class Outputs

A global PlantCV output class.

class plantcv.Outputs

An Outputs class has been added that automatically stores measurements and images collected by the following functions:

  • analyze_bound_horizontal
  • analyze_bound_vertical
  • analyze_color
  • analyze_nir_intensity
  • analyze_object
  • fluor_fvfm
  • report_size_marker_area
  • watershed

An instance of Outputs is created on import automatically as plantcv.outputs. The function pcv.print_results will print out all the stored measurments data to a text file.

Methods

Methods are accessed as plantcv.outputs.method.

clear: Clears the contents of both measurements and image

Example

from plantcv import plantcv as pcv

######## Pipeline steps here ########

# Find shape properties, output shape image (optional)
shape_header, shape_data, shape_img = pcv.analyze_object(img, obj, mask)

# Write shape data to results file
pcv.print_results(filename=args.result)

# Will will print out results again, so clear the outputs before running NIR analysis 
pcv.outputs.clear()

######## More pipeline steps here ########

nhist_header, nhist_data, nir_imgs = pcv.analyze_nir_intensity(nir2, nir_combinedmask, 256)
nshape_header, nshape_data, nir_hist = pcv.analyze_object(nir2, nir_combined, nir_combinedmask)

# Write the NIR and shape data to a file 
pcv.print_results(filename=args.coresult)