Plantcv

[](https://doi.org/10.5281/zenodo.4770879)

**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.

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

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

* A new `sample` input was added to the `Outputs.add_observations` class method.
* Observations stored in `Outputs` class instances have an extra hierarchical layer to account for sample names. To access an observation, the sample name needs to be included, for example:
* `pcv.resize` deprecated and replaced with `pcv.transform.resize` and `pcv.transform.resize_factor`

python
pcv.outputs.observations["sample_name"]["variable_name"]

* Updates `plantcv.plot_image` and various other plotting methods to create a new figure for each plot. PlantCV now works better with the `%matplotlib notebook` plotting method in Jupyter.
* Fixes an issue where `plantcv.visualize.pseudocolor` plotted the image even when debug mode was disabled.
* Various documentation updates, corrections, and reformatting.

* Refactored plantcv.fluor_fvfm which is now plantcv.photosynthesis.analyze_fvfm to be consistent with the naming of other analysis functions. Input parameters are unchanged.