normalization.py 7.6 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
import multiprocessing
from PyMca5.PyMcaPhysics.xas.XASClass import XASClass
Wout De Nolf's avatar
flake8    
Wout De Nolf committed
35
from est.core.process.process import Process
36
from est.core.process.process import _NexusDatasetDef
payno's avatar
payno committed
37
from est.core.types import Spectrum, XASObject
38

payno's avatar
payno committed
39
40
41
_logger = logging.getLogger(__name__)


payno's avatar
payno committed
42
def process_spectr_norm(
payno's avatar
payno committed
43
    spectrum: Spectrum,
payno's avatar
payno committed
44
45
46
47
48
49
    configuration,
    overwrite=True,
    callbacks=None,
    output=None,
    output_dict=None,
):
50
51
    """

52
53
54
55
56
57
    :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
58
    :param callbacks: callback to execute.
59
60
    :param output: list to store the result, needed for pool processing
    :type: multiprocessing.manager.list
61
62
63
    :param output_dict: key is input spectrum, value is index in the output
                        list.
    :type: dict
64
    :return: processed spectrum
65
66
    :rtype: tuple (configuration, spectrum)
    """
payno's avatar
payno committed
67
    assert isinstance(spectrum, 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
    """
payno's avatar
payno committed
117
118
    normalization_obj = PyMca_normalization(inputs={"xas_obj": xas_obj})
    return normalization_obj.run()
119
120


121
_USE_MULTIPROCESSING_POOL = False
payno's avatar
payno committed
122
# note: we cannot use multiprocessing pool with pypushflow for now.
123
124


125
class PyMca_normalization(
126
127
128
129
130
    Process,
    name="normalization",
    input_names=["xas_obj"],
    output_names=["xas_obj"],
    optional_input_names=["normalization"],
131
):
132
    def set_properties(self, properties):
payno's avatar
payno committed
133
134
        if "_pymcaSettings" in properties:
            self._settings = properties["_pymcaSettings"]
135

136
    def run(self):
137
138
        """

139
140
141
        :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
142
143
        :return: updated XASObject
        :rtype: :class:`.XASObject`
144
        """
145
        xas_obj = self.inputs.xas_obj
146
        if xas_obj is None:
147
            raise ValueError("xas_obj should be provided")
148
        _xas_obj = self.getXasObject(xas_obj)
149
150

        if _xas_obj.energy is None:
payno's avatar
payno committed
151
            _logger.error("Energy not specified, unable to normalize spectra")
152
153
            return

154
155
156
        if self.inputs.normalization:
            self.setConfiguration(self.inputs.normalization)
            _xas_obj.configuration["Normalization"] = self.inputs.normalization
157
        self._advancement.reset(max_=_xas_obj.n_spectrum)
158
        self._advancement.startProcess()
159
        self._pool_process(xas_obj=_xas_obj)
160
        self._advancement.endProcess()
161
162
        if _xas_obj.normalized_energy is None:
            raise ValueError("Fail to compute normalize energy")
payno's avatar
payno committed
163
        self.register_process(
164
165
166
167
168
169
            _xas_obj,
            data_keys=(
                _NexusDatasetDef("NormalizedEnergy"),
                _NexusDatasetDef("NormalizedMu"),
                _NexusDatasetDef("NormalizedSignal"),
            ),
payno's avatar
payno committed
170
        )
171
        self.outputs.xas_obj = _xas_obj.to_dict()
172
173
174
175
        return _xas_obj

    def _pool_process(self, xas_obj):
        """process normalization from a pool"""
176
177
        assert isinstance(xas_obj, XASObject)
        if not _USE_MULTIPROCESSING_POOL:
payno's avatar
payno committed
178
            for spectrum in xas_obj.spectra.data.flat:
payno's avatar
payno committed
179
180
181
182
183
184
                process_spectr_norm(
                    spectrum=spectrum,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=True,
                )
185
186
        else:
            from multiprocessing import Manager
payno's avatar
payno committed
187

188
189
190
            manager = Manager()
            output_dict = {}
            res_list = manager.list()
payno's avatar
payno committed
191
            for i_spect, spect in enumerate(xas_obj.spectra.data.flat):
192
193
194
195
                res_list.append(None)
                output_dict[spect] = i_spect

            with multiprocessing.Pool(5) as p:
payno's avatar
payno committed
196
197
198
199
200
201
202
203
                partial_ = functools.partial(
                    process_spectr_norm,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=False,
                    output=res_list,
                    output_dict=output_dict,
                )
204
205
206
207
208
209
                p.map(partial_, xas_obj.spectra)

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

210
211
212
213
214
    def definition(self):
        return "Normalization of the spectrum"

    def program_version(self):
        import PyMca5
payno's avatar
payno committed
215

216
217
        return PyMca5.version()

218
219
    @staticmethod
    def program_name():
payno's avatar
payno committed
220
        return "pymca_normalization"
221

222
    __call__ = run