Source code for

The data-file handling functions


# Copyright (c) 2013, yt Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file COPYING.txt, distributed with this software.

import numpy as np
from yt.utilities.on_demand_imports import _h5py as h5py
from yt.funcs import \
from yt.geometry.selection_routines import GridSelector
from yt.utilities.io_handler import \

def _grid_dname(grid_id):
    return "/data/grid_%010i" % grid_id

def _field_dname(grid_id, field_name):
    return "%s/%s" % (_grid_dname(grid_id), field_name)

# TODO all particle bits were removed
[docs]class IOHandlerGDFHDF5(BaseIOHandler): _dataset_type = "grid_data_format" _offset_string = 'data:offsets=0' _data_string = 'data:datatype=0' def _read_fluid_selection(self, chunks, selector, fields, size): from sys import version rv = {} chunks = list(chunks) if isinstance(selector, GridSelector): if not (len(chunks) == len(chunks[0].objs) == 1): raise RuntimeError grid = chunks[0].objs[0] h5f = h5py.File(grid.filename, 'r') gds = h5f.get(_grid_dname( for ftype, fname in fields: if self.ds.field_ordering == 1: rv[(ftype, fname)] = gds.get(fname).value.swapaxes(0, 2) else: rv[(ftype, fname)] = gds.get(fname).value h5f.close() return rv if size is None: size = sum((grid.count(selector) for chunk in chunks for grid in chunk.objs)) if any((ftype != "gdf" for ftype, fname in fields)): raise NotImplementedError for field in fields: ftype, fname = field fsize = size # check the dtype instead rv[field] = np.empty(fsize, dtype="float64") ngrids = sum(len(chunk.objs) for chunk in chunks) mylog.debug("Reading %s cells of %s fields in %s blocks", size, [fn for ft, fn in fields], ngrids) ind = 0 for chunk in chunks: fid = None for grid in chunk.objs: if grid.filename is None: continue if fid is None: if version < '3': fid =,h5py.h5f.ACC_RDONLY) else: fid =,'utf-8'),h5py.h5f.ACC_RDONLY) if self.ds.field_ordering == 1: # check the dtype instead data = np.empty(grid.ActiveDimensions[::-1], dtype="float64") data_view = data.swapaxes(0, 2) else: # check the dtype instead data_view = data = np.empty(grid.ActiveDimensions, dtype="float64") for field in fields: ftype, fname = field if version < '3': dg =, _field_dname(, fname)) else: dg =, bytes(_field_dname(, fname),'utf-8')), h5py.h5s.ALL, data) # caches nd =, data_view, rv[field], ind) ind += nd # I don't get that part, only last nd is added if fid is not None: fid.close() return rv