def colocalization(self): imgR = self.Images[0].npimage imgG = self.Images[1].npimage self.m_colocalizationHeatmap = colocalizationDetection.coloc(imgR,imgG) #Histogram = colocalizationDetection.getAngleHistogram(imgR, imgG, self.m_dims) pearsonCoeff = colocalizationDetection.calcPearsonCorrelationCoeff(imgR, imgG) MR, MG = colocalizationDetection.calcMandersColocalizationCoeffs(imgR, imgG) overlap = colocalizationDetection.calcOverlapCoeff(imgR, imgG) self.recalculateResult()
def colocalization(self): self.main_window.statusBar().showMessage('beginning colocalization calculations') imgR = self.m_npimages[0] imgG = self.m_npimages[1] #worker.smooth_image_according_to_heatmatrix(imgG, self.heatmatrix, self.m_factor) if self.heatmatrix != []: imgG = worker.smooth_image_according_to_heatmatrix_new(imgG, self.heatmatrix, self.m_factor) #Histogram = colocalizationDetection.getAngleHistogram(imgR, imgG, self.m_dims) pearsonCoeff = colocalizationDetection.calcPearsonCorrelationCoeff(imgR, imgG) MR, MG = colocalizationDetection.calcMandersColocalizationCoeffs(imgR, imgG) overlap = colocalizationDetection.calcOverlapCoeff(imgR, imgG) self.m_colocalizationHeatmap = colocalizationDetection.createColocHeatmap(imgR,imgG) self.m_colocalizationHeatmap = colocalizationDetection.coloc(imgR,imgG) self.recalculateResult() print overlap message='Pearson = %.3f '%pearsonCoeff+' Manders Green = %.3f '%MG+' Manders Red = %.3f '%MR+' overlap coeff= %.3f '%overlap self.main_window.statusBar().showMessage(message)
def connectSignals(self): QtCore.QObject.connect(self.ui.actionColocalization, QtCore.SIGNAL("triggered()"), self.colocalization) QtCore.QObject.connect(self.ui.actionToggle_colocalization_heatmap, QtCore.SIGNAL("triggered()"), self.toggleColocalizationHeatmap) QtCore.QObject.connect(self.ui.actionToggle_Images, QtCore.SIGNAL("triggered()"), self.toggleImages) self.ui.setSigmaSlider.valueChanged.connect(self.setSigmaSliderChanged) self.ui.setSigmaSpinBox.valueChanged.connect(self.setSigmaSpinBoxChanged) self.ui.thresholdSlider.valueChanged.connect(self.thresholdSliderChanged) self.ui.thresholdSpinBox.valueChanged.connect(self.thresholdSpinBoxChanged) self.ui.doSmoothingButton.clicked.connect(self.doSmoothing) self.ui.thresholdButton.clicked.connect(self.doThreshold) self.ui.actionOpen_File.triggered.connect(self.getFilename) self.ui.actionSave_File.triggered.connect(self.saveFile) self.ui.actionSave_Features.triggered.connect(self.saveFeatures) self.ui.actionReset.triggered.connect(self.reset) self.ui.actionShow_covariance_matrix.triggered.connect(self.showCovar) self.ui.actionCalculate_distance_matrix.triggered.connect(self.calcDistanceMatrix) self.ui.actionShow_Heatmatrix.triggered.connect(self.showHeatmatrix) self.ui.addFileButton.clicked.connect(self.getFilename) self.ui.zoomInButton.clicked.connect(self.zoomInButton_clicked) self.ui.zoomOutButton.clicked.connect(self.zoomOutButton_clicked) self.ui.findConnectedComponentsButton.clicked.connect(self.findConnectedComponents) self.ui.cutOffButton.clicked.connect(self.cutOff) QtCore.QObject.connect(self.scene, QtCore.SIGNAL("cursorMoved(float, float, float)"), self.displayStats) if 0: self.addFile('/home/herrmannsdoerfer/Desktop/SampleCells/01-control/confocal/Pos075_S001C0 - AveProj.tif') self.addFile('/home/herrmannsdoerfer/Desktop/SampleCells/01-control/confocal/Pos075_S001C1 - AveProj.tif') if 0: self.addFile('/home/herrmannsdoerfer/Desktop/SampleCells/01-control/confocal/Pos081_S001C0 - AveProj.tif') self.addFile('/home/herrmannsdoerfer/Desktop/SampleCells/01-control/confocal/Pos081_S001C1 - AveProj.tif') imgR, imgG = colocalizationDetection.coloc(self.Images[0].npimage,self.Images[1].npimage) self.Images[0].npimage =imgR self.Images[1].npimage =imgG self.recalculateResult() if 0: self.Images.append(ImageData()) self.Images.append(ImageData()) imgR=np.zeros((3810,2960,4)) imgG=np.zeros((3810,2960,4)) self.m_numberImages=2 imgR[...,2]=vigra.impex.readImage('/home/herrmannsdoerfer/Desktop/SampleCellsUnedited/01-control/storm/Pos11_2_aligned.tif', index = 0).swapaxes(0,1).view(np.ndarray).astype(np.float32)[:,:,0] imgG[...,1]=vigra.impex.readImage('/home/herrmannsdoerfer/Desktop/SampleCellsUnedited/01-control/storm/Pos11_2_aligned.tif', index = 1).swapaxes(0,1).view(np.ndarray).astype(np.float32)[:,:,0] self.Images[0].npimage =imgR self.Images[1].npimage =imgG self.showHeatmatrix() if 0: self.addFile('/home/herrmannsdoerfer/master/workspace/PythonPrograms/Colocalization/ColocBlockRed.txt') self.addFile('/home/herrmannsdoerfer/master/workspace/PythonPrograms/Colocalization/ColocBlockGreen.txt') self.showHeatmatrix() if 0: self.addFile('/home/herrmannsdoerfer/master/workspace/PythonPrograms/Colocalization/ColocBlockRed.txt') self.addFile('/home/herrmannsdoerfer/master/workspace/PythonPrograms/Colocalization/ColocBlockGreen.txt') #self.showHeatmatrix() imgR, imgG = colocalizationDetection.Colocdetection(self.Images[0].npimage,self.Images[1].npimage) self.Images[0].npimage =imgR self.Images[1].npimage =imgG self.recalculateResult()