#/*########################################################################## # Copyright (C) 2004-2014 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. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import sys import numpy from PyMca5.PyMcaGui import PyMcaQt as qt from PyMca5.PyMcaGui import PlotWindow from PyMca5.PyMcaMath.fitting import SpecfitFuns class StripParametersWidget(qt.QWidget): sigStripParametersWidgetSignal = qt.pyqtSignal(object) def __init__(self, parent=None): qt.QWidget.__init__(self, parent) self.build() def build(self): self.mainLayout = qt.QGridLayout(self) self.mainLayout.setContentsMargins(11, 11, 11, 11) self.mainLayout.setSpacing(6) #strip algorithm self.stripComboLabel = qt.QLabel(self) self.stripComboLabel.setText("Non-analytical (or estimation) background algorithm") self.stripCombo = qt.QComboBox(self) self.stripCombo.addItem(str("Strip")) self.stripCombo.addItem(str("SNIP")) self.stripCombo.activated[int].connect(self._stripComboActivated) #SNIP width self.snipWidthLabel = qt.QLabel(self) self.snipWidthLabel.setText(str("SNIP Background Width")) self.snipWidthSpin = qt.QSpinBox(self) self.snipWidthSpin.setMaximum(300) self.snipWidthSpin.setMinimum(0) self.snipWidthSpin.valueChanged[int].connect(self._emitSignal) #Strip width self.stripWidthLabel = qt.QLabel(self) self.stripWidthLabel.setText(str("Strip Background Width")) self.stripWidthSpin = qt.QSpinBox(self) self.stripWidthSpin.setMaximum(100) self.stripWidthSpin.setMinimum(1) self.stripWidthSpin.valueChanged[int].connect(self._emitSignal) #Strip iterations self.stripIterLabel = qt.QLabel(self) self.stripIterLabel.setText(str("Strip Background Iterations")) self.stripIterValue = qt.QLineEdit(self) validator = qt.QIntValidator(self.stripIterValue) self.stripIterValue._v = validator self.stripIterValue.editingFinished[()].connect(self._emitSignal) #Strip smoothing self.stripFilterLabel = qt.QLabel(self) self.stripFilterLabel.setText(str("Strip Background Smoothing Width (Savitsky-Golay)")) self.stripFilterSpin = qt.QSpinBox(self) self.stripFilterSpin.setMinimum(1) self.stripFilterSpin.setMaximum(40) self.stripFilterSpin.setSingleStep(2) self.stripFilterSpin.valueChanged[int].connect(self._emitSignal) #anchors self.anchorsContainer = qt.QWidget(self) anchorsContainerLayout = qt.QHBoxLayout(self.anchorsContainer) anchorsContainerLayout.setContentsMargins(0, 0, 0, 0) anchorsContainerLayout.setSpacing(2) self.stripAnchorsFlagCheck = qt.QCheckBox(self.anchorsContainer) self.stripAnchorsFlagCheck.setText(str("Strip Background use Anchors")) self.stripAnchorsFlagCheck.stateChanged[int].connect( \ self._emitSignal) anchorsContainerLayout.addWidget(self.stripAnchorsFlagCheck) #self.iterSpin = qt.QSpinBox(self) #self.iterSpin.setMinimum(1) maxnchannel = 16384*4 self.stripAnchorsList = [] for i in range(4): anchorSpin = qt.QSpinBox(self.anchorsContainer) anchorSpin.setMinimum(0) anchorSpin.setMaximum(maxnchannel) anchorSpin.valueChanged[int].connect(self._emitSignal) anchorsContainerLayout.addWidget(anchorSpin) self.stripAnchorsList.append(anchorSpin) self.mainLayout.setColumnStretch(0, 1) row = 0 self.mainLayout.addWidget(self.stripComboLabel, row, 0) self.mainLayout.addWidget(self.stripCombo, row, 4) row += 1 self.mainLayout.addWidget(self.snipWidthLabel,row, 0) self.mainLayout.addWidget(self.snipWidthSpin, row, 4) row += 1 self.mainLayout.addWidget(self.stripWidthLabel, row, 0) self.mainLayout.addWidget(self.stripWidthSpin, row, 4) row += 1 self.mainLayout.addWidget(self.stripIterLabel, row, 0) self.mainLayout.addWidget(self.stripIterValue, row, 4) row += 1 self.mainLayout.addWidget(self.stripFilterLabel, row, 0) self.mainLayout.addWidget(self.stripFilterSpin, row, 4) row += 1 self.mainLayout.addWidget(self.anchorsContainer, row, 0, 1, 5) self._stripComboActivated(0) def _stripComboActivated(self, iValue): if iValue == 1: self.setSNIP(True) else: self.setSNIP(False) def setSNIP(self, bValue): if bValue: self.snipWidthSpin.setEnabled(True) self.stripWidthSpin.setEnabled(False) #self.stripFilterSpin.setEnabled(False) self.stripIterValue.setEnabled(False) self.stripCombo.setCurrentIndex(1) else: self.snipWidthSpin.setEnabled(False) #self.stripFilterSpin.setEnabled(True) self.stripWidthSpin.setEnabled(True) self.stripIterValue.setEnabled(True) self.stripCombo.setCurrentIndex(0) def setParameters(self, ddict): if 'fit' in ddict: pars = ddict['fit'] else: pars = ddict key = "stripalgorithm" if key in pars: stripAlgorithm = int(pars[key]) self.setSNIP(stripAlgorithm) key = "snipwidth" if key in pars: self.snipWidthSpin.setValue(int(pars[key])) key = "stripwidth" if key in pars: self.stripWidthSpin.setValue(int(pars[key])) key = "stripiterations" if key in pars: self.stripIterValue.setText("%d" % int(pars[key])) key = "stripfilterwidth" if key in pars: self.stripFilterSpin.setValue(int(pars[key])) key = "stripanchorsflag" if key in pars: self.stripAnchorsFlagCheck.setChecked(int(pars[key])) key = "stripanchorslist" if key in pars: anchorslist = pars[key] if anchorslist in [None, 'None']: anchorslist = [] for spin in self.stripAnchorsList: spin.setValue(0) i = 0 for value in anchorslist: self.stripAnchorsList[i].setValue(int(value)) i += 1 def getParameters(self): pars = {} pars["stripalgorithm"] = int(self.stripCombo.currentIndex()) pars["stripconstant"]= 1.0 pars["snipwidth"] = self.snipWidthSpin.value() txt = str(self.stripIterValue.text()) if len(txt): pars["stripiterations"]= int(txt) else: pars["stripiterations"] = 0 pars["stripwidth"]= self.stripWidthSpin.value() pars["stripfilterwidth"] = self.stripFilterSpin.value() pars["stripanchorsflag"] = int(self.stripAnchorsFlagCheck.isChecked()) pars["stripanchorslist"] = [] for spin in self.stripAnchorsList: pars["stripanchorslist"].append(spin.value()) return pars def _emitSignal(self, dummy=None): ddict= {} ddict['event']='ParametersChanged' ddict['parameters'] = self.getParameters() self.sigStripParametersWidgetSignal.emit(ddict) class StripBackgroundWidget(qt.QWidget): 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 = StripParametersWidget(self) self.graphWidget = PlotWindow.PlotWindow(self, newplot=False, plugins=False, fit=False) self.mainLayout.addWidget(self.parametersWidget) self.mainLayout.addWidget(self.graphWidget) self.getParameters = self.parametersWidget.getParameters self.setParameters = self.parametersWidget.setParameters self._x = None self._y = None self.parametersWidget.sigStripParametersWidgetSignal.connect( \ self._slot) def setData(self, x, y): self._x = x self._y = y self.update() def _slot(self, ddict): self.update() def update(self): if self._y is None: return pars = self.getParameters() #smoothed data y = numpy.ravel(numpy.array(self._y)).astype(numpy.float) ysmooth = SpecfitFuns.SavitskyGolay(y, pars['stripfilterwidth']) 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]) #loop for anchors x = self._x niter = pars['stripiterations'] anchorslist = [] if pars['stripanchorsflag']: if pars['stripanchorslist'] is not None: ravelled = x for channel in pars['stripanchorslist']: if channel <= ravelled[0]:continue index = numpy.nonzero(ravelled >= channel)[0] if len(index): index = min(index) if index > 0: anchorslist.append(index) if niter > 1000: stripBackground = SpecfitFuns.subac(ysmooth, pars['stripconstant'], niter, pars['stripwidth'], anchorslist) #final smoothing stripBackground = SpecfitFuns.subac(stripBackground, pars['stripconstant'], 500,1, anchorslist) elif niter > 0: stripBackground = SpecfitFuns.subac(ysmooth, pars['stripconstant'], niter, pars['stripwidth'], anchorslist) else: stripBackground = 0.0 * ysmooth + ysmooth.min() if len(anchorslist) == 0: anchorslist = [0, len(ysmooth)-1] anchorslist.sort() snipBackground = 0.0 * ysmooth lastAnchor = 0 width = pars['snipwidth'] for anchor in anchorslist: if (anchor > lastAnchor) and (anchor < len(ysmooth)): snipBackground[lastAnchor:anchor] =\ SpecfitFuns.snip1d(ysmooth[lastAnchor:anchor], width, 0) lastAnchor = anchor if lastAnchor < len(ysmooth): snipBackground[lastAnchor:] =\ SpecfitFuns.snip1d(ysmooth[lastAnchor:], width, 0) self.graphWidget.addCurve(x, y, \ legend='Input Data',\ replace=True, replot=False) self.graphWidget.addCurve(x, stripBackground,\ legend='Strip Background',\ replot=False) self.graphWidget.addCurve(x, snipBackground,\ legend='SNIP Background', replot=True) class StripBackgroundDialog(qt.QDialog): 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 = StripBackgroundWidget(self) self.setData = self.parametersWidget.setData self.getParameters = self.parametersWidget.getParameters self.setParameters = self.parametersWidget.setParameters 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(qt.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) def sizeHint(self): return qt.QSize(int(1.5*qt.QDialog.sizeHint(self).width()), qt.QDialog.sizeHint(self).height()) if __name__ == "__main__": a = qt.QApplication(sys.argv) a.lastWindowClosed.connect(a.quit) w = StripBackgroundDialog() def mySlot(ddict): print(ddict) w.parametersWidget.parametersWidget.\ sigStripParametersWidgetSignal.connect(mySlot) x = numpy.arange(1000.).astype(numpy.float32) y = 100 + x + 100 * numpy.exp(-0.5*(x-500) * (x-500)/ 30.) w.setData(x, y) w.exec_() #a.exec_()