Merge branch 'master' of https://github.com/AntSimi/py-eddy-tracker

Author: CoriPegliasco

examples/02_eddy_identification/pet_sla_and_adt.py

@@ -55,32 +55,32 @@ def update_axes(ax, mappable=None):
 # over filtered
 ax = start_axes(f"ADT (m) filtered ({wavelength}km)")
 m = g.display(ax, "adt", vmin=-0.15, vmax=0.15)
-a_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_a_sla)
+a_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_c_adt)
 ax.legend(), update_axes(ax, m)
 
 ax = start_axes(f"SLA (m) filtered ({wavelength}km)")
 m = g.display(ax, "sla", vmin=-0.15, vmax=0.15)
-a_sla.display(ax, **kwargs_c_adt), c_sla.display(ax, **kwargs_c_sla)
+a_sla.display(ax, **kwargs_a_sla), c_sla.display(ax, **kwargs_c_sla)
 ax.legend(), update_axes(ax, m)
 
 # %%
 # over raw
 ax = start_axes("ADT (m)")
 m = g.display(ax, "adt_raw", vmin=-0.15, vmax=0.15)
-a_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_a_sla)
+a_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_c_adt)
 ax.legend(), update_axes(ax, m)
 
 ax = start_axes("SLA (m)")
 m = g.display(ax, "sla_raw", vmin=-0.15, vmax=0.15)
-a_sla.display(ax, **kwargs_c_adt), c_sla.display(ax, **kwargs_c_sla)
+a_sla.display(ax, **kwargs_a_sla), c_sla.display(ax, **kwargs_c_sla)
 ax.legend(), update_axes(ax, m)
 
 # %%
 # Display detection
 ax = start_axes("Eddies detected")
 a_adt.display(ax, **kwargs_a_adt)
-a_sla.display(ax, **kwargs_c_adt)
-c_adt.display(ax, **kwargs_a_sla)
+a_sla.display(ax, **kwargs_a_sla)
+c_adt.display(ax, **kwargs_c_adt)
 c_sla.display(ax, **kwargs_c_sla)
 ax.legend()
 update_axes(ax)

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/02_eddy_identification/pet_sla_and_adt.ipynb

@@ -102,7 +102,7 @@
       },
       "outputs": [],
       "source": [
-        "ax = start_axes(f\"ADT (m) filtered ({wavelength}km)\")\nm = g.display(ax, \"adt\", vmin=-0.15, vmax=0.15)\na_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_a_sla)\nax.legend(), update_axes(ax, m)\n\nax = start_axes(f\"SLA (m) filtered ({wavelength}km)\")\nm = g.display(ax, \"sla\", vmin=-0.15, vmax=0.15)\na_sla.display(ax, **kwargs_c_adt), c_sla.display(ax, **kwargs_c_sla)\nax.legend(), update_axes(ax, m)"
+        "ax = start_axes(f\"ADT (m) filtered ({wavelength}km)\")\nm = g.display(ax, \"adt\", vmin=-0.15, vmax=0.15)\na_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_c_adt)\nax.legend(), update_axes(ax, m)\n\nax = start_axes(f\"SLA (m) filtered ({wavelength}km)\")\nm = g.display(ax, \"sla\", vmin=-0.15, vmax=0.15)\na_sla.display(ax, **kwargs_a_sla), c_sla.display(ax, **kwargs_c_sla)\nax.legend(), update_axes(ax, m)"
       ]
     },
     {
@@ -120,7 +120,7 @@
       },
       "outputs": [],
       "source": [
-        "ax = start_axes(\"ADT (m)\")\nm = g.display(ax, \"adt_raw\", vmin=-0.15, vmax=0.15)\na_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_a_sla)\nax.legend(), update_axes(ax, m)\n\nax = start_axes(\"SLA (m)\")\nm = g.display(ax, \"sla_raw\", vmin=-0.15, vmax=0.15)\na_sla.display(ax, **kwargs_c_adt), c_sla.display(ax, **kwargs_c_sla)\nax.legend(), update_axes(ax, m)"
+        "ax = start_axes(\"ADT (m)\")\nm = g.display(ax, \"adt_raw\", vmin=-0.15, vmax=0.15)\na_adt.display(ax, **kwargs_a_adt), c_adt.display(ax, **kwargs_c_adt)\nax.legend(), update_axes(ax, m)\n\nax = start_axes(\"SLA (m)\")\nm = g.display(ax, \"sla_raw\", vmin=-0.15, vmax=0.15)\na_sla.display(ax, **kwargs_a_sla), c_sla.display(ax, **kwargs_c_sla)\nax.legend(), update_axes(ax, m)"
       ]
     },
     {
@@ -138,7 +138,7 @@
       },
       "outputs": [],
       "source": [
-        "ax = start_axes(\"Eddies detected\")\na_adt.display(ax, **kwargs_a_adt)\na_sla.display(ax, **kwargs_c_adt)\nc_adt.display(ax, **kwargs_a_sla)\nc_sla.display(ax, **kwargs_c_sla)\nax.legend()\nupdate_axes(ax)"
+        "ax = start_axes(\"Eddies detected\")\na_adt.display(ax, **kwargs_a_adt)\na_sla.display(ax, **kwargs_a_sla)\nc_adt.display(ax, **kwargs_c_adt)\nc_sla.display(ax, **kwargs_c_sla)\nax.legend()\nupdate_axes(ax)"
       ]
     },
     {

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

@@ -20,27 +20,33 @@
         "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/GridFiltering",
-        "src/scripts/EddyId",
         "src/scripts/EddySubSetter",
         "src/scripts/EddyTranslate",
         "src/scripts/EddyTracking",
         "src/scripts/EddyFinalTracking",
         "src/scripts/EddyMergeCorrespondances",
-        "src/scripts/ZarrDump",
         "src/scripts/GUIEddy",
     ],
     zip_safe=False,
     entry_points=dict(
         console_scripts=[
-            "MergeEddies = py_eddy_tracker.appli:merge_eddies",
-            "EddyNetworkGroup = py_eddy_tracker.network:build_network",
-            "EddyAnim = py_eddy_tracker.appli:anim"
+            # 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
+            "EddyNetworkGroup = py_eddy_tracker.appli.network:build_network",
+            "EddyNetworkBuildPath = py_eddy_tracker.appli.network:divide_network",
+            # anim/gui
+            "EddyAnim = py_eddy_tracker.appli.gui:anim",
+            # misc
+            "ZarrDump = py_eddy_tracker.appli.misc:zarrdump",
         ]
     ),
     package_data={

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
@@ -385,6 +386,17 @@ 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",
@@ -418,6 +430,17 @@ 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",
@@ -579,5 +602,6 @@ 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

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+"""
+===========================================================================
+This file is part of py-eddy-tracker.
+
+    py-eddy-tracker is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    py-eddy-tracker is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with py-eddy-tracker.  If not, see <http://www.gnu.org/licenses/>.
+
+Copyright (c) 2014-2020 by Evan Mason
+Email: [email protected]
+===========================================================================
+"""
+from netCDF4 import Dataset
+from .. import EddyParser
+from ..observations.tracking import TrackEddiesObservations
+
+
+def merge_eddies():
+    parser = EddyParser("Merge eddies")
+    parser.add_argument("filename", nargs="+", help="all file to merge")
+    parser.add_argument("out", help="output file")
+    parser.add_argument(
+        "--add_rotation_variable", help="add rotation variables", action="store_true"
+    )
+    parser.add_argument(
+        "--include_var", nargs="+", type=str, help="use only listed variable"
+    )
+    args = parser.parse_args()
+
+    if args.include_var is None:
+        with Dataset(args.filename[0]) as h:
+            args.include_var = h.variables.keys()
+
+    obs = TrackEddiesObservations.load_file(
+        args.filename[0], raw_data=True, include_vars=args.include_var
+    )
+    if args.add_rotation_variable:
+        obs = obs.add_rotation_type()
+    for filename in args.filename[1:]:
+        other = TrackEddiesObservations.load_file(
+            filename, raw_data=True, include_vars=args.include_var
+        )
+        if args.add_rotation_variable:
+            other = other.add_rotation_type()
+        obs = obs.merge(other)
+    obs.write_file(filename=args.out)