Created
August 30, 2018 18:31
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Extract JSON metadata from all HDF5 groups
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| from __future__ import print_function, division, unicode_literals | |
| import os | |
| import numpy as np | |
| import h5py | |
| import json | |
| import sys | |
| if sys.version_info.major == 3: | |
| unicode = str | |
| def get_attr(h5_object, attr_name): | |
| """ | |
| Returns the attribute from the h5py object | |
| Parameters | |
| ---------- | |
| h5_object : h5py.Dataset, h5py.Group or h5py.File object | |
| object whose attribute is desired | |
| attr_name : str | |
| Name of the attribute of interest | |
| Returns | |
| ------- | |
| att_val : object | |
| value of attribute, in certain cases (byte strings or list of byte strings) reformatted to readily usable forms | |
| """ | |
| if not isinstance(h5_object, (h5py.Dataset, h5py.Group, h5py.File)): | |
| raise TypeError('h5_object should be a h5py.Dataset, h5py.Group or h5py.File object') | |
| if not isinstance(attr_name, (str, unicode)): | |
| raise TypeError('attr_name should be a string') | |
| if attr_name not in h5_object.attrs.keys(): | |
| raise KeyError("'{}' is not an attribute in '{}'".format(attr_name, h5_object.name)) | |
| att_val = h5_object.attrs.get(attr_name) | |
| if isinstance(att_val, np.bytes_) or isinstance(att_val, bytes): | |
| att_val = att_val.decode('utf-8') | |
| elif type(att_val) == np.ndarray: | |
| if sys.version_info.major == 3: | |
| if att_val.dtype.type in [np.bytes_, np.object_]: | |
| att_val = np.array([str(x, 'utf-8') for x in att_val]) | |
| return att_val | |
| def get_attributes(h5_object, attr_names=None): | |
| """ | |
| Returns attribute associated with some DataSet. | |
| Parameters | |
| ---------- | |
| h5_object : h5py.Dataset | |
| Dataset object reference. | |
| attr_names : string or list of strings, optional, default = all (DataSet.attrs). | |
| Name of attribute object to return. | |
| Returns | |
| ------- | |
| Dictionary containing (name,value) pairs of attributes | |
| """ | |
| if not isinstance(h5_object, (h5py.Dataset, h5py.Group, h5py.File)): | |
| raise TypeError('h5_object should be a h5py.Dataset, h5py.Group or h5py.File object') | |
| if attr_names is None: | |
| attr_names = h5_object.attrs.keys() | |
| else: | |
| if isinstance(attr_names, (str, unicode)): | |
| attr_names = [attr_names] | |
| if not isinstance(attr_names, (list, tuple)): | |
| raise TypeError('attr_names should be a string or list / tuple of strings') | |
| if not np.all([isinstance(x, (str, unicode)) for x in attr_names]): | |
| raise TypeError('attr_names should be a string or list / tuple of strings') | |
| att_dict = {} | |
| for attr in attr_names: | |
| try: | |
| att_dict[attr] = get_attr(h5_object, attr) | |
| except KeyError: | |
| raise KeyError('%s is not an attribute of %s' % (str(attr), h5_object.name)) | |
| return att_dict | |
| def clean_attributes(metadata): | |
| attrs_to_delete = [] | |
| for key, val in metadata.items(): | |
| if type(val) in [np.uint16, np.uint8, np.uint, np.uint32, np.int, np.int16, np.int32, np.int64]: | |
| metadata[key] = int(val) | |
| if type(val) in [np.float, np.float16, np.float32, np.float64]: | |
| metadata[key] = float(val) | |
| if type(val) in [np.bool, np.bool_]: | |
| metadata[key] = bool(val) | |
| if isinstance(val, np.ndarray): | |
| metadata[key] = val.tolist() | |
| if isinstance(val, h5py.Reference): | |
| attrs_to_delete.append(key) | |
| for key in attrs_to_delete: | |
| del metadata[key] | |
| return metadata | |
| def get_attrs_from_groups(parent): | |
| metadata_tree = dict() | |
| for item_name, obj in parent.items(): | |
| if isinstance(obj, h5py.Group): | |
| temp = clean_attributes(get_attributes(obj)) | |
| sub_attrs = get_attrs_from_groups(obj) | |
| temp.update(sub_attrs) | |
| metadata_tree[item_name] = temp | |
| return metadata_tree | |
| def h5_atts_to_json(h5_path, root_only=False): | |
| if not h5_path.endswith('.h5'): | |
| print('Provided file did not have an h5 extension.') | |
| return | |
| with h5py.File(h5_path, mode='r') as h5_f: | |
| if root_only: | |
| metadata = get_attributes(h5_f) | |
| else: | |
| metadata = get_attrs_from_groups(h5_f) | |
| metadata = clean_attributes(metadata) | |
| json_path = h5_path.replace('.h5','.json') | |
| with open(json_path, mode='w') as json_handle: | |
| json.dump(metadata, json_handle) | |
| def extract_json_from_all_h5(root_dir, root_only=False): | |
| root_dir = os.path.abspath(root_dir) | |
| for item in os.listdir(root_dir): | |
| item_path = os.path.join(root_dir, item) | |
| if os.path.isdir(item_path): | |
| extract_json_from_all_h5(item_path) | |
| else: | |
| if item.endswith('.h5'): | |
| h5_atts_to_json(item_path, root_only=root_only) | |
| print('Finished generating JSON for ' + item) |
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