Processing diffuse scattering for mac1 dataset H8¶
Background files¶
Import using DIALS
cd /nfs/chess/user/spm82/mdx/als_20250624/macrodomain_H8
mkdir -p dials_background
cd dials_background
dials.import /nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H8/H8_air_10_*.cbf image_range=1,360
mdx2 processing¶
cd /nfs/chess/user/spm82/mdx/als_20250624/macrodomain_H8
mkdir -p mdx2
cd mdx2
mdx2.import_data ../dials_background/imported.expt --chunks 5 211 493 --nproc 5 --outfile bkg_data.nxs
mdx2.bin_image_series bkg_data.nxs 5 20 20 --valid_range 0 100 --outfile binned.nxs --nproc 64
mdx2.import_data ../dials_360/DataFiles/AUTOMATIC_DEFAULT_scaled.expt --chunks 50 211 493 --nproc 5
mdx2.import_geometry ../dials_360/DataFiles/AUTOMATIC_DEFAULT_scaled.expt
mdx2.find_peaks geometry.nxs data.nxs --count_threshold 20 --nproc 64
mdx2.mask_peaks geometry.nxs data.nxs peaks.nxs --sigma_cutoff 3 --nproc 64
mdx2.integrate geometry.nxs data.nxs --mask mask.nxs --subdivide 2 2 4 --nproc 64
mdx2.correct geometry.nxs integrated.nxs --background binned.nxs
mdx2.scale corrected.nxs --mca2020
mdx2.merge corrected.nxs --scale scales.nxs
mdx2: 1.0.3 Python 3.10.18 Installed in: /nfs/chess/user/spm82/dev/mdx2/mdx2
mdx2 scaling model¶
/nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r") /nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r")
Isotropic average¶
/nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r") /nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r") /nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r")
NXgroup('hkl_table')
<Axes: xlabel='s'>
Map slice visualization¶
22:47:53 INFO | Starting mdx2.map at 2026-02-08 22:47:53 22:47:53 INFO | Parameters(geom='mdx2/geometry.nxs', hkl='mdx2/merged_sub.nxs', symmetry=True, limits=(-80.0, 80.0, -80.0, 80.0, 0.0, 1.0), signal='isoavg', outfile='mdx2/slice_isoavg.nxs') 22:47:53 INFO | Loading HKL table and geometry... /nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r") 22:47:54 INFO | Map region: 22:47:54 INFO | h: -80.0 to 80.0 (321 points) 22:47:54 INFO | k: -80.0 to 80.0 (321 points) 22:47:54 INFO | l: 0.0 to 1.0 (5 points) 22:47:54 INFO | Generating Miller index grid... 22:47:54 INFO | Mapping Miller indices to asymmetric unit... 22:47:54 INFO | Looking up 'isoavg' values in data table... 22:48:00 INFO | Saving map to mdx2/slice_isoavg.nxs... 22:48:01 INFO | Map creation completed successfully 22:48:01 SUCCESS | mdx2.map completed in 8.03 seconds 22:48:05 INFO | Starting mdx2.map at 2026-02-08 22:48:05 22:48:05 INFO | Parameters(geom='mdx2/geometry.nxs', hkl='mdx2/merged_sub.nxs', symmetry=True, limits=(-80.0, 80.0, -80.0, 80.0, 0.0, 1.0), signal='intensity', outfile='mdx2/slice.nxs') 22:48:05 INFO | Loading HKL table and geometry... /nfs/chess/user/spm82/dev/mdx2/mdx2/io.py:68: UserWarning: mdx2 version mismatch: file version None, installed version 1.0.3 nxroot = nxload(filename, "r") 22:48:06 INFO | Map region: 22:48:06 INFO | h: -80.0 to 80.0 (321 points) 22:48:06 INFO | k: -80.0 to 80.0 (321 points) 22:48:06 INFO | l: 0.0 to 1.0 (5 points) 22:48:06 INFO | Generating Miller index grid... 22:48:06 INFO | Mapping Miller indices to asymmetric unit... 22:48:06 INFO | Looking up 'intensity' values in data table... 22:48:13 INFO | Saving map to mdx2/slice.nxs... 22:48:13 INFO | Map creation completed successfully 22:48:13 SUCCESS | mdx2.map completed in 7.90 seconds
