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# coding: utf-8
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2015-2020 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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.
"""Module for writing sparse frames in HDF5 in the Nexus style"""
__author__ = "Jerome Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "20/11/2020"
__status__ = "production"
__docformat__ = 'restructuredtext'
import json
from collections import OrderedDict
import logging
logger = logging.getLogger(__name__)
import numpy
from .. import version
from .nexus import Nexus, get_isotime
try:
import hdf5plugin
except:
cmp = {}
else:
cmp = hdf5plugin.Bitshuffle()
def _generate_densify_script(integer):
"Provide a script to densify those data"
res = """#python
import numpy
frames = []
masked = numpy.where(numpy.logical_not(numpy.isfinite(mask)))
for idx, bg in enumerate(background_avg):
dense = numpy.interp(mask, radius, bg)
flat = dense.ravel()
start, stop = frame_ptr[idx:idx+2]
flat[index[start:stop]] = intensity[start:stop]"""
if integer:
res += """
dense = numpy.round(dense)
dense[masked] = dummy"""
else:
res += """
dense[masked] = numpy.NaN"""
res += """
frames.append(dense.astype(intensity.dtype))
"""
return res
def save_sparse(filename, frames, beamline="beamline", ai=None, source=None, extra={}):
"""Write the list of frames into a HDF5 file
:param filename: name of the file
:param frames: list of sparse frames (as built by sparsify)
:param beamline: name of the beamline as text
:param ai: Instance of geometry or azimuthal integrator
:param source: list of input files
:param extra: dict with extra metadata
:return: None
"""
assert len(frames)
with Nexus(filename, mode="w", creator="pyFAI_%s" % version) as nexus:
instrument = nexus.new_instrument(instrument_name=beamline)
entry = instrument.parent
sparse_grp = nexus.new_class(entry, "sparse_frames", class_type="NXdata")
entry.attrs["default"] = sparse_grp.name
sparse_grp["frame_ptr"] = numpy.concatenate(([0], numpy.cumsum([i.intensity.size for i in frames]))).astype(dtype=numpy.uint32)
index = numpy.concatenate([i.index for i in frames]).astype(numpy.uint32)
intensity = numpy.concatenate([i.intensity for i in frames])
is_integer = numpy.issubdtype(intensity.dtype, numpy.integer)
sparse_grp["script"] = _generate_densify_script(is_integer)
sparse_grp.create_dataset("index", data=index, **cmp)
sparse_grp.create_dataset("intensity", data=intensity, **cmp)
radius = frames[0].radius
mask = frames[0].mask
dummy = frames[0].dummy
if dummy is None:
if is_integer:
dummy = 0
else:
dummy = numpy.NaN
sparse_grp.create_dataset("dummy", data=dummy)
rds = sparse_grp.create_dataset("radius", data=radius, dtype=numpy.float32)
rds.attrs["interpretation"] = "spectrum"
mskds = sparse_grp.create_dataset("mask", data=mask, **cmp)
mskds.attrs["interpretation"] = "image"
background_avg = numpy.vstack([f.background_avg for f in frames])
background_std = numpy.vstack([f.background_std for f in frames])
bgavgds = sparse_grp.create_dataset("background_avg", data=background_avg, **cmp)
bgavgds.attrs["interpretation"] = "spectrum"
bgavgds.attrs["signal"] = 1
bgavgds.attrs["long_name"] = "Average value of background"
bgstdds = sparse_grp.create_dataset("background_std", data=background_std, **cmp)
sparse_grp["errors"] = bgstdds
bgstdds.attrs["interpretation"] = "spectrum"
bgstdds.attrs["long_name"] = "Standard deviation of background"
sparse_grp.attrs["signal"] = "background_avg"
try:
sparse_grp.attrs["axes"] = [".", "radius"]
except TypeError:
logger.error("Please upgrade your installation of h5py !!!")
if ai is not None:
sparsify_grp = nexus.new_class(entry, "sparsify", class_type="NXprocess")
sparsify_grp["program"] = "pyFAI"
sparsify_grp["sequence_index"] = 1
sparsify_grp["version"] = version
sparsify_grp["date"] = get_isotime()
if source is not None:
sparsify_grp["source"] = source
config_grp = nexus.new_class(sparsify_grp, "configuration", class_type="NXnote")
config_grp["type"] = "text/json"
parameters = OrderedDict([("geometry", ai.get_config()),
("sparsify", extra)])
config_grp["data"] = json.dumps(parameters, indent=2, separators=(",\r\n", ": "))
detector_grp = nexus.new_class(instrument, ai.detector.name.replace(" ", "_"), "NXdetector")
dist_ds = detector_grp.create_dataset("distance", data=ai.dist)
dist_ds.attrs["units"] = "m"
xpix_ds = detector_grp.create_dataset("x_pixel_size", data=ai.pixel2)
xpix_ds.attrs["units"] = "m"
ypix_ds = detector_grp.create_dataset("y_pixel_size", data=ai.pixel1)
ypix_ds.attrs["units"] = "m"
f2d = ai.getFit2D()
xbc_ds = detector_grp.create_dataset("beam_center_x", data=f2d["centerX"])
xbc_ds.attrs["units"] = "pixel"
ybc_ds = detector_grp.create_dataset("beam_center_y", data=f2d["centerY"])
ybc_ds.attrs["units"] = "pixel"
if ai.wavelength is not None:
monochromator_grp = nexus.new_class(instrument, "monchromator", "NXmonochromator")
wl_ds = monochromator_grp.create_dataset("wavelength", data=numpy.float32(ai.wavelength * 1e10))
wl_ds.attrs["units"] = "Å"
# wl_ds.attrs["resolution"] = 0.014
# nrj_ds = monochromator_grp.create_dataset("energy", data=numpy.floaself.energy)
# nrj_ds.attrs["units"] = "keV"
# #nrj_ds.attrs["resolution"] = 0.014
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