packages feed

hnetcdf 0.3.0.0 → 0.4.0.0

raw patch · 12 files changed

+175/−514 lines, 12 filesdep −hmatrixdep ~HUnitdep ~QuickCheckdep ~containers

Dependencies removed: hmatrix

Dependency ranges changed: HUnit, QuickCheck, containers, directory, either, errors, filepath, repa, test-framework, test-framework-hunit, test-framework-quickcheck2, transformers, vector

Files

Data/NetCDF.hs view
@@ -237,7 +237,7 @@   readAttr' nc var n l NcAttrDouble nc_get_att_double  -- | Helper function for attribute reading.-readAttr' :: Show a => Int -> Int -> String -> Int -> ([a] -> NcAttr)+readAttr' :: Int -> Int -> String -> Int -> ([a] -> NcAttr)           -> (Int -> Int -> String -> Int -> IO (Int, [a])) -> Access NcAttr readAttr' nc var n l w rf = chk $ do   tmp <- rf nc var n l
− Data/NetCDF/HMatrix.hs 
@@ -1,51 +0,0 @@-{-# LANGUAGE FlexibleInstances, ConstraintKinds, TypeFamilies #-}-{-# LANGUAGE MultiParamTypeClasses, ScopedTypeVariables, GADTs #-}-{-# OPTIONS_GHC -fno-warn-orphans -fwarn-missing-methods #-}--- | NetCDF store instance for HMatrix vectors and matrices.-module Data.NetCDF.HMatrix-       ( HVector (..)-       , HMatrix (..)-       ) where--import Data.NetCDF.Store--import qualified Numeric.Container as C-import qualified Numeric.LinearAlgebra.Util as C-import Foreign.C-import Data.Packed.Vector-import Data.Packed.Development--newtype HVector a = HVector (C.Vector a)-                  deriving (Eq, Show)--instance NcStore HVector where-  type NcStoreExtraCon HVector a = C.Element a-  toForeignPtr (HVector v) = fst3 $ unsafeToForeignPtr v-  fromForeignPtr p s = HVector $ unsafeFromForeignPtr p 0 (Prelude.product s)-  smap f (HVector v) = HVector $ C.mapVector f v--data HMatrix a = HMatrix (C.Matrix a)--instance NcStore HMatrix where-  type NcStoreExtraCon HMatrix a = C.Element a-  toForeignPtr (HMatrix m) = fst3 $ unsafeToForeignPtr $ C.flatten m-  fromForeignPtr p s =-    let c = last s-        d = product s-    in HMatrix $ matrixFromVector RowMajor (d `div` c) (last s) $-       unsafeFromForeignPtr p 0 (Prelude.product s)-  smap f (HMatrix m) = HMatrix $ C.mapMatrix f m--instance C.Element CShort-instance C.Element CInt-instance C.Element CFloat-instance C.Element CDouble--instance C.Container C.Vector CFloat-instance C.Container C.Vector CDouble--instance C.Indexable (C.Vector CFloat) CFloat where (!) = (@>)-instance C.Indexable (C.Vector CDouble) CDouble where (!) = (@>)--fst3 :: (a, b, c) -> a-fst3 (x, _, _) = x
Data/NetCDF/PutGet.hs view
@@ -109,5 +109,5 @@  -- | Helper function for dealing with size (start, count, stride) -- arrays.-withSizeArray :: (Storable a, Integral a) => [a] -> (Ptr CULong -> IO b) -> IO b+withSizeArray :: Integral a => [a] -> (Ptr CULong -> IO b) -> IO b withSizeArray = withArray . liftM fromIntegral
Data/NetCDF/Raw/Attributes.chs view
@@ -5,6 +5,7 @@ module Data.NetCDF.Raw.Attributes where  import Data.Char+import Data.Word  import Data.NetCDF.Raw.Utils @@ -17,10 +18,9 @@ -- int nc_put_att_text(int ncid, int varid, const char *name, --                     size_t len, const char *op); nc_put_att_text :: Int -> Int -> String -> Int -> String -> IO Int-nc_put_att_text nc var name xtype v = do+nc_put_att_text nc var name _ v = do   let ncid = fromIntegral nc       varid = fromIntegral var-      ncxtype = fromIntegral xtype       ncsize = fromIntegral $ length v   let tv = map convChar v   withCString name $ \namep -> do@@ -34,7 +34,7 @@   nc_put_att_text'_ :: CInt -> CInt -> CString -> CULong                      -> Ptr CChar -> IO CInt -nc_put_att :: (Storable a, Storable b, Show b) =>+nc_put_att :: Storable b =>               (CInt -> CInt -> CString -> CInt -> CULong -> Ptr b -> IO CInt)             -> (a -> b) -> Int -> Int -> String -> Int -> [a] -> IO Int nc_put_att cfn conv nc var name xtype v = do@@ -171,7 +171,7 @@ {#fun nc_del_att { `Int', `Int', `String' } -> `Int' #}  -nc_get_att :: (Storable a, Storable b) =>+nc_get_att :: Storable a =>               (CInt -> CInt -> CString -> Ptr a -> IO CInt)             -> (a -> b) -> Int -> Int -> String -> Int -> IO (Int, [b]) nc_get_att cfn conv nc var name cnt = do
Data/NetCDF/Raw/Utils.hs view
@@ -4,14 +4,20 @@  module Data.NetCDF.Raw.Utils        ( module Data.NetCDF.Raw.Utils-       , module Foreign        , module Foreign.C+       , module Foreign.Ptr+       , module Foreign.Storable+       , module Foreign.Marshal.Array+       , module Foreign.Marshal.Alloc        , unsafePerformIO        ) where  import Control.Monad (liftM)-import Foreign hiding (unsafePerformIO) import Foreign.C+import Foreign.Ptr+import Foreign.Storable+import Foreign.Marshal.Array+import Foreign.Marshal.Alloc import System.IO.Unsafe (unsafePerformIO)  ncMaxName, ncMaxDims, ncMaxVars, ncMaxAttrs, ncMaxVarDims :: Int@@ -30,17 +36,17 @@ peekFloatConv :: (Storable a, RealFloat a, RealFloat b) => Ptr a -> IO b peekFloatConv = liftM realToFrac . peek -withIntArray :: (Storable a, Integral a) => [a] -> (Ptr CInt -> IO b) -> IO b+withIntArray :: Integral a => [a] -> (Ptr CInt -> IO b) -> IO b withIntArray = withArray . liftM fromIntegral -withIntPtrConv :: (Storable a, Storable b, Integral a, Integral b)+withIntPtrConv :: (Storable b, Integral a, Integral b)                   => a -> (Ptr b -> IO c) -> IO c withIntPtrConv val f =   alloca $ \ptr -> do     poke ptr (fromIntegral val)     f ptr -withFloatPtrConv :: (Storable a, Storable b, RealFloat a, RealFloat b)+withFloatPtrConv :: (Storable b, RealFloat a, RealFloat b)                     => a -> (Ptr b -> IO c) -> IO c withFloatPtrConv val f =   alloca $ \ptr -> do
Data/NetCDF/Store.hs view
@@ -1,4 +1,4 @@-{-# LANGUAGE FlexibleInstances, ConstraintKinds, TypeFamilies #-}+{-# LANGUAGE ConstraintKinds, TypeFamilies #-} -- | The /store polymorphism/ for the functions to get the values of -- NetCDF variables relies on a simple `NcStore` typeclass for -- converting between /store/ values and @ForeignPtr@s.
README.markdown view
@@ -1,6 +1,8 @@ hnetcdf ======= +[![Build Status](https://travis-ci.org/ian-ross/hnetcdf.svg?branch=master)](https://travis-ci.org/ian-ross/hnetcdf)+ Haskell NetCDF library: as well as conventional low-level FFI bindings to the functions in the NetCDF library (in the `Data.NetCDF.Raw` modules), `hnetcdf` provides a higher-level Haskell interface
examples/example1.hs view
@@ -55,7 +55,7 @@   Right slice1tmp <- getA nc zvar [0, 0, 0] [1, nlat, nlon] :: SVRet CShort   let slice1 = SV.map (/ 9.8) $ coardsScale zvar slice1tmp :: SV.Vector CDouble   putStrLn $ "length slice1 = " ++ show (length slice1)-  let idx i j = (nlat - i) * nlon + (j - 1)+  let idx i j = (nlat - j) * nlon + (i - 1)   putStrLn $ "lon(i=25) = " ++ show (lon SV.! (25 - 1))   putStrLn $ "lat(j=40) = " ++ show (lat SV.! (nlat - 40))   putStrLn $ "slice1(i=25,j=40) = " ++ show (slice1 SV.! idx 25 40)
− examples/example3.hs 
@@ -1,68 +0,0 @@-module Main where--import Prelude hiding (length, sum)-import Control.Applicative ((<$>))-import Data.NetCDF-import Data.NetCDF.HMatrix-import qualified Data.Map as M-import Foreign.C-import Foreign.Storable-import Numeric.Container--type VRet a = IO (Either NcError (HVector a))-type MRet a = IO (Either NcError (HMatrix a))--main :: IO ()-main = do-  -- Open file and access some basic metadata.-  Right nc <- openFile "z500-short.nc"-  putStrLn $ "Name: " ++ ncName nc-  putStrLn $ "Dims: " ++ show (M.keys $ ncDims nc)-  putStr $ unlines $ map (\(n, s) -> "  " ++ n ++ ": " ++ s) $-    M.toList $ flip M.map (ncDims nc) $-    \d -> show (ncDimLength d) ++ if ncDimUnlimited d then " (UNLIM)" else ""-  putStrLn $ "Vars: " ++ show (M.keys $ ncVars nc)-  putStrLn $ "Global attributes: " ++ show (M.keys $ ncAttrs nc)--  -- Get dimension sizes.-  let Just ntime = ncDimLength <$> ncDim nc "time"-      Just nlat = ncDimLength <$> ncDim nc "latitude"-      Just nlon = ncDimLength <$> ncDim nc "longitude"--  -- Get longitude variable: metadata, then all values, then a slice-  -- of values.-  let (Just lonvar) = ncVar nc "longitude"-  Right (HVector lon) <- get nc lonvar :: VRet CFloat-  let mlon = mean lon-  putStrLn $ "longitude: " ++ show lon ++ " -> " ++ show mlon-  Right (HVector lon2) <- getS nc lonvar [0] [72] [2] :: VRet CFloat-  let mlon2 = mean lon2-  putStrLn $ "longitude (every 2): " ++ show lon2 ++ " -> " ++ show mlon2--  -- Get latitude variable: metadata, then all values, then a slice of-  -- values.-  let (Just latvar) = ncVar nc "latitude"-  Right (HVector lat) <- get nc latvar :: VRet CFloat-  let mlat = mean lat-  putStrLn $ "latitude: " ++ show lat ++ " -> " ++ show mlat-  Right (HVector lat2) <- getS nc latvar [0] [37] [2] :: VRet CFloat-  let mlat2 = mean lat2-  putStrLn $ "latitude (every 2): " ++ show lat2 ++ " -> " ++ show mlat2--  -- Get Z500 variable: get a slice, do COARDS short -> double-  -- scaling, convert units.-  let (Just zvar) = ncVar nc "z500"-  putStrLn $ "z500 dims: " ++ show (map ncDimName $ ncVarDims zvar)-  Right slice1tmp <--    getA nc zvar [0, 0, 0] [1, nlat, nlon] :: MRet CShort-  let (HMatrix slice1tmp2) = coardsScale zvar slice1tmp :: HMatrix CDouble-      slice1 = cmap ((/ 9.8) . realToFrac) slice1tmp2 :: Matrix Double-  putStrLn $ "size slice1 = " ++-    show (rows slice1) ++ " x " ++ show (cols slice1)-  putStrLn $ "lon(i=25) = " ++ show (lon @> (25 - 1))-  putStrLn $ "lat(j=40) = " ++ show (lat @> (nlat - 40))-  let v @!! (i, j) = v @@> (nlat - i, j - 1)-  putStrLn $ "slice1(i=25,j=40) = " ++ show (slice1 @!! (25, 40))--mean :: (Storable a, Fractional a) => Vector a -> a-mean xs = (foldVector (+) 0 xs) / fromIntegral (dim xs)
hnetcdf.cabal view
@@ -1,178 +1,161 @@-name:                hnetcdf-version:             0.3.0.0-synopsis:            Haskell NetCDF library+name: hnetcdf+version: 0.4.0.0+cabal-version: >=1.8+build-type: Simple+license: BSD3+license-file: LICENSE+copyright: Copyright (2013) Ian Ross+maintainer: ian@skybluetrades.net+homepage: https://github.com/ian-ross/hnetcdf+synopsis: Haskell NetCDF library description:-  Bindings to the Unidata NetCDF library, along with a higher-level-  Haskell interface that attempts to provide container polymorphic-  data access (initially just Storable vectors and Repa arrays).-license:             BSD3-license-file:        LICENSE-author:              Ian Ross-maintainer:          ian@skybluetrades.net-copyright:           Copyright (2013) Ian Ross-category:            Data-build-type:          Simple-extra-source-files:  README.markdown CHANGELOG.markdown-cabal-version:       >=1.8-homepage:            https://github.com/ian-ross/hnetcdf-data-files:          test/tst-raw-get-put.nc test/tst-bathymetry.nc+    Bindings to the Unidata NetCDF library, along with a higher-level+    Haskell interface that attempts to provide container polymorphic+    data access (initially just Storable vectors and Repa arrays).+category: Data+author: Ian Ross+data-files:+    test/tst-raw-get-put.nc+    test/tst-bathymetry.nc+extra-source-files:+    README.markdown+    CHANGELOG.markdown  source-repository head-  type:     git-  location: https://github.com/ian-ross/hnetcdf---Library-  exposed-modules:     Data.NetCDF-                       Data.NetCDF.Vector-                       Data.NetCDF.Repa-                       Data.NetCDF.HMatrix-                       Data.NetCDF.Metadata-                       Data.NetCDF.PutGet-                       Data.NetCDF.Storable-                       Data.NetCDF.Store-                       Data.NetCDF.Types-                       Data.NetCDF.Utils-                       Data.NetCDF.Raw-                       Data.NetCDF.Raw.Base-                       Data.NetCDF.Raw.PutGet-                       Data.NetCDF.Raw.Attributes-                       Data.NetCDF.Raw.Utils---                       Data.NetCDF.Raw.NetCDF4-  build-depends:       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       either                      >= 3.4.1    && < 5,-                       errors                      >= 1.4.2    && < 1.5,-                       filepath                    >= 1.3      && < 1.4,-                       hmatrix                     >= 0.16.0.2 && < 0.17,-                       repa,-                       transformers                >= 0.2      && < 0.5,-                       vector                      >= 0.9      && < 0.11-  build-tools:         c2hs-  extra-libraries:     netcdf-  ghc-options:         -Wall--Test-Suite test-raw-metadata-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-raw-metadata.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       vector                      >= 0.9      && < 0.11,-                       repa,-                       test-framework              >= 0.3,-                       test-framework-hunit,-                       test-framework-quickcheck2  >= 0.3,-                       HUnit,-                       QuickCheck-  extra-libraries:     netcdf--Test-Suite test-raw-get-put-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-raw-get-put.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       vector                      >= 0.9      && < 0.11,-                       repa,-                       directory                   >= 1.1      && < 1.3,-                       test-framework              >= 0.3,-                       test-framework-hunit,-                       test-framework-quickcheck2  >= 0.3,-                       HUnit,-                       QuickCheck-  extra-libraries:     netcdf--Test-Suite test-raw-attributes-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-raw-attributes.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       vector                      >= 0.9      && < 0.11,-                       repa,-                       directory                   >= 1.1      && < 1.3,-                       test-framework              >= 0.3,-                       test-framework-hunit,-                       test-framework-quickcheck2  >= 0.3,-                       HUnit,-                       QuickCheck-  extra-libraries:     netcdf--Test-Suite test-get-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-get.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       errors                      >= 1.4.2    && < 1.5,-                       hmatrix                     >= 0.16.0.2 && < 0.17,-                       repa,-                       vector                      >= 0.9      && < 0.11,-                       directory                   >= 1.1      && < 1.3,-                       test-framework              >= 0.3,-                       test-framework-hunit,-                       test-framework-quickcheck2  >= 0.3,-                       HUnit,-                       QuickCheck-  extra-libraries:     netcdf--Test-Suite test-put-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-put.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       errors                      >= 1.4.2    && < 1.5,-                       vector                      >= 0.9      && < 0.11,-                       directory                   >= 1.1      && < 1.3-  extra-libraries:     netcdf+    type: git+    location: https://github.com/ian-ross/hnetcdf -Test-Suite test-hmatrix-  type:                exitcode-stdio-1.0-  hs-source-dirs:      test-  main-is:             test-hmatrix.hs-  build-depends:       hnetcdf,-                       base                        >= 4.3      && < 5,-                       containers                  >= 0.4      && < 0.6,-                       errors                      >= 1.4.2    && < 1.5,-                       vector                      >= 0.9      && < 0.11,-                       directory                   >= 1.1      && < 1.3,-                       hmatrix                     >= 0.16.0.2 && < 0.17,-                       test-framework              >= 0.3,-                       test-framework-hunit,-                       test-framework-quickcheck2  >= 0.3,-                       HUnit,-                       QuickCheck-  extra-libraries:     netcdf+library+    build-depends:+        base           >= 4.3     && <5,+        containers     >= 0.5.0.0 && <0.6,+        either         >= 4.4     && <4.5,+        errors         >= 2.0     && <2.2,+        filepath       >= 1.4     && <1.5,+        repa           >= 3.4     && <3.5,+        transformers   >= 0.2     && <0.6,+        vector         >= 0.10.9  && <0.12+    exposed-modules:+        Data.NetCDF+        Data.NetCDF.Vector+        Data.NetCDF.Repa+        Data.NetCDF.Metadata+        Data.NetCDF.PutGet+        Data.NetCDF.Storable+        Data.NetCDF.Store+        Data.NetCDF.Types+        Data.NetCDF.Utils+        Data.NetCDF.Raw+        Data.NetCDF.Raw.Base+        Data.NetCDF.Raw.PutGet+        Data.NetCDF.Raw.Attributes+        Data.NetCDF.Raw.Utils+    build-tools: c2hs -any+    extra-libraries:+        netcdf+    ghc-options: -Wall -Executable example1-  hs-source-dirs:   examples-  main-is:          example1.hs-  build-depends:    hnetcdf,-                    base                           >= 4.3      && < 5,-                    containers                     >= 0.4      && < 0.6,-                    vector                         >= 0.9      && < 0.11+executable example1+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        vector+    main-is: example1.hs+    hs-source-dirs: examples -Executable example2-  hs-source-dirs:   examples-  main-is:          example2.hs-  build-depends:    hnetcdf,-                    base                           >= 4.3      && < 5,-                    containers                     >= 0.4      && < 0.6,-                    vector                         >= 0.9      && < 0.11,-                    repa+executable example2+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        vector,+        repa+    main-is: example2.hs+    hs-source-dirs: examples -Executable example3-  hs-source-dirs:   examples-  main-is:          example3.hs-  build-depends:    hnetcdf,-                    base                           >= 4.3      && < 5,-                    containers                     >= 0.4      && < 0.6,-                    vector                         >= 0.9      && < 0.11,-                    hmatrix+test-suite test-raw-metadata+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        vector,+        repa,+        test-framework              >= 0.8     && <0.9,+        test-framework-hunit        >= 0.3     && <0.4,+        test-framework-quickcheck2  >= 0.3     && <0.4,+        HUnit                       >= 1.2.5.2 && <1.4,+        QuickCheck                  >= 2.8.1   && <2.9+    type: exitcode-stdio-1.0+    main-is: test-raw-metadata.hs+    extra-libraries:+        netcdf+    hs-source-dirs: test+test-suite test-raw-get-put+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        vector,+        repa,+        directory,+        test-framework,+        test-framework-hunit,+        test-framework-quickcheck2,+        HUnit,+        QuickCheck+    type: exitcode-stdio-1.0+    main-is: test-raw-get-put.hs+    extra-libraries:+        netcdf+    hs-source-dirs: test+test-suite test-raw-attributes+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        vector,+        repa,+        directory,+        test-framework,+        test-framework-hunit,+        test-framework-quickcheck2,+        HUnit,+        QuickCheck+    type: exitcode-stdio-1.0+    main-is: test-raw-attributes.hs+    extra-libraries:+        netcdf+    hs-source-dirs: test+test-suite test-get+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        errors,+        repa,+        vector,+        directory,+        test-framework,+        test-framework-hunit,+        test-framework-quickcheck2,+        HUnit,+        QuickCheck+    type: exitcode-stdio-1.0+    main-is: test-get.hs+    extra-libraries:+        netcdf+    hs-source-dirs: test+test-suite test-put+    build-depends:+        hnetcdf -any,+        base           >= 4.3     && <5,+        containers,+        errors,+        vector,+        directory+    type: exitcode-stdio-1.0+    main-is: test-put.hs+    extra-libraries:+        netcdf+    hs-source-dirs: test
test/test-get.hs view
@@ -8,13 +8,11 @@ import Data.Array.Repa.Repr.ForeignPtr (F) import Control.Error import Control.Monad-import Numeric.Container as C import Foreign.C  import Data.NetCDF import qualified Data.NetCDF.Vector as V import qualified Data.NetCDF.Repa as R-import qualified Data.NetCDF.HMatrix as H  main :: IO () main = defaultMain tests@@ -45,9 +43,6 @@     , testCase "Read (float, Repa)" (getVarRepa infile "vf" fwit)     , testCase "Read (int, Repa)" (getVarRepa infile "vi" iwit)     , testCase "Read (short, Repa)" (getVarRepa infile "vs" swit)-    , testCase "Read (float, hmatrix)" (getVarHMV infile "vf" fwit)-    , testCase "Read (int, hmatrix)" (getVarHMV infile "vi" iwit)-    , testCase "Read (short, hmatrix)" (getVarHMV infile "vs" swit)     ],     testGroup "Variable slice access functions"     [ testCase "Read (float, SV)" (getVarASV infile "vf" fwit)@@ -56,9 +51,6 @@     , testCase "Read (float, Repa)" (getVarARepa infile "vf" fwit)     , testCase "Read (int, Repa)" (getVarARepa infile "vi" iwit)     , testCase "Read (short, Repa)" (getVarARepa infile "vs" swit)-    , testCase "Read (float, hmatrix)" (getVarAHMV infile "vf" fwit)-    , testCase "Read (int, hmatrix)" (getVarAHMV infile "vi" iwit)-    , testCase "Read (short, hmatrix)" (getVarAHMV infile "vs" swit)     ],     testGroup "Strided slice access functions"     [ testCase "Read (float, SV)" (getVarSSV infile "vf" fwit)@@ -67,9 +59,6 @@     , testCase "Read (float, Repa)" (getVarSRepa infile "vf" fwit)     , testCase "Read (int, Repa)" (getVarSRepa infile "vi" iwit)     , testCase "Read (short, Repa)" (getVarSRepa infile "vs" swit)-    , testCase "Read (float, hmatrix)" (getVarSHMV infile "vf" fwit)-    , testCase "Read (int, hmatrix)" (getVarSHMV infile "vi" iwit)-    , testCase "Read (short, hmatrix)" (getVarSHMV infile "vs" swit)     ]   ] @@ -77,8 +66,6 @@ type SVRet a = IO (Either NcError (SV.Vector a)) type RepaRet3 a = IO (Either NcError (R.Array F R.DIM3 a)) type RepaRet1 a = IO (Either NcError (R.Array F R.DIM1 a))-type HMVRet a = IO (Either NcError (H.HVector a))-type HMMRet a = IO (Either NcError (H.HMatrix a))   --------------------------------------------------------------------------------@@ -165,32 +152,7 @@             (and $ zipWith (==) tstvals truevals)   void $ closeFile nc -getVarHMV :: forall a. (Eq a, Num a, Show a, NcStorable a, Element a)-          => FilePath -> String -> a -> Assertion-getVarHMV f v _ = do-  enc <- openFile f-  assertBool "failed to open file" $ isRight enc-  let Right nc = enc-  case ncVar nc v of-    Nothing -> assertBool "missing variable" False-    Just var -> do-      eval <- get nc var :: HMVRet a-      case eval of-        Left e -> assertBool ("read error: " ++ show e) False-        Right (H.HVector val) -> do-          let [nz, ny, nx] = map ncDimLength $ ncVarDims var-              truevals = [fromIntegral $ ix + 10 * iy + 100 * iz |-                          ix <- [1..nx], iy <- [1..ny], iz <- [1..nz]]-              idxs = [(iz - 1) * ny * nx + (iy - 1) * nx + (ix - 1) |-                      ix <- [1..nx], iy <- [1..ny], iz <- [1..nz]]-              tstvals = [val C.@> i | i <- idxs]-          assertBool ("value error: " ++ show tstvals ++-                      " instead of " ++ show truevals)-            (and $ zipWith (==) tstvals truevals)-  void $ closeFile nc -- -------------------------------------------------------------------------------- -- --  VARIABLE SLICE READ@@ -291,54 +253,7 @@               assertBool ("3: value error: " ++ show tstvals ++                           " instead of " ++ show truevals) (tstvals == truevals) -getVarAHMV :: forall a. (Num a, Show a, Eq a, NcStorable a, Element a)-           => FilePath -> String -> a -> Assertion-getVarAHMV f v _ = do-  enc <- openFile f-  assertBool "failed to open file" $ isRight enc-  let Right nc = enc-  case ncVar nc v of-    Nothing -> assertBool "missing variable" False-    Just var -> do-      let [nz, ny, nx] = map ncDimLength $ ncVarDims var-      forM_ [1..nx] $ \ix -> do-        forM_ [1..ny] $ \iy -> do-          let start = [0, iy-1, ix-1]-              count = [nz, 1, 1]-          eval <- getA nc var start count :: HMVRet a-          case eval of-            Left e -> assertBool ("read error: " ++ show e) False-            Right vals -> do-              let truevals = H.HVector $ C.buildVector (fromIntegral nz)-                             (\iz -> fromIntegral $ ix + 10 * iy + 100 * (iz+1))-              assertBool ("1: value error: " ++ show vals ++-                          " instead of " ++ show truevals) (vals == truevals)-      forM_ [1..nx] $ \ix -> do-        forM_ [1..nz] $ \iz -> do-          let start = [iz-1, 0, ix-1]-              count = [1, ny, 1]-          eval <- getA nc var start count :: HMVRet a-          case eval of-            Left e -> assertBool ("read error: " ++ show e) False-            Right vals -> do-              let truevals = H.HVector $ C.buildVector (fromIntegral ny)-                             (\iy -> fromIntegral $ ix + 10 * (iy+1) + 100 * iz)-              assertBool ("2: value error: " ++ show vals ++-                          " instead of " ++ show truevals) (vals == truevals)-      forM_ [1..ny] $ \iy -> do-        forM_ [1..nz] $ \iz -> do-          let start = [iz-1, iy-1, 0]-              count = [1, 1, nx]-          eval <- getA nc var start count :: HMVRet a-          case eval of-            Left e -> assertBool ("read error: " ++ show e) False-            Right vals -> do-              let truevals = H.HVector $ C.buildVector (fromIntegral nx)-                             (\ix -> fromIntegral $ (ix+1) + 10 * iy + 100 * iz)-              assertBool ("3: value error: " ++ show vals ++-                          " instead of " ++ show truevals) (vals == truevals) - -------------------------------------------------------------------------------- -- --  STRIDED SLICE READ@@ -465,62 +380,3 @@                 assertBool ("3: value error: " ++ show tstvals ++                             " instead of " ++ show truevals)                   (tstvals == truevals)--getVarSHMV :: forall a. (Num a, Show a, Eq a, NcStorable a, Element a)-          => FilePath -> String -> a -> Assertion-getVarSHMV f v _ = do-  enc <- openFile f-  assertBool "failed to open file" $ isRight enc-  let Right nc = enc-  case ncVar nc v of-    Nothing -> assertBool "missing variable" False-    Just var -> do-      let [nz, ny, nx] = map ncDimLength $ ncVarDims var-      forM_ [1..nx] $ \ix -> do-        forM_ [1..ny] $ \iy -> do-          forM_ [1..nz] $ \s -> do-            let start = [0, iy-1, ix-1]-                count = [(nz + s - 1) `div` s, 1, 1]-                stride = [s, 1, 1]-            eval <- getS nc var start count stride :: HMVRet a-            case eval of-              Left e -> assertBool ("read error: " ++ show e) False-              Right vals -> do-                let truevals = H.HVector $ C.buildVector-                               (fromIntegral $ (nz + s - 1) `div` s)-                               (\iz -> fromIntegral $-                                       ix + 10 * iy + 100 * (iz * s + 1))-                assertBool ("1: value error: " ++ show vals ++-                            " instead of " ++ show truevals) (vals == truevals)-      forM_ [1..nx] $ \ix -> do-        forM_ [1..nz] $ \iz -> do-          forM_ [1..ny] $ \s -> do-            let start = [iz-1, 0, ix-1]-                count = [1, (ny + s - 1) `div` s, 1]-                stride = [1, s, 1]-            eval <- getS nc var start count stride :: HMVRet a-            case eval of-              Left e -> assertBool ("read error: " ++ show e) False-              Right vals -> do-                let truevals = H.HVector $ C.buildVector-                               (fromIntegral $ (ny + s - 1) `div` s)-                               (\iy -> fromIntegral $-                                       ix + 10 * (iy * s + 1) + 100 * iz)-                assertBool ("2: value error: " ++ show vals ++-                            " instead of " ++ show truevals) (vals == truevals)-      forM_ [1..ny] $ \iy -> do-        forM_ [1..nz] $ \iz -> do-          forM_ [1..nx] $ \s -> do-            let start = [iz-1, iy-1, 0]-                count = [1, 1, (nx + s - 1) `div` s]-                stride = [1, 1, s]-            eval <- getS nc var start count stride :: HMVRet a-            case eval of-              Left e -> assertBool ("read error: " ++ show e) False-              Right vals -> do-                let truevals = H.HVector $ C.buildVector-                               (fromIntegral $ (nx + s - 1) `div` s)-                               (\ix -> fromIntegral $-                                       (ix * s + 1) + 10 * iy + 100 * iz)-                assertBool ("3: value error: " ++ show vals ++-                            " instead of " ++ show truevals) (vals == truevals)
− test/test-hmatrix.hs 
@@ -1,67 +0,0 @@-{-# LANGUAGE ScopedTypeVariables #-}--import Test.Framework (defaultMain, testGroup, Test)-import Test.Framework.Providers.HUnit-import Test.Framework.Providers.QuickCheck2-import Test.HUnit hiding (Test, assert)-import Test.QuickCheck-import Test.QuickCheck.Monadic--import qualified Data.Map as M-import Data.Maybe-import qualified Data.Vector.Storable as SV-import Numeric.LinearAlgebra.HMatrix-import Control.Error-import Control.Monad-import Foreign.C--import Data.NetCDF-import Data.NetCDF.Vector-import Data.NetCDF.HMatrix--type HMatrixRet a = IO (Either NcError (HMatrix a))--main :: IO ()-main = defaultMain tests--tests :: [Test]-tests =-  [ testGroup "HMatrix handling"-    [ testCase "Data ordering" hmatrixDataOrdering-    ]-  ]--hmatrixDataOrdering :: Assertion-hmatrixDataOrdering = do-  let xdim = NcDim "x" 5 False-      ydim = NcDim "y" 10 False-      ncout = emptyNcInfo "tst-hmatrix.nc" #-           addNcDim xdim #-           addNcDim ydim #-           addNcVar (NcVar "x" NcDouble [xdim] M.empty) #-           addNcVar (NcVar "y" NcDouble [ydim] M.empty) #-           addNcVar (NcVar "z1" NcDouble [ydim, xdim] M.empty) #-           addNcVar (NcVar "z2" NcDouble [ydim, xdim] M.empty)-      z1 = cmap realToFrac $ matrix 5 [1..50] :: Matrix CDouble-      z2 = fromColumns $ toColumns z1 :: Matrix CDouble-  let write nc = do-        let xvar = fromJust $ ncVar nc "x"-            yvar = fromJust $ ncVar nc "y"-            z1var = fromJust $ ncVar nc "z1"-            z2var = fromJust $ ncVar nc "z2"-        put nc xvar $ SV.fromList [1..5 :: CDouble]-        put nc yvar $ SV.fromList [1..10 :: CDouble]-        put nc z1var $ HMatrix z1-        put nc z2var $ HMatrix z2-        return ()-  withCreateFile ncout write (putStrLn . ("ERROR: " ++) . show)-  let read nc = do-        let z1var = fromJust $ ncVar nc "z1"-            z2var = fromJust $ ncVar nc "z2"-        Right (HMatrix z1) <- get nc z1var :: HMatrixRet CDouble-        Right (HMatrix z2) <- get nc z2var :: HMatrixRet CDouble-        return (z1, z2)-  (z1tst, z2tst) <--    withReadFile "tst-hmatrix.nc" read (error . ("ERROR: " ++) . show)-  assertBool "Straightforward write/read" (flatten z1tst == flatten z1)-  assertBool "Columnar write/read" (flatten z2tst == flatten z2)