Added flags for LAC data and georeferencing for increased accuracy

pygac_fdr/reader.py

@@ -40,30 +40,52 @@
 )
 
 
-def read_gac(filename, reader_kwargs=None):
-    """Read and calibrate AVHRR GAC level 1b data using satpy.
+def read_file(filename, reader_kwargs=None):
+    """Read and calibrate AVHRR GAC/LAC level 1b data using satpy.
 
     Args:
-        filename (str): AVHRR GAC level 1b file
+        filename (str): AVHRR GAC/LAC level 1b file
         reader_kwargs (dict): Keyword arguments to be passed to the reader.
+
     Returns:
         The loaded data in a satpy.Scene object.
     """
-    scene = satpy.Scene(
-        filenames=[filename], reader="avhrr_l1b_gaclac", reader_kwargs=reader_kwargs
-    )
+    scene = satpy.Scene(filenames=[filename], reader="avhrr_l1b_gaclac", reader_kwargs=reader_kwargs)
     scene.load(BANDS)
+    if reader_kwargs.get("dem") is not None:
+        AUX_DATA.append("tc_latitude")
+        AUX_DATA.append("tc_longitude")
+    if reader_kwargs.get("reference_image") is not None:
+        AUX_DATA.append("gcp_x")
+        AUX_DATA.append("gcp_y")
+        AUX_DATA.append("gcp_longitude")
+        AUX_DATA.append("gcp_latitude")
+        AUX_DATA.append("gcp_x_corrected")
+        AUX_DATA.append("gcp_y_corrected")
+        AUX_DATA.append("gcp_x_displacement")
+        AUX_DATA.append("gcp_y_displacement")
+    if reader_kwargs.get("compute_uncertainties"):
+        AUX_DATA.extend(("random_uncertainty",
+                         "systematic_uncertainty",
+                         "channel_covariance_ratio",
+                         "uncertainty_flags"))
     scene.load(AUX_DATA)
 
     # Add additional metadata
     basename = os.path.basename(filename)
-    fname_info = trollsift.parse(GAC_FORMAT, basename)
-    orbit_number_end = (
-        fname_info["orbit_number"] // 100 * 100 + fname_info["end_orbit_last_digits"]
-    )
     scene.attrs.update(
         {
             "gac_filename": basename,
+        }
+    )
+    try:
+        fname_info = trollsift.parse(GAC_FORMAT, basename)
+    except ValueError:
+        return scene
+
+    orbit_number_end = fname_info["orbit_number"] // 100 * 100 + fname_info["end_orbit_last_digits"]
+    scene.attrs.update(
+        {
             "orbit_number_start": fname_info["orbit_number"],
             "orbit_number_end": orbit_number_end,
             "ground_station": fname_info["station"],

bin/pygac-fdr-crop → pygac_fdr/runners/crop.py

@@ -23,7 +23,8 @@
 
 from pygac_fdr.crop import CROP_OVERLAP_BEGINNING, CROP_OVERLAP_END, crop
 
-if __name__ == "__main__":
+
+def main():
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("filename", type=str, help="pygac-fdr output file")
     parser.add_argument(

bin/pygac-fdr-dump → pygac_fdr/runners/dump.py

@@ -23,7 +23,8 @@
 
 from pygac_fdr.metadata import MetadataCollector
 
-if __name__ == "__main__":
+
+def main():
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("dbfile", help="Metadata database")
     parser.add_argument("-n", help="Maximum number of rows to be printed", type=int)

bin/pygac-fdr-mda-collect → pygac_fdr/runners/mda_collect.py

@@ -34,7 +34,7 @@
 for reading a long list of filenames from an arguments file.
 """
 
-if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser(
         description=__doc__, fromfile_prefix_chars="@", epilog=tooltip
     )

bin/pygac-fdr-mda-update → pygac_fdr/runners/mda_update.py

@@ -22,7 +22,8 @@
 from pygac_fdr.metadata import MetadataUpdater, read_metadata_from_database
 from pygac_fdr.utils import logging_on
 
-if __name__ == "__main__":
+
+def main():
     parser = argparse.ArgumentParser(description="Update metadata in level 1c files")
     parser.add_argument(
         "--dbfile",

bin/pygac-fdr-run → pygac_fdr/runners/run.py

@@ -20,13 +20,13 @@
 import logging
 import re
 import tarfile
-from contextlib import closing
+from contextlib import closing, suppress
 
 import satpy
 from satpy.readers import FSFile
 
 from pygac_fdr.config import read_config
-from pygac_fdr.reader import read_gac
+from pygac_fdr.reader import read_file
 from pygac_fdr.utils import LOGGER_NAME, TarFileSystem, logging_on
 from pygac_fdr.writer import NetcdfWriter
 
@@ -44,9 +44,7 @@ def __fspath__(self):
 def process_file(filename, config):
     LOG.info("Processing file {}".format(filename))
     try:
-        scene = read_gac(
-            filename, reader_kwargs=config["controls"].get("reader_kwargs")
-        )
+        scene = read_file(filename, reader_kwargs=config["controls"].get("reader_kwargs"))
         writer = NetcdfWriter(
             output_dir=config["output"].get("output_dir"),
             global_attrs=config.get("global_attrs"),
@@ -56,8 +54,18 @@ def process_file(filename, config):
             engine=config["netcdf"].get("engine"),
             debug=config["controls"].get("debug"),
         )
+
         writer.write(scene=scene)
         success = True
+        if image_config := config["output"].get("image"):
+            composite = image_config["composite"]
+            scene.load([composite])
+            area = image_config["area"]
+            scn = scene.resample(area)
+            overlay = None
+            with suppress(KeyError):
+                overlay = {'coast_dir': image_config["coastlines_dir"], 'color': 'red'}
+            scn.save_dataset(composite, base_dir=config["output"].get("output_dir"), overlay=overlay)
     except Exception as err:
         if config["controls"]["debug"]:
             raise
@@ -81,23 +89,17 @@ def process_tarball(tarball, config):
     else:
         LOG.info("Successfully processed all files in {}".format(tarball))
 
-
-if __name__ == "__main__":
+def main():
     # Parse command line arguments
-    parser = argparse.ArgumentParser(
-        description="Read & calibrate AVHRR GAC data and write results to netCDF"
-    )
-    parser.add_argument(
-        "--cfg", required=True, type=str, help="Path to pygac-fdr configuration file."
-    )
+    parser = argparse.ArgumentParser(description="Read & calibrate AVHRR GAC data and write results to netCDF")
+    parser.add_argument("--cfg", required=True, type=str, help="Path to pygac-fdr configuration file.")
     parser.add_argument(
         "--output-dir",
         help="Output directory. Overrides entry in the configuration file.",
     )
     parser.add_argument(
         "--tle-dir",
-        help="Directory containing TLE files. Overrides entry in the configuration"
-        " file.",
+        help="Directory containing TLE files. Overrides entry in the configuration file.",
     )
     parser.add_argument(
         "--debug",
@@ -106,12 +108,11 @@ def process_tarball(tarball, config):
         "next file. Overrides entry in the configuration file.",
     )
     parser.add_argument("--verbose", action="store_true", help="Increase verbosity")
-    parser.add_argument(
-        "--log-all", action="store_true", help="Enable logging for all modules"
-    )
-    parser.add_argument(
-        "filenames", nargs="+", help="AVHRR GAC level 1b files to be processed"
-    )
+    parser.add_argument("--log-all", action="store_true", help="Enable logging for all modules")
+    parser.add_argument("filenames", nargs="+", help="AVHRR GAC level 1b files to be processed")
+    parser.add_argument("--georef", type=str, help="Path to reference GeoTiff file for georeferencing")
+    parser.add_argument("--dem", type=str, help="Path to digital elevation model GeoTiff file for orthocorrection")
+    parser.add_argument("--with-uncertainties", action="store_true", help="Compute uncertainties")
     args = parser.parse_args()
     logging_on(logging.DEBUG if args.verbose else logging.INFO, for_all=args.log_all)
 
@@ -122,6 +123,12 @@ def process_tarball(tarball, config):
         config["output"]["output_dir"] = args.output_dir
     if args.tle_dir:
         config["controls"]["reader_kwargs"]["tle_dir"] = args.tle_dir
+    if args.georef:
+        config["controls"]["reader_kwargs"]["reference_image"] = args.georef
+    if args.dem:
+        config["controls"]["reader_kwargs"]["dem"] = args.dem
+    if args.with_uncertainties:
+        config["controls"]["reader_kwargs"]["compute_uncertainties"] = args.with_uncertainties
     if args.debug:
         config["controls"]["debug"] = args.debug
 

bin/pygac-fdr-val-collect → pygac_fdr/runners/val_collect.py

@@ -32,7 +32,8 @@
 for reading a long list of filenames from an arguments file.
 """
 
-if __name__ == "__main__":
+
+def main():
     parser = argparse.ArgumentParser(
         description=__doc__, fromfile_prefix_chars="@", epilog=tooltip
     )

bin/pygac-fdr-val-plot → pygac_fdr/runners/val_plot.py

@@ -256,7 +256,7 @@ def draw_hovmoeller(channel, data):
     return fig
 
 
-if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("dbfiles", nargs="+", help="Statistics databases")
     parser.add_argument("--cache", help="Cache directory, defaults to %(default)s", default='./cache')