def OnUnmix(self, event):
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
usds = self._getUSDataSources()
fns = os.path.split(self.image.filename)[1]
im = ImageStack(usds, titleStub='%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
# grab events from the first data source TODO - do this need to be smarter?
try:
im.events = usds[0].getEvents()
except:
logger.warning('No Events found when coalescing UnsplitDataSource')
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
print(im.data[:, :, 1, 1].shape)
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
def OnUnmixMax(self, event):
#unmix and take brightest channel
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
usds = self._getUSDataSources()
fns = os.path.split(self.image.filename)[1]
zm = usds[0].shape[2] / 2
maxs = [u[:, :, zm].max() for u in usds]
im = ImageStack(usds[np.argmax(maxs)], titleStub='%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
def OnApplyShiftmap(self, event):
"""apply a vectorial correction for chromatic shift to an image - this
is a generic vectorial shift compensation, rather than the secial case
correction used with the splitter."""
from scipy import ndimage
import numpy as np
from PYME.DSView import ImageStack, ViewIm3D
from PYME.IO.MetaDataHandler import get_camera_roi_origin
dlg = ShiftmapSelectionDialog(self.dsviewer, self.image)
succ = dlg.ShowModal()
if (succ == wx.ID_OK):
#self.ds = example.CDataStack(fdialog.GetPath().encode())
#self.ds =
ds = []
shiftFiles = {}
X, Y, Z = np.mgrid[0:self.image.data.shape[0], 0:self.image.data.shape[1], 0:self.image.data.shape[2]]
vx, vy, vz = self.image.voxelsize_nm
roi_x0, roi_y0 = get_camera_roi_origin(self.image.mdh)
for ch in range(self.image.data.shape[3]):
sfFilename = dlg.GetChanFilename(ch)
shiftFiles[ch] = sfFilename
data = self.image.data[:,:,:, ch]
if os.path.exists(sfFilename):
spx, spy, dz = np.load(sfFilename)
dx = spx.ev(vx*(X+roi_x0), vy*(Y+roi_y0))/vx
dy = spy.ev(vx*(X+roi_x0), vy*(Y+roi_y0))/vy
dz = dz/vz
ds.append(ndimage.map_coordinates(data, [X+dx, Y+dy, Z+dz], mode='nearest'))
else:
ds.append(data)
fns = os.path.split(self.image.filename)[1]
im = ImageStack(ds, titleStub = '%s - corrected' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
im.mdh.setEntry('ChromaCorrection.ShiftFilenames', shiftFiles)
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
dlg.Destroy()
def OnUnmixMax(self, event):
#unmix and take brightest channel
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
mdh = self.image.mdh
if 'chroma.dx' in mdh.getEntryNames():
sf = (mdh['chroma.dx'], mdh['chroma.dy'])
elif global_shiftfield:
sf = global_shiftfield
else:
#self.OnSetShiftField()
#sf = (mdh['chroma.dx'], mdh['chroma.dy'])
sf = None
flip = True
if 'Splitter.Flip' in mdh.getEntryNames() and not mdh['Splitter.Flip']:
flip = False
ROIX1 = mdh.getEntry('Camera.ROIPosX')
ROIY1 = mdh.getEntry('Camera.ROIPosY')
ROIX2 = ROIX1 + mdh.getEntry('Camera.ROIWidth')
ROIY2 = ROIY1 + mdh.getEntry('Camera.ROIHeight')
um0 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2],
0, flip, sf)
um1 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2], 1
, flip, sf)
fns = os.path.split(self.image.filename)[1]
zm = um0.shape[2]/2
if um0[:,:,zm].max() > um1[:,:,zm].max():
im = ImageStack(um0, titleStub = '%s - unsplit' % fns)
else:
im = ImageStack(um1, titleStub = '%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
def OnUnmix(self, event):
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
mdh = self.image.mdh
if 'chroma.dx' in mdh.getEntryNames():
sf = (mdh['chroma.dx'], mdh['chroma.dy'])
elif global_shiftfield:
sf = global_shiftfield
else:
sf = None
flip = True
if 'Splitter.Flip' in mdh.getEntryNames() and not mdh['Splitter.Flip']:
flip = False
chanROIs = None
if 'Splitter.Channel0ROI' in mdh.getEntryNames():
chanROIs = [mdh['Splitter.Channel0ROI'],mdh['Splitter.Channel1ROI']]
ROIX1 = mdh.getEntry('Camera.ROIPosX')
ROIY1 = mdh.getEntry('Camera.ROIPosY')
ROIX2 = ROIX1 + mdh.getEntry('Camera.ROIWidth')
ROIY2 = ROIY1 + mdh.getEntry('Camera.ROIHeight')
um0 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2],
0, flip, sf, chanROIs=chanROIs, voxelsize=self.image.voxelsize)
um1 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2], 1
, flip, sf, chanROIs=chanROIs, voxelsize=self.image.voxelsize)
fns = os.path.split(self.image.filename)[1]
im = ImageStack([um0, um1], titleStub = '%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
#print im.data[:,:,1,1].shape
dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
def dark(dsviewer):
from PYME.DSView import ViewIm3D, ImageStack
im = ImageStack(dsviewer.image.data[:, :, :].astype('f').mean(2),
mdh=dsviewer.image.mdh)
ViewIm3D(im)
def flat(dsviewer):
from PYME.DSView import ViewIm3D, ImageStack
import numpy as np
dark = ImageStack(
load_prompt=
"Select corresponding DARK image (should have been calculated first)"
).data[:, :, 0].squeeze().astype('f')
illum = 0 * dark
for i in range(dsviewer.image.data.shape[2]):
illum += dsviewer.image.data[:, :, i].squeeze().astype('f') - dark
illum /= dsviewer.image.data.shape[2]
im = ImageStack(illum.mean() / illum, mdh=dsviewer.image.mdh)
ViewIm3D(im)
def OnUnmix(self, event):
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
from scipy import linalg
mdh = self.image.mdh
if 'Camera.ADOffset' in mdh.getEntryNames():
offset = mdh['Camera.ADOffset']
else:
offset = 0
dlg = UnMixSettingsDlg(self.dsviewer, offset=offset)
if dlg.ShowModal() == wx.ID_OK:
mm = dlg.GetMixMatrix()
off = dlg.GetOffset()
mmi = linalg.inv(mm)
ch0 = self.image.data[:, :, :, 0] - off
ch1 = self.image.data[:, :, :, 1] - off
um0 = mmi[0, 0] * ch0 + mmi[0, 1] * ch1
um1 = mmi[1, 0] * ch0 + mmi[1, 1] * ch1
im = ImageStack([um0, um1], titleStub='Unmixed Image')
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
im.mdh['Unmixing.MixMatrix'] = mm
im.mdh['Unmixing.Offset'] = off
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
def OnUnmix(self, event):
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
from scipy import linalg
mdh = self.image.mdh
if 'Camera.ADOffset' in mdh.getEntryNames():
offset = mdh['Camera.ADOffset']
else:
offset = 0
dlg = UnMixSettingsDlg(self.dsviewer, offset=offset)
if dlg.ShowModal() == wx.ID_OK:
mm = dlg.GetMixMatrix()
off = dlg.GetOffset()
mmi = linalg.inv(mm)
ch0 = self.image.data[:,:,:,0] - off
ch1 = self.image.data[:,:,:,1] - off
um0 = mmi[0,0]*ch0 + mmi[0,1]*ch1
um1 = mmi[1,0]*ch0 + mmi[1,1]*ch1
im = ImageStack([um0, um1], titleStub = 'Unmixed Image')
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
im.mdh['Unmixing.MixMatrix'] = mm
im.mdh['Unmixing.Offset'] = off
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
def OnUnmixMax(self, event):
#unmix and take brightest channel
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
mdh = self.image.mdh
if 'chroma.dx' in mdh.getEntryNames():
sf = (mdh['chroma.dx'], mdh['chroma.dy'])
elif global_shiftfield:
sf = global_shiftfield
else:
#self.OnSetShiftField()
#sf = (mdh['chroma.dx'], mdh['chroma.dy'])
sf = None
flip = True
if 'Splitter.Flip' in mdh.getEntryNames() and not mdh['Splitter.Flip']:
flip = False
ROIX1 = mdh.getEntry('Camera.ROIPosX')
ROIY1 = mdh.getEntry('Camera.ROIPosY')
ROIX2 = ROIX1 + mdh.getEntry('Camera.ROIWidth')
ROIY2 = ROIY1 + mdh.getEntry('Camera.ROIHeight')
um0 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2], 0,
flip, sf)
um1 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2], 1,
flip, sf)
fns = os.path.split(self.image.filename)[1]
zm = um0.shape[2] / 2
if um0[:, :, zm].max() > um1[:, :, zm].max():
im = ImageStack(um0, titleStub='%s - unsplit' % fns)
else:
im = ImageStack(um1, titleStub='%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
def OnApplyShiftmap(self, event):
"""apply a vectorial correction for chromatic shift to an image - this
is a generic vectorial shift compensation, rather than the secial case
correction used with the splitter."""
from scipy import ndimage
import numpy as np
from PYME.DSView import ImageStack, ViewIm3D
dlg = ShiftmapSelectionDialog(self.dsviewer, self.image)
succ = dlg.ShowModal()
if succ == wx.ID_OK:
# self.ds = example.CDataStack(fdialog.GetPath().encode())
# self.ds =
ds = []
shiftFiles = {}
X, Y, Z = np.mgrid[0 : self.image.data.shape[0], 0 : self.image.data.shape[1], 0 : self.image.data.shape[2]]
vx = self.image.mdh["voxelsize.x"] * 1e3
vy = self.image.mdh["voxelsize.y"] * 1e3
vz = self.image.mdh["voxelsize.z"] * 1e3
x0 = 1
y0 = 1
if "Camera.ROIPosX" in self.image.mdh.getEntryNames():
x0 = self.image.mdh["Camera.ROIPosX"]
y0 = self.image.mdh["Camera.ROIPosY"]
for ch in range(self.image.data.shape[3]):
sfFilename = dlg.GetChanFilename(ch)
shiftFiles[ch] = sfFilename
data = self.image.data[:, :, :, ch]
if os.path.exists(sfFilename):
spx, spy, dz = np.load(sfFilename)
dx = spx.ev(vx * (X + x0 - 1), vy * (Y + y0 - 1)) / vx
dy = spy.ev(vx * (X + x0 - 1), vy * (Y + y0 - 1)) / vy
dz = dz / vz
ds.append(ndimage.map_coordinates(data, [X + dx, Y + dy, Z + dz], mode="nearest"))
else:
ds.append(data)
fns = os.path.split(self.image.filename)[1]
im = ImageStack(ds, titleStub="%s - corrected" % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh["Parent"] = self.image.filename
im.mdh.setEntry("ChromaCorrection.ShiftFilenames", shiftFiles)
if "fitResults" in dir(self.image):
im.fitResults = self.image.fitResults
# im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == "visGUI":
mode = "visGUI"
else:
mode = "lite"
dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
dlg.Destroy()
def OnOpenRaw(self, event):
from PYME.DSView import ViewIm3D, ImageStack
ViewIm3D(ImageStack(), mode='visGUI', glCanvas=self.glCanvas)
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 reconstruct_pipeline_from_image_file(self, event=None, filename=None):
from PYME.DSView import ImageStack
im = ImageStack(filename=filename)
self.reconstruct_pipeline_from_image(im)
def OnUnmix(self, event):
#from PYME.Analysis import deTile
from PYME.DSView import ViewIm3D, ImageStack
mdh = self.image.mdh
if 'chroma.dx' in mdh.getEntryNames():
sf = (mdh['chroma.dx'], mdh['chroma.dy'])
elif global_shiftfield:
sf = global_shiftfield
else:
sf = None
flip = True
if 'Splitter.Flip' in mdh.getEntryNames() and not mdh['Splitter.Flip']:
flip = False
chanROIs = None
if 'Splitter.Channel0ROI' in mdh.getEntryNames():
chanROIs = [
mdh['Splitter.Channel0ROI'], mdh['Splitter.Channel1ROI']
]
ROIX1 = mdh.getEntry('Camera.ROIPosX')
ROIY1 = mdh.getEntry('Camera.ROIPosY')
ROIX2 = ROIX1 + mdh.getEntry('Camera.ROIWidth')
ROIY2 = ROIY1 + mdh.getEntry('Camera.ROIHeight')
um0 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2],
0,
flip,
sf,
chanROIs=chanROIs,
voxelsize=self.image.voxelsize)
um1 = UnsplitDataSource.DataSource(self.image.data,
[ROIX1, ROIY1, ROIX2, ROIY2],
1,
flip,
sf,
chanROIs=chanROIs,
voxelsize=self.image.voxelsize)
fns = os.path.split(self.image.filename)[1]
im = ImageStack([um0, um1], titleStub='%s - unsplit' % fns)
im.mdh.copyEntriesFrom(self.image.mdh)
im.mdh['Parent'] = self.image.filename
if 'fitResults' in dir(self.image):
im.fitResults = self.image.fitResults
#im.mdh['Processing.GaussianFilter'] = sigmas
if self.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
#print im.data[:,:,1,1].shape
dv = ViewIm3D(im,
mode=mode,
glCanvas=self.dsviewer.glCanvas,
parent=wx.GetTopLevelParent(self.dsviewer))
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
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)
