Processing diffuse scattering for mac1 dataset H6¶

Background images¶

Import using DIALS

cd /nfs/chess/user/spm82/mdx/als_20250624/macrodomain_H6
mkdir -p dials_background
cd dials_background
dials.import /nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H6/H6_air_7_*.cbf image_range=1,90 

Note, if you use template=stuff_#####.cbf instead, it only loads the first header, and the rest of the exposure times in imported.expt are zero! This produces infinities in output of mdx2.bin_image_series

mdx2 processing¶

cd /nfs/chess/user/spm82/mdx/als_20250624/macrodomain_H6
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
mdx2.import_data ../dials/DataFiles/AUTOMATIC_DEFAULT_scaled.expt --chunks 50 211 493 --nproc 5
mdx2.import_geometry ../dials/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: 1.0.0

mdx2 scaling model¶

Isotropic average¶

Reading crystal from mdx2/geometry.nxs
  importing as Crystal from mdx2.geometry
Reading symmetry from mdx2/geometry.nxs
  importing as Symmetry from mdx2.geometry
Reading hkl_table from mdx2/merged.nxs
  importing as HKLTable from mdx2.data
Reading hkl_table from mdx2/merged.nxs
  importing as HKLTable from mdx2.data
Exporting <class 'mdx2.data.HKLTable'> to nexus object
  writing hkl_table to mdx2/merged_sub.nxs

NXgroup('hkl_table')

<Axes: xlabel='s'>

Map slice visualization¶

Reading hkl_table from mdx2/merged_sub.nxs
  importing as HKLTable from mdx2.data
Reading crystal from mdx2/geometry.nxs
  importing as Crystal from mdx2.geometry
Reading symmetry from mdx2/geometry.nxs
  importing as Symmetry from mdx2.geometry
map region:
  h from -80.0 to 80.0 (321 grid points)
  k from -80.0 to 80.0 (321 grid points)
  l from 0.0 to 1.0 (5 grid points)
generating Miller index array
mapping Miller indices to asymmetric unit
looking up isoavg in data table
preparing output array
Exporting <class 'mdx2.geometry.GridData'> to nexus object
  writing isoavg to mdx2/slice_isoavg.nxs
done!
Reading hkl_table from mdx2/merged_sub.nxs
  importing as HKLTable from mdx2.data
Reading crystal from mdx2/geometry.nxs
  importing as Crystal from mdx2.geometry
Reading symmetry from mdx2/geometry.nxs
  importing as Symmetry from mdx2.geometry
map region:
  h from -80.0 to 80.0 (321 grid points)
  k from -80.0 to 80.0 (321 grid points)
  l from 0.0 to 1.0 (5 grid points)
generating Miller index array
mapping Miller indices to asymmetric unit
looking up intensity in data table
preparing output array
Exporting <class 'mdx2.geometry.GridData'> to nexus object
  writing intensity to mdx2/slice.nxs
done!

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