Add a low pass filter option to remove noisy data to answer at AntSimi#42

Author: AntSimi

CHANGELOG.rst

@@ -9,6 +9,16 @@ and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0
 [Unreleased]
 ------------
 
+Fixed
+^^^^^
+- Use `safe_load` for yaml load
+
+Added
+^^^^^
+- Identification file could be load in memory before to be read with netcdf library to get speed up in case of slow disk
+- Add a filter option in EddyId to be able to remove fine scale (like noise) with same filter order than high scale
+  filter
+
 [3.3.0] - 2020-12-03
 --------------------
 Added

src/py_eddy_tracker/appli/grid.py

@@ -69,13 +69,21 @@ def eddy_id(args=None):
     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)
+    help = (
+        "Wavelength for mesoscale filter in km to remove low scale if 2 args is given first one will be"
+        "used to remove high scale and second value to remove low scale"
+    )
+    parser.add_argument(
+        "--cut_wavelength", default=[500], type=float, help=help, nargs="+"
+    )
     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(
+        "--lat_max", default=85, type=float, help="Maximal latitude filtered"
+    )
     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")
@@ -102,14 +110,25 @@ def eddy_id(args=None):
         action=DictAction,
     )
     args = parser.parse_args(args) if args else parser.parse_args()
+
+    cut_wavelength = args.cut_wavelength
+    nb_cw = len(cut_wavelength)
+    if nb_cw > 2 or nb_cw == 0:
+        raise Exception("You must specify 1 or 2 values for cut wavelength.")
+    elif nb_cw == 1:
+        cut_wavelength = [0, *cut_wavelength]
+    inf_bnds, upper_bnds = cut_wavelength
+
     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,
+        nb_step_to_be_mle=0,
     )
+
     a, c = identification(
         args.filename,
         args.longitude,
@@ -119,7 +138,9 @@ def eddy_id(args=None):
         args.u,
         args.v,
         unregular=args.unregular,
-        cut_wavelength=args.cut_wavelength,
+        cut_wavelength=upper_bnds,
+        cut_highwavelength=inf_bnds,
+        lat_max=args.lat_max,
         filter_order=args.filter_order,
         indexs=args.indexs,
         sampling=args.sampling,
@@ -141,6 +162,8 @@ def identification(
     v="None",
     unregular=False,
     cut_wavelength=500,
+    cut_highwavelength=0,
+    lat_max=85,
     filter_order=1,
     indexs=None,
     **kwargs
@@ -150,6 +173,9 @@ def identification(
     if u == "None" and v == "None":
         grid.add_uv(h)
         u, v = "u", "v"
+    kw_filter = dict(order=filter_order, lat_max=lat_max)
+    if cut_highwavelength != 0:
+        grid.bessel_low_filter(h, cut_highwavelength, **kw_filter)
     if cut_wavelength != 0:
-        grid.bessel_high_filter(h, cut_wavelength, order=filter_order)
+        grid.bessel_high_filter(h, cut_wavelength, **kw_filter)
     return grid.eddy_identification(h, u, v, date, **kwargs)