implement VSIM Dumpreader

tested if methods return right value (except getderived all methods
implemented). Using _const.axesidentify for x,y,z,px,py,pz; weight and
ID not included. All other methods should behave like for sdf.
Neverthelerss additional esting required--

.gitignore

@@ -1,5 +1,6 @@
 *~
 *.pyc
+*.odt
 .project
 .pydevproject
 *.egg-info

postpic/datareader/__init__.py

@@ -314,13 +314,18 @@ def chooseCode(code):
     Args:
       code : string
         Possible options are:
-          - "EPOCH": .sdf files written by EPOCH1D, EPOCH2D or EPOCH3D.
           - "DUMMY": dummy class creating fake data.
+          - "EPOCH": .sdf files written by EPOCH1D, EPOCH2D or EPOCH3D.
+          - "VSIM": .hdf5 files written by VSim.
     '''
     if code in ['EPOCH', 'epoch', 'EPOCH1D', 'EPOCH2D', 'EPOCH3D']:
         from epochsdf import Sdfreader, Visitreader
         setdumpreadercls(Sdfreader)
         setsimreadercls(Visitreader)
+    elif code in ['VSim', 'VSIM', 'vsim']:
+        from vsimhdf5 import Hdf5reader
+        setdumpreadercls(Hdf5reader)
+        # no Simulationsreader implemented yet
     elif code in ['DUMMY', 'dummy']:
         from dummy import Dummyreader, Dummysim
         setdumpreadercls(Dummyreader)

postpic/datareader/vsimhdf5.py

@@ -0,0 +1,147 @@
+#
+# This file is part of postpic.
+#
+# postpic 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.
+#
+# postpic 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 postpic. If not, see <http://www.gnu.org/licenses/>.
+#
+# Georg Wittig, Stephan Kuschel 2014
+
+'''
+Reader for HDF5 File format written by the VSim Code:
+http://www.txcorp.com/support/vsim-support-menu/vsim-documentation
+Dependecies:
+h5py  The Python actual reader for hdf5 file format.
+Georg Wittig, Stephan Kuschel 2014
+'''
+from . import Dumpreader_ifc
+from . import Simulationreader_ifc
+from .. import _const
+
+
+import h5py
+import numpy as np
+import os
+
+__all__ = ['Hdf5reader']
+
+
+class Hdf5reader(Dumpreader_ifc):
+    '''
+    The Reader implementation for HDF5 Data written by the VSim Code.
+    as argument h5file can be any *.h5 file of the dump of consideration.
+    '''
+    def __init__(self, h5file, **kwargs):
+        '''
+        Initializes the Hdf5reader for a specific h5file.
+        '''
+        super(self.__class__, self).__init__(h5file, **kwargs)
+        if not os.path.isfile(h5file):
+            raise IOError('File "' + str(h5file) + '" doesnt exist.')
+        self.h5file = h5file
+        filelist = [f for f in os.listdir(".") if f.endswith(".h5")]
+        self._time = h5py.File(h5file)["time"].attrs["vsTime"]
+        # all dumped h5 files at one time
+        self._dumplist = [f for f in filelist
+                          if self._time == h5py.File(f)["time"].attrs["vsTime"]]
+
+    def keys(self):
+        keys = []
+        for f in self._dumplist:
+            for a in h5py.File(f):
+                if a not in keys:
+                    keys.append(a)
+        return keys
+
+    def __getitem__(self, key):
+        ''' delivers one dataset with the key key.'''
+        for f in self._dumplist:
+            for a in h5py.File(f):
+                if a == key:
+                    return h5py.File(f)[key]
+        # print " couldn't find key ", key
+        return None
+
+    def timestep(self):
+        ''' returns the timestem 0.5*DX/c  '''
+        temp = self["compGridGlobal"]
+        NX = temp.attrs["vsNumCells"][0]
+        xl = temp.attrs["vsLowerBounds"][0]
+        xu = temp.attrs["vsUpperBounds"][0]
+        LX = abs(xu-xl)
+        return 0.5*(LX/NX)/299792458.
+
+    def time(self):
+        return self._time
+
+    def simdimensions(self):
+        return self["compGridGlobal"].attrs["vsNumCells"].shape[0]
+
+    def dataE(self, axis, **kwargs):
+        # x, y, z, px, py, pz same as in sdf. weigt and ID not included.
+        axis = _const.axesidentify[axis]
+        try:
+            return np.float64(self["ElecMultiField"][..., axis])
+        except:
+            return None
+
+    def dataB(self, axis, **kwargs):
+        # x, y, z, px, py, pz same as in sdf. wweigt and ID not included.
+        axis = _const.axesidentify[axis]
+        try:
+            return np.float64(self["MagMultiField"][..., axis])
+        except:
+            return None
+
+    def grid(self, axis):
+        ''' returns the array of the positions of all cells on axis = axis.  '''
+        # x, y, z, px, py, pz same as in sdf. weigt and ID not included.
+        axis = _const.axesidentify[axis]
+        temp = self["compGridGlobal"]
+        return np.linspace(temp.attrs["vsLowerBounds"][axis],
+                           temp.attrs["vsUpperBounds"][axis], temp.attrs["vsNumCells"][axis])
+
+    def listSpecies(self):
+        ''' returns all h5 dumps that have a attribute "mass" '''
+        SpeciesList = []
+        for f in self._dumplist:
+            for k in h5py.File(f):
+                for a in h5py.File(f)[k].attrs:
+                    if a == "mass":
+                        SpeciesList.append(k)
+                        break
+        return SpeciesList
+
+    def getSpecies(self, species, attrib):
+        '''
+        Returns one of the attributes out of (x,y,z,px,py,pz,weight,ID) of
+        this particle species.
+        returning None means that this particle property wasnt dumped.
+        Note that this is different from returning an empty list!
+        '''
+        # x, y, z, px, py, pz same as in sdf. weigt and ID not included.
+        attrib = _const.axesidentify[attrib]
+        attrib = {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 9: 6, 10: 7}[attrib]
+        try:
+            return np.float64(self[species])[:, attrib]
+        except:
+            return None
+
+    def getderived(self):
+        '''
+        Returns all Keys starting with "Derived/".
+        '''
+        pass
+
+    def __str__(self):
+        return '<Hdf5reader at "' + str(self.dumpidentifier) + '">'
+