original_inputs.py

import time
import numpy as np
from pathlib import Path
from vesuvio_analysis.core_functions.bootstrap import runBootstrap
from vesuvio_analysis.core_functions.bootstrap_analysis import runAnalysisOfStoredBootstrap
from vesuvio_analysis.core_functions.run_script import runScript
from mantid.api import AnalysisDataService

scriptName =  Path(__file__).name.split(".")[0]  # Take out .py
experimentPath = Path(__file__).absolute().parent / "experiments" / scriptName  # Path to the repository
ipFilesPath = Path(__file__).absolute().parent / "vesuvio_analysis" / "ip_files"


class LoadVesuvioBackParameters:
    runs="43066-43076"         # 77K         # The numbers of the runs to be analysed
    empty_runs="41876-41923"   # 77K         # The numbers of the empty runs to be subtracted
    spectra='3-134'                          # Spectra to be analysed
    mode='DoubleDifference'
    ipfile=ipFilesPath / "ip2019.par"   

    subEmptyFromRaw = True         # Flag to control wether empty ws gets subtracted from raw
    scaleEmpty = 1       # None or scaling factor 
    scaleRaw = 1


class LoadVesuvioFrontParameters:
    runs='43066-43076'         # 100K        # The numbers of the runs to be analysed
    empty_runs='43868-43911'   # 100K        # The numbers of the empty runs to be subtracted
    spectra='144-182'                        # Spectra to be analysed
    mode='SingleDifference'
    ipfile=ipFilesPath / "ip2018_3.par" 

    subEmptyFromRaw = False         # Flag to control wether empty ws gets subtracted from raw
    scaleEmpty = 1       # None or scaling factor 
    scaleRaw = 1


class GeneralInitialConditions:
    """Used to define initial conditions shared by both Back and Forward scattering"""
    
    transmission_guess =  0.8537        # Experimental value from VesuvioTransmission
    multiple_scattering_order, number_of_events = 2, 1.e5
    # Sample slab parameters
    vertical_width, horizontal_width, thickness = 0.1, 0.1, 0.001  # Expressed in meters


class BackwardInitialConditions(GeneralInitialConditions):
    InstrParsPath = ipFilesPath / "ip2018_3.par" 

    HToMassIdxRatio = 19.0620008206  # Set to zero or None when H is not present
    massIdx = 0

    # Masses, instrument parameters and initial fitting parameters
    masses = np.array([12, 16, 27])
    # noOfMasses = len(masses)

    initPars = np.array([ 
    # Intensities, NCP widths, NCP centers   
            1, 12, 0.,    
            1, 12, 0.,   
            1, 12.5, 0.    
        ])
    bounds = np.array([
            [0, np.nan], [8, 16], [-3, 1],
            [0, np.nan], [8, 16], [-3, 1],
            [0, np.nan], [11, 14], [-3, 1]
        ])
    constraints = ()

    noOfMSIterations = 3     #4
    firstSpec = 3    #3
    lastSpec = 134    #134

    maskedSpecAllNo = np.array([18, 34, 42, 43, 59, 60, 62, 118, 119, 133])

    # Boolean Flags to control script
    MSCorrectionFlag = True
    GammaCorrectionFlag = False

    # # Parameters of workspaces in input_ws
    tofBinning='275.,1.,420'                    # Binning of ToF spectra
    maskTOFRange = None
    
    # Original data uses histogram data instead of point data
    runHistData = True
    normVoigt = False


class ForwardInitialConditions(GeneralInitialConditions):

    masses = np.array([1.0079, 12, 16, 27]) 

    initPars = np.array([ 
    # Intensities, NCP widths, NCP centers  
        1, 4.7, 0, 
        1, 12.71, 0.,    
        1, 8.76, 0.,   
        1, 13.897, 0.    
    ])
    bounds = np.array([
        [0, np.nan], [3, 6], [-3, 1],
        [0, np.nan], [12.71, 12.71], [-3, 1],
        [0, np.nan], [8.76, 8.76], [-3, 1],
        [0, np.nan], [13.897, 13.897], [-3, 1]
    ])
    constraints = ()

    noOfMSIterations = 3   #4
    firstSpec = 144   #144
    lastSpec = 182    #182

    # Boolean Flags to control script
    MSCorrectionFlag = True
    GammaCorrectionFlag = True

    maskedSpecAllNo = np.array([173, 174, 179])

    tofBinning="110,1,430"                 # Binning of ToF spectra
    maskTOFRange = None
  
    # Original data uses histogram data instead of point data
    runHistData = True
    normVoigt = False


class YSpaceFitInitialConditions:
    anything = True


class UserScriptControls:
    runRoutine = True
    
    # Choose main procedure to run
    procedure = "BACKWARD"   # Options: None, "BACKWARD", "FORWARD", "JOINT"

    # Choose on which ws to perform the fit in y space
    fitInYSpace = None    # Options: None, "BACKWARD", "FORWARD", "JOINT"


class BootstrapInitialConditions:
    runBootstrap = False


start_time = time.time()

wsBackIC = LoadVesuvioBackParameters
wsFrontIC = LoadVesuvioFrontParameters  
bckwdIC = BackwardInitialConditions
fwdIC = ForwardInitialConditions
yFitIC = YSpaceFitInitialConditions
bootIC = BootstrapInitialConditions
userCtr = UserScriptControls

runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)

AnalysisDataService.clear()
userCtr.procedure = "FORWARD"

runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)


end_time = time.time()
print("\nRunning time: ", end_time-start_time, " seconds")