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

   1 {-# LANGUAGE CPP #-}
   2 {-# LANGUAGE OverloadedStrings #-}
   3
   4 module Hkl.Projects.Diffabs.Martinetto
   5        ( martinetto
   6        , martinetto'
   7        ) where
   8
   9 import Control.Concurrent (setNumCapabilities)
  10 import Control.Concurrent.Async (mapConcurrently)
  11 import Data.Array.Repa (DIM1, ix1)
  12 import Data.Char (toUpper)
  13 import Numeric.LinearAlgebra (ident)
  14 import System.FilePath ((</>))
  15 import Text.Printf (printf)
  16
  17 import Prelude hiding (concat, lookup, readFile, writeFile)
  18
  19 import Hkl
  20
  21 -- | Samples
  22
  23 project :: FilePath
  24 project = "/nfs/ruche-diffabs/diffabs-users/99160066/"
  25
  26 published :: FilePath
  27 published = project </> "published-data"
  28
  29 beamlineUpper :: Beamline -> String
  30 beamlineUpper b = [Data.Char.toUpper x | x <- show b]
  31
  32 nxs' :: FilePath -> NxEntry -> (NxEntry -> DataFrameH5Path) -> Nxs
  33 nxs' f e h = Nxs f e (h e)
  34
  35 nxs :: FilePath -> NxEntry -> (NxEntry -> DataFrameH5Path) -> XrdSource
  36 nxs f e h = XrdSourceNxs (nxs' f e h)
  37
  38 h5path' :: NxEntry -> DataFrameH5Path
  39 h5path' nxentry =
  40     DataFrameH5Path { h5pImage = DataItemH5 (nxentry </> image) StrictDims
  41                     , h5pGamma = DataItemH5 (nxentry </> beamline </> gamma) ExtendDims
  42                     , h5pDelta = DataItemH5 (nxentry </> delta) ExtendDims
  43                     , h5pWavelength = DataItemH5 (nxentry </> beamline </> wavelength) StrictDims
  44                     }
  45         where
  46           beamline :: String
  47           beamline = beamlineUpper Diffabs
  48
  49           image = "scan_data/data_53"
  50           gamma = "d13-1-cx1__EX__DIF.1-GAMMA__#1/raw_value"
  51           delta = "scan_data/actuator_1_1"
  52           wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
  53
  54 sampleCalibration :: XRDCalibration
  55 sampleCalibration = XRDCalibration { xrdCalibrationName = "calibration"
  56                                    , xrdCalibrationOutputDir = published </> "calibration"
  57                                    , xrdCalibrationEntries = entries
  58                                    }
  59     where
  60
  61       idxs :: [Int]
  62       idxs = [3, 6, 9, 15, 18, 21, 24, 27, 30, 33, 36, 39, 43]
  63
  64       entry :: Int -> XRDCalibrationEntry
  65       entry idx = XRDCalibrationEntryNxs
  66                 { xrdCalibrationEntryNxs'Nxs = nxs' (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path'
  67                 , xrdCalibrationEntryNxs'Idx = idx
  68                 , xrdCalibrationEntryNxs'NptPath = published </> "calibration" </> printf "XRD18keV_26.nxs_%02d.npt" idx
  69                 }
  70
  71       entries :: [XRDCalibrationEntry]
  72       entries = [ entry idx | idx <- idxs]
  73
  74
  75 sampleRef :: XRDRef
  76 sampleRef = XRDRef "reference"
  77             (published </> "calibration")
  78             (XrdRefNxs
  79              (nxs' (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path')
  80              6 -- BEWARE only the 6th poni was generated with the right Xpad_flat geometry.
  81             )
  82
  83 h5path :: NxEntry -> DataFrameH5Path
  84 h5path nxentry =
  85   DataFrameH5Path { h5pImage = DataItemH5 (nxentry </> image) StrictDims
  86                   , h5pGamma = DataItemH5 (nxentry </> beamline </> gamma) ExtendDims
  87                   , h5pDelta = DataItemH5 (nxentry </> delta) ExtendDims
  88                   , h5pWavelength = DataItemH5 (nxentry </> beamline </> wavelength) StrictDims
  89                   }
  90   where
  91     beamline :: String
  92     beamline = beamlineUpper Diffabs
  93
  94     image = "scan_data/data_58"
  95     gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
  96     delta = "scan_data/actuator_1_1"
  97     wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
  98
  99 bins :: DIM1
 100 bins = ix1 8000
 101
 102 multibins :: DIM1
 103 multibins = ix1 25000
 104
 105 threshold :: Threshold
 106 threshold = Threshold 800
 107
 108 ceo2 :: XRDSample
 109 ceo2 = XRDSample "CeO2"
 110        (published </> "CeO2")
 111        [ XrdNxs bins multibins threshold n | n <-
 112          [ nxs (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path' ]
 113        ]
 114
 115 n27t2 :: XRDSample
 116 n27t2 = XRDSample "N27T2"
 117         (published </> "N27T2")
 118         [ XrdNxs bins multibins threshold n | n <-
 119           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "N27T2_14.nxs") "scan_14" h5path
 120           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "N27T2_17.nxs") "scan_17" h5path
 121           ]
 122         ]
 123
 124 r23 :: XRDSample
 125 r23 = XRDSample "R23"
 126         (published </> "R23")
 127         [ XrdNxs bins multibins threshold n | n <-
 128           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R23_6.nxs") "scan_6" h5path
 129           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R23_12.nxs") "scan_12" h5path
 130           ]
 131         ]
 132
 133 r18 :: XRDSample
 134 r18 = XRDSample "R18"
 135         (published </> "R18")
 136         [ XrdNxs bins multibins threshold n | n <-
 137           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R18_20.nxs") "scan_20" h5path
 138           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R18_24.nxs") "scan_24" h5path
 139           ]
 140         ]
 141
 142 a3 :: XRDSample
 143 a3 = XRDSample "A3"
 144         (published </> "A3")
 145         [ XrdNxs bins multibins threshold n | n <-
 146           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_13.nxs") "scan_13" h5path
 147           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_14.nxs") "scan_14" h5path
 148           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A3_15.nxs") "scan_15" h5path
 149           ]
 150         ]
 151
 152 a2 :: XRDSample
 153 a2 = XRDSample "A2"
 154         (published </> "A2")
 155         [ XrdNxs bins multibins threshold n | n <-
 156          [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A2_14.nxs") "scan_14" h5path
 157          , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "A2_17.nxs") "scan_17" h5path
 158          ]
 159         ]
 160
 161 a26 :: XRDSample
 162 a26 = XRDSample "A26"
 163       (published </> "A26")
 164       [ XrdNxs bins multibins threshold n | n <-
 165         [ nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_50.nxs") "scan_50" h5path
 166         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_51.nxs") "scan_51" h5path
 167         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_52.nxs") "scan_52" h5path
 168         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_53.nxs") "scan_53" h5path
 169         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_54.nxs") "scan_54" h5path
 170         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_55.nxs") "scan_55" h5path
 171         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_56.nxs") "scan_56" h5path
 172         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_57.nxs") "scan_57" h5path
 173         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_58.nxs") "scan_58" h5path
 174         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "A26_59.nxs") "scan_59" h5path
 175         ]
 176       ]
 177
 178 d2 :: XRDSample
 179 d2 = XRDSample "D2"
 180         (published </> "D2")
 181         [ XrdNxs bins multibins threshold n | n <-
 182           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D2_16.nxs") "scan_16" h5path
 183           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D2_17.nxs") "scan_17" h5path
 184           ]
 185         ]
 186
 187 d3 :: XRDSample
 188 d3 = XRDSample "D3"
 189         (published </> "D3")
 190         [ XrdNxs bins multibins threshold n | n <-
 191           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D3_14.nxs") "scan_14" h5path
 192           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D3_15.nxs") "scan_15" h5path
 193           ]
 194         ]
 195
 196 f30 :: XRDSample
 197 f30 = XRDSample "F30"
 198       (published </> "F30")
 199       [ XrdNxs bins multibins threshold n | n <-
 200         [ nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "F30_11.nxs") "scan_11" h5path
 201         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "F30_12.nxs") "scan_12" h5path
 202         , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "F30_13.nxs") "scan_13" h5path
 203         ]
 204       ]
 205
 206 r11 :: XRDSample
 207 r11 = XRDSample "R11"
 208         (published </> "R11")
 209         [ XrdNxs bins multibins threshold n | n <-
 210           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_5.nxs") "scan_5" h5path
 211           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_6.nxs") "scan_6" h5path
 212           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R11_7.nxs") "scan_7" h5path
 213           ]
 214         ]
 215
 216 d16 :: XRDSample
 217 d16 = XRDSample "D16"
 218         (published </> "D16")
 219         [ XrdNxs bins multibins threshold n | n <-
 220           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_12.nxs") "scan_12" h5path
 221           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_15.nxs") "scan_15" h5path
 222           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "D16_17.nxs") "scan_17" h5path
 223           ]
 224         ]
 225
 226 k9a2 :: XRDSample
 227 k9a2 = XRDSample "K9A2"
 228        (published </> "K9A2")
 229         [ XrdNxs bins multibins threshold n | n <-
 230           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "K9A2_1_31.nxs") "scan_31" h5path
 231           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "K9A2_1_32.nxs") "scan_32" h5path
 232           ]
 233         ]
 234
 235 r34n1 :: XRDSample
 236 r34n1 = XRDSample "R34N1"
 237         (published </> "R34N1")
 238         [ XrdNxs bins multibins threshold n | n <-
 239           [ nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R34N1_28.nxs") "scan_28" h5path
 240           , nxs (project </> "2016" </> "Run2" </> "2016-03-27" </> "R34N1_37.nxs") "scan_37" h5path
 241           ]
 242         ]
 243
 244 r35n1 :: XRDSample
 245 r35n1 = XRDSample "R35N1"
 246         (published </> "R35N1")
 247         [ XrdNxs bins multibins threshold n | n <-
 248           [ nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "R35N1_25.nxs") "scan_19" h5path
 249           , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "R35N1_26.nxs") "scan_20" h5path
 250           , nxs (project </> "2016" </> "Run2" </> "2016-03-26" </> "R35N1_27.nxs") "scan_21" h5path
 251           ]
 252         ]
 253
 254 -- meshSample :: String
 255 -- meshSample = project </> "2016" "Run2" "2016-03-28" "MELLE_29.nxs"
 256 -- scan_29 scan_data actuator_1_1 actuator_2_1 data_58 (images)
 257
 258 -- | Main
 259
 260 martinetto :: IO ()
 261 martinetto = do
 262   -- lire le ou les ponis de référence ainsi que leur géométrie
 263   -- associée.
 264
 265   -- let samples = [ceo2, a2, a3, a26, d2, d3, d16, f30, k9a2, n27t2, r11, r18, r23, r34n1, r35n1]
 266   let samples = [ceo2]
 267
 268   p <- getPoniExtRef sampleRef
 269
 270   -- flip the ref poni in order to fit the reality
 271   -- let poniextref = Hkl.PyFAI.PoniExt.flip p
 272   let poniextref = p
 273   -- integrate each step of the scan
 274   _ <- mapConcurrently (integrate poniextref) samples
 275
 276   -- plot de la figure. (script python ou autre ?)
 277   return ()
 278
 279 martinetto' :: IO ()
 280 martinetto' = do
 281   let samples = [ceo2, a2, a3, a26, d2, d3, d16, f30, k9a2, n27t2, r11, r18, r23, r34n1, r35n1]
 282
 283   p <- getPoniExtRef sampleRef
 284
 285   -- flip the ref poni in order to fit the reality
 286   -- let poniextref = p
 287   let poniextref = setPose p (MyMatrix HklB (ident 3))
 288   -- let poniextref = setPose (Hkl.PyFAI.PoniExt.flip p) (MyMatrix HklB (ident 3))
 289
 290   -- full calibration
 291   poniextref' <- calibrate sampleCalibration poniextref Xpad32
 292   -- print p
 293   print poniextref
 294   print poniextref'
 295
 296   -- integrate each step of the scan
 297   setNumCapabilities 2
 298   _ <- mapM_ (integrateMulti poniextref') samples
 299   return ()