pre_edge.py 11.6 KB
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# 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__ = "06/07/2019"


import functools
import logging
from Orange.widgets import gui
from Orange.widgets.settings import Setting
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from Orange.widgets.widget import OWWidget
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from Orange.widgets.widget import Input, Output
import Orange.data
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from silx.gui import qt
from silx.gui.plot import LegendSelector
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import est.core.process.larch.pre_edge
from orangecontrib.est.process import _ProcessForOrangeMixIn
from orangecontrib.est.process import ProcessRunnable
from est.core.types import XASObject
from est.gui.XasObjectViewer import XasObjectViewer, ViewType
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from est.gui.XasObjectViewer import (
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    _plot_raw,
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    _plot_edge,
    _plot_norm,
    _plot_norm_area,
    _plot_post_edge,
    _plot_pre_edge,
)
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from est.gui.larch.pre_edge import _MPreEdgeParameters
from orangecontrib.est.progress import QProgress
from orangecontrib.est.utils import Converter
from orangecontrib.est.widgets.container import _ParameterWindowContainer
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_logger = logging.getLogger(__file__)

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_USE_THREAD = False
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class _PreEdgeWindow(qt.QMainWindow):
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    def __init__(self, parent=None):
        qt.QMainWindow.__init__(self, parent)

        # xas object viewer
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        mapKeys = ["mu", "norm", "norm_area"]
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        self.xasObjViewer = XasObjectViewer(mapKeys=mapKeys)
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        self.xasObjViewer._spectrumViews[0]._plotWidget.getXAxis().setLabel(
            "Energy (eV)"
        )
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        self.setCentralWidget(self.xasObjViewer)
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        self._parametersWindow = _ParameterWindowContainer(
            parent=self, parametersWindow=_MPreEdgeParameters
        )
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        dockWidget = qt.QDockWidget(parent=self)

        # parameters window
        dockWidget.setWidget(self._parametersWindow)
        self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
        dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
        dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)

        # legend selector
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        self.legendDockWidget = LegendSelector.LegendsDockWidget(
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            parent=self, plot=self.xasObjViewer._spectrumViews[0]._plotWidget
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        )
        self.legendDockWidget.setAllowedAreas(
            qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea
        )
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        self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
        self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)

        # volume key selection
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        self.addDockWidget(
            qt.Qt.RightDockWidgetArea, self.xasObjViewer._mapView.keySelectionDocker
        )
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        # plot settings
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        for ope in (
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            _plot_raw,
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            _plot_norm,
            _plot_norm_area,
            _plot_pre_edge,
            _plot_post_edge,
            _plot_edge,
        ):
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            self.xasObjViewer._spectrumViews[0].addCurveOperation(ope)

        self.setWindowFlags(qt.Qt.Widget)

        # connect signal / slot
        self.xasObjViewer.viewTypeChanged.connect(self._updateLegendView)

        # set up
        self._updateLegendView()

    def _updateLegendView(self):
        index, viewType = self.xasObjViewer.getViewType()
        self.legendDockWidget.setVisible(viewType is ViewType.spectrum)
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        self.xasObjViewer._mapView.keySelectionDocker.setVisible(
            viewType is ViewType.map
        )
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    def getNCurves(self):
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        return len(self.xasObjViewer._spectrumViews[0]._plotWidget.getAllCurves())
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class PreEdgeOW(
    _ProcessForOrangeMixIn,
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    OWWidget,
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):
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    """
    Widget used for signal extraction
    """
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    name = "pre edge"
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    id = "orange.widgets.est.larch.pre_edge.PreEdgeOW"
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    description = """
    pre edge subtraction, normalization for XAFS
    This performs a number of steps:
       1. determine E0 (if not supplied) from max of deriv(mu)
       2. fit a line of polynomial to the region below the edge
       3. fit a polynomial to the region above the edge
       4. extrapolate the two curves to E0 to determine the edge jump
       5. estimate area from emin_area to norm2, to get norm_area
    """
    icon = "icons/pre_edge.png"
    priority = 2
    category = "esrfWidgets"
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    keywords = ["spectroscopy", "preedge", "pre", "edge", "normalization"]
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    want_main_area = True
    resizing_enabled = True
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    allows_cycle = False
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    ewokstaskclass = est.core.process.larch.pre_edge.Larch_pre_edge
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    _larchSettings = Setting(dict())
    """Store the configuration of the larch configuration"""

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    class Inputs:
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        xas_obj = Input("xas_obj", XASObject, default=True)
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        # simple compatibility for some Orange widget and especialy the
        # 'spectroscopy add-on'
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        data_table = Input("Data", Orange.data.Table)
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    class Outputs:
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        xas_obj = Output("xas_obj", XASObject)
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        # by default we want to avoid sending 'Orange.data.Table' to avoid
        # loosing the XASObject flow process and results.

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    def __init__(self):
        super().__init__()
        self._latest_xas_obj = None
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        self._window = _PreEdgeWindow(parent=self)
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        layout = gui.vBox(self.mainArea, "pre edge").layout()
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        layout.addWidget(self._window)
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        self._window.xasObjViewer.setWindowTitle("spectra")
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        # manage settings
        if self._larchSettings != dict():
            self._window._parametersWindow.setParameters(self._larchSettings)

        # connect signals / slots
        self._window._parametersWindow.sigChanged.connect(self._updateProcess)

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        # required to display advancement
        if _USE_THREAD is False:
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            self._advancement = QProgress("pre_edge")
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            self._advancement.sigProgress.connect(self._setProgressValue)

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        # set up (insure settings will be store
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        self._update_settings()
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        # self.handleNewSignals()
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    def _updateProcess(self):
        self._update_settings()
        if self._latest_xas_obj:
            self.process(self._latest_xas_obj)

    def _update_settings(self):
        self._larchSettings = self._window._parametersWindow.getParameters()

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    @Inputs.data_table
    def processFrmDataTable(self, data_table):
        if data_table is None:
            return
        self.process(Converter.toXASObject(data_table=data_table))

    @Inputs.xas_obj
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    def process(self, xas_obj):
        if xas_obj is None:
            return

        if not self._canProcess():
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            _logger.warning(
                "There is some processing on going already, will"
                "not process the new dataset"
            )
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        self._latest_xas_obj = xas_obj
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        # e0 can be defined from the flow previously
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        if "e0" in xas_obj.configuration:
            conf = {"e0": xas_obj.configuration["e0"]}
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            self._window._parametersWindow.setParameters(conf)
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        self._startProcess()

        # setup the normalization process
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        inputs = {"xas_obj": xas_obj}
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        if _USE_THREAD is True:
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            # larch is using sqlite3 for database. access to the database
            # require a 'connection' and 'cursor'. theoretically we should be
            # able to access it from a single thread using something like:
            #
            # import sqlite3
            # from larch.xray import xraydb
            # import os
            #
            # dbname = 'xraydata.db'
            # parent, _ = os.path.split(xraydb.__file__)
            # file_ = os.path.join(parent, dbname)
            # if not os.path.exists(file_):
            #     raise IOError('%s does not exists' % file_)
            # self.connection = sqlite3.connect(file_)
            # cursor = self.connection.cursor()
            # self._processingThread = PreEdgeThread(advancement=self._advancement,
            #                                        args=(self.connection, cursor))
            # working until at one point (in time) the database is closed by larch
            # or there is some concurrency failling ?
            # so fo rnow we are making the processing in the main thread that
            # larch is happy about and splitting it in a way to avoid gui
            # freeze
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            process_obj = QLarch_pre_edge(inputs=inputs)
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            process_obj._advancement.sigProgress.connect(self._setProgressValue)
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            process_obj.set_properties(
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                {"_larchSettings": self._window._parametersWindow.getParameters()}
            )
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            # update the processing thread
            thread = self.getProcessingThread()
            thread.init(process_obj=process_obj, xas_obj=self._latest_xas_obj)
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            self._callback_finish = functools.partial(
                self._endProcess, self._latest_xas_obj
            )
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            thread.finished.connect(self._callback_finish)
            # start processing
            thread.start(priority=qt.QThread.LowPriority)
        else:
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            # manage advancement
            self._advancement.setAdvancement(0)
            self._advancement.setMaxSpectrum(self._latest_xas_obj.n_spectrum)
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            process_obj = est.core.process.larch.pre_edge.Larch_pre_edge(inputs=inputs)
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            process_obj.advancement = self._advancement
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            process_obj.set_properties(
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                {"_larchSettings": self._window._parametersWindow.getParameters()}
            )
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            # hack (reason explained in the thread part)
            # to avoid gui freeze, processevents after each spectrum process
            process_obj.addCallback(qt.QApplication.instance().processEvents)
            process_obj.addCallback(self._advancement.increaseAdvancement)
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            process_obj.run()
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            self._callback_finish = None
            self._endProcess(self._latest_xas_obj)
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class QLarch_pre_edge(est.core.process.larch.pre_edge.Larch_pre_edge):
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    """
    Normalization able to give advancement using qt.Signal and QThreadPool
    """

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    def __init__(self, *args, **kwargs):
        est.core.process.larch.pre_edge.Larch_pre_edge.__init__(self, *args, **kwargs)
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        self._advancement = QProgress("pre_edge")
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    def _pool_process(self, xas_obj):
        self.pool = qt.QThreadPool()
        self.pool.setMaxThreadCount(5)
        for spectrum in xas_obj.spectra:
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            runnable = ProcessRunnable(
                fct=est.core.process.larch.pre_edge.process_spectr_pre_edge,
                spectrum=spectrum,
                configuration=xas_obj.configuration,
                callback=self._advancement.increaseAdvancement,
            )
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            self.pool.start(runnable)
        self.pool.waitForDone()