#/*########################################################################## # Copyright (C) 2004-2020 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__ = "Mauro Rovezzi - ID26, V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import sys import numpy import logging _logger = logging.getLogger(__name__) try: from matplotlib.mlab import griddata GRIDDATA = "matplotlib" except ImportError: # matplotlib 3.x got rid of griddata try: from scipy.interpolate import griddata GRIDDATA = "scipy" except ImportError: GRIDDATA = None _logger.info("matplotlib.mlab.griddata not available") from PyMca5 import Plugin1DBase from PyMca5.PyMcaGui import MaskImageWidget from PyMca5.PyMcaGui import PyMcaQt as qt class MultipleScanToMeshPlugin(Plugin1DBase.Plugin1DBase): """ This plugin attempts to create an image from multiple scans. It is aimed at dealing with: - ID26 RIXS Data - Meshes generated line by line. """ def __init__(self, plotWindow, **kw): Plugin1DBase.Plugin1DBase.__init__(self, plotWindow, **kw) self.methodDict = {} self.methodDict['RIXS Etransfer'] = [self._energyTransfer, "Show RIXS E transfer image", None] self.methodDict['RIXS Eout'] = [self._energyAnalyzer, "Show RIXS E out image", None] self.methodDict['Mesh'] = [self._mesh, "Show mesh image", None] self._rixsWidget = 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, ... """ names = list(self.methodDict.keys()) names.sort() return names 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. """ try: self.methodDict[name][0]() except: _logger.error(sys.exc_info()) raise def _mesh(self): return self._energyTransfer(mode="mesh") def _energyAnalyzer(self): return self._energyTransfer(mode="energyout") def _energyTransfer(self, mode="energytransfer"): allCurves = self.getAllCurves() nCurves = len(allCurves) if nCurves < 2: msg = "RIXS scans are built combining several single scans" raise ValueError(msg) self._xLabel = self.getGraphXLabel() self._yLabel = self.getGraphYLabel() if self._xLabel not in \ ["energy", "Energy", "Spec.Energy", "arr_hdh_ene", "Mono.Energy"]: msg = "X axis does not correspond to a supported RIXS scan" raise ValueError(msg) motorNames = allCurves[0][3]["MotorNames"] CHESS = False if self._xLabel == "Spec.Energy": # ID26 fixedMotorMne = "Mono.Energy" elif (self._xLabel == "Energy") and ("xes_dn_ana" in motorNames): # CHESS fixedMotorMne = "xes_dn_ana" CHESS = True msg = "Please use CHESS provided plugin. Contact beamline staff" raise RuntimeError(msg) elif (self._xLabel == "energy") and ("xes_en" in motorNames): # BM20 case fixedMotorMne = "xes_en" elif "Spec.Energy" in motorNames: # ID26 fixedMotorMne = "Spec.Energy" else: # TODO: Show a combobox to allow the selection of the "motor" msg = "Cannot automatically recognize motor mnemomnic to be used" raise ValueError(msg) fixedMotorIndex = allCurves[0][3]["MotorNames"].index(fixedMotorMne) #get the min and max values of the curves if fixedMotorMne != "Mono.Energy": xMin = allCurves[0][0][0] # ID26 data are already ordered xMax = allCurves[0][0][-1] minValues = numpy.zeros((nCurves,), numpy.float64) minValues[0] = xMin nData = len(allCurves[0][0]) i = 0 for curve in allCurves[1:]: i += 1 tmpMin = curve[0][0] tmpMax = curve[0][-1] minValues[i] = tmpMin if tmpMin < xMin: xMin = tmpMin if tmpMax > xMax: xMax =tmpMax nData += len(curve[0]) else: info = allCurves[0][3] xMin = info["MotorValues"][fixedMotorIndex] xMax = xMin nData = 0 i = 0 minValues = numpy.zeros((nCurves,), numpy.float64) for curve in allCurves: info = curve[3] tmpMin = info['MotorValues'][fixedMotorIndex] tmpMax = info['MotorValues'][fixedMotorIndex] minValues[i] = tmpMin if tmpMin < xMin: xMin = tmpMin if tmpMax > xMax: xMax =tmpMax nData += len(curve[0]) i += 1 #sort the curves orderIndex = minValues.argsort() #print "ORDER INDEX = ", orderIndex # express data in eV if (xMax - xMin) < 5.0 : # it seems data need to be multiplied factor = 1000. else: factor = 1.0 motor2Values = numpy.zeros((nCurves,), numpy.float64) xData = numpy.zeros((nData,), numpy.float32) yData = numpy.zeros((nData,), numpy.float32) zData = numpy.zeros((nData,), numpy.float32) start = 0 for i in range(nCurves): idx = orderIndex[i] curve = allCurves[idx] info = curve[3] nPoints = max(curve[0].shape) end = start + nPoints x = curve[0] z = curve[1] x.shape = -1 z.shape = -1 if fixedMotorMne == "Mono.Energy": xData[start:end] = info["MotorValues"][fixedMotorIndex] * factor yData[start:end] = x * factor elif CHESS: xData[start:end] = x * factor #yData[start:end] = info["MotorValues"][fixedMotorIndex] thetaDeg = 78.1119 + 0.5 * (info["MotorValues"][fixedMotorIndex] + 5.25) yData[start:end] = 12398.4 / (1.656446 * numpy.sin(numpy.pi*thetaDeg/180.)) else: xData[start:end] = x * factor yData[start:end] = info["MotorValues"][fixedMotorIndex] * factor zData[start:end] = z start = end # construct the grid in steps of eStep eV eStep = 0.05 n = int((xMax - xMin) * (factor / eStep)) grid0 = numpy.linspace(xMin * factor, xMax * factor, n) grid1 = numpy.linspace(yData.min(), yData.max(), n) # create the meshgrid xx, yy = numpy.meshgrid(grid0, grid1) if 0: # get the interpolated values etData = xData - yData grid3 = numpy.linspace(etData.min(), etData.max(), n) xx, yy = numpy.meshgrid(grid0, grid3) try: zz = griddata(xData, etData, zData, xx, yy) except RuntimeError: zz = griddata(xData, etData, zData, xx, yy, interp='linear') # show them if self._rixsWidget is None: self._rixsWidget = MaskImageWidget.MaskImageWidget(\ imageicons=False, selection=False, profileselection=True, scanwindow=self) shape = zz.shape xScale = (xx.min(), (xx.max() - xx.min())/float(zz.shape[1])) yScale = (yy.min(), (yy.max() - yy.min())/float(zz.shape[0])) self._rixsWidget.setImageData(zz, xScale=xScale, yScale=yScale) self._rixsWidget.setXLabel("Incident Energy (eV)") self._rixsWidget.setYLabel("Energy Transfer (eV)") self._rixsWidget.show() elif 1: if mode == "mesh": etData = yData else: etData = xData - yData grid3 = numpy.linspace(etData.min(), etData.max(), n) # create the meshgrid xx, yy = numpy.meshgrid(grid0, grid3) # get the interpolated values if GRIDDATA == "matplotlib": try: zz = griddata(xData, etData, zData, xx, yy) except: # Natural neighbor interpolation not always possible zz = griddata(xData, etData, zData, xx, yy, interp='linear') elif GRIDDATA == "scipy": zz = griddata((xData, etData), zData, (xx, yy), method='cubic') else: raise RuntimeError("griddata function not available") if self._rixsWidget is None: self._rixsWidget = MaskImageWidget.MaskImageWidget(\ imageicons=False, selection=False, aspect=True, profileselection=True, scanwindow=self) self._rixsWidget.setLineProjectionMode('X') #actualMax = zData.max() #actualMin = zData.min() #zz = numpy.where(numpy.isfinite(zz), zz, actualMax) shape = zz.shape xScale = (xx.min(), (xx.max() - xx.min())/float(zz.shape[1])) if mode == "energyout": yScale = (yy.min() + yData.min(), (yy.max() - yy.min())/float(zz.shape[0])) else: yScale = (yy.min(), (yy.max() - yy.min())/float(zz.shape[0])) self._rixsWidget.setXLabel("Incident Energy (eV)") if mode == "mesh": self._rixsWidget.setYLabel("Emitted Energy (eV)") elif mode == "energyout": self._rixsWidget.setYLabel("Emitted Energy (eV)") else: self._rixsWidget.setYLabel("Energy Transfer (eV)") self._rixsWidget.setImageData(zz, xScale=xScale, yScale=yScale) # self._rixsWidget.graph.replot() self._rixsWidget.show() self._rixsWidget.raise_() return MENU_TEXT = "MultipleScanToMeshPlugin" def getPlugin1DInstance(plotWindow, **kw): ob = MultipleScanToMeshPlugin(plotWindow) return ob if __name__ == "__main__": from PyMca5.PyMcaGraph import Plot app = qt.QApplication([]) #w = ConfigurationWidget() #w.exec() #sys.exit(0) _logger.setLevel(logging.DEBUG) 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())