merge

Author: adelepoulle

README.md

@@ -2,7 +2,24 @@
 
 ### How do I get set up? ###
 
-To avoid problem with installation, maybe prefer virtual environnement.
+To avoid problems with installation, use of the virtualenv Python virtual environment is recommended.
+
+Then use pip to install all dependencies (numpy, scipy, matplotlib, netCDF4, cython, pyproj, Shapely, ...), e.g.:
 
 * ** pip install cython numpy matplotlib scipy netCDF4 shapely pyproj**
-* ** python setup.py install**
+
+Then run the following to install the eddy tracker:
+
+* ** python setup.py install**
+
+Two executables are now available in your PATH: EddyIdentification and EddyTracking
+
+Edit the corresponding yaml files and then run the code, e.g.:
+
+* ** EddyIdentification eddy_identification.yaml**
+
+for identification, followed by:
+
+* ** EddyTracking tracking.yaml**
+
+for tracking.

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="pyEddyTracker",
-    version='2.0.3',
+    version='3.0.0',
     description="Py-Eddy-Tracker libraries",
     classifiers=['Development Status :: Alpha',
                  'Topic :: Eddy',

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
@@ -81,8 +81,9 @@ 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_e
     - shape_error_s
 
 TRACK_ARRAY_VARIABLES:

share/tracking.yaml

@@ -4,17 +4,17 @@ DIAGNOSTIC_TYPE: 'SLA'
 
 PATHS:
   # Files produces with EddyIdentification
-  FILES_PATTERN: id_track/acyc_eddy_stat_19930*.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
-VIRTUAL_LEGNTH_MAX: 0
+VIRTUAL_LENGTH_MAX: 0
 
 CLASS:
     MODULE: py_eddy_tracker.featured_tracking.old_tracker_reference

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

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
 
 ===========================================================================
 
@@ -509,7 +508,7 @@ def solve_conflict(cost):
 
     @staticmethod
     def solve_simultaneous(cost):
-        mask = -cost.mask
+        mask = ~cost.mask
         # Count number of link by self obs and other obs
         self_links = mask.sum(axis=1)
         other_links = mask.sum(axis=0)
@@ -533,7 +532,7 @@ def solve_simultaneous(cost):
             # Cost to resolve conflict
             cost_reduce = cost[i_self_keep][:, i_other_keep]
             shape = cost_reduce.shape
-            nb_conflict = (-cost_reduce.mask).sum()
+            nb_conflict = (~cost_reduce.mask).sum()
             logging.debug('Shape conflict matrix : %s, %d conflicts', shape, nb_conflict)
 
             if nb_conflict >= (shape[0] + shape[1]):
@@ -637,7 +636,7 @@ def tracking(self, other):
             dist[mask_accept_dist])
 
         cost_mat = ma.empty(mask_accept_dist.shape, dtype='f4')
-        cost_mat.mask = -mask_accept_dist
+        cost_mat.mask = ~mask_accept_dist
         cost_mat[mask_accept_dist] = cost_values
 
         i_self, i_other = self.solve_function(cost_mat)
@@ -727,8 +726,8 @@ def filled_by_interpolation(self, mask):
             var = field[0]
             if var in ['n', 'virtual', 'track'] or var in self.array_variables:
                 continue
-            self.obs[var][mask] = interp(index[mask], index[-mask],
-                                         self.obs[var][-mask])
+            self.obs[var][mask] = interp(index[mask], index[~mask],
+                                         self.obs[var][~mask])
 
     def extract_longer_eddies(self, nb_min, nb_obs, compress_id=True):
         """Select eddies which are longer than nb_min

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
 ===========================================================================
 
 
@@ -203,7 +203,7 @@ 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
 
 ===========================================================================
 
@@ -88,7 +87,7 @@ def __init__(self, contlon, contlat, eddy, grd):
         self.amplitude = 0  # atleast_1d(0.)
         self.local_extrema = None  # int(0)
         self.local_extrema_inds = None
-        self.sla = ma.array(self.sla, mask=-self.mask)
+        self.sla = ma.array(self.sla, mask=~self.mask)
 
     @property
     def islice(self):