EIGER2CBF(1)

📦
version 0.14.0 · 2 versions
, in debian bookworm

🎀 eiger2cbf — the bestie cut 🎀

okay so real quick: this is eiger2cbf, and it lives in section 1 of the manual, aka User Commands. buckle up, it's a good one 💖

💖 NAME 💖

eiger2cbf — a portable image converter built on the FabIO library that takes Eiger frames (including the ones from LIMA, yes those too) and exports them to CBF, while fully cosplaying the header of a Dectris Pilatus. it's giving fake-it-till-you-make-it and honestly? iconic behavior. 👑

✨ DESCRIPTION ✨

here's how you summon it, bestie:

usage: eiger2cbf [-h] [-V] [-v] [--debug] [-o OUTPUT] [-m MASK] [-O OFFSET] [-D DUMMY] [--pilatus] [--dry-run] [-e ENERGY] [-w WAVELENGTH] [-d DISTANCE] [-b BEAM BEAM] [--alpha ALPHA] [--kappa KAPPA] [--chi CHI] [--phi PHI] [--omega OMEGA] [--rotation ROTATION] [--transpose] [--flip-ud] [--flip-lr] [IMAGE ...]

so what it does: portable image converter based on FabIO library to export Eiger frames (including the ones from LIMA) to CBF and mimic the header from Dectris Pilatus. that's the whole mission statement. 🦋

🫶 positional arguments

  • IMAGE — file with input images. and yes, you can pass more than one, go off. 🌸

💅 options

  • -h, --help — show this help message and exit. the classic, the beloved, the "help me I forgot the flag" 💀
  • -V, --version — output version and exit. short and sweet, no notes.
  • -v, --verbose — show information for each conversions. so you actually see what's happening for every single one. 👀
  • --debug — show debug information. for when you need the whole lore. 🔍

👑 main arguments

  • -o OUTPUT, --output OUTPUT — output directory and filename template: eiger2cbf/frame_{index:04d}.cbf. that template is literally the default, bestie, so you know what it's gonna name your stuff if you don't say otherwise.
  • -m MASK, --mask MASK — Read masked pixel from this file. mask girlies stay winning. 🎭
  • -O OFFSET, --offset OFFSET — index offset. CrysalisPro likes indexes to start at 1, Python starts at 0, and this flag is the peace treaty between them. 🕊️
  • -D DUMMY, --dummy DUMMY — Set masked values to this dummy value. yes it's called dummy, no we're not being mean. 🫶
  • --pilatus — Select an image shape similar to Pilatus detectors for compatibility with Crysalis. it's not a Pilatus, it's just dressed like one for the function. 💅

🌈 optional behaviour arguments

  • --dry-run — do everything except modifying the file system. it's the rehearsal, not the show. absolutely the move before you commit to anything. ✨

🧪 Experimental setup options

  • -e ENERGY, --energy ENERGY — Energy of the incident beam in keV. beam energy, let's go. ⚡
  • -w WAVELENGTH, --wavelength WAVELENGTH — Wavelength of the incident beam in ??. (that's what the page says, we're not editorializing, we're just reporting.) 🌊
  • -d DISTANCE, --distance DISTANCE — Detector distance in meters. meters!! not mm, not cm, meters. 🫡
  • -b BEAM BEAM, --beam BEAM BEAM — Direct beam in pixels x, y. two values, x then y, no cap. 📍

🌀 Goniometer setup

  • --alpha ALPHA — Goniometer angle alpha value in deg.
  • --kappa KAPPA — Goniometer angle kappa value in deg.
  • --chi CHI — Goniometer angle chi value in deg. or formula f(index)
  • --phi PHI — Goniometer angle phi value in deg. or formula f(index)
  • --omega OMEGA — Goniometer angle omega value in deg. or formula f(index) like '-180+index*0.1

like, you can hand it a plain number or a whole little formula that depends on the index. main character energy, fr fr. 📐

🎀 Image preprocessing (Important: applied in this order!)

okay listen, this heading is doing a LOT of shouting and it deserves to, because the order matters. do not shuffle these. 🙈

  • --rotation ROTATION — Rotate the initial image by this value in degrees. Must be a multiple of 90??. so like, quarter turns only, bestie, don't get creative. 🔄
  • --transpose — Flip the x/y axis. axes said "we're switching places". 🔀
  • --flip-ud — Flip the image upside-down. 🙃
  • --flip-lr — Flip the image left-right. ↔️
and the receipts, because you'll want them: return codes: 0 means a success. 1 means the conversion contains a failure, 2 means there was an error in the arguments. so 0 = slay, 1 = the conversion itself said no, 2 = you said it wrong. 💀

and that's the whole page, bestie. this was eiger2cbf 0.14.0, dated November 2022 — go convert some frames, you've got this. 🫶✨🌸

📦 where this page comes from