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+{-# LANGUAGE CPP #-}
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE UnicodeSyntax #-}
+
+module Hkl.Projects.Diffabs.Melle
+ ( melle ) where
+
+-- import Control.Concurrent (setNumCapabilities)
+-- import Control.Concurrent.Async (mapConcurrently)
+import Data.Array.Repa (DIM1, ix1)
+-- import Data.Char (toUpper)
+-- import Numeric.LinearAlgebra (ident)
+import System.FilePath ((</>))
+import Text.Printf (printf)
+
+-- import Prelude hiding (concat, lookup, readFile, writeFile)
+
+import Hkl
+
+published ∷ FilePath
+published = "/nfs/ruche-diffabs/diffabs-soleil/com-diffabs/Reguer/USERSexperiences/melle"
+
+-- | TODO
+
+-- | MELLE / VIALAS
+-- Session 1 MACRO - 16-17 février 2016 (Logbook n° 42 p 169)
+-- Session 2 MICRO KB --28 mars 2016 (Logbook 42 + Logbook 43 p3)
+-- Session 3 MICRO pinhole - 22-24 juillet 2016 (Logbook 44 p33)
+-- Session 4 MACRO - septembre 2016 (Logbook 44 p63)
+
+-- | Session 1
+
+-- macrofaisceau
+-- 16keV
+-- Λ = 0,775
+-- detection : XPAD S140 / image = data 54
+-- sample : ω = 5 et χ = 70
+
+-- calibration = beam direct
+
+-- - 3 MESH pour 3 positions du détecteur de diffraction (delta = -4, 3, 10),
+
+-- macro python:
+-- for i in range (10):
+-- myx = -12+i*0,5
+-- mv(samplex, myx)
+-- ascan(sampley, -8, 12, 100, 10)
+
+-- scan_26 à 55.nxs
+-- diffabs-soleil/com-diffabs/2016/Run1/2016-02-16 ou 02-17
+
+-- 2THETA = 1 DELTA SCAN
+-- scan_56 = ascan(delta, -4, 70, 18, 3)
+-- scan_58 = ascan(delta, -4, 70, 18, 3)
+
+
+-- | Session 2
+
+-- microbeam
+-- 18keV, ?= 0,6888Å
+-- detection : XPAD 3.2 / image = data 58
+-- sample : ? = 5° et ? = 80°.
+-- calibration CeO2
+-- data dans le dossier du proposal de Philippe Charlier 2015 1386
+-- voir aussi script Martinetto proposal IHR 99160066
+-- scan_25 = ascan(delta, -14.5, 60.5, 75, 0.5)
+-- scan_26 = ascan(delta, -14, 60, 75, 1)
+-- scan_27 = ascan(delta, -14, 60, 46, 1)
+
+-- MESH : MELLE_29.nxs
+-- dossier: diffabs-soleil/com-diffabs/2016/Run2/2016-03-28
+
+-- calibration
+
+project2 :: FilePath
+project2 = "/nfs/ruche-diffabs/diffabs-users/99160066/"
+
+published2:: FilePath
+published2 = project2 </> "published-data"
+
+h5path2 :: NxEntry -> DataFrameH5Path XrdOneD
+h5path2 nxentry =
+ XrdOneDH5Path
+ (DataItemH5 (nxentry </> image) StrictDims)
+ (DataItemH5 (nxentry </> beamline </> gamma) ExtendDims)
+ (DataItemH5 (nxentry </> delta) ExtendDims)
+ (DataItemH5 (nxentry </> beamline </> wavelength) StrictDims)
+ where
+ beamline :: String
+ beamline = beamlineUpper Diffabs
+
+ image = "scan_data/data_53"
+ gamma = "d13-1-cx1__EX__DIF.1-GAMMA__#1/raw_value"
+ delta = "scan_data/actuator_1_1"
+ wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
+
+sampleCalibration2 :: XRDCalibration Xpad32
+sampleCalibration2 = XRDCalibration { xrdCalibrationName = "calibration2"
+ , xrdCalibrationOutputDir = published </> "calibration2"
+ , xrdCalibrationDetector = Xpad32
+ , xrdCalibrationCalibrant = CeO2
+ , xrdCalibrationEntries = entries
+ }
+ where
+ idxs :: [Int]
+ idxs = [3, 6, 9, 15, 18, 21, 24, 27, 30, 33, 36, 39, 43]
+
+ entry :: Int -> XRDCalibrationEntry
+ entry idx = XRDCalibrationEntryNxs
+ { xrdCalibrationEntryNxs'Nxs = mkNxs (published2 </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path2
+ , xrdCalibrationEntryNxs'Idx = idx
+ , xrdCalibrationEntryNxs'NptPath = published2 </> "calibration" </> printf "XRD18keV_26.nxs_%02d.npt" idx
+ }
+
+ entries :: [XRDCalibrationEntry]
+ entries = [ entry idx | idx <- idxs]
+
+sampleRef2 :: XRDRef
+sampleRef2 = XRDRef "reference"
+ (published2 </> "calibration")
+ (XrdRefNxs
+ (mkNxs (published2 </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path2)
+ 6 -- BEWARE only the 6th poni was generated with the right Xpad_flat geometry.
+ )
+
+bins :: DIM1
+bins = ix1 8000
+
+multibins :: DIM1
+multibins = ix1 25000
+
+threshold :: Maybe Threshold
+threshold = Just (Threshold 800)
+
+skipedFrames :: [Int]
+skipedFrames = []
+
+melleScan :: XRDSample
+melleScan = XRDSample "CeO2"
+ (published </> "xrd" </> "session2" </> "oned")
+ [ XrdNxs bins multibins threshold skipedFrames (XrdSourceNxs n) | n <-
+ [ mkNxs (project </> "2016" </> "Run2" </> "2016-03-23" </> "XRD18keV_25.nxs") "scan_25" h5path2
+ , mkNxs (project </> "2016" </> "Run2" </> "2016-03-23" </> "XRD18keV_26.nxs") "scan_26" h5path2
+ , mkNxs (project </> "2016" </> "Run2" </> "2016-03-23" </> "XRD18keV_27.nxs") "scan_27" h5path2
+ ]
+ ]
+ where
+ project ∷ FilePath
+ project = "/nfs/ruche-diffabs/diffabs-users/20151386/"
+
+
+melleMesh :: XrdMeshSample
+melleMesh = XrdMeshSample "MELLE_29"
+ (published </> "xrd" </> "session2" </> "mesh")
+ [ XrdMesh bins multibins threshold (XrdMeshSourceNxs n) | n <-
+ [ mkNxs (project2' </> "2016" </> "Run2" </> "2016-03-28" </> "MELLE_29.nxs") "scan_29" h5path2'
+ ]
+ ]
+ where
+ project2' :: FilePath
+ project2' = "/nfs/ruche-diffabs/diffabs-users/99160066/"
+
+ h5path2' :: NxEntry -> DataFrameH5Path XrdMesh
+ h5path2' nxentry =
+ XrdMeshH5Path
+ (DataItemH5 (nxentry </> image) StrictDims)
+ (DataItemH5 (nxentry </> meshX) StrictDims)
+ (DataItemH5 (nxentry </> meshY) StrictDims)
+ (DataItemH5 (nxentry </> beamline </> gamma) ExtendDims)
+ (DataItemH5 (nxentry </> beamline </> delta) ExtendDims)
+ (DataItemH5 (nxentry </> beamline </> wavelength) StrictDims)
+ where
+ beamline :: String
+ beamline = beamlineUpper Diffabs
+
+ image = "scan_data/data_58"
+ meshX = "scan_data/actuator_1_1"
+ meshY = "scan_data/actuator_2_1"
+ gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
+ delta = "D13-1-CX1__EX__DIF.1-DELTA__#1/raw_value"
+ wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
+
+
+session2 :: IO ()
+session2 = do
+ -- compute the ref poni
+ p ← getPoniExtRef sampleRef2
+ poniextref <- calibrate sampleCalibration2 p
+
+ -- integrate the mesh
+ let mflat = Nothing
+ integrateMesh (XrdMeshParams poniextref mflat CsrOcl) [melleMesh]
+
+ -- integrate the scan parts
+ let params = XrdOneDParams poniextref mflat Csr
+ integrate params [melleScan]
+ integrateMulti params [melleScan]
+
+ return ()
+
+-- | session 4
+-- macro
+-- 18keV, ?= 0,6888Å
+-- detection : XPAD 3.2
+
+session4 ∷ IO ()
+session4 = do
+ -- calibration
+ p ← getPoniExtRef sampleRef
+ poniextref <- calibrate sampleCalibration p
+
+-- calibration : CeO2
+-- On peut utiliser la calib de IHR_30, mais il faut prendre en compte le décentrage.
+-- IHR_56
+-- IHR_58
+-- sont deux autres possibilité de calibration.
+-- diffabs-soleil\com-diffabs\2016\Run4\2016-09-07
+
+ -- | set the integration parameters
+ let mflat = Nothing
+ let params = XrdOneDParams poniextref mflat Csr
+
+ -- integrate each step of the scan
+ integrate params [ceo2]
+
+-- 1 seul "MESH"(20, 49) à partir d'une serie 2THETA
+-- IHR_63 à 95
+-- diffabs-soleil\com-diffabs\2016\Run4\2016-09-07
+-- IHR_96 à 190
+-- diffabs-soleil\com-diffabs\2016\Run4\2016-09-08
+-- obtenu via la macro suivante.
+-- for i in range(20):
+-- myx = -11 + i
+-- mv(txs, myx) # exhantillon à 45 degree donc ce double déplacement correspond au vrai x
+-- mv(tys, myx)
+-- for j in range(29):
+-- myy = 12 + j
+-- mv(tabV, myy)
+-- ascan(δ, -13.6, 30, 109, 5)
+
+ return ()
+
+ where
+
+ project :: FilePath
+ project = "/nfs/ruche-diffabs/diffabs-soleil/com-diffabs/"
+
+ published' :: FilePath
+ published' = project </> "2016" </> "Run4B" </> "OutilsMetallo_CarolineHamon"
+
+ sampleRef :: XRDRef
+ sampleRef = XRDRef "reference"
+ (published' </> "xrd" </> "calibration")
+ (XrdRefNxs
+ (mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_30.nxs") "scan_30" h5path')
+ 33
+ )
+
+ h5path' :: NxEntry -> DataFrameH5Path XrdOneD
+ h5path' nxentry =
+ XrdOneDH5Path
+ (DataItemH5 (nxentry </> image) StrictDims)
+ (DataItemH5 (nxentry </> beamline </> gamma) ExtendDims)
+ (DataItemH5 (nxentry </> delta) ExtendDims)
+ (DataItemH5 (nxentry </> beamline </> wavelength) StrictDims)
+ where
+ beamline :: String
+ beamline = beamlineUpper Diffabs
+
+ image = "scan_data/data_02"
+ gamma = "D13-1-CX1__EX__DIF.1-GAMMA__#1/raw_value"
+ delta = "scan_data/actuator_1_1"
+ wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
+
+ sampleCalibration :: XRDCalibration Xpad32
+ sampleCalibration = XRDCalibration { xrdCalibrationName = "calibration"
+ , xrdCalibrationOutputDir = published' </> "xrd" </> "calibration" -- TODO pourquoi ce output
+ , xrdCalibrationDetector = Xpad32
+ , xrdCalibrationCalibrant = CeO2
+ , xrdCalibrationEntries = entries
+ }
+ where
+
+ idxs :: [Int]
+ idxs = [5, 33, 100, 246, 300, 436]
+
+ entry :: Int -> XRDCalibrationEntry
+ entry idx = XRDCalibrationEntryNxs
+ { xrdCalibrationEntryNxs'Nxs = mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_30.nxs") "scan_30" h5path'
+ , xrdCalibrationEntryNxs'Idx = idx
+ , xrdCalibrationEntryNxs'NptPath = published' </> "xrd" </> "calibration" </> printf "IHR_30.nxs_%02d.npt" idx
+ }
+
+ entries :: [XRDCalibrationEntry]
+ entries = [ entry idx | idx <- idxs]
+
+ bins :: DIM1
+ bins = ix1 1000
+
+ multibins :: DIM1
+ multibins = ix1 10000
+
+ threshold :: Maybe Threshold
+ threshold = Just (Threshold 5000)
+
+ skipedFrames :: [Int]
+ skipedFrames = []
+
+ ceo2 :: XRDSample
+ ceo2 = XRDSample "CeO2"
+ (published </> "session4" </> "xrd" </> "CeO2")
+ [ XrdNxs bins multibins threshold skipedFrames (XrdSourceNxs n) | n <-
+ [ mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_29.nxs") "scan_29" h5path'
+ , mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_30.nxs") "scan_30" h5path'
+ , mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_56.nxs") "scan_56" h5path'
+ , mkNxs (project </> "2016" </> "Run4" </> "2016-09-07" </> "IHR_58.nxs") "scan_58" h5path'
+ ]
+ ]
+
+-- ** session 5
+-- micro
+-- 18.05keV
+-- detection XPAD S140
+
+-- calibration CeO2
+-- gam = 9 phi = 170
+-- 18p1kev_71
+-- gam = 9 phi = 175
+-- 18p1kev_73
+-- gam = 0 phi = 205
+-- 18p1kev_74
+-- gam = 0.3 phi = 205
+-- 18p1kev_75
+-- ruche-diffabs\diffabs-users\99170085\2017\Run3\2017-05-14
+
+-- FLAT (à verifier si suffisant) (faire la somme des trois fichiers)
+-- 18p1kev_82
+-- 18p1kev_83
+-- 18p1kev_84
+-- ruche-diffabs\diffabs-users\99170085\2017\Run3\2017-05-14
+
+-- FLY -- ????
+-- flyscan_16602
+-- diffabs-soleil\com-diffabs\2017\Run3\fly_IHRSol
+
+-- 2THETA = 1 DELTA SCAN
+-- 18p1kev_85
+-- 18p1kev_86
+-- ruche-diffabs\diffabs-users\99170085\2017\Run3\2017-05-14
+
+-- | Samples
+
+-- published :: FilePath
+-- published = project </> "published-data"
+
+-- beamlineUpper :: Beamline -> String
+-- beamlineUpper b = [Data.Char.toUpper x | x <- show b]
+
+-- nxs :: FilePath -> NxEntry -> (NxEntry -> DataFrameH5Path) -> Nxs
+-- nxs f e h = Nxs f e (h e)
+
+-- nxs' :: FilePath -> NxEntry -> (NxEntry -> a) -> Nxs' a
+-- nxs' f e h = Nxs' f e (h e)
+
+-- h5path :: NxEntry -> DataFrameH5Path
+-- h5path nxentry =
+-- DataFrameH5Path { h5pImage = DataItem (nxentry </> image) StrictDims
+-- , h5pGamma = DataItem (nxentry </> beamline </> gamma) ExtendDims
+-- , h5pDelta = DataItem (nxentry </> delta) ExtendDims
+-- , h5pWavelength = DataItem (nxentry </> beamline </> wavelength) StrictDims
+-- }
+-- where
+-- beamline :: String
+-- beamline = beamlineUpper Diffabs
+
+-- image = "scan_data/data_53"
+-- gamma = "d13-1-cx1__EX__DIF.1-GAMMA__#1/raw_value"
+-- delta = "scan_data/actuator_1_1"
+-- wavelength = "D13-1-C03__OP__MONO__#1/wavelength"
+
+-- sampleCalibration :: XRDCalibration
+-- sampleCalibration = XRDCalibration { xrdCalibrationName = "calibration"
+-- , xrdCalibrationOutputDir = published </> "calibration"
+-- , xrdCalibrationEntries = entries
+-- }
+-- where
+
+-- idxs :: [Int]
+-- idxs = [3, 6, 9, 15, 18, 21, 24, 27, 30, 33, 36, 39, 43]
+
+-- entry :: Int -> XRDCalibrationEntry
+-- entry idx = XRDCalibrationEntryNxs
+-- { xrdCalibrationEntryNxs'Nxs = nxs (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path
+-- , xrdCalibrationEntryNxs'Idx = idx
+-- , xrdCalibrationEntryNxs'NptPath = published </> "calibration" </> printf "XRD18keV_26.nxs_%02d.npt" idx
+-- }
+
+-- entries :: [XRDCalibrationEntry]
+-- entries = [ entry idx | idx <- idxs]
+
+
+-- sampleRef :: XRDRef
+-- sampleRef = XRDRef "reference"
+-- (published </> "calibration")
+-- (nxs (published </> "calibration" </> "XRD18keV_26.nxs") "scan_26" h5path)
+-- 6 -- BEWARE only the 6th poni was generated with the right Xpad_flat geometry.
+
+-- bins :: DIM1
+-- bins = ix1 8000
+
+-- multibins :: DIM1
+-- multibins = ix1 25000
+
+-- threshold :: Threshold
+-- threshold = Threshold 800
+
+
+-- p <- getPoniExtRef sampleRef
+
+-- -- flip the ref poni in order to fit the reality
+-- -- let poniextref = p
+-- let poniextref = setPose p (MyMatrix HklB (ident 3))
+-- -- let poniextref = setPose (Hkl.PyFAI.PoniExt.flip p) (MyMatrix HklB (ident 3))
+
+-- -- full calibration
+-- poniextref' <- calibrate sampleCalibration poniextref Xpad32
+-- -- print p
+-- print poniextref
+-- print poniextref'
+
+-- -- integrate each step of the scan
+-- _ <- mapM_ (integrateMesh poniextref') samples
+
+-- return ()
+
+melle ∷ IO ()
+melle = do
+ session2
+ session4
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