#/*########################################################################## # 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 from PyMca5.PyMcaGui import PyMcaQt as qt from PyMca5.PyMcaGui import PyMca_Icons IconDict = PyMca_Icons.IconDict from PyMca5.PyMcaGui import MaskImageWidget from PyMca5.PyMcaGui import ScanWindow from PyMca5.PyMcaMath import SNIPModule OBJECT3D = False try: from PyMca5.Object3D import Object3DScene OBJECT3D = True except: try: # Frozen version handling from Object3D import Object3DScene OBJECT3D = True except: OBJECT3D = False class SNIP1DParametersWidget(qt.QWidget): sigSNIPParametersSignal = qt.pyqtSignal(object) def __init__(self, parent = None, length=2000, smooth=False): qt.QWidget.__init__(self, parent) self.mainLayout = qt.QGridLayout(self) self.mainLayout.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) i = 0 self.parametersDict = {'roi_min':0, 'roi_max':length, 'width':min(30, length/10), 'smoothing':1} textLabels = ["SNIP background width (2 to 3 times fwhm) :", "Minimum channel considered:", "Maximum channel considered:", "Preliminar smoothing level:"] if smooth: textLabels[0] = "SNIP width :" self.parametersDict['width'] = 3 for text in textLabels: label = qt.QLabel(self) label.setText(text) self.mainLayout.addWidget(label, i, 0) #self.mainLayout.addWidget(qt.HorizontalSpacer(self), i, 1) i +=1 i = 0 self.widgetDict = {} for key in ['width', 'roi_min', 'roi_max', 'smoothing']: self.widgetDict[key] = qt.QSpinBox(self) self.widgetDict[key].setMinimum(0) self.widgetDict[key].setMaximum(self.parametersDict['roi_max']) self.widgetDict[key].setValue(self.parametersDict[key]) self.widgetDict[key].valueChanged[int].connect(self._updateParameters) self.mainLayout.addWidget(self.widgetDict[key], i, 1) i += 1 self.widgetDict['smoothing'].setMaximum(100) def _updateParameters(self, val): for key in ['width', 'roi_min', 'roi_max', 'smoothing']: self.parametersDict[key] = self.widgetDict[key].value() ddict = {} ddict['event']='SNIPParametersChanged' ddict.update(self.parametersDict) self.sigSNIPParametersSignal.emit(ddict) def getParameters(self): return self.parametersDict def setParameters(self, ddict=None): if ddict is None: return actualKeys = self.widgetDict.keys() for key in ddict.keys(): if key in actualKeys: w = self.widgetDict[key] #w.setMaximum(max(ddict[key], w.value())) #w.setMinimum(min(ddict[key], w.value())) w.setValue(ddict[key]) self._updateParameters("dummy") class SNIP2DParametersWidget(qt.QWidget): sigSNIPParametersSignal = qt.pyqtSignal(object) def __init__(self, parent = None, shape=(4000,4000)): qt.QWidget.__init__(self, parent) self.mainLayout = qt.QGridLayout(self) self.mainLayout.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) i = 0 self.parametersDict = {'roi_min':[0,0], 'roi_max':[shape[0], shape[1]], 'width':min(30, int(min(shape)/10)), 'smoothing':1} for text in ["SNIP background width (2 to 3 times fwhm) :", "Minimum ROI channels considered:", "Maximum ROI channels considered:", "Pleliminar smoothing level:"]: label = qt.QLabel(self) label.setText(text) self.mainLayout.addWidget(label, i, 0) #self.mainLayout.addWidget(qt.HorizontalSpacer(self), i, 1) i +=1 i = 0 self.widgetDict = {} for key in ['width', 'roi_min', 'roi_max', 'smoothing']: if key in ['width', 'smoothing']: spinBox = qt.QSpinBox(self) spinBox.setMinimum(0) spinBox.setMaximum(min(self.parametersDict['roi_max'])) spinBox.setValue(self.parametersDict[key]) spinBox.valueChanged[int].connect(self._updateParameters) self.mainLayout.addWidget(spinBox, i, 2) self.widgetDict[key] = spinBox elif 1: lineEdit = qt.QLineEdit(self) validator = qt.QIntValidator(lineEdit) lineEdit.setValidator(validator) lineEdit._validator = validator lineEdit.setText("%d" % self.parametersDict[key][0]) lineEdit.editingFinished[()].connect( \ self._updateParameters) self.mainLayout.addWidget(lineEdit, i, 1) self.widgetDict[key] = [lineEdit] lineEdit = qt.QLineEdit(self) validator = qt.QIntValidator(lineEdit) lineEdit.setValidator(validator) lineEdit._validator = validator lineEdit.setText("%d" % self.parametersDict[key][1]) lineEdit.editingFinished.connect(self._updateParameters) self.mainLayout.addWidget(lineEdit, i, 2) self.widgetDict[key].append(lineEdit) else: spinBox = qt.QSpinBox(self) spinBox.setMinimum(0) spinBox.setMaximum(self.parametersDict['roi_max'][0]) spinBox.setValue(self.parametersDict[key][0]) spinBox.valueChanged[int].connect(self._updateParameters) self.mainLayout.addWidget(spinBox, i, 1) self.widgetDict[key] = [spinBox] spinBox = qt.QSpinBox(self) spinBox.setMinimum(0) spinBox.setMaximum(self.parametersDict['roi_max'][1]) spinBox.setValue(self.parametersDict[key][1]) spinBox.valueChanged[int].connect(self._updateParameters) self.mainLayout.addWidget(spinBox, i, 2) self.widgetDict[key].append(spinBox) i += 1 self.widgetDict['smoothing'].setMaximum(100) def _updateParameters(self, val=None): for key in ['width', 'smoothing']: self.parametersDict[key] = self.widgetDict[key].value() for key in ['roi_min', 'roi_max']: self.parametersDict[key] = [int(self.widgetDict[key][0].text()), int(self.widgetDict[key][1].text())] ddict = {} ddict['event']='SNIPParametersChanged' ddict.update(self.parametersDict) self.sigSNIPParametersSignal.emit(ddict) def getParameters(self): return self.parametersDict def setParameters(self): raise NotImplemented("Set parameters not implemented for SNIP 2D") class SNIPWindow(qt.QWidget): def __init__(self, parent, data, image=None, x=None, smooth=False): qt.QWidget.__init__(self, parent) self.setWindowTitle("SNIP Configuration Window") self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) if image is None: image = False if data.shape == 2: if 1 not in data.shape: image = True else: spectrum = data.ravel() else: spectrum = data elif not image: spectrum = data self.__smooth = smooth self.__image = image if self.__image: self.spectrum = None else: if x is None: self.xValues = range(len(spectrum)) else: self.xValues = x if self.__image: self.image = data self.graphWidget = MaskImageWidget.MaskImageWidget(self, colormap=True, selection=False, imageicons=False, standalonesave=True) self.parametersWidget = SNIP2DParametersWidget(self, shape=self.image.shape) self.graph = self.graphWidget.graphWidget.graph self.graphWidget.setImageData(data) self.mainLayout.addWidget(self.parametersWidget) self.mainLayout.addWidget(self.graphWidget) self.o3dScene = None else: self.image = None self.spectrum = spectrum self.parametersWidget = SNIP1DParametersWidget(self, length=len(spectrum), smooth=smooth) self.graph = ScanWindow.ScanWindow(self) self.graph.newCurve(self.xValues, spectrum, "Spectrum", replace=True) self.mainLayout.addWidget(self.parametersWidget) self.mainLayout.addWidget(self.graph) self.xMarkers = [] self.yMarkers = [] self.getParameters = self.parametersWidget.getParameters self.setParameters = self.parametersWidget.setParameters self.parametersWidget.sigSNIPParametersSignal.connect( \ self.updateGraph) self.updateGraph(self.getParameters()) def updateGraph(self, ddict): width = ddict['width'] roi_min = ddict['roi_min'] roi_max = ddict['roi_max'] smoothing = ddict['smoothing'] if self.__image: if self.xMarkers == []: xMin, xMax = self.graph.getGraphXLimits() yMin, yMax = self.graph.getGraphYLimits() xMean = 0.5 * (xMin + xMax) yMean = 0.5 * (yMin + yMax) self.xMarkers.append(self.graph.insertXMarker(roi_min[1], legend='C Min', text='C Min')) self.xMarkers.append(self.graph.insertXMarker(roi_max[1], legend='C Max', text='C Max')) self.yMarkers.append(self.graph.insertYMarker(roi_min[0], legend='R Min', text='R Min')) self.yMarkers.append(self.graph.insertYMarker(roi_max[0], legend='R Max', text='R Max')) else: self.graph.insertXMarker(roi_min[1], legend='C Min', text='C Min') self.graph.insertXMarker(roi_max[1], legend='C Max', text='C Max') self.graph.insertYMarker(roi_min[0], legend='R Min', text='R Min') self.graph.insertYMarker(roi_max[0], legend='R Max', text='R Max') self.background = SNIPModule.getImageBackground(self.image, width, roi_min=roi_min, roi_max=roi_max, smoothing=smoothing) difference = self.image-self.background self.graphWidget.setImageData(difference) if OBJECT3D: if self.o3dScene is None: self.o3dScene = Object3DScene.Object3DScene() self.o3dScene.show() if 0: imageData =(self.image * 1).astype(numpy.float32) backgroundData = (self.background * 1).astype(numpy.float32) self.o3dScene.mesh(imageData, z=imageData * 1, legend='Data', update_scene=True) self.o3dScene.mesh(backgroundData, z=backgroundData , legend='Background', update_scene=True) else: self.o3dScene.mesh(difference, z=difference, legend='Data-Background') self.o3dScene.show() else: self.background = SNIPModule.getSpectrumBackground(self.spectrum, width, roi_min=roi_min, roi_max=roi_max, smoothing=smoothing) if self.__smooth: legend0 = "Smoothed Spectrum" else: legend0 = "Background" self.graph.addCurve(self.xValues, self.background, legend0, replace=False) #Force information update legend = self.graph.getActiveCurve(just_legend=True) if legend.startswith(legend0[0:5]): self.graph.setActiveCurve(legend) class SNIPDialog(qt.QDialog): def __init__(self, parent, data, x=None, smooth=False): qt.QDialog.__init__(self, parent) self.setWindowTitle("SNIP Configuration Dialog") self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setContentsMargins(10, 10, 10, 10) self.mainLayout.setSpacing(2) self.__image = False self.__smooth = smooth if len(data.shape) == 2: if 1 not in data.shape: image = data self.__image = True else: spectrum = data.ravel() else: spectrum = data if self.__image: self.parametersWidget = SNIPWindow(self, image, image=True, x=x) else: self.parametersWidget = SNIPWindow(self, spectrum, image=False, x=x, smooth=smooth) self.graph = self.parametersWidget.graph self.mainLayout.addWidget(self.parametersWidget) hbox = qt.QWidget(self) hboxLayout = qt.QHBoxLayout(hbox) hboxLayout.setContentsMargins(0, 0, 0, 0) hboxLayout.setSpacing(0) 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(self.okButton) hboxLayout.addWidget(qt.HorizontalSpacer(hbox)) hboxLayout.addWidget(self.dismissButton) self.mainLayout.addWidget(hbox) self.dismissButton.clicked.connect(self.reject) self.okButton.clicked.connect(self.accept) def getParameters(self): parametersDict = self.parametersWidget.getParameters() if self.__image: parametersDict['function'] = SNIPModule.subtractSnip2DBackgroundFromStack elif self.__smooth: parametersDict['function'] = SNIPModule.replaceStackWithSnip1DBackground else: parametersDict['function'] = SNIPModule.subtractSnip1DBackgroundFromStack parametersDict['arguments'] = [parametersDict['width'], parametersDict['roi_min'], parametersDict['roi_max'], parametersDict['smoothing']] return parametersDict def setParameters(self, ddict0): if 'arguments' in ddict0: ddict = {} ddict['width'] = ddict0['arguments'][0] ddict['roi_min'] = ddict0['arguments'][1] ddict['roi_max'] = ddict0['arguments'][2] ddict['smoothing'] = ddict0['arguments'][3] self.parametersWidget.setParameters(ddict) else: self.parametersWidget.setParameters(ddict0) if __name__ == "__main__": import numpy app = qt.QApplication([]) if 0: noise = numpy.random.randn(1000.) y=numpy.arange(1000.) w = SNIPDialog(None, y+numpy.sqrt(y)* noise) elif len(sys.argv) > 1: from PyMca5.PyMcaIO import EdfFile edf = EdfFile.EdfFile(sys.argv[1]) data = edf.GetData(0) w = SNIPDialog(None, data) else: x, y = numpy.ogrid[0:200:200j, 0:200:200j] data = 50 * numpy.exp(-(x-64)*(x-64)/20.) +\ 50 * numpy.exp(-(y-128)*(y-128)/20.) +\ 100 * numpy.exp(-(1./20) * ((x-64)*(x-64) + (y-128)*(y-128))) w = SNIPDialog(None, data) w.show() ret=w.exec_() if ret: print(w.getParameters())