Read CropReporter Fluorescence Image Files

Reads .DAT image data into numpy ndarray and reshapes the frames into a datacube before identifying and extracting fdark, fmin, and fmax as separate numpy ndarrays.

plantcv.photosynthesis.read_cropreporter(filename)

returns fdark, fmin, fmax

  • Parameters:

    • filename - image file to be read (possibly including a path)

  • Context:

    • Reads in file to be processed and does so using the metadata contained within a corresponding .INF file
  • Notes:
    • This function assumes a specific pattern between .DAT image files and their corresponding .INF file. We assume that for every image file xx_PSD_xxx.DAT there will be a corresponding metadata file with the same path named xx_HDR_xxx.INF
  • Example use: 
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 = "print"

#read in image
fdark, fmin, fmax = pcv.photosynthesis.read_cropreporter(filename="PSII_PSD_20200826_22_rep6.DAT")

Source Code: Here