Adapt to titanlib 0.3.0

bin/oi2soda

@@ -5,5 +5,5 @@ import surfex
 
 if __name__ == "__main__":
 
-    args = surfex.parse_args_oi2soda(sys.argv[1:])
-    surfex.run_oi2soda(args)
+    kwargs = surfex.parse_args_oi2soda(sys.argv[1:])
+    surfex.run_oi2soda(**kwargs)

setup.py

@@ -172,6 +172,7 @@ def get_version(rel_path):
         'bin/perturbed_offline',
         'bin/pgd',
         'bin/plot_field',
+        'bin/plot_points',
         'bin/plot_timeseries',
         'bin/prep',
         'bin/set_geo_from_obs_set',

surfex/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.0.1a12'
+__version__ = '0.0.1a13'
 
 from .file import *
 from .geo import *

surfex/cli.py

@@ -427,7 +427,7 @@ def run_masterodb(**kwargs):
             if kwargs["config"] is not None:
                 config_exp = kwargs["config"]
         if config_exp is None:
-            config_exp = surfex.__path__[0] + "/../scheduler/config/config_exp_surfex.toml"
+            config_exp = surfex.__path__[0] + "/cfg/config_exp_surfex.toml"
         print("Using default config from: " + config_exp)
         input_data = toml.load(open(config_exp, "r"))
         config = surfex.ConfigurationFromHarmonie(os.environ, input_data)
@@ -1202,8 +1202,8 @@ def run_bufr2json(**kwargs):
     bufr_set.write_json_file(output, indent=indent)
 
 
-def parse_args_plot_field(argv):
-    parser = ArgumentParser("Plot field")
+def parse_args_plot_points(argv):
+    parser = ArgumentParser("Plot points")
     parser.add_argument('-g', '--geo', dest="geo", type=str, help="Domain/points json geometry definition file",
                         default=None, required=False)
     parser.add_argument('-v', '--variable', dest="variable", type=str, help="Variable name", required=False)
@@ -1215,7 +1215,7 @@ def parse_args_plot_field(argv):
                         required=False)
     parser.add_argument('-o', '--output', dest="output", type=str, help="Output file", default=None,
                         required=False)
-
+    parser.add_argument("--interpolator", type=str, default="nearest", required=False, help="Interpolator")
     grib = parser.add_argument_group('grib', 'Grib1/2 settings (-it grib1 or -it grib2)')
     grib.add_argument('--indicatorOfParameter', type=int, help="Indicator of parameter [grib1]", default=None)
     grib.add_argument('--timeRangeIndicator', type=int, help="Time range indicator [grib1]", default=0)
@@ -1257,7 +1257,7 @@ def parse_args_plot_field(argv):
     return kwargs
 
 
-def run_plot_field(**kwargs):
+def run_plot_points(**kwargs):
 
     debug = False
     if "debug" in kwargs:
@@ -1277,13 +1277,15 @@ def run_plot_field(**kwargs):
         filepattern = kwargs["inputfile"]
     inputtype = kwargs["inputtype"]
     output = kwargs["output"]
+    interpolator = "nearest"
+    if "interpolator" in kwargs:
+        interpolator = kwargs["interpolator"]
 
     geo = None
     if geo_file is not None:
         domain_json = json.load(open(geo_file, "r"))
         geo = surfex.geo.get_geo_object(domain_json)
 
-    geo_input = None
     contour = True
     var = "field_to_read"
     if inputtype == "grib1":
@@ -1306,7 +1308,8 @@ def run_plot_field(**kwargs):
             "parameter": par,
             "type": lt,
             "level": lev,
-            "tri": tri
+            "tri": tri,
+            "interpolator": interpolator
         }
 
     elif inputtype == "grib2":
@@ -1354,7 +1357,8 @@ def run_plot_field(**kwargs):
             "filepattern": filepattern,
             "fcint": 10800,
             "file_inc": 10800,
-            "offset": 0
+            "offset": 0,
+            "interpolator": interpolator
         }
 
     elif inputtype == "surfex":
@@ -1390,7 +1394,8 @@ def run_plot_field(**kwargs):
             "geo_input": geo_input,
             "fcint": 10800,
             "file_inc": 10800,
-            "offset": 0
+            "offset": 0,
+            "interpolator": interpolator
         }
 
     elif inputtype == "obs":
@@ -1439,7 +1444,6 @@ def run_plot_field(**kwargs):
     converter = "none"
     converter = surfex.read.Converter(converter, validtime, defs, converter_conf, inputtype, validtime, debug=debug)
     field = surfex.ConvertedInput(geo, var, converter).read_time_step(validtime, cache)
-    # field = np.reshape(field, [geo.nlons, geo.nlats])
 
     if field is None:
         raise Exception("No field read")
@@ -1789,7 +1793,11 @@ def run_timeseries2json(**kwargs):
     obs_set = kwargs["obs_set"]
     start = datetime.strptime(starttime, "%Y%m%d%H")
     end = datetime.strptime(endtime, "%Y%m%d%H")
-    geo_in = kwargs["geo_in"]
+    geo_in = None
+    if "geo_in" in kwargs:
+        geo_in = kwargs["geo_in"]
+    if isinstance(geo_in, str):
+        geo_in = json.load(open(geo_in, "r"))
 
     # Get lon and lats from station list
     if lons is None and lats is None:

surfex/file.py

@@ -1047,6 +1047,7 @@ def points(self, var, geo_out, validtime=None, interpolation=None, cache=None):
 
         points, interpolator = SurfexIO.interpolate_field(self, field, geo_in, geo_out, interpolation=interpolation,
                                                           cache=cache)
+
         return points, interpolator
 
 

surfex/interpolation.py

@@ -77,6 +77,8 @@ def __init__(self, geo_in, geo_out, cache=None, distance_check=True,  distance_l
             cached_interpolator = cache.get_interpolator("nearest", geo_in, geo_out)
 
         print(geo_in.identifier())
+        if geo_out is None:
+            geo_out = geo_in
         print(geo_out.identifier())
         if cached_interpolator is not None:
             print("Using cached interpolator")
@@ -156,8 +158,7 @@ def __init__(self, geo_in, geo_out, cache=None, distance_check=True,  distance_l
                 values_vec = np.arange(nx * ny)
                 x = np.floor_divide(values_vec, ny)
                 y = np.mod(values_vec, ny)
-                grid_points =  np.column_stack((x, y))
-
+                grid_points = np.column_stack((x, y))
 
             Interpolation.__init__(self, "nearest", nx, ny, var_lons, var_lats)
             self.index = grid_points

surfex/read.py

@@ -27,6 +27,18 @@ def print_info(self):
         raise NotImplementedError('users must define read_time_step to use this base class')
 
 
+class Points(object):
+    def __init__(self, values, interpolator):
+        self.values = values
+        self.interpolator = interpolator
+
+
+class TwoDField(object):
+    def __init__(self, values, geo):
+        self.values = values
+        self.geo = geo
+
+
 # Direct data can be ead with this class with converter = None
 class ConvertedInput(ReadData):
     """
@@ -105,7 +117,7 @@ def remove_existing_file(f_in, f_out):
 #######################################################
 
 
-class Converter:
+class Converter(object):
     """
     Main interface to read a field is done through a converter.
     The converter name is default "None" to read a plain field without any conversion.
@@ -229,7 +241,8 @@ def read_time_step(self, geo, validtime, cache):
         # print("Time in converter: "+self.name+" "+validtime.strftime('%Y%m%d%H'))
 
         gravity = 9.81
-        field = np.empty(geo.npoints)
+        field = None
+        # field = np.empty(geo.npoints)
         # Specific reading for each converter
         if self.name == "none":
             field = self.var.read_variable(geo, validtime, cache)

surfex/titan.py

@@ -384,7 +384,8 @@ def test(self, dataset, mask, code=105):
             lons = np.asarray(lons)
             elevs = np.asarray(elevs)
             values = np.asarray(values)
-            answer = tit.sct(lats, lons, elevs, values, self.num_min, self.num_max, self.inner_radius,
+            points = tit.Points(lats, lons, elevs)
+            answer = tit.sct(points, values, self.num_min, self.num_max, self.inner_radius,
                              self.outer_radius, self.num_iterations, self.num_min_prof, self.min_elev_diff,
                              self.min_horizonal_scale, self.vertical_scale, self.pos, self.neg, self.eps2)
 
@@ -492,7 +493,8 @@ def test(self, dataset, mask, code=104):
             elevs.append(dataset.elevs[i])
             values.append(dataset.values[i])
 
-        status, flags = tit.buddy_check(lats, lons, elevs, values,
+        points = tit.Points(lats, lons, elevs)
+        status, flags = tit.buddy_check(points, values,
                                         self.distance_lim, self.priorities,
                                         self.buddies_min, self.thresholds, self.diff_elev_max,
                                         self.adjust_for_elev_diff, self.obs_to_check)
@@ -563,7 +565,8 @@ def test(self, dataset, mask, code=103):
             val = dataset.values[mask[o]] + self.offset[o]
             values.append(val)
 
-        flags = tit.range_check_climatology(lats, lons, elevs, values, self.unixtime, self.maxvals, self.minvals)
+        points = tit.Points(lats, lons, elevs)
+        flags = tit.range_check_climatology(points, values, self.unixtime, self.maxvals, self.minvals)
 
         global_flags = dataset.flags
         for i in range(0, len(mask)):
@@ -1094,7 +1097,8 @@ def __init__(self, var, settings, tests, datasources, an_time, debug=False, core
         for i in range(0, len(lons)):
             observations.append(surfex.Observation(obstimes[i], lons[i], lats[i], values[i], elev=elevs[i],
                                                    stid=stids[i], varname=varnames[i]))
-        self.titan_dataset = tit.Dataset(lats, lons, elevs, values)
+        points = tit.Points(lats, lons, elevs)
+        self.titan_dataset = tit.Dataset(points, values)
         if passed_tests is None:
             passed_tests = []
             for i in range(0, len(lons)):

test/test_plot.py

@@ -19,8 +19,8 @@ def test_plot_grib1(self):
             "-o", "unittest_output_plot_grib1.png",
             "--debug"
             ]
-        kwargs = surfex.parse_args_plot_field(argv)
-        surfex.run_plot_field(**kwargs)
+        kwargs = surfex.parse_args_plot_points(argv)
+        surfex.run_plot_points(**kwargs)
 
     def test_plot_grib2(self):
         argv = [
@@ -36,8 +36,8 @@ def test_plot_grib2(self):
             "-o", "unittest_output_plot_grib2.png",
             "--debug"
             ]
-        kwargs = surfex.parse_args_plot_field(argv)
-        surfex.run_plot_field(**kwargs)
+        kwargs = surfex.parse_args_plot_points(argv)
+        surfex.run_plot_points(**kwargs)
 
     def test_plot_netcdf(self):
         argv = [
@@ -49,8 +49,8 @@ def test_plot_netcdf(self):
             "-o", "unittest_output_plot_nc.png",
             "--debug"
             ]
-        kwargs = surfex.parse_args_plot_field(argv)
-        surfex.run_plot_field(**kwargs)
+        kwargs = surfex.parse_args_plot_points(argv)
+        surfex.run_plot_points(**kwargs)
 
     def test_plot_obs_frost_json(self):
         argv = [
@@ -62,5 +62,5 @@ def test_plot_obs_frost_json(self):
             "-o", "unittest_output_plot_obs_frost_json.png",
             "--debug"
             ]
-        kwargs = surfex.parse_args_plot_field(argv)
-        surfex.run_plot_field(**kwargs)
+        kwargs = surfex.parse_args_plot_points(argv)
+        surfex.run_plot_points(**kwargs)