def OnGenShiftmapQuad(self, event):
from PYME.Analysis.points import twoColour, twoColourPlot
from PYME.IO.MetaDataHandler import get_camera_roi_origin
pipeline = self.visFr.pipeline
vs = pipeline.mdh.voxelsize_nm
roi_x0, roi_y0 = get_camera_roi_origin(pipeline.mdh)
x0 = (roi_x0)*vs[0]
y0 = (roi_y0)*vs[1]
lx = len(pipeline.filter['x'])
bbox = None#[0,(pipeline.mdh['Camera.ROIWidth'] + 1)*vs[0], 0,(pipeline.mdh['Camera.ROIHeight'] + 1)*vs[1]]
dx, dy, spx, spy, good = twoColour.genShiftVectorFieldQ(pipeline.filter['x']+.1*np.random.randn(lx) + x0, pipeline.filter['y']+.1*np.random.randn(lx) + y0, pipeline.filter['fitResults_dx'], pipeline.filter['fitResults_dy'], pipeline.filter['fitError_dx'], pipeline.filter['fitError_dy'], bbox=bbox)
#twoColourPlot.PlotShiftField(dx, dy, spx, spy)
twoColourPlot.PlotShiftField2(spx, spy, pipeline.mdh['Splitter.Channel0ROI'][2:], voxelsize=vs)
twoColourPlot.PlotShiftResiduals(pipeline['x'][good] + x0, pipeline['y'][good] + y0, pipeline['fitResults_dx'][good], pipeline['fitResults_dy'][good], spx, spy)
from six.moves import cPickle
defFile = os.path.splitext(os.path.split(self.visFr.GetTitle())[-1])[0] + '.sf'
fdialog = wx.FileDialog(None, 'Save shift field as ...',
wildcard='Shift Field file (*.sf)|*.sf', style=wx.FD_SAVE, defaultDir = nameUtils.genShiftFieldDirectoryPath(), defaultFile=defFile)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
fpath = fdialog.GetPath()
#save as a pickle containing the data and voxelsize
fid = open(fpath, 'wb')
cPickle.dump((spx, spy), fid, 2)
fid.close()
def OnShowShiftMap(self, event=None):
from PYME.Analysis.points import twoColour, twoColourPlot
mdh = self.pipeline.mdh
vs = [mdh['voxelsize.x']*1e3, mdh['voxelsize.y']*1e3, mdh['voxelsize.z']*1e3]
dx = mdh.getEntry('chroma.dx')
dy = mdh.getEntry('chroma.dy')
shape = mdh['Splitter.Channel0ROI'][2:]
twoColourPlot.PlotShiftField2(dx,dy,shape,vs)
def OnGenShiftmapQuadz(self, event):
from PYME.Analysis.points import twoColour, twoColourPlot
pipeline = self.visFr.pipeline
vs = [
pipeline.mdh['voxelsize.x'] * 1e3,
pipeline.mdh['voxelsize.y'] * 1e3, 200.
]
z0 = (pipeline['z'] * pipeline['A']).sum() / pipeline['A'].sum()
lx = len(pipeline.filter['x'])
bbox = None #[0,(pipeline.mdh['Camera.ROIWidth'] + 1)*vs[0], 0,(pipeline.mdh['Camera.ROIHeight'] + 1)*vs[1]]
dx, dy, spx, spy, good = twoColour.genShiftVectorFieldQz(
pipeline.filter['x'] + .1 * pylab.randn(lx),
pipeline.filter['y'] + .1 * pylab.randn(lx),
pipeline.filter['z'] - z0,
pipeline.filter['fitResults_dx'],
pipeline.filter['fitResults_dy'],
pipeline.filter['fitError_dx'],
pipeline.filter['fitError_dy'],
bbox=bbox)
#twoColourPlot.PlotShiftField(dx, dy, spx, spy)
twoColourPlot.PlotShiftField2(spx,
spy,
pipeline.mdh['Splitter.Channel0ROI'][2:],
voxelsize=vs)
twoColourPlot.PlotShiftResiduals(pipeline['x'][good],
pipeline['y'][good],
pipeline['fitResults_dx'][good],
pipeline['fitResults_dy'][good], spx,
spy, pipeline.filter['z'][good] - z0)
from six.moves import cPickle
defFile = os.path.splitext(os.path.split(
self.visFr.GetTitle())[-1])[0] + '.sf'
fdialog = wx.FileDialog(
None,
'Save shift field as ...',
wildcard='Shift Field file (*.sf)|*.sf',
style=wx.FD_SAVE,
defaultDir=nameUtils.genShiftFieldDirectoryPath(),
defaultFile=defFile)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
fpath = fdialog.GetPath()
#save as a pickle containing the data and voxelsize
fid = open(fpath, 'wb')
cPickle.dump((spx, spy), fid, 2)
fid.close()
def _loadSF(self, filename):
self.mdh = MetaDataHandler.NestedClassMDHandler(MetaData.BareBones)
self.mdh.setEntry('chroma.ShiftFilename', filename)
dx, dy = numpy.load(filename)
self.mdh.setEntry('chroma.dx', dx)
self.mdh.setEntry('chroma.dy', dy)
#Completely guessing dimensions as it it not logged in the file
x = numpy.linspace(0, 256 * 70, 256)
y = numpy.linspace(0, 512 * 70, 512)
xs, ys = numpy.meshgrid(x, y)
self.data = [
dx.ev(xs.ravel(), ys.ravel()).reshape(xs.shape)[::-1, :].T,
dy.ev(xs.ravel(), ys.ravel()).reshape(xs.shape)[::-1, :].T
]
from PYME.Analysis.points import twoColourPlot
twoColourPlot.PlotShiftField2(dx, dy, [256, 512])
self.mode = 'default'