endocal 16.8.8rc1

A compact GUI application for optical distortion calibration of endoscopes

endocal

endocal is a cross-platform, compact GUI application for optical distortion calibration of endoscopes. It uses the [OpenCV][opencv] camera calibration module.

endocal was developed by Dzhoshkun I. Shakir as part of the [GIFT-Surg project][giftsurg] at the [Translational Imaging Group][tig] in the [Centre for Medical Image Computing][cmic] at [University College London (UCL)][ucl].

License

Copyright (c) 2016, [University College London][ucl]. endocal is available as free open-source software under a BSD 3-Clause Licence.

Features

• Lightweight, compact GUI application for optical distortion calibration of endoscopes

• Command-line application for generating [ASCII DXF files](http://www.autodesk.com/techpubs/autocad/acadr14/dxf/) for use in calibration target fabrication (translated from Matlab scripts developed by Daniil I. Nikitichev)

System requirements

• [OpenCV][opencv]

• [pip](https://pip.pypa.io/en/stable/installing/)

• (Online calibration) Video source supported by [OpenCV][opencv_docs] (see esp. the OpenCV tutorials related to video IO)

How to install / remove

Note: Please check out [these hints](doc/issues.md) if you encounter any issues with endocal.

To install: pip install endocal.

To test your installation type: endocal-test:

• See [this screenshot](endocal/res/screenshot-start.png) for what to expect on launching the application.

• To perform an optical distortion calibration, follow the instructions shown in red on top of the window. While acquiring calibration data, detected calibration pattern blobs will be emphasized with a virtual overlay as in [this screenshot](endocal/res/screenshot-detection.png).

• All data for each calibration will be saved in the sub-folder of a folder called tmp-sample_001, created within the current folder. These include: * Calibration parameters saved as calibration.yml * Frames used for calibration saved as indexed image files, e.g. frame_009.jpg

• After performing a calibration, the application will automatically show the undistorted images to the right as shown in [this screenshot](endocal/res/screenshot-undistort.png).

To remove: pip uninstall endocal.

How to use

Calibration: endocal –help shows details of what input parameters are expected. Examples include: * Using all frames stored as indexed files e.g. frame_009.jpg: ` endocal --pattern-specs 3 11 3 1 --output-folder ./calibration-results --input /data/offline/frame_%03d.jpg ` * Using online video stream from a frame-grabber (attached to an endoscope) that is mounted as /dev/video0 on Linux: ` endocal --input 0 --pattern-specs 3 11 3 1 --output-folder ./calibration-results ` * Using a 700 x 700 sub-frame of the whole endoscopic video frame (1920 x 1080): ` endocal --input 0 --pattern-specs 3 11 3 1 --output-folder ./calibration-results --roi 620 200 700 700 `

ASCII DXF file generation: For instance to generate an asymmetric grid of circles each with a diameter of 1 mm to be etched by a laser cutter with a beam width of 45 μm (microns): ` dxf --laser-beam-width 45 --diameter 1 --output-file output.dxf ` Here the grid is saved to file output.dxf and the corresponding (ellipse) legend to output-legend.dxf (legend filename always inferred from main DXF filename).

Supported platforms

endocal was tested so far on:

• Linux: Ubuntu 14.04.3 LTS 64-bit, elementary OS Freya 0.3.2 64-bit

• Mac OS X: El Capitan 10.11.3

• Windows: 10 Professional 64-bit

It is highly likely that it will work on other platforms as well, due to the small number of dependencies.

Funding

This work was supported through an Innovative Engineering for Health award by the [Wellcome Trust][wellcometrust] [WT101957], the [Engineering and Physical Sciences Research Council (EPSRC)][epsrc] [NS/A000027/1] and a [National Institute for Health Research][nihr] Biomedical Research Centre [UCLH][uclh]/UCL High Impact Initiative.

[tig]: http://cmictig.cs.ucl.ac.uk [giftsurg]: http://www.gift-surg.ac.uk [cmic]: http://cmic.cs.ucl.ac.uk [ucl]: http://www.ucl.ac.uk [nihr]: http://www.nihr.ac.uk/research [uclh]: http://www.uclh.nhs.uk [epsrc]: http://www.epsrc.ac.uk [wellcometrust]: http://www.wellcome.ac.uk [opencv]: http://opencv.org/ [opencv_docs]: http://docs.opencv.org/