mia-3dprop...boundingbox(1)

📦
version 2.4.7 · 4 versions
, in ubuntu resolute, ubuntu stonking
bestie, you opened mia-3dprop...boundingbox(1) from the General Commands Manual, and it's literally all about proposing a bounding box for an image. No cap. 💅✨

🌸 NAME 🌸

mia-3dpropose-boundingbox — evaluate a bounding box for the image. That's it, that's the whole name vibe. 🎀

🚀 SYNOPSIS 🚀

mia-3dpropose-boundingbox -i <in-file> [options]

Okay so you run it with -i <in-file> and then any options you want. Slay. 💖

📝 DESCRIPTION 📝

mia-3dpropose-boundingbox is the main character here: it evaluates a box that contains all the pixels of a given mask image. 🫶

If the input image is not a binary image, a pre-filter must be applied that converts the input image into a mask. Like, no pre-filter? Then you're not getting your mask-based bounding box moment. Periodt. 💅

⚙️ OPTIONS ⚙️

📁 File-IO 📁

  • -i --in-file=(input, required); io — input image(s) to be filtered. For supported file types see PLUGINS:3dimage/io. ✨

🆘 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 🏷️

🎛️ Parameters 🎛️

  • -f --filter= — Filter to be applied to the image before the bounding box is evaluated. Must return a bit-valued image. For supported plugins see PLUGINS:3dimage/filter. 🔍
  • -p --padding=0; uint in [0, inf) — Padding of boundaries. 🧸

🧵 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). 🧠

🔌 PLUGINS: 1d/spacialkernel 🔌

cdiff

Central difference filter kernel, mirror boundary conditions are used.

(no parameters)

gauss

spacial Gauss filter kernel, supported parameters are:

  • w = 1; uint in [0, inf) — half filter width.

scharr

This plugin provides the 1D folding kernel for the Scharr gradient filter.

(no parameters)

🌀 PLUGINS: 1d/splinebc 🌀

mirror

Spline interpolation boundary conditions that mirror on the boundary.

(no parameters)

repeat

Spline interpolation boundary conditions that repeats the value at the boundary.

(no parameters)

zero

Spline interpolation boundary conditions that assumes zero for values outside.

(no parameters)

✨ PLUGINS: 1d/splinekernel ✨

bspline

B-spline kernel creation, supported parameters are:

  • d = 3; int in [0, 5] — Spline degree.

omoms

OMoms-spline kernel creation, supported parameters are:

  • d = 3; int in [3, 3] — Spline degree.

🧩 PLUGINS: 3dimage/combiner 🧩

absdiff

Image combiner 'absdiff'

(no parameters)

add

Image combiner 'add'

(no parameters)

div

Image combiner 'div'

(no parameters)

mul

Image combiner 'mul'

(no parameters)

sub

Image combiner 'sub'

(no parameters)

🎀 PLUGINS: 3dimage/filter 🎀

bandpass

intensity bandpass filter, supported parameters are:

  • max = 3.40282e+38; float — maximum of the band.
  • min = 0; float — minimum of the band.

binarize

image binarize filter, supported parameters are:

  • max = 3.40282e+38; float — maximum of accepted range.
  • min = 0; float — minimum of accepted range.

close

morphological close, supported parameters are:

  • hint = black; string — a hint at the main image content (black|white).
  • shape = [sphere:r=2]; factory — structuring element. For supported plug-ins see PLUGINS:3dimage/shape.

combiner

Combine two images with the given combiner operator. If 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run. Supported parameters are:

  • image =(input, required, io) — second image that is needed in the combiner. For supported file types see PLUGINS:3dimage/io.
  • op =(required, factory) — Image combiner to be applied to the images. For supported plug-ins see PLUGINS:3dimage/combiner.
  • reverse = 0; bool — reverse the order in which the images passed to the combiner.

convert

image pixel format conversion filter, supported parameters are:

  • a = 1; float — linear conversion parameter a.
  • b = 0; float — linear conversion parameter b.
  • map = opt; dict — conversion mapping. Supported values are:
    • copy — copy data when converting
    • linear — apply linear transformation x -> a*x+b
    • range — apply linear transformation that maps the input data type range to the output data type range
    • opt — apply a linear transformation that maps the real input range to the full output range
    • optstat — apply a linear transform that maps based on input mean and variation to the full output range
  • repn = ubyte; dict — output pixel type. Supported values 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

crop

Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept. Supported parameters are:

  • end = [[4294967295,4294967295,4294967295]]; streamable — end of cropping range, maximum = (-1,-1,-1).
  • start = [[0,0,0]]; streamable — begin of cropping range.

dilate

3d image stack dilate filter, supported parameters are:

  • hint = black; string — a hint at the main image content (black|white).
  • shape = [sphere:r=2]; factory — structuring element. For supported plug-ins see PLUGINS:3dimage/shape.

distance

Evaluate the 3D distance transform of an image. If the image is a binary mask, then result of the distance transform in each point corresponds to the Euclidian distance to the mask. If the input image is of a scalar pixel value, then the this scalar is interpreted as heighfield and the per pixel value adds to the distance.

(no parameters)

downscale

Downscale the input image by using a given block size to define the downscale factor. Prior to scaling the image is filtered by a smoothing filter to eliminate high frequency data and avoid aliasing artifacts. Supported parameters are:

  • b = [[1,1,1]]; 3dbounds — blocksize.
  • bx = 1; uint in [1, inf) — blocksize in x direction.
  • by = 1; uint in [1, inf) — blocksize in y direction.
  • bz = 1; uint in [1, inf) — blocksize in z direction.
  • kernel = gauss; factory — smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize. For supported plug-ins see PLUGINS:1d/spacialkernel.

erode

3d image stack erode filter, supported parameters are:

  • hint = black; string — a hint at the main image content (black|white).
  • shape = [sphere:r=2]; factory — structuring element. For supported plug-ins see PLUGINS:3dimage/shape.

gauss

isotropic 3D gauss filter, supported parameters are:

  • w = 1; int in [0, inf) — filter width parameter.

gradnorm

3D image to gradient norm filter

(no parameters)

growmask

Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if they have a lower intensity that is above the given threshold. Supported parameters are:

  • min = 1; float — lower threshold for mask growing.
  • ref =(input, required, io) — reference image for mask region growing. For supported file types see PLUGINS:3dimage/io.
  • shape = 6n; factory — neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape.

invert

intensity invert filter

(no parameters)

isovoxel

This filter scales an image to make the voxel size isometric and its size to correspond to the given value, supported parameters are:

  • interp = [bspline:d=3]; factory — interpolation kernel to be used. For supported plug-ins see PLUGINS:1d/splinekernel.
  • size = 1; float in (0, inf) — isometric target voxel size.

kmeans

3D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image. Supported parameters are:

  • c = 3; int in [2, inf) — number of classes.
  • label — okay so this one labels the connected components of a binary image, i.e. it finds all the lil blobby besties that are touching and gives each squad its own number 🫶💖 its supported parameters are:
    • n = 6n; factory — the neighborhood mask. Want to know which plug-ins you can plug in here? Go look at PLUGINS:3dimage/shape ✨
  • labelmap — an image filter that remaps label id's. Heads up: this is only applicable to images with integer valued intensities/labels, no faking it with floats bestie 💅 its supported parameters are:
    • map =(input, required, string) — the label mapping file.
  • labelscale — a filter that only creates output voxels that are already created in the input image. The scaling is done with a voting algorithm that picks the target pixel value based on the highest pixel count of a certain label in the corresponding source region. And if the region has two labels with the same count? The one with the lower number wins, periodt 👑 its supported parameters are:
    • out-size =(required, 3dbounds) — target size, given as two coma separated values.
  • load — loads the input image from a file and uses it to replace the current image in the pipeline, like a lil glow-up swap 🌸 its supported parameters are:
    • file =(input, required, io) — name of the input file to load from. (yes the original literally has two periods, we keep it 💀) For supported file types see PLUGINS:3dimage/io
  • lvdownscale — this is a label voting downscale filter. It downscales a 3D image by blocks, and for each block the (non-zero) label that shows up the most times in that block gets issued as the output pixel in the target image. If two labels appear the same number of times, the one with the lower absolute value wins — tie goes to the smaller number, no cap 🎀 its supported parameters are:
    • b = [[1,1,1]]; 3dbounds — blocksize for the downscaling. Each block gets represented by one pixel in the target image.
  • mask — masks an image: one image is taken from the parameters list and the other comes from the normal filter input. Both images must be of the same dimensions and one of them must be binary. The attributes of the image coming through the filter pipeline are preserved, and the output pixel type corresponds to the input image that is not binary 🦋 its supported parameters are:
    • input =(input, required, io) — second input image file name. For supported file types see PLUGINS:3dimage/io
  • mean — 3D image mean filter, the classic smoothing vibe ✨ its supported parameters are:
    • w = 1; int in [1, inf) — half filter width.
  • median — median 3d filter, so good at killing noise fr fr 🌈 its supported parameters are:
    • w = 1; int in [1, inf) — filter width parameter.
  • mlv — Mean of Least Variance 3D image filter, iykyk 💜 its supported parameters are:
    • w = 1; int in [1, inf) — filter width parameter.
  • msnormalizer — 3D image mean-sigma normalizing filter, it's giving very normalized bestie energy 💅 its supported parameters are:
    • w = 1; int in [1, inf) — half filter width.
  • open — morphological open 🌸 its supported parameters are:
    • hint = black; string — a hint at the main image content (black|white).
    • shape = [sphere:r=2]; factory — the structuring element. For supported plug-ins see PLUGINS:3dimage/shape
  • reorient — 3D image reorientation filter, aka spin that image around the main character energy 💫 its supported parameters are:
    • map = xyz; dict — the oriantation mapping to be applied. Supported values are:
      • xyz ‐ keep orientation
      • p-yzx ‐ permutate x->z->y->x
      • p-zxy ‐ permutate x->y->z->x
      • f-yz ‐ flip y-z
      • f-xy ‐ flip x-y
      • f-xz ‐ flip x-z
      • r-x90 ‐ rotate around x-axis clockwise 90 degree
      • r-x180 ‐ rotate around x-axis clockwise 180 degree
      • r-x270 ‐ rotate around x-axis clockwise 270 degree
      • r-y90 ‐ rotate around y-axis clockwise 90 degree
      • r-y180 ‐ rotate around y-axis clockwise 180 degree
      • r-y270 ‐ rotate around y-axis clockwise 270 degree
      • r-z90 ‐ rotate around z-axis clockwise 90 degree
      • r-z180 ‐ rotate around z-axis clockwise 180 degree
      • r-z270 ‐ rotate around z-axis clockwise 270 degree
  • resize — resizes an image. The original data is centered within the new sized image, cute and symmetrical 🎀 its supported parameters are:
    • size = [[0,0,0]]; streamable — new size of the image. A size 0 indicates to keep the size for the corresponding dimension.
  • sandp — salt and pepper 3d filter, the spicy one 🌶️✨ its supported parameters are:
    • thresh = 100; float in [0, inf) — thresh value.
    • w = 1; int in [1, inf) — filter width parameter.
  • scale — 3D image filter that scales to a given target size, living its resized dream 💖 its supported parameters are:
    • interp = [bspline:d=3]; factory — interpolation kernel to be used. For supported plug-ins see PLUGINS:1d/splinekernel
    • s = [[0,0,0]]; 3dbounds — target size to set all components at once (component 0:use input image size).
    • sx = 0; uint in [0, inf) — target size in x direction (0:use input image size).
    • sy = 0; uint in [0, inf) — target size in y direction (0:use input image size).
    • sz = 0; uint in [0, inf) — target size in y direction (0:use input image size).
  • scharr — the 3D Scharr filter for gradient evaluation 🔥 Big heads-up though: the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable. Do it, trust 💅 its supported parameters are:
    • dir = x; dict — Gradient direction. Supported values are:
      • x ‐ gradient in x-direction
      • y ‐ gradient in y-direction
      • z ‐ gradient in z-direction
  • selectbig — a filter that creats a binary mask representing the intensity with the highest pixel count. The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined 😭 so don't come crying to me about it. The input pixel must have an integral pixel type.
    • (no parameters)
  • sepconv — 3D image intensity separaple convolution filter, the separated-convolution slay 🌈 its supported parameters are:
    • kx = [gauss:w=1]; factory — filter kernel in x-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
    • ky = [gauss:w=1]; factory — filter kernel in y-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
    • kz = [gauss:w=1]; factory — filter kernel in z-direction. For supported plug-ins see PLUGINS:1d/spacialkernel
  • sobel — the 2D Sobel filter for gradient evaluation ✨ same warning as its Scharr bestie: the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable. No cap 💅 its supported parameters are:
    • dir = x; dict — Gradient direction. Supported values are:
      • x ‐ gradient in x-direction
      • y ‐ gradient in y-direction
      • z ‐ gradient in z-direction
  • sws — seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image, iconic behaviour honestly 👑 its supported parameters are:
    • grad = 0; bool — Interpret the input image as gradient.
    • mark = 0; bool — Mark the segmented watersheds with a special gray scale value.
    • n = [sphere:r=1]; factory — Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape
    • seed =(input, required, string) — seed input image containing the labels for the initial regions.
  • tee — saves the input image to a file and also passes it through to the next filter, like a lil splitter bestie that refuses to choose 🫶 its supported parameters are:
    • file =(output, required, io) — name of the output file to save the image too. (yes, "too", we keep it 💀) For supported file types see PLUGINS:3dimage/io
  • thinning — 3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image Processing, 56(6):462-478, 1994. This implementation only supports the 26 neighbourhood, so that's the vibe check 🦋
    • (no parameters)
  • transform — transforms the input image with the given transformation 🪄 its supported parameters are:
    • file =(input, required, io) — Name of the file containing the transformation. For supported file types see PLUGINS:3dtransform/io
    • imgboundary = ; factory — override image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc
    • imgkernel = ; factory — override image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel
  • variance — 3D image variance filter, math girlie ✨ its supported parameters are:
    • w = 1; int in [1, inf) — half filter width.
  • ws — basic watershead segmentation, the lowkey version of the seeded one 💜 its supported parameters are:
    • evalgrad = 0; bool — Set to 1 if the input image does not represent a gradient norm image.
    • mark = 0; bool — Mark the segmented watersheds with a special gray scale value.
    • n = [sphere:r=1]; factory — Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape
    • thresh = 0; float in [0, 1) — Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined.

🔌 PLUGINS: 3dimage/io 🎀

okay bestie, this is the whole roster of file formats this thing can read and write for 3D images. every plugin, every extension, every element type — no skipping, we're doing this right 💅

  • 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)
experimental, bestie. it's giving "we're testing this, don't be shocked if it acts up" 💀

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: 3dimage/shape 🌸

tiny but mighty, these are the little shape-makers. ✨

  • 18n — 18n neighborhood 3D shape creator

(no parameters)

  • 26n — 26n neighborhood 3D shape creator

(no parameters)

  • 6n — 6n neighborhood 3D shape creator

(no parameters)

  • sphere — closed spherical shape neighborhood including the pixels within a given radius r., supported parameters are:
    • r = 2; float in (0, inf)
      • sphere radius.

🦋 PLUGINS: 3dtransform/io 👑

the transformation-file formats, aka where your 3D transforms go to live 💜

  • bbs — binary (non-portable) serialized IO of 3D transformations

Recognized file extensions: .bbs

"non-portable" is right there in the name bestie, don't say nobody told you 🙈
  • 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 💖

so like. we're evaluating a bounding box with boundary padding of 5 of a mask that came from a binarization with a minimum value 10.10 and a boundary padding of 5, from image image.v. iconic, tbh.

mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

🫶 AUTHOR(s) 🫶

Gert Wollny

(one guy, carrying this whole plugin ecosystem on his back, no cap 🎀)

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.

fr fr, no warranty at all. run --copyright if you want the receipts.

aaaand that's the whole page bestie, we did it 💅✨ so this is mia-3dprop...boundingbox(1) from the USER COMMANDS crew, version v2.4.7 — that's the version and the source tag, and the footer date is the classic 2015-ish era of this manpage. go forth and bounding-box responsibly, ily, bye 🦋💖

📦 where this page comes from