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()