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Flexbrdf/hytools/glint/hochberg_2003.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
+
+
+def apply_hochberg_2003_correction(hy_obj, data, dimension, index):
+    """
+    Glint correction algorithm following:
+
+    Hochberg, EJ, Andréfouët, S and Tyler, MR. 2003.
+    Sea surface correction of high spatial resolution Ikonos images to
+    improve bottom mapping in near‐shore environments..
+    IEEE Transactions on Geoscience and Remote Sensing, 41: 1724–1729.
+    """
+
+    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
+
+    if 'hochberg_correction' not in hy_obj.ancillary:
+        hy_obj.ancillary['hochberg_correction'] = (
+            get_hochberg_correction(hy_obj)
+        )
+
+    if dimension == 'line':
+        correction = hy_obj.ancillary['hochberg_correction'][index, :][:,np.newaxis]
+
+    elif dimension == 'column':
+        correction = hy_obj.ancillary['hochberg_correction'][:, index][np.newaxis,:]
+
+    elif dimension == 'band':
+        correction = hy_obj.ancillary['hochberg_correction']
+
+    elif dimension == 'chunk':
+        x1, x2, y1, y2 = index
+        correction = hy_obj.ancillary['hochberg_correction'][y1:y2, x1:x2]
+
+    elif dimension == 'pixels':
+        y, x = index
+        correction = hy_obj.ancillary['hochberg_correction'][y, x]
+
+    return data - correction
+
+def get_hochberg_correction(hy_obj):
+    """
+    Calculates the hochberg correction across entire image.
+    Uses the NIR or SWIR wavelengths to find the amount of signal
+    attributed to glint. Zeros out non-water pixels
+    """
+
+    if isinstance(hy_obj.glint['correction_wave'],list):
+        nir_swir_array = np.zeros((hy_obj.lines,hy_obj.columns))
+        for wave in hy_obj.glint['correction_wave']:
+            nir_swir_array+= hy_obj.get_wave(wave)
+        nir_swir_array/=len(hy_obj.glint['correction_wave'])
+    else:
+        nir_swir_array = np.copy(hy_obj.get_wave(hy_obj.glint['correction_wave']))
+
+    nir_swir_array[~hy_obj.mask['apply_glint']] = 0
+
+    nir_swir_min = np.percentile(
+        nir_swir_array[nir_swir_array > 0], .001
+    )
+
+    hochberg_correction = nir_swir_array - nir_swir_min
+    hochberg_correction[~hy_obj.mask['apply_glint']] = 0
+
+    return hochberg_correction