SAXS diffraction pattern indexing the easy way.
Once you have started Julia, enter Pkg mode by typing ] and run add Himalaya command. You will see something like this
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.8.0-beta3 (2022-03-29)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(@v1.8) pkg> add Himalaya
And that's it!
The following code is an example of how to use Himalaya to index the integration of a diffraction pattern.
using DelimitedFiles
using Himalaya
load_integration(path) = readdlm(path, ' ', Float64, '\n')
# `integration` contains the values in a tot_file
integration = load_integration("my-high-impact-sample_tot.dat")
qs, logIs = integration[:, 1], log10.(integration[:, 2])
# indices of peaks in the integration array
peak_locations, peak_proms = findpeaks(logIs)
peak_qs = qs[peak_locations]
# compute phases matching identified peaks
indices = indexpeaks(peak_qs, peak_proms)
# Example `indices`
# 3-element Vector{Index}:
# Index(::Pn3m, 0.05344, [0.05344 0.06556 0.07508 0.09239 0.10668 0.11317 ⋅ 0.12486]
# Index(::Im3m, 0.05344, [0.05344 0.07508 0.09239 0.10668 ⋅ 0.13049 ⋅ ⋅ ⋅]
# Index(::Pn3m, 0.07508, [0.07508 0.09239 0.10668 0.13049 ⋅ ⋅ ⋅ ⋅]
index = first(indices)
score(index) # => 6.4996...
d, R² = fit(index) # => d = 117.8585...Å; R² = 0.9999...You can also get Indexs for a specific phase as follows
indexpeaks(Hexagonal, peak_qs, peak_proms)
# 6-element Vector{Index}:
# Index(::Hexagonal, 0.06426, [0.06426 0.11144 0.12876 0.16771 0.19368 ⋅ ⋅])
# Index(::Hexagonal, 0.07855, [0.07855 0.13655 0.15732 ⋅ ⋅ ⋅ ⋅])
# Index(::Hexagonal, 0.09673, [0.09673 0.16771 0.19368 0.25645 0.29107 ⋅ ⋅])
# ...You can use ?Phase to see the list of available phases (? enters help mode).