Source code for mth5.helpers

# -*- coding: utf-8 -*-
Helper functions for HDF5

Created on Tue Jun  2 12:37:50 2020

    Jared Peacock (

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# Imports
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from import Iterable
import inspect
import numpy as np
import h5py
import gc

from mth5.utils.mth5_logger import setup_logger

logger = setup_logger(__name__)

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# Acceptable compressions
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COMPRESSION = ["lzf", "gzip", "szip", None]
    "lzf": [None],
    "gzip": range(10),
    "szip": ["ec-8", "ee-10", "nn-8", "nn-10"],
    None: [None],

[docs]def validate_compression(compression, level): """ validate that the input compression is supported. :param compression: type of lossless compression :type compression: string, [ 'lzf' | 'gzip' | 'szip' | None ] :param level: compression level if supported :type level: string for 'szip' or int for 'gzip' :return: compression type :rtype: string :return: compressiong level :rtype: string for 'szip' or int for 'gzip' :raises: ValueError if comporession or level are not supported :raises: TypeError if compression level is not a string """ if compression is None: return None, None if not isinstance(compression, (str, type(None))): msg = "compression type must be a string, not {0}".format(type(compression)) logger.error(msg) raise TypeError(msg) if not compression in COMPRESSION: msg = ( f"Compression type {compression} not supported. " + f"Supported options are {COMPRESSION}" ) logger.error(msg) raise ValueError(msg) if compression == "lzf": level = COMPRESSION_LEVELS["lzf"][0] elif compression == " gzip": if not isinstance(level, (int)): msg = "Level type for gzip must be an int, not {0}.".format( type(level) + f" Options are {0}".format(COMPRESSION_LEVELS["gzip"]) ) logger.error(msg) raise TypeError(msg) elif compression == " szip": if not isinstance(level, (str)): msg = "Level type for szip must be an str, not {0}.".format( type(level) ) + " Options are {0}".format(COMPRESSION_LEVELS["szip"]) logger.error(msg) raise TypeError(msg) if not level in COMPRESSION_LEVELS[compression]: msg = ( f"compression level {level} not supported for {compression}." + " Options are {0}".format(COMPRESSION_LEVELS[compression]) ) logger.error(msg) raise ValueError(msg) return compression, level
[docs]def recursive_hdf5_tree(group, lines=[]): if isinstance(group, (, h5py._hl.files.File)): for key, value in group.items(): lines.append("-{0}: {1}".format(key, value)) recursive_hdf5_tree(value, lines) elif isinstance(group, h5py._hl.dataset.Dataset): for key, value in group.attrs.items(): lines.append("\t-{0}: {1}".format(key, value)) return "\n".join(lines)
[docs]def close_open_files(): for obj in gc.get_objects(): try: if isinstance(obj, h5py.File): msg = "Found HDF5 File object " print(msg) try: msg = "{0}, ".format(obj.filename) obj.flush() obj.close() msg += "Closed File" except: msg += "File already closed." except: print("Object {} does not have __class__")
[docs]def get_tree(parent): """ Simple function to recursively print the contents of an hdf5 group Parameters ---------- parent : :class:`h5py.Group` HDF5 (sub-)tree to print """ lines = ["{0}:".format(, "=" * 20] if not isinstance(parent, (h5py.File, h5py.Group)): raise TypeError("Provided object is not a h5py.File or h5py.Group " "object") def fancy_print(name, obj): # lines.append(name) spacing = " " * 4 * (name.count("/") + 1) group_name = name[name.rfind("/") + 1 :] if isinstance(obj, h5py.Group): lines.append("{0}|- Group: {1}".format(spacing, group_name)) lines.append("{0}{1}".format(spacing, (len(group_name) + 10) * "-")) elif isinstance(obj, h5py.Dataset): lines.append("{0}--> Dataset: {1}".format(spacing, group_name)) lines.append("{0}{1}".format(spacing, (len(group_name) + 15) * ".")) # lines.append( parent.visititems(fancy_print) return "\n".join(lines)
[docs]def to_numpy_type(value): """ Need to make the attributes friendly with Numpy and HDF5. For numbers and bool this is straight forward they are automatically mapped in h5py to a numpy type. But for strings this can be a challenge, especially a list of strings. HDF5 should only deal with ASCII characters or Unicode. No binary data is allowed. """ if value is None: return "none" # For now turn references into a generic string if isinstance(value, h5py.h5r.Reference): value = str(value) if isinstance( value, ( str, np.str_, int, float, bool, complex, np.int_, np.float_, np.bool_, np.complex_, ), ): return value if isinstance(value, Iterable): if np.any([type(x) in [str, bytes, np.str_] for x in value]): return np.array(value, dtype="S") else: return np.array(value) else: raise TypeError("Type {0} not understood".format(type(value)))
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[docs]def inherit_doc_string(cls): for base in inspect.getmro(cls): if base.__doc__ is not None: cls.__doc__ = base.__doc__ break return cls