contrib/haskell/src/Hkl/Diffabs/Martinetto.hs

   1 {-# LANGUAGE CPP #-}
   2 {-# LANGUAGE OverloadedStrings #-}
   3
   4 module Hkl.Diffabs.Martinetto
   5        ( main_martinetto ) where
   6
   7 #if __GLASGOW_HASKELL__ < 710
   8 import Control.Applicative ((<$>), (<*>))
   9 #endif
  10 import Control.Monad (forM_, forever)
  11 import Control.Monad.IO.Class (liftIO)
  12 import Control.Monad.Morph (hoist)
  13 import Data.Attoparsec.Text
  14 import Data.ByteString.Char8 (pack)
  15 import Data.Char (toUpper)
  16 import Data.Either
  17 import Data.Text (Text, intercalate, pack)
  18 import Data.Text.IO (readFile, writeFile)
  19 import Data.Vector.Storable (concat, head)
  20 import Hkl.C (geometryDetectorRotationGet)
  21 import Hkl.H5 ( Dataset
  22               , File
  23               , closeDataset
  24               , get_position
  25               , lenH5Dataspace
  26               , openDataset
  27               , withH5File )
  28 import Hkl.PyFAI
  29 import Hkl.Types
  30 import Numeric.Units.Dimensional.Prelude (meter, nano, (/~), (*~))
  31 import System.Directory (createDirectoryIfMissing)
  32 import System.FilePath ((</>), dropExtension, takeFileName, takeDirectory)
  33 import Prelude hiding (concat, lookup, readFile, writeFile)
  34
  35 import Pipes (Consumer, Pipe, lift, (>->), runEffect, await, yield)
  36 import Pipes.Prelude (toListM)
  37 import Pipes.Safe (MonadSafe(..), runSafeT, bracket)
  38 import Text.Printf (printf)
  39
  40 -- | Types
  41
  42 type NxEntry = String
  43 type OutputBaseDir = FilePath
  44 type PoniGenerator = MyMatrix Double -> Int -> IO PoniExt
  45 type SampleName = String
  46
  47 data XRDRef = XRDRef SampleName OutputBaseDir Nxs Int
  48
  49 data XRDSample = XRDSample SampleName OutputBaseDir [Nxs]-- ^ nxss
  50
  51 data Nxs = Nxs FilePath NxEntry DataFrameH5Path deriving (Show)
  52
  53 data PoniExt = PoniExt Poni (MyMatrix Double) deriving (Show)
  54
  55 data DifTomoFrame =
  56   DifTomoFrame { df_nxs :: Nxs -- ^ nexus of the current frame
  57                , df_n :: Int -- ^ index of the current frame
  58                , df_geometry :: Geometry -- ^ diffractometer geometry
  59                , df_poniext :: PoniExt -- ^ the ref poniext
  60                } deriving (Show)
  61
  62 class Frame t where
  63   len :: t -> IO (Maybe Int)
  64   row :: t -> Int -> IO DifTomoFrame
  65
  66 data DataFrameH5Path =
  67   DataFrameH5Path { h5pImage :: DataItem
  68                   , h5pGamma :: DataItem
  69                   , h5pDelta :: DataItem
  70                   , h5pWavelength :: DataItem
  71                   } deriving (Show)
  72
  73 data DataFrameH5 =
  74   DataFrameH5 { h5nxs :: Nxs
  75               , h5gamma :: Dataset
  76               , h5delta :: Dataset
  77               , h5wavelength :: Dataset
  78               , ponigen :: PoniGenerator
  79               }
  80
  81 instance Frame DataFrameH5 where
  82   len d =  lenH5Dataspace (h5delta d)
  83
  84   row d idx = do
  85     let nxs' = h5nxs d
  86     let mu = 0.0
  87     let komega = 0.0
  88     let kappa = 0.0
  89     let kphi = 0.0
  90     gamma <- get_position (h5gamma d) 0
  91     delta <- get_position (h5delta d) idx
  92     wavelength <- get_position (h5wavelength d) 0
  93     let source = Source (Data.Vector.Storable.head wavelength *~ nano meter)
  94     let positions = concat [mu, komega, kappa, kphi, gamma, delta]
  95     let geometry =  Geometry K6c source positions Nothing
  96     let detector = Detector DetectorType0D
  97     m <- geometryDetectorRotationGet geometry detector
  98     poniext <- ponigen d (MyMatrix HklB m) idx
  99     return DifTomoFrame { df_nxs = nxs'
 100                         , df_n = idx
 101                         , df_geometry = geometry
 102                         , df_poniext = poniext
 103                         }
 104
 105 -- | Samples
 106
 107 -- project = "/nfs/ruche-diffabs/diffabs-users/99160066/"
 108 -- project = "/home/experiences/instrumentation/picca/data/99160066"
 109 project :: FilePath
 110 project = "/home/picca/data/99160066"
 111
 112 published :: FilePath
 113 published = project </> "published-data"
 114
 115 beamlineUpper :: Beamline -> String
 116 beamlineUpper b = [toUpper x | x <- show b]
 117
 118 nxs :: FilePath -> NxEntry -> (NxEntry -> DataFrameH5Path ) -> Nxs
 119 nxs f e h5path = Nxs f e (h5path e)
 120
 121 calibration :: XRDRef
 122 calibration = XRDRef "calibration"
 123               (published </> "calibration")
 124               (nxs (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path)
 125               0
 126   where
 127     beamline :: String
 128     beamline = beamlineUpper Diffabs
 129
 130     image = "scan_data/data_53"
 131     gamma = "d13-1-cx1__EX__DIF.1-GAMMA__#1/raw_value"
 132     delta = "scan_data/trajectory_1_1"
 133     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 134
 135     h5path :: NxEntry -> DataFrameH5Path
 136     h5path nxentry =
 137       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 138                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 139                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 140                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 141                       }
 142
 143 n27t2 :: XRDSample
 144 n27t2 = XRDSample "N27T2"
 145         (published </> "N27T2")
 146         [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "N27T2_14.nxs") "scan_14" h5path
 147         , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "N27T2_17.nxs") "scan_17" h5path
 148         ]
 149   where
 150     beamline :: String
 151     beamline = beamlineUpper Diffabs
 152
 153     image = "scan_data/data_53"
 154     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 155     delta = "scan_data/trajectory_1_1"
 156     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 157
 158     h5path :: NxEntry -> DataFrameH5Path
 159     h5path nxentry =
 160       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 161                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 162                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 163                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 164                       }
 165
 166 r34n1 :: XRDSample
 167 r34n1 = XRDSample "R34N1"
 168         (published </> "R34N1")
 169          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R34N1_28.nxs") "scan_28" h5path
 170          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R34N1_37.nxs") "scan_37" h5path
 171          ]
 172   where
 173     beamline :: String
 174     beamline = beamlineUpper Diffabs
 175
 176     image = "scan_data/data_53"
 177     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 178     delta = "scan_data/trajectory_1_1"
 179     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 180
 181     h5path :: NxEntry -> DataFrameH5Path
 182     h5path nxentry =
 183       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 184                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 185                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 186                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 187                       }
 188
 189 r23 :: XRDSample
 190 r23 = XRDSample "R23"
 191         (published </> "R23")
 192          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R23_6.nxs") "scan_6" h5path
 193          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R23_12.nxs") "scan_12" h5path
 194          ]
 195   where
 196     beamline :: String
 197     beamline = beamlineUpper Diffabs
 198
 199     image = "scan_data/data_53"
 200     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 201     delta = "scan_data/trajectory_1_1"
 202     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 203
 204     h5path :: NxEntry -> DataFrameH5Path
 205     h5path nxentry =
 206       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 207                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 208                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 209                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 210                       }
 211
 212 r18 :: XRDSample
 213 r18 = XRDSample "R18"
 214         (published </> "R18")
 215          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R18_20.nxs") "scan_20" h5path
 216          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R18_24.nxs") "scan_24" h5path
 217          ]
 218   where
 219     beamline :: String
 220     beamline = beamlineUpper Diffabs
 221
 222     image = "scan_data/data_53"
 223     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 224     delta = "scan_data/trajectory_1_1"
 225     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 226
 227     h5path :: NxEntry -> DataFrameH5Path
 228     h5path nxentry =
 229       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 230                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 231                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 232                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 233                       }
 234
 235 a3 :: XRDSample
 236 a3 = XRDSample "A3"
 237         (published </> "A3")
 238          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_13.nxs") "scan_13" h5path
 239          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_14.nxs") "scan_14" h5path
 240          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_15.nxs") "scan_15" h5path
 241          ]
 242   where
 243     beamline :: String
 244     beamline = beamlineUpper Diffabs
 245
 246     image = "scan_data/data_53"
 247     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 248     delta = "scan_data/trajectory_1_1"
 249     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 250
 251     h5path :: NxEntry -> DataFrameH5Path
 252     h5path nxentry =
 253       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 254                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 255                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 256                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 257                       }
 258
 259 a2 :: XRDSample
 260 a2 = XRDSample "A2"
 261         (published </> "A2")
 262          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A2_14.nxs") "scan_14" h5path
 263          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A2_17.nxs") "scan_17" h5path
 264          ]
 265   where
 266     beamline :: String
 267     beamline = beamlineUpper Diffabs
 268
 269     image = "scan_data/data_53"
 270     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 271     delta = "scan_data/trajectory_1_1"
 272     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 273
 274     h5path :: NxEntry -> DataFrameH5Path
 275     h5path nxentry =
 276       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 277                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 278                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 279                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 280                       }
 281
 282 d2 :: XRDSample
 283 d2 = XRDSample "D2"
 284         (published </> "D2")
 285          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D2_16.nxs") "scan_16" h5path
 286          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D2_17.nxs") "scan_17" h5path
 287          ]
 288   where
 289     beamline :: String
 290     beamline = beamlineUpper Diffabs
 291
 292     image = "scan_data/data_53"
 293     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 294     delta = "scan_data/trajectory_1_1"
 295     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 296
 297     h5path :: NxEntry -> DataFrameH5Path
 298     h5path nxentry =
 299       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 300                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 301                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 302                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 303                       }
 304
 305 d3 :: XRDSample
 306 d3 = XRDSample "D3"
 307         (published </> "D3")
 308          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D3_14.nxs") "scan_14" h5path
 309          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D3_15.nxs") "scan_15" h5path
 310          ]
 311   where
 312     beamline :: String
 313     beamline = beamlineUpper Diffabs
 314
 315     image = "scan_data/data_53"
 316     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 317     delta = "scan_data/trajectory_1_1"
 318     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 319
 320     h5path :: NxEntry -> DataFrameH5Path
 321     h5path nxentry =
 322       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 323                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 324                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 325                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 326                       }
 327
 328 r11 :: XRDSample
 329 r11 = XRDSample "R11"
 330         (published </> "R11")
 331          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_5.nxs") "scan_5" h5path
 332          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_6.nxs") "scan_6" h5path
 333          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_7.nxs") "scan_7" h5path
 334          ]
 335   where
 336     beamline :: String
 337     beamline = beamlineUpper Diffabs
 338
 339     image = "scan_data/data_53"
 340     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 341     delta = "scan_data/trajectory_1_1"
 342     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 343
 344     h5path :: NxEntry -> DataFrameH5Path
 345     h5path nxentry =
 346       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 347                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 348                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 349                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 350                       }
 351
 352 d16 :: XRDSample
 353 d16 = XRDSample "D16"
 354         (published </> "D16")
 355          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_12.nxs") "scan_12" h5path
 356          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_15.nxs") "scan_15" h5path
 357          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_17.nxs") "scan_17" h5path
 358          ]
 359   where
 360     beamline :: String
 361     beamline = beamlineUpper Diffabs
 362
 363     image = "scan_data/data_53"
 364     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 365     delta = "scan_data/trajectory_1_1"
 366     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 367
 368     h5path :: NxEntry -> DataFrameH5Path
 369     h5path nxentry =
 370       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 371                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 372                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 373                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 374                       }
 375
 376 k9a2 :: XRDSample
 377 k9a2 = XRDSample "K9A2"
 378        (published </> "K9A2")
 379        [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "K9A2_1_31.nxs") "scan_31" h5path
 380        , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "K9A2_1_32.nxs") "scan_32" h5path
 381        ]
 382   where
 383     beamline :: String
 384     beamline = beamlineUpper Diffabs
 385
 386     image = "scan_data/data_53"
 387     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
 388     delta = "scan_data/trajectory_1_1"
 389     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
 390
 391     h5path :: NxEntry -> DataFrameH5Path
 392     h5path nxentry =
 393       DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
 394                       , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
 395                       , h5pDelta = DataItem (nxentry </> delta) ExtendDims
 396                       , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
 397                       }
 398
 399 -- {-# ANN module "HLint: ignore Use camelCase" #-}
 400
 401
 402 -- import Graphics.Rendering.Chart.Easy
 403 -- import Graphics.Rendering.Chart.Backend.Diagrams
 404
 405 -- plotPonies :: FilePath -> [PoniEntry] -> IO ()
 406 -- plotPonies f entries = toFile def f $ do
 407 --     layout_title .= "Ponies"
 408 --     setColors [opaque blue]
 409 --     let values = map extract entries
 410 --     plot (line "am" [values [0,(0.5)..400]])
 411 --     -- plot (points "am points" (signal [0,7..400]))
 412 --     where
 413 --       extract (PoniEntry _ _ (Length poni1) _ _ _ _ _ _) = poni1
 414
 415 -- | Usual methods
 416
 417
 418 poniFromFile :: FilePath -> IO Poni
 419 poniFromFile filename = do
 420   content <- readFile filename
 421   return $ case parseOnly poniP content of
 422     Left _     -> error $ "Can not parse the " ++ filename ++ " poni file"
 423     Right poni -> poni
 424
 425 getPoniExtRef :: XRDRef -> IO PoniExt
 426 getPoniExtRef (XRDRef _ output nxs'@(Nxs f _ _) idx) = do
 427   poniExtRefs <- withH5File f $ \h5file ->
 428     runSafeT $ toListM ( withDataFrameH5 h5file nxs' (gen output f) yield
 429                          >-> hoist lift (frames' [idx]))
 430   return $ df_poniext (Prelude.head poniExtRefs)
 431   where
 432     gen :: FilePath -> FilePath -> MyMatrix Double -> Int -> IO PoniExt
 433     gen root nxs'' m idx' = do
 434       poni <- poniFromFile $ root </> scandir ++ printf "_%02d.poni" idx'
 435       return $ PoniExt poni m
 436       where
 437         scandir = takeFileName nxs''
 438
 439 integrate :: PoniExt -> XRDSample -> IO ()
 440 integrate ref (XRDSample _ output nxss) = mapM_ (integrate' ref output) nxss
 441
 442 integrate' :: PoniExt -> OutputBaseDir -> Nxs -> IO ()
 443 integrate' ref output nxs'@(Nxs f _ _) = do
 444   Prelude.print f
 445   withH5File f $ \h5file ->
 446       runSafeT $ runEffect $
 447         withDataFrameH5 h5file nxs' (gen ref) yield
 448         >-> hoist lift (frames
 449                         >-> savePonies (pgen output f)
 450                         >-> savePy 300)
 451   where
 452     gen :: PoniExt -> MyMatrix Double -> Int -> IO PoniExt
 453     gen ref' m _idx = return $ computeNewPoni ref' m
 454
 455     pgen :: OutputBaseDir -> FilePath -> Int -> FilePath
 456     pgen o nxs'' idx = o </> scandir </>  scandir ++ printf "_%02d.poni" idx
 457       where
 458         scandir = (dropExtension . takeFileName) nxs''
 459
 460 computeNewPoni :: PoniExt -> MyMatrix Double -> PoniExt
 461 computeNewPoni (PoniExt p1 mym1) mym2 = PoniExt p2 mym2
 462   where
 463     p2 = map rotate p1
 464
 465     rotate :: PoniEntry -> PoniEntry
 466     rotate e = rotatePoniEntry e mym1 mym2
 467
 468 createPy :: Int -> (DifTomoFrame, FilePath) -> Text
 469 createPy nb (f, poniFileName) =
 470   intercalate "\n" $
 471   map Data.Text.pack ["#!/bin/env python"
 472                      , ""
 473                      , "from h5py import File"
 474                      , "from pyFAI import load"
 475                      , ""
 476                      , "PONIFILE = " ++ show p
 477                      , "NEXUSFILE = " ++ show nxs'
 478                      , "IMAGEPATH = " ++ show i
 479                      , "IDX = " ++ show idx
 480                      , "N = " ++ show nb
 481                      , "OUTPUT = " ++ show out
 482                      , "WAVELENGTH = " ++ show (w /~ meter)
 483                      , ""
 484                      , "ai = load(PONIFILE)"
 485                      , "ai.wavelength = WAVELENGTH"
 486                      , "with File(NEXUSFILE) as f:"
 487                      , "    img = f[IMAGEPATH][IDX]"
 488                      , "    ai.integrate1d(img, N, filename=OUTPUT)"
 489                      ]
 490   where
 491     p = takeFileName poniFileName
 492     (Nxs nxs' _ h5path) = df_nxs f
 493     (DataItem i _) = h5pImage h5path
 494     idx = df_n f
 495     out = (dropExtension . takeFileName) poniFileName ++ ".dat"
 496     (Geometry _ (Source w) _ _) = df_geometry f
 497
 498 -- | Pipes
 499
 500 withDataFrameH5 :: (MonadSafe m) => File -> Nxs -> PoniGenerator -> (DataFrameH5 -> m r) -> m r
 501 withDataFrameH5 h nxs'@(Nxs _ _ d) gen = Pipes.Safe.bracket (liftIO $ before) (liftIO . after)
 502   where
 503     -- before :: File -> DataFrameH5Path -> m DataFrameH5
 504     before :: IO DataFrameH5
 505     before =  DataFrameH5
 506               <$> return nxs'
 507               <*> openDataset' h (h5pGamma d)
 508               <*> openDataset' h (h5pDelta d)
 509               <*> openDataset' h (h5pWavelength d)
 510               <*> return gen
 511
 512     -- after :: DataFrameH5 -> IO ()
 513     after d' = do
 514       closeDataset (h5gamma d')
 515       closeDataset (h5delta d')
 516       closeDataset (h5wavelength d')
 517
 518     -- openDataset' :: File -> DataItem -> IO Dataset
 519     openDataset' hid (DataItem name _) = openDataset hid (Data.ByteString.Char8.pack name) Nothing
 520
 521 savePonies :: (Int -> FilePath) -> Pipe DifTomoFrame (DifTomoFrame, FilePath) IO ()
 522 savePonies g = forever $ do
 523   f <- await
 524   let filename = g (df_n f)
 525   lift $ createDirectoryIfMissing True (takeDirectory filename)
 526   lift $ writeFile filename (content (df_poniext f))
 527   lift $ Prelude.print $ "--> " ++ filename
 528   yield (f, filename)
 529     where
 530       content :: PoniExt -> Text
 531       content (PoniExt poni _) = poniToText poni
 532
 533 savePy :: Int-> Consumer (DifTomoFrame, FilePath) IO ()
 534 savePy n = forever $ do
 535   f@(_, poniFileName) <- await
 536   let directory = takeDirectory poniFileName
 537   let pyFileName = dropExtension poniFileName ++ ".py"
 538   lift $ createDirectoryIfMissing True directory
 539   lift $ writeFile pyFileName (createPy n f)
 540   lift $ Prelude.print $ "--> " ++ pyFileName
 541
 542 frames :: (Frame a) => Pipe a DifTomoFrame IO ()
 543 frames = do
 544   d <- await
 545   (Just n) <- lift $ len d
 546   forM_ [0..n-1] (\i -> do
 547                      f <- lift $ row d i
 548                      yield f)
 549
 550 frames' :: (Frame a) => [Int] -> Pipe a DifTomoFrame IO ()
 551 frames' idxs = do
 552   d <- await
 553   forM_ idxs (\i -> do
 554                  f <- lift $ row d i
 555                  yield f)
 556
 557 -- | Main
 558
 559 main_martinetto :: IO ()
 560 main_martinetto = do
 561   -- lire le ou les ponis de référence ainsi que leur géométrie
 562   -- associée.
 563
 564   let samples = [n27t2, r34n1, r23, r18, a2, a3, d2, d3, r11, d16, k9a2]
 565
 566   poniextref <- getPoniExtRef calibration
 567
 568   -- calculer et écrire pour chaque point d'un scan un poni correspondant à la bonne géométries.
 569
 570   mapM_ (integrate poniextref) samples
 571
 572   -- plotPoni "/tmp/*.poni" "/tmp/plot.txt"
 573
 574   -- créer le script python d'intégration multi géométrie
 575
 576   -- l'executer pour faire l'intégration.
 577
 578   -- plot de la figure. (script python ou autre ?)