DIFF_TOMO(1)

💖 DIFF_TOMO(1) 💖

okay so bestie, welcome to DIFF_TOMO(1), the manual page that's giving very niche science-girlboss energy, and I'm gonna walk you through every single line of it because you deserve to understand it fr fr 🧚✨

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✨ NAME ✨

diff_tomo — GUI interface for reduction of diffraction tomography experiments 🎀

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🌸 DESCRIPTION 🌸

okay first thing, here's the usage line, copied EXACTLY, no edits, no cap:

usage: diff_map [options] -p ponifile imagefiles* If the number of files is too large, use double quotes like "*.edf"

(yes it says diff_map, that's not me being sloppy, that's literally what's written 💅)

So like. Azimuthal integration for diffraction imaging. Diffraction mapping is an experiment where 2D diffraction patterns get recorded while you do a 2D scan. Diff_map is a graphical application (built on top of pyFAI and h5py, iconic combo honestly 👑) which lets you reduce that 4D dataset down into a 3D dataset that contains the two motion dimensions plus the many diffraction angles — and by many I mean thousands, it's giving data hoarder 😭.

The resulting dataset can be opened using PyMca roitool, where the 1d dataset has to be selected as the last dimension. This result file aims at being NeXus compliant, which, slay. ✨

This tool can also be used for diffraction tomography experiments, considering the slow scan direction as the rotation. main character energy tbh 🔥

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🫶 positional arguments 🫶

• FILE — List of files to integrate. Mandatory without GUI. Like, no GUI? You need this. Periodt.

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💅 options 💅

• -h, --help — show this help message and exit 🙈
• -V, --version — show program's version number and exit ⭐
• -o FILE, --output FILE — HDF5 File where the processed map will be saved. Mandatory without GUI, so don't forget it bestie 🍓
• -v, --verbose — switch to verbose/debug mode, default: quiet 🤫
• -P FILE, --prefix FILE — Prefix or common base for all files 🎀
• -e EXTENSION, --extension EXTENSION — Process all files with this extension 🌸
• -t FAST, --fast FAST — number of points for the fast motion. Mandatory without GUI 🦋
• -r SLOW, --slow SLOW — number of points for slow motion. Mandatory without GUI 🦋
• -c NPT_RAD, --npt NPT_RAD — number of points in diffraction powder pattern. Mandatory without GUI 💜
• --npt-azim NPT_AZIM — number of points in azimuthal direction, 1 for 1D integration ✨
• -d FILE, --dark FILE — list of dark images to average and subtract (comma separated list) 🌈
• -f FILE, --flat FILE — list of flat images to average and divide (comma separated list) 🌈
• -m FILE, --mask FILE — file containing the mask, no mask by default 🫶
• -p FILE, --poni FILE — file containing the diffraction parameter (poni-file), Mandatory without GUI 👑
• -O OFFSET, --offset OFFSET — do not process the first files 🙈
• -g, --gpu — process using OpenCL on GPU, ok speed demon 💀
• -S, --stats — show statistics at the end ⭐
• --gui — Use the Graphical User Interface 🖥️
• --no-gui — Do not use the Graphical User Interface 🚫
• --config CONFIG — provide a JSON configuration file 📄

Bugs: Many, see hereafter: 1. If the number of files is too large, use double quotes "*.edf" 2. There is a known bug on Debian7 where importing a large number of file can take much longer than the integration itself: consider passing files in the command line

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and that's the whole vibe check, bestie — no skips, no summaries, we read everything together 💖

this was diff_tomo from pyFAI version ... , dated February 2023 — and if you made it to the bottom of this page you're literally an icon, go hydrate and run your integration 🧚💜✨