Data reduction, visualization and analysis of ARCS data.
This document explains the steps to reduction of data and how to visualize and analyze using DAVE.
Initial setup - permission and accessing python files.
1. Establish the use of the DANSE Dr.Chops routines, and ARCS routines.
$source ~5us/ARCSreduction.sh
This command also copies over a series of text files and python routines to
the current directory.
2. Ensure that multiprocessor analysis is currently set-up for your account.
If steps 2a)-2d) were already performed previously, then you only need to
perform step 2e) to make certain mpd is currently running.
a) Make a text file in home directory called .mpd.conf
b) The only line of this file is password=yourpassword, where yourpassword
is a password of your choice
c) Change the read and write permissions of this file to only be yours
$chmod 600 ~/.mpd.conf
d) Create the text file mpd.hosts in your home directory. The only
text in this file is
localhost:16
e) check that mpi is running using the command
$mpd &
$ mpirun -n 4 mpipython.exe -c 'import mpi; w=mpi.world(); print w.rank'
# Output should be integers 1, 2, 3, and 4 in a random sequence.
Data Reduction and Visualizing
Initial setup - permission and accessing python files.
1. Establish the use of the DANSE Dr.Chops routines, and ARCS routines.
$source ~5us/ARCSreduction.sh
This command also copies over a series of text files and python routines to
the current directory.
2. Ensure that multiprocessor analysis is currently set-up for your account.
If steps 2a)-2d) were already performed previously, then you only need to
perform step 2e) to make certain mpd is currently running.
a) Make a text file in home directory called .mpd.conf
b) The only line of this file is password=yourpassword, where yourpassword
is a password of your choice
c) Change the read and write permissions of this file to only be yours
$chmod 600 ~/.mpd.conf
d) Create the text file mpd.hosts in your home directory. The only
text in this file is
localhost:16
e) check that mpi is running using the command
$mpd &
$ mpirun -n 4 mpipython.exe -c 'import mpi; w=mpi.world(); print w.rank'
# Output should be integers 1, 2, 3, and 4 in a random sequence.
Data Reduction and Visualizing
The reduction routines make use of the vanadium masking and calibration files. The data reduction make use of two text files.
Data reduction text files are datatext.dat and datamask.dat. Text files can be edited with the available text editors (emacs, gedit, etc)
Example of a datatext.dat file is as below.
===================================================================================
IPTS-5959, 24041, 63.60, 16.64, -14, 63, 1.0, 0, 1, 0, 23181, 1, 2, 10, 1, SrVO_65_5K_10
IPTS-5959, 24042, 63.60, 16.64, -14, 63, 1.0, 0, 1, 0, 23181, 1, 2, 7.5, 1, SrVO_65_5K_7.5
# IPTSnumber,
# monochromatic run number(s),
# Ei (meV), [use a negative number if you want software to calculate Ei]
# toffset (microseconds),
# emin (meV) (smallest value of energy transfer),
# emax (meV) (largest value of energy transfer),
# ebin (meV),
# qbin (inv. Angstroms), set to 0 for automatic qbinning.
# ki/kf flag,
# set = 0 for double differential cross-section.
# set = 1 to perform this multiplicative normalization (S(Q,W)).
# NOTE: when .nxspe files are used with DAVE-DCSMslice, the "view intensity as"
# option recognizes your choice of ki/kf and scales the data appropriately.
# time-independent background range, values in microseconds to use for the
# time independent background, set = 0 for no tibg
# vanadium run number(s)
# masking flag (0 no mask, 1 mask w/vandium, 2 mask w/sample,
# 3 mask w/sample and vanadium)
# pixel resolution = 2, 4, 8 etc. for changing resoloution of output mslice
# file, 1 = 128 pixels per tube, 2 = 64 pixels per tube,
# 4 = 32 pixels per tube
# ANGLE value, -999 automatically reads the CCR12 motor angle
# positive or negative number, will use that number for the angle and not
# read the file. Use 0 for powders
# sparsefile value = 0 for all files, 1 for sparse files
# friendlyfilename - text which will be used to generate friendly filenames
# of the output, and the subdirectory of the output data.
# friendlyfilename must follow rules for text of directory names in *nix
# need to check masking and union of masks.
===================================================================================
Note – for a particular Ei need to change only the monochromatic run number(s), Angle Value and Filename.
One can comment out a line by starting the line with the # symbol.
Example for a different Ei is as below,
IPTS-5959, 24117, 115.78, 10.12, -20, 116, 2.0, 0, 1, 0, 23181, 1, 2, 10, 1, SrVO_120_5K_10
Note that, the absolute value of emax should not be larger than Ei
Ebin must divide well into the range of energy transfers established by emin and emax.
If vandium IPTS number is 0 then, vandium normalization will not be done, AND, one can only choose masking flag = 0 or =2.
One can include multiple run numbers in a single line by listing the run numbers separated by spaces, and or hyphenating the first and last run number for series of consecutive measurements
Use a negative number for the nominal incident energy if you want the software to calculate Ei and the time-offset automatically
2. Run this script using the command
(Before that go to the folder, IPTS-xxx/shared)
datareduce.py datatext.dat datamaskTEMPLATE.dat
It will take time to reduce the data and create files.
3. Copy all the folders with same incident energy to another folder for easy access.
cp SrVO_120*/*.* nxspe_120_5k
After that you are ready to use MSlice in DAVE.
4. Open DAVE. Go to Data Reduction -> NCNR -> DCS Data Reduction.
First select the file type by going to File->FileType->NXSPE
Select Sample Type = Diffuse Scattering Multiple E
Energy Range = All
Browse for the folder containing *.nxspe files, where you copied in last step.
5. Select all the data files, and load data
6. Enter lattice parameters.
7. Enter Crystal Orientation, depending on the scattering plane of the crystal
8. Click Calculate Projections
9. After that you can plot either Slice or Cut or Volume depending on the interest.
10. Few examples are shown below.
