add network functions and clean some file/share

Author: AntSimi

examples/08_tracking_manipulation/pet_track_anim.py

@@ -6,7 +6,7 @@
 
 """
 from py_eddy_tracker.observations.tracking import TrackEddiesObservations
-from py_eddy_tracker.appli import Anim
+from py_eddy_tracker.appli.gui import Anim
 import py_eddy_tracker_sample
 
 # %%

notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb

@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "from py_eddy_tracker.observations.tracking import TrackEddiesObservations\nfrom py_eddy_tracker.appli import Anim\nimport py_eddy_tracker_sample"
+        "from py_eddy_tracker.observations.tracking import TrackEddiesObservations\nfrom py_eddy_tracker.appli.gui import Anim\nimport py_eddy_tracker_sample"
       ]
     },
     {

setup.py

@@ -20,12 +20,11 @@
         "Programming Language :: Python",
     ],
     keywords="eddy science, eddy tracking, eddy tracker",
-    author="emason",
+    author="emason & adelepoulle",
     author_email="[email protected]",
     packages=find_packages("src"),
     package_dir={"": "src"},
     scripts=[
-        "src/scripts/EddyId",
         "src/scripts/EddySubSetter",
         "src/scripts/EddyTranslate",
         "src/scripts/EddyTracking",
@@ -38,6 +37,7 @@
         console_scripts=[
             # grid
             "GridFiltering = py_eddy_tracker.appli.grid:grid_filtering",
+            "EddyId = py_eddy_tracker.appli.grid:eddy_id",
             # eddies
             "MergeEddies = py_eddy_tracker.appli.eddies:merge_eddies",
             # network

share/eddy_identification.yaml

@@ -31,12 +31,13 @@ def start_logger():
     FORMAT_LOG = (
         "%(levelname)-8s %(asctime)s %(module)s.%(funcName)s :\n\t\t\t\t\t%(message)s"
     )
-    # set up logging to CONSOLE
-    console = logging.StreamHandler()
-    console.setFormatter(ColoredFormatter(FORMAT_LOG))
     logger = logging.getLogger("pet")
-    # add the handler to the root logger
-    logger.addHandler(console)
+    if len(logger.handlers) == 0:
+        # set up logging to CONSOLE
+        console = logging.StreamHandler()
+        console.setFormatter(ColoredFormatter(FORMAT_LOG))
+        # add the handler to the root logger
+        logger.addHandler(console)
     return logger
 
 
@@ -50,7 +51,7 @@ class ColoredFormatter(logging.Formatter):
     )
 
     def __init__(self, message):
-        super(ColoredFormatter, self).__init__(message)
+        super().__init__(message)
 
     def format(self, record):
         color = self.COLOR_LEVEL.get(record.levelname, "")
@@ -60,15 +61,15 @@ def format(self, record):
         record.funcName = model % record.funcName
         record.module = model % record.module
         record.levelname = model % record.levelname
-        return super(ColoredFormatter, self).format(record)
+        return super().format(record)
 
 
 class EddyParser(ArgumentParser):
     """General parser for applications
     """
 
     def __init__(self, *args, **kwargs):
-        super(EddyParser, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.add_base_argument()
 
     def add_base_argument(self):
@@ -85,7 +86,7 @@ def add_base_argument(self):
     def parse_args(self, *args, **kwargs):
         logger = start_logger()
         # Parsing
-        opts = super(EddyParser, self).parse_args(*args, **kwargs)
+        opts = super().parse_args(*args, **kwargs)
         # set current level
         logger.setLevel(getattr(logging, opts.logging_level.upper()))
         return opts
@@ -395,6 +396,17 @@ def parse_args(self, *args, **kwargs):
             axis="X",
         ),
     ),
+    num_point_e=dict(
+        attr_name=None,
+        nc_name="num_point_e",
+        nc_type="u2",
+        nc_dims=("obs",),
+        nc_attr=dict(
+            longname="number of point for effective contour",
+            units="ordinal",
+            description="Number of point for effective contour, if greater than NbSample, there is a resampling",
+        ),
+    ),
     contour_lon_s=dict(
         attr_name=None,
         nc_name="speed_contour_longitude",
@@ -428,6 +440,17 @@ def parse_args(self, *args, **kwargs):
             axis="X",
         ),
     ),
+    num_point_s=dict(
+        attr_name=None,
+        nc_name="num_point_s",
+        nc_type="u2",
+        nc_dims=("obs",),
+        nc_attr=dict(
+            longname="number of point for speed contour",
+            units="ordinal",
+            description="Number of point for speed contour, if greater than NbSample, there is a resampling",
+        ),
+    ),
     shape_error_e=dict(
         attr_name=None,
         nc_name="effective_contour_shape_error",
@@ -590,5 +613,6 @@ def parse_args(self, *args, **kwargs):
         VAR_DESCR_inv[key_old] = key
 
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions

src/py_eddy_tracker/__init__.py

@@ -20,11 +20,12 @@
 Email: [email protected]
 ===========================================================================
 """
+from datetime import datetime
 from .. import EddyParser
-from ..dataset.grid import RegularGridDataset
+from ..dataset.grid import RegularGridDataset, UnRegularGridDataset
 
 
-def grid_parser():
+def filtering_parser():
     parser = EddyParser("Grid filtering")
     parser.add_argument("filename")
     parser.add_argument("grid")
@@ -49,7 +50,7 @@ def grid_parser():
 
 
 def grid_filtering():
-    args = grid_parser().parse_args()
+    args = filtering_parser().parse_args()
 
     h = RegularGridDataset(args.filename, args.longitude, args.latitude)
     if args.low:
@@ -61,3 +62,76 @@ def grid_filtering():
             args.grid, args.cut_wavelength, order=args.filter_order, extend=args.extend
         )
     h.write(args.filename_out)
+
+
+def eddy_id(args=None):
+    parser = EddyParser("Eddy Identification")
+    parser.add_argument("filename")
+    parser.add_argument("datetime")
+    parser.add_argument("h")
+    parser.add_argument("u", help="If it s None, it will be deduce from h")
+    parser.add_argument("v", help="If it s None, it will be deduce from h")
+    parser.add_argument("longitude")
+    parser.add_argument("latitude")
+    parser.add_argument("path_out")
+    help = "Wavelength for mesoscale filter in km"
+    parser.add_argument("--cut_wavelength", default=500, type=float, help=help)
+    parser.add_argument("--filter_order", default=3, type=int)
+    help = "Step between 2 isoline in m"
+    parser.add_argument("--isoline_step", default=0.002, type=float, help=help)
+    help = "Error max accepted to fit circle in percent"
+    parser.add_argument("--fit_errmax", default=55, type=float, help=help)
+    parser.add_argument("--height_unit", default=None, help="Force height unit")
+    parser.add_argument("--speed_unit", default=None, help="Force speed unit")
+    parser.add_argument("--unregular", action="store_true", help="if grid is unregular")
+    help = "Output will be wrote in zarr"
+    parser.add_argument("--zarr", action="store_true", help=help)
+    args = parser.parse_args(args) if args else parser.parse_args()
+
+    date = datetime.strptime(args.datetime, "%Y%m%d")
+    kwargs = dict(
+        step=args.isoline_step,
+        shape_error=args.fit_errmax,
+        pixel_limit=(5, 2000),
+        force_height_unit=args.height_unit,
+        force_speed_unit=args.speed_unit,
+    )
+    a, c = identification(
+        args.filename,
+        args.longitude,
+        args.latitude,
+        date,
+        args.h,
+        args.u,
+        args.v,
+        unregular=args.unregular,
+        cut_wavelength=args.cut_wavelength,
+        filter_order=args.filter_order,
+        **kwargs
+    )
+    out_name = date.strftime("%(path)s/%(sign_type)s_%Y%m%d.nc")
+    a.write_file(path=args.path_out, filename=out_name, zarr_flag=args.zarr)
+    c.write_file(path=args.path_out, filename=out_name, zarr_flag=args.zarr)
+
+
+def identification(
+    filename,
+    lon,
+    lat,
+    date,
+    h,
+    u="None",
+    v="None",
+    unregular=False,
+    cut_wavelength=500,
+    filter_order=1,
+    **kwargs
+):
+    grid_class = UnRegularGridDataset if unregular else RegularGridDataset
+    grid = grid_class(filename, lon, lat)
+    if u == "None" and v == "None":
+        grid.add_uv(h)
+        u, v = "u", "v"
+    if cut_wavelength != 0:
+        grid.bessel_high_filter(h, cut_wavelength, order=filter_order)
+    return grid.eddy_identification(h, u, v, date, **kwargs)