Plot Histograms for Hyperspectral Images

This is a plotting method that is used to examine the distribution of signal within an hyperspectral image for specific wavelengths. This function is an application of the histogram function.

plantcv.visualize.hyper_histogram(hsi, mask=None, bins=100, lower_bound=None, upper_bound=None, title=None, wvlengths=[480, 550, 670])

returns fig_hist

  • Parameters:

    • hsi - Spectral_data
    • mask - Optional binary mask made from selected contours.
    • bins - Number of class to divide spectrum into (default bins=100).
    • lower_bound - Lower bound of range to be shown in the histogram (default lower_range=None).
    • upper_bound - Upper bound of range to be shown in the histogram.
    • title - The title for the histogram (default title=None)
    • wvlengths - Interested wavelengths (in nanometers) to show histogram of (default wvlengths=[480, 550, 670])

  • Context:

    • Examine the distribution of the signal, this can help select a value for calling the binary thresholding function.
    • If the provided wavelength is in the range of visible spectrum, the color corresponds to the wavelength would be used as the histogram color

  • Example use:

Hyperspectral image

Screenshot

Mask

Screenshot


from plantcv import plantcv as pcv

pcv.params.debug = "plot"

# Showing histograms for 3 default wavelengths
hist_figure1 = pcv.visualize.hyper_histogram(hsi=hsi, mask=mask)

# Showing the histogram for a single wavelength (700nm)
hist_figure2 = pcv.visualize.hyper_histogram(hsi=hsi, mask=mask, wvlengths=[700])

# Showing the histogram for two wavelengths 
hist_figure3 = pcv.visualize.hyper_histogram(hsi=hsi, mask=mask, wvlengths=[380, 970])

# Showing the histogram for multiple wavelengths
hist_figure4 = pcv.visualize.hyper_histogram(hsi=hsi, mask=mask, 
                                             wvlengths=[379, 409, 439, 469, 499, 529, 559, 568, 
                                                        619, 649, 679, 709, 739, 769, 799, 
                                                        829, 859, 889, 
                                                        919, 949, 979, 1000])

Histogram of signal intensity

hist_default

hist_single

hist_two

hist_multiple

To plot all wavelengths (not recommended for hyperspectral images supporting a large number of bands):

# Plot not shown
hist_all_wv = pcv.visualize.hyper_histogram(hsi=hsi, mask=mask, wvlengths=list(hsi.wavelength_dict.keys()))

Source Code: Here