Simlei Reader working but probably buggy

postpic/datareader/smileih5.py

@@ -20,7 +20,7 @@
 
 from __future__ import absolute_import, division, print_function, unicode_literals
 
-from . import OpenPMDreader
+from .openPMDh5 import OpenPMDreader
 from . import Simulationreader_ifc
 from .. import helper
 import os.path
@@ -30,7 +30,7 @@
 __all__ = ['SmileiReader', 'SmileiSeries']
 
 
-def createh5indexfile(indexfile, fnames):
+def _generateh5indexfile(indexfile, fnames):
  '''
  Creates a h5 index file called indexfile containing external links to all h5
  datasets which are in in the h5 filelist fnames. This is fast as datasets
@@ -43,8 +43,8 @@ def createh5indexfile(indexfile, fnames):
  # indexfile already exists. do not recreate
  return
 
- dirname = osp.dirname(fnames[0])
- indexfile = osp.join(dirname, indexfile)
+ dirname = os.path.dirname(fnames[0])
+ indexfile = os.path.join(dirname, indexfile)
 
  def visitf(key):
  # key is a string
@@ -58,40 +58,64 @@ def visitf(key):
  hf.visit(visitf)
 
 
+def _getindexfile(path):
+ '''
+ Returns the name of the index file after the file has been
+ generated (File generation only if it doesnt exist)
+ '''
+ indexfile = os.path.join(path, '.postpic-smilei-index.h5')
+ if not os.path.isfile(indexfile):
+ # find all h5 files
+ h5files = glob.glob(os.path.join(path, '*.h5'))
+ print('generating index file "{}" from the following'
+ 'h5 files: {}'.format(indexfile, h5files))
+ _generateh5indexfile(indexfile, h5files)
+ return indexfile
+
+
 class SmileiReader(OpenPMDreader):
  '''
- The Smilei reader will combine the information of different h5 files.
- Should work by pointing to the directory of the simulation
- `simreader = SmileiReader('path/to/simulation/*.h5', 1000)`,
+ The Smilei reader can read a single h5 file or combine the information of
+ all h5 files in the same directory.
+ Use either
+ `simreader = SmileiReader('path/to/simulation/fields0.h5', 1000)`,
  where 1000 points to iteration 1000 of the simulation.
+ or use
+ `simreader = SmileiReader('path/to/simulation/', 1000)`
+ to combine all h5 files in this directory.
+ Internally the second command will create a new file called
+ `.postpic-smilei-index.h5` which contains external links to all
+ datasets in this directory.
 
  Args:
  h5file : String
- A String containing the relative Path to the h5 files of the simulation.
- Will be expanded using glob. Hidden files starting with `.` will be ignored.
+ A String containing the relative Path to the h5 files of the simulation
+ or the path to a single h5 file.
+ Hidden files starting with `.` will be ignored.
 
- 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, h5filesstr, iteration=None):
+ 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__(h5filesstr)
+ super(OpenPMDreader, self).__init__(h5file)
  # Smilei uses multiple h5 files and also the iteration encoding differs from openPMD.
- h5files = glob.glob(h5filesstr)
- if len(h5files) == 0:
-  raise IOError('No h5 files found matching {}'.format(h5filesstr))
- path = os.path.basename(h5filesstr)
- indexfile = os.path.join(path, '.postpic_smilei_index.h5')
- createh5indexfile(indexfile, h5files)
-
- self._h5 = h5py.File(indexfile, 'r')
- self._iteration = int(iteration)
- if self._iteration is None:
+ if os.path.isfile(h5file):
+  self._h5 = h5py.File(h5file, 'r')
+ elif os.path.isdir(h5file):
+  indexfile = _getindexfile(h5file)
+  self._h5 = h5py.File(indexfile, 'r')
+ else:
+ raise IOError('"{}" is neither a h5 file nor a directory'
+  'containing h5 files'.format(h5file))
+
+ if iteration is None:
  self._iteration = int(list(self._h5['data'].keys())[0])
+ else:
+ self._iteration = int(iteration)
  self._data = self._h5['/data/{:010d}/'.format(self._iteration)]
  self.attrs = self._data.attrs
 
@@ -104,17 +128,27 @@ def __init__(self, h5filesstr, iteration=None):
  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)
+ return '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)
+ return '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']
+ return ['Ex', 'Ey', 'Ez',
+ 'Bx', 'By', 'Bz']
+
+ def getderived(self):
+ '''
+ return all other fields dumped, except E and B.
+ '''
+ ret = []
+ self['.'].visit(ret.append)
+ # TODO: remove E and B fields and particles from list
+ ret.sort()
+ return ret
 
  def __str__(self):
  return '<SmileiReader at "{}" at iteration {:d}>'.format(self.dumpidentifier,
@@ -129,7 +163,7 @@ class SmileiSeries(Simulationreader_ifc):
  but possibly containing different data.
  `simreader = SmileiSeries('path/to/simulation/')`
 
- Or point this to a single file an you will only get the
+ Alternatively point this to a single file an you will only get
  the iterations which are present in that file:
  `simreader = SmileiSeries('path/to/simulation/fields0.h5')`
  '''
@@ -143,7 +177,10 @@ def __init__(self, h5file, dumpreadercls=SmileiReader, **kwargs):
  with h5py.File(h5file, 'r') as h5:
  self._dumpkeys = list(h5['data'].keys())
  elif os.path.isdir(h5file):
- pass # TODO
+ indexfile = _getindexfile(h5file)
+ self._h5 = h5py.File(indexfile, 'r')
+ with h5py.File(indexfile, 'r') as h5:
+ self._dumpkeys = list(h5['data'].keys())
  else:
  raise IOError('{} does not exist.'.format(h5file))