crysm 1.0.0

Continuous rotation electron diffraction (cRED) data analysis helper cli

CRYSM

Installation

The package can be installed from PyPI using

pip install crysm

This exposes the crysm command. To see available commands, run crysm --help. The commands correspond to the decorated functions in src/main.py.

Installation of uv

In this package, uv is used for package management. To install on linux/mac, run

curl -LsSf https://astral.sh/uv/install.sh | sh

and on windows (in powershell)

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Usage

The functionality of this library can be found by typing crysm --help or reading the functions in src/main.py. Below are some examples.

Example 1: Finding correction factors for the central cross from a flatfield image

crysm find-center-cross-correction 24bit/flatfield_200kV_24bit.mib
> For image: 24bit/flatfield_200kV_24bit.mib:
>   Mean value of cross: 40151.59
>   Mean value of central four pixels: 74076.75
>   Mean value of rest of image: 18284.44
> Suggested arguments for correction:
>  --additional-pixels 4 --correction-factor 2.196 --central-four-factor 4.051
> Number of additional pixels should be verified with detector manufacturer

This command can also take multiple images, but they should be collected with the same parameters (unlike the example below):

crysm find-center-cross-correction 24bit/flatfield_200kV_24bit.mib 12bit/flatfield_200kV_12bit.mib 6bit/flatfield_200kV_6bit.mib                                          3.11   17:08:04
> For image: 24bit/flatfield_200kV_24bit.mib:
>   Mean value of cross: 40151.59
>   Mean value of central four pixels: 74076.75
>   Mean value of rest of image: 18284.44
>   Additional pixels: 4
>   Correction factor: 2.196
>   Central four factor: 4.051
> For image: 12bit/flatfield_200kV_12bit.mib:
>   Mean value of cross: 2013.16
>   Mean value of central four pixels: 3716.25
>   Mean value of rest of image: 916.51
>   Additional pixels: 4
>   Correction factor: 2.197
>   Central four factor: 4.055
> For image: 6bit/flatfield_200kV_6bit.mib:
>   Mean value of cross: 39.97
>   Mean value of central four pixels: 63.00
>   Mean value of rest of image: 18.22
>   Additional pixels: 4
>   Correction factor: 2.194
>   Central four factor: 3.457
> Suggested arguments for correction:
>  --additional-pixels 4 --correction-factor 2.195 --central-four-factor 3.854
> Number of additional pixels should be verified with detector manufacturer

Example 2: Correcting the central cross of a calibration image

crysm pets-correct-center-cross-calibration --additional-pixels 4 --correction-factor 2.196 --central-four-factor 4.051 SAED_150cm.mib WIDE_150cm.tiff
> Wrote corrected image to WIDE_150cm.tiff

Example 3: Correcting the central cross of a pets project

crysm pets-correct-center-cross --additional-pixels 4 --correction-factor 2.196 --central-four-factor 4.051
> Using cred project C:\Users\iverks\progging\master\cRED_070325\experiment_5
> 100%|█████████████████████████████████████████████████████████████████████████████| 1093/1093 [00:10<00:00, 109.19it/s]
> Wrote 1093 corrected images to C:\Users\iverks\progging\master\cRED_070325\experiment_5\tiff_corr

Developers

In order to install the package locally, run

uv tool install -e .

The crysm command is then available globally.

• pets/run_shelx.py depends on the internal format of .pts2-files, future updates might break
• lib/find_cred_project.py depends on the existence of cRED_log.txt, which Stef Smeets has hinted at removing in the future. Beware.
• To publish a new update to PyPi, bump the version number in pyproject.toml, then run uv publish. Developer permissions must be acquired first.