Read Image

Reads image into numpy ndarray and splits the path and image filename (*see note about when mode='envi'). Most modes of use of this function is a wrapper for the OpenCV function imread.

plantcv.readimage(filename, mode="native")

returns img, path, image filename

  • Parameters:

    • filename - image file to be read (possibly including a path)
    • mode - return mode of image ("native," "rgb,", "rgba", "csv", "envi", or "gray"), defaults to "native"

  • Context:

    • Reads in file to be processed
  • Notes:
    • In most cases, the alpha channel in RGBA image data is unused (and causes issue when used as RGB image data), so unless specificed as mode='rgba' the pcv.readimage() function will read RGBA data in as an RGB image under default settings (mode='native'). However, if the alpha channel is needed users can specify mode='rgba'.
    • Comma separated data can be read in with mode='csv' so that, for example, thermal data can be used in downstream analysis, such as pcv.analyze_thermal_values
    • ENVI hyperspectral data can be read in with mode="envi" where the filename parameter is the raw data file. This mode of reading in data expects a filename.hdr file which gets used for shaping the hyperspectral datacube and labeling bands of data to the corresponding wavelength. An instance of the Spectral_data class is created while reading in the data and this instance is returned to the user rather than the usual img, path, filename that is returned under other modes of pcv.readimage.
  • Example use:

Note

ENVI mode currently supports Band Interleaved by Line (BIL), Band Interleaved by Pixel (BIP) Band Sequential (BSQ) raw data formats.

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
img, path, img_filename = pcv.readimage(filename="home/user/images/test-image.png", mode="native")

Source Code: Here