mia-raw2volume(1)

📦
version 2.4.7 · 3 versions
, in ubuntu jammy, ubuntu noble

✨ mia-raw2volume ✨

okay bestie, so this is a page from the General Commands Manual — the command is mia-raw2volume, and it's literally the glow-up station where your raw, unhinged byte soup becomes a real 3D image with actual metadata. 💖 Let's get into it.

🌸 NAME 🌸

mia-raw2volume — Convert raw data into a 3D image

🎀 SYNOPSIS 🎀

mia-raw2volume -i <in-file> -o <out-file> -s <size> [options]

🦋 DESCRIPTION 🦋

mia-raw2volume — this program is used to convert raw data into 3D images with apropriate metadata. (yes, "apropriate" is spelled exactly like that in the original, we don't fix people's spelling here, we respect it 💅)

Basically: you hand it a pile of raw bytes, you tell it how big the thing is, and it hands you back a proper 3D image. It's giving main character energy for your data. 😌

💅 OPTIONS 💅

  • -i, --in-file=(input, required); string — input file name. Required! No input, no party.
  • -o, --out-file=(output, required); io — output file name. Also required! For supported file types see PLUGINS:3dimage/io
  • -r, --repn=ubyte — input pixel type. The options are:
    • bit ‐ binary data
    • sbyte ‐ signed 8 bit
    • ubyte ‐ unsigned 8 bit
    • sshort ‐ signed 16 bit
    • ushort ‐ unsigned 16 bit
    • sint ‐ signed 32 bit
    • uint ‐ unsigned 32 bit
    • slong ‐ signed 64 bit
    • ulong ‐ unsigned 64 bit
    • float ‐ floating point 32 bit
    • double ‐ floating point 64 bit
    • none ‐ no pixel type defined
  • -b, --big-endian — input data is big endian. Endianness check, bestie, don't skip it 🙈
  • -f, --scale=[1,1,1] — scale of input voxels <FX,FY,FZ>
  • -k, --skip=0 — skip number of bytes from beginning of file
  • -s, --size=(required); 3dbounds — size of input <NX,NY,NZ> (yes, required, again 💀)

🌈 Help & Info 🌈

  • -V, --verbose=warning — verbosity of output, print messages of given level and higher priorities. Supported priorities starting at 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
  • -h, --help — print this help
  • -?, --usage — print a short help
  • --version — print the version number and exit

⚙️ Processing ⚙️

  • --threads=-1 — Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation). (yep, "Maxiumum" and the missing space after the comma are both in the original — iconic, we keep them 🫶)

🧚 PLUGINS: 3dimage/io 🧚

These are all the file formats that can show up on either end of your conversion, plus what pixel types each one fucks with. Go off, format support.

  • 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

🍓 EXAMPLE 🍓

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

Look at that line going places. It's long, it's dramatic, it works. 💖

👑 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'.

bestie this is the real legal bit, don't sleep on it — ABSOLUTELY NO WARRANTY, fr fr. 💀

okay that's the whole page!! 🌟 this is from v2.4.7, filed under USER COMMANDS, and the page is literally called mia-raw2volume(1) — go convert something and slay, you got this 🫶✨

📦 where this page comes from