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", "normalize", "csv", "envi", "arcgis", "gray", "nd2", or "thermal"), 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, 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 must 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.
    • Nikon microscope images can be read in using mode="nd2".
    • FLIR thermal images can be read in using mode="thermal".
    • Hyperspectral data can be read in with mode="envi" where the filename parameter is the raw data file. There is also support for ArcGis style hyperspectral images (mode="arcgis"). These modes 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. There is some flexibility in formats of images supported but encourage people to reach out on GitHub and collaborate with the PlantCV community to expand our support.
    • A wide variety of images can be read with mode=normalize which may be useful for special cases, such as 16-bit color images that otherwise may behave unexpectedly. This mode will normalize images to values to be between 0 and 255 using cv2.normalize.
  • 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 = "plot"

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

Source Code: Here