Merge branch 'master' of github.com:VACUMM/vacumm

* 'master' of github.com:VACUMM/vacumm:
  Introduction of atmospheric and wave variables
  Add new classes for MesoNh, Sympĥonie and WW3 models
  mars3d model : add t,z,y,xaxis_name class attributes
  fix vacumm.validator.valid.ValidXYT.py : bad import
  fix vacumm.diag.dynamics : bad indexes

lib/python/vacumm/data/misc/dataset.py

@@ -2075,14 +2075,22 @@ def torect(self, var, curvsel=None):
 class AtmosSurfaceDataset(Dataset):
 
     # For auto-declaring methods
-    auto_generic_var_names = ['senhf', 'lathf', 'lhf', 'swhf', 'lwhf', 'evap', 'rain',
-        'taux', 'tauy', 'u10m', 'v10m']
+    auto_generic_var_names = ['nethf', 'senhf', 'hfsen', 'lathf', 'hflat', 'swhf', 'lwhf', 'evap', 'rain',
+        'taux', 'tauy', 'u10m', 'v10m', 't2m', 'hu2m', 'z0a', 'cda', 'cha', 'cea']
 
 @getvar_decmets
 class OceanSurfaceDataset(Dataset):
 
     # For auto-declaring methods
-    auto_generic_var_names = ['sst', 'sss', 'ssh', 'usurf', 'vsurf', 'hs']
+    auto_generic_var_names = ['sst', 'sss', 'ssh', 'usurf', 'vsurf']
+
+@getvar_decmets
+class WaveSurfaceDataset(Dataset):
+    # For auto-declaring methods
+    auto_generic_var_names = ['hs','mss','mssx','mssy','mss','dir','fp','t0m1','lm',
+        'ubot','uubr','vubr','bhd','foc','utwo','vtwo','utaw','vtaw','uuss','vuss','utus','vtus',
+        'fbb','utbb','vtbb','mapsta','bathy','wlv','ucur','vcur','uwnd','vwnd','dp','cha','utaw','vtaw']
+
 
 @getvar_decmets
 class OceanDataset(OceanSurfaceDataset):
@@ -3663,11 +3671,15 @@ def plot_ped(self, select, **kwargs):
         m.post_plot(**plotkw)
         return m,c
 
+@getvar_decmets
 class AtmosDataset(AtmosSurfaceDataset):
     name = 'atmos'
     description = 'Generic atmospheric dataset'
-    ncobj_specs = {}
+    default_depth_search_mode = None
 
+    # For auto-declaring methods
+    auto_generic_var_names = ['oro','wdir','wspd','ua','va','wa','tair','pa',
+        'tkea']
 
 def _at_(at, squeezet=False, focus=None, prefix=False):
     """Convert location letters"""

lib/python/vacumm/data/model/__init__.py

@@ -50,3 +50,6 @@
 import mars3d
 import nemo
 import swan
+import mesonh
+import symphonie
+import ww3

lib/python/vacumm/data/model/mars3d.py

@@ -69,10 +69,22 @@ class Mars3D(OceanDataset,AtmosSurfaceDataset):
     #: Positive up?
     positive = 'up'
 
+    #: Name of time axis
+    taxis_name = 'time'
+
+    #: Name of vertical axis
+    zaxis_name = 'levels'
+
+    #: Name of meridional / j axis
+    yaxis_name = 'nj'
+
+    #: Name of zonal / i axis
+    xaxis_name = 'ni'
+
     # Local specs
     ncobj_specs = {
 
-        # salinity
+        # diffusivity
         'kz':{'search':{'id':['kzm']}},
 
         # sea surface temperature

lib/python/vacumm/data/model/mesonh.py

@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+# -*- coding: utf8 -*-
+#
+# Copyright or © or Copr. Actimar/IFREMER (2010-2017)
+# 
+# [email protected]
+#
+# This software is a computer program whose purpose is to provide
+# utilities for handling oceanographic and atmospheric data,
+# with the ultimate goal of validating the MARS model from IFREMER.
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+# 
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+# 
+
+
+
+__author__ = 'Valerie Garnier'
+__email__ = '[email protected]'
+__date__ = '2015-07-08'
+__doc__ = 'MesoNH model data manipulation'
+
+
+from vacumm.data import register_dataset
+from vacumm.data.misc.dataset import AtmosDataset,OceanSurfaceDataset
+
+
+class MesoNH(AtmosDataset,OceanSurfaceDataset):
+    """:class:`~vacumm.data.misc.dataset.Dataset` class to read the
+    MesoNH ocean model outputs
+    
+    Read the :class:`~vacumm.data.misc.dataset.Dataset` for more information
+    """
+
+    name = 'mesonh'
+    description = "The MesoNH non-hydrostatic mesoscale atmospheric model of the French research community"
+
+
+# remplacer names par id a priori ?
+
+    ncobj_specs = {
+
+        # sea surface zonal wind
+        'usurf':{
+            'inherit':'ua',   # relatif a la methode get_ua et non au nom de variable
+            'select':{'level':slice(0, None)},
+            'squeeze':'z',
+        }
+        ,
+        # sea surface meridional wind
+        'vsurf':{
+            'inherit':'v3d', # heritage des specs
+            'select':{'level':slice(0, None)},
+            'squeeze':'z',
+        }
+
+    }
+
+    positive = 'up'
+
+    def nbcells(self):
+
+        """
+        For MesoNH, the number of cells along X and Y axes must be a multiple of 2,3,5
+        """ 
+
+        list_nb_cells = []
+        for l in range(10): 
+            for m in range(10):
+               for n in range(10):
+                   list_nb_cells.append( (2**l*3**m*5**n,l,m,n) )
+
+        return sorted(list_nb_cells)
+
+#: Alias for :class:`MesoNH`
+mesonh = MesoNH
+
+# Register the class
+register_dataset(mesonh)
+
+
+if __name__ == '__main__' :
+
+    nb_cell = mesonh.mesonh().nb_cells()
+    print nb_cell[0:100]
+    from vacumm.data import DS
+    from vacumm.misc.plot import map2 as map
+    #map(sshmod[0, Ellipsis], res=None)
+    print "test utus"
+    f = DS('/temp/vgarnier/AMICO/WORKENV_METHODO/AROME/./AROME_IROISE_20110901-0000_20110910-0000.nc','mesonh')
+    xwind = f.get_u10m()
+    xxx
+    #f.get_depth()
+    xxxx
+

lib/python/vacumm/data/model/symphonie.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+# -*- coding: utf8 -*-
+#
+# Copyright or © or Copr. Actimar/IFREMER (2010-2017)
+# 
+# [email protected]
+#
+# This software is a computer program whose purpose is to provide
+# utilities for handling oceanographic and atmospheric data,
+# with the ultimate goal of validating the MARS model from IFREMER.
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+# 
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+# 
+
+
+
+__author__ = 'Valerie Garnier'
+__email__ = '[email protected]'
+__date__ = '2012-11-14'
+__doc__ = 'SYMPHONIE model data manipulation'
+
+
+from vacumm.data import register_dataset
+from vacumm.data.misc.dataset import OceanDataset
+
+
+class Symphonie(OceanDataset):
+    """:class:`~vacumm.data.misc.dataset.Dataset` class to read the
+    SYMPHONIE ocean model outputs
+    
+    Read the :class:`~vacumm.data.misc.dataset.Dataset` for more information
+    """
+
+    name = 'symphonie'
+    description = "The Symphonie ocean model from Laboratoire d'Aerologie"    
+
+    ncobj_specs = {
+
+# remplacer names par id a priori ?
+        # depth
+        'depth':{'search':{'id':['depth_t']}}, 
+
+        # sea surface height
+        'ssh':{'search':{'id':['ssh_ib']}}, 
+
+        # temperature
+        'temp':{'search':{'id':['tem']}}, 
+
+        # salinity
+        'sal':{'search':{'id':['sal']}}, 
+
+        # zonal current (3d)
+#useless ?        'u3d':{'search':{'id':['u']}}, 
+
+        # zonal current (barotrope)
+        #'ubt':{'search':{'id': ['vosaline']}},
+
+        # meridional current (3d)
+#useless ?        'v3d':{'search':{'id':['v']}}, 
+
+        # meridional current (2d)
+        #'vbt':{'search':{'id':['vomecrty']}}
+
+    }
+
+
+    positive = 'up'
+
+
+#: Alias for :class:`Symphonie`
+symp = Symphonie
+
+# Register the class
+register_dataset(symp)
+
+if __name__ == '__main__' :
+    from vacumm.data import setup_dataset
+    from vacumm.misc.plot import map2 as map
+    #f = setup_dataset('symphonie', dataset='/home2/creizic/pgarreau/SIMED/SYMPHONIE/LION/GV_MFSTEP-SYS4_20040702_ASLV.nc')
+    #sshmod = f.get_ssh()
+    #map(sshmod[0, Ellipsis], res=None)
+#    f = DS('symphonie', dataset='/home2/creizic/pgarreau/SIMED/SYMPHONIE/SST/20100501_000118.nc')
+    print "test temperature"
+    f = setup_dataset('symp', '/home2/creizic/pgarreau/SIMED/SYMPHONIE/SST/20100501_000118.nc')
+#    f = setup_dataset('symphonie', '/home2/creizic/pgarreau/SIMED/SYMPHONIE/SST/20100501_000118.nc')
+    temp = f.get_temp()
+    xxx
+    #f.get_depth()
+    xxxx
+