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Diffstat (limited to 'silx/io/nxdata/write.py')
| -rw-r--r-- | silx/io/nxdata/write.py | 203 |
1 files changed, 0 insertions, 203 deletions
diff --git a/silx/io/nxdata/write.py b/silx/io/nxdata/write.py deleted file mode 100644 index e9ac3ac..0000000 --- a/silx/io/nxdata/write.py +++ /dev/null @@ -1,203 +0,0 @@ -# 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. -# -# ###########################################################################*/ - -import os -import logging - -import h5py -import numpy -import six - -__authors__ = ["P. Knobel"] -__license__ = "MIT" -__date__ = "17/04/2018" - - -_logger = logging.getLogger(__name__) - - -def _str_to_utf8(text): - return numpy.array(text, dtype=h5py.special_dtype(vlen=six.text_type)) - - -def save_NXdata(filename, signal, axes=None, - signal_name="data", axes_names=None, - signal_long_name=None, axes_long_names=None, - signal_errors=None, axes_errors=None, - title=None, interpretation=None, - nxentry_name="entry", nxdata_name=None): - """Write data to an NXdata group. - - .. note:: - - No consistency checks are made regarding the dimensionality of the - signal and number of axes. The user is responsible for providing - meaningful data, that can be interpreted by visualization software. - - :param str filename: Path to output file. If the file does not - exists, it is created. - :param numpy.ndarray signal: Signal array. - :param List[numpy.ndarray] axes: List of axes arrays. - :param str signal_name: Name of signal dataset, in output file - :param List[str] axes_names: List of dataset names for axes, in - output file - :param str signal_long_name: *@long_name* attribute for signal, or None. - :param axes_long_names: None, or list of long names - for axes - :type axes_long_names: List[str, None] - :param numpy.ndarray signal_errors: Array of errors associated with the - signal - :param axes_errors: List of arrays of errors - associated with each axis - :type axes_errors: List[numpy.ndarray, None] - :param str title: Graph title (saved as a "title" dataset) or None. - :param str interpretation: *@interpretation* attribute ("spectrum", - "image", "rgba-image" or None). This is only needed in cases of - ambiguous dimensionality, e.g. a 3D array which represents a RGBA - image rather than a stack. - :param str nxentry_name: Name of group in which the NXdata group - is created. By default, "/entry" is used. - - .. note:: - - The Nexus format specification requires for NXdata groups - be part of a NXentry group. - The specified group should have attribute *@NX_class=NXentry*, in - order for the created file to be nexus compliant. - :param str nxdata_name: Name of NXdata group. If omitted (None), the - function creates a new group using the first available name ("data0", - or "data1"...). - Overwriting an existing group (or dataset) is not supported, you must - delete it yourself prior to calling this function if this is what you - want. - :return: True if save was successful, else False. - """ - if h5py is None: - raise ImportError("h5py could not be imported, but is required by " - "save_NXdata function") - - if axes_names is not None: - assert axes is not None, "Axes names defined, but missing axes arrays" - assert len(axes) == len(axes_names), \ - "Mismatch between number of axes and axes_names" - - if axes is not None and axes_names is None: - axes_names = [] - for i, axis in enumerate(axes): - axes_names.append("dim%d" % i if axis is not None else ".") - if axes is None: - axes = [] - - # Open file in - if os.path.exists(filename): - errmsg = "Cannot write/append to existing path %s" - if not os.path.isfile(filename): - errmsg += " (not a file)" - _logger.error(errmsg, filename) - return False - if not os.access(filename, os.W_OK): - errmsg += " (no permission to write)" - _logger.error(errmsg, filename) - return False - mode = "r+" - else: - mode = "w-" - - with h5py.File(filename, mode=mode) as h5f: - # get or create entry - if nxentry_name is not None: - entry = h5f.require_group(nxentry_name) - if "default" not in h5f.attrs: - # set this entry as default - h5f.attrs["default"] = _str_to_utf8(nxentry_name) - if "NX_class" not in entry.attrs: - entry.attrs["NX_class"] = u"NXentry" - else: - # write NXdata into the root of the file (invalid nexus!) - entry = h5f - - # Create NXdata group - if nxdata_name is not None: - if nxdata_name in entry: - _logger.error("Cannot assign an NXdata group to an existing" - " group or dataset") - return False - else: - # no name specified, take one that is available - nxdata_name = "data0" - i = 1 - while nxdata_name in entry: - _logger.info("%s item already exists in NXentry group," + - " trying %s", nxdata_name, "data%d" % i) - nxdata_name = "data%d" % i - i += 1 - - data_group = entry.create_group(nxdata_name) - data_group.attrs["NX_class"] = u"NXdata" - data_group.attrs["signal"] = _str_to_utf8(signal_name) - if axes: - data_group.attrs["axes"] = _str_to_utf8(axes_names) - if title: - # not in NXdata spec, but implemented by nexpy - data_group["title"] = title - # better way imho - data_group.attrs["title"] = _str_to_utf8(title) - - signal_dataset = data_group.create_dataset(signal_name, - data=signal) - if signal_long_name: - signal_dataset.attrs["long_name"] = _str_to_utf8(signal_long_name) - if interpretation: - signal_dataset.attrs["interpretation"] = _str_to_utf8(interpretation) - - for i, axis_array in enumerate(axes): - if axis_array is None: - assert axes_names[i] in [".", None], \ - "Axis name defined for dim %d but no axis array" % i - continue - axis_dataset = data_group.create_dataset(axes_names[i], - data=axis_array) - if axes_long_names is not None: - axis_dataset.attrs["long_name"] = _str_to_utf8(axes_long_names[i]) - - if signal_errors is not None: - data_group.create_dataset("errors", - data=signal_errors) - - if axes_errors is not None: - assert isinstance(axes_errors, (list, tuple)), \ - "axes_errors must be a list or a tuple of ndarray or None" - assert len(axes_errors) == len(axes_names), \ - "Mismatch between number of axes_errors and axes_names" - for i, axis_errors in enumerate(axes_errors): - if axis_errors is not None: - dsname = axes_names[i] + "_errors" - data_group.create_dataset(dsname, - data=axis_errors) - if "default" not in entry.attrs: - # set this NXdata as default - entry.attrs["default"] = nxdata_name - - return True |