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 namedxx_HDR_xxx.INF
- This function assumes a specific pattern between .DAT image files and their corresponding .INF file.
We assume that for every image file
- 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