mia-3disos...rom-volume(1)

🦋 mia-3disosurface-from-volume 🦋

okay bestie, welcome to the manual page for mia-3disosurface-from-volume, straight outta the General Commands Manual section. this is the girl who pulls a whole iso-surface out of a 3D image and i am so excited to introduce you two 💖

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✨ NAME ✨

mia-3disosurface-from-volume — extract an ist-surface froma a 3D image.

(no cap, that's literally what it says. we do not fix the typo, we respect the typo. it's part of the lore 👑)

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✨ SYNOPSIS ✨

mia-3disosurface-from-volume -i <in-file> -o <out-file> [options]

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✨ DESCRIPTION ✨

so mia-3disosurface-from-volume is that program 🫶 — you hand it a gray scale image, it hands you back an iso-surface, and the way it does that is by marching tetrahedra. iconic algorithm behaviour, honestly.

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✨ OPTIONS ✨

🎀 File-IO

• -i, --in-file=(input, required); io — the input image. it's required, bestie, you can't skip it. for supported file types see PLUGINS:3dimage/io ✨
• -o, --out-file=(output, required); io — the output mesh. also required! for supported file types see PLUGINS:mesh/io ✨

🎀 Help & Info

• -V, --verbose=warning — how chatty do you want it? prints messages at the given level and everything with higher priority. 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

🎀 Image options

• -s, --iso-value=128 — iso-value of iso surface to be extracted
• -b, --bordered — put an empty border around the image to ensure a closed surface (so the mesh doesn't have raggedy open edges, we love a closed surface 💅)

🎀 Mesh options

• -f, --max-faces=-1 — maximum number of Faces,
• -e, --max-edges=-1 — maximum number of Edges
• -c, --max-cost=0.1 — maximum cost for edge collaps
• -r, --ratio=4 — ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized
• -w, --reverse-winding — reverse the winding of the triangles in order to make normals point away from the high intensity area

🎀 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).

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🌈 PLUGINS: 3dimage/io 🌈

all the file formats your input image can be, bestie. screenshot this. 🧚

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

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🌸 PLUGINS: mesh/io 🌸

and these are the formats your output mesh can be. so many options, we're obsessed. 💖

datapool — Virtual IO to and from the internal data pool

• Recognized file extensions: .@

off — plugin to load/store some Geomview OFF files. Supported is only the ASCII format 3D meshes with normales and per-vertex RGB colors. Alpha values and texture coordinates, as well as per face properties are ignored. Polygons are read and triangulated.

• Recognized file extensions: .OFF, .off

ply — Ply triangle mesh input/output support

• Recognized file extensions: .PLY, .ply

stl — STL mesh io plugin

• Recognized file extensions: .STL, .stl

vista — Vista/Simbio triangle mesh input/output support

• Recognized file extensions: .-, .V, .VMESH, .v, .vmesh

vtk — A subset of VTK mesh in-and output: Triangle meshes are written, and triangle meshes and triangle strips are read. Additional per-vertex attributes are supported: 'normals', 'colors' for three component colors, and 'scale' for a scalar value attached to each vertex. The data is written by the vtkPolyDataWriter in binary format.

• Recognized file extensions: .VTK, .VTKMESH, .vtk, .vtkmesh

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⭐ EXAMPLE ⭐

extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

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💜 AUTHOR(s) 💜

Gert Wollny

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💜 COPYRIGHT 💜

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'.

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okay that's the whole thing, bestie 🫶 this page lives in the USER COMMANDS corner of the manual, it's v2.4.7, and it was dated by the good people of Leipzig, Germany and Madrid, Spain (1999‐2015 energy 🌍). go extract some iso-surfaces, you're gonna slay. periodt. 💅✨