diff options
Diffstat (limited to 'silx/io/dictdump.py')
| -rw-r--r-- | silx/io/dictdump.py | 158 |
1 files changed, 106 insertions, 52 deletions
diff --git a/silx/io/dictdump.py b/silx/io/dictdump.py index ae7a457..1860b7f 100644 --- a/silx/io/dictdump.py +++ b/silx/io/dictdump.py @@ -41,13 +41,13 @@ else: h5py_missing = False from .configdict import ConfigDict -from .utils import is_group, is_file - -from silx.io import open as h5open +from .utils import is_group +from .utils import is_file as is_h5_file_like +from .utils import open as h5open __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "10/02/2017" +__date__ = "16/06/2017" logger = logging.getLogger(__name__) @@ -82,6 +82,76 @@ def _prepare_hdf5_dataset(array_like): return array +class _SafeH5FileWrite(object): + """Context manager returning a :class:`h5py.File` object. + + If this object is initialized with a file path, we open the file + and then we close it on exiting. + + If a :class:`h5py.File` instance is provided to :meth:`__init__` rather + than a path, we assume that the user is responsible for closing the + file. + + This behavior is well suited for handling h5py file in a recursive + function. The object is created in the initial call if a path is provided, + and it is closed only at the end when all the processing is finished. + """ + def __init__(self, h5file, mode="w"): + """ + + :param h5file: HDF5 file path or :class:`h5py.File` instance + :param str mode: Can be ``"r+"`` (read/write, file must exist), + ``"w"`` (write, existing file is lost), ``"w-"`` (write, fail if + exists) or ``"a"`` (read/write if exists, create otherwise). + This parameter is ignored if ``h5file`` is a file handle. + """ + self.raw_h5file = h5file + self.mode = mode + + def __enter__(self): + if not isinstance(self.raw_h5file, h5py.File): + self.h5file = h5py.File(self.raw_h5file, self.mode) + self.close_when_finished = True + else: + self.h5file = self.raw_h5file + self.close_when_finished = False + return self.h5file + + def __exit__(self, exc_type, exc_val, exc_tb): + if self.close_when_finished: + self.h5file.close() + + +class _SafeH5FileRead(object): + """Context manager returning a :class:`h5py.File` or a + :class:`silx.io.spech5.SpecH5` or a :class:`silx.io.fabioh5.File` object. + + The general behavior is the same as :class:`_SafeH5FileWrite` except + that SPEC files and all formats supported by fabio can also be opened, + but in read-only mode. + """ + def __init__(self, h5file): + """ + + :param h5file: HDF5 file path or h5py.File-like object + """ + self.raw_h5file = h5file + + def __enter__(self): + if not is_h5_file_like(self.raw_h5file): + self.h5file = h5open(self.raw_h5file) + self.close_when_finished = True + else: + self.h5file = self.raw_h5file + self.close_when_finished = False + + return self.h5file + + def __exit__(self, exc_type, exc_val, exc_tb): + if self.close_when_finished: + self.h5file.close() + + def dicttoh5(treedict, h5file, h5path='/', mode="w", overwrite_data=False, create_dataset_args=None): @@ -142,40 +212,32 @@ def dicttoh5(treedict, h5file, h5path='/', if h5py_missing: raise h5py_import_error - if not isinstance(h5file, h5py.File): - h5f = h5py.File(h5file, mode) - else: - h5f = h5file - if not h5path.endswith("/"): h5path += "/" - for key in treedict: - - if isinstance(treedict[key], dict) and len(treedict[key]): - # non-empty group: recurse - dicttoh5(treedict[key], h5f, h5path + key, - overwrite_data=overwrite_data, - create_dataset_args=create_dataset_args) + with _SafeH5FileWrite(h5file, mode=mode) as h5f: + for key in treedict: + if isinstance(treedict[key], dict) and len(treedict[key]): + # non-empty group: recurse + dicttoh5(treedict[key], h5f, h5path + key, + overwrite_data=overwrite_data, + create_dataset_args=create_dataset_args) - elif treedict[key] is None or (isinstance(treedict[key], dict) and - not len(treedict[key])): - # Create empty group - h5f.create_group(h5path + key) + elif treedict[key] is None or (isinstance(treedict[key], dict) and + not len(treedict[key])): + # Create empty group + h5f.create_group(h5path + key) - else: - ds = _prepare_hdf5_dataset(treedict[key]) - # can't apply filters on scalars (datasets with shape == () ) - if ds.shape == () or create_dataset_args is None: - h5f.create_dataset(h5path + key, - data=ds) else: - h5f.create_dataset(h5path + key, - data=ds, - **create_dataset_args) - - if isinstance(h5file, string_types): - h5f.close() + ds = _prepare_hdf5_dataset(treedict[key]) + # can't apply filters on scalars (datasets with shape == () ) + if ds.shape == () or create_dataset_args is None: + h5f.create_dataset(h5path + key, + data=ds) + else: + h5f.create_dataset(h5path + key, + data=ds, + **create_dataset_args) def _name_contains_string_in_list(name, strlist): @@ -228,26 +290,18 @@ def h5todict(h5file, path="/", exclude_names=None): if h5py_missing: raise h5py_import_error - if not is_file(h5file): - h5f = h5open(h5file) - else: - h5f = h5file - - ddict = {} - for key in h5f[path]: - if _name_contains_string_in_list(key, exclude_names): - continue - if is_group(h5f[path + "/" + key]): - ddict[key] = h5todict(h5f, - path + "/" + key, - exclude_names=exclude_names) - else: - # Convert HDF5 dataset to numpy array - ddict[key] = h5f[path + "/" + key][...] - - if not is_file(h5file): - # close file, if we opened it - h5f.close() + with _SafeH5FileRead(h5file) as h5f: + ddict = {} + for key in h5f[path]: + if _name_contains_string_in_list(key, exclude_names): + continue + if is_group(h5f[path + "/" + key]): + ddict[key] = h5todict(h5f, + path + "/" + key, + exclude_names=exclude_names) + else: + # Convert HDF5 dataset to numpy array + ddict[key] = h5f[path + "/" + key][...] return ddict |