From 5acd7c4a4d89a3efa41646172973280038d65899 Mon Sep 17 00:00:00 2001 From: Xiaodong Huang Date: Tue, 12 Nov 2024 22:51:12 +0000 Subject: [PATCH 1/2] upoad the nisar l2 cube interpolator --- nisar_l2_cube_interpolator/README.md | 3 + nisar_l2_cube_interpolator/environment.yml | 15 + nisar_l2_cube_interpolator/pyproject.toml | 43 ++ .../src/nisar_l2_cube_interpolator.py | 426 ++++++++++++++++++ 4 files changed, 487 insertions(+) create mode 100644 nisar_l2_cube_interpolator/README.md create mode 100644 nisar_l2_cube_interpolator/environment.yml create mode 100644 nisar_l2_cube_interpolator/pyproject.toml create mode 100644 nisar_l2_cube_interpolator/src/nisar_l2_cube_interpolator.py diff --git a/nisar_l2_cube_interpolator/README.md b/nisar_l2_cube_interpolator/README.md new file mode 100644 index 0000000..4042ee4 --- /dev/null +++ b/nisar_l2_cube_interpolator/README.md @@ -0,0 +1,3 @@ +# nisar_l2_cube_interpolator + +A python script to interpolate the NISAR L2 products metadata cube \ No newline at end of file diff --git a/nisar_l2_cube_interpolator/environment.yml b/nisar_l2_cube_interpolator/environment.yml new file mode 100644 index 0000000..a6ed6b2 --- /dev/null +++ b/nisar_l2_cube_interpolator/environment.yml @@ -0,0 +1,15 @@ +name: nisar_l2_cube +channels: + - conda-forge + - defaults + +dependencies: + - python + - h5py + - libgdal-netcdf + - gdal + - libgdal-hdf5 + - numpy + - scipy + - rasterio + - pip \ No newline at end of file diff --git a/nisar_l2_cube_interpolator/pyproject.toml b/nisar_l2_cube_interpolator/pyproject.toml new file mode 100644 index 0000000..6ee026d --- /dev/null +++ b/nisar_l2_cube_interpolator/pyproject.toml @@ -0,0 +1,43 @@ +[build-system] +requires = [ + "setuptools", + "gdal", + "h5py", + "numpy", + "scipy", + "rasterio", +] +build-backend = "setuptools.build_meta" + +[project] +name = "nisar_l2_cube_interpolator" +requires-python = ">=3.10" + +description = "NISAR L2 3D metadata datacube interpolator" + +# README format is auto-detected from the extension as GitHub-flavored Markdown +readme = "README.md" + +authors = [ + { name = "Xiaodong Huang", email = "xiaodong.huang@jpl.nasa.gov" }, +] + +dependencies = [ + "python", + "h5py", + "gdal", + "numpy", + "scipy", + "rasterio", +] + +dynamic = ["version"] + +[tool.setuptools.dynamic] +version = {attr = "nisar_l2_cube_interpolator.__version__"} + +[tool.setuptools.packages.find] +where = ["src"] + +[project.scripts] +nisarqa = "nisar_l2_cube_interpolator.__main__:main" \ No newline at end of file diff --git a/nisar_l2_cube_interpolator/src/nisar_l2_cube_interpolator.py b/nisar_l2_cube_interpolator/src/nisar_l2_cube_interpolator.py new file mode 100644 index 0000000..3e5101a --- /dev/null +++ b/nisar_l2_cube_interpolator/src/nisar_l2_cube_interpolator.py @@ -0,0 +1,426 @@ + +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on 10/23/2024 + +@author: Xiaodong Huang @JPL Caltech +""" + +import argparse +import os +import time +import warnings + +import h5py +import numpy as np +import rasterio +from osgeo import gdal, osr +from rasterio.coords import BoundingBox +from rasterio.warp import transform_bounds +from scipy.interpolate import RegularGridInterpolator + +# GCOV datasets in its radar grid datacube +GCOV_RADAR_GRID_DATASETS = ['alongTrackUnitVectorX', + 'alongTrackUnitVectorY', + 'elevationAngle', + 'groundTrackVelocity', + 'incidenceAngle', + 'losUnitVectorX', + 'losUnitVectorY', + 'zeroDopplerAzimuthTime', + 'slantRange'] + +# GSLC datasets in its radar grid datacube +GSLC_RADAR_GRID_DATASETS = GCOV_RADAR_GRID_DATASETS + +# GOFF datasets in its radar grid datacube +GOFF_RADAR_GRID_DATASETS = \ + GCOV_RADAR_GRID_DATASETS[:-2] + ['parallelBaseline', + 'perpendicularBaseline', + 'referenceSlantRange', + 'referenceZeroDopplerAzimuthTime', + 'secondarySlantRange', + 'secondaryZeroDopplerAzimuthTime'] + +# GUNW datasets in its radar grid datacube +GUNW_RADAR_GRID_DATASETS = \ + GOFF_RADAR_GRID_DATASETS + ['hydrostaticTroposphericPhaseScreen', + 'wetTroposphericPhaseScreen', + 'combinedTroposphericPhaseScreen', + 'slantRangeSolidEarthTidesPhase'] + +def get_parser(): + ''' + Command line parser. + ''' + descr = 'Interpolate the NISAR L2 3D metadata datacube' + parser = argparse.ArgumentParser(description=descr) + + parser.add_argument(type=str, + dest='input_file', + help='Input NISAR L2 file') + + parser.add_argument('--dem', + '--dem-file', + dest='input_dem_file', + required=True, + type=str, + help='Reference DEM file') + + parser.add_argument('--out', + '--output', + dest='output_file', + type=str, + required=True, + help='Output file of the interplated 2D dataset') + + parser.add_argument('--frequency', + '--freq', + type=str, + default='A', + dest='frequency', + choices=['A', 'B'], + help='Frequency band, default: A') + + parser.add_argument('--polarization', + '--pol', + type=str, + default='HH', + dest='polarization', + choices=['HH', 'HV', 'VH', 'VV'], + help='Polarizations, default: HH') + + parser.add_argument('--cube-interp-method', + dest='cube_interp_method', + type=str, + default='linear', + choices=['linear', 'nearest', 'slinear', 'cubic', + 'quintic', 'pchip'], + help='Datacube interpolation method' + ' of the python RegularGridInterpolator, default: linear') + + parser.add_argument('--dem-resample-method', + dest='dem_resample_method', + type=str, + default='cubicspline', + choices=['near', 'bilinear', 'cubic', 'cubicspline', + 'lanczos', 'average','med'], + help='DEM interpolation method, default: cubicspline') + + parser.add_argument('--out-resampled-dem', + '--out-dem', + type=str, + default=None, + dest='out_resampled_dem', + help='Output of the resampled dem, default: None') + + parser.add_argument('--out-format', + dest='out_format', + default='GTiff', + help="The raster format of the output," + " must be the GDAL supported raster format, default: GTiff") + + parser.add_argument('--force-resample-dem', + action='store_true', + dest='force_resample_dem', + help='Force resample dem') + + parser.add_argument('--gunw-ds-name', + dest='gunw_dataset_name', + default='unwrappedInterferogram', + choices=['unwrappedInterferogram', + 'wrappedInterferogram', + 'pixelOffsets'], + help='GUNW dataset names, default: unwrappedInterferogram') + + parser.add_argument('--cube-ds-name', + dest='cube_dataset_name', + required=True, + default='incidenceAngle', + choices=GUNW_RADAR_GRID_DATASETS + ['zeroDopplerAzimuthTime', + 'slantRange'], + help='3D metadata datacube names') + return parser.parse_args() + + +def compute_coverage_area(dem_bounds, ds_bounds): + x_min = max(dem_bounds.left, ds_bounds.left) + y_min = max(dem_bounds.bottom, ds_bounds.bottom) + x_max = min(dem_bounds.right, ds_bounds.right) + y_max = min(dem_bounds.top, ds_bounds.top) + + if x_min < x_max and y_min < y_max: + return (x_max - x_min) * (y_max - y_min) / \ + ((ds_bounds.right - ds_bounds.left)*\ + (ds_bounds.top - ds_bounds.bottom)) * 100.0 + else: + return 0.0 + +def resample_dem(input_dem_path, + out_epsg, + out_start_x, + out_start_y, + out_spacing_x, + out_spacing_y, + out_length, + out_width, + force_resample = False, + dem_resample_method = 'cubicspline', + out_path = None): + + # Check the DEM coverage over the dataset + # raise warning if the coverage is less than 100.0 + with rasterio.open(input_dem_path) as src: + dem_bounds = src.bounds + original_crs = src.crs + target_crs = f'EPSG:{out_epsg}' + + # DEM bounds to the target CRS + dem_bounds = \ + transform_bounds(original_crs, target_crs, + dem_bounds.left, dem_bounds.bottom, + dem_bounds.right, dem_bounds.top) + dem_bounds = BoundingBox(left = dem_bounds[0], + bottom = dem_bounds[1], + right = dem_bounds[2], + top = dem_bounds[3]) + # the dataset bounds + ds_bounds = BoundingBox(left=out_start_x, + bottom=out_start_y + out_length * out_spacing_y, + right=out_start_x + out_width * out_spacing_x, + top=out_start_y) + coverage_area = round(compute_coverage_area(dem_bounds, ds_bounds),2) + if coverage_area < 100.0: + warnings.warn( + f"DEM only covers {coverage_area}% of the dataset!", + UserWarning) + + # If the DEM exists and the resample is not forced, + # then read it from the existing file + if ((out_path is not None) and + (os.path.exists(out_path)) and + (not force_resample)): + des = gdal.Open(out_path) + band = des.GetRasterBand(1) + resampled_dem = band.ReadAsArray() + else: + # Resample the DEM using GDALWarp + input_raster = gdal.Open(input_dem_path) + output_extent = (out_start_x, + out_start_y + out_length * out_spacing_y, + out_start_x + out_width * out_spacing_x, + out_start_y) + + gdalwarp_options = gdal.WarpOptions(format="MEM", + outputType = gdal.GDT_Float32, + dstSRS=f"EPSG:{out_epsg}", + xRes=out_spacing_x, + yRes=np.abs(out_spacing_y), + resampleAlg=dem_resample_method, + outputBounds=output_extent) + + dst_ds = gdal.Warp("", input_raster, options=gdalwarp_options) + resampled_dem = dst_ds.ReadAsArray() + + # Save to the harddrive if the out_path is not None + if out_path is not None: + driver = gdal.GetDriverByName('GTiff') + data_type = gdal.GDT_Float32 + des = driver.Create(out_path, out_width, out_length, 1, data_type) + + # Write data to the hard drive + band = des.GetRasterBand(1) + band.WriteArray(resampled_dem) + + # Set the geotransform + geotransform = (out_start_x, out_spacing_x, 0, + out_start_y, 0, out_spacing_y) + des.SetGeoTransform(geotransform) + + # Set the projection + srs = osr.SpatialReference() + srs.ImportFromEPSG(out_epsg) + des.SetProjection(srs.ExportToWkt()) + + return resampled_dem + + +def interpolate_L2_datacube(nisar_L2_product_path, + dem_path, + cube_ds_name, + out_ds_path, + cube_interp_method = 'linear', + gunw_geogrid_ds_name = None, + frequency = 'A', + polarization = 'HH', + force_resample_dem = False, + dem_resample_method = 'cubicspline', + out_dem_file = None, + out_format = "GTiff"): + """ + Interpolate the 3D metadata datacube in the NISAR L2 product + """ + + with h5py.File(nisar_L2_product_path) as f: + # get the product type in the HDF5, and it must be + # 'GCOV', 'GSLC', 'GUNW', or 'GOFF' + product_type = f['science/LSAR/identification/productType'][()].astype(str) + if product_type not in ['GCOV', 'GSLC', 'GUNW', 'GOFF']: + err_str = f'Product type {product_type} is not supproted' + raise ValueError(err_str) + + # Check the cube dataset name in the radar grid metadata cube + if product_type == 'GCOV': + if cube_ds_name not in GCOV_RADAR_GRID_DATASETS: + err_str = f"{product_type} does not have {cube_ds_name} in its datacube," + " please pick up one of:\n"+\ + ','.join(GCOV_RADAR_GRID_DATASETS) + raise ValueError(err_str) + elif product_type == 'GSLC': + if cube_ds_name not in GSLC_RADAR_GRID_DATASETS: + err_str = f"{product_type} does not have {cube_ds_name} in its datacube," + " please pick up one of:\n"+\ + ','.join(GSLC_RADAR_GRID_DATASETS) + raise ValueError(err_str) + elif product_type == 'GOFF': + if cube_ds_name not in GOFF_RADAR_GRID_DATASETS: + err_str = f"{product_type} does not have {cube_ds_name} in its datacube," + " please pick up one of:\n"+\ + ','.join(GOFF_RADAR_GRID_DATASETS) + raise ValueError(err_str) + elif product_type == 'GUNW': + if cube_ds_name not in GUNW_RADAR_GRID_DATASETS: + err_str = f"{product_type} does not have {cube_ds_name} in its datacube," + " please pick up one of:\n"+\ + ','.join(GUNW_RADAR_GRID_DATASETS) + raise ValueError(err_str) + + # Get the X, Y, and Z coordindates of the datacube + xcoords = f[f'/science/LSAR/{product_type}' + '/metadata/radarGrid/xCoordinates'][()] + ycoords = f[f'/science/LSAR/{product_type}' + '/metadata/radarGrid/yCoordinates'][()] + zcoords = f[f'/science/LSAR/{product_type}' + '/metadata/radarGrid/heightAboveEllipsoid'][()] + + # Get the datacube datataset + ds_name = f'/science/LSAR/{product_type}/metadata/radarGrid/{cube_ds_name}' + if ds_name not in f: + err_str = f'{ds_name} is not in the radar grid metadata cube of {product_type}' + raise ValueError(err_str) + + # cube dataset + ds_cube = f[ds_name][()] + + # Build the regular grid interpolator + # and check the first dimension since the Baseline top/bottom mode only has 2 heights + ds_cube_shape = ds_cube.shape + if ds_cube_shape[0] == 2: + interplator = RegularGridInterpolator( + (np.array([zcoords[0], zcoords[-1]]), + ycoords, xcoords), ds_cube, method = cube_interp_method) + else: + interplator = RegularGridInterpolator( + (zcoords, ycoords, xcoords),ds_cube, method = cube_interp_method) + + # Get the geogrid of the product in the L2 product and check if + # the frequency is in the product + group_name = f'/science/LSAR/{product_type}/grids/frequency{frequency}/' + if group_name not in f: + err_str = f'Frequency {frequency} is not in the product' + raise ValueError(err_str) + + out_epsg = 4326 + if product_type == 'GUNW': + if gunw_geogrid_ds_name is None: + gunw_ds_name = 'unwrappedInterferogram' + else: + gunw_ds_name = gunw_geogrid_ds_name + ds_x = f[f'{group_name}/{gunw_ds_name}/{polarization}/xCoordinates'][()] + ds_y = f[f'{group_name}/{gunw_ds_name}/{polarization}/yCoordinates'][()] + out_epsg = int(f[f'{group_name}/{gunw_ds_name}/{polarization}/projection'][()]) + elif product_type == 'GOFF': + ds_x = f[f'{group_name}/pixelOffsets/{polarization}/layer1/xCoordinates'][()] + ds_y = f[f'{group_name}/pixelOffsets/{polarization}/layer1/yCoordinates'][()] + out_epsg = int(f[f'{group_name}/pixelOffsets/{polarization}/layer1/projection'][()]) + else: + ds_x = f[f'{group_name}/xCoordinates'][()] + ds_y = f[f'{group_name}/yCoordinates'][()] + out_epsg = int(f[f'{group_name}/projection'][()]) + + # Resample the DEM to be the same geogrid with the dataset + ds_dem_data = resample_dem(dem_path, out_epsg, + ds_x[0], ds_y[0], + ds_x[1] - ds_x[0], + ds_y[1] - ds_y[0], + len(ds_y), len(ds_x), + force_resample_dem, + dem_resample_method, + out_dem_file) + + # Build the meshgrid for the interpolator + y, x = np.meshgrid(ds_y, ds_x, + indexing='ij') + pts = np.stack([ds_dem_data.ravel(), + y.ravel(), + x.ravel()]).T + + # Interpolating the points + interp_pts = interplator(pts) + group_name = \ + f"NETCDF:{nisar_L2_product_path}://science/LSAR/{product_type}/grids/frequency{frequency}" + if product_type == 'GCOV': + src = rasterio.open(f"{group_name}/{[polarization]*2}", + driver = 'netCDF') + if product_type == 'GSLC': + src = rasterio.open(f"{group_name}/{polarization}", + driver = 'netCDF') + if product_type == 'GUNW': + if ((gunw_geogrid_ds_name is None) or + (gunw_geogrid_ds_name == 'unwrappedInterferogram')): + gunw_ds_name = f'{gunw_geogrid_ds_name}/{polarization}/coherenceMagnitude' + elif gunw_geogrid_ds_name == 'wrappedInterferogram': + gunw_ds_name = f'{gunw_geogrid_ds_name}/{polarization}/coherenceMagnitude' + elif gunw_geogrid_ds_name == 'pixelOffsets': + gunw_ds_name = f'{gunw_geogrid_ds_name}/{polarization}/alongTrackOffset' + src = rasterio.open(f"{group_name}/{gunw_ds_name}", + driver = 'netCDF') + if product_type == 'GOFF': + src = rasterio.open( + f"{group_name}/pixelOffsets/{polarization}/layer1/alongTrackOffset", + driver = 'netCDF') + + # Write the data to the harddrive + out_meta = src.meta.copy() + out_meta.update({"driver": out_format, + "height": src.shape[0], + "width": src.shape[1], + "dtype": 'float32', + 'nodata': 0.0, + }) + + with rasterio.open(out_ds_path, "w", **out_meta) as dest: + dest.write(interp_pts.reshape(src.shape),1) + +def main(): + parser = get_parser() + t_all = time.time() + interpolate_L2_datacube(parser.input_file, + parser.input_dem_file, + parser.cube_dataset_name, + parser.output_file, + parser.cube_interp_method, + parser.gunw_dataset_name, + parser.frequency, + parser.polarization, + parser.force_resample_dem, + parser.dem_resample_method, + parser.out_resampled_dem, + parser.out_format) + t_all_elapsed = time.time() - t_all + print(f"Successfully ran the {parser.cube_dataset_name}" + f" interpolation in {t_all_elapsed:.3f} seconds") + +if __name__ == "__main__": + main() \ No newline at end of file From 6750c20fcd705adea956909613c65d4c4a79df8e Mon Sep 17 00:00:00 2001 From: Xiaodong Huang Date: Tue, 12 Nov 2024 22:58:25 +0000 Subject: [PATCH 2/2] remove the pyproject.toml --- nisar_l2_cube_interpolator/pyproject.toml | 43 ----------------------- 1 file changed, 43 deletions(-) delete mode 100644 nisar_l2_cube_interpolator/pyproject.toml diff --git a/nisar_l2_cube_interpolator/pyproject.toml b/nisar_l2_cube_interpolator/pyproject.toml deleted file mode 100644 index 6ee026d..0000000 --- a/nisar_l2_cube_interpolator/pyproject.toml +++ /dev/null @@ -1,43 +0,0 @@ -[build-system] -requires = [ - "setuptools", - "gdal", - "h5py", - "numpy", - "scipy", - "rasterio", -] -build-backend = "setuptools.build_meta" - -[project] -name = "nisar_l2_cube_interpolator" -requires-python = ">=3.10" - -description = "NISAR L2 3D metadata datacube interpolator" - -# README format is auto-detected from the extension as GitHub-flavored Markdown -readme = "README.md" - -authors = [ - { name = "Xiaodong Huang", email = "xiaodong.huang@jpl.nasa.gov" }, -] - -dependencies = [ - "python", - "h5py", - "gdal", - "numpy", - "scipy", - "rasterio", -] - -dynamic = ["version"] - -[tool.setuptools.dynamic] -version = {attr = "nisar_l2_cube_interpolator.__version__"} - -[tool.setuptools.packages.find] -where = ["src"] - -[project.scripts] -nisarqa = "nisar_l2_cube_interpolator.__main__:main" \ No newline at end of file