Make Mask of Napari Points¶

This function is to generate a mask from Napari point information. This application of this function could be to get information about image at particular points (e.g. color or intensity information)

plantcv.annotate.napari_points_mask(img, viewer)

returns dictionary of masks (one for each class where the class label is the key to access)

• Parameters:

  • img - image data (compatible with gray, RGB, and hyperspectral data. If data is hyperspecral it should be the array e.g. hyperspectral.array_data)
  • viewer = Napari Viewer with point classes labeled (likely created with napari_label_classes). The size of the points in the mask will be determined from the viewer parameters.

• Context:

  • This function can be used to generate a mask from Napari points in order to get information about point data.

• Example use:

  • An application of this function might be collection of color data for the Naive Bayes module.

import plantcv.plantcv as pcv 
import plantcv.annotate as pcvan
import napari

# Create an instance of the Points class
img, path, name = pcv.readimage("./wheat.png")

# Should open interactive napari viewer
viewer = pcvan.napari_label_classes(img=img, classes=['background','healthy', 'rust', 'chlorosis'], size=4)

maskdict = pcvan.napari_points_mask(img, viewer)

pcv.plot_image(maskdict['background'])
pcv.plot_image(maskdict['healthy'])
pcv.plot_image(maskdict['rust'])
pcv.plot_image(maskdict['chlorosis'])

Background Mask

Healthy Mask

Rust Mask

Chlorosis Mask

Source Code: Here