Plantcv

[](https://doi.org/10.5281/zenodo.2532116)

PlantCV v3.0.2 only changes PyPI authentication information.

[](https://doi.org/10.5281/zenodo.2531970)

PlantCV v3.0.1 adds a new Travis CI build method on git tags that should also trigger auto-deployment to PyPI.

* `plantcv.fill` is now significantly faster using a scikit-image backend
* `plantcv.median_blur` now allows the kernel size to be asymmetric (a two-element tuple)
* Fixed issues with Read the Docs rendering
* Documentation was updated to fix typos, command examples, etc.
* Some test data was reduced in size to shrink the memory footprint during build tests
* Fixed some package usage syntax to avoid future method deprecation issues
* Added color card mask helper function
* Added color card checker analysis function
* Added color card auto detection method (thanks to bhive01 for the method inspiration)
* Improved code testing coverage to 98%
* Added method to read raw Bayer images
* Updated `plantcv.fluor_fvfm` to accept 8-bit images in addition to 16-bit images
* Added conda environment YAML configuration files for quick conda installation

PlantCV v3.0.dev2 is an early release in the v3 release cycle. A full v3 will be released at a later date. While this is an early release, it should be considered essentially production-ready. Note that this release breaks previous syntax/functionality with the goal of making things easier. Updating existing code to the new styles should be fairly straightforward.

[](https://doi.org/10.5281/zenodo.1408271)

Overview of changes:

* The input and output `device` has been eliminated for all functions. The step counter still exists in the background.
* The input `debug` has been eliminated for all functions. It can now be set globally with the class `Params`: https://plantcv.readthedocs.io/en/latest/params/.
* The output location of images printed in debug mode can now be set using the `plantcv.params.debug_outdir` global setting: https://plantcv.readthedocs.io/en/latest/params/
* Some function arguments were refactored. Many were changed to make it more explicit what type of input image is required. The new vocabulary is generally: `img` = all image types, `rgb_img` = RGB images only, `gray_img` = Grayscale images only, `bin_img` or `mask` = Binary images only. Some other inputs were renamed for consistency and/or PEP8 formatting guidelines. All function call changes are summarized here: https://plantcv.readthedocs.io/en/latest/updating/#updating-to-v3.
* Several functions were removed and replaced with updated versions.
* `define_roi`: replaced with the functions in the subpackage `roi`.
* `analyze_bound`: replaced with the functions `analyze_bound_horizontal` and `analyze_bound_vertical`.
* `rotate_img`: replaced with the function `rotate`.
* The threshold functions `binary_threshold`, `adaptive_threshold`, `otsu_auto_threshold`, and `triangle_auto_threshold` were moved to a new subpackage and are now: `plantcv.threshold.binary`, `plantcv.threshold.gaussian`, `plantcv.threshold.mean`, `plantcv.threshold.otsu`, `plantcv.threshold.triangle`.
* These changes are also summarized here: https://plantcv.readthedocs.io/en/latest/updating/#updating-to-v3.
* Testing coverage was increased to 94%.
* Some additional general documentation and docstring reformatting for consistency.
* The FAQ was updated.

[](https://doi.org/10.5281/zenodo.1296371)

Some features already included in the v3 release:

* Distance transformation
* Release of PlantCV through Docker containerization
* Full and tested Python2/3 and OpenCV2/3 compatibility
* Global settings and simplified API framework
* New boundary line tools
* Simplified region of interest (ROI) tools
* Color correction/standardization
* Package namespace reorganization
* Documentation improvements and bug fixes

The PlantCV release v2.1 is an update to the v2.0 release. The release contains some minor bug fixes and updated documentation based on feedback we received for the PlantCV v2.0 preprint.

[](https://doi.org/10.5281/zenodo.1035894)