#/*########################################################################## # 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. # #############################################################################*/ """ This stack plugin provides filtering and background subtraction methods: - Savitzky-Golay Filtering (smoothing) - Deglitch with SNIP 1D Background - Subtract SNIP 1D Background - Subtract SNIP 2D Background - Subtract active curve """ __author__ = "V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import logging from PyMca5 import StackPluginBase from PyMca5.PyMcaGui import SGWindow from PyMca5.PyMcaGui import SNIPWindow from PyMca5.PyMcaGui import PyMca_Icons as PyMca_Icons import numpy _logger = logging.getLogger(__name__) class BackgroundStackPlugin(StackPluginBase.StackPluginBase): def __init__(self, stackWindow, **kw): if _logger.getEffectiveLevel() == logging.DEBUG: StackPluginBase.pluginBaseLogger.setLevel(logging.DEBUG) StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw) SGtext = "Replace current stack by a\n" SGtext += "Savitsky-Golay treated one." SNIP1Dtext = "Replace current stack by a\n" SNIP1Dtext += "SNIP1D treated one." SNIP2Dtext = "Replace current stack by a\n" SNIP2Dtext += "SNIP2D treated one." self.methodDict = {} function = self.replaceStackWithSavitzkyGolayFiltering info = SGtext icon = PyMca_Icons.substract self.methodDict["Savitzky-Golay Filtering"] = [function, info, icon] function = self.subtract1DSnipBackground info = SNIP1Dtext self.methodDict["Subtract SNIP 1D Background"] = [function, info, icon] function = self.replaceWith1DSnipBackground info = "Smooth and replace current stack\n" info += "by its SNIP1D background." self.methodDict["Deglitch with SNIP 1D Background"] = [function, info, PyMca_Icons.smooth] function = self.subtract2DSnipBackground info = SNIP2Dtext self.methodDict["Subtract SNIP 2D Background"] = [function, info, icon] function = self.subtractActiveCurve info = "Replace current stack by one in which\nthe active curve has been subtracted" self.methodDict["Subtract active curve"] = [function, info, icon] self.__methodKeys = ["Savitzky-Golay Filtering", "Deglitch with SNIP 1D Background", "Subtract SNIP 1D Background", "Subtract SNIP 2D Background", "Subtract active curve"] def stackUpdated(self): self.dialogWidget = None #Methods implemented by the plugin def getMethods(self): return self.__methodKeys def getMethodToolTip(self, name): return self.methodDict[name][1] def getMethodPixmap(self, name): return self.methodDict[name][2] def applyMethod(self, name): return self.methodDict[name][0]() def replaceStackWithSavitzkyGolayFiltering(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: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] stack = self.getStackDataObject() function(stack, *arguments) self.setStack(stack) def subtract1DSnipBackground(self, smooth=False): activeCurve = self.getActiveCurve() if activeCurve is None: return x, spectrum, legend, info = activeCurve snipWindow = SNIPWindow.SNIPDialog(None, spectrum, x=x, smooth=smooth) snipWindow.graph.setGraphXLabel(info['xlabel']) snipWindow.graph.setGraphYLabel(info['ylabel']) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec() if ret: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] stack = self.getStackDataObject() function(stack, *arguments) self.setStack(stack) def replaceWith1DSnipBackground(self): return self.subtract1DSnipBackground(smooth=True) def subtract2DSnipBackground(self): imageList = self.getStackROIImagesAndNames() if imageList is None: return imageList, imageNames = imageList if not len(imageList): return snipWindow = SNIPWindow.SNIPDialog(None, imageList[0] * 1) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec() if ret: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] stack = self.getStackDataObject() function(stack, *arguments) self.setStack(stack) def subtractActiveCurve(self): curve = self.getActiveCurve() if curve is None: raise ValueError("No active curve") x, y, legend, info = curve[:4] stack = self.getStackDataObject() if not isinstance(stack.data, numpy.ndarray): text = "This method does not work with dynamically loaded stacks" raise TypeError(text) x0, y0, legend0, info0 = self.getStackOriginalCurve()[:4] if self.getGraphXLabel().upper() not in ["CHANNEL", "POINTS"]: # get the used calibration a, b, c = info.get("McaCalib", [0.0, 1,0, 0.0]) x0 = a + b * x0 + c * x0 * x0 interpolate = True if x0.size == x.size: if numpy.allclose(x, x0): interpolate = False if interpolate: xmin = max(x.min(), x0.min()) xmax = min(x.max(), x0.max()) selection = (x0 >= xmin) & (x0 <= xmax) idx = numpy.nonzero(selection)[0] if not idx.size: raise ValueError("Curves do not overlap") xwork = x0[idx] # we have got the final x values, interpolate into the # curve to be subtracted ywork = numpy.interp(xwork, x, y) #proceed to subtract the data notIdx = numpy.nonzero(selection == False)[0] mcaIndex = stack.info.get('McaIndex', -1) if mcaIndex in [-1, 2]: #for i in range(stack.data.shape[-1]): stack.data[:, :, idx] = stack.data[:, :, idx] - ywork stack.data[:, :, notIdx] = 0.0 elif mcaIndex == 0: counter = 0 for i in range(stack.data.shape[0]): if i in idx: stack.data[i] -= ywork[counter] counter += 1 else: stack.data[i] = 0.0 else: raise ValueError("Invalid 1D index %d" % mcaIndex) else: mcaIndex = stack.info.get('McaIndex', -1) if mcaIndex in [-1, 2]: for i in range(stack.data.shape[-1]): stack.data[:, :, i] -= y[i] elif mcaIndex == 0: for i in range(stack.data.shape[0]): stack.data[i] -= y[i] else: raise ValueError("Invalid 1D index %d" % mcaIndex) self.setStack(stack) MENU_TEXT = "Stack Filtering Options" def getStackPluginInstance(stackWindow, **kw): ob = BackgroundStackPlugin(stackWindow) return ob