#/*########################################################################## # Copyright (C) 2004-2017 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 plugin provides 3 methods: - subtract a SNIP1D background from the active curve - apply a Savitsky-Golay filter on the active curve - smooth and replace current curve by its SNIP1D background (deglitch) """ __author__ = "V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import numpy from PyMca5 import Plugin1DBase from PyMca5.PyMcaGui import SGWindow from PyMca5.PyMcaGui import SNIPWindow from PyMca5.PyMcaGui import PyMca_Icons class BackgroundScanPlugin(Plugin1DBase.Plugin1DBase): def __init__(self, plotWindow, **kw): Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw) SGtext = "Replace active curve by a\n" SGtext += "Savitsky-Golay treated one." SNIP1Dtext = "Replace active curve by a\n" SNIP1Dtext += "SNIP1D treated one." self.methodDict = {} function = self.replaceActiveCurveWithSavitzkyGolayFiltering info = SGtext icon = PyMca_Icons.substract self.methodDict["Savitzky-Golay Filtering"] =[function, info, icon] function = self.subtract1DSnipBackgroundFromActiveCurve info = SNIP1Dtext self.methodDict["Subtract SNIP 1D Background"] =[function, info, icon] function = self.deglitchActiveCurveWith1DSnipBackground info = "Smooth and replace current curve\n" info += "by its SNIP1D background." self.methodDict["Deglitch with SNIP 1D Background"] =[function, info, PyMca_Icons.smooth] self.__methodKeys = ["Subtract SNIP 1D Background", "Savitzky-Golay Filtering", "Deglitch with SNIP 1D Background"] self.subtract1DSnipParameters = None self.deglitch1DSnipParameters = 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, ... """ if 0: names = self.methodDict.keys() names.sort() return names else: return self.__methodKeys 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 replaceActiveCurveWithSavitzkyGolayFiltering(self): activeCurve = self.getActiveCurve() if activeCurve is None: return x, spectrum, legend, info = activeCurve snipWindow = SGWindow.SGDialog(None, spectrum, x=x) snipWindow.graph.setGraphXLabel(info['xlabel']) snipWindow.graph.setGraphYLabel(info['ylabel']) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec_() if ret: ydata = snipWindow.parametersWidget.background xdata = snipWindow.parametersWidget.xValues operations = info.get("operations", []) operations.append("SG Filtered") info['operations'] = operations self.addCurve(xdata, ydata, legend=legend, info=info, replot=True) def subtract1DSnipBackgroundFromActiveCurve(self, smooth=False): activeCurve = self.getActiveCurve() if activeCurve is None: return x, spectrum, legend, info = activeCurve snipWindow = SNIPWindow.SNIPDialog(None, spectrum, x=x, smooth=False) if self.subtract1DSnipParameters is not None: snipWindow.setParameters(self.subtract1DSnipParameters) snipWindow.graph.setGraphXLabel(info['xlabel']) snipWindow.graph.setGraphYLabel(info['ylabel']) snipWindow.show() ret = snipWindow.exec_() if ret: ydata = snipWindow.parametersWidget.spectrum -\ snipWindow.parametersWidget.background xdata = snipWindow.parametersWidget.xValues operations = info.get("operations", []) operations.append("SNIP Background Removal") info['operations'] = operations self.removeCurve(legend, replot=False) self.addCurve(xdata, ydata, legend=legend +" Net", info=info, replot=True) self.subtract1DSnipParameters = snipWindow.getParameters() def deglitchActiveCurveWith1DSnipBackground(self): activeCurve = self.getActiveCurve() if activeCurve is None: return x, spectrum, legend, info = activeCurve snipWindow = SNIPWindow.SNIPDialog(None, spectrum, x=x, smooth=True) if self.deglitch1DSnipParameters is not None: snipWindow.setParameters(self.deglitch1DSnipParameters) snipWindow.graph.setGraphXLabel(info['xlabel']) snipWindow.graph.setGraphYLabel(info['ylabel']) snipWindow.show() ret = snipWindow.exec_() if ret: ydata = snipWindow.parametersWidget.background xdata = snipWindow.parametersWidget.xValues operations = info.get("operations", []) operations.append("SNIP Deglith") info['operations'] = operations self.addCurve(xdata, ydata, legend=legend, info=info, replot=True) self.deglitch1DSnipParameters = snipWindow.getParameters() MENU_TEXT = "Background subtraction tools" def getPlugin1DInstance(plotWindow, **kw): ob = BackgroundScanPlugin(plotWindow) return ob if __name__ == "__main__": from PyMca5.PyMcaGui import PyMcaQt as qt app = qt.QApplication([]) from PyMca5.PyMcaGraph import Plot x = numpy.arange(100.) y = x * x plot = Plot.Plot() plot.addCurve(x, y, "dummy") plot.addCurve(x+100, -x*x) plugin = getPlugin1DInstance(plot) for method in plugin.getMethods(): print(method, ":", plugin.getMethodToolTip(method)) plugin.applyMethod(plugin.getMethods()[0]) curves = plugin.getAllCurves() for curve in curves: print(curve[2]) print("LIMITS = ", plugin.getGraphYLimits()) #app = qt.QApplication()