mia-2dseries2sets(1)

💖 NAME 💖

mia-2dseries2sets — bestie, this thing scoops up a whole series of images and sorts them into sets. That's the whole vibe. 🎀

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✨ SYNOPSIS ✨

mia-2dseries2sets -o <out-directory> [options] <PLUGINS:2dimage/io>

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🌸 DESCRIPTION 🌸

Okay so, mia-2dseries2sets is the friend who takes literally every image file you hand it as a free parameter on the command line and goes "mmkay, let me organize these" — it builds segmentation sets out of the info it finds inside those images. 👑

What info, you ask? Two things, and only two things:

• the z-location of the slice 🧊
• the acquisition number 🔢

The code is tailored to use the matching descriptors defined in the DICOM standard, so like, it speaks DICOM's language natively, no cap.

Here's the tea: every image that shares the same slice location gets grouped together into one segmentation set 🫶, and inside that set they're ordered by their acquisition number. And because floating point values are little chaos gremlins that will betray you, the slice locations get rounded to three digits accuracy so the comparison actually, you know, works. 💅

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💅 OPTIONS 💅

• -o --out-directory=(required, output); string — the output directory. It needs to already exist and be writable, so like, don't come crying to me if you point it at a folder that isn't there. 🙈
• --no-copy — don't copy the image files to the output directory. Just... sets, no copies. 🦋

🎀 Help & Info 🎀

• -V --verbose=warning — how chatty do you want this program to be? It prints messages of the given level and higher priorities. 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 than or equal to the number of logical processor cores in the machine. (-1: automatic estimation). So if you set this to like 9000 on a 4-core laptop, that's on you bestie. 💀

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🌈 PLUGINS: 2dimage/io 🌈

• bmp — BMP 2D-image input/output support. The 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

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⭐ EXAMPLE ⭐

Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default). ✨

mia-2dseries2sets -o /home/user/series
       /net/dicoms/patient1/series1/*.dcm

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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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And that's the whole page, bestie 💜 this was the mia-2dseries2sets(1) manual out of the USER COMMANDS section, sitting at version v2.4.7 — go forth and sort your slices, you absolute icon. 🦋💖