ft.py

# coding: utf-8
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__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "06/11/2019"

import functools
import logging
import multiprocessing

import numpy
from PyMca5.PyMcaPhysics.xas.XASClass import XASClass
from est.core.process.process import _input_desc
from est.core.process.process import _output_desc
from est.core.process.process import Process
from est.core.process.process import _NexusDatasetDef
from est.core.types import XASObject, Spectrum

_logger = logging.getLogger(__name__)


def process_spectr_ft(
    spectrum,
    configuration,
    overwrite=True,
    callbacks=None,
    output=None,
    output_dict=None,
):
    """

    :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
    :param callback: callback to execute.
    :param output: list to store the result, needed for pool processing
    :type: multiprocessing.manager.list
    :param output_dict: key is input spectrum, value is index in the output
                        list.
    :type: dict
    :return: processed spectrum
    :rtype: tuple (configuration, spectrum)
    """
    _logger.debug(
        "start fourier transform on spectrum (%s, %s)" % (spectrum.x, spectrum.y)
    )
    pymca_xas = XASClass()
    if spectrum.energy is None or spectrum.mu is None:
        _logger.error(
            "Energy and or Mu is/are not specified, unable to " "compute exafs"
        )
        return None, None

    if configuration is not None:
        pymca_xas.setConfiguration(configuration)
    pymca_xas.setSpectrum(energy=spectrum.energy, mu=spectrum.mu)

    if "EXAFSSignal" not in spectrum:
        _logger.warning(
            "exafs has not been processed yet, unable to process" "fourier transform"
        )
        return None, None

    if "EXAFSNormalized" not in spectrum:
        _logger.warning("ft window need to be defined first")
        return None, None

    cleanMu = spectrum["EXAFSSignal"]
    kValues = spectrum["EXAFSKValues"]

    dataSet = numpy.zeros((cleanMu.size, 2), numpy.float)
    dataSet[:, 0] = kValues
    dataSet[:, 1] = cleanMu

    set2 = dataSet.copy()
    set2[:, 1] = spectrum["EXAFSNormalized"]

    # remove points with k<2
    goodi = (set2[:, 0] >= spectrum["KMin"]) & (set2[:, 0] <= spectrum["KMax"])
    set2 = set2[goodi, :]

    if set2.size == 0:
        ft = {"FTImaginary": numpy.nan, "FTIntensity": numpy.nan, "FTRadius": numpy.nan}
    else:
        ft = pymca_xas.fourierTransform(
            set2[:, 0], set2[:, 1], kMin=spectrum["KMin"], kMax=spectrum["KMax"]
        )
        assert "FTIntensity" in ft
        assert "FTRadius" in ft
        assert ft["FTRadius"] is not None
        assert ft["FTIntensity"] is not None
    if callbacks:
        for callback in callbacks:
            callback()

    if overwrite:
        spectrum_ = spectrum
    else:
        spectrum_ = Spectrum()
        spectrum_.update(spectrum)
    assert spectrum_
    spectrum_.ft = ft

    if output is not None:
        assert output_dict is not None
        output[output_dict[spectrum]] = spectrum_
    return configuration, spectrum_


def pymca_ft(xas_obj):
    """

    :param xas_obj: object containing the configuration and spectra to process
    :type: Union[XASObject, dict]
    :return: spectra dict
    :rtype: dict
    """
    ft_obj = PyMca_ft()
    assert xas_obj is not None
    return ft_obj.process(xas_obj=xas_obj)


_USE_MULTIPROCESSING_POOL = False
# note: we cannot use multiprocessing pool with pypushflow for now.


class PyMca_ft(Process):

    _INPUT_NAMES = set(["xas_obj"])

    _OUTPUT_NAMES = set(["xas_obj"])

    def __init__(self, varinfo=None, **inputs):
        Process.__init__(self, name="ft", varinfo=varinfo, **inputs)

    def set_properties(self, properties):
        if "_pymcaSettings" in properties:
            self._settings = properties["_pymcaSettings"]

    def run(self, xas_obj=None):
        """

        :param xas_obj: object containing the configuration and spectra to process
        :type: Union[XASObject, dict]
        :return: spectra dict
        :rtype: dict
        """
        if xas_obj is None:
            xas_obj = self.inputs.xas_obj
        _xas_obj = self.getXasObject(xas_obj=xas_obj)
        if self._settings:
            _xas_obj.configuration["FT"] = self._settings

        self._advancement.reset(max_=_xas_obj.n_spectrum)
        self._advancement.startProcess()
        self._pool_process(xas_obj=_xas_obj)
        self._advancement.endProcess()
        assert hasattr(_xas_obj.spectra.data.flat[0], "ft")
        assert hasattr(_xas_obj.spectra.data.flat[0].ft, "intensity")
        assert hasattr(_xas_obj.spectra.data.flat[0].ft, "imaginary")
        self.register_process(
            _xas_obj,
            data_keys=(
                _NexusDatasetDef("ft.radius"),
                _NexusDatasetDef("ft.intensity"),
                _NexusDatasetDef("ft.imaginary"),
            ),
        )
        self.outputs.xas_obj = _xas_obj.to_dict()
        return _xas_obj

    def _pool_process(self, xas_obj):
        assert isinstance(xas_obj, XASObject)
        if not _USE_MULTIPROCESSING_POOL:
            for spectrum in xas_obj.spectra:
                process_spectr_ft(
                    spectrum=spectrum,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=True,
                )
        else:
            from multiprocessing import Manager

            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(1) as p:
                partial_ = functools.partial(
                    process_spectr_ft,
                    configuration=xas_obj.configuration,
                    callbacks=self.callbacks,
                    overwrite=False,
                    output=res_list,
                    output_dict=output_dict,
                )
                p.map(partial_, xas_obj.spectra)

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

    def definition(self):
        return "fourier transform"

    def program_version(self):
        import PyMca5

        return PyMca5.version()

    @staticmethod
    def program_name():
        return "pymca_ft"

    __call__ = run


if __name__ == "__main__":
    import sys
    import yaml

    xas_object_yaml_file = sys.argv[1]
    _logger.debug("Load xas object from {}".format(xas_object_yaml_file))
    with open(xas_object_yaml_file, "r") as file:
        ddict = yaml.load(file)["input_data"]
        xas_object = XASObject.from_dict(ddict)
    print("******* do ft ********")
    res_xas_object = pymca_ft(xas_obj=xas_object)
    res_xas_object._create_saving_pt()

    # dump resulting object
    with open(xas_object_yaml_file, "w") as file:
        yaml.dump({"input_data": res_xas_object.to_dict()}, file)

    # dump resulting object into output_normalization file
    with open("output_ft.yaml", "w") as file:
        yaml.dump({"input_data": res_xas_object.to_dict()}, file)