autobk.py

# coding: utf-8
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__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "04/10/2021"


import functools
import logging
from Orange.widgets import gui
from Orange.widgets.settings import Setting
from Orange.widgets.widget import OWWidget
from Orange.widgets.widget import Input, Output
import Orange.data
from silx.gui import qt
from silx.gui.plot import LegendSelector
import est.core.process.larch.autobk
from orangecontrib.est.process import _ProcessForOrangeMixIn
from est.core.types import XASObject
from est.gui.XasObjectViewer import XasObjectViewer, ViewType
from est.gui.XasObjectViewer import (
    _plot_bkg,
    _plot_spectrum,
    _plot_knots,
    _plot_chi,
)
from est.gui.larch.autobk import _AutobkParameters
from orangecontrib.est.progress import QProgress
from orangecontrib.est.utils import Converter
from orangecontrib.est.widgets.container import _ParameterWindowContainer

_logger = logging.getLogger(__file__)

_USE_THREAD = False


class AutobkWindow(qt.QMainWindow):
    def __init__(self, parent=None):
        qt.QMainWindow.__init__(self, parent)

        # xas object viewer
        mapKeys = ["mu", "bkg", "chie", "k", "chi", "e0"]
        self.xasObjViewer = XasObjectViewer(
            mapKeys=mapKeys, spectrumPlots=("background", "chi(k)")
        )
        self.xasObjViewer._spectrumViews[0]._plotWidget.getXAxis().setLabel(
            "Energy (eV)"
        )
        self.xasObjViewer._spectrumViews[0]._plotWidget.getYAxis().setLabel(
            "Absorption (a.u.)"
        )
        self.setCentralWidget(self.xasObjViewer)
        self._parametersWindow = _ParameterWindowContainer(
            parent=self, parametersWindow=_AutobkParameters
        )
        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)

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

        # chi legend selector
        self._chiLegendDockWidget = LegendSelector.LegendsDockWidget(
            parent=self, plot=self.xasObjViewer._spectrumViews[1]._plotWidget
        )
        self._chiLegendDockWidget.setAllowedAreas(
            qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea
        )
        self._chiLegendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
        self.addDockWidget(qt.Qt.RightDockWidgetArea, self._chiLegendDockWidget)

        # volume key selection
        self.addDockWidget(
            qt.Qt.RightDockWidgetArea, self.xasObjViewer._mapView.keySelectionDocker
        )

        # plot settings
        for ope in (_plot_bkg, _plot_spectrum, _plot_knots):
            self.xasObjViewer._spectrumViews[0].addCurveOperation(ope)

        self.xasObjViewer._spectrumViews[1].addCurveOperation(_plot_chi)

        self.setWindowFlags(qt.Qt.Widget)

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

        # set up
        self._updateLegendView()

    def getNCurves(self):
        return len(self.xasObjViewer._spectrumViews[0]._plotWidget.getAllCurves())

    def _updateLegendView(self):
        index, viewType = self.xasObjViewer.getViewType()
        self.bkgLegendDockWidget.setVisible(
            viewType is ViewType.spectrum and index == 0
        )
        self._chiLegendDockWidget.setVisible(
            viewType is ViewType.spectrum and index == 1
        )
        self.xasObjViewer._mapView.keySelectionDocker.setVisible(
            viewType is ViewType.map
        )


class AutobkOW(_ProcessForOrangeMixIn, OWWidget):
    """
    Widget used for signal extraction
    """

    name = "autobk"
    id = "orange.widgets.est.larch.autobk"
    description = "background removal"
    icon = "icons/autobk.png"
    priority = 1
    category = "esrfWidgets"
    keywords = ["spectroscopy", "autobk", "background"]

    want_main_area = True
    resizing_enabled = True
    allows_cycle = False

    _larchSettings = Setting(dict())
    # kept for compatibility
    static_input = Setting({"xas_obj": None, "autobk": None})
    """Store the configuration of the larch configuration"""

    ewokstaskclass = est.core.process.larch.autobk.Larch_autobk

    class Inputs:
        xas_obj = Input("xas_obj", XASObject, default=True)
        # simple compatibility for some Orange widget and especialy the
        # 'spectroscopy add-on'
        data_table = Input("Data", Orange.data.Table)

    class Outputs:
        xas_obj = Output("xas_obj", XASObject)
        # by default we want to avoid sending 'Orange.data.Table' to avoid
        # loosing the XASObject flow process and results.

    def __init__(self):
        super().__init__()
        self._latest_xas_obj = None
        self._window = AutobkWindow(parent=self)
        layout = gui.vBox(self.mainArea, "autobk").layout()
        layout.addWidget(self._window)
        self._window.xasObjViewer.setWindowTitle("spectra")

        # manage settings
        larch_settings = self.static_input.get("autobk", None)
        if larch_settings is None:
            larch_settings = self._larchSettings
        if larch_settings != dict():
            self._window._parametersWindow.setParameters(larch_settings)

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

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

        # set up (insure settings will be store
        self._update_settings()

        # self.handleNewSignals()

    def _updateProcess(self):
        """Update settings keeping current xas obj"""
        self._update_settings()
        if self._latest_xas_obj:
            self.process(self._latest_xas_obj)

    def _update_settings(self):
        self._larchSettings = self._window._parametersWindow.getParameters()
        self.static_input = {
            "autobk": self._window._parametersWindow.getParameters(),
            "xas_obj": None,
        }

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

        if not self._canProcess():
            _logger.warning(
                "There is some processing on going already, will"
                "not process the new dataset"
            )

        self._latest_xas_obj = xas_obj
        self._startProcess()

        # setup the normalization process
        inputs = {"xas_obj": xas_obj}
        if _USE_THREAD is True:
            # note: for now with larch with cannot do thread computation (see
            # PreEdgeOW )
            process_obj = QLarch_autobk(inputs=inputs)
            process_obj._advancement.sigProgress.connect(self._setProgressValue)
            process_obj.set_properties(
                {"_larchSettings": self._window._parametersWindow.getParameters()}
            )

            # update the processing thread
            thread = self.getProcessingThread()
            thread.init(process_obj=process_obj, xas_obj=self._latest_xas_obj)
            self._callback_finish = functools.partial(
                self._endProcess, self._latest_xas_obj
            )
            thread.finished.connect(self._callback_finish)
            # start processing
            thread.start(priority=qt.QThread.LowPriority)
        else:
            # manage advancement
            self._advancement.setAdvancement(0)
            self._advancement.setMaxSpectrum(self._latest_xas_obj.n_spectrum)
            process_obj = est.core.process.larch.autobk.Larch_autobk(inputs=inputs)
            process_obj.advancement = self._advancement
            process_obj.set_properties(
                {"_larchSettings": self._window._parametersWindow.getParameters()}
            )
            # 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)
            process_obj.run()
            self._callback_finish = None
            self._endProcess(self._latest_xas_obj)


class QLarch_autobk(est.core.process.larch.autobk.Larch_autobk):
    """
    Normalization able to give advancement using qt.Signal and QThreadPool
    """

    def __init__(self, *args, **kwargs):
        est.core.process.larch.autobk.Larch_autobk.__init__(self, *args, **kwargs)
        self._advancement = QProgress("autobk")

    def _pool_process(self, xas_obj):
        self.pool = qt.QThreadPool()
        self.pool.setMaxThreadCount(5)
        for spectrum in xas_obj.spectra:
            runnable = ProcessRunnable(
                fct=est.core.process.larch.autobk.process_spectr_autobk,
                spectrum=spectrum,
                configuration=xas_obj.configuration,
                callback=self._advancement.increaseAdvancement,
            )
            self.pool.start(runnable)
        self.pool.waitForDone()