first draft of smilei reader

postpic/datareader/__init__.py

@@ -188,6 +188,10 @@ def chooseCode(code):
         from .vsimhdf5 import Hdf5reader, VSimReader
         setdumpreadercls(Hdf5reader)
         setsimreadercls(VSimReader)
+    elif code.lower() in ['smilei']:
+        from .smileih5 import SmileiReader, SmileiSeries
+        setdumpreadercls(SmileiReader)
+        setsimreadercls(SmileiSeries)
     elif code.lower() in ['dummy']:
         from .dummy import Dummyreader, Dummysim
         setdumpreadercls(Dummyreader)

postpic/datareader/openPMDh5.py

@@ -46,16 +46,23 @@ class OpenPMDreader(Dumpreader_ifc):
     Args:
       h5file : String
         A String containing the relative Path to the .h5 file.
+
+    Kwargs:
+      iteration: Integer
+        An integer indicating the iteration to be loaded. Default is None, leading
+        to the first iteration found in the h5file.
     '''
 
-    def __init__(self, h5file, **kwargs):
+    def __init__(self, h5file, iteration=None, **kwargs):
         super(OpenPMDreader, self).__init__(h5file, **kwargs)
         import os.path
         import h5py
         if not os.path.isfile(h5file):
             raise IOError('File "' + str(h5file) + '" doesnt exist.')
         self._h5 = h5py.File(h5file, 'r')
-        self._iteration = int(list(self._h5['data'].keys())[0])
+        self._iteration = iteration
+        if self._iteration is None:
+            self._iteration = int(list(self._h5['data'].keys())[0])
         self._data = self._h5['/data/{:d}/'.format(self._iteration)]
         self.attrs = self._data.attrs
 

postpic/datareader/smileih5.py

+#
+# 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/>.
+#
+# Stephan Kuschel, 2023
+# Carolin Goll, 2023
+
+
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+from . import OpenPMDreader
+from . import Simulationreader_ifc
+import numpy as np
+import re
+from .. import helper
+from ..helper_fft import fft
+
+__all__ = ['SmileiReader', 'SmileiSeries']
+
+
+class SmileiReader(OpenPMDreader):
+    '''
+    The Reader implementation for Data written in the hdf5 file
+    format following openPMD_ naming conventions.
+
+    Args:
+      h5file : String
+        A String containing the relative Path to the .h5 file.
+
+    Kwargs:
+      iteration : Integer
+        An integer indicating the iteration to be loaded. Default is None, leading
+        to the first iteration found in the h5file to be loaded.
+    '''
+
+    def __init__(self, h5file, iteration=None):
+        # The class given to super is the OpenPMDreader class, not the SmileiReader class.
+        # This is on purpose to NOT run the `OpenPMDreader.__init__`.
+        super(OpenPMDreader, self).__init__(h5file)
+        # Smilei uses multiple h5 files and also the iteration encoding differs from openPMD.
+        import os.path
+        import h5py
+        if not os.path.isfile(h5file):
+            raise IOError('File "{}" doesnt exist.'.format(h5file))
+        self._h5 = h5py.File(h5file, 'r')
+        self._iteration = iteration
+        if self._iteration is None:
+            self._iteration = int(list(self._h5['data'].keys())[0])
+        self._data = self._h5['/data/{:010d}/'.format(self._iteration)]
+        self.attrs = self._data.attrs
+
+# --- Level 0 methods ---
+
+# --- Level 1 methods ---
+
+# --- Level 2 methods ---
+
+    def _keyE(self, component, **kwargs):
+        # Smilei deviates from openPMD standard: Ex instead of E/x
+        axsuffix = {0: 'x', 1: 'y', 2: 'z', 90: 'r', 91: 't'}[helper.axesidentify[component]]
+        return 'fields/E{}'.format(axsuffix)
+
+    def _keyB(self, component, **kwargs):
+        # Smilei deviates from openPMD standard: Bx instead of B/x
+        axsuffix = {0: 'x', 1: 'y', 2: 'z', 90: 'r', 91: 't'}[helper.axesidentify[component]]
+        return 'fields/B{}'.format(axsuffix)
+
+    def _simgridkeys(self):
+        # Smilei deviates from openPMD standard: Ex instead of E/x
+        return ['fields/Ex', 'fields/Ey', 'fields/Ez',
+                'fields/Bx', 'fields/By', 'fields/Bz']
+
+    def __str__(self):
+        return '<SmileiReader at "{}", iteration {:d}>'.format(self.dumpidentifier,
+                                                               self.timestep())
+
+
+class SmileiSeries(Simulationreader_ifc):
+    '''
+    Reads a time series of dumps from a given directory.
+    The simidentifier is expanded using glob in order to
+    find matching files.
+    '''
+
+    def __init__(self, h5file, dumpreadercls=SmileiReader, **kwargs):
+        super(SmileiSeries, self).__init__(h5file, **kwargs)
+        self.dumpreadercls = dumpreadercls
+        self.h5file = h5file
+        if not os.path.isfile(h5file):
+            raise IOError('File "{}" doesnt exist.'.format(h5file))
+        with h5py.File(h5file, 'r') as h5:
+            self._dumpkeys = list(h5['data'].keys())
+
+    def _getDumpreader(self, n):
+        '''
+        Do not use this method. It will be called by __getitem__.
+        Use __getitem__ instead.
+        '''
+        return self.dumpreadercls(self._dumpkeys[n])
+
+    def __len__(self):
+        return len(self._dumpkeys)
+
+    def __str__(self):
+        return '<SmileiSeries based on "{}">'.format(self.simidentifier)