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)
