diff options
Diffstat (limited to 'silx/io/nxdata/parse.py')
| -rw-r--r-- | silx/io/nxdata/parse.py | 111 |
1 files changed, 106 insertions, 5 deletions
diff --git a/silx/io/nxdata/parse.py b/silx/io/nxdata/parse.py index cce47ab..6bd18d6 100644 --- a/silx/io/nxdata/parse.py +++ b/silx/io/nxdata/parse.py @@ -1,7 +1,7 @@ # coding: utf-8 # /*########################################################################## # -# Copyright (c) 2017-2019 European Synchrotron Radiation Facility +# Copyright (c) 2017-2020 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 @@ -41,6 +41,7 @@ Other public functions: """ +import json import numpy import six @@ -53,13 +54,83 @@ from ._utils import get_attr_as_unicode, INTERPDIM, nxdata_logger, \ __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "15/02/2019" +__date__ = "24/03/2020" class InvalidNXdataError(Exception): pass +class _SilxStyle(object): + """NXdata@SILX_style parser. + + :param NXdata nxdata: + NXdata description for which to extract silx_style information. + """ + + def __init__(self, nxdata): + naxes = len(nxdata.axes) + self._axes_scale_types = [None] * naxes + self._signal_scale_type = None + + stylestr = get_attr_as_unicode(nxdata.group, "SILX_style") + if stylestr is None: + return + + try: + style = json.loads(stylestr) + except json.JSONDecodeError: + nxdata_logger.error( + "Ignoring SILX_style, cannot parse: %s", stylestr) + return + + if not isinstance(style, dict): + nxdata_logger.error( + "Ignoring SILX_style, cannot parse: %s", stylestr) + + if 'axes_scale_types' in style: + axes_scale_types = style['axes_scale_types'] + + if isinstance(axes_scale_types, str): + # Convert single argument to list + axes_scale_types = [axes_scale_types] + + if not isinstance(axes_scale_types, list): + nxdata_logger.error( + "Ignoring SILX_style:axes_scale_types, not a list") + else: + for scale_type in axes_scale_types: + if scale_type not in ('linear', 'log'): + nxdata_logger.error( + "Ignoring SILX_style:axes_scale_types, invalid value: %s", str(scale_type)) + break + else: # All values are valid + if len(axes_scale_types) > naxes: + nxdata_logger.error( + "Clipping SILX_style:axes_scale_types, too many values") + axes_scale_types = axes_scale_types[:naxes] + elif len(axes_scale_types) < naxes: + # Extend axes_scale_types with None to match number of axes + axes_scale_types = [None] * (naxes - len(axes_scale_types)) + axes_scale_types + self._axes_scale_types = tuple(axes_scale_types) + + if 'signal_scale_type' in style: + scale_type = style['signal_scale_type'] + if scale_type not in ('linear', 'log'): + nxdata_logger.error( + "Ignoring SILX_style:signal_scale_type, invalid value: %s", str(scale_type)) + else: + self._signal_scale_type = scale_type + + axes_scale_types = property( + lambda self: self._axes_scale_types, + doc="Tuple of NXdata axes scale types (None, 'linear' or 'log'). List[str]") + + signal_scale_type = property( + lambda self: self._signal_scale_type, + doc="NXdata signal scale type (None, 'linear' or 'log'). str") + + class NXdata(object): """NXdata parser. @@ -76,6 +147,7 @@ class NXdata(object): """ def __init__(self, group, validate=True): super(NXdata, self).__init__() + self._plot_style = None self.group = group """h5py-like group object with @NX_class=NXdata. @@ -147,6 +219,8 @@ class NXdata(object): # excludes scatters self.signal_is_1d = self.signal_is_1d and len(self.axes) <= 1 # excludes n-D scatters + self._plot_style = _SilxStyle(self) + def _validate(self): """Fill :attr:`issues` with error messages for each error found.""" if not is_group(self.group): @@ -250,8 +324,18 @@ class NXdata(object): "dimensions as axis '%s'." % axis_name) # test dimensions of errors associated with signal + + signal_errors = signal_name + "_errors" if "errors" in self.group and is_dataset(self.group["errors"]): - if self.group["errors"].shape != self.group[signal_name].shape: + errors = "errors" + elif signal_errors in self.group and is_dataset(self.group[signal_errors]): + errors = signal_errors + else: + errors = None + if errors: + if self.group[errors].shape != self.group[signal_name].shape: + # In principle just the same size should be enough but + # NeXus documentation imposes to have the same shape self.issues.append( "Dataset containing standard deviations must " + "have the same dimensions as the signal.") @@ -629,9 +713,26 @@ class NXdata(object): if not self.is_valid: raise InvalidNXdataError("Unable to parse invalid NXdata") - if "errors" not in self.group: + # case of signal + signal_errors = self.signal_dataset_name + "_errors" + if "errors" in self.group and is_dataset(self.group["errors"]): + errors = "errors" + elif signal_errors in self.group and is_dataset(self.group[signal_errors]): + errors = signal_errors + else: return None - return self.group["errors"] + return self.group[errors] + + @property + def plot_style(self): + """Information extracted from the optional SILX_style attribute + + :raises: InvalidNXdataError + """ + if not self.is_valid: + raise InvalidNXdataError("Unable to parse invalid NXdata") + + return self._plot_style @property def is_scatter(self): |