#/*########################################################################## # Copyright (C) 2004-2022 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF. # # 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 plugin uses a median filter smoothing to remove glitches from curves. A configuration widget can be used to configure the median filter (width and threshold), and the user can choose to apply it on the active curve or on all curves. """ __author__ = "T. Rueter - ESRF" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" from PyMca5 import Plugin1DBase from PyMca5.PyMcaMath.PyMcaSciPy.signal import medfilt1d from PyMca5.PyMcaGui import PyMcaQt as qt import numpy import logging _logger = logging.getLogger(__name__) class MedianFilterScanDeglitchPlugin(Plugin1DBase.Plugin1DBase): """ Median-filter-based deglitching """ def __init__(self, plotWindow, **kw): Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw) self.methodDict = { 'Apply to active curve': [self.removeSpikesActive, 'Apply sliding median filter to active curve', None], 'Apply to all curves': [self.removeSpikesAll, 'Apply sliding median filter to all curves', None], 'Configure median filter': [self.configureFilter, 'Set threshold and width of the filter', None] } self._methodList = ['Configure median filter', 'Apply to active curve', 'Apply to all curves'] self.threshold = 0.66 self.width = 9 self._widget = None #Methods to be implemented by the plugin def getMethods(self, plottype=None): """ A list with the NAMES associated to the callable methods that are applicable to the specified plot. Plot type can be "SCAN", "MCA", None, ... """ return list(self._methodList) def getMethodToolTip(self, name): """ Returns the help associated to the particular method name or None. """ return self.methodDict[name][1] def getMethodPixmap(self, name): """ Returns the pixmap associated to the particular method name or None. """ return self.methodDict[name][2] def applyMethod(self, name): """ The plugin is asked to apply the method associated to name. """ self.methodDict[name][0]() return def configureFilter(self): if self._widget is None: # construct a widget msg = qt.QDialog() msg.setWindowTitle("Deglitch Configuration") msgLayout = qt.QGridLayout() buttonLayout = qt.QHBoxLayout() inpThreshold = qt.QDoubleSpinBox() inpThreshold.setRange(0.,10.) inpThreshold.setSingleStep(.1) inpThreshold.setValue(self.threshold) inpThreshold.setToolTip('Increase width for broad spikes') inpWidth = qt.QSpinBox() inpWidth.setRange(1,101) inpWidth.setSingleStep(2) inpWidth.setValue(self.width) inpWidth.setToolTip('Set low threshold for multiple spikes of different markedness') labelWidth = qt.QLabel('Width (must be odd)') labelThreshold = qt.QLabel('Threshold (multiple of deviation)') buttonOK = qt.QPushButton('Ok') buttonOK.clicked.connect(msg.accept) buttonCancel = qt.QPushButton('Cancel') buttonCancel.clicked.connect(msg.reject) allActiveBG = qt.QButtonGroup() buttonAll = qt.QCheckBox('Apply to All') buttonActive = qt.QCheckBox('Apply to Active') allActiveBG.addButton(buttonAll, 0) allActiveBG.addButton(buttonActive, 1) buttonActive.setChecked(True) buttonLayout.addWidget(qt.HorizontalSpacer()) buttonLayout.addWidget(buttonOK) buttonLayout.addWidget(buttonCancel) msgLayout.addWidget(labelWidth,0,0) msgLayout.addWidget(inpWidth,0,1) msgLayout.addWidget(labelThreshold,1,0) msgLayout.addWidget(inpThreshold,1,1) msgLayout.addWidget(buttonActive,2,0) msgLayout.addWidget(buttonAll,2,1) msgLayout.addLayout(buttonLayout,3,0,1,2) msg.setLayout(msgLayout) msg.inputWidth = inpWidth msg.inputThreshold = inpThreshold msg.applyToAll = buttonAll self._widget = msg self._widget.buttonActive = buttonActive self._widget.buttonAll = buttonAll if self._widget.exec(): self.threshold = float(self._widget.inputThreshold.value()) self.width = int(self._widget.inputWidth.value()) if not (self.width%2): self.width += 1 if self._widget.buttonAll.isChecked(): _logger.debug('AllChecked') self.removeSpikesAll() elif self._widget.buttonActive.isChecked(): _logger.debug('ActiveChecked') self.removeSpikesActive() def removeSpikesAll(self): self.medianThresholdFilter(False, self.threshold, self.width) def removeSpikesActive(self): self.medianThresholdFilter(True, self.threshold, self.width) def medianThresholdFilter(self, activeOnly, threshold, length): if activeOnly: active = self.getActiveCurve() if not active: return else: x, y, legend, info = active[:4] self.removeCurve(legend) spectra = [active] else: spectra = self.getAllCurves() for (idx, spec) in enumerate(spectra): x, y, legend, info = spec[:4] xlabel=info.get("xlabel", None) ylabel=info.get("ylabel", None) filtered = medfilt1d(y, length) diff = filtered-y mean = diff.mean() sigma = (y-mean)**2 sigma = numpy.sqrt(sigma.sum()/float(len(sigma))) ynew = numpy.where(abs(diff) > threshold * sigma, filtered, y) legend = info.get('selectionlegend',legend) + ' SR' if (idx==0) and (len(spectra)!=1): self.addCurve(x, ynew, legend, info, xlabel=xlabel, ylabel=ylabel, replace=True, replot=False) elif idx == (len(spectra)- 1): self.addCurve(x, ynew, legend, info, xlabel=xlabel, ylabel=ylabel, replace=False, replot=True) else: self.addCurve(x, ynew, legend, info, xlabel=xlabel, ylabel=ylabel, replace=False, replot=False) #self._plotWindow.replot() MENU_TEXT = "Remove glitches from curves" def getPlugin1DInstance(plotWindow, **kw): ob = MedianFilterScanDeglitchPlugin(plotWindow) return ob if __name__ == "__main__": from PyMca5.PyMcaGui import PlotWindow app = qt.QApplication([]) sw = PlotWindow.PlotWindow() x = numpy.linspace(0, 1999, 2000) y0 = x/100. + 100.*numpy.exp(-(x-500)**2/1000.) + 50.*numpy.exp(-(x-1200)**2/5000.) + 100.*numpy.exp(-(x-1700)**2/500.) + 10 * numpy.random.random(2000) y1 = x/100. + 100.*numpy.exp(-(x-600)**2/1000.) + 50.*numpy.exp(-(x-1000)**2/5000.) + 100.*numpy.exp(-(x-1500)**2/500.) + 10 * numpy.random.random(2000) for idx in range(20): y0[idx*100] = 500. * numpy.random.random(1) y1[idx*100] = 500. * numpy.random.random(1) sw.addCurve(x, y0, legend="Curve0") sw.addCurve(x, y1, legend="Curve1") sw.setActiveCurve("Curve0") plugin = getPlugin1DInstance(sw) plugin.configureFilter() sw.show() app.exec()