Source code for silx.gui.fit.BackgroundWidget

# coding: utf-8
#/*##########################################################################
# Copyright (C) 2004-2021 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# 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.
#
# #########################################################################*/
"""This module provides a background configuration widget
:class:`BackgroundWidget` and a corresponding dialog window
:class:`BackgroundDialog`.

.. image:: img/BackgroundDialog.png
   :height: 300px
"""
import sys
import numpy
from silx.gui import qt
from silx.gui.plot import PlotWidget
from silx.math.fit import filters

__authors__ = ["V.A. Sole", "P. Knobel"]
__license__ = "MIT"
__date__ = "28/06/2017"


class HorizontalSpacer(qt.QWidget):
    def __init__(self, *args):
        qt.QWidget.__init__(self, *args)
        self.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Expanding,
                                          qt.QSizePolicy.Fixed))


class BackgroundParamWidget(qt.QWidget):
    """Background configuration composite widget.

    Strip and snip filters parameters can be adjusted using input widgets.

    Updating the widgets causes :attr:`sigBackgroundParamWidgetSignal` to
    be emitted.
    """
    sigBackgroundParamWidgetSignal = qt.pyqtSignal(object)

    def __init__(self, parent=None):
        qt.QWidget.__init__(self, parent)

        self.mainLayout = qt.QGridLayout(self)
        self.mainLayout.setColumnStretch(1, 1)

        # Algorithm choice ---------------------------------------------------
        self.algorithmComboLabel = qt.QLabel(self)
        self.algorithmComboLabel.setText("Background algorithm")
        self.algorithmCombo = qt.QComboBox(self)
        self.algorithmCombo.addItem("Strip")
        self.algorithmCombo.addItem("Snip")
        self.algorithmCombo.activated[int].connect(
                self._algorithmComboActivated)

        # Strip parameters ---------------------------------------------------
        self.stripWidthLabel = qt.QLabel(self)
        self.stripWidthLabel.setText("Strip Width")

        self.stripWidthSpin = qt.QSpinBox(self)
        self.stripWidthSpin.setMaximum(100)
        self.stripWidthSpin.setMinimum(1)
        self.stripWidthSpin.valueChanged[int].connect(self._emitSignal)

        self.stripIterLabel = qt.QLabel(self)
        self.stripIterLabel.setText("Strip Iterations")
        self.stripIterValue = qt.QLineEdit(self)
        validator = qt.QIntValidator(self.stripIterValue)
        self.stripIterValue._v = validator
        self.stripIterValue.setText("0")
        self.stripIterValue.editingFinished[()].connect(self._emitSignal)
        self.stripIterValue.setToolTip(
                "Number of iterations for strip algorithm.\n" +
                "If greater than 999, an 2nd pass of strip filter is " +
                "applied to remove artifacts created by first pass.")

        # Snip parameters ----------------------------------------------------
        self.snipWidthLabel = qt.QLabel(self)
        self.snipWidthLabel.setText("Snip Width")

        self.snipWidthSpin = qt.QSpinBox(self)
        self.snipWidthSpin.setMaximum(300)
        self.snipWidthSpin.setMinimum(0)
        self.snipWidthSpin.valueChanged[int].connect(self._emitSignal)


        # Smoothing parameters -----------------------------------------------
        self.smoothingFlagCheck = qt.QCheckBox(self)
        self.smoothingFlagCheck.setText("Smoothing Width (Savitsky-Golay)")
        self.smoothingFlagCheck.toggled.connect(self._smoothingToggled)

        self.smoothingSpin = qt.QSpinBox(self)
        self.smoothingSpin.setMinimum(3)
        #self.smoothingSpin.setMaximum(40)
        self.smoothingSpin.setSingleStep(2)
        self.smoothingSpin.valueChanged[int].connect(self._emitSignal)

        # Anchors ------------------------------------------------------------

        self.anchorsGroup = qt.QWidget(self)
        anchorsLayout = qt.QHBoxLayout(self.anchorsGroup)
        anchorsLayout.setSpacing(2)
        anchorsLayout.setContentsMargins(0, 0, 0, 0)

        self.anchorsFlagCheck = qt.QCheckBox(self.anchorsGroup)
        self.anchorsFlagCheck.setText("Use anchors")
        self.anchorsFlagCheck.setToolTip(
                "Define X coordinates of points that must remain fixed")
        self.anchorsFlagCheck.stateChanged[int].connect(
                self._anchorsToggled)
        anchorsLayout.addWidget(self.anchorsFlagCheck)

        maxnchannel = 16384 * 4    # Fixme ?
        self.anchorsList = []
        num_anchors = 4
        for i in range(num_anchors):
            anchorSpin = qt.QSpinBox(self.anchorsGroup)
            anchorSpin.setMinimum(0)
            anchorSpin.setMaximum(maxnchannel)
            anchorSpin.valueChanged[int].connect(self._emitSignal)
            anchorsLayout.addWidget(anchorSpin)
            self.anchorsList.append(anchorSpin)

        # Layout ------------------------------------------------------------
        self.mainLayout.addWidget(self.algorithmComboLabel, 0, 0)
        self.mainLayout.addWidget(self.algorithmCombo, 0, 2)
        self.mainLayout.addWidget(self.stripWidthLabel, 1, 0)
        self.mainLayout.addWidget(self.stripWidthSpin, 1, 2)
        self.mainLayout.addWidget(self.stripIterLabel, 2, 0)
        self.mainLayout.addWidget(self.stripIterValue, 2, 2)
        self.mainLayout.addWidget(self.snipWidthLabel, 3, 0)
        self.mainLayout.addWidget(self.snipWidthSpin, 3, 2)
        self.mainLayout.addWidget(self.smoothingFlagCheck, 4, 0)
        self.mainLayout.addWidget(self.smoothingSpin, 4, 2)
        self.mainLayout.addWidget(self.anchorsGroup, 5, 0, 1, 4)

        # Initialize interface -----------------------------------------------
        self._setAlgorithm("strip")
        self.smoothingFlagCheck.setChecked(False)
        self._smoothingToggled(is_checked=False)
        self.anchorsFlagCheck.setChecked(False)
        self._anchorsToggled(is_checked=False)

    def _algorithmComboActivated(self, algorithm_index):
        self._setAlgorithm("strip" if algorithm_index == 0 else "snip")

    def _setAlgorithm(self, algorithm):
        """Enable/disable snip and snip input widgets, depending on the
        chosen algorithm.
        :param algorithm: "snip" or "strip"
        """
        if algorithm not in ["strip", "snip"]:
            raise ValueError(
                    "Unknown background filter algorithm %s" % algorithm)

        self.algorithm = algorithm
        self.stripWidthSpin.setEnabled(algorithm == "strip")
        self.stripIterValue.setEnabled(algorithm == "strip")
        self.snipWidthSpin.setEnabled(algorithm == "snip")

    def _smoothingToggled(self, is_checked):
        """Enable/disable smoothing input widgets, emit dictionary"""
        self.smoothingSpin.setEnabled(is_checked)
        self._emitSignal()

    def _anchorsToggled(self, is_checked):
        """Enable/disable all spin widgets defining anchor X coordinates,
        emit signal.
        """
        for anchor_spin in self.anchorsList:
            anchor_spin.setEnabled(is_checked)
        self._emitSignal()

    def setParameters(self, ddict):
        """Set values for all input widgets.

        :param dict ddict: Input dictionary, must have the same
            keys as the dictionary output by :meth:`getParameters`
        """
        if "algorithm" in ddict:
            self._setAlgorithm(ddict["algorithm"])

        if "SnipWidth" in ddict:
            self.snipWidthSpin.setValue(int(ddict["SnipWidth"]))

        if "StripWidth" in ddict:
            self.stripWidthSpin.setValue(int(ddict["StripWidth"]))

        if "StripIterations" in ddict:
            self.stripIterValue.setText("%d" % int(ddict["StripIterations"]))

        if "SmoothingFlag" in ddict:
            self.smoothingFlagCheck.setChecked(bool(ddict["SmoothingFlag"]))

        if "SmoothingWidth" in ddict:
            self.smoothingSpin.setValue(int(ddict["SmoothingWidth"]))

        if "AnchorsFlag" in ddict:
            self.anchorsFlagCheck.setChecked(bool(ddict["AnchorsFlag"]))

        if "AnchorsList" in ddict:
            anchorslist = ddict["AnchorsList"]
            if anchorslist in [None, 'None']:
                anchorslist = []
            for spin in self.anchorsList:
                spin.setValue(0)

            i = 0
            for value in anchorslist:
                self.anchorsList[i].setValue(int(value))
                i += 1

    def getParameters(self):
        """Return dictionary of parameters defined in the GUI

        The returned dictionary contains following values:

            - *algorithm*: *"strip"* or *"snip"*
            - *StripWidth*: width of strip iterator
            - *StripIterations*: number of iterations
            - *StripThreshold*: curvature parameter (currently fixed to 1.0)
            - *SnipWidth*: width of snip algorithm
            - *SmoothingFlag*: flag to enable/disable smoothing
            - *SmoothingWidth*: width of Savitsky-Golay smoothing filter
            - *AnchorsFlag*: flag to enable/disable anchors
            - *AnchorsList*: list of anchors (X coordinates of fixed values)
        """
        stripitertext = self.stripIterValue.text()
        stripiter = int(stripitertext) if len(stripitertext) else 0

        return {"algorithm": self.algorithm,
                "StripThreshold": 1.0,
                "SnipWidth": self.snipWidthSpin.value(),
                "StripIterations": stripiter,
                "StripWidth": self.stripWidthSpin.value(),
                "SmoothingFlag": self.smoothingFlagCheck.isChecked(),
                "SmoothingWidth": self.smoothingSpin.value(),
                "AnchorsFlag": self.anchorsFlagCheck.isChecked(),
                "AnchorsList": [spin.value() for spin in self.anchorsList]}

    def _emitSignal(self, dummy=None):
        self.sigBackgroundParamWidgetSignal.emit(
            {'event': 'ParametersChanged',
             'parameters': self.getParameters()})


[docs]class BackgroundWidget(qt.QWidget): """Background configuration widget, with a plot to preview the results. Strip and snip filters parameters can be adjusted using input widgets, and the computed backgrounds are plotted next to the original data to show the result.""" def __init__(self, parent=None): qt.QWidget.__init__(self, parent) self.setWindowTitle("Strip and SNIP Configuration Window") self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) self.parametersWidget = BackgroundParamWidget(self) self.graphWidget = PlotWidget(parent=self) self.mainLayout.addWidget(self.parametersWidget) self.mainLayout.addWidget(self.graphWidget) self._x = None self._y = None self.parametersWidget.sigBackgroundParamWidgetSignal.connect(self._slot)
[docs] def getParameters(self): """Return dictionary of parameters defined in the GUI The returned dictionary contains following values: - *algorithm*: *"strip"* or *"snip"* - *StripWidth*: width of strip iterator - *StripIterations*: number of iterations - *StripThreshold*: strip curvature (currently fixed to 1.0) - *SnipWidth*: width of snip algorithm - *SmoothingFlag*: flag to enable/disable smoothing - *SmoothingWidth*: width of Savitsky-Golay smoothing filter - *AnchorsFlag*: flag to enable/disable anchors - *AnchorsList*: list of anchors (X coordinates of fixed values) """ return self.parametersWidget.getParameters()
[docs] def setParameters(self, ddict): """Set values for all input widgets. :param dict ddict: Input dictionary, must have the same keys as the dictionary output by :meth:`getParameters` """ return self.parametersWidget.setParameters(ddict)
[docs] def setData(self, x, y, xmin=None, xmax=None): """Set data for the original curve, and _update strip and snip curves accordingly. :param x: Array or sequence of curve abscissa values :param y: Array or sequence of curve ordinate values :param xmin: Min value to be displayed on the X axis :param xmax: Max value to be displayed on the X axis """ self._x = x self._y = y self._xmin = xmin self._xmax = xmax self._update(resetzoom=True)
def _slot(self, ddict): self._update() def _update(self, resetzoom=False): """Compute strip and snip backgrounds, update the curves """ if self._y is None: return pars = self.getParameters() # smoothed data y = numpy.ravel(numpy.array(self._y)).astype(numpy.float64) if pars["SmoothingFlag"]: ysmooth = filters.savitsky_golay(y, pars['SmoothingWidth']) f = [0.25, 0.5, 0.25] ysmooth[1:-1] = numpy.convolve(ysmooth, f, mode=0) ysmooth[0] = 0.5 * (ysmooth[0] + ysmooth[1]) ysmooth[-1] = 0.5 * (ysmooth[-1] + ysmooth[-2]) else: ysmooth = y # loop for anchors x = self._x niter = pars['StripIterations'] anchors_indices = [] if pars['AnchorsFlag'] and pars['AnchorsList'] is not None: ravelled = x for channel in pars['AnchorsList']: if channel <= ravelled[0]: continue index = numpy.nonzero(ravelled >= channel)[0] if len(index): index = min(index) if index > 0: anchors_indices.append(index) stripBackground = filters.strip(ysmooth, w=pars['StripWidth'], niterations=niter, factor=pars['StripThreshold'], anchors=anchors_indices) if niter >= 1000: # final smoothing stripBackground = filters.strip(stripBackground, w=1, niterations=50*pars['StripWidth'], factor=pars['StripThreshold'], anchors=anchors_indices) if len(anchors_indices) == 0: anchors_indices = [0, len(ysmooth)-1] anchors_indices.sort() snipBackground = 0.0 * ysmooth lastAnchor = 0 for anchor in anchors_indices: if (anchor > lastAnchor) and (anchor < len(ysmooth)): snipBackground[lastAnchor:anchor] =\ filters.snip1d(ysmooth[lastAnchor:anchor], pars['SnipWidth']) lastAnchor = anchor if lastAnchor < len(ysmooth): snipBackground[lastAnchor:] =\ filters.snip1d(ysmooth[lastAnchor:], pars['SnipWidth']) self.graphWidget.addCurve(x, y, legend='Input Data', replace=True, resetzoom=resetzoom) self.graphWidget.addCurve(x, stripBackground, legend='Strip Background', resetzoom=False) self.graphWidget.addCurve(x, snipBackground, legend='SNIP Background', resetzoom=False) if self._xmin is not None and self._xmax is not None: self.graphWidget.getXAxis().setLimits(self._xmin, self._xmax)
[docs]class BackgroundDialog(qt.QDialog): """QDialog window featuring a :class:`BackgroundWidget`""" def __init__(self, parent=None): qt.QDialog.__init__(self, parent) self.setWindowTitle("Strip and Snip Configuration Window") self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) self.parametersWidget = BackgroundWidget(self) self.mainLayout.addWidget(self.parametersWidget) hbox = qt.QWidget(self) hboxLayout = qt.QHBoxLayout(hbox) hboxLayout.setContentsMargins(0, 0, 0, 0) hboxLayout.setSpacing(2) self.okButton = qt.QPushButton(hbox) self.okButton.setText("OK") self.okButton.setAutoDefault(False) self.dismissButton = qt.QPushButton(hbox) self.dismissButton.setText("Cancel") self.dismissButton.setAutoDefault(False) hboxLayout.addWidget(HorizontalSpacer(hbox)) hboxLayout.addWidget(self.okButton) hboxLayout.addWidget(self.dismissButton) self.mainLayout.addWidget(hbox) self.dismissButton.clicked.connect(self.reject) self.okButton.clicked.connect(self.accept) self.output = {} """Configuration dictionary containing following fields: - *SmoothingFlag* - *SmoothingWidth* - *StripWidth* - *StripIterations* - *StripThreshold* - *SnipWidth* - *AnchorsFlag* - *AnchorsList* """ # self.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(self.updateOutput) # def updateOutput(self, ddict): # self.output = ddict
[docs] def accept(self): """Update :attr:`output`, then call :meth:`QDialog.accept` """ self.output = self.getParameters() super(BackgroundDialog, self).accept()
[docs] def sizeHint(self): return qt.QSize(int(1.5*qt.QDialog.sizeHint(self).width()), qt.QDialog.sizeHint(self).height())
[docs] def setData(self, x, y, xmin=None, xmax=None): """See :meth:`BackgroundWidget.setData`""" return self.parametersWidget.setData(x, y, xmin, xmax)
[docs] def getParameters(self): """See :meth:`BackgroundWidget.getParameters`""" return self.parametersWidget.getParameters()
[docs] def setParameters(self, ddict): """See :meth:`BackgroundWidget.setPrintGeometry`""" return self.parametersWidget.setParameters(ddict)
[docs] def setDefault(self, ddict): """Alias for :meth:`setPrintGeometry`""" return self.setParameters(ddict)
def getBgDialog(parent=None, default=None, modal=True): """Instantiate and return a bg configuration dialog, adapted for configuring standard background theories from :mod:`silx.math.fit.bgtheories`. :return: Instance of :class:`BackgroundDialog` """ bgd = BackgroundDialog(parent=parent) # apply default to newly added pages bgd.setParameters(default) return bgd def main(): # synthetic data from silx.math.fit.functions import sum_gauss x = numpy.arange(5000) # (height1, center1, fwhm1, ...) 5 peaks params1 = (50, 500, 100, 20, 2000, 200, 50, 2250, 100, 40, 3000, 75, 23, 4000, 150) y0 = sum_gauss(x, *params1) # random values between [-1;1] noise = 2 * numpy.random.random(5000) - 1 # make it +- 5% noise *= 0.05 # 2 gaussians with very large fwhm, as background signal actual_bg = sum_gauss(x, 15, 3500, 3000, 5, 1000, 1500) # Add 5% random noise to gaussians and add background y = y0 + numpy.average(y0) * noise + actual_bg # Open widget a = qt.QApplication(sys.argv) a.lastWindowClosed.connect(a.quit) def mySlot(ddict): print(ddict) w = BackgroundDialog() w.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(mySlot) w.setData(x, y) w.exec() #a.exec() if __name__ == "__main__": main()