Fix copy of the HDF5 group geolocationGrid (#775)

* add option to update scales list when copying HDF5 datasets

* update h5_prep geolocationGrid copy using cp_h5_meta_data() with new attach_scales_list parameter

* update copy of the group geolocationGrid for L1 and L2 products

* rename output dataset zeroDopplerTime to zeroDopplerAzimuthTime

* substitute coordiantes with coordinates

* Update python/packages/pybind_nisar/workflows/h5_prep.py

Co-Authored-By: Liang Yu <[email protected]>

* simplify test for re-attaching HDF5 coordinates

Co-authored-by: Liang Yu <[email protected]>

Author: 2 people

cxx/isce3/geocode/GeocodePolygon.cpp

@@ -27,7 +27,7 @@ GeocodePolygon<T>::GeocodePolygon(
     pyre::journal::info_t _info("isce.geometry.GeocodePolygon");
 
     if (x_vect.size() != y_vect.size()) {
-        std::string error_msg = "ERROR number of X- and Y-coordiantes"
+        std::string error_msg = "ERROR number of X- and Y-coordinates"
                                 " do not match: " + std::to_string(x_vect.size()) +
                                 " != " + std::to_string(y_vect.size());
         throw isce3::except::InvalidArgument(ISCE_SRCINFO(), error_msg);

cxx/isce3/geometry/boundingbox.h

@@ -31,7 +31,7 @@ namespace isce3{
     * @param[in] numiter       Max number of iterations for convergence
     *
     * The outputs of this method is an OGRLinearRing.
-    * Transformer from radar geometry coordinates to map coordiantes with a DEM
+    * Transformer from radar geometry coordinates to map coordinates with a DEM
     * The sequence of walking the perimeter is always in the following order :
     * <ul>
     * <li> Start at Early Time, Near Range edge. Always the first point of the polygon.

doc/sphinx/geometry/getGeoPerimeter.rst

@@ -5,7 +5,7 @@
 getGeoPerimeter
 ==================
 
-This is an extension of Rdr2Geo but only performs the transformation of radar coordiantes to 
+This is an extension of Rdr2Geo but only performs the transformation of radar coordinates to 
 map cordinates at the edges of the swath and returns a GeoJson string representing the Perimeter
 of the radar grid. The Geojson form allows one to use the result directly with other GIS software
 and REST interfaces.

python/packages/pybind_nisar/h5/bulk.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3 #
 
 def cp_h5_meta_data(src_h5, dst_h5, src_path, dst_path=None,
-        excludes=None, renames=None, flag_overwrite=False): 
+        excludes=None, renames=None, flag_overwrite=False,
+        attach_scales_list = None): 
     '''
     Copy HDF5 node contents
 
@@ -21,6 +22,12 @@ def cp_h5_meta_data(src_h5, dst_h5, src_path, dst_path=None,
     renames : dict of (str, str), optional
         Dict where keys are source node names and vales
         are destination node names
+    flag_overwrite :  bool, optional
+        If flag_overwrite, delete existing dataset
+    attach_scales_list : list, optional
+        List of new dimensions (scales) to overwrite
+        existing dimensions attributes in destination
+        datasets
     '''
 
     import h5py
@@ -42,7 +49,8 @@ def cp_h5_meta_data(src_h5, dst_h5, src_path, dst_path=None,
     if dst_parent_path not in dst_h5:
         dst_h5.create_group(dst_parent_path)
 
-    if excludes or renames:
+    if excludes or renames or attach_scales_list is not None:
+
         # copy dataset piecemeal from src_h5:src_path to dst_h5:dst_path
         # create dst_path if needed
         if dst_path not in dst_h5:
@@ -60,12 +68,17 @@ def cp_h5_meta_data(src_h5, dst_h5, src_path, dst_path=None,
             src_sub_path = os.path.join(src_path, subnode_src)
             node_obj = src_h5[src_sub_path]
 
-            # if flag_overwrite, delete exising dataset
+            # if flag_overwrite, delete existing dataset
             if flag_overwrite and subnode_dst in dst_group:
                 del dst_group[subnode_dst]
 
             # copy group/dataset
             dst_group.copy(node_obj, subnode_dst)
+            if (attach_scales_list is not None and 
+                    'DIMENSION_LIST' in node_obj.attrs.keys()):
+                dst_group[subnode_dst].attrs.__delitem__('DIMENSION_LIST')
+                for i, dim in enumerate(attach_scales_list):
+                    dst_group[subnode_dst].dims[i].attach_scale(dim)
     else:
         dst_group = dst_h5[dst_parent_path]
 

python/packages/pybind_nisar/workflows/h5_prep.py

@@ -147,20 +147,31 @@ def cp_geocode_meta(cfg, output_hdf5, dst):
         if is_geocoded:
             cp_h5_meta_data(src_h5, dst_h5, f'{src_meta_path}/attitude',
                             f'{dst_meta_path}/attitude')
-            if dst not in ['GCOV', 'GSLC']:
+            if dst != 'GCOV':
                 # the lines below should be deleted after radar-grid
                 # cubes are added to all L2 workflows
+                yds = dst_h5.create_dataset(f'{dst_meta_path}/radarGrid/yCoordinates',
+                    data = src_h5[f'{src_meta_path}/geolocationGrid/zeroDopplerTime'])                 
+                xds = dst_h5.create_dataset(f'{dst_meta_path}/radarGrid/xCoodinates',
+                    data = src_h5[f'{src_meta_path}/geolocationGrid/slantRange'])
                 cp_h5_meta_data(src_h5, dst_h5,
                                 f'{src_meta_path}/geolocationGrid',
                                 f'{dst_meta_path}/radarGrid',
-                                renames={'coordinateX': 'xCoordinates',
-                                         'coordinateY': 'yCoordinates',
-                                         'zeroDopplerTime': 'zeroDopplerAzimuthTime'})
+                                renames={'coordinateX': 'slantRange',
+                                         'coordinateY': 'zeroDopplerAzimuthTime'},
+                                excludes=['slantRange', 'zeroDopplerTime'],
+                                attach_scales_list = [yds, xds])
         else:
             # RUNW and RIFG have no attitude group and have geolocation grid
+            yds = dst_h5.create_dataset(f'{dst_meta_path}/geolocationGrid/zeroDopplerTime',
+                    data = src_h5[f'{src_meta_path}/geolocationGrid/zeroDopplerTime'])                 
+            xds = dst_h5.create_dataset(f'{dst_meta_path}/geolocationGrid/slantRange',
+                    data = src_h5[f'{src_meta_path}/geolocationGrid/slantRange'])
             cp_h5_meta_data(src_h5, dst_h5,
                             f'{src_meta_path}/geolocationGrid',
-                            f'{dst_meta_path}/geolocationGrid')
+                            f'{dst_meta_path}/geolocationGrid',
+                            excludes=['zeroDopplerTime', 'slantRange'],
+                            attach_scales_list = [yds, xds])
 
         # copy processingInformation/algorithms group (common across products)
         cp_h5_meta_data(src_h5, dst_h5,