mia-3dtransform(1)

📦
version 2.4.7 · 3 versions
, in debian bookworm, ubuntu jammy

💖 mia-3dtransform(1) — the manual, but make it cute 💖

okay bestie, welcome to the General Commands Manual page for mia-3dtransform — yes that's the manual name, yes you're in the right place, and yes we're about to transform a whole entire 3D image together. grab a snack. 🍓

✨ NAME ✨

mia-3dtransform — Transform a 3D image. literally that's the whole job. she transforms. 💅

🌈 SYNOPSIS 🌈

mia-3dtransform -i <in-file> -o <out-file> -t <transformation> [options]

three required besties (-i, -o, -t) and then whatever else you feel like sprinkling on top. 🫶

🦋 DESCRIPTION 🦋

mia-3dtransform transforms a 3D image by applying a given 3D transformation. that's it. that's the vibe. you hand her an image, you hand her a transformation, she gives you back a transformed image. iconic behaviour, no notes. ✨

🎀 OPTIONS 🎀

the required girlies (io)

  • -i, --in-file=(input, required); io — the input image, bestie. mandatory, no skipping. for supported file types see PLUGINS:3dimage/io down below 👇
  • -o, --out-file=(output, required); io — the transformed image goes here. also mandatory. for supported file types see PLUGINS:3dimage/io 👇
  • -t, --transformation=(input, required); io — the transformation file. yes, also mandatory. for supported file types see PLUGINS:3dtransform/io 👇

the override girlies

  • -p, --interpolator= — override the interpolator that the transformation brought with her. you're the boss now. 👑
  • -b, --boundary=mirror — override the boundary conditions provided by the transformation. heads up though: this one is only used if the interpolator is also overridden. so don't come for her alone, she needs -p as her plus-one. 🙈

🧚 Help & Info 🧚

  • -V, --verbose=warning — verbosity of output; prints messages of the given level and higher priorities. the supported priorities, starting at the lowest level, are:
    • trace ‐ Function call trace
    • debug ‐ Debug output
    • info ‐ Low level messages
    • message ‐ Normal messages
    • warning ‐ Warnings
    • fail ‐ Report test failures
    • error ‐ Report errors
    • fatal ‐ Report only fatal errors
  • --copyright — print copyright information. the receipts. 🧾
  • -h, --help — print this help
  • -?, --usage — print a short help
  • --version — print the version number and exit

💅 Processing 💅

  • --threads=-1 — Maximum number of threads to use for processing. this number should be lower than or equal to the number of logical processor cores in the machine. (-1 means: automatic estimation — she'll figure it out herself, main character energy ✨)

🌸 PLUGINS: 3dimage/io 🌸

all the file formats she'll read and write for 3D images, fr fr:

  • analyze — Analyze 7.5 image
    • Recognized file extensions: .HDR, .hdr
    • Supported element types: unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit
  • datapool — Virtual IO to and from the internal data pool
    • Recognized file extensions: .@
  • dicom — Dicom image series as 3D
    • Recognized file extensions: .DCM, .dcm
    • Supported element types: signed 16 bit, unsigned 16 bit
  • hdf5 — HDF5 3D image IO
    • Recognized file extensions: .H5, .h5
    • Supported element types: binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit
  • inria — INRIA image
    • Recognized file extensions: .INR, .inr
    • Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
  • mhd — MetaIO 3D image IO using the VTK implementation (experimental).
    • Recognized file extensions: .MHA, .MHD, .mha, .mhd
    • Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
  • nifti — NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with dicomtonifti --no-reorder from the vtk-dicom package.
    • Recognized file extensions: .NII, .nii
    • Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit
  • vff — VFF Sun raster format
    • Recognized file extensions: .VFF, .vff
    • Supported element types: unsigned 8 bit, signed 16 bit
  • vista — Vista 3D
    • Recognized file extensions: .-, .V, .VISTA, .v, .vista
    • Supported element types: binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
  • vti — 3D image VTK-XML in- and output (experimental).
    • Recognized file extensions: .VTI, .vti
    • Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit
  • vtk — 3D VTK image legacy in- and output (experimental).
    • Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage
    • Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

🦄 PLUGINS: 3dtransform/io 🦄

and here's where transformations live, in case you were wondering:

  • bbs — Binary (non-portable) serialized IO of 3D transformations
    • Recognized file extensions: .bbs
  • datapool — Virtual IO to and from the internal data pool
    • Recognized file extensions: .@
  • vista — Vista storage of 3D transformations
    • Recognized file extensions: .v, .v3dt
  • xml — XML serialized IO of 3D transformations
    • Recognized file extensions: .x3dt

⭐ EXAMPLE ⭐

Transform an image input.v by the transfromation stored in trans.v by using nearest neighbour interpolation ans store the result in output.v

mia-3dtransform -i input.v -t trans.v  -o output.v  -p bspline:d=0

look at her go. 😭 she ate that. 🔥

👑 AUTHOR(s) 👑

Gert Wollny

This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option --copyright.

no warranty bestie, I mean it. read the license, it's giving legal realness. 🧾

okay that's the whole page, mwah 💋

this was USER COMMANDS version v2.4.7 of mia-3dtransform(1) — go transform something gorgeous ✨🦋💖

📦 where this page comes from