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Flexbrdf/hytools/glint/gao_2021.py

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+# -*- coding: utf-8 -*-
+"""
+HyTools:  Hyperspectral image processing library
+Copyright (C) 2021 University of Wisconsin
+
+Authors: Evan Greenberg.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, version 3 of the License.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+import numpy as np
+from ..masks import mask_create
+
+
+REFRACTIVE_INDICES = np.array([
+    [200, 1.396],
+    [225, 1.373],
+    [250, 1.362],
+    [275, 1.354],
+    [300, 1.349],
+    [325, 1.346],
+    [350, 1.343],
+    [375, 1.341],
+    [400, 1.339],
+    [425, 1.338],
+    [450, 1.337],
+    [475, 1.336],
+    [500, 1.335],
+    [525, 1.334],
+    [550, 1.333],
+    [575, 1.333],
+    [600, 1.332],
+    [625, 1.332],
+    [650, 1.331],
+    [675, 1.331],
+    [700, 1.331],
+    [725, 1.33],
+    [750, 1.33],
+    [775, 1.33],
+    [800, 1.329],
+    [825, 1.329],
+    [850, 1.329],
+    [875, 1.328],
+    [900, 1.328],
+    [925, 1.328],
+    [950, 1.327],
+    [975, 1.327],
+    [1000, 1.327],
+    [1200, 1.324],
+    [1400, 1.321],
+    [1600, 1.317],
+    [1800, 1.312],
+    [2000, 1.306],
+    [2200, 1.296],
+    [2400, 1.279],
+    [2600, 1.242],
+    [2650, 1.219],
+    [2700, 1.188],
+    [2750, 1.157],
+    [2800, 1.142],
+    [2850, 1.149],
+    [2900, 1.201],
+    [2950, 1.292],
+    [3000, 1.371]
+])
+
+
+def apply_gao_2021_correction(hy_obj, data, dimension, index):
+    """
+    Glint correction algorithm following:
+
+    Gao BC, Li RR.
+    Correction of Sunglint Effects in High Spatial Resolution
+    Hyperspectral Imagery Using SWIR or NIR Bands and Taking Account of
+    Spectral Variation of Refractive Index of Water.
+    Adv Environ Eng Res 2021;2(3):16; doi:10.21926/aeer.2103017.
+    """
+
+
+    if 'apply_glint' not in hy_obj.mask:
+        hy_obj.gen_mask(mask_create,'apply_glint',hy_obj.glint['apply_mask'])
+
+    if hy_obj.mask['apply_glint'].sum() == 0:
+        return data
+
+    hy_obj.glint['correction_band'] = hy_obj.wave_to_band(hy_obj.glint['correction_wave'])
+
+    if 'gao_b_simu' not in hy_obj.ancillary:
+        hy_obj.ancillary['gao_b_simu'] = get_b_simu(hy_obj)
+
+    if 'gao_rto' not in hy_obj.ancillary:
+        hy_obj.ancillary['gao_rto'] = get_rto(hy_obj)
+
+    if dimension == 'line':
+        rto_line = hy_obj.ancillary['gao_rto'][index, :]
+        rto_line = np.reshape(rto_line, (len(rto_line), 1))
+        correction = rto_line * hy_obj.ancillary['gao_b_simu']
+
+    elif dimension == 'column':
+        rto_col = hy_obj.ancillary['gao_rto'][:, index]
+        rto_col = np.reshape(rto_col, (len(rto_col), 1))
+        correction = rto_col * hy_obj.ancillary['gao_b_simu']
+
+    elif (dimension == 'band'):
+        correction = (
+            hy_obj.ancillary['gao_b_simu'][0, :][index]
+            * hy_obj.ancillary['gao_rto']
+        )
+
+    elif dimension == 'chunk':
+        x1, x2, y1, y2 = index
+        rto_chunk = hy_obj.ancillary['gao_rto'][y1:y2, x1:x2]
+        rto_chunk = np.reshape(
+            rto_chunk,
+            (
+                rto_chunk.shape[0],
+                rto_chunk.shape[1],
+                1
+            )
+        )
+        correction = rto_chunk * hy_obj.ancillary['gao_b_simu']
+
+    elif dimension == 'pixels':
+        y, x = index
+        rto_pixels = hy_obj.ancillary['gao_rto'][y, x]
+        rto_pixels = np.reshape(rto_pixels, (len(rto_pixels), 1))
+        correction = rto_pixels * hy_obj.ancillary['gao_b_simu']
+
+    return data - correction
+
+
+def zenith_refracted(theta, n):
+    """
+    Find zenith of the outgoing reflected light
+    n is the refractive index of water at a specific wavelength
+    """
+    theta_p = np.degrees(
+        np.arcsin(np.sin(np.radians(theta)) / n)
+    )
+
+    return theta_p
+
+
+def fresnel_reflectence(theta, theta_p):
+    """
+    Uses the fresnel equation to find the
+    percentege of incident light reflected
+    """
+    theta_rad = np.radians(theta)
+    theta_p_rad = np.radians(theta_p)
+
+    return (
+        (
+            (np.sin(theta_rad - theta_p_rad)**2)
+            / (np.sin(theta_rad + theta_p_rad)**2)
+        ) + (
+            (np.tan(theta_rad - theta_p_rad)**2)
+            / (np.tan(theta_rad + theta_p_rad)**2)
+        )
+    ) / 2
+
+
+def fresnel_spectra(theta, xs, ns):
+    """
+    Solves for the spectrum of reflected light
+    according to fresnels equations
+    """
+    spectra = []
+    for x in xs:
+        n = np.interp(x, ns[:, 0], ns[:, 1])
+        theta_p = zenith_refracted(theta, n)
+        spectra.append(fresnel_reflectence(theta, theta_p))
+
+    return np.array(spectra)
+
+
+def get_b_simu(hy_obj):
+    b_simu = fresnel_spectra(
+        10**-5,
+        hy_obj.wavelengths,
+        REFRACTIVE_INDICES
+    )
+
+    return np.reshape(
+        b_simu, (1, len(b_simu))
+    )
+
+
+def get_rto(hy_obj):
+    b_ref = hy_obj.get_wave(hy_obj.glint['correction_wave'])
+
+    b_ref_min = np.percentile(
+        b_ref[
+            (hy_obj.mask['apply_glint'])
+            & (b_ref > 0)
+        ],
+        .0001
+    )
+    b_ref = b_ref - b_ref_min
+
+    rto = (
+        b_ref
+        / hy_obj.ancillary['gao_b_simu'][0, :][hy_obj.glint['correction_band']]
+    )
+    rto[~hy_obj.mask['apply_glint']] = 0
+
+    return rto