dir++    files <- getDirectoryContents dir+    mapM_ putStrLn files+     putStr "Checking foreign libraries..."      args <- getArgs

@@ -1,5 +1,5 @@ Name:               hstatistics-Version:            0.1.0.3+Version:            0.1.0.4 License:            GPL License-file:       LICENSE Copyright:          (c) A.V.H. McPhail 2010

@@ -36,13 +36,14 @@  --import Numeric.LinearAlgebra.Linear -import Control.Monad(when)+--import Control.Monad(when)  import Foreign hiding(shift)-import Foreign.ForeignPtr+--import Foreign.ForeignPtr --import Foreign.Marshal.Alloc(alloca)-import Foreign.C.Types(CInt,CChar)-import Foreign.C.String(newCString,peekCString)+--import Foreign.C.Types(CInt,CChar)+import Foreign.C.Types(CInt)+--import Foreign.C.String(newCString,peekCString)  --import GHC.ForeignPtr           (mallocPlainForeignPtrBytes) 

@@ -32,13 +32,14 @@  --import Numeric.LinearAlgebra.Linear -import Control.Monad(when)+--import Control.Monad(when)  import Foreign hiding(shift)-import Foreign.ForeignPtr+--import Foreign.ForeignPtr --import Foreign.Marshal.Alloc(alloca)-import Foreign.C.Types(CInt,CUInt,CChar)-import Foreign.C.String(newCString,peekCString)+--import Foreign.C.Types(CInt,CUInt,CChar)+import Foreign.C.Types(CInt,CUInt)+--import Foreign.C.String(newCString,peekCString)  --import GHC.ForeignPtr           (mallocPlainForeignPtrBytes) 

@@ -14,13 +14,13 @@ -----------------------------------------------------------------------------  module Numeric.GSL.Fitting.Linear (-                                   linear, linear_w+                                   linear, linear_w, linear_est                              ) where  -----------------------------------------------------------------------------  import Data.Packed.Vector-import Data.Packed.Matrix+--import Data.Packed.Matrix import Data.Packed.Development  --import Numeric.LinearAlgebra.Linear@@ -28,7 +28,7 @@ --import Control.Monad(when)  import Foreign-import Foreign.ForeignPtr+--import Foreign.ForeignPtr --import Foreign.Marshal.Alloc(alloca) import Foreign.C.Types(CInt) --import Foreign.C.String(newCString,peekCString)@@ -45,22 +45,27 @@ -- | fits the model Y = C X linear :: Vector Double    -- ^ x data        -> Vector Double    -- ^ y data-       -> (Vector Double,Vector Double,Matrix Double,Matrix Double,Matrix Double,Matrix Double) -- ^ (c_0,c_1,cov_00,cov_01,cov_11,chi_sq)+       -> (Double,Double,Double,Double,Double,Double) -- ^ (c_0,c_1,cov_00,cov_01,cov_11,chi_sq) linear x y = unsafePerformIO $ do-           let s = dim x-           c0 <- createVector 1-           c1 <- createVector 1-           cov00 <- createMatrix RowMajor s s-           cov01 <- createMatrix RowMajor s s-           cov11 <- createMatrix RowMajor s s-           chi_sq <- createMatrix RowMajor s s-           app8 fitting_linear vec x vec y vec c0 vec c1 mat cov00 mat cov01 mat cov11 mat chi_sq "linear"-           return (c0,c1,cov00,cov01,cov11,chi_sq)+           alloca $ \c0 ->+               alloca $ \c1 ->+                   alloca $ \chi_sq -> +                       alloca $ \cov00 -> +                           alloca $ \cov01 -> +                               alloca $ \cov11 -> do+                                                  app2 (fitting_linear c0 c1 chi_sq cov00 cov01 cov11) vec x vec y "linear"+                                                  c0' <- peek c0+                                                  c1' <- peek c1+                                                  cov00' <- peek cov00+                                                  cov01' <- peek cov01+                                                  cov11' <- peek cov11+                                                  chi_sq' <- peek chi_sq+                                                  return (c0',c1',cov00',cov01',cov11',chi_sq')   ----------------------------------------------------------------------------- -foreign import ccall "fitting-aux.h linear" fitting_linear :: CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> IO CInt+foreign import ccall "fitting-aux.h linear" fitting_linear :: Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> IO CInt  ----------------------------------------------------------------------------- @@ -68,21 +73,47 @@ linear_w :: Vector Double    -- ^ x data          -> Vector Double    -- ^ x weights          -> Vector Double    -- ^ y data-         -> (Vector Double,Vector Double,Matrix Double,Matrix Double,Matrix Double,Matrix Double) -- ^ (c_0,c_1,cov_00,cov_01,cov_11,chi_sq)+         -> (Double,Double,Double,Double,Double,Double) -- ^ (c_0,c_1,cov_00,cov_01,cov_11,chi_sq) linear_w x w y = unsafePerformIO $ do-             let s = dim x-             c0 <- createVector 1-             c1 <- createVector 1-             cov00 <- createMatrix RowMajor s s-             cov01 <- createMatrix RowMajor s s-             cov11 <- createMatrix RowMajor s s-             chi_sq <- createMatrix RowMajor s s-             app9 fitting_linear_w vec x vec w vec y vec c0 vec c1 mat cov00 mat cov01 mat cov11 mat chi_sq "linear_w"-             return (c0,c1,cov00,cov01,cov11,chi_sq)+             alloca $ \c0 ->+                 alloca $ \c1 ->+                     alloca $ \chi_sq ->+                       alloca $ \cov00 -> +                           alloca $ \cov01 -> +                               alloca $ \cov11 -> do+                                                  app3 (fitting_linear_w c0 c1 chi_sq cov00 cov01 cov11) vec x vec w vec y "linear_w"+                                                  c0' <- peek c0+                                                  c1' <- peek c1+                                                  cov00' <- peek cov00+                                                  cov01' <- peek cov01+                                                  cov11' <- peek cov11+                                                  chi_sq' <- peek chi_sq+                                                  return (c0',c1',cov00',cov01',cov11',chi_sq') +----------------------------------------------------------------------------- +foreign import ccall "fitting-aux.h linear_weighted" fitting_linear_w :: Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> IO CInt+ ----------------------------------------------------------------------------- -foreign import ccall "fitting-aux.h linear_weighted" fitting_linear_w :: CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> CInt -> CInt -> Ptr Double -> IO CInt+-- | computes the fitted function and standard deviation at the input point+linear_est :: Double          -- ^ x data point+           -> Double          -- ^ c0+           -> Double          -- ^ c1+           -> Double          -- ^ cov00+           -> Double          -- ^ cov01+           -> Double          -- ^ cov11+           -> (Double,Double) -- ^ (y,error)+linear_est x c0 c1 cov00 cov01 cov11 = unsafePerformIO $ do+                                       alloca $ \y ->+                                           alloca $ \e -> do+                                               check "linear_est" $ fitting_linear_est x c0 c1 cov00 cov01 cov11 y e+                                               y' <- peek y+                                               e' <- peek e+                                               return (y',e')++-----------------------------------------------------------------------------++foreign import ccall "fitting-aux.h linear_estimate" fitting_linear_est :: Double -> Double -> Double -> Double -> Double -> Double -> Ptr Double -> Ptr Double -> IO CInt  -----------------------------------------------------------------------------

@@ -40,13 +40,14 @@  --import Numeric.LinearAlgebra.Linear -import Control.Monad+--import Control.Monad  import Foreign hiding(shift)-import Foreign.ForeignPtr-import Foreign.Marshal.Alloc(alloca)+--import Foreign.ForeignPtr+--import Foreign.Marshal.Alloc(alloca) import Foreign.C.Types(CInt,CChar)-import Foreign.C.String(newCString,peekCString)+--import Foreign.C.String(newCString,peekCString)+import Foreign.C.String(newCString) --import Control.Monad(when)  --import GHC.ForeignPtr           (mallocPlainForeignPtrBytes)@@ -108,7 +109,7 @@ fromLimitsIO n (l,u) = do                          h <- histogram_new (fromIntegral n)                          h' <- newForeignPtr histogram_free h-                         withForeignPtr h' (\f -> histogram_set_ranges_uniform f l u)+                         check "set_ranges_uniform" $ withForeignPtr h' (\f -> histogram_set_ranges_uniform f l u)                          return $ H n h'  foreign import ccall "gsl-histogram.h gsl_histogram_set_ranges" histogram_set_ranges :: HistHandle -> CInt -> Ptr Double -> IO CInt@@ -190,9 +191,7 @@  -- | add 1.0 to the correct bin, fails silently if the value is outside the range incrementIO :: Histogram -> Double -> IO ()-incrementIO (H _ h) x = do-                       withForeignPtr h (\f -> histogram_increment f x)-                       return ()+incrementIO (H _ h) x = withForeignPtr h (\f -> check "increment" $ histogram_increment f x)  -- | add 1.0 to the correct bin for each element of the vector, fails silently if the value is outside the range incrementListIO :: Histogram -> [Double] -> IO ()@@ -206,9 +205,7 @@  -- | adds the weight (second Double) to the bin appropriate for the value (first Double) accumulateIO :: Histogram -> Double -> Double -> IO ()-accumulateIO (H _ h) x w = do-                           withForeignPtr h (\f -> histogram_accumulate f x w)-                           return ()+accumulateIO (H _ h) x w = withForeignPtr h (\f -> check "accumulate" $ histogram_accumulate f x w)  -- | add the weight (snd) to the correct bin for each (fst) element of the list, fails silently if the value is outside the range accumulateListIO :: Histogram -> [(Double,Double)] -> IO ()@@ -232,7 +229,7 @@ getRange (H _ h) b = unsafePerformIO $ do                    alloca $ \l ->                        alloca $ \u -> do-                       withForeignPtr h (\f -> histogram_get_range f (fromIntegral b) l u)+                       check "get_range" $ withForeignPtr h (\f -> histogram_get_range f (fromIntegral b) l u)                        l' <- peek l                        u' <- peek u                        return (l',u')@@ -251,9 +248,7 @@  -- | reset all the bins to zero reset :: Histogram -> IO ()-reset (H _ h) = do-                 withForeignPtr h histogram_reset-                 return ()+reset (H _ h) = withForeignPtr h histogram_reset  foreign import ccall "gsl-histogram.h gsl_histogram_increment" histogram_increment :: HistHandle -> Double -> IO CInt foreign import ccall "gsl-histogram.h gsl_histogram_accumulate" histogram_accumulate :: HistHandle -> Double -> Double -> IO CInt@@ -458,7 +453,7 @@                         p <- histogram_pdf_new $ fromIntegral b                          p' <- newForeignPtr histogram_pdf_free p                         withForeignPtr p' $ \p'' -> -                            withForeignPtr h $ \h' -> histogram_pdf_init p'' h'+                            withForeignPtr h $ \h' -> check "pdf_init" $ histogram_pdf_init p'' h'                         return $ P p'  -- | given a randomm from the uniform distribution [0,1], draw a random sample from the PDF

@@ -41,14 +41,15 @@  --import Numeric.LinearAlgebra.Linear -import Control.Monad+--import Control.Monad+--import Control.Monad(when)  import Foreign hiding(shift)-import Foreign.ForeignPtr-import Foreign.Marshal.Alloc(alloca)+--import Foreign.ForeignPtr+--import Foreign.Marshal.Alloc(alloca) import Foreign.C.Types(CInt,CChar)-import Foreign.C.String(newCString,peekCString)---import Control.Monad(when)+--import Foreign.C.String(newCString,peekCString)+import Foreign.C.String(newCString)  --import GHC.ForeignPtr           (mallocPlainForeignPtrBytes) @@ -114,7 +115,7 @@ fromLimitsIO nx ny (lx,ux) (uy,ly) = do                                    h <- histogram2d_new (fromIntegral nx) (fromIntegral ny)                                    h' <- newForeignPtr histogram2d_free h-                                   withForeignPtr h' (\f -> histogram2d_set_ranges_uniform f lx ux ly uy)+                                   check "set_ranges_uniform" $ withForeignPtr h' (\f -> histogram2d_set_ranges_uniform f lx ux ly uy)                                    return $ H nx ny h'  foreign import ccall "gsl-histogram2d.h gsl_histogram2d_set_ranges" histogram2d_set_ranges :: Hist2DHandle -> Ptr Double -> CInt -> Ptr Double -> CInt -> IO CInt@@ -203,7 +204,7 @@ -- | add 1.0 to the correct bin, fails silently if the value is outside the range incrementIO :: Histogram2D -> Double -> Double -> IO () incrementIO (H _ _ h) x y = do-                            withForeignPtr h (\f -> histogram2d_increment f x y)+                            check "increment" $ withForeignPtr h (\f -> histogram2d_increment f x y)                             return ()  -- | add 1.0 to the correct bin for each element of the vector pair, fails silently if the value is outside the range@@ -219,7 +220,7 @@ -- | Adds the weight (third Double) to the bin appropriate for the value (first two Doubles) accumulateIO :: Histogram2D -> Double -> Double -> Double -> IO () accumulateIO (H _ _ h) x y w = do-                               withForeignPtr h (\f -> histogram2d_accumulate f x y w)+                               check "accumulate" $ withForeignPtr h (\f -> histogram2d_accumulate f x y w)                                return ()  -- | add the weight (third) to the correct bin for each vector pair element, fails silently if the value is outside the range@@ -242,7 +243,7 @@ getXRange (H _ _ h) b = unsafePerformIO $ do                         alloca $ \l ->                             alloca $ \u -> do-                            withForeignPtr h (\f -> histogram2d_get_xrange f (fromIntegral b) l u)+                            check "get_xrange" $ withForeignPtr h (\f -> histogram2d_get_xrange f (fromIntegral b) l u)                             l' <- peek l                             u' <- peek u                             return (l',u')@@ -252,7 +253,7 @@ getYRange (H _ _ h) b = unsafePerformIO $ do                         alloca $ \l ->                             alloca $ \u -> do-                            withForeignPtr h (\f -> histogram2d_get_yrange f (fromIntegral b) l u)+                            check "get_yrange" $ withForeignPtr h (\f -> histogram2d_get_yrange f (fromIntegral b) l u)                             l' <- peek l                             u' <- peek u                             return (l',u')@@ -283,9 +284,7 @@  -- | reset all the bins to zero reset :: Histogram2D -> IO ()-reset (H _ _ h) = do-                 withForeignPtr h histogram2d_reset-                 return ()+reset (H _ _ h) = withForeignPtr h histogram2d_reset  foreign import ccall "gsl-histogram2d.h gsl_histogram2d_increment" histogram2d_increment :: Hist2DHandle -> Double -> Double -> IO CInt foreign import ccall "gsl-histogram2d.h gsl_histogram2d_accumulate" histogram2d_accumulate :: Hist2DHandle -> Double -> Double -> Double -> IO CInt@@ -520,7 +519,7 @@                               p' <- newForeignPtr histogram2d_pdf_free p                               withForeignPtr p' $ \p'' ->                                    withForeignPtr h $ \h' -> do-                                                histogram2d_pdf_init p'' h'+                                                check "pdf_init" $ histogram2d_pdf_init p'' h'                                                 return $ P p'  -- | given a randomm from the uniform distribution [0,1], draw a random sample from the PDF

@@ -37,13 +37,14 @@  --import Numeric.LinearAlgebra.Linear -import Control.Monad(when)+--import Control.Monad(when)  import Foreign hiding(shift)-import Foreign.ForeignPtr+--import Foreign.ForeignPtr --import Foreign.Marshal.Alloc(alloca) import Foreign.C.Types(CInt,CChar)-import Foreign.C.String(newCString,peekCString)+--import Foreign.C.String(newCString,peekCString)+import Foreign.C.String(newCString)  --import GHC.ForeignPtr           (mallocPlainForeignPtrBytes) 

@@ -50,7 +50,7 @@  import Foreign import Foreign.C.Types(CInt)-import Foreign.Marshal.Alloc(alloca)+--import Foreign.Marshal.Alloc(alloca)  ----------------------------------------------------------------------------- 

@@ -1,28 +1,29 @@ #include <gsl/gsl_fit.h> -int linear(int xs, const double* x, int ys, const double* y,-	   int c0s, double* c0, int c1s, double* c1,-	   int cov00x, int cov00y, double* cov00,-	   int cov01x, int cov01y, double* cov01,-	   int cov11x, int cov11y, double* cov11,-	   int chi_sqx, int chi_sqy, double* chi_sq)+int linear(double* c0, double* c1, double* chi_sq,+	   double* cov00, double* cov01, double* cov11,+	   int xs, const double* x, int ys, const double* y) {-  if (xs != ys || xs != c0s || xs != c1s) return 2000; //BAD_SIZE+  if (xs != ys) return 2000; //BAD_SIZE      return gsl_fit_linear(x,1,y,1,xs,c0,c1,cov00,cov01,cov11,chi_sq); } -int linear_weighted(int xs, const double* x, int ws, const double * w, -		    int ys, const double* y,-		    int c0s, double* c0, int c1s, double* c1,-		    int cov00x, int cov00y, double* cov00,-		    int cov01x, int cov01y, double* cov01,-		    int cov11x, int cov11y, double* cov11,-		    int chi_sqx, int chi_sqy, double* chi_sq)+int linear_weighted(double* c0, double* c1, double* chi_sq,+		    double* cov00, double* cov01, double* cov11,+		    int xs, const double* x, +		    int ws, const double * w, +		    int ys, const double* y) {-  if (xs != ys || xs != ws || xs != c0s || xs != c1s) return 2000; //BAD_SIZE+  if (xs != ys || xs != ws) return 2000; //BAD_SIZE      return gsl_fit_wlinear(x,1,w,1,y,1,xs,c0,c1,cov00,cov01,cov11,chi_sq); }  +int linear_estimate(double x, double c0, double c1, +		    double cov00, double cov01, double cov11,+		    double* y, double* e)+{+  return gsl_fit_linear_est(x,c0,c1,cov00,cov01,cov11,y,e);+}