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Add an option in the GCOV workflow to assign values to regions with missing radar samples #48

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ffd8aa7
Add an option in the GCOV workflow to assign values to regions with m…
gshiroma Jun 30, 2025
d20b793
Merge branch 'isce-framework:develop' into gcov_fill_no_data
gshiroma Jul 1, 2025
a68b4d0
Merge branch 'isce-framework:develop' into gcov_fill_no_data
gshiroma Aug 11, 2025
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94 changes: 69 additions & 25 deletions cxx/isce3/geocode/GeocodeCov.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
isce3::io::Raster& input_raster, isce3::io::Raster& output_raster,
isce3::io::Raster& dem_raster, geocodeOutputMode output_mode,
bool flag_az_baseband_doppler, bool flatten, double geogrid_upsampling,
bool flag_upsample_radar_grid, bool flag_apply_rtc,
float shadow_no_data_value, bool flag_upsample_radar_grid,
bool flag_apply_rtc,
isce3::geometry::rtcInputTerrainRadiometry input_terrain_radiometry,
isce3::geometry::rtcOutputTerrainRadiometry output_terrain_radiometry,
int exponent, float rtc_min_value_db, double rtc_geogrid_upsampling,
Expand Down Expand Up @@ -158,7 +159,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
bool flag_run_geocode_interp = output_mode == geocodeOutputMode::INTERP;
if (flag_run_geocode_interp && !flag_complex_to_real)
geocodeInterp<T>(radar_grid, input_raster, output_raster, dem_raster,
flag_apply_rtc, flag_az_baseband_doppler, flatten,
shadow_no_data_value, flag_apply_rtc,
flag_az_baseband_doppler, flatten,
input_terrain_radiometry, output_terrain_radiometry,
rtc_min_value_db, rtc_geogrid_upsampling, rtc_algorithm,
rtc_area_beta_mode,
Expand All @@ -174,7 +176,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
(std::is_same<T, double>::value ||
std::is_same<T, std::complex<double>>::value))
geocodeInterp<double>(radar_grid, input_raster, output_raster,
dem_raster, flag_apply_rtc, flag_az_baseband_doppler, flatten,
dem_raster, shadow_no_data_value,
flag_apply_rtc, flag_az_baseband_doppler, flatten,
input_terrain_radiometry, output_terrain_radiometry,
rtc_min_value_db, rtc_geogrid_upsampling, rtc_algorithm,
rtc_area_beta_mode,
Expand All @@ -188,7 +191,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
dem_interp_method);
else if (flag_run_geocode_interp)
geocodeInterp<float>(radar_grid, input_raster, output_raster,
dem_raster, flag_apply_rtc, flag_az_baseband_doppler, flatten,
dem_raster, shadow_no_data_value,
flag_apply_rtc, flag_az_baseband_doppler, flatten,
input_terrain_radiometry, output_terrain_radiometry,
rtc_min_value_db, rtc_geogrid_upsampling, rtc_algorithm,
rtc_area_beta_mode,
Expand All @@ -202,7 +206,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
dem_interp_method);
else if (!flag_complex_to_real)
geocodeAreaProj<T>(radar_grid, input_raster, output_raster, dem_raster,
geogrid_upsampling, flag_upsample_radar_grid, flag_apply_rtc,
geogrid_upsampling, shadow_no_data_value,
flag_upsample_radar_grid, flag_apply_rtc,
input_terrain_radiometry, output_terrain_radiometry,
rtc_min_value_db, rtc_geogrid_upsampling, rtc_algorithm,
rtc_area_beta_mode,
Expand All @@ -218,7 +223,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
else if (std::is_same<T, double>::value ||
std::is_same<T, std::complex<double>>::value)
geocodeAreaProj<double>(radar_grid, input_raster, output_raster,
dem_raster, geogrid_upsampling, flag_upsample_radar_grid,
dem_raster, geogrid_upsampling, shadow_no_data_value,
flag_upsample_radar_grid,
flag_apply_rtc, input_terrain_radiometry,
output_terrain_radiometry, rtc_min_value_db,
rtc_geogrid_upsampling, rtc_algorithm, rtc_area_beta_mode,
Expand All @@ -233,7 +239,8 @@ void Geocode<T>::geocode(const isce3::product::RadarGridParameters& radar_grid,
dem_interp_method);
else
geocodeAreaProj<float>(radar_grid, input_raster, output_raster,
dem_raster, geogrid_upsampling, flag_upsample_radar_grid,
dem_raster, geogrid_upsampling, shadow_no_data_value,
flag_upsample_radar_grid,
flag_apply_rtc, input_terrain_radiometry,
output_terrain_radiometry, rtc_min_value_db,
rtc_geogrid_upsampling, rtc_algorithm, rtc_area_beta_mode,
Expand All @@ -253,8 +260,8 @@ template<class T_out>
void Geocode<T>::geocodeInterp(
const isce3::product::RadarGridParameters& radar_grid,
isce3::io::Raster& inputRaster, isce3::io::Raster& outputRaster,
isce3::io::Raster& demRaster, bool flag_apply_rtc,
bool flag_az_baseband_doppler, bool flatten,
isce3::io::Raster& demRaster, float shadow_no_data_value,
bool flag_apply_rtc, bool flag_az_baseband_doppler, bool flatten,
isce3::geometry::rtcInputTerrainRadiometry input_terrain_radiometry,
isce3::geometry::rtcOutputTerrainRadiometry output_terrain_radiometry,
float rtc_min_value_db, double rtc_geogrid_upsampling,
Expand Down Expand Up @@ -860,9 +867,10 @@ void Geocode<T>::geocodeInterp(
rdrBlockWidth, rdrBlockLength, azimuthFirstLine,
rangeFirstPixel, interp.get(), radar_grid,
flag_az_baseband_doppler, flatten, phase_screen_raster,
phase_screen_array, rtc_min_value,
phase_screen_array, shadow_no_data_value, rtc_min_value,
abs_cal_factor_effective, clip_min, clip_max,
flag_apply_rtc, rtc_area_array, rtc_area_sigma0_array, out_geo_rtc_band,
flag_apply_rtc, rtc_area_array, rtc_area_sigma0_array,
out_geo_rtc_band,
out_geo_rtc_array, out_geo_rtc_gamma0_to_sigma0_band,
out_geo_rtc_gamma0_to_sigma0_array,
input_layover_shadow_mask_raster,
Expand Down Expand Up @@ -947,7 +955,7 @@ inline void Geocode<T>::_interpolate(
const bool flag_az_baseband_doppler, const bool flatten,
isce3::io::Raster* phase_screen_raster,
isce3::core::Matrix<float>& phase_screen_array,
float rtc_min_value,
float shadow_no_data_value, float rtc_min_value,
double abs_cal_factor_effective,
float clip_min, float clip_max, bool flag_apply_rtc,
const isce3::core::Matrix<float>& rtc_area,
Expand Down Expand Up @@ -1036,6 +1044,21 @@ inline void Geocode<T>::_interpolate(
}

if (flag_has_invalid_sample) {

// set NaN values according to T_out, i.e. real (NaN)
// or complex (NaN, NaN)
T_out v = static_cast<T_out>(shadow_no_data_value);
geoDataBlock(i, j) = v;

if (flag_apply_rtc && out_geo_rtc != nullptr) {
out_geo_rtc_array(i, j) =
std::numeric_limits<float>::quiet_NaN();
}
if (flag_apply_rtc &&
out_geo_rtc_gamma0_to_sigma0 != nullptr) {
out_geo_rtc_gamma0_to_sigma0_array(i, j) =
std::numeric_limits<float>::quiet_NaN();
}
continue;
}
}
Expand Down Expand Up @@ -1866,7 +1889,8 @@ void Geocode<T>::geocodeAreaProj(
const isce3::product::RadarGridParameters& radar_grid,
isce3::io::Raster& input_raster, isce3::io::Raster& output_raster,
isce3::io::Raster& dem_raster, double geogrid_upsampling,
bool flag_upsample_radar_grid, bool flag_apply_rtc,
float shadow_no_data_value, bool flag_upsample_radar_grid,
bool flag_apply_rtc,
isce3::geometry::rtcInputTerrainRadiometry input_terrain_radiometry,
isce3::geometry::rtcOutputTerrainRadiometry output_terrain_radiometry,
float rtc_min_value_db, double rtc_geogrid_upsampling,
Expand Down Expand Up @@ -1910,10 +1934,10 @@ void Geocode<T>::geocodeAreaProj(
const float upsampled_radar_grid_nlooks = radar_grid_nlooks / 2;
geocodeAreaProj<T_out>(upsampled_radar_grid, input_raster,
output_raster, dem_raster, geogrid_upsampling,
flag_upsample_radar_grid, flag_apply_rtc,
input_terrain_radiometry, output_terrain_radiometry,
rtc_min_value_db, rtc_geogrid_upsampling, rtc_algorithm,
rtc_area_beta_mode,
shadow_no_data_value, flag_upsample_radar_grid,
flag_apply_rtc, input_terrain_radiometry,
output_terrain_radiometry, rtc_min_value_db,
rtc_geogrid_upsampling, rtc_algorithm, rtc_area_beta_mode,
abs_cal_factor, clip_min, clip_max, min_nlooks,
upsampled_radar_grid_nlooks, out_off_diag_terms, out_geo_rdr,
out_geo_dem, out_geo_nlooks, out_geo_rtc,
Expand Down Expand Up @@ -2271,7 +2295,8 @@ void Geocode<T>::geocodeAreaProj(
is_radar_grid_single_block, rdrData, block_size_y,
block_size_with_upsampling_y, block_y, block_size_x,
block_size_with_upsampling_x, block_x, numdone,
progress_block, geogrid_upsampling, nbands,
progress_block, geogrid_upsampling,
shadow_no_data_value, nbands,
nbands_off_diag_terms, dem_interp_method, dem_raster,
out_off_diag_terms, out_geo_rdr, out_geo_dem,
out_geo_nlooks, out_geo_rtc,
Expand All @@ -2298,7 +2323,8 @@ void Geocode<T>::geocodeAreaProj(
is_radar_grid_single_block, rdrDataT, block_size_y,
block_size_with_upsampling_y, block_y, block_size_x,
block_size_with_upsampling_x, block_x, numdone,
progress_block, geogrid_upsampling, nbands,
progress_block, geogrid_upsampling,
shadow_no_data_value, nbands,
nbands_off_diag_terms, dem_interp_method, dem_raster,
out_off_diag_terms, out_geo_rdr, out_geo_dem,
out_geo_nlooks, out_geo_rtc,
Expand Down Expand Up @@ -2486,7 +2512,8 @@ void Geocode<T>::_runBlock(
int block_size_y, int block_size_with_upsampling_y, int block_y,
int block_size_x, int block_size_with_upsampling_x, int block_x,
long long& numdone, const long long& progress_block,
double geogrid_upsampling, int nbands, int nbands_off_diag_terms,
double geogrid_upsampling, float shadow_no_data_value,
int nbands, int nbands_off_diag_terms,
isce3::core::dataInterpMethod dem_interp_method,
isce3::io::Raster& dem_raster, isce3::io::Raster* out_off_diag_terms,
isce3::io::Raster* out_geo_rdr, isce3::io::Raster* out_geo_dem,
Expand Down Expand Up @@ -3355,13 +3382,34 @@ void Geocode<T>::_runBlock(
out_mask_array(i, j) = 0;
}

// x, y positions are binned by integer quotient (floor)
const int x = static_cast<int>(j / geogrid_upsampling);
const int y = static_cast<int>(i / geogrid_upsampling);

// ignoring boundary or low-sampled area elements
if (std::isnan(nlooks) || nlooks == 0 ||
nlooks < isce3::core::AREA_PROJECTION_MIN_VALID_SAMPLES_RATIO *
std::abs(w_total) ||
(!std::isnan(min_nlooks) &&
nlooks * radar_grid_nlooks <= min_nlooks))
nlooks * radar_grid_nlooks <= min_nlooks)) {

if (!std::isnan(shadow_no_data_value)) {

T_out v = static_cast<T_out>(shadow_no_data_value);
for (int band = 0; band < nbands; ++band) {
geoDataBlock[band]->operator()(y, x) = v;
}
if (nbands_off_diag_terms > 0) {

T2 v2 = static_cast<T2>(shadow_no_data_value);
for (int band = 0; band < nbands_off_diag_terms; ++band) {
geoDataBlockOffDiag[band]->operator()(y, x) = v2;
}
}
}

continue;
}

/*
If we need to output the mask layer AND the geogrid pixel contains
Expand Down Expand Up @@ -3410,10 +3458,6 @@ void Geocode<T>::_runBlock(
out_geo_rdr_r(i + 1, j + 1) = x11;
}

// x, y positions are binned by integer quotient (floor)
const int x = static_cast<int>(j / geogrid_upsampling);
const int y = static_cast<int>(i / geogrid_upsampling);

if (flag_apply_rtc) {
area_total /= nlooks;
if (out_geo_rtc_gamma0_to_sigma0 != nullptr) {
Expand Down
35 changes: 29 additions & 6 deletions cxx/isce3/geocode/GeocodeCov.h
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,10 @@ class Geocode {
* baseband (using Doppler centroid) before interpolation
* @param[in] flatten Flatten the geocoded SLC
* @param[in] geogrid_upsampling Geogrid upsampling
* @param[in] shadow_no_data_value Value to represent areas without
* valid radar samples. If output is complex (e.g., off-diagonal terms),
* this value will be used for the real-part whereas the imaginary part
* will be set to 0
* @param[in] flag_upsample_radar_grid Double the radar grid sampling rate
* @param[in] flag_apply_rtc Apply radiometric terrain correction
* (RTC)
Expand Down Expand Up @@ -151,6 +155,7 @@ class Geocode {
geocodeOutputMode output_mode = geocodeOutputMode::INTERP,
bool flag_az_baseband_doppler = false, bool flatten = false,
double geogrid_upsampling = 1,
float shadow_no_data_value = std::numeric_limits<float>::quiet_NaN(),
bool flag_upsample_radar_grid = false, bool flag_apply_rtc = false,
isce3::geometry::rtcInputTerrainRadiometry
input_terrain_radiometry = isce3::geometry::
Expand Down Expand Up @@ -222,6 +227,12 @@ class Geocode {
* `abs_cal_factor parameters`, which default to `false` and `1`,
* respectively.
* @param[in] dem_raster Input DEM raster
* @param[in] shadow_no_data_value Value to represent areas without
* valid radar samples. If output is complex (e.g., off-diagonal terms),
* this value will be used for the real-part whereas the imaginary part
* will be set to 0
* @param[in] flag_apply_rtc Apply radiometric terrain correction
* (RTC)
* @param[in] flag_az_baseband_doppler Shift SLC azimuth spectrum to
* baseband (using Doppler centroid) before interpolation
* @param[in] input_terrain_radiometry Input terrain radiometry
Expand Down Expand Up @@ -288,7 +299,9 @@ class Geocode {
template<class T_out>
void geocodeInterp(const isce3::product::RadarGridParameters& radar_grid,
isce3::io::Raster& input_raster, isce3::io::Raster& output_raster,
isce3::io::Raster& dem_raster, bool flag_apply_rtc = false,
isce3::io::Raster& dem_raster,
float shadow_no_data_value = std::numeric_limits<float>::quiet_NaN(),
bool flag_apply_rtc = false,
bool flag_az_baseband_doppler = false, bool flatten = false,
isce3::geometry::rtcInputTerrainRadiometry
input_terrain_radiometry = isce3::geometry::
Expand Down Expand Up @@ -356,6 +369,10 @@ class Geocode {
* respectively.
* @param[in] dem_raster Input DEM raster
* @param[in] geogrid_upsampling Geogrid upsampling
* @param[in] shadow_no_data_value Value to represent areas without
* valid radar samples. If output is complex (e.g., off-diagonal terms),
* this value will be used for the real-part whereas the imaginary part
* will be set to 0
* @param[in] flag_upsample_radar_grid Double the radar grid sampling rate
* @param[in] flag_apply_rtc Apply radiometric terrain correction
* (RTC)
Expand Down Expand Up @@ -433,6 +450,7 @@ class Geocode {
isce3::io::Raster& input_raster, isce3::io::Raster& output_raster,
isce3::io::Raster& dem_raster,
double geogrid_upsampling = 1,
float shadow_no_data_value = std::numeric_limits<float>::quiet_NaN(),
bool flag_upsample_radar_grid = false,
bool flag_apply_rtc = false,
isce3::geometry::rtcInputTerrainRadiometry input_terrain_radiometry =
Expand Down Expand Up @@ -621,7 +639,9 @@ class Geocode {
int block_size_y, int block_size_with_upsampling_y, int block_y,
int block_size_x, int block_size_with_upsampling_x, int block_x,
long long& numdone, const long long& progress_block,
double geogrid_upsampling, int nbands, int nbands_off_diag_terms,
double geogrid_upsampling,
float shadow_no_data_value,
int nbands, int nbands_off_diag_terms,
isce3::core::dataInterpMethod dem_interp_method,
isce3::io::Raster& dem_raster,
isce3::io::Raster* out_off_diag_terms,
Expand Down Expand Up @@ -672,8 +692,11 @@ class Geocode {
* @param[in] flatten flag to flatten the geocoded SLC
* @param[in] phase_screen_raster Phase screen raster
* @param[in] phase_screen_array Phase screen array
* @param[in] rtc_min_value_db Minimum value for the RTC area factor.
* Radar data with RTC area factor below this limit will be set to NaN.
* @param[in] shadow_no_data_value Value to represent areas without
* valid radar samples. If output is complex (e.g., off-diagonal terms),
* this value will be used for the real-part whereas the imaginary part
* will be set to 0
* @param[in] rtc_min_value Minimum value for the RTC area factor.
* @param[in] abs_cal_factor Absolute calibration factor applied
* to real-valued output datasets (assumed to be proportional to
* power/intensity). If the output is complex valued, its considered
Expand Down Expand Up @@ -724,8 +747,8 @@ class Geocode {
const bool flag_az_baseband_doppler, const bool flatten,
isce3::io::Raster* phase_screen_raster,
isce3::core::Matrix<float>& phase_screen_array,
float rtc_min_value, double abs_cal_factor,
float clip_min, float clip_max,
float shadow_no_data_value, float rtc_min_value,
double abs_cal_factor, float clip_min, float clip_max,
bool flag_run_rtc, const isce3::core::Matrix<float>& rtc_area,
const isce3::core::Matrix<float>& rtc_area_sigma,
isce3::io::Raster* out_geo_rtc,
Expand Down
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