def OnExtractPSF(self, event):
if (len(self.PSFLocs) > 0):
from PYME.Analysis.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, offsets = extractImages.getPSF3D(
self.image.data[:, :, :, chnum],
self.PSFLocs,
psfROISize,
psfBlur,
expand_z=self.cbExpandROI.GetValue())
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler(self.image.mdh)
self.write_metadata(mdh, 'default')
mdh['ImageType'] = 'PSF'
im = ImageStack(data=psf, mdh=mdh, titleStub='Extracted PSF')
im.defaultExt = '*.tif' #we want to save as PSF by default
ViewIm3D(im,
mode='psf',
parent=wx.GetTopLevelParent(self.dsviewer))
def OnSubtractBackground(self, event):
from PYME.IO.image import ImageStack
from PYME.DSView import ViewIm3D
from PYME.Analysis.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)
def OnExtractMultiviewPSF(self, event):
if (len(self.PSFLocs) > 0):
from PYME.Analysis.PSFEst import extractImages
psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')]
psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')]
psfs = []
for chnum in range(self.image.data.shape[3]):
alignZ = (chnum > 0) and self.cbAlignZ.GetValue()
#always align the first channel
psf, offsets = extractImages.getPSF3D(
self.image.data[:, :, :, chnum],
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=alignZ,
expand_z=self.cbExpandROI.GetValue())
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler(self.image.mdh)
self.write_metadata(mdh, 'Multiview')
mdh['ImageType'] = 'PSF'
im = ImageStack(data=psfs, mdh=mdh, titleStub='Extracted PSF')
im.defaultExt = '*.tif' #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.Analysis.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 = []
offsetsAllChannel = []
#extract first channel (always aligned)
psf, offsets = extractImages.getPSF3D(self.image.data[:, :, :,
0].squeeze(),
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=True)
if self.chType.GetSelection() == 0:
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
offsetsAllChannel.append(offsets)
alignZ = self.cbAlignZ.GetValue()
z_offset = offsets[2]
#extract subsequent channels, aligning if necessary, otherwise offsetting by the calculated offset for the first channel
for i in range(1, self.image.data.shape[3]):
psf, offsets = extractImages.getPSF3D(
self.image.data[:, :, :, i].squeeze(),
self.PSFLocs,
psfROISize,
psfBlur,
centreZ=alignZ,
z_offset=z_offset)
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
psfs.append(psf)
offsetsAllChannel.append(offsets)
psf = numpy.concatenate(psfs, 0)
offsetsAllChannel = numpy.asarray(offsetsAllChannel)
offsetsAllChannel -= offsetsAllChannel[0]
print(offsetsAllChannel)
# from pylab import *
# import cPickle
# imshow(psf.max(2))
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import NestedClassMDHandler
mdh = NestedClassMDHandler(self.image.mdh)
self.write_metadata(mdh, 'Split', offsetsAllChannel[:, 2])
mdh['ImageType'] = 'PSF'
im = ImageStack(data=psf, mdh=mdh, titleStub='Extracted PSF')
im.defaultExt = '*.tif' #we want to save as PSF by default
ViewIm3D(im,
mode='psf',
parent=wx.GetTopLevelParent(self.dsviewer))
def OnCalibrateMultiview(self, event):
"""
CalibrateMultiview loops over all channels described in the metadata and runs CalibrateAstigmatism on each one.
Results are stored in a library of dictionaries and are saved into a jason astigmatism map file (.am)
Args:
event: GUI event
Returns:
nothing
"""
# first make sure the user is calling the right function
try:
chanSizeX = self.image.mdh['Multiview.ROISize'][0]
except KeyError:
raise KeyError(
'You are not looking at multiview data, or the metadata is incomplete'
)
if len(self.PSFLocs) > 0:
print(
'Place cursor on bead in first multiview channel and press Calibrate Multiview Astigmatism'
)
self.OnClearTags(event)
return
from PYME.Analysis.PSFEst import extractImages
from PYME.DSView.modules import psfTools
import scipy.interpolate as terp
import numpy as np
from PYME.IO.FileUtils import nameUtils
import os
import json
zrange = np.nan * np.ones(2)
rsx, rsy, rsz = [int(s) for s in self.tPSFROI.GetValue().split(',')]
# astigDat = []
astigLib = {}
for ii in range(self.numChan):
# grab PSFs, currently relying on user to pick psf in first channel
xmin, xmax = [(self.do.xp - rsx + ii * chanSizeX),
(self.do.xp + rsx + ii * chanSizeX + 1)]
# dz returns offset in units of frames, dx dy are in pixels
dx, dy, dz = extractImages.getIntCenter(
self.image.data[xmin:xmax,
(self.do.yp - rsy):(self.do.yp + rsy + 1), :,
0])
self.PSFLocs.append((self.do.xp + dx, self.do.yp + dy, dz))
self.view.psfROIs = self.PSFLocs
self.view.Refresh()
psfROISize = [int(s) for s in self.tPSFROI.GetValue().split(',')]
psfBlur = [float(s) for s in self.tPSFBlur.GetValue().split(',')]
psf = extractImages.getPSF3D(self.image.data[:, :, :, 0],
[self.PSFLocs[ii]], psfROISize,
psfBlur)
if self.cbBackgroundCorrect.GetValue():
#widefield image - do special background subtraction
psf = extractImages.backgroundCorrectPSFWF(psf)
from PYME.DSView.dsviewer import ImageStack, ViewIm3D
im = ImageStack(data=psf,
mdh=self.image.mdh,
titleStub='Extracted PSF, Chan %i' % ii)
im.defaultExt = '*.psf' #we want to save as PSF by default
ViewIm3D(im,
mode='psf',
parent=wx.GetTopLevelParent(self.dsviewer))
calibrater = psfTools.PSFTools(self.dsviewer, im)
astigLib['PSF%i' % ii] = (calibrater.OnCalibrateAstigmatism(
event, plotIt=False))
# the next line is only ok if each frame is at a different z position, which it should be
astigLib['PSF%i' %
ii]['z'] += dz * self.image.mdh['voxelsize.z'] * 1.e3
# -- spline interpolate --
# find region of dsigma which is monotonic
dsig = terp.UnivariateSpline(
astigLib['PSF%i' % ii]['z'],
astigLib['PSF%i' %
ii]['dsigma']) #, s=1.5*len(astigDat[ii]['z']))
# mask where the sign is the same as the center
zvec = np.linspace(astigLib['PSF%i' % ii]['z'].min(),
astigLib['PSF%i' % ii]['z'].max(), 1000)
sgn = np.sign(np.diff(dsig(zvec)))
halfway = len(sgn) / 2
notmask = sgn != sgn[halfway]
# find z range for spline generation
lowerZ = zvec[np.where(notmask[:halfway])[0].max()]
upperZ = zvec[(len(sgn) / 2 +
np.where(notmask[halfway:])[0].min() - 1)]
astigLib['PSF%i' % ii]['zrange'] = [lowerZ, upperZ]
zrange = [
np.nanmin([lowerZ, zrange[0]]),
np.nanmax([upperZ, zrange[1]])
]
#lowsubZ , upsubZ = np.absolute(astigDat[ii]['z'] - zvec[lowerZ]), np.absolute(astigDat[ii]['z'] - zvec[upperZ])
#lowZLoc = np.argmin(lowsubZ)
#upZLoc = np.argmin(upsubZ)
#
#astigLib['sigxTerp%i' % ii] = terp.UnivariateSpline(astigLib['PSF%i' % ii]['z'], astigLib['PSF%i' % ii]['sigmax'],
# bbox=[lowerZ, upperZ])
#astigLib['sigyTerp%i' % ii] = terp.UnivariateSpline(astigLib['PSF%i' % ii]['z'], astigLib['PSF%i' % ii]['sigmay'],
# bbox=[lowerZ, upperZ])
astigLib['PSF%i' % ii]['z'] = astigLib['PSF%i' % ii]['z'].tolist()
astigLib['zRange'] = np.round(zrange).tolist()
astigLib['numChan'] = self.numChan
psfTools.plotAstigCalibration(astigLib)
# save to json file
#defFile = os.path.splitext(os.path.split(self.visFr.GetTitle())[-1])[0] + '.am'
fdialog = wx.FileDialog(
None,
'Save Astigmatism Calibration as ...',
wildcard='AstigMAPism file (*.am)|*.am',
style=wx.FD_SAVE,
defaultDir=nameUtils.genShiftFieldDirectoryPath(
)) #, defaultFile=defFile)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
fpath = fdialog.GetPath()
fid = open(fpath, 'wb')
json.dump(astigLib, fid)
fid.close()