Updated copyright headers. New version will be 3.0.0

Author: emason

share/eddy_identification.yaml

@@ -1,42 +1,41 @@
+
 # Two diagnostics, based on SLA (e.g., Chelton et al, 2011)
 DIAGNOSTIC_TYPE: 'SLA'
 
 # Specify domain
 DOMAIN:
-  #~ THE_DOMAIN: 'Global'
   THE_DOMAIN: 'Regional'
-  LONMIN: -100
-  LONMAX: -5
-  LATMIN: 10
-  LATMAX: 45
-  DATE_STR: 2014-12-27
-  DATE_END: 2014-12-31
+  LONMIN: -40
+  LONMAX: -10
+  LATMIN: 18
+  LATMAX: 34
+  DATE_STR: 2007-06-27
+  DATE_END: 2009-12-31
 
 DATASET:
     # Path to data
-    #~ DATA_DIR: '/data/PVA/Externe/global/delayed-time/grids/msla/all-sat-merged/h/2014/'
-    DATA_DIR: '/home/adelepoulle/2014/'
+    DATA_DIR: '/marula/emason/data/altimetry/global/delayed-time/grids/msla/all-sat-merged/h/'
     # Model to select file
     FILES_MODEL: dt_global_allsat_msla_h_????????_????????.nc
     # Model to extract date (regular expression)
     DATE_REGEXP: dt_global_allsat_msla_h_([0-9]*)_[0-9]*.nc
     # Model to transfer date to python datetime
     DATE_MODEL: '%Y%m%d'
     # Grid Name to compute analysis
-    VAR_NAME: Grid_0001
+    VAR_NAME: sla
     # Longitude variable
-    LON_NAME: NbLongitudes
+    LON_NAME: lon
     # Latitude variable
-    LAT_NAME: NbLatitudes
+    LAT_NAME: lat
     # Step to do SUBSAMPLING (1 no subsampling)
     SUBSAMPLING: 1
 
 PATHS:
   # Obtain file from:
   # http://www-po.coas.oregonstate.edu/research/po/research/rossby_radius/
-  RW_PATH: 'rossrad.dat'
+  RW_PATH: '/home/emason/Dropbox/rossrad.dat'
   # Path for saving of outputs
-  SAVE_DIR: 'test/'
+  SAVE_DIR: '/home/emason/toto/'
 
   # Reference Julian day (Julian date at Jan 1, 1992)
 JDAY_REFERENCE: 2448623.
@@ -46,10 +45,11 @@ CONTOUR_PARAMETER:
   # Set SLA contour spacing (cm)
   CONTOUR_PARAMETER_SLA:
     MAX_SLA: 100.
-    INTERVAL: 0.5
+    INTERVAL: 0.25
+    #~ INTERVAL: 1
 
 # Shape error (see Kurian et al 2011)
-SHAPE_ERROR: 55. # % (Mason et al 2014 use 55%)
+SHAPE_ERROR: 95. # % (Mason et al 2014 use 55%)
 
 # Filtering
 SMOOTHING: Yes
@@ -60,9 +60,9 @@ SMOOTHING_SLA:
 
 # Min and max permitted eddy radii [degrees] and amplitudes (cm)
 # 0.4 for DT10, 0.35 for DT14
-RADMIN: 0.35
+RADMIN: 0.15
 RADMAX: 4.461
-AMPMIN: 0.
+AMPMIN: 0.005
 AMPMAX: 150.
 
 # MPM14 use 1; CSS11 have no limit
@@ -81,6 +81,7 @@ EVOLVE_AREA_MAX: 500 # max change in area
 # - speed-based contour points
 # - shape test values
 # - profiles of swirl velocity from effective contour inwards
+# Useful for working with ARGO data    
 TRACK_EXTRA_VARIABLES:
     - shape_error
     - shape_error_s

share/tracking.yaml

@@ -4,13 +4,14 @@ DIAGNOSTIC_TYPE: 'SLA'
 
 PATHS:
   # Files produces with EddyIdentification
-  FILES_PATTERN: id_track/acyc_eddy_stat_19930*.nc
+  FILES_PATTERN: /data/adelepoulle/Test/Test_eddy/20160330_brasilia_comparaison/brasil/Anticyclonic_*.nc
+  FILES_PATTERN: /home/emason/toto/Anticyclonic_*.nc
   # Path and filename of Chelton et al (1998) Rossby radius data
   # Obtain file from:
   # http://www-po.coas.oregonstate.edu/research/po/research/rossby_radius/
-  RW_PATH: 'rossrad.dat'
+  RW_PATH: '/home/emason/Dropbox/rossrad.dat'
   # Path for saving of outputs
-  SAVE_DIR: 'tracks_acyc_test/'
+  SAVE_DIR: '/home/emason/toto/'
 
 # Minimum number of observations to store eddy
 TRACK_DURATION_MIN: 4

src/py_eddy_tracker/__init__.py

@@ -1,4 +1,32 @@
 # -*- 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) 2014-2017 by Antoine Delepoulle and Evan Mason
+Email: [email protected]
+===========================================================================
+
+__init__.py
+
+Version 3.0.0
+
+===========================================================================
+
+"""
 from argparse import ArgumentParser
 import logging
 

src/py_eddy_tracker/grid/__init__.py

@@ -1,4 +1,32 @@
 # -*- 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) 2014-2017 by Antoine Delepoulle and Evan Mason
+Email: [email protected]
+===========================================================================
+
+__init__.py
+
+Version 3.0.0
+
+===========================================================================
+"""
+
 from netCDF4 import Dataset
 from scipy import interpolate
 from scipy import spatial
@@ -347,6 +375,11 @@ def get_aviso_f_pm_pn(self):
         lonv = self.half_interp(self.lonpad[:-1], self.lonpad[1:])
         latv = self.half_interp(self.latpad[:-1], self.latpad[1:])
 
+        print 'self.lonpad.shape',self.lonpad.shape
+        print 'self.latpad.shape',self.latpad.shape
+        print 'self.lon.shape',self._lon.shape
+        print 'self.lat.shape',self._lat.shape
+
         # Get p_m and p_n
         p_m = zeros(self.lonpad.shape)
         p_m[:, 1:-1] = self.haversine_dist(lonu[:, :-1], latu[:, :-1],

src/py_eddy_tracker/grid/aviso.py

@@ -1,4 +1,31 @@
 # -*- 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) 2014-2017 by Evan Mason and Antoine Delepoulle
+Email: [email protected]
+===========================================================================
+
+aviso.py
+
+Version 3.0.0
+
+===========================================================================
+"""
 from matplotlib.dates import date2num
 from scipy import ndimage
 from scipy import spatial

src/py_eddy_tracker/observations.py

@@ -16,14 +16,13 @@
     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) 2014-2015 by Evan Mason
+Copyright (c) 2014-2017 by Evan Mason and Antoine Delepoulle
 Email: [email protected]
 ===========================================================================
 
+observations.py
 
-py_eddy_tracker_amplitude.py
-
-Version 2.0.3
+Version 3.0.0
 
 ===========================================================================
 
@@ -392,6 +391,7 @@ def mask_function(self, other):
 
     @staticmethod
     def cost_function(records_in, records_out, distance):
+        m = EddiesObservations.across_ground(records_in, records_out, distance)
         cost = ((records_in['amplitude'] - records_out['amplitude']
                  ) / records_in['amplitude']
                 ) ** 2
@@ -401,7 +401,7 @@ def cost_function(records_in, records_out, distance):
         cost += (distance / 125) ** 2
         cost **= 0.5
         # Mask value superior at 60 % of variation
-        # return ma.array(cost, mask=m)
+        return ma.array(cost, mask=m)
         return cost
 
     def circle_mask(self, other, radius=100):

src/py_eddy_tracker/property_functions.py

@@ -17,13 +17,13 @@
     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) 2014-2015 by Evan Mason
+Copyright (c) 2014-2017 by Evan Mason and Antoine Delepoulle
 Email: [email protected]
 ===========================================================================
 
-py_eddy_tracker_classes.py
+property_functions.py
 
-Version 2.0.3
+Version 3.0.0
 ===========================================================================
 
 
@@ -206,7 +206,7 @@ def get_uavg(eddy, contours, centlon_e, centlat_e, poly_eff, grd,
                             poly_eff.vertices[:, 1].copy())
 
     theseglon, theseglat = uniform_resample(
-        theseglon, theseglat, method='akima')
+        theseglon, theseglat, method='interp1d')
 
     if 'RectBivariate' in eddy.interp_method:
         uavg = eddy.uspd_coeffs.ev(theseglat[1:], theseglon[1:]).mean()
@@ -261,7 +261,7 @@ def get_uavg(eddy, contours, centlon_e, centlat_e, poly_eff, grd,
             continue
         any_inner_contours = True
 
-        seglon, seglat = (poly_i.vertices[:, 0], poly_i.vertices[:, 1])
+        seglon, seglat = (poly_i.vertices[:, 0].copy(), poly_i.vertices[:, 1].copy())
         seglon, seglat = uniform_resample(seglon, seglat, method='interp1d')
 
         # Interpolate uspd to seglon, seglat, then get mean

src/py_eddy_tracker/property_objects.py

@@ -16,14 +16,13 @@
     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) 2014-2015 by Evan Mason
+Copyright (c) 2014-2017 by Evan Mason and Antoine Delepoulle
 Email: [email protected]
 ===========================================================================
 
+property_objects.py
 
-py_eddy_tracker_amplitude.py
-
-Version 2.0.3
+Version 3.0.0
 
 ===========================================================================
 
@@ -55,7 +54,7 @@ class Amplitude (object):
       grd:
         A grid object
     """
-    ___slots__ = (
+    __slots__ = (
         'eddy',
         'sla',
         'h_0',

src/py_eddy_tracker/tracking.py

@@ -16,14 +16,13 @@
     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) 2014-2015 by Evan Mason
+Copyright (c) 2014-2017 by Evan Mason and Antoine Delepoulle
 Email: [email protected]
 ===========================================================================
 
+tracking.py
 
-py_eddy_tracker_amplitude.py
-
-Version 2.0.3
+Version 3.0.0
 
 ===========================================================================
 

src/py_eddy_tracker/tracking_objects.py

@@ -17,14 +17,14 @@
     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) 2014-2015 by Evan Mason
+Copyright (c) 2014-2017 by Evan Mason and Antoine Delepoulle
 Email: [email protected]
 ===========================================================================
 
 
-make_eddy_tracker_list_obj.py
+tracking_objects.py
 
-Version 2.0.3
+Version 3.0.0
 
 
 ===========================================================================