PlantCV v3.1.0

PlantCV v3.1.0 addresses several bugs and usability issues. Big thanks to @HaleySchuhl and @dschneiderch!

• All analysis functions now output visualization images rather than attempting to save them directly. This removes the filename input parameter and gives users the flexibility to save, plot, etc. what they want to where they want.
• A new function pseudocolor was added to give users the ability and flexibility to take grayscale images and colorize them with any matplotlib colormap, autocrop them to the plant (or other object), mask out background, etc. This function can be used with the changes made above to customize visualization of output images. Colorized images have a built-in color scale bar.
• Due to the changes above, the plot_colorbar function was removed as it's no longer used.
• Histograms are now plotted with plotnine instead of matplotlib.
• A Canny edge detection function was added (canny_edge_detect).
• A color standard card auto-detection method (transform.find_color_card) was added.

PlantCV v3.0.5

This release modifies the Travis CI build procedure to use dependencies installed from PyPI rather than conda. This should fix issues with deployed versions of PlantCV on PyPI and allow us to identify dependency incompatibilities faster. It also decreased build and testing types by more than half.

PlantCV v3.0.4

This release fixes an issue that prevents PlantCV from being installed with OpenCV v4, which is not currently supported. The documentation and docstrings were thoroughly revised for correctness, completeness, and consistency. The installation instructions were updated to include methods for installing PlantCV from PyPI and Bioconda.

PlantCV v3.0.3

PlantCV v3.0.3 fixes some minor issues with PyPI deployment.

PlantCV v3.0.2

PlantCV v3.0.2 only changes PyPI authentication information.

PlantCV v3.0.1

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

PlantCV v3.0

With PlantCV v3.0 PlantCV should be available on PyPI (if all goes well). Big thanks to @HaleySchuhl and @dschneiderch for all the pull requests and all the other contributors.

PlantCV v3.0 contains the following new features/changes:

• 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

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.

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.

PlantCV v3.0.dev1

PlantCV v3.0.dev1 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.

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

PlantCV v2.1

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.