def OnDeconvICTM(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog,DeconvProgressDialog,DeconvProgressPanel
dlg = DeconvSettingsDialog(self.dsviewer, beadMode, self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, decThread, richardsonLucy
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
#self.dlgDeconProg = DeconvProgressDialog(self.dsviewer, nIter)
#self.dlgDeconProg.Show()
vx = self.image.mdh.getEntry('voxelsize.x')
vy = self.image.mdh.getEntry('voxelsize.y')
vz = self.image.mdh.getEntry('voxelsize.z')
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(), (1e3*vx, 1e3*vy, 1e3*vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
#psf, vs = numpy.load(dlg.GetPSFFilename())
#psf = numpy.atleast_3d(psf)
psfFilename, psf, vs = dlg.GetPSF(vshint = vx)
decMDH['Deconvolution.PSFFile'] = dlg.GetPSFFilename()
if not (vs.x == vx and vs.y == vy and vs.z ==vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x/vx, vs.y/vy, vs.z/vz])
data = self.image.data[:,:,:, dlg.GetChannel()].astype('f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:,:,numpy.floor(dz/2):(psf.shape[2]-numpy.ceil(dz/2))]
print((data.shape, psf.shape))
if dlg.GetPadding():
padsize = numpy.array(dlg.GetPadSize())
decMDH['Deconvolution.Padding'] = padsize
dp = numpy.ones(numpy.array(data.shape) + 2*padsize, 'f')*data.mean()
weights = numpy.zeros_like(dp)
px, py, pz = padsize
#print data.shape, dp[px:-(px+1), py:-(py+1), pz:-(pz+1)].shape
dp[px:-px, py:-py, pz:-pz] = data
#if dlg.GetRemovePadding():
# data = dp[px:-px, py:-py, pz:-pz]#should be a slice
#else:
# data = dp
weights[px:-px, py:-py, pz:-pz] = 1.
weights = weights.ravel()
else:
dp = data
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq, data, psf, self.image.seriesName, blocksize={'y': bs, 'x': bs, 'z': 256})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp.shape)
self.decT = decThread.decThread(self.dec, dp, regLambda, nIter, weights, bg = bg)
self.decT.start()
tries = 0
while tries < 10 and not hasattr(self.dec, 'fs'):
time.sleep(1)
tries += 1
if dlg.GetPadding() and dlg.GetRemovePadding():
fs = self.dec.fs[px:-px, py:-py, pz:-pz]
else:
fs = self.dec.fs
im = ImageStack(data = fs, mdh = decMDH, titleStub = 'Deconvolution Result')
mode = 'lite'
if beadMode:
mode = 'psf'
im.defaultExt = '*.psf' #we want to save as PSF by default
self.res = ViewIm3D(im, mode=mode, parent=wx.GetTopLevelParent(self.dsviewer))
#self.res = View3D(fs, 'Deconvolution Result', mdh=decMDH, parent=wx.GetTopLevelParent(self.dsviewer), mode=mode)
self.dlgDeconProg = DeconvProgressPanel(self.res, nIter)
self.pinfo1 = aui.AuiPaneInfo().Name("deconvPanel").Top().Caption('Deconvolution Progress').DestroyOnClose(True).CloseButton(False)#.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self.res._mgr.AddPane(self.dlgDeconProg, self.pinfo1)
self.res._mgr.Update()
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def OnDeconvMovie(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog #,DeconvProgressDialog,DeconvProgressPanel
#import multiprocessing
dlg = DeconvSettingsDialog(self.dsviewer, beadMode, self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, richardsonLucy #, decThread
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
#self.dlgDeconProg = DeconvProgressDialog(self.dsviewer, nIter)
#self.dlgDeconProg.Show()
vx = self.image.mdh.getEntry('voxelsize.x')
vy = self.image.mdh.getEntry('voxelsize.y')
vz = self.image.mdh.getEntry('voxelsize.z')
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(), (1e3*vx, 1e3*vy, 1e3*vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
#psf, vs = numpy.load(dlg.GetPSFFilename())
#psf = numpy.atleast_3d(psf)
psfFilename, psf, vs = dlg.GetPSF(vshint = vx)
decMDH['Deconvolution.PSFFile'] = psfFilename
if not (vs.x == vx and vs.y == vy):# and vs.z ==vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x/vx, vs.y/vy, 1])
data = self.image.data[:,:,:, dlg.GetChannel()].astype('f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
#print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:,:,numpy.floor(dz/2):(psf.shape[2]-numpy.ceil(dz/2))]
print((data.shape, psf.shape))
dp = numpy.array(data)
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq, data, psf, self.image.seriesName, blocksize={'y': bs, 'x': bs, 'z': 256})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp[:,:,0:1].shape)
#print dp.__class__
#self.decT = decThread.decThread(self.dec, dp, regLambda, nIter, weights)
#self.decT.start()
# p = multiprocessing.Pool()
# slices = [(self.dec, psf, dp[:,:,i:(i+1)],regLambda, nIter, weights) for i in range(dp.shape[2])]
# r = p.map(_pt, slices)
# res = numpy.concatenate(r, 2)
res = numpy.concatenate([self.dec.deconv(dp[:,:,i:(i+1)], regLambda, nIter, weights, bg=bg).reshape(self.dec.shape) for i in range(dp.shape[2])], 2)
im = ImageStack(data = res, mdh = decMDH, titleStub = 'Deconvolution Result')
mode = 'lite'
self.res = ViewIm3D(im, mode=mode, parent=wx.GetTopLevelParent(self.dsviewer))
def OnDeconvMovie(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog #,DeconvProgressDialog,DeconvProgressPanel
#import multiprocessing
dlg = DeconvSettingsDialog(self.dsviewer, beadMode,
self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, richardsonLucy #, decThread
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
vx, vy, vz = self.image.voxelsize_nm
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(), (vx, vy, vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
psfFilename, psf, vs = dlg.GetPSF(vshint=vx)
decMDH['Deconvolution.PSFFile'] = psfFilename
if not (vs.x == vx and vs.y == vy): # and vs.z ==vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x / vx, vs.y / vy, 1])
data = self.image.data[:, :, :, dlg.GetChannel()].astype(
'f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
#print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:, :,
numpy.floor(dz / 2):(psf.shape[2] -
numpy.ceil(dz / 2))]
print((data.shape, psf.shape))
dp = numpy.array(data)
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq,
data,
psf,
self.image.seriesName,
blocksize={
'y': bs,
'x': bs,
'z': 256
})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp[:, :, 0:1].shape)
#print dp.__class__
#self.decT = decThread.decThread(self.dec, dp, regLambda, nIter, weights)
#self.decT.start()
# p = multiprocessing.Pool()
# slices = [(self.dec, psf, dp[:,:,i:(i+1)],regLambda, nIter, weights) for i in range(dp.shape[2])]
# r = p.map(_pt, slices)
# res = numpy.concatenate(r, 2)
res = numpy.concatenate([
self.dec.deconv(
dp[:, :, i:(i + 1)], regLambda, nIter, weights,
bg=bg).reshape(self.dec.shape)
for i in range(dp.shape[2])
], 2)
im = ImageStack(data=res,
mdh=decMDH,
titleStub='Deconvolution Result')
mode = 'lite'
self.res = ViewIm3D(im,
mode=mode,
parent=wx.GetTopLevelParent(self.dsviewer))
def OnDeconvICTM(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog, DeconvProgressPanel
dlg = DeconvSettingsDialog(self.dsviewer, beadMode,
self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, decThread, richardsonLucy
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
vx, vy, vz = self.image.voxelsize_nm
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(), (vx, vy, vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
psfFilename, psf, vs = dlg.GetPSF(vshint=vx)
if psf.shape[2] < 2:
raise RuntimeError(
'Expepected a 3D PSF for 3D deconvolution. For 2D deconvolution use the DeconvMovie function'
)
decMDH['Deconvolution.PSFFile'] = dlg.GetPSFFilename()
if not (vs.x == vx and vs.y == vy and vs.z == vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x / vx, vs.y / vy, vs.z / vz])
#crop PSF in z if bigger than stack
if psf.shape[2] > self.image.data.shape[2]:
dz = psf.shape[2] - self.image.data.shape[2]
psf = psf[:, :,
int(numpy.floor(dz / 2)):int(psf.shape[2] -
numpy.ceil(dz / 2))]
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
if beadMode and self.image.data.shape[3] > 1:
#special case for deconvolving multi-channel PSFs
data = np.concatenate([
self.image.data[:, :, :, i].astype('f') - dlg.GetOffset()
for i in range(self.image.data.shape[3])
], 0)
else:
data = self.image.data[:, :, :, dlg.GetChannel()].astype(
'f') - dlg.GetOffset()
if dlg.GetPadding():
padsize = numpy.array(dlg.GetPadSize())
decMDH['Deconvolution.Padding'] = padsize
dp = numpy.ones(numpy.array(data.shape) + 2 * padsize,
'f') * data.mean()
weights = numpy.zeros_like(dp)
px, py, pz = padsize
dp[px:-px, py:-py, pz:-pz] = data
weights[px:-px, py:-py, pz:-pz] = 1.
weights = weights.ravel()
else:
dp = data
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq,
data,
psf,
self.image.seriesName,
blocksize={
'y': bs,
'x': bs,
'z': 256
})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp.shape)
self.decT = decThread.decThread(self.dec,
dp,
regLambda,
nIter,
weights,
bg=bg)
self.decT.start()
tries = 0
while not hasattr(self.dec, 'fs'):
if tries > 60:
self.decT.kill()
raise RuntimeError(
'Initialization not complete after 60s, giving up.'
)
time.sleep(1)
tries += 1
if dlg.GetPadding() and dlg.GetRemovePadding():
fs = self.dec.fs[px:-px, py:-py, pz:-pz]
else:
fs = self.dec.fs
if beadMode and self.image.data.shape[3] > 1:
#special case for bead deconvolution - unwind the stacking
nChans = self.image.data.shape[3]
xs = int(fs.shape[0] / nChans)
#NOTE: this relies on the slicing returning a view into the underlying data, not a copy
fs = [
fs[(i * xs):((i + 1) * xs), :, :]
for i in range(nChans)
]
im = ImageStack(data=fs,
mdh=decMDH,
titleStub='Deconvolution Result')
mode = 'lite'
if beadMode and im.data.shape[1] < 100:
mode = 'psf'
im.defaultExt = '*.psf' #we want to save as PSF by default
self.res = ViewIm3D(im,
mode=mode,
parent=wx.GetTopLevelParent(self.dsviewer))
#self.res = View3D(fs, 'Deconvolution Result', mdh=decMDH, parent=wx.GetTopLevelParent(self.dsviewer), mode=mode)
self.dlgDeconProg = DeconvProgressPanel(self.res, nIter)
self.pinfo1 = aui.AuiPaneInfo().Name("deconvPanel").Top(
).Caption('Deconvolution Progress').DestroyOnClose(
True
).CloseButton(
False
) #.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self.res._mgr.AddPane(self.dlgDeconProg, self.pinfo1)
self.res._mgr.Update()
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def OnDeconvICTM(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog, DeconvProgressDialog, DeconvProgressPanel
dlg = DeconvSettingsDialog(self.dsviewer, beadMode,
self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, decThread, richardsonLucy
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
#self.dlgDeconProg = DeconvProgressDialog(self.dsviewer, nIter)
#self.dlgDeconProg.Show()
vx = self.image.mdh.getEntry('voxelsize.x')
vy = self.image.mdh.getEntry('voxelsize.y')
vz = self.image.mdh.getEntry('voxelsize.z')
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(),
(1e3 * vx, 1e3 * vy, 1e3 * vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
#psf, vs = numpy.load(dlg.GetPSFFilename())
#psf = numpy.atleast_3d(psf)
psfFilename, psf, vs = dlg.GetPSF(vshint=vx)
decMDH['Deconvolution.PSFFile'] = dlg.GetPSFFilename()
if not (vs.x == vx and vs.y == vy and vs.z == vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x / vx, vs.y / vy, vs.z / vz])
data = self.image.data[:, :, :, dlg.GetChannel()].astype(
'f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:, :,
numpy.floor(dz / 2):(psf.shape[2] -
numpy.ceil(dz / 2))]
print((data.shape, psf.shape))
if dlg.GetPadding():
padsize = numpy.array(dlg.GetPadSize())
decMDH['Deconvolution.Padding'] = padsize
dp = numpy.ones(numpy.array(data.shape) + 2 * padsize,
'f') * data.mean()
weights = numpy.zeros_like(dp)
px, py, pz = padsize
#print data.shape, dp[px:-(px+1), py:-(py+1), pz:-(pz+1)].shape
dp[px:-px, py:-py, pz:-pz] = data
#if dlg.GetRemovePadding():
# data = dp[px:-px, py:-py, pz:-pz]#should be a slice
#else:
# data = dp
weights[px:-px, py:-py, pz:-pz] = 1.
weights = weights.ravel()
else:
dp = data
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq,
data,
psf,
self.image.seriesName,
blocksize={
'y': bs,
'x': bs,
'z': 256
})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp.shape)
self.decT = decThread.decThread(self.dec,
dp,
regLambda,
nIter,
weights,
bg=bg)
self.decT.start()
tries = 0
while tries < 10 and not hasattr(self.dec, 'fs'):
time.sleep(1)
tries += 1
if dlg.GetPadding() and dlg.GetRemovePadding():
fs = self.dec.fs[px:-px, py:-py, pz:-pz]
else:
fs = self.dec.fs
im = ImageStack(data=fs,
mdh=decMDH,
titleStub='Deconvolution Result')
mode = 'lite'
if beadMode:
mode = 'psf'
im.defaultExt = '*.psf' #we want to save as PSF by default
self.res = ViewIm3D(im,
mode=mode,
parent=wx.GetTopLevelParent(self.dsviewer))
#self.res = View3D(fs, 'Deconvolution Result', mdh=decMDH, parent=wx.GetTopLevelParent(self.dsviewer), mode=mode)
self.dlgDeconProg = DeconvProgressPanel(self.res, nIter)
self.pinfo1 = aui.AuiPaneInfo().Name("deconvPanel").Top(
).Caption('Deconvolution Progress').DestroyOnClose(
True
).CloseButton(
False
) #.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self.res._mgr.AddPane(self.dlgDeconProg, self.pinfo1)
self.res._mgr.Update()
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)