hGRS 1.1.1__tar.gz

hgrs-1.1.1/LICENSE

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+
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+      To apply the Apache License to your work, attach the following
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+   Copyright [2025] [Tristan Harmel]
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hgrs-1.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: hGRS
+Version: 1.1.1
+Summary: hGRS processor for atmospheric correction of high-spatial resolution and hyperspectral satellite images
+Author-email: Tristan Harmel <tristan.harmel@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/Tristanovsk/hgrs
+Project-URL: Documentation, https://hgrs.readthedocs.io
+Keywords: PRISMA,EnMAP,atmospheric correction,EO satellite
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: h5netcdf
+Requires-Dist: netCDF4
+Requires-Dist: h5py
+Requires-Dist: scipy
+Requires-Dist: rasterio>=1.3.10
+Requires-Dist: xarray>=2024.06.0
+Requires-Dist: rioxarray>=0.15.0
+Requires-Dist: geopandas>=0.14.4
+Requires-Dist: zarr
+Requires-Dist: numba
+Requires-Dist: omnicloudmask
+Requires-Dist: xesmf
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: bumpver; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: pip-tools; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Dynamic: license-file

hgrs-1.1.1/README.md

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+# hGRS package
+## Hyperspectral Glint Removal System for hyperspectral remote sensing of the aquatic environment
+
+# WARNING: this is a working version between collaborators please do not use it as is. Stable version will come soon.
+
+### Prerequisites
+
+If you want to get visualization tool, you first need to install the following libraries (more secure with Anaconda):
+
+```
+conda install -c conda-forge hvplot bokeh panel datashader jupyter jupyterlab
+```
+
+### Installing
+
+First, clone [the repository](https://github.com/Tristanovsk/prismapy#) and execute the following command in the
+local copy:
+
+```
+pip install . 
+```
+
+Optional dependency, if you want to use the reprojection feature for PRISMA please install xemsf:
+
+```commandline
+conda install xesmf
+```
+
+## Examples
+![example spectra](fig/check_spectra.png)
+
+![example l2c](fig/test_L2C_Garda.png)
+![example l1c](fig/test_L1C_Garda_water.png)
+
+
+
+

hgrs-1.1.1/docs/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/hgrs/__init__.py

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+'''
+v1.0.0 open and visualize
+v1.0.1 orient North of rasters (waiting for proper georeference)
+v1.0.2 improvement of solar irradiance data and convolution for reflectance conversion
+v1.0.3 development of the process kernel
+v1.0.4 reorganizing modules
+v1.0.5 investigate solar irradiance reference model
+v1.0.6: add reprojection feature
+v1.0.7: 2025-11-07 correct bug for Earth-Sun distance, option to remove bad EnMAP bands, refactoring
+v1.1.0: new processor for aerosol optical thickness based on non-negativity of retrieved reflectance
+v1.1.1: clean up and check which function gaussian, supergaussian is the most suited for spectral integration
+'''
+__version__ = '1.1.1'
+
+from .utils import Reproj, Misc
+from .auxdata import AuxData, SolarIrradiance
+from .hgrs_kernel import Algo, WaterVapor, Aerosol, Product, Spectral
+from .hgrs_process import Process
+from .driver import Driver
+
+
+import logging
+
+#init logger
+logger = logging.getLogger()
+
+level = logging.getLevelName("INFO")
+logger.setLevel(level)

hgrs-1.1.1/docs/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/hgrs/auxdata.py

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+import os
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+import rioxarray as rio
+
+import h5py
+import netCDF4 as nc
+import scipy.interpolate
+import scipy.integrate
+
+import matplotlib.pyplot as plt
+import cartopy.crs as crs
+import cartopy.feature as cf
+
+import datetime
+
+from pkg_resources import resource_filename
+
+opj = os.path.join
+
+# ******************************************************************************************************
+dir, filename = os.path.split(__file__)
+
+thuillier_file = resource_filename(__package__, 'data/aux/ref_atlas_thuillier3.nc')
+gueymard_file = resource_filename(__package__, 'data/aux/NewGuey2003.dat')
+kurucz_file = resource_filename(__package__, 'data/aux/kurucz_0.1nm.dat')
+tsis_file = resource_filename(__package__,
+                              'data/aux/hybrid_reference_spectrum_p1nm_resolution_c2022-11-30_with_unc.nc')
+
+sunglint_eps_file = resource_filename(__package__, 'data/aux/mean_rglint_small_angles_vza_le_12_sza_le_60.txt')
+rayleigh_file = resource_filename(__package__, 'data/aux/rayleigh_bodhaine.txt')
+
+
+class AuxData():
+    def __init__(self, wl=None):
+        # load data from raw files
+        self.solar_irr = SolarIrradiance()
+        self.sunglint_eps = pd.read_csv(sunglint_eps_file, sep=r'\s+', index_col=0).to_xarray()
+        self.rayleigh()
+        self.pressure_rot_ref = 1013.25
+
+        # reproject onto desired wavelengths
+        if wl is not None:
+            self.solar_irr = self.solar_irr.interp(wl=wl)
+            self.sunglint_eps = self.sunglint_eps['mean'].interp(wl=wl)
+            self.rot = self.rot.interp(wl=wl)
+
+    def rayleigh(self):
+        '''
+        Rayleigh Optical Thickness for
+        P=1013.25mb,
+        T=288.15K,
+        CO2=360ppm
+        from
+        Bodhaine, B.A., Wood, N.B, Dutton, E.G., Slusser, J.R. (1999). On Rayleigh
+        Optical Depth Calculations, J. Atmos. Ocean Tech., 16, 1854-1861.
+        '''
+        data = pd.read_csv(rayleigh_file, skiprows=16, sep=' ', header=None)
+        data.columns = ('wl', 'rot', 'dpol')
+        self.rot = data.set_index('wl').to_xarray().rot
+
+
+class SolarIrradiance():
+    def __init__(self, wl=None):
+        # load data from raw files
+        self.wl_min = 300
+        self.wl_max = 2600
+
+        self.gueymard = self.read_gueymard()
+        self.kurucz = self.read_kurucz()
+        self.thuillier = self.read_thuillier()
+        self.tsis = self.read_tsis()
+
+    def read_tsis(self):
+        '''
+        Open TSIS data and convert them into xarray in mW/m2/nm
+        :return:
+        '''
+        tsis = xr.open_dataset(tsis_file)
+        tsis = tsis.set_index(wavelength='Vacuum Wavelength').rename(
+            {'wavelength': 'wl'})  # set_coords('Vacuum Wavelength')
+        # convert
+        tsis['SSI'] = tsis.SSI * 1000  # .plot(lw=0.5)
+        tsis.SSI.attrs['units'] = 'mW m-2 nm-1'
+        tsis.SSI.attrs['long_name'] = 'Solar Spectral Irradiance Reference Spectrum (mW m-2 nm-1)'
+        tsis.SSI.attrs['reference'] = 'Coddington, O. M., Richard, E. C., Harber, D., et al. (2021).' + \
+                                      'The TSIS-1 Hybrid Solar Reference Spectrum. Geophysical Research Letters,' + \
+                                      '48(12), e2020GL091709. https://doi.org/10.1029/2020GL091709'
+        return tsis.SSI.sel(wl=slice(self.wl_min,self.wl_max))
+
+    def read_thuillier(self):
+        '''
+        Open Thuillier data and convert them into xarray in mW/m2/nm
+        :return:
+        '''
+        solar_irr = xr.open_dataset(thuillier_file).squeeze().data.drop('time') * 1e3
+        solar_irr = solar_irr.rename({'wavelength': 'wl'})
+        # keep spectral range of interest UV-SWIR
+        solar_irr = solar_irr[(solar_irr.wl <= self.wl_max) & (solar_irr.wl >= self.wl_min)]
+        solar_irr.attrs['units'] = 'mW/m2/nm'
+        return solar_irr
+
+    def read_gueymard(self):
+        '''
+        Open Thuillier data and convert them into xarray in mW/m2/nm
+        :return:
+        '''
+        solar_irr = pd.read_csv(gueymard_file, sep=r'\s+', skiprows=30, header=None)
+        solar_irr.columns = ['wl', 'data']
+        solar_irr = solar_irr.set_index('wl').data.to_xarray()
+        # keep spectral range of interest UV-SWIR
+        solar_irr = solar_irr[(solar_irr.wl <= self.wl_max) & (solar_irr.wl >= self.wl_min)]
+        solar_irr.attrs['units'] = 'mW/m2/nm'
+        solar_irr.attrs['reference'] = 'Gueymard, C. A., Solar Energy, Volume 76, Issue 4,2004, ISSN 0038-092X'
+        return solar_irr
+
+    def read_kurucz(self):
+        '''
+        Open Kurucz data and convert them into xarray in mW/m2/nm
+        :return:
+        '''
+        solar_irr = pd.read_csv(kurucz_file, sep=r'\s+', skiprows=11, header=None)
+        solar_irr.columns = ['wl', 'data']
+        solar_irr = solar_irr.set_index('wl').data.to_xarray()
+        # keep spectral range of interest UV-SWIR
+        solar_irr = solar_irr[(solar_irr.wl <= self.wl_max) & (solar_irr.wl >= self.wl_min)]
+        solar_irr.attrs['units'] = 'mW/m2/nm'
+        solar_irr.attrs['reference'] = 'Kurucz, R.L., Synthetic infrared spectra, in Infrared Solar Physics, ' + \
+                                       'IAU Symp. 154, edited by D.M. Rabin and J.T. Jefferies, Kluwer, Acad., ' + \
+                                       'Norwell, MA, 1992.'
+        return solar_irr
+
+    def interp(self, wl=[440, 550, 660, 770, 880]):
+        '''
+        Interpolation on new wavelengths
+        :param wl: wavelength in nm
+        :return: update variables of the class
+        '''
+        self.thuillier = self.thuillier.interp(wl=wl)
+        self.gueymard = self.gueymard.interp(wl=wl)
+
+    @staticmethod
+    def Gamma2sigma(Gamma):
+        '''Function to convert FWHM (Gamma) to standard deviation (sigma)'''
+        return Gamma * np.sqrt(2.) / (np.sqrt(2. * np.log(2.)) * 2.)
+
+    @staticmethod
+    def gaussian(x, mu, sigma):
+        return 1 / (sigma * np.sqrt(2 * np.pi)) * np.exp(-(x - mu) ** 2 / (2 * sigma ** 2))
+
+    def convolve(self, F0, fwhm, info={}):
+        '''
+        Convolve with spectral response of sensor based on full width at half maximum of each band
+        :param F0: xarray solar irradiance to convolve, coord=wl
+        :param fwhm: xarray with data=fwhm containing full width at half maximum in nm, and coords=wl
+        :param info: optional parameter to feed the attributes of the output xarray
+        :return:
+        '''
+        wl_ref = F0.wl
+        F0_int = []
+        for fwhm_ in fwhm:
+            sig = self.Gamma2sigma(fwhm_.values)
+            rsr = self.gaussian(wl_ref, fwhm_.wl.values, sig)
+
+            F0_ = (F0 * rsr).integrate('wl') / np.trapz(rsr, wl_ref)
+            F0_int.append(F0_.values)
+        return xr.DataArray(F0_int, name='F0',
+                            coords={'wl': fwhm.wl.values},
+                            attrs=info)