normalization.py 6.99 KB
Newer Older
payno's avatar
payno committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2016-2017 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.
#
# ###########################################################################*/

__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "06/11/2019"


31
import functools
payno's avatar
payno committed
32
import logging
33
34
35
36
import multiprocessing

from PyMca5.PyMcaPhysics.xas.XASClass import XASClass

payno's avatar
payno committed
37
38
from est.core.process.process import Process, Progress
from est.core.types import Spectrum, XASObject
39

payno's avatar
payno committed
40
41
42
_logger = logging.getLogger(__name__)


payno's avatar
payno committed
43
44
45
46
47
48
49
50
def process_spectr_norm(
    spectrum,
    configuration,
    overwrite=True,
    callbacks=None,
    output=None,
    output_dict=None,
):
51
52
    """

53
54
55
56
57
58
    :param spectrum: spectrum to process
    :type: :class:`.Spectrum`
    :param configuration: configuration of the pymca normalization
    :type: dict
    :param overwrite: False if we want to return a new Spectrum instance
    :type: bool
59
    :param callbacks: callback to execute.
60
61
    :param output: list to store the result, needed for pool processing
    :type: multiprocessing.manager.list
62
63
64
    :param output_dict: key is input spectrum, value is index in the output
                        list.
    :type: dict
65
    :return: processed spectrum
66
67
    :rtype: tuple (configuration, spectrum)
    """
payno's avatar
payno committed
68
    _logger.debug("start normalization on spectrum (%s, %s)" % (spectrum.x, spectrum.y))
69
    if spectrum.energy is None or spectrum.mu is None:
payno's avatar
payno committed
70
71
72
        _logger.error(
            "Energy and or Mu is/are not specified, unable to " "compute exafs"
        )
73
        return None, None
74
    pymca_xas = XASClass()
payno's avatar
payno committed
75
    pymca_xas.setSpectrum(energy=spectrum.energy, mu=spectrum.mu)
76
    if configuration is not None:
payno's avatar
payno committed
77
78
79
        if "e0" in configuration:
            configuration["E0Value"] = configuration["e0"]
            configuration["E0Method"] = "Manual"
80
        pymca_xas.setConfiguration(configuration)
81
    configuration = pymca_xas.getConfiguration()
82
83
84
85
86
87
88
89
    try:
        res = pymca_xas.normalize()
        ddict = spectrum.to_dict()
        ddict.update(res)
        spectrum_ = Spectrum.from_dict(ddict)
    except (IndexError, ValueError) as e:
        _logger.error(e)
        return None, None
90
91
92
    if callbacks:
        for callback in callbacks:
            callback()
93
94
95
96
97
98
99
100
101
102
103
104
105

    def get_output(orignal_spec, res_spec):
        if overwrite:
            orignal_spec.update(res_spec)
            return orignal_spec
        else:
            return res_spec

    if output is not None:
        assert output_dict is not None
        output[output_dict[spectrum]] = get_output(spectrum, spectrum_)

    return configuration, get_output(spectrum, spectrum_)
106
107


108
def pymca_normalization(xas_obj):
payno's avatar
payno committed
109
    """
110

111
112
113
114
    :param xas_obj: object containing the configuration and spectra to process
    :type: Union[XASObject, dict]. If is a dict, should contain configuration or
                                 spectra keys. Otherwise is simply the spectra
    :return: spectra dict
115
    :rtype: dict
payno's avatar
payno committed
116
    """
117
118
    normalization_obj = PyMca_normalization()
    return normalization_obj.process(xas_obj=xas_obj)
119
120


121
122
123
124
_USE_MULTIPROCESSING_POOL = False
# note: we cannot use multiprocessing pool with push workflow for now.


125
class PyMca_normalization(Process):
126
    def __init__(self):
payno's avatar
payno committed
127
        Process.__init__(self, "normalization")
128
        self._advancement = Progress(self.name)
129

130
    def set_properties(self, properties):
payno's avatar
payno committed
131
132
        if "_pymcaSettings" in properties:
            self._settings = properties["_pymcaSettings"]
133
134
135
136

    def process(self, xas_obj):
        """

137
138
139
        :param xas_obj: object containing the configuration and spectra to process
        :type: Union[XASObject, dict]. If is a dict, should contain configuration or
                                     spectra keys. Otherwise is simply the spectra
140
141
        :return: updated XASObject
        :rtype: :class:`.XASObject`
142
        """
143
        _xas_obj = self.getXasObject(xas_obj)
144
145

        if _xas_obj.energy is None:
payno's avatar
payno committed
146
            _logger.error("Energy not specified, unable to normalize spectra")
147
148
            return

149
        if self._settings:
payno's avatar
payno committed
150
            _xas_obj.configuration["Normalization"] = self._settings
151

152
        self._advancement.reset(max_=_xas_obj.n_spectrum)
153
        self._advancement.startProcess()
154
        self._pool_process(xas_obj=_xas_obj)
155
        self._advancement.endProcess()
payno's avatar
payno committed
156
157
158
        self.register_process(
            _xas_obj, data_keys=("NormalizedEnergy", "NormalizedMu", "NormalizedSignal")
        )
159
160
161
162
        return _xas_obj

    def _pool_process(self, xas_obj):
        """process normalization from a pool"""
163
164
165
        assert isinstance(xas_obj, XASObject)
        if not _USE_MULTIPROCESSING_POOL:
            for spectrum in xas_obj.spectra:
payno's avatar
payno committed
166
167
168
169
170
171
                process_spectr_norm(
                    spectrum=spectrum,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=True,
                )
172
173
        else:
            from multiprocessing import Manager
payno's avatar
payno committed
174

175
176
177
178
179
180
181
182
            manager = Manager()
            output_dict = {}
            res_list = manager.list()
            for i_spect, spect in enumerate(xas_obj.spectra):
                res_list.append(None)
                output_dict[spect] = i_spect

            with multiprocessing.Pool(5) as p:
payno's avatar
payno committed
183
184
185
186
187
188
189
190
                partial_ = functools.partial(
                    process_spectr_norm,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=False,
                    output=res_list,
                    output_dict=output_dict,
                )
191
192
193
194
195
196
                p.map(partial_, xas_obj.spectra)

            # then update local spectrum
            for spectrum, res in zip(xas_obj.spectra, res_list):
                spectrum.update(res)

197
198
199
200
201
    def definition(self):
        return "Normalization of the spectrum"

    def program_version(self):
        import PyMca5
payno's avatar
payno committed
202

203
204
205
        return PyMca5.version()

    def program_name(self):
payno's avatar
payno committed
206
        return "pymca_normalization"
207
208

    __call__ = process