Fill holes in binary 2D & 3D images fast.

Overview

PyPI version

Fill Voids

# PYTHON
import fill_voids

img = ... # 2d or 3d binary image 
filled_image = fill_voids.fill(img, in_place=False) # in_place allows editing of original image
filled_image, N = fill_voids.fill(img, return_fill_count=True) # returns number of voxels filled in
(labels, sx, sy, sz); // 3D // let labels now represent a 512x512 2D image size_t fill_ct = fill_voids::binary_fill_holes (labels, sx, sy); // 2D ">
// C++ 
#include "fill_voids.hpp"

size_t sx, sy, sz;
sx = sy = sz = 512;

uint8_t* labels = ...; // 512x512x512 binary image

// modifies labels as a side effect, returns number of voxels filled in
size_t fill_ct = fill_voids::binary_fill_holes<uint8_t>(labels, sx, sy, sz); // 3D

// let labels now represent a 512x512 2D image
size_t fill_ct = fill_voids::binary_fill_holes<uint8_t>(labels, sx, sy); // 2D

Filling five labels using SciPy binary_fill_holes vs fill_voids from a 512x512x512 densely labeled connectomics segmentation. (black) fill_voids 1.1.0 (blue) fill_voids 1.1.0 with `in_place=True` (red) scipy 1.4.1
Fig. 1: Filling five labels using SciPy binary_fill_holes vs fill_voids from a 512x512x512 densely labeled connectomics segmentation. (black) fill_voids 1.1.0 (blue) fill_voids 1.1.0 with `in_place=True` (red) scipy 1.4.1. In this test, fill_voids (`in_place=False`) is significantly faster than scipy with lower memory usage.

This library contains both 2D and 3D void filling algorithms, similar in function to scipy.ndimage.morphology.binary_fill_holes, but with an eye towards higher performance. The SciPy hole filling algorithm uses slow serial dilations.

The current version of this library uses a scan line flood fill of the background labels and then labels everything not filled as foreground.

pip Installation

pip install fill-voids

If there's no binary for your platform and you have a C++ compiler try:

sudo apt-get install python3-dev # This is for Ubuntu, but whatever is appropriate for you
pip install numpy
pip install fill-voids --no-binary :all:

Current Algorithm

  1. Raster scan and mark every foreground voxel 2 for pre-existing foreground.
  2. Raster scan each face of the current image and the first time a black pixel (0) is encountered after either starting or enountering a foreground pixel, add that location to a stack.
  3. Flood fill (six connected) with the visited background color (1) in sequence from each location in the stack that is not already foreground.
  4. Write out a binary image the same size as the input mapped as buffer != 1 (i.e. 0 or 2). This means non-visited holes and foreground will be marked as 1 for foreground and the visited background will be marked as 0.

We improve performance significantly by using libdivide to make computing x,y,z coordinates from array index faster, by scanning right and left to take advantage of machine memory speed, by only placing a neighbor on the stack when we've either just started a scan or just passed a foreground pixel while scanning.

Multi-Label Concept

Similarly to the connected-components-3d and euclidean-distance-3d projects, in connectomics, it can be common to want to apply void filling algorithms to all labels within a densely packed volume. A multi-label algorithm can be much faster than even the fastest serial application of a binary algorithm. Here's how this might go given an input image I:

  1. Compute M = max(I)
  2. Perform the fill as in the binary algorithm labeling the surrounding void as M+1. This means all voids are now either legitimate and can be filled or holes in-between labels.
  3. Raster scan through the volume. If a new void is encountered, we must determine if it is fillable or an in-between one which will not be filled.
  4. On encountering the void, record the last label seen and contour trace around it. If only that label is encountered during contour tracing, it is fillable. If another label is encountered, it is not fillable.
  5. During the contour trace, mark the trace using an integer not already used, such as M+2. If that label is encountered in the future, you'll know what to fill between it and the next label encountered based on the fillable determination. This phase stops when either the twin of the first M+2 label is encountered or when futher contour tracing isn't possible (in the case of single voxel gaps).
  6. (Inner Labels) If another label is encountered in the middle of a void, contour trace around it and mark the boundary with the same M+2 label that started the current fill.
Hide sensitive information in images

Data-Preserved Script allowing to blur the most sensitive information on images. Prerequisites Before you begin, ensure you have met the following req

2 Dec 01, 2021
Easily turn large sets of image urls to an image dataset. Can download, resize and package 100M urls in 20h on one machine.

img2dataset Easily turn large sets of image urls to an image dataset. Can download, resize and package 100M urls in 20h on one machine. Also supports

Romain Beaumont 1.4k Jan 01, 2023
Art directed cropping, useful for responsive images

Art direction sets a focal point and can be used when you need multiple copies of the same Image but also in in different proportions.

Daniel 1 Aug 16, 2022
Simple Python package to convert an image into a quantized image using a customizable palette

Simple Python package to convert an image into a quantized image using a customizable palette. Resulting image can be displayed by ePaper displays such as Waveshare displays.

Luis Obis 3 Apr 13, 2022
Make your master artistic punk avatar through machine learning world famous paintings

Master-art-punk Make your master artistic punk avatar through machine learning world famous paintings. 通过机器学习世界名画制作属于你的大师级艺术朋克头像 Nowadays, NFT is beco

蒋虎成 23 Jan 04, 2022
Paper backup of files using QR codes

Generate paper backups for Linux. Currently command-linux Linux only. Takes any file, and outputs a "paper backup": a printable black-and-white pdf fu

Zachary Vance 27 Dec 28, 2022
Black-white image converter - Black-white photo colorization

Black-white image converter - Black-white photo colorization

1 Jan 02, 2022
Blender addon - convert empty image reference to image plane

Reference to image plane Convert reference images to a textured image mesh plane. As if it was imported with import image as plane Use on drag'n'dropp

Samuel Bernou 6 Nov 25, 2022
Hacking github graph with a easy python script

Hacking-Github-Graph Hacking github graph with a easy python script Requirements git latest version installed. A text editor (eg: vs code, sublime tex

SENPAI LEGEND 1 Nov 01, 2021
🖼️ Draw Images or GIFs in your terminal

Drawitor Draw Images/GIFs in your terminal. Install pip install drawitor CLI Tool drawitor cat_dancing.gif Library The library is written in a simple

Eliaz Bobadilla 7 Dec 15, 2022
PSD (Photoshop, Krita, Gimp...) -> Godot.

limage v0.2.2 Features Getting Started Tags Settings Todo Customizer Changes Solutions WARNING: Requires Python to be installed PSD (Photoshop, Krita,

21 Nov 10, 2022
A procedural Blender pipeline for photorealistic training image generation

BlenderProc2 A procedural Blender pipeline for photorealistic rendering. Documentation | Tutorials | Examples | ArXiv paper | Workshop paper Features

DLR-RM 1.8k Jan 02, 2023
The ctypes-based simple ImageMagick binding for Python

Wand Wand is a ctypes-based simple ImageMagick binding for Python, supporting 2.7, 3.3+, and PyPy. All functionalities of MagickWand API are implement

Eric McConville 1.2k Dec 30, 2022
A tool for hiding data inside of images

Stegenography-tool a tool for hiding data inside of images Quick test: do python steg-encode.py test/message.txt test/covid19.png to generate the test

luke 2 Nov 02, 2021
Pyconvert is a python script that you can use to convert image files to another image format! (eg. PNG to ICO)

Pyconvert is a python script that you can use to convert image files to another image format! (eg. PNG to ICO)

1 Jan 16, 2022
Bringing vtk.js into Dash and Python

Dash VTK Dash VTK lets you integrate the vtk.js visualization pipeline directly into your Dash app. It is powered by react-vtk-js. Docs Demo Explorer

Plotly 88 Nov 29, 2022
Qrgenerator - A qr generator app using python3

qrgenerator by Mal4D Hi welcome into qr code generator using python by Mal4d Lin

Mal4D 1 Jan 09, 2022
Repair broken bookmarks to referenced files in Apple Photos

Repair Apple Photos Bookmarks Work in progress to repair file location bookmarks in Apple Photos. Background Starting in macOS 10.15/Catalina, photos

Rhet Turnbull 10 Nov 03, 2022
Using P5.js, Processing and Python to create generative art

Experiments in Generative Art Using Python, Processing, and P5.js Quick Links Daily Sketches March 2021. | Gallery | Repo | Done using P5.js Genuary 2

Ram Narasimhan 33 Jul 06, 2022
Tool made for the FWA Yearbook Team to resize multiple images quickly.

ImageResize Tool Tool made for the FWA Yearbook Team to resize multiple images quickly. Make sure to check this repo for future updates How to Use The

LGobin 1 Jan 07, 2022