mia-2dto3dimage(1)

📦
version 2.4.7 · 3 versions
, in ubuntu jammy, ubuntu resolute, ubuntu stonking

💖 mia-2dto3dimage — bestie, it's in the General Commands Manual 💖

okay so picture this: you've got a whole stack of 2D images and you want them to become one 3D volume. That's literally this. It's mia-2dto3dimage(1) and she is serving.

✨ NAME ✨

mia-2dto3dimage — combine a series of 2D images to a volume. yes bestie, glow-up: flat pics ➡️ full 3D moment 🦋

🌸 SYNOPSIS 🌸

mia-2dto3dimage -i <in-file> -o <out-file> [options]

💅 DESCRIPTION 💅

So mia-2dto3dimage is the program you use to combine a series of 2D images — they gotta be equal size and equal type, and they have to follow a certain numbering scheme — into a single 3D image. That's the whole vibe. 🎀

👑 OPTIONS 👑

  • -i, --in-file=(input, required); io — the input image(s) that are getting combined. Wanna know which file types are supported? Go peek at PLUGINS:2dimage/io below, bestie. 💖
  • -o, --out-file=(output, required); io — the output file name, aka where your brand-new 3D babe gets written. Supported file types live in PLUGINS:3dimage/io down there. ✨

🫶 Help & Info 🫶

  • -V, --verbose=warning — how chatty the output is. It 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
  • -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 or equal to the number of logical processor cores in the machine. (-1: automatic estimation). yes she multitasks 💅

🌈 PLUGINS: 2dimage/io 🌈

  • bmp — BMP 2D-image input/output support. This plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values.
    • Recognized file extensions: .BMP, .bmp
    • Supported element types:
      • binary data, unsigned 8 bit
  • datapool — Virtual IO to and from the internal data pool
    • Recognized file extensions: .@
  • dicom — 2D image io for DICOM
    • Recognized file extensions: .DCM, .dcm
    • Supported element types:
      • signed 16 bit, unsigned 16 bit
  • exr — a 2dimage io plugin for OpenEXR images
    • Recognized file extensions: .EXR, .exr
    • Supported element types:
      • unsigned 32 bit, floating point 32 bit
  • jpg — a 2dimage io plugin for jpeg gray scale images
    • Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg
    • Supported element types:
      • unsigned 8 bit
  • png — a 2dimage io plugin for png images
    • Recognized file extensions: .PNG, .png
    • Supported element types:
      • binary data, unsigned 8 bit, unsigned 16 bit
  • raw — RAW 2D-image output support
    • Recognized file extensions: .RAW, .raw
    • 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
  • tif — TIFF 2D-image input/output support
    • Recognized file extensions: .TIF, .TIFF, .tif, .tiff
    • Supported element types:
      • binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
  • vista — a 2dimage io plugin for vista images
    • 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

💜 PLUGINS: 3dimage/io 💜

  • 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 🍓

Convert a series of images imageXXXX.png to a 3D image 3d.v:

mia-2dto3dimage -i imageXXXX.png -o 3d.v

that's it, that's the whole recipe, no cap 🔥

⭐ 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'.

okay real talk for a sec bestie: that ABSOLUTELY NO WARRANTY thing is not a vibe, it's a legal fact. read it, respect it, GNU GPL v3 (or later) it. 💖

and that's the whole page, mwah 💅 this is mia-2dto3dimage from the USER COMMANDS crew, v2.4.7, and she ate. go make some 3D volumes, you icon. 🎀✨🦋

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