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itkioopenslide's Introduction

ITKIOOpenSlide

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Overview

This is an InsightToolkit (ITK) ExternalModule to provide an ImageIO for the OpenSlide library supported file formats. These are generally TIFF-based microscopy formats.

To use this module, clone it into the Modules/External directory in the ITK source tree.

Note that the OpenSlide library (http://openslide.org) must be available.

Note: This module is currently a work in progress.

License

This software is distributed under the Apache 2.0 license. Please see the LICENSE file for details.

itkioopenslide's People

Contributors

dzenanz avatar hjmjohnson avatar jhlegarreta avatar mseng10 avatar nslay avatar thewtex avatar

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itkioopenslide's Issues

ITKIOOpenSlide functionality is not implemented

I found this ImageIO and was surprised that none of it was implemented.

I went ahead and implemented it myself. I've added abilities to support all of OpenSlide's features in a way that is flexible enough for ITK. I've tested it for accessing level (!= 0) and associated images.

However, I'm still experimenting with ITK IO streaming to deal with level 0 images! ITK seems to use 32 bit integers for sizes and that can cause overflows (e.g. images being 60000 x 70000). I added sanity checks that try to catch these problems.

https://github.com/nslay/ITKIOOpenSlide

Does it look good? Do you want to pull it?

Improve tests.

The existing tests should be improved:

  • The ITK testing macros should be used (e.g. TRY_EXPECT_NO_EXCEPTION, EXERCISE_BASIC_OBJECT_METHODS, etc.) to avoid boilerplate code.
  • The tests should run as long as possible and return the status code at the end (i.e. use a testStatus in and change its value as tests fail: requires changing the test design).
  • Improve the argument check message.
  • Remove the unnecessary message prints.
  • The coding style should conform to the ITK coding style (Appendix Three).

Fix CI builds

As noted in PR #22, OpenSlide does not build with Visual Studio, so the AppVeyor build should be disabled for now.

Also, the macOS and Linux builds have many dependencies, so may be tools like Conan.io should be considered.

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