use of slots to try to manage leaks

Author: adelepoulle

src/py_eddy_tracker/grid/__init__.py

@@ -10,7 +10,7 @@
 from ..tracking_objects import nearest
 
 
-class PyEddyTracker(object):
+class BaseData(object):
     """
     Base object
 
@@ -29,7 +29,42 @@ class PyEddyTracker(object):
       ROMS:   get_ROMS_f_pm_pn
 
     """
-
+    
+    __slots__ = (
+        'zero_crossing',
+        'slice_i',
+        'slice_j',
+        'slice_i_pad',
+        'slice_j_pad',
+        'slice_i_unpad',
+        'slice_j_unpad',
+        'eke',
+        'u_val',
+        'upad',
+        'v_val',
+        'vpad',
+        '_uspd',
+        'm_val',
+        'm_x',
+        'm_y',
+        '_lon',
+        '_lat',
+        '_f_val',
+        '_gof',
+        '_pm',
+        '_pn',
+        '_dx',
+        '_dy',
+        '_umask',
+        '_vmask',
+        'grid_filename',
+        'grid_date',
+        'domain',
+        'pad',
+        'shape',
+        'mask',
+        )
+    
     GRAVITY = 9.81
     earth_radius = 6371315.0
 
@@ -73,7 +108,7 @@ def read_nc(self, varname, indices=slice(None)):
           indices : slice
         """
         with Dataset(self.grid_filename) as h_nc:
-            return h_nc.variables[varname][:][indices]
+            return h_nc.variables[varname][indices]
 
     @property
     def nc_variables(self):
@@ -120,7 +155,7 @@ def set_initial_indices(self):
         lonmin, lonmax = self.lonmin, self.lonmax
         latmin, latmax = self.latmin, self.latmax
 
-        logging.info('Setting initial indices to *%s* domain', self.the_domain)
+        logging.info('Setting initial indices to *%s* domain', self.domain)
         logging.info('lonmin = %s, lonmax = %s, latmin = %s, latmax = %s',
                      lonmin, lonmax, latmin, latmax)
         latmin_offset = latmin + (0.5 * (latmax - latmin))
@@ -287,7 +322,6 @@ def get_aviso_f_pm_pn(self):
         p_n[-1] = p_n[-2]
         self._dy = p_n
         self._pn = reciprocal(p_n)
-        return self
 
     def u2rho_2d(self, uu_in):
         """
@@ -343,27 +377,19 @@ def set_basemap(self, with_pad=True):
         logging.info('Computing Basemap')
         # Create Basemap instance for Mercator projection.
         self.m_val = Proj(
-            '+proj=merc '
-            '+llcrnrlon=%(llcrnrlon)f '
-            '+llcrnrlat=%(llcrnrlat)f '
-            '+urcrnrlon=%(urcrnrlon)f '
-            '+urcrnrlat=%(urcrnrlat)f '
-            '+lat_ts=%(lat_ts)f' %
-            dict(
-                llcrnrlon=self.lonmin - 1,
-                urcrnrlon=self.lonmax + 1,
-                llcrnrlat=self.latmin - 1,
-                urcrnrlat=self.latmax + 1,
-                lat_ts=0.5 * (self.latmin + self.latmax)
-                )
+            proj='merc',
+            llcrnrlon=self.lonmin - 1,
+            urcrnrlon=self.lonmax + 1,
+            llcrnrlat=self.latmin - 1,
+            urcrnrlat=self.latmax + 1,
+            lat_ts=0.5 * (self.latmin + self.latmax)
             )
 
         if with_pad:
             x_val, y_val = self.m_val(self.lonpad, self.latpad)
         else:
             x_val, y_val = self.m_val(self.lon, self.lat)
         self.m_x, self.m_y = x_val, y_val
-        return self
 
     def set_geostrophic_velocity(self, zeta):
         """
@@ -382,7 +408,6 @@ def set_geostrophic_velocity(self, zeta):
         self.vpad[:] = self.u2rho_2d(
             ma.array((zeta1 - zeta2) *0.5 * (pm1 + pm2), mask=self.umask))
         self.vpad *= self.gof
-        return self
 
     def set_u_v_eke(self, pad=2):
         """
@@ -425,7 +450,6 @@ def set_interp_coeffs(self, sla, uspd):
             self.lat[:, 0], self.lon[0], sla, kx=1, ky=1)
         self.uspd_coeffs = interpolate.RectBivariateSpline(
             self.lat[:, 0], self.lon[0], uspd, kx=1, ky=1)
-        return self
 
     @staticmethod
     def create_index_inverse(slice_to_inverse, size):

src/py_eddy_tracker/grid/aviso.py

@@ -8,10 +8,10 @@
 import logging
 from netCDF4 import Dataset
 
-from . import PyEddyTracker
+from . import BaseData
 
 
-class AvisoGrid(PyEddyTracker):
+class AvisoGrid(BaseData):
     """
     Class to satisfy the need of the eddy tracker
     to have a grid class
@@ -20,6 +20,26 @@ class AvisoGrid(PyEddyTracker):
             m=100.,
             cm=1.,
             )
+    __slots__ = (
+        'lonmin',
+        'lonmax',
+        'latmin',
+        'latmax',
+        'lon_name',
+        'lat_name',
+        'grid_name',
+        '_lon',
+        '_lat',
+        'fillval',
+        '_angle',
+        'sla_coeffs',
+        'uspd_coeffs',
+        '__lon',
+        '__lat',
+        '__lonpad',
+        '__latpad',
+        'labels',
+        )
 
     def __init__(self, aviso_file, the_domain,
                  lonmin, lonmax, latmin, latmax, grid_name, lon_name,
@@ -30,7 +50,7 @@ def __init__(self, aviso_file, the_domain,
         super(AvisoGrid, self).__init__()
         logging.info('Initialising the *AVISO_grid*')
         self.grid_filename = aviso_file
-        self.the_domain = the_domain
+        self.domain = the_domain
         self.lonmin = float(lonmin)
         self.lonmax = float(lonmax)
         self.latmin = float(latmin)
@@ -50,12 +70,12 @@ def __init__(self, aviso_file, the_domain,
         self._lon, self._lat = meshgrid(self._lon, self._lat)
         self._angle = zeros(self._lon.shape)
 
-        if 'MedSea' in self.the_domain:
+        if 'MedSea' in self.domain:
             self._lon -= 360.
 
         # zero_crossing, used for handling a longitude range that
         # crosses zero degree meridian
-        if lonmin < 0 and lonmax >= 0 and 'MedSea' not in self.the_domain:
+        if lonmin < 0 and lonmax >= 0 and 'MedSea' not in self.domain:
             self.zero_crossing = True
 
         self.sla_coeffs = None
@@ -73,6 +93,9 @@ def __init__(self, aviso_file, the_domain,
 #         self.shape = (self.f_coriolis.shape[0] - pad2,
 #                       self.f_coriolis.shape[1] - pad2)
 
+    def set_filename(self, file_name):
+        self.grid_filename = file_name
+    
     def get_aviso_data(self, aviso_file):
         """
         Read nc data from AVISO file
@@ -104,10 +127,9 @@ def get_aviso_data(self, aviso_file):
             zeta = zeta.T
 
         zeta *= self.KNOWN_UNITS[units]  # units to cm
-        if hasattr(zeta, 'mask'):
-            return zeta
-        else:
-            return ma.array(zeta)
+        if not hasattr(zeta, 'mask'):
+            zeta = ma.array(zeta)
+        return zeta
 
     def set_mask(self, sla):
         """
@@ -116,7 +138,7 @@ def set_mask(self, sla):
             self.mask = None
         else:
             self.mask = sla.mask.copy()
-            if 'Global' in self.the_domain:
+            if 'Global' in self.domain:
 
                 # Close Drake Passage
                 minus70 = argmin(abs(self.lonpad[0] + 70))
@@ -156,14 +178,14 @@ def set_mask(self, sla):
                 plus9 = argmin(abs(self.latpad[:, 0] - 9))
                 sea_label = self.labels[plus9, plus200]
                 self.mask += self.labels != sea_label
-        return self
 
     def fillmask(self, data, mask):
         """
         Fill missing values in an array with an average of nearest
         neighbours
         From http://permalink.gmane.org/gmane.comp.python.scientific.user/19610
         """
+        raise Exception('Use convolution to fill data')
         assert data.ndim == 2, 'data must be a 2D array.'
         fill_value = 9999.99
         data[mask == 0] = fill_value

src/py_eddy_tracker/property_functions.py

@@ -394,6 +394,9 @@ def collection_loop(contours, grd, eddy, x_i=None, c_s_xi=None):
         # Loop over individual c_s contours (i.e., every eddy in field)
         for cont in contour_paths:
             # Filter for closed contours
+            
+            # I don't understand the cost of this addition
+            #~ eddy.swirl.is_valid(eddy.swirl.level_index[corrected_coll_index] + i_cont)
             if not cont.isvalid:
                 continue
             centlon_e, centlat_e, eddy_radius_e, aerr = cont.fit_circle()