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__init__.py
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__init__.py
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from __future__ import absolute_import, division, print_function
import logging
import os
import sys
import warnings
import libtbx.load_env
import dxtbx.format.Registry
if sys.version_info.major == 2:
warnings.warn(
"Python 2 is no longer supported. "
"If you need Python 2.7 support please use the DIALS 2.2 release branch.",
UserWarning,
)
# Ensures that HDF5 has the conda_base plugin path configured.
#
# Ideally this will be properly configured by the conda environment.
# However, currently the dials-installer will not install a path-correct
# conda_base folder, so it needs to be updated manually.
# Warn if user is using an old hdf5-external-filter-plugins
# Remove after DIALS 3.3 release branch is made
_legacy_plugin_path = libtbx.env.under_base(os.path.join("lib", "plugins"))
_new_plugin_path = libtbx.env.under_base(os.path.join("lib", "hdf5", "plugin"))
# Find out which plugin path we need to inject
if os.path.exists(_legacy_plugin_path) and not os.path.exists(_new_plugin_path):
# Set up the plugin path for HDF5 to pick up compression plugins from legacy location
_hdf5_plugin_path = _legacy_plugin_path
warnings.warn(
"You are using an outdated version of the hdf5-external-filter-plugins package.\n"
"Please update your environment using 'conda install hdf5-external-filter-plugins'",
UserWarning,
)
else:
_hdf5_plugin_path = _new_plugin_path
# Inject via the environment if h5py not used yet, or else use h5py
if "h5py" not in sys.modules:
os.environ["HDF5_PLUGIN_PATH"] = (
_hdf5_plugin_path + os.pathsep + os.getenv("HDF5_PLUGIN_PATH", "")
)
else:
# We've already loaded h5py, so setting the environment variable won't work
# We need to use the h5py API to add a plugin path
import h5py
h5_plugin_paths = [h5py.h5pl.get(i).decode() for i in range(h5py.h5pl.size())]
if _hdf5_plugin_path not in h5_plugin_paths:
h5py.h5pl.prepend(_hdf5_plugin_path.encode())
logging.getLogger("dxtbx").addHandler(logging.NullHandler())
class IncorrectFormatError(RuntimeError):
"""
An exception class for an incorrect format error
"""
def __init__(self, format_instance, filename):
super(IncorrectFormatError, self).__init__(
"Could not open %s as %s" % (filename, str(format_instance))
)
self.args = (format_instance, filename)
def load(filename):
"""Use DXTBX to load the input filename.
:param filename: The input filename
:type filename: os.PathLike or str or bytes
:returns: A dxtbx Format-subclass instance for the file type
:raises IOError: if the file format could not be determined
"""
# Unwrap PEP-519-style objects. This covers py.path, pathlib, ...
if hasattr(filename, "__fspath__"):
filename = filename.__fspath__()
format_instance = dxtbx.format.Registry.get_format_class_for_file(filename)
return format_instance(filename)