PlantCV v3.14.1

What's Changed

• Update segment_sort.py by @jdavidpeery in #892
• update documentation for visualize_colorspace by @jdavidpeery in #894
• fix bug in dtype_dict in hyperspectral read_data by @JorgeGtz in #890
• New docs page for pr review process by @jdavidpeery in #895
• Document default values by @jdavidpeery in #899
• Fix overindented docstrings by @nfahlgren in #901
• Remove unnecessary use of comprehension by @deepsource-autofix in #904
• Iterate dictionary directly by @deepsource-autofix in #905
• Remove blank lines after docstring by @deepsource-autofix in #900
• Group imports from same package by @deepsource-autofix in #903
• Doc updates by @HaleySchuhl in #910
• Hsi filename pattern matching by @HaleySchuhl in #916

Full Changelog: v3.14...v3.14.1

PlantCV v3.14

What's Changed

• Finish refactor debugging by @nfahlgren in #848
• add line return to Sample Images function by @HaleySchuhl in #856
• Add deepsource.io config file to repository by @nfahlgren in #858
• Reorganize tests into separate modules by @nfahlgren in #850
• Replace symlinks with image files by @nfahlgren in #861
• Remove unnecessary whitespace by @deepsource-autofix in #865
• Remove commented out code by @deepsource-autofix in #866
• Merge isinstance calls by @deepsource-autofix in #867
• Replace multiple == checks with in by @deepsource-autofix in #868
• Refactor unnecessary else / elif when if block has a return statement by @deepsource-autofix in #870
• Remove blank lines after docstring by @deepsource-autofix in #871
• Remove blank lines after docstring by @deepsource-autofix in #872
• Remove blank lines after docstring by @deepsource-autofix in #873
• Use literal syntax instead of function calls to create data structure by @deepsource-autofix in #874
• Update analysis_approach.md by @ygarrot in #876
• Update versioneer from 0.18 to 0.21 by @nfahlgren in #864
• Omit coverage for the file _version.py by @nfahlgren in #877
• Imported name is not used anywhere in the module PY-W2000 by @nfahlgren in #869
• added sample column to case without variables by @stiphyMT in #882
• support for other dtypes in color correction by @JorgeGtz in #885

New Contributors

• @deepsource-autofix made their first contribution in #865
• @ygarrot made their first contribution in #876
• @stiphyMT made their first contribution in #882

Full Changelog: v3.13.4...v3.14

PlantCV v3.13.4

What's Changed

• Update dependency OpenCV to v4 by @nfahlgren in #846

Full Changelog: v3.13.3...v3.13.4

PlantCV v3.13.3

What's Changed

• Use fewer contours in testing roi_objects by @JorgeGtz in #844
• Update hyperspectral calibration function by @nfahlgren and @JorgeGtz in #845. Thanks to @billygrahamram for bringing the issue to our attention and providing the sample data

Full Changelog: v3.13.2...v3.13.3

PlantCV v3.13.2

What's Changed

• Scale color correction matrices to 0-255 in quick color check by @JorgeGtz in #831
• Fix bug in channel order in color correction by @JorgeGtz in #832
• Trigger GitHub Actions deployment workflow when a release is published by @nfahlgren in #833

Full Changelog: v3.13.1...v3.13.2

PlantCV v3.13.1

What's Changed

• Fix line endings when switching between macOS/Linux and Windows by @nfahlgren in #811
• Increase flexibility for processing hyperspectral ENVI header files by @typelogic in #813
• Configure most functions to use the _debug module by @dschneiderch in #807
• Cast contour tuple as a list in find_objects by @JorgeGtz in #830
• Fix bug in color correction by @JorgeGtz in #829

New Contributors

• @typelogic made their first contribution in #813

Full Changelog: v3.13.0...v3.13.1

PlantCV v3.13.0

PlantCV Version 3.13 Updates

• Update imports to discontinue the deprecation warnings in pcv.watershed
• Update scikit-image requirement to scikit-image>=0.13
• Reorganizes our tutorials in several ways:
  • There is now a main tutorials page that is organized as a gallery of tutorial "cards" that can be filtered by keyword tags. Each card has a launch Binder button to access the interactive tutorial and a link to the static tutorial.
  • The tutorial card images and links to notebooks are remote and can be hosted from any GitHub (or other) repository.
  • The static tutorial pages are now grouped in a directory called "tutorials."
  • The static tutorial pages now only have a launch Binder button and render the complete Jupyter notebooks using nbviewer, rather than having a page that recreates the workflow and has a script version of the workflow.
• Added pcv.transform.gamma_correct which performs gamma correction on the input image (wrapper of the skimage gamma correction function).
• Updated the debug method in the backend within more miscellaneous functions.
• Expand the functionality of the metadata matcher portion of plantcv-workflow to support the matching of multiple metadata values.
  • Syntax at the command line (--match id:1,id:2,id:3)
  • Also supports lists in configuration file based parallelization
• Updates plantcv.hyperspectral.read_data to support Band Sequential (BSQ) in addition to Band Interleaved by Line (BIL) raw data formats for ENVI type multi/hyperspectral datasets.
• Adds pcv.visualize.obj_sizes function for annotating the sizes of separate objects onto a visualization.
• Add pcv.visualize. obj_size_ecdf for a new way to visualize: empirical cumulative distribution function (eCDF).
• Converted to base python classes int and bool since numpy is deprecating np.int and np.bool datatypes.
• Update the fill_segments function in the morphology sub-package
  • The added observations are corrected.
  • Also return the filled_mask (which is a label image as an output) along with the filled_image as outputs.
  • The filled_img is generate by calling the added colorize_label_img visualization function.

PlantCV v3.12.1

PlantCV Version 3.12.1 Updates

• Bugfix (from #770 ) for an update since OpenCV function pointPolygonTest was impacting 3 analysis functions from PCV.

• Numpy is deprecating np.int and np.bool; converted these to base python classes int and bool.

PlantCV v3.12.0

PlantCV Version 3.12 Updates

• Updated the pcv.apply_mask(), changed the rgb_img parameter to img since the function is now able to handle grayscale, NIR, and hyperspectral data.
• Add json datatype check in the add_observation method.
• Started to move some internal code within functions across the package to start using a debug module rather than having repetitive code for plotting/printing debugging images.
• Extend the pcv.cluster_contours_splitimg functionality to grayscale images.
• Added a bounding parameter to pcv.clustered_contours() function so circles can be turned on or off (default behavior as on).
• Added a pcv.deprecation_warning function for warning statements internal use within functions.
  • Add a "verbose" variable to pcv.params such that users have the option to turn off (deprecation) warnings by setting it to "False".
• Update and resolve a bug within the random_sample utility function so that it works as intended on datasets with subdirectories.
• Added a new method (save_results) to the Outputs class. outputs.save_results supports two output formats, JSON and CSV. The code from plantcv.print_results was moved to the save_results method and a deprecation warning is now printed via print_results. When run with outformat = "json", outputs.save_results has the same functionality as plantcv.print_results. When run with outformat = "csv", a single CSV table in "long" format is produced that is compatible with use in R. CSV format is useful for a user who runs workflows only in Jupyter or wants to utilize data for testing from Jupyter. The output format JSON must be used for parallel workflows as before.
  • Users will need to migrate workflows from pcv.print_results(args.result) to pcv.outputs.save_results(args.result) before pcv.print_results is removed.
• Addition of RGB2CMYK function to PlantCV to allow the conversion of images from the RGB colour space to CMYK colour space and split the channels.
• Updated the way PlantCV handles subdaily timestamps for parallelization. Now will work with months and days even where there are no years.

Version 3.12.0 breaking changes

• pcv.apply_mask(), changed the rgb_img parameter to img
• pcv.cluster_contours_splitimg, changed the rgb_img parameter to img

PlantCV v3.11.1

Release v3.11.1

This release is an update of v3.11.0 to correctly trigger a deployment to PyPI and conda-forge.