Plot chlorophyll fluorescence induction curves

Creates a chart of chlorophyll fluorescence induction curves from a PSII_Data instance. The photosynthesis subpackage is dependent on a PSII_Data instance file structure as created by photosynthesis.read_cropreporter. Plots the mean level of fluorescence per object/label per frame/timepoint. The PSII_Data Fm and Fm' frames are labeled and the chart can be used to decide whether to use auto_fm in pcv.analyze.yii and pcv.analyze.npq.

plantcv.visualize.chlorophyll_fluorescence(ps_da, labeled_mask, n_labels=1, label="object")

returns chlorophyll fluorescence induction curve chart

  • Parameters:
    • ps_da - photosynthesis xarray DataArray ("ojip_light" or "ojip_dark")
    • labeled_mask - Labeled mask of objects (32-bit).
    • n_labels - Total number expected individual objects (default = 1).
    • label - optional label parameter, modifies the prefix of the group plotting label
  • Context:
    • Used to visualize chlorophyll florescence induction curves.
  • Example use:

Example image with labels marking three leaves


from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), 
# or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "plot"

chart = pcv.visualize.chlorophyll_fluorescence(ps_da=ps.ojip_dark, labeled_mask=labeled_mask, n_labels=3, label="object")

Chlorophyll fluorescence induction curve chart


Source Code: Here