Source code for yt.utilities.file_handler

A wrapper class for h5py file objects.


# 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.

from yt.utilities.on_demand_imports import _h5py as h5py
from yt.utilities.on_demand_imports import NotAModule
from contextlib import contextmanager

[docs]def valid_hdf5_signature(fn): signature = b'\x89HDF\r\n\x1a\n' try: with open(fn, 'rb') as f: header = return header == signature except: return False
[docs]def warn_h5py(fn): needs_h5py = valid_hdf5_signature(fn) if needs_h5py and isinstance(h5py.File, NotAModule): raise RuntimeError("This appears to be an HDF5 file, " "but h5py is not installed.")
[docs]class HDF5FileHandler(object): handle = None def __init__(self, filename): self.handle = h5py.File(filename, 'r') def __getitem__(self, key): return self.handle[key] def __contains__(self, item): return item in self.handle def __len__(self): return len(self.handle) @property def attrs(self): return self.handle.attrs
[docs] def keys(self): return list(self.handle.keys())
[docs] def items(self): return list(self.handle.items())
[docs] def close(self): if self.handle is not None: self.handle.close()
[docs]class FITSFileHandler(HDF5FileHandler): def __init__(self, filename): from yt.utilities.on_demand_imports import _astropy if isinstance(filename, _astropy.pyfits.hdu.image._ImageBaseHDU): self.handle = _astropy.pyfits.HDUList(filename) elif isinstance(filename, _astropy.pyfits.HDUList): self.handle = filename else: self.handle = filename, memmap=True, do_not_scale_image_data=True, ignore_blank=True) self._fits_files = [] def __del__(self): for f in self._fits_files: f.close() del self._fits_files del self.handle self.handle = None
[docs] def close(self): self.handle.close()
[docs]def valid_netcdf_classic_signature(filename): signature_v1 = b'CDF\x01' signature_v2 = b'CDF\x02' try: with open(filename, 'rb') as f: header = return (header == signature_v1 or header == signature_v2) except: return False
[docs]def warn_netcdf(fn): # There are a few variants of the netCDF format. classic = valid_netcdf_classic_signature(fn) # NetCDF-4 Classic files are HDF5 files constrained to the Classic # data model used by netCDF-3. netcdf4_classic = valid_hdf5_signature(fn) and fn.endswith(('.nc', '.nc4')) needs_netcdf = classic or netcdf4_classic from yt.utilities.on_demand_imports import _netCDF4 as netCDF4 if needs_netcdf and isinstance(netCDF4.Dataset, NotAModule): raise RuntimeError("This appears to be a netCDF file, but the " "python bindings for netCDF4 are not installed.")
[docs]class NetCDF4FileHandler(object): def __init__(self, filename): self.filename = filename @contextmanager
[docs] def open_ds(self): from yt.utilities.on_demand_imports import _netCDF4 as netCDF4 ds = netCDF4.Dataset(self.filename) yield ds ds.close()