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# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2017-2018 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
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
"""Utility functions used by NXdata validation and parsing."""
import copy
import numpy
import logging
from silx.io import is_dataset
from silx.utils.deprecation import deprecated
from silx.third_party import six
__authors__ = ["P. Knobel"]
__license__ = "MIT"
__date__ = "17/04/2018"
nxdata_logger = logging.getLogger("silx.io.nxdata")
INTERPDIM = {"scalar": 0,
"spectrum": 1,
"image": 2,
"rgba-image": 3, # "hsla-image": 3, "cmyk-image": 3, # TODO
"vertex": 1} # 3D scatter: 1D signal + 3 axes (x, y, z) of same legth
"""Number of signal dimensions associated to each possible @interpretation
attribute.
"""
@deprecated(since_version="0.8.0", replacement="get_attr_as_unicode")
def get_attr_as_string(*args, **kwargs):
return get_attr_as_unicode(*args, **kwargs)
def get_attr_as_unicode(item, attr_name, default=None):
"""Return item.attrs[attr_name] as unicode or as a
list of unicode.
Numpy arrays of strings or bytes returned by h5py are converted to
lists of unicode.
:param item: Group or dataset
:param attr_name: Attribute name
:param default: Value to be returned if attribute is not found.
:return: item.attrs[attr_name]
"""
attr = item.attrs.get(attr_name, default)
if isinstance(attr, six.binary_type):
# byte-string
return attr.decode("utf-8")
elif isinstance(attr, numpy.ndarray) and not attr.shape:
if isinstance(attr[()], six.binary_type):
# byte string as ndarray scalar
return attr[()].decode("utf-8")
else:
# other scalar, possibly unicode
return attr[()]
elif isinstance(attr, numpy.ndarray) and len(attr.shape):
if hasattr(attr[0], "decode"):
# array of byte-strings
return [element.decode("utf-8") for element in attr]
else:
# other array, most likely unicode objects
return [element for element in attr]
else:
return copy.deepcopy(attr)
def get_uncertainties_names(group, signal_name):
# Test consistency of @uncertainties
uncertainties_names = get_attr_as_unicode(group, "uncertainties")
if uncertainties_names is None:
uncertainties_names = get_attr_as_unicode(group[signal_name], "uncertainties")
if isinstance(uncertainties_names, six.text_type):
uncertainties_names = [uncertainties_names]
return uncertainties_names
def get_signal_name(group):
"""Return the name of the (main) signal in a NXdata group.
Return None if this info is missing (invalid NXdata).
"""
signal_name = get_attr_as_unicode(group, "signal", default=None)
if signal_name is None:
nxdata_logger.info("NXdata group %s does not define a signal attr. "
"Testing legacy specification.", group.name)
for key in group:
if "signal" in group[key].attrs:
signal_name = key
signal_attr = group[key].attrs["signal"]
if signal_attr in [1, b"1", u"1"]:
# This is the main (default) signal
break
return signal_name
def get_auxiliary_signals_names(group):
"""Return list of auxiliary signals names"""
auxiliary_signals_names = get_attr_as_unicode(group, "auxiliary_signals",
default=[])
if isinstance(auxiliary_signals_names, (six.text_type, six.binary_type)):
auxiliary_signals_names = [auxiliary_signals_names]
return auxiliary_signals_names
def validate_auxiliary_signals(group, signal_name, auxiliary_signals_names):
"""Check data dimensionality and size. Return False if invalid."""
issues = []
for asn in auxiliary_signals_names:
if asn not in group or not is_dataset(group[asn]):
issues.append(
"Cannot find auxiliary signal dataset '%s'" % asn)
elif group[signal_name].shape != group[asn].shape:
issues.append("Auxiliary signal dataset '%s' does not" % asn +
" have the same shape as the main signal.")
return issues
def validate_number_of_axes(group, signal_name, num_axes):
issues = []
ndims = len(group[signal_name].shape)
if 1 < ndims < num_axes:
# ndim = 1 with several axes could be a scatter
issues.append(
"More @axes defined than there are " +
"signal dimensions: " +
"%d axes, %d dimensions." % (num_axes, ndims))
# case of less axes than dimensions: number of axes must match
# dimensionality defined by @interpretation
elif ndims > num_axes:
interpretation = get_attr_as_unicode(group[signal_name], "interpretation")
if interpretation is None:
interpretation = get_attr_as_unicode(group, "interpretation")
if interpretation is None:
issues.append("No @interpretation and not enough" +
" @axes defined.")
elif interpretation not in INTERPDIM:
issues.append("Unrecognized @interpretation=" + interpretation +
" for data with wrong number of defined @axes.")
elif interpretation == "rgba-image":
if ndims != 3 or group[signal_name].shape[-1] not in [3, 4]:
issues.append(
"Inconsistent RGBA Image. Expected 3 dimensions with " +
"last one of length 3 or 4. Got ndim=%d " % ndims +
"with last dimension of length %d." % group[signal_name].shape[-1])
if num_axes != 2:
issues.append(
"Inconsistent number of axes for RGBA Image. Expected "
"3, but got %d." % ndims)
elif num_axes != INTERPDIM[interpretation]:
issues.append(
"%d-D signal with @interpretation=%s " % (ndims, interpretation) +
"must define %d or %d axes." % (ndims, INTERPDIM[interpretation]))
return issues
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