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 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 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 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 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 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()
