mia-2dimagestack-cmeans(1)

💖 mia-2dimagestack-cmeans 💖

okay bestie, so this is a page from the General Commands Manual, and it's all about a little tool called mia-2dimagestack-cmeans. Say it with me: mia-2dimagestack-cmeans. Iconic name, no notes. 🎀

---

✨ NAME ✨

mia-2dimagestack-cmeans — Calculate the c-means classification for a series of images. 🧚

---

✨ SYNOPSIS ✨

mia-2dimagestack-cmeans -i <in-file> -o <out-probmap> [options]

---

✨ DESCRIPTION ✨

So here's the tea, bestie 🫖 — mia-2dimagestack-cmeans does three things in a row, and it does them in this exact order:

1. first it evaluates a sparse histogram of an input image series,
2. then it runs a c-means classification over that histogram,
3. and then it writes the probability mapping for the original intensity values.

That's it, that's the whole vibe. Three steps, one program, slay. 💅

---

✨ OPTIONS ✨

📁 File-IO

• -i, --in-file=(input, required); io — the input image(s) to be filtered. For the supported file types, go peek at PLUGINS:2dimage/io 👀
• -o, --out-probmap=(output, required); string — save the probability map to this file. That's the output, bestie, it has to go somewhere. 🎀

🆘 Help & Info

• -V, --verbose=warning — verbosity of output; 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

🎛️ Parameters

• -T, --histogram-thresh=5; float in [0, 50] — percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.
• -C, --classes=kmeans:nc=3 — C-means class initializer. For the supported plugins, check out PLUGINS:1d/cmeans. 🌸

⚙️ 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).

ngl bestie, yes, the original really does say "Maxiumum". We keep it. Character for character. That's the rule. 😭

---

🔌 PLUGINS: 1d/cmeans

These are your c-means class initializer options, and there are three of them:

• even — C-Means initializer that sets the initial class centers as evenly distributed over [0,1]. Supported parameters are:
  • nc =(required, ulong) — Number of classes to use for the fuzzy-cmeans classification.
• kmeans — C-Means initializer that sets the initial class centers by using a k-means classification. Supported parameters are:
  • nc =(required, ulong) — Number of classes to use for the fuzzy-cmeans classification.
• predefined — C-Means initializer that sets pre-defined values for the initial class centers. Supported parameters are:
  • cc =(required, vdouble) — Initial class centers fuzzy-cmeans classification (normalized to range [0,1]).

---

🔌 PLUGINS: 2dimage/io

Your file-type roster, bestie. Every one of these is a whole mood. ✨

• 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

---

✨ EXAMPLE ✨

okay so the vibe here is: run the program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if available), and run cmeans with three classes on the non-zero pixels. 💜

mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt
       --histogram-tresh=5 --classes 3

---

✨ AUTHOR(s) ✨

Gert Wollny 👑

---

✨ 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.

---

and that's the whole page, bestie 🫶 this is USER COMMANDS material, version v2.4.7 of the manual for mia-2dimagestack-cmeans, and honestly? it ate. go forth and c-means. 💖✨🎀🦋🌸💅