def test_mask_spectra_wavelengths_actual_data(): filename = resource_filename(sbc.__name__, "tests/data/siop/aw_340_900_lw2002_1nm.csv") # load_spectral_library returns a dictionary. Popitem simply extracts the # only value. We don't care about the key in this instance. one = sbc.load_spectral_library(filename).popitem()[1] one_wavs, one_values = one[0], one[1] assert one_wavs.min() == 340 assert one_wavs.max() == 901 filename = resource_filename(sbc.__name__, "tests/data/siop/WL_aphy_1nm.hdr") two = sbc.load_spectral_library(filename).popitem()[1] two_wavs, two_values = two[0], two[1] assert two_wavs.min() == 350 assert two_wavs.max() == 800 # generate the mask mask = sbc.spectra_find_common_wavelengths(one, two) assert len(mask) == len(two_wavs) # mask the larger spectra to the smaller set of wavelengths masked_wavs, masked_values = sbc.spectra_apply_wavelength_mask(one, mask) assert masked_wavs.min() == mask[0] assert masked_wavs.max() == mask[-1] assert len(masked_wavs) == len(mask) assert len(masked_values) == len(mask)
def test_mask_spectra_wavelengths(): one = (np.asarray([1, 2, 3, 4, 5]), np.asarray([10, 20, 30, 40, 50])) two = (np.asarray([2, 3, 4]), np.asarray([2, 3, 4])) mask = sbc.spectra_find_common_wavelengths(one, two) masked_wavs, masked_values = sbc.spectra_apply_wavelength_mask(one, mask) assert len(masked_wavs) == len(mask) assert len(masked_values) == len(mask) assert np.allclose(masked_wavs, [2, 3, 4]) assert np.allclose(masked_values, [20, 30, 40])
def input_prepare(siop, envmeta, image_info, error_name): a_water = siop['a_water'] a_ph_star = siop['a_ph_star'] substrates = siop['substrates'] substrate_names = siop['substrate_names'] sensor_filter = image_info['sensor_filter'] observed_rrs_width = image_info['observed_rrs_width'] observed_rrs_height = image_info['observed_rrs_height'] nedr = image_info['nedr'] wavelengths = sbc.spectra_find_common_wavelengths(a_water, a_ph_star, *substrates) #TODO check not empty #print('Common wavelength range: {0} - {1}'.format(min(wavelengths), max(wavelengths))) #Use the common wavelengths to mask the inputs: a_water = sbc.spectra_apply_wavelength_mask(a_water, wavelengths) a_ph_star = sbc.spectra_apply_wavelength_mask(a_ph_star, wavelengths) for i, substrate in enumerate(substrates): substrates[i] = sbc.spectra_apply_wavelength_mask( substrate, wavelengths) print('awater: min: {0} max: {1}'.format(min(a_water[0]), max(a_water[0]))) print('a_ph_star: min: {0} max: {1}'.format(min(a_ph_star[0]), max(a_ph_star[0]))) for substrate_name, substrate in zip(substrate_names, substrates): print('{0}: min: {1} max: {2}'.format(substrate_name, min(substrate[0]), max(substrate[0]))) """Truncate the sensor filter to match the common wavelength range It remains to be seen whether this is the best approach, but it works for this demo. An alternative approach would be to truncate the entire band for any band that falls outside the common wavelength range. If this approach, or something based on it, is valid, then this should be moved into a sambuca_core function with appropriate unit tests.""" filter_mask = (sensor_filter[0] >= wavelengths.min()) & (sensor_filter[0] <= wavelengths.max()) sensor_filter = sensor_filter[0][filter_mask], sensor_filter[ 1][:, filter_mask] fixed_parameters = sb.create_fixed_parameter_set( wavelengths=wavelengths, a_water=a_water, a_ph_star=a_ph_star, substrates=substrates, sub1_frac=None, sub2_frac=None, sub3_frac=None, chl=None, cdom=None, nap=None, depth=None, a_cdom_slope=siop['a_cdom_slope'], a_nap_slope=siop['a_nap_slope'], bb_ph_slope=siop['bb_ph_slope'], bb_nap_slope=siop['bb_nap_slope'], lambda0cdom=siop['lambda0cdom'], lambda0nap=siop['lambda0nap'], lambda0x=siop['lambda0x'], x_ph_lambda0x=siop['x_ph_lambda0x'], x_nap_lambda0x=siop['x_nap_lambda0x'], a_cdom_lambda0cdom=siop['a_cdom_lambda0cdom'], a_nap_lambda0nap=siop['a_nap_lambda0nap'], bb_lambda_ref=siop['bb_lambda_ref'], water_refractive_index=siop['water_refractive_index'], theta_air=envmeta['theta_air'], off_nadir=envmeta['off_nadir'], q_factor=envmeta['q_factor']) result_recorder = sb.ArrayResultWriter(observed_rrs_height, observed_rrs_width, sensor_filter, nedr, fixed_parameters) error_dict = { 'alpha': sb.distance_alpha, 'alpha_f': sb.distance_alpha_f, 'lsq': sb.distance_lsq, 'f': sb.distance_f } objective = sb.SciPyObjective( sensor_filter, fixed_parameters, error_function=error_dict[error_name.lower()], nedr=nedr) siop['a_water'] = a_water siop['a_ph_star'] = a_ph_star siop['substrates'] = substrates siop['substrate_names'] = substrate_names image_info['sensor_filter'] = sensor_filter image_info['observed_rrs_width'] = observed_rrs_width image_info['observed_rrs_height'] = observed_rrs_height image_info['nedr'] = nedr #print ('EXIT PREPARE') return wavelengths, siop, image_info, fixed_parameters, result_recorder, objective
def sam_obs(): if __name__ == 'sen2coral2.obs': print( os.path.isfile( 'bioopti_data\\..\\sambuca\\reference\\wl_alos_data\\inputs\\WL_ALOS_R_0_sub120.img' )) base_path = 'bioopti_data\\' observed_rrs_base_path = base_path + '..\\sambuca\\reference\\wl_alos_data\\inputs\\' observed_rrs_raster_path = join(observed_rrs_base_path, 'WL_ALOS_R_0_sub120.img') sensor_filter_path = join(base_path, 'sensor_filters') sensor_filter_name = 'ALOS' substrate_path = join(base_path, 'Substrates') substrate1_name = 'moreton_bay_speclib:white Sand' substrate2_name = 'moreton_bay_speclib:brown Mud' substrate3_name = 'moreton_bay_speclib:Syringodium isoetifolium' substrate4_name = 'moreton_bay_speclib:brown algae' substrate5_name = 'moreton_bay_speclib:green algae' #substrate_names= ( substrate1_name, substrate2_name) #substrate_names= ( substrate1_name, substrate2_name, substrate3_name) #substrate_names= ( substrate1_name, substrate2_name, substrate3_name, substrate4_name) substrate_names = (substrate1_name, substrate2_name, substrate3_name, substrate4_name, substrate5_name) aphy_star_path = join(base_path, 'SIOP/WL08_aphy_1nm.hdr') aphy_star_name = 'wl08_aphy_1nm:WL08_aphy_star_mean_correct.csv:C2' awater_path = join(base_path, 'SIOP/aw_350_900_lw2002_1nm.csv') awater_name = 'aw_350_900_lw2002_1nm:a_water' nedr_path = join(observed_rrs_base_path, 'WL_ALOS_NEDR_0_4bands.hdr') sensor_filter_path = join(base_path, 'sensor_filters') sensor_filter_name = 'ALOS' observed_rrs_width = 0 observed_rrs_height = 0 observed_rrs = None with rasterio.drivers(): with rasterio.open(observed_rrs_raster_path) as src: print('Observed rrs file: ', observed_rrs_raster_path) print('Width, height: ', src.width, src.height) print('crs: ', src.crs) print('affine: ', src.affine) print('num bands: ', src.count) print('band indicies: ', src.indexes) observed_rrs_width = src.width observed_rrs_height = src.height observed_rrs = src.read() all_substrates = sbc.load_all_spectral_libraries(substrate_path) substrates = [] for substrate_name in substrate_names: substrates.append(all_substrates[substrate_name]) # load all filters from the given directory sensor_filters = sbc.load_sensor_filters(sensor_filter_path) # We don't need to do this, but it lets us see the name of all loaded filters sensor_filters.keys() # retrieve the specified filter sensor_filter = sensor_filters[sensor_filter_name] #Plot the sensor filter: #plot_items.clear() #Python 3.3 and later only aphy_star = sbc.load_spectral_library(aphy_star_path)[aphy_star_name] awater = sbc.load_spectral_library(awater_path)[awater_name] nedr = sbc.load_spectral_library( nedr_path, validate=False)['wl_alos_nedr_0_4bands:33'] nedr wavelengths = sbc.spectra_find_common_wavelengths( awater, aphy_star, *substrates) print('Common wavelength range: {0} - {1}'.format( min(wavelengths), max(wavelengths))) #Use the common wavelengths to mask the inputs: awater = sbc.spectra_apply_wavelength_mask(awater, wavelengths) aphy_star = sbc.spectra_apply_wavelength_mask(aphy_star, wavelengths) for i, substrate in enumerate(substrates): substrates[i] = sbc.spectra_apply_wavelength_mask( substrate, wavelengths) print('awater: min: {0} max: {1}'.format(min(awater[0]), max(awater[0]))) print('aphy_star: min: {0} max: {1}'.format(min(aphy_star[0]), max(aphy_star[0]))) for substrate_name, substrate in zip(substrate_names, substrates): print('{0}: min: {1} max: {2}'.format(substrate_name, min(substrate[0]), max(substrate[0]))) """Truncate the sensor filter to match the common wavelength range It remains to be seen whether this is the best approach, but it works for this demo. An alternative approach would be to truncate the entire band for any band that falls outside the common wavelength range. If this approach, or something based on it, is valid, then this should be moved into a sambuca_core function with appropriate unit tests.""" filter_mask = (sensor_filter[0] >= wavelengths.min()) & ( sensor_filter[0] <= wavelengths.max()) sensor_filter = sensor_filter[0][filter_mask], sensor_filter[ 1][:, filter_mask] xstart = 0 xend = 10 xspan = xend - xstart ystart = 0 yend = 120 print('CIAO ', xstart) num_pixels = xspan * (yend - ystart) assert xend <= observed_rrs_width assert yend <= observed_rrs_height fixed_parameters = sb.create_fixed_parameter_set( wavelengths=wavelengths, a_water=awater, a_ph_star=aphy_star, substrates=substrates, ) result_recorder = sb.ArrayResultWriter(observed_rrs_width, observed_rrs_height, sensor_filter, nedr, fixed_parameters) objective = sb.SciPyObjective(sensor_filter, fixed_parameters, error_function=sb.distance_f, nedr=nedr) return wavelengths, observed_rrs, observed_rrs_width, observed_rrs_height, awater, aphy_star, substrates, nedr, sensor_filter, xstart, xend, ystart, yend, num_pixels, fixed_parameters, result_recorder, objective
print('{0}: min: {1} max: {2}'.format(substrate_name, min(substrate[0]), max(substrate[0]))) # In[87]: wavelengths = sbc.spectra_find_common_wavelengths(awater, aphy_star, *substrates) print('Common wavelength range: {0} - {1}'.format(min(wavelengths), max(wavelengths))) # Use the common wavelengths to mask the inputs: # In[88]: awater = sbc.spectra_apply_wavelength_mask(awater, wavelengths) aphy_star = sbc.spectra_apply_wavelength_mask(aphy_star, wavelengths) for i, substrate in enumerate(substrates): substrates[i] = sbc.spectra_apply_wavelength_mask( substrate, wavelengths) print('awater: min: {0} max: {1}'.format(min(awater[0]), max(awater[0]))) print('aphy_star: min: {0} max: {1}'.format(min(aphy_star[0]), max(aphy_star[0]))) for substrate_name, substrate in zip(substrate_names, substrates): print('{0}: min: {1} max: {2}'.format(substrate_name, min(substrate[0]), max(substrate[0]))) # ## Truncate the sensor filter to match the common wavelength range # It remains to be seen whether this is the best approach, but it works for this demo.