diff options
Diffstat (limited to 'silx/io/dictdump.py')
| -rw-r--r-- | silx/io/dictdump.py | 125 |
1 files changed, 118 insertions, 7 deletions
diff --git a/silx/io/dictdump.py b/silx/io/dictdump.py index da1bc5c..f2318e0 100644 --- a/silx/io/dictdump.py +++ b/silx/io/dictdump.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2019 European Synchrotron Radiation Facility +# Copyright (C) 2016-2020 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -154,14 +154,19 @@ def dicttoh5(treedict, h5file, h5path='/', any other data type, it is cast into a numpy array and written as a :mod:`h5py` dataset. Dictionary keys must be strings and cannot contain the ``/`` character. + + If dictionary keys are tuples they are interpreted to set h5 attributes. + The tuples should have the format (dataset_name,attr_name) .. note:: This function requires `h5py <http://www.h5py.org/>`_ to be installed. - :param treedict: Nested dictionary/tree structure with strings as keys - and array-like objects as leafs. The ``"/"`` character is not allowed - in keys. + :param treedict: Nested dictionary/tree structure with strings or tuples as + keys and array-like objects as leafs. The ``"/"`` character can be used + to define sub trees. If tuples are used as keys they should have the + format (dataset_name,attr_name) and will add a 5h attribute with the + corresponding value. :param h5file: HDF5 file name or handle. If a file name is provided, the function opens the file in the specified mode and closes it again before completing. @@ -186,10 +191,12 @@ def dicttoh5(treedict, h5file, h5path='/', "Europe": { "France": { "Isère": { - "Grenoble": "18.44 km2" + "Grenoble": 18.44, + ("Grenoble","unit"): "km2" }, "Nord": { - "Tourcoing": "15.19 km2" + "Tourcoing": 15.19, + ("Tourcoing","unit"): "km2" }, }, }, @@ -207,7 +214,11 @@ def dicttoh5(treedict, h5file, h5path='/', h5path += "/" with _SafeH5FileWrite(h5file, mode=mode) as h5f: - for key in treedict: + if isinstance(treedict, dict) and h5path != "/": + if h5path not in h5f: + h5f.create_group(h5path) + + for key in filter(lambda k: not isinstance(k, tuple), treedict): if isinstance(treedict[key], dict) and len(treedict[key]): # non-empty group: recurse dicttoh5(treedict[key], h5f, h5path + key, @@ -253,6 +264,106 @@ def dicttoh5(treedict, h5file, h5path='/', data=ds, **create_dataset_args) + # deal with h5 attributes which have tuples as keys in treedict + for key in filter(lambda k: isinstance(k, tuple), treedict): + if (h5path + key[0]) not in h5f: + # Create empty group if key for attr does not exist + h5f.create_group(h5path + key[0]) + logger.warning( + "key (%s) does not exist. attr %s " + "will be written to ." % (h5path + key[0], key[1]) + ) + + if key[1] in h5f[h5path + key[0]].attrs: + if not overwrite_data: + logger.warning( + "attribute %s@%s already exists. Not overwriting." + "" % (h5path + key[0], key[1]) + ) + continue + + # Write attribute + value = treedict[key] + + # Makes list/tuple of str being encoded as vlen unicode array + # Workaround for h5py<2.9.0 (e.g. debian 10). + if (isinstance(value, (list, tuple)) and + numpy.asarray(value).dtype.type == numpy.unicode_): + value = numpy.array(value, dtype=h5py.special_dtype(vlen=str)) + + h5f[h5path + key[0]].attrs[key[1]] = value + + +def dicttonx( + treedict, + h5file, + h5path="/", + mode="w", + overwrite_data=False, + create_dataset_args=None, +): + """ + Write a nested dictionary to a HDF5 file, using string keys as member names. + The NeXus convention is used to identify attributes with ``"@"`` character, + therefor the dataset_names should not contain ``"@"``. + + :param treedict: Nested dictionary/tree structure with strings as keys + and array-like objects as leafs. The ``"/"`` character can be used + to define sub tree. The ``"@"`` character is used to write attributes. + + Detais on all other params can be found in doc of dicttoh5. + + Example:: + + import numpy + from silx.io.dictdump import dicttonx + + gauss = { + "entry":{ + "title":u"A plot of a gaussian", + "plot": { + "y": numpy.array([0.08, 0.19, 0.39, 0.66, 0.9, 1., + 0.9, 0.66, 0.39, 0.19, 0.08]), + "x": numpy.arange(0,1.1,.1), + "@signal": "y", + "@axes": "x", + "@NX_class":u"NXdata", + "title:u"Gauss Plot", + }, + "@NX_class":u"NXentry", + "default":"plot", + } + "@NX_class": u"NXroot", + "@default": "entry", + } + + dicttonx(gauss,"test.h5") + """ + + def copy_keys_keep_values(original): + # create a new treedict with with modified keys but keep values + copy = dict() + for key, value in original.items(): + if "@" in key: + newkey = tuple(key.rsplit("@", 1)) + else: + newkey = key + if isinstance(value, dict): + copy[newkey] = copy_keys_keep_values(value) + else: + copy[newkey] = value + return copy + + nxtreedict = copy_keys_keep_values(treedict) + dicttoh5( + nxtreedict, + h5file, + h5path=h5path, + mode=mode, + overwrite_data=overwrite_data, + create_dataset_args=create_dataset_args, + ) + def _name_contains_string_in_list(name, strlist): if strlist is None: |