def OnExtractPSF(self, event): if (len(self.PSFLocs) > 0): from PYME.PSFEst import extractImages chnum = self.chChannel.GetSelection() psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')] psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')] #print psfROISize psf = extractImages.getPSF3D(self.image.data[:, :, :, chnum], self.PSFLocs, psfROISize, psfBlur) if self.chType.GetSelection() == 0: #widefield image - do special background subtraction psf = extractImages.backgroundCorrectPSFWF(psf) # from pylab import * # import cPickle # imshow(psf.max(2)) from PYME.DSView.dsviewer_npy_nb import ImageStack, ViewIm3D im = ImageStack(data=psf, mdh=self.image.mdh, titleStub='Extracted PSF') im.defaultExt = '*.psf' #we want to save as PSF by default ViewIm3D(im, mode='psf', parent=wx.GetTopLevelParent(self.dsviewer))
def OnExtractSplitPSF(self, event): if (len(self.PSFLocs) > 0): from PYME.PSFEst import extractImages chnum = self.chChannel.GetSelection() psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')] psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')] #print psfROISize psfs = [] for i in range(self.image.data.shape[3]): psf = extractImages.getPSF3D(self.image.data[:,:,:,i], self.PSFLocs, psfROISize, psfBlur) if self.chType.GetSelection() == 0: #widefield image - do special background subtraction psf = extractImages.backgroundCorrectPSFWF(psf) psfs.append(psf) psf = numpy.concatenate(psfs, 0) # from pylab import * # import cPickle # imshow(psf.max(2)) from PYME.DSView.dsviewer_npy_nb import ImageStack, ViewIm3D im = ImageStack(data = psf, mdh = self.image.mdh, titleStub = 'Extracted PSF') im.defaultExt = '*.psf' #we want to save as PSF by default ViewIm3D(im, mode='psf', parent=wx.GetTopLevelParent(self.dsviewer))
def OnSubtractBackground(self, event): from PYME.DSView.image import ImageStack from PYME.DSView import ViewIm3D from PYME.PSFEst import extractImages d_bg = extractImages.backgroundCorrectPSFWF(self.image.data[:,:,:]) im = ImageStack(d_bg, titleStub = 'Filtered Image') im.mdh.copyEntriesFrom(self.image.mdh) im.mdh['Parent'] = self.image.filename dv = ViewIm3D(im, mode='psf', glCanvas=self.dsviewer.glCanvas)