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mandi_autoreduce.config
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mandi_autoreduce.config
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# Configuration file for MANDI data reduction - automatic profile fitting
#
# Part 1
# Peak Integration ==> .integrate and .mat files
# Part 2
# Peak Intensity Normalization ==> .mtz
#
# ==========================================================================
# Configuration parameters for Part1
# Peak Integration
# ==========================================================================
# Each line can either start with a comment, indicated by a '#' mark or start
# with a parameter name and value, optionally followed by a comment. ALL
# parameters used by the script must be specified. If a required parameter
# is not specified, the script will terminate with a message indicating which
# parameter was missing.
#
# **************************************************************************
# Parameters needed by ReduceOneSCD_Run.py, to process ONE run.
# **************************************************************************
#
instrument_name MANDI # prefix for run file names
#
# Specify calibration file(s). SNAP requires two calibration files, one
# for each bank. If the default detector position is to be used, specify
# None as the calibration file name.
calibration_file_1 None
calibration_file_2 None
data_directory /SNS/MANDI/IPTS-8776/nexus/
#
# Number of peaks to find, per run, both for getting the UB matrix,
# AND to determine how many peaks are integrated, if peak positions are
# NOT predicted.
#
num_peaks_to_find 150
#
# min_d, max_d and tolerance control indexing peaks. max_d is also
# used to specify a threshold for the separation between peaks
# returned by FindPeaksMD, so it should be specified somewhat larger
# than the largest cell edge in the Niggli reduced cell for the
# sample.
#
min_d 65.0
max_d 120.0
tolerance 0.15
#
# unit cell parameters for the sample. These will be used if the UB
# matrix cannot be found by FindUBUsingFFT, in which case autoreduction
# will fall back on FindUBUsingLatticeParameters
#
unitcell_a 73.3
unitcell_b 73.3
unitcell_c 99.0
unitcell_alpha 90
unitcell_beta 90
unitcell_gamma 120
force_lattice_parameters True #Will reindex using the given cell rather than allowing
#Mantid to determine its own cell.
#
# If predicted peak positions are to be integrated,
# the integrate_predicted_peaks flag should be set to True and the range
# of wavelengths and d-spacings must be specified
#
integrate_predicted_peaks True
min_pred_wl 2.0
max_pred_wl 4.0
min_pred_dspacing 2.3
max_pred_dspacing 15.0
#
# This is set to only use spherical integration. We only need this as a rough comparison to profile
# fitted intensities to serve as a sanity check.
#
peak_radius 0.020
bkg_inner_radius 0.021
bkg_outer_radius 0.023
#
# A couple of things for the IntegrateThingsProfileFitting algorithm. These are explained in the
# IntegrateProfileFitting's documentation.
#
moderator_file /SNS/MANDI/shared/ProfileFitting/bl11_moderatorCoefficients_2018.dat
strong_peaks_params_file None
intensity_cutoff 200
edge_cutoff 3
frac_stop 0.05
min_ppl_frac 0.9
max_ppl_frac 1.1
dq_max 0.15
# ==========================================================================
# Configuration parameters for Part 3
# Generate mtz file from all applicable runs. This will run intensities through
# lauenorm (from the laugen package) to do wavelength and image normalization. The
# output is a merged and unmerged mtz file containing F's for further analysis.
# ==========================================================================
#
first_run_number 9113 #First run number that you want to include in creating the mtz files
spacegroup_number 154 #Space group number for laueNorm.
mtz_name betalac #name for mtz files resulting from laueNorm
lauenorm_edge_pixels 1 #number of pixels from the edge to exclude
lauenorm_scale_peaks 3. #Value to scale peak intensitys and sigmas by
lauenorm_min_d 1.2 #Minimum d value to output for laueNorm
lauenorm_min_wl 2.0 #Min wavelength to output for laueNorm
lauenorm_max_wl 4.0 #Max wavelength to output for lauenorm
lauenorm_min_isi 1.0 #Min I/sigma to output for laueNorm
lauenorm_mini 0.0 #Min I to output for laueNorm
lauenorm_applysinsq True #If true, will multiply intensities and sigmas by sin(theta)**2
#Allowing lauenorm to apply the wavelength component of the Lorentz
#correction.
# The next lines are directories for lauenorm. Do not edit them unless you know exactly what you
# are doing.
pbpDir /SNS/MANDI/shared/laue3/ #pbp directory for laueNorm. Must contain multidiags.out (from laugen). Should end with /
laueLibDir /SNS/MANDI/shared/laue3/laue/laue_install/lib/ #library file for lauegen. Should end with /
lauenormBin /SNS/MANDI/shared/laue3/laue/laue_install/bin/lauenorm #Binary file for lauenorm.
lauenormSetupScript /SNS/snfs1/instruments/MANDI/shared/laue3/laue/laue.setup-sh