Update GCOV and GSLC writer to geocode the inputDataExceptionMask (UInt16) dataset

python/packages/nisar/products/XML/L2/nisar_L2_GCOV.xml

@@ -367,12 +367,29 @@
         <integer name="/science/LSAR/GCOV/grids/frequencyA/inputDataExceptionMask"
               shape="realDataFrequencyAShape"
               signed="false"
-              width="8">
+              width="16">
           <annotation app="conformance"
                       lang="en"
                       DIMENSION_LIST="HDF5 internal attribute"
                       valid_min="0"
-                      grid_mapping="projection">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip)</annotation>
+                      _FillValue="65535"
+                      rslcValidPixelFractionHH="Ratio of fully focused pixels to total number of pixels in the input RSLC HH mask"
+                      rawValidPulseFractionHH="Ratio of valid pulse count to total pulses required to form the input RSLC HH image"
+                      rslcValidPixelFractionHV="Ratio of fully focused pixels to total number of pixels in the input RSLC HV mask"
+                      rawValidPulseFractionHV="Ratio of valid pulse count to total pulses required to form the input RSLC HV image"
+                      rslcValidPixelFractionVH="Ratio of fully focused pixels to total number of pixels in the input RSLC VH mask"
+                      rawValidPulseFractionVH="Ratio of valid pulse count to total pulses required to form the input RSLC VH image"
+                      rslcValidPixelFractionVV="Ratio of fully focused pixels to total number of pixels in the input RSLC VV mask"
+                      rawValidPulseFractionVV="Ratio of valid pulse count to total pulses required to form the input RSLC VV image"
+                      rslcValidPixelFractionRH="Ratio of fully focused pixels to total number of pixels in the input RSLC RH mask"
+                      rawValidPulseFractionRH="Ratio of valid pulse count to total pulses required to form the input RSLC RH image"
+                      rslcValidPixelFractionRV="Ratio of fully focused pixels to total number of pixels in the input RSLC RV mask"
+                      rawValidPulseFractionRV="Ratio of valid pulse count to total pulses required to form the input RSLC RV image"
+                      rslcValidPixelFractionLH="Ratio of fully focused pixels to total number of pixels in the input RSLC LH mask"
+                      rawValidPulseFractionLH="Ratio of valid pulse count to total pulses required to form the input RSLC LH image"
+                      rslcValidPixelFractionLV="Ratio of fully focused pixels to total number of pixels in the input RSLC LV mask"
+                      rawValidPulseFractionLV="Ratio of valid pulse count to total pulses required to form the input RSLC LV image"
+                      grid_mapping="projection">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip). Also includes OR of validity mask bits, where each bit is set on for fully-focused data or off for partially focused or missing data (256:HH, 512:HV, 1024:VH, 2048:VV, 4096:LH, 8192:LV, 16384:RH, 32768:RV)</annotation>
         </integer>
         <real name="/science/LSAR/GCOV/grids/frequencyA/HHHH"
               shape="realDataFrequencyAShape"
@@ -782,12 +799,29 @@
         <integer name="/science/LSAR/GCOV/grids/frequencyB/inputDataExceptionMask"
               shape="realDataFrequencyBShape"
               signed="false"
-              width="8">
+              width="16">
           <annotation app="conformance"
                       lang="en"
                       DIMENSION_LIST="HDF5 internal attribute"
                       valid_min="0"
-                      grid_mapping="projection">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip)</annotation>
+                      _FillValue="65535"
+                      rslcValidPixelFractionHH="Ratio of fully focused pixels to total number of pixels in the input RSLC HH mask"
+                      rawValidPulseFractionHH="Ratio of valid pulse count to total pulses required to form the input RSLC HH image"
+                      rslcValidPixelFractionHV="Ratio of fully focused pixels to total number of pixels in the input RSLC HV mask"
+                      rawValidPulseFractionHV="Ratio of valid pulse count to total pulses required to form the input RSLC HV image"
+                      rslcValidPixelFractionVH="Ratio of fully focused pixels to total number of pixels in the input RSLC VH mask"
+                      rawValidPulseFractionVH="Ratio of valid pulse count to total pulses required to form the input RSLC VH image"
+                      rslcValidPixelFractionVV="Ratio of fully focused pixels to total number of pixels in the input RSLC VV mask"
+                      rawValidPulseFractionVV="Ratio of valid pulse count to total pulses required to form the input RSLC VV image"
+                      rslcValidPixelFractionRH="Ratio of fully focused pixels to total number of pixels in the input RSLC RH mask"
+                      rawValidPulseFractionRH="Ratio of valid pulse count to total pulses required to form the input RSLC RH image"
+                      rslcValidPixelFractionRV="Ratio of fully focused pixels to total number of pixels in the input RSLC RV mask"
+                      rawValidPulseFractionRV="Ratio of valid pulse count to total pulses required to form the input RSLC RV image"
+                      rslcValidPixelFractionLH="Ratio of fully focused pixels to total number of pixels in the input RSLC LH mask"
+                      rawValidPulseFractionLH="Ratio of valid pulse count to total pulses required to form the input RSLC LH image"
+                      rslcValidPixelFractionLV="Ratio of fully focused pixels to total number of pixels in the input RSLC LV mask"
+                      rawValidPulseFractionLV="Ratio of valid pulse count to total pulses required to form the input RSLC LV image"
+                      grid_mapping="projection">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip). Also includes OR of validity mask bits, where each bit is set on for fully-focused data or off for partially focused or missing data (256:HH, 512:HV, 1024:VH, 2048:VV, 4096:LH, 8192:LV, 16384:RH, 32768:RV)</annotation>
         </integer>
         <real name="/science/LSAR/GCOV/grids/frequencyB/HHHH"
               shape="realDataFrequencyBShape"

python/packages/nisar/products/XML/L2/nisar_L2_GSLC.xml

@@ -361,12 +361,29 @@
         <integer name="/science/LSAR/GSLC/grids/frequencyA/inputDataExceptionMask"
               shape="realDataFrequencyAShape"
               signed="false"
-              width="8">
+              width="16">
           <annotation app="conformance"
                       lang="en"
                       DIMENSION_LIST="HDF5 internal attribute"
                       grid_mapping="projection"
-                      valid_min="0">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip)</annotation>
+                      _FillValue="65535"
+                      rslcValidPixelFractionHH="Ratio of fully focused pixels to total number of pixels in the input RSLC HH mask"
+                      rawValidPulseFractionHH="Ratio of valid pulse count to total pulses required to form the input RSLC HH image"
+                      rslcValidPixelFractionHV="Ratio of fully focused pixels to total number of pixels in the input RSLC HV mask"
+                      rawValidPulseFractionHV="Ratio of valid pulse count to total pulses required to form the input RSLC HV image"
+                      rslcValidPixelFractionVH="Ratio of fully focused pixels to total number of pixels in the input RSLC VH mask"
+                      rawValidPulseFractionVH="Ratio of valid pulse count to total pulses required to form the input RSLC VH image"
+                      rslcValidPixelFractionVV="Ratio of fully focused pixels to total number of pixels in the input RSLC VV mask"
+                      rawValidPulseFractionVV="Ratio of valid pulse count to total pulses required to form the input RSLC VV image"
+                      rslcValidPixelFractionRH="Ratio of fully focused pixels to total number of pixels in the input RSLC RH mask"
+                      rawValidPulseFractionRH="Ratio of valid pulse count to total pulses required to form the input RSLC RH image"
+                      rslcValidPixelFractionRV="Ratio of fully focused pixels to total number of pixels in the input RSLC RV mask"
+                      rawValidPulseFractionRV="Ratio of valid pulse count to total pulses required to form the input RSLC RV image"
+                      rslcValidPixelFractionLH="Ratio of fully focused pixels to total number of pixels in the input RSLC LH mask"
+                      rawValidPulseFractionLH="Ratio of valid pulse count to total pulses required to form the input RSLC LH image"
+                      rslcValidPixelFractionLV="Ratio of fully focused pixels to total number of pixels in the input RSLC LV mask"
+                      rawValidPulseFractionLV="Ratio of valid pulse count to total pulses required to form the input RSLC LV image"
+                      valid_min="0">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip). Also includes OR of validity mask bits, where each bit is set on for fully-focused data or off for partially focused or missing data (256:HH, 512:HV, 1024:VH, 2048:VV, 4096:LH, 8192:LV, 16384:RH, 32768:RV)</annotation>
         </integer>
         <real name="/science/LSAR/GSLC/grids/frequencyA/HH"
               shape="complexDataFrequencyAShape"
@@ -630,12 +647,29 @@
         <integer name="/science/LSAR/GSLC/grids/frequencyB/inputDataExceptionMask"
               shape="realDataFrequencyBShape"
               signed="false"
-              width="8">
+              width="16">
           <annotation app="conformance"
                       lang="en"
                       DIMENSION_LIST="HDF5 internal attribute"
                       grid_mapping="projection"
-                      valid_min="0">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip)</annotation>
+                      _FillValue="65535"
+                      rslcValidPixelFractionHH="Ratio of fully focused pixels to total number of pixels in the input RSLC HH mask"
+                      rawValidPulseFractionHH="Ratio of valid pulse count to total pulses required to form the input RSLC HH image"
+                      rslcValidPixelFractionHV="Ratio of fully focused pixels to total number of pixels in the input RSLC HV mask"
+                      rawValidPulseFractionHV="Ratio of valid pulse count to total pulses required to form the input RSLC HV image"
+                      rslcValidPixelFractionVH="Ratio of fully focused pixels to total number of pixels in the input RSLC VH mask"
+                      rawValidPulseFractionVH="Ratio of valid pulse count to total pulses required to form the input RSLC VH image"
+                      rslcValidPixelFractionVV="Ratio of fully focused pixels to total number of pixels in the input RSLC VV mask"
+                      rawValidPulseFractionVV="Ratio of valid pulse count to total pulses required to form the input RSLC VV image"
+                      rslcValidPixelFractionRH="Ratio of fully focused pixels to total number of pixels in the input RSLC RH mask"
+                      rawValidPulseFractionRH="Ratio of valid pulse count to total pulses required to form the input RSLC RH image"
+                      rslcValidPixelFractionRV="Ratio of fully focused pixels to total number of pixels in the input RSLC RV mask"
+                      rawValidPulseFractionRV="Ratio of valid pulse count to total pulses required to form the input RSLC RV image"
+                      rslcValidPixelFractionLH="Ratio of fully focused pixels to total number of pixels in the input RSLC LH mask"
+                      rawValidPulseFractionLH="Ratio of valid pulse count to total pulses required to form the input RSLC LH image"
+                      rslcValidPixelFractionLV="Ratio of fully focused pixels to total number of pixels in the input RSLC LV mask"
+                      rawValidPulseFractionLV="Ratio of valid pulse count to total pulses required to form the input RSLC LV image"
+                      valid_min="0">Bitwise OR of input data exception codes for each image pixel (0: no anomaly, 2: NISAR LSAR qFSP-H1 sample slip). Also includes OR of validity mask bits, where each bit is set on for fully-focused data or off for partially focused or missing data (256:HH, 512:HV, 1024:VH, 2048:VV, 4096:LH, 8192:LV, 16384:RH, 32768:RV)</annotation>
         </integer>
         <real name="/science/LSAR/GSLC/grids/frequencyB/HH"
               shape="complexDataFrequencyBShape"

python/packages/nisar/products/writers/BaseL2WriterSingleInput.py

@@ -1655,7 +1655,8 @@ def geocode_lut(self, output_h5_group, input_h5_group=None,
                     input_ds_name_list=None,
                     skip_if_not_present=False,
                     compute_stats=False,
-                    data_interpolator=None):
+                    data_interpolator=None,
+                    fill_value=None):
         """
         Geocode a look-up table (LUT) from the input product in
         radar coordinates to the output product in map coordinates
@@ -1694,6 +1695,12 @@ def geocode_lut(self, output_h5_group, input_h5_group=None,
             Otherwise, if the LUT contains < 5 rows or columns, bilinear
             interpolation will be used. Otherwise, biquintic interpolation
             will be used.
+        fill_value : float, optional
+            Value to populate the HDF5 dataset attribute "_FillValue".
+            Defaults to "nan" or "(nan+nanj)" if the raster layer
+            is real- or complex-valued, respectively. If the layer data
+            type is integer and `fill_value` is None, the attribute "_FillValue"
+            will not be populated as an attribute of the HDF5 dataset.
 
         Returns
         -------
@@ -1770,7 +1777,8 @@ def geocode_lut(self, output_h5_group, input_h5_group=None,
             output_h5_group_path,
             skip_if_not_present,
             compute_stats,
-            data_interpolator)
+            data_interpolator,
+            fill_value=fill_value)
 
     def geocode_metadata_group(self,
                                frequency,
@@ -1781,7 +1789,8 @@ def geocode_metadata_group(self,
                                output_h5_group_path,
                                skip_if_not_present,
                                compute_stats=False,
-                               data_interpolator=None):
+                               data_interpolator=None,
+                               fill_value=None):
         """
         Geocode look-up tables (LUTs) from the input product in
         radar coordinates to the output product in map coordinates
@@ -1822,6 +1831,12 @@ def geocode_metadata_group(self,
             Otherwise, if the LUT contains < 5 rows or columns, bilinear
             interpolation will be used. Otherwise, biquintic interpolation
             will be used.
+        fill_value : float, optional
+            Value to populate the HDF5 dataset attribute "_FillValue".
+            Defaults to "nan" or "(nan+nanj)" if the raster layer
+            is real- or complex-valued, respectively. If the layer data
+            type is integer and `fill_value` is None, the attribute "_FillValue"
+            will not be populated as an attribute of the HDF5 dataset.
 
         Returns
         -------
@@ -2182,6 +2197,7 @@ def geocode_metadata_group(self,
                             metadata_geogrid,
                             compute_stats,
                             data_interpolator=data_interpolator,
+                            fill_value=fill_value,
                             **geocode_kwargs)
 
         input_temp.close()
@@ -2196,6 +2212,7 @@ def geocode_raster(self,
                        metadata_geogrid,
                        compute_stats,
                        data_interpolator=None,
+                       fill_value=None,
                        **geocode_kwargs):
         """
         Geocode an ISCE3 Raster object containing look-up tables (LUTs)
@@ -2223,6 +2240,12 @@ def geocode_raster(self,
             output raster layer. Defaults to False.
         data_interpolator: str, optional
             Interpolation algorithm to use for geocoding
+        fill_value : float, optional
+            Value to populate the HDF5 dataset attribute "_FillValue".
+            Defaults to "nan" or "(nan+nanj)" if the raster layer
+            is real- or complex-valued, respectively. If the layer data
+            type is integer and `fill_value` is None, the attribute "_FillValue"
+            will not be populated as an attribute of the HDF5 dataset.
         **geocode_kwargs
             Keyword arguments to be passed to the `geocode()`.
         """
@@ -2254,7 +2277,7 @@ def geocode_raster(self,
             geo = isce3.geocode.GeocodeCFloat32()
         elif input_raster_obj.datatype() == gdal.GDT_CFloat64:
             geo = isce3.geocode.GeocodeCFloat64()
-        elif input_raster_obj.datatype() == gdal.GDT_Byte:
+        elif input_raster_obj.datatype() in (gdal.GDT_Byte, gdal.GDT_Int16, gdal.GDT_UInt16):
             geo = isce3.geocode.GeocodeFloat32()
         else:
             err_str = 'Unsupported raster type for geocoding'
@@ -2321,6 +2344,7 @@ def geocode_raster(self,
         save_dataset(temp_output.name, self.output_hdf5_obj,
                      output_h5_group_path,
                      yds, xds, output_ds_name_list,
+                     fill_value=fill_value,
                      compute_stats=compute_stats)
 
         temp_output.close()