def plot_into_subplot(self, subplot):
res = pyprosail.run(1.5, 40, 8, 0, 0.1, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile)
data_series = ProSAILSeries("ProSAIL Output", xdata=res[:,0],
ydata=res[:,1])
subplot.add_data_series(data_series)
return True
def update_plot(self, evnt):
"""
Event handler for frequency slider change events.
"""
ewt = self.sliders['EWT'].GetValue()
chloro = self.sliders['Chloro'].GetValue()
carot = self.sliders['Carot'].GetValue()
N = self.sliders['N'].GetValue()
res = pyprosail.run(N, chloro, carot, 0, ewt, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile)
#change the data in the series object
self.series.set_xy_data(xdata=res[:,0], ydata=res[:,1])
#draw our changes on the display
self.series.update()
def GetReflectance(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF): spectrum = pyprosail.run(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF) #spectrum = pyprosail.run(1.5, chloro, 8, 0, 0.01, .009, 1, LAI, 0.01, 30, 0, 10, 0, pyprosail.Planophile) #spectrum = pyprosail.run(1.5, chloro, 8, 0, 0.01, .009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile) ''' pyprosail.run arguments N - Structure co-efficient chloro - Chlorophyll content (ug per cm^2) caroten - Carotenoid content (ug per cm^2) brown - Brown pigment content (arbitrary units) EWT - Equivalent Water Thickness (cm) LMA - Leaf Mass per unit area (g per cm^2) soil_reflectance - Soil reflectance: wet soil = 0, dry soil = 1 LAI - Leaf Area Index hot_spot - Hot spot parameter solar_zenith - Solar zenith angle (degrees) solar_azimuth - Solar azimuth angle (degrees) view_zenith - View zenith angle (degrees) view_azimuth - View azimuth angle (degrees) LIDF - Leaf distibution function parameter(s) (see below) ''' return spectrum
def electrons_in_pixel(wavelength_qe, b_qe, g_qe, r_qe, nir_qe, integration_time, const, detector_pixel_width, focal_length, diameter_obscuration, diameter_apreture, scene_albedo, atmospheric_transmission, gain, gain_step, hr_from_noon, latitude, bit_depth, full_well_e, dark_current_e_per_s, read_noise_e, temperature, dark_noise_2x_temperature, dark_noise_measure_temperature):
pixel_e = []
pixel_e_per_10nm = numpy.zeros((len(wavelength_qe),4))
solar_radiance = numpy.zeros(len(wavelength_qe))
# pixel_etendue_center_field
# detector_pixel_width = 0.009 # mm
focal_length = 1368 # mm
diameter_obscuration = 29.0 # mm
diameter_apreture = 89.0 # mm
area_of_optics = ( diameter_apreture ** 2 - diameter_obscuration ** 2 ) / 4 * math.pi
solid_angle_FOV = ( numpy.arctan( detector_pixel_width / ( 2 * focal_length ) ) * 2 ) ** 2 # steradians
pixel_etendue_center_field = solid_angle_FOV * area_of_optics / 100 # sr-cm^2
print 'pixel etendue, center of field: \t', pixel_etendue_center_field, ' sr-cm2'
gain_multiplier = ( 10 ** ( gain_step / 20 ) ) ** gain
print 'gain: \t\t\t\t', gain, '\ngain multiplier: \t\t', gain_multiplier
optics_transmission = .9 # 0-1
for w in range(0,len(wavelength_qe)):
source_spectral_radiance = solar_blackbody(wavelength_qe[w]) * ( wavelength_qe[1] - wavelength_qe[0] ) * ( const[1] / const[2] ) ** 2 # W/cm2/sr/10nm
spectral_radiance = source_spectral_radiance * optics_transmission * 1000.0 # mW/cm2-sr-10nm
total_photon_power = spectral_radiance * pixel_etendue_center_field # mW/10nm
power_per_photon = const[3] * const[0] / ( wavelength_qe[w] *1e-6) * 1000 # mW/photon/sec or mJ/photon
photon_flux = total_photon_power / power_per_photon # photons/sec/10nm
reflectance = crop_reflectance_vector(pyprosail.run(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF), wavelength_qe[w])
replaced_with_prosail = atmospheric_transmission * reflectance * numpy.cos( latitude * math.pi / 180.0 ) * numpy.cos( math.pi * hr_from_noon / 12.0 ) # all the reflectance modeling that PROSAIL does; careful here! Prosail may use latitude and LToD to calculate reflectance only and not take into account illumination
photons_at_pixel = photon_flux * ( integration_time / 1000000.0 ) * replaced_with_prosail # photons/10nm
# print 'photons in the pixel: ' + str(photons_at_pixel)
# print b_qe
pixel_e_per_10nm[w,0] = b_qe[w] * photons_at_pixel
pixel_e_per_10nm[w,1] = g_qe[w] * photons_at_pixel
pixel_e_per_10nm[w,2] = r_qe[w] * photons_at_pixel
pixel_e_per_10nm[w,3] = nir_qe[w] * photons_at_pixel
sum_e = numpy.zeros(4)
for i in range(0, len(sum_e)):
sum_e[i] = sum(pixel_e_per_10nm[:,i])
# sum_e = sum(pixel_e_per_10nm[:,0])
# sum_e = sum(pixel_e_per_10nm[:,1])
# sum_e = sum(pixel_e_per_10nm[:,2])
# sum_e = sum(pixel_e_per_10nm[:,3])
int_sum_e = [int(f) for f in sum_e]
print "b,g,r,n e-: \t\t\t", int_sum_e
# DN = sum_e * gain_multiplier
DN = e_to_DN(sum_e * gain_multiplier, full_well_e, bit_depth)
int_DN = [int(f) for f in DN]
print "b,g,r,n DN: \t\t\t", int_DN
# print "green e-: \t", int(sum_g)
# print "red e-: \t", int(sum_r)
# print "NIR e-: \t", int(sum_n)
max_b = max(pixel_e_per_10nm[:,0])
max_g = max(pixel_e_per_10nm[:,1])
max_r = max(pixel_e_per_10nm[:,2])
max_n = max(pixel_e_per_10nm[:,3])
max_y = max(max_b, max_g, max_r, max_n)
'''
fit_plotting(wavelength_qe, pixel_e_per_10nm[:,0], 'photons at pixel', 'wavelength [um]', 'blue photons', 'b-', max_y)
fit_plotting(wavelength_qe, pixel_e_per_10nm[:,1], 'photons at pixel', 'wavelength [um]', 'green photons', 'g-', max_y)
fit_plotting(wavelength_qe, pixel_e_per_10nm[:,2], 'photons at pixel', 'wavelength [um]', 'red photons', 'r-', max_y)
fit_plotting(wavelength_qe, pixel_e_per_10nm[:,3], 'photons at pixel', 'wavelength [um]', 'NIR photons', 'k-', max_y)
plt.show()
'''
# pixel_e_total = numpy.asarray()
# max_y = max(solar_radiance)
# fit_plotting(wavelength_qe, solar_radiance, 'solar radiance', 'wavelength [um]', 'W/cm2/sr/10nm', 'b-', max_y)
# plt.show()
descretization_noise_e = ( full_well_e / gain_multiplier / 2 ** bit_depth ) / ( 12 ** 0.5 )
print 'Descretization Noise, e-: \t', descretization_noise_e
dark_noise = dark_current_e_per_s * ( integration_time / 1000000.0 ) * 2 ** ( ( temperature -dark_noise_measure_temperature ) / dark_noise_2x_temperature )
print 'Dark Noise, e-: \t\t', dark_noise ** 0.5
print 'Read Noise, e-: \t\t', read_noise_e
print 'Shot Noise, e-: \t\t', sum_e ** 0.5
noise_e = ( sum_e + dark_noise + descretization_noise_e ** 2 + read_noise_e ** 2 ) ** 0.5 # root-sum-squared noise
noise_DN = e_to_DN(noise_e * gain_multiplier, full_well_e, bit_depth)
print "b,g,r,n noise, DN: \t\t", noise_DN
bar_plot_DN(DN, noise_DN)
snr_DN = DN / noise_DN
plt.annotate('SNR = ' + str(round(snr_DN[0],2)), xy=(0.25, 2), xytext=(0.25, 1),)
plt.annotate('SNR = ' + str(round(snr_DN[1],2)), xy=(0.25, 2), xytext=(1.25, 1),)
plt.annotate('SNR = ' + str(round(snr_DN[2],2)), xy=(0.25, 2), xytext=(2.25, 1),)
plt.annotate('SNR = ' + str(round(snr_DN[3],2)), xy=(0.25, 2), xytext=(3.25, 1),)
snr_DN = DN / noise_DN
# bar_plot_SNR(snr_DN, 0)
print "b,g,r,n SNR, DN: \t\t", snr_DN
name = 'NDVI'
index_DN = get_index(name, DN)
index_noise = get_index_noise(name, noise_DN, index_DN, DN) # must send the standard deviation
index_ann = name + ': ' + str(round(index_DN,3))
index_noise_ann = name + ' noise: ' + str(round(index_noise,3))
index_snr_ann = name + ' SNR: ' + str(round(index_DN / index_noise,2))
print index_ann
print index_noise_ann
print index_snr_ann
plt.annotate( index_ann + '\n' + index_noise_ann + '\n' + index_snr_ann, xy=(0.25, 2), xytext=(0.1, 100),)
plt.savefig('NDVI' + '_' + str(chloro) + '_' + str(LAI) + '_test.png')
plt.show()
return
def GetReflectance(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF): spectrum = pyprosail.run(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF) #spectrum = pyprosail.run(1.5, chloro, 8, 0, 0.01, .009, 1, LAI, 0.01, 30, 0, 10, 0, pyprosail.Planophile) #spectrum = pyprosail.run(1.5, chloro, 8, 0, 0.01, .009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile) return spectrum
### ITERATE PROSAIL MODELLING FOR EACH PIXEL IN THE DATA FILE. IT READS THE LAI, CHLORO AND EWT TRAIT COMBINATIONS FROM THE FILE ###
### GENERATES SPECTRA USING PROSAIL. COMPARES WITH THE ACTUAL SPECTRA FROM THE SENTINEL-2 SCENCE USING SPECTRAL ANGLE MAPPER ###
### OPTIONS TO PLOT, PAUSE AND PRINT RESULTS ARE CURRENTLY COMMENTED ###
for irow in range(np.shape(data)[0]):
rowvars = data.iloc[irow]
if rowvars['flagsbyfiveall_1'] == 1:
if rowvars['B8A_1'] > 0.1:
LAI = rowvars['LAI_1']
chloro = rowvars['CAB_1'] * rowvars['LAI_1']
EWT = rowvars['CWC_1'] * rowvars['LAI_1']
solar_zenith = rowvars['sun_zenith_1']
solar_azimuth = rowvars['sun_azimuth_1']
view_zenith = rowvars['view_zenith_mean_1']
view_azimuth = rowvars['view_azimuth_mean_1']
specout = pyprosail.run(N, chloro, caroten, brown, EWT, LMA, psoil,
LAI, hot_spot, solar_zenith, solar_azimuth,
view_zenith, view_azimuth, LIDF)
# print LAI, chloro, EWT, solar_zenith, solar_azimuth, view_zenith, view_azimuth
s2out = pd.DataFrame(columns={
'B2', 'B3', 'B4', 'B5', 'B6', 'B7', 'B8A', 'B11', 'B12'
})
s2outt = np.array([[520, 560, 665, 705, 740, 783, 865, 1610, 2190],
np.zeros(9)])
for ib, band in enumerate(bandslist):
weigthedvalue = 0
bandname = 'S2A_SR_AV_' + band
sumvalue = np.sum(s2sens[bandname])
for ix in np.where(s2sens[bandname] != 0)[0]:
iwl = np.where(
(specout[:, 0] *
1000) == int(s2sens['SR_WL'].iloc[ix]))[0][0]
hot_spot = []
LAD_inclination = []
LAD_bimodality = []
s_az = []
s_za = []
v_az = []
v_za = []
nir_v = []
brightness = []
# set the wavelengths to use in calculating nir_v
red_wl = 0.680
nir_wl = 0.800
# set a dummy run of prosail to find the index for each wavelength
spec = pyprosail.run(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
red_band = np.where(spec[:,0] == red_wl)[0][0]
nir_band = np.where(spec[:,0] == nir_wl)[0][0]
# create a function to calculate nir_v
def calc_nir_v(red, nir):
return nir * (nir - red) / (nir + red)
# and some functions to optimize linear and logistic fits for plotting later
def func_sigmoid(x, x0, k, a, c):
return a / (1 + np.exp(-k * (x - x0))) + c
def func_linear(x, m, b):
return m * x + b
def func_fit(x, y, function):
s.atmos_profile = AtmosProfile.PredefinedType(atmos_profile[atmos_profile_ind[i]])
s.aot550 = aot[i]
geo.solar_a = solar_a[i]
geo.solar_z = solar_z[i]
geo.view_a = view_a[i]
geo.view_z = view_z[i]
s.geometry = geo
ground_refl = ground_reflectance[ground_reflectance_ind[i]]
# loop through each veg / wood / soil bundle
for j in range(n_bundles):
# load prosail and run the canopy model
LIDF = (LAD_inclination[j], LAD_bimodality[j])
spectrum = pyprosail.run(N[j], chloro[j], caroten[j],
brown[j], EWT[j], LMA[j], soil_reflectance[j],
LAI[j], hot_spot[j], solar_z_prosail, solar_a_prosail,
view_z_prosail, view_a_prosail, LIDF)
# set the prosail modeled spectrum as ground spectrum in sixs
s.ground_reflectance = ground_refl(spectrum)
# generate the output spectrum
if target_sensor == 'custom':
wavelengths, results = run_sixs_params(s, wl, output_name = output_type)
else:
wavelengths, results = run_sixs_params(s, output_name = output_type)
# convert output to array for ease of output
results = np.asarray(results)
# add the modeled spectrum to the output array
import pyprosail res = pyprosail.run(1.5, 40, 8, 0, 0.01, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile) print res