Update runconfig fields from camel case to snake case (#911)

* update runconfig parameters from camel case to snake case

* update runconfig parameters from camel case to snake case (2)

* update runconfig parameters from camel case to snake case (3)

* Update share/nisar/examples/alos_to_nisar_l0b.py

Co-authored-by: Geoffrey M Gunter <[email protected]>

* Update share/nisar/examples/alos2_to_nisar_l1.py

Co-authored-by: Geoffrey M Gunter <[email protected]>

Co-authored-by: Geoffrey M Gunter <[email protected]>

Author: 2 people

python/packages/nisar/workflows/bandpass_insar.py

@@ -20,14 +20,14 @@ def run(cfg: dict):
     run bandpass
     '''
     # pull parameters from cfg
-    ref_hdf5 = cfg['InputFileGroup']['InputFilePath']
-    sec_hdf5 = cfg['InputFileGroup']['SecondaryFilePath']
+    ref_hdf5 = cfg['input_file_group']['input_file_path']
+    sec_hdf5 = cfg['input_file_group']['secondary_file_path']
     freq_pols = cfg['processing']['input_subset']['list_of_frequencies']
     blocksize = cfg['processing']['bandpass']['lines_per_block']
     window_function = cfg['processing']['bandpass']['window_function']
     window_shape = cfg['processing']['bandpass']['window_shape']
     fft_size = cfg['processing']['bandpass']['range_fft_size']
-    scratch_path = pathlib.Path(cfg['ProductPathGroup']['ScratchPath'])
+    scratch_path = pathlib.Path(cfg['product_path_group']['scratch_path'])
 
     # init parameters shared by frequency A and B
     ref_slc = SLC(hdf5file=ref_hdf5)
@@ -67,7 +67,7 @@ def run(cfg: dict):
             base_slc = sec_slc
 
             # update reference SLC path 
-            cfg['InputFileGroup']['InputFilePath'] = ref_slc_output
+            cfg['input_file_group']['input_file_path'] = ref_slc_output
             target_output = ref_slc_output
 
         elif target == 'sec':
@@ -76,7 +76,7 @@ def run(cfg: dict):
             base_slc = ref_slc
 
             # update secondary SLC path 
-            cfg['InputFileGroup']['SecondaryFilePath'] = sec_slc_output
+            cfg['input_file_group']['secondary_file_path'] = sec_slc_output
             target_output = sec_slc_output
 
         if os.path.exists(target_output):

python/packages/nisar/workflows/crossmul.py

@@ -23,16 +23,16 @@ def run(cfg: dict, output_hdf5: str = None, resample_type='coarse'):
     run crossmul
     '''
     # pull parameters from cfg
-    ref_hdf5 = cfg['InputFileGroup']['InputFilePath']
-    sec_hdf5 = cfg['InputFileGroup']['SecondaryFilePath']
+    ref_hdf5 = cfg['input_file_group']['input_file_path']
+    sec_hdf5 = cfg['input_file_group']['secondary_file_path']
     freq_pols = cfg['processing']['input_subset']['list_of_frequencies']
     flatten = cfg['processing']['crossmul']['flatten']
 
     if flatten is not None:
         flatten_path = cfg['processing']['crossmul']['flatten']
 
     if output_hdf5 is None:
-        output_hdf5 = cfg['ProductPathGroup']['SASOutputFile']
+        output_hdf5 = cfg['product_path_group']['sas_output_file']
 
     # init parameters shared by frequency A and B
     ref_slc = SLC(hdf5file=ref_hdf5)

python/packages/nisar/workflows/crossmul_runconfig.py

@@ -21,8 +21,8 @@ def yaml_check(self, resample_type):
         '''
         error_channel = journal.error('CrossmulRunConfig.yaml_check')
 
-        scratch_path = self.cfg['ProductPathGroup']['ScratchPath']
-        # if coregistered_slc_path not provided, use ScratchPath as source for coregistered SLCs
+        scratch_path = self.cfg['product_path_group']['scratch_path']
+        # if coregistered_slc_path not provided, use scratch_path as source for coregistered SLCs
         if 'coregistered_slc_path' not in self.cfg['processing']['crossmul']:
             self.cfg['processing']['crossmul']['coregistered_slc_path'] = scratch_path
 

python/packages/nisar/workflows/dense_offsets.py

@@ -22,9 +22,9 @@ def run(cfg: dict):
     '''
 
     # Pull parameters from cfg
-    ref_hdf5 = cfg['InputFileGroup']['InputFilePath']
-    sec_hdf5 = cfg['InputFileGroup']['SecondaryFilePath']
-    scratch_path = pathlib.Path(cfg['ProductPathGroup']['ScratchPath'])
+    ref_hdf5 = cfg['input_file_group']['input_file_path']
+    sec_hdf5 = cfg['input_file_group']['secondary_file_path']
+    scratch_path = pathlib.Path(cfg['product_path_group']['scratch_path'])
     freq_pols = cfg['processing']['input_subset']['list_of_frequencies']
     offset_params = cfg['processing']['dense_offsets']
 

python/packages/nisar/workflows/dense_offsets_runconfig.py

@@ -21,7 +21,7 @@ def yaml_check(self):
         '''
 
         error_channel = journal.error('DenseOffsetsRunConfig.yaml_check')
-        scratch_path = self.cfg['ProductPathGroup']['ScratchPath']
+        scratch_path = self.cfg['product_path_group']['scratch_path']
 
         # If coregistered_slc_path is None, assume that we run dense_offsets
         # as part of insar.py. In this case, coregistered_slc_path comes

python/packages/nisar/workflows/focus.py

@@ -88,7 +88,7 @@ def get_window(win: Struct, msg=''):
 
 
 def get_chirp(cfg: Struct, raw: Raw, frequency: str, tx: str):
-    if cfg.DynamicAncillaryFileGroup.Waveform:
+    if cfg.dynamic_ancillary_file_group.waveform:
         log.warning("Ignoring input waveform file.  Using analytic chirp.")
     chirp = raw.getChirp(frequency, tx)
     log.info(f"Chirp length = {len(chirp)}")
@@ -110,9 +110,9 @@ def parse_rangecomp_mode(mode: str):
 
 def get_orbit(cfg: Struct):
     log.info("Loading orbit")
-    if cfg.DynamicAncillaryFileGroup.Orbit:
+    if cfg.dynamic_ancillary_file_group.orbit:
         log.warning("Ignoring input orbit file.  Using L0B orbits.")
-    rawfiles = cfg.InputFileGroup.InputFilePath
+    rawfiles = cfg.input_file_group.input_file_path
     if len(rawfiles) > 1:
         raise NotImplementedError("Can't concatenate orbit data.")
     raw = open_rrsd(rawfiles[0])
@@ -121,9 +121,9 @@ def get_orbit(cfg: Struct):
 
 def get_attitude(cfg: Struct):
     log.info("Loading attitude")
-    if cfg.DynamicAncillaryFileGroup.Pointing:
+    if cfg.dynamic_ancillary_file_group.pointing:
         log.warning("Ignoring input pointing file.  Using L0B attitude.")
-    rawfiles = cfg.InputFileGroup.InputFilePath
+    rawfiles = cfg.input_file_group.input_file_path
     if len(rawfiles) > 1:
         raise NotImplementedError("Can't concatenate attitude data.")
     raw = open_rrsd(rawfiles[0])
@@ -194,7 +194,7 @@ def get_dem(cfg: Struct):
     dem = isce3.geometry.DEMInterpolator(
         height=cfg.processing.dem.reference_height,
         method=cfg.processing.dem.interp_method)
-    fn = cfg.DynamicAncillaryFileGroup.DEMFile
+    fn = cfg.dynamic_ancillary_file_group.dem_file
     if fn:
         log.info(f"Loading DEM {fn}")
         dem.load_dem(fn)
@@ -286,7 +286,7 @@ def make_doppler(cfg: Struct, frequency='A'):
     dem = get_dem(cfg)
     opt = cfg.processing.doppler
     az = np.radians(opt.azimuth_boresight_deg)
-    rawfiles = cfg.InputFileGroup.InputFilePath
+    rawfiles = cfg.input_file_group.input_file_path
 
     fc, lut = make_doppler_lut(rawfiles,
                                az=az, orbit=orbit, attitude=attitude,
@@ -489,7 +489,7 @@ def get_range_deramp(grid: isce3.product.RadarGridParameters) -> np.ndarray:
 def focus(runconfig):
     # Strip off two leading namespaces.
     cfg = runconfig.runconfig.groups
-    rawfiles = cfg.InputFileGroup.InputFilePath
+    rawfiles = cfg.input_file_group.input_file_path
     if len(rawfiles) <= 0:
         raise IOError("need at least one raw data file")
     if len(rawfiles) > 1:
@@ -552,20 +552,20 @@ def focus(runconfig):
     polygon = isce3.geometry.get_geo_perimeter_wkt(ogrid["A"], orbit,
                                                    zerodop, dem)
 
-    output_slc_path = os.path.abspath(cfg.ProductPathGroup.SASOutputFile)
+    output_slc_path = os.path.abspath(cfg.product_path_group.sas_output_file)
 
     output_dir = os.path.dirname(output_slc_path)
     os.makedirs(output_dir, exist_ok=True)
 
-    product = cfg.PrimaryExecutable.ProductType
+    product = cfg.primary_executable.product_type
     log.info(f"Creating output {product} product {output_slc_path}")
     slc = SLC(output_slc_path, mode="w", product=product)
     slc.set_orbit(orbit) # TODO acceleration, orbitType
     if attitude:
         slc.set_attitude(attitude, orbit.reference_epoch)
     slc.copy_identification(raw, polygon=polygon,
-        track=cfg.Geometry.RelativeOrbitNumber,
-        frame=cfg.Geometry.FrameNumber,
+        track=cfg.Geometry.relative_orbit_number,
+        frame=cfg.Geometry.frame_number,
         start_time=ogrid["A"].sensing_datetime(0),
         end_time=ogrid["A"].sensing_datetime(ogrid["A"].length - 1))
 
@@ -592,7 +592,7 @@ def focus(runconfig):
                              **vars(cfg.processing.azcomp.geo2rdr))
 
     # Scratch directory for intermediate outputs
-    scratch_dir = os.path.abspath(cfg.ProductPathGroup.ScratchPath)
+    scratch_dir = os.path.abspath(cfg.product_path_group.scratch_path)
     os.makedirs(scratch_dir, exist_ok=True)
 
     # main processing loop
@@ -724,7 +724,7 @@ def main(argv):
     args = yaml_parser.parse()
     configure_logging()
     cfg = validate_config(load_config(args.run_config_path))
-    echofile = cfg.runconfig.groups.ProductPathGroup.SASConfigFile
+    echofile = cfg.runconfig.groups.product_path_group.sas_config_file
     if echofile:
         log.info(f"Logging configuration to file {echofile}.")
         dump_config(cfg, echofile)

python/packages/nisar/workflows/gcov.py

@@ -27,19 +27,19 @@ def run(cfg):
     '''
 
     # pull parameters from cfg
-    input_hdf5 = cfg['InputFileGroup']['InputFilePath']
-    output_hdf5 = cfg['ProductPathGroup']['SASOutputFile']
+    input_hdf5 = cfg['input_file_group']['input_file_path']
+    output_hdf5 = cfg['product_path_group']['sas_output_file']
     freq_pols = cfg['processing']['input_subset']['list_of_frequencies']
     flag_fullcovariance = cfg['processing']['input_subset']['fullcovariance']
     flag_symmetrize_cross_pol_channels = \
         cfg['processing']['input_subset']['symmetrize_cross_pol_channels']
-    scratch_path = cfg['ProductPathGroup']['ScratchPath']
+    scratch_path = cfg['product_path_group']['scratch_path']
 
     radar_grid_cubes_geogrid = cfg['processing']['radar_grid_cubes']['geogrid']
     radar_grid_cubes_heights = cfg['processing']['radar_grid_cubes']['heights']
 
     # DEM parameters
-    dem_file = cfg['DynamicAncillaryFileGroup']['DEMFile']
+    dem_file = cfg['dynamic_ancillary_file_group']['dem_file']
     dem_margin = cfg['processing']['dem_margin']
     dem_interp_method_enum = cfg['processing']['dem_interpolation_method_enum']
 

python/packages/nisar/workflows/gcov_runconfig.py

@@ -76,7 +76,7 @@ def load(self):
             Default margin as the length of 50 pixels
             (max of X and Y pixel spacing).
             '''
-            dem_file = self.cfg['DynamicAncillaryFileGroup']['DEMFile']
+            dem_file = self.cfg['dynamic_ancillary_file_group']['dem_file']
             dem_raster = isce3.io.Raster(dem_file)
             dem_margin = 50 * max([dem_raster.dx, dem_raster.dy])
             self.cfg['processing']['dem_margin'] = dem_margin

python/packages/nisar/workflows/geo2rdr.py

@@ -21,9 +21,9 @@ def run(cfg):
     '''
 
     # Pull parameters from cfg dict
-    sec_hdf5 = cfg['InputFileGroup']['SecondaryFilePath']
-    dem_file = cfg['DynamicAncillaryFileGroup']['DEMFile']
-    scratch_path = pathlib.Path(cfg['ProductPathGroup']['ScratchPath'])
+    sec_hdf5 = cfg['input_file_group']['secondary_file_path']
+    dem_file = cfg['dynamic_ancillary_file_group']['dem_file']
+    scratch_path = pathlib.Path(cfg['product_path_group']['scratch_path'])
     freq_pols = cfg['processing']['input_subset']['list_of_frequencies']
     threshold = cfg['processing']['geo2rdr']['threshold']
     numiter = cfg['processing']['geo2rdr']['maxiter']

python/packages/nisar/workflows/geo2rdr_runconfig.py

@@ -18,7 +18,7 @@ def yaml_check(self):
         '''
         # Use scratch as topo_path if none given in YAML
         if 'topo_path' not in self.cfg['processing']['geo2rdr']:
-            self.cfg['processing']['geo2rdr']['topo_path'] = self.cfg['ProductPathGroup']['ScratchPath']
+            self.cfg['processing']['geo2rdr']['topo_path'] = self.cfg['product_path_group']['scratch_path']
 
         # Check topo directory structure
         topo_path = self.cfg['processing']['geo2rdr']['topo_path']