merge again

isce2_topsapp/__main__.py

@@ -221,11 +221,14 @@ def gunw_slc():
         additional_attributes.append(iono_attr['ionosphere'])
         additional_2d_layers.append("ionosphereBurstRamps")
         additional_attributes.append(iono_attr['ionosphereBurstRamps'])
+        additional_2d_layers.append('ionosphere')
+    if args.unfiltered_coherence:
+        additional_2d_layers.append('unfilteredCoherence')
 
     additional_2d_layers = additional_2d_layers or None
 
     custom_event_product = False
-
+    # TODO - figure out CUSTOM determination
     nc_path = package_gunw_product(
         isce_data_directory=Path.cwd(),
         reference_properties=ref_properties,

isce2_topsapp/packaging.py

@@ -220,7 +220,7 @@ def perform_netcdf_packaging(*,
     subprocess.check_call(cmd, shell=True)
     os.chdir(cwd)
 
-    out_nc_file = merged_dir/f'{gunw_id}.nc'
+    out_nc_file = merged_dir / f'{gunw_id}.nc'
 
     # Check if the netcdf file was created
     assert out_nc_file.exists()
@@ -235,10 +235,6 @@ def package_additional_layers_into_gunw(gunw_path: Path,
     # 1. Do any additional processing/formatting outside of GUNW
     # 2. Add layer into GUNW
     # 3. Update Version
-    if not set(additional_2d_layers).issubset(set(PERMISSIBLE_2D_LAYERS)):
-        raise RuntimeError('Additional 2d layers must be subset of '
-                           f'{PERMISSIBLE_2D_LAYERS}')
-
     if 'ionosphere' in additional_2d_layers:
         # current working directory is ISCE directory
         _ = format_ionosphere_for_gunw(isce_data_directory, gunw_path)

isce2_topsapp/packaging_utils/additional_layers.json

@@ -7,6 +7,7 @@
                 "attrs": {
                         "standard_name": "ionospherePhaseCorrection",
                         "long_name": "ionospherePhaseCorrection",
+                        "units": "rad",
                         "description": "Estimated ionosphere phase correction"
                 }
         },

isce2_topsapp/packaging_utils/additional_layers.py

@@ -5,38 +5,46 @@
 import xarray as xr
 
 LAYER_JSON = Path(__file__).parents[0] / 'additional_layers.json'
-ADDITIONAL_LAYERS = json.load(open(LAYER_JSON))
+ADDITIONAL_LAYERS_DATA = json.load(open(LAYER_JSON))
 
 
 def add_2d_layer(layer_name: str,
                  gunw_netcdf_path: Path,
                  additional_attrs: dict = None) -> Path:
     """
     Combines a lot of standard formatting of the netcdf via rioxarray and
-    deletes the previous placeholder (we assume it exists via the placeholder).
+    deletes the previous placeholder if there is one.
 
-    We also assume any additional processing specific to GUNW is done outside of
+    We assume any additional processing specific to GUNW is done outside of
     this function.
     """
 
-    layer_data = ADDITIONAL_LAYERS[layer_name]
+    layer_data = ADDITIONAL_LAYERS_DATA[layer_name]
 
     dst_group = layer_data['dst_group']
     dst_variable = layer_data['dst_variable']
     band_number = layer_data['src_band_number']
-    if not isinstance(band_number, int) or (band_number < 0):
+    possible_layers = list(ADDITIONAL_LAYERS_DATA.keys())
+
+    if layer_name not in possible_layers:
+        ValueError('layer_name must be in {", ".join(possible_layers)}')
+
+    if not isinstance(band_number, int) or (band_number < 1):
         ValueError('Layers must select individual layers from outputs i.e '
                    '1, 2, ...')
     if additional_attrs:
         layer_data['attrs'].update(additional_attrs)
 
-    # The layers generally already exist within the file
+    # If the layers already exist within the file, we need to delete them otherwise the dummy placeholder
+    # Causes type errors when attempting to overwrite
     with h5py.File(gunw_netcdf_path, mode='a') as file:
         if dst_group in file:
             # Delete the variable to be written to
             if dst_variable in file[dst_group]:
                 del file[dst_group][dst_variable]
-            # Delete the group if there are no variables left
+            # Delete the group if there are no variables left to ensure correct type of arrays.
+            # If there are variables left, this routine appends the new array to the group (assumes same dims
+            # as existing arrays)
             if len(file[dst_group].keys()) == 0:
                 del file[dst_group]
 

isce2_topsapp/packaging_utils/ionosphere.py

@@ -8,6 +8,19 @@
 
 def format_ionosphere_for_gunw(isce_directory: Path,
                                gunw_netcdf_path: Path) -> Path:
+    """Resamples the ionosphere to approximately 1 km using origin of product
+
+    Parameters
+    ----------
+    isce_directory : Path
+        The so-called "scratch" directory
+    gunw_netcdf_path : Path
+
+    Returns
+    -------
+    Path
+        gunw_path
+    """
     with rasterio.open(isce_directory / "merged/topophase.ion.geo") as ds:
         X_ion = ds.read(1)
         p_ion = ds.profile

isce2_topsapp/topsapp_proc.py

@@ -49,7 +49,7 @@ def topsapp_processing(*,
                        esd_coherence_threshold: float = .7,
                        output_resolution: int = 90,
                        do_dense_offsets: bool = False,
-                       ampcor_window_size=16):
+                       ampcor_window_size: int = 64):
     swaths = swaths or [1, 2, 3]
     # for [ymin, ymax, xmin, xmax]
     extent_isce = [extent[k] for k in [1, 3, 0, 2]]
@@ -75,6 +75,9 @@ def topsapp_processing(*,
     if estimate_ionosphere_delay:
         geocode_list.append('merged/topophase.ion')
 
+    if do_dense_offsets:
+        geocode_list.append('merged/dense_offsets.bil')
+
     topsApp_xml = template.render(orbit_directory=orbit_directory,
                                   output_reference_directory='reference',
                                   output_secondary_directory='secondary',