def getNeighbourDists(self, forceRetriang=False):
from PYME.Analysis.LMVis import visHelpers
if forceRetriang or not 'neighbourDistances' in self.GeneratedMeasures.keys(
):
statNeigh = statusLog.StatusLogger(
"Calculating mean neighbour distances ...")
self.GeneratedMeasures['neighbourDistances'] = np.array(
visHelpers.calcNeighbourDists(
self.getTriangles(forceRetriang)))
return self.GeneratedMeasures['neighbourDistances']
def genIm(self, dlg, imb, mdh):
pixelSize = dlg.getPixelSize()
jitParamName = dlg.getJitterVariable()
jitScale = dlg.getJitterScale()
mdh['Rendering.JitterVariable'] = jitParamName
mdh['Rendering.JitterScale'] = jitScale
jitVals = self._genJitVals(jitParamName, jitScale)
if dlg.getSoftRender():
status = statusLog.StatusLogger("Rendering triangles ...")
return visHelpers.rendJitTriang2(self.pipeline.colourFilter['x'],self.pipeline.colourFilter['y'], dlg.getNumSamples(), jitVals, dlg.getMCProbability(),imb, pixelSize)
else:
return self.visFr.glCanvas.genJitTim(dlg.getNumSamples(),self.pipeline.colourFilter['x'],self.pipeline.colourFilter['y'], jitVals, dlg.getMCProbability(),pixelSize)
def getTriangles(self, recalc=False):
from matplotlib import delaunay
if self.Triangles == None or recalc:
statTri = statusLog.StatusLogger("Generating Triangulation ...")
self.Triangles = delaunay.Triangulation(
self.colourFilter['x'] +
.1 * np.random.normal(size=len(self.colourFilter['x'])),
self.colourFilter['y'] +
.1 * np.random.normal(size=len(self.colourFilter['x'])))
#reset things which will have changed
self.edb = None
try:
self.GeneratedMeasures.pop('neighbourDistances')
except KeyError:
pass
return self.Triangles
def Generate(self, event=None):
jitVars = ['1.0']
jitVars += self.pipeline.colourFilter.keys()
self.genMeas = self.pipeline.GeneratedMeasures.keys()
if not 'neighbourDistances' in self.genMeas:
self.genMeas.append('neighbourDistances')
if not 'neighbourErrorMin' in self.genMeas:
self.genMeas.append('neighbourErrorMin')
jitVars += self.genMeas
if 'z' in self.pipeline.mapping.keys():
zvals = self.pipeline.mapping['z']
else:
zvals = None
dlg = genImageDialog.GenImageDialog(self.mainWind, mode=self.mode, defaultPixelSize=self._defaultPixelSize, colours=self.pipeline.colourFilter.getColourChans(), zvals = zvals, jitterVariables = jitVars, jitterVarDefault=self._getDefaultJitVar(jitVars), jitterVarDefaultZ=self._getDefaultZJitVar(jitVars))
ret = dlg.ShowModal()
bCurr = wx.BusyCursor()
if ret == wx.ID_OK:
mdh = MetaDataHandler.NestedClassMDHandler()
mdh['Rendering.Method'] = self.name
if 'imageID' in self.pipeline.mdh.getEntryNames():
mdh['Rendering.SourceImageID'] = self.pipeline.mdh['imageID']
mdh['Rendering.SourceFilename'] = self.pipeline.filename
mdh.Source = MetaDataHandler.NestedClassMDHandler(self.pipeline.mdh)
for cb in renderMetadataProviders:
cb(mdh)
pixelSize = dlg.getPixelSize()
status = statusLog.StatusLogger('Generating %s Image ...' % self.name)
imb = self._getImBounds()
#record the pixel origin in nm from the corner of the camera for futrue overlays
if 'Source.Camera.ROIPosX' in mdh.getEntryNames():
#a rendered image with information about the source ROI
voxx, voxy = 1e3*mdh['Source.voxelsize.x'], 1e3*mdh['Source.voxelsize.y']
ox = (mdh['Source.Camera.ROIPosX'] - 1)*voxx + imb.x0
oy = (mdh['Source.Camera.ROIPosY'] - 1)*voxy + imb.y0
if 'Source.Positioning.PIFoc' in mdh.getEntryNames():
oz = mdh['Source.Positioning.PIFoc']*1e3
else:
oz = 0
else:
ox = imb.x0
oy = imb.y0
oz = 0
mdh['Origin.x'] = ox
mdh['Origin.y'] = oy
mdh['Origin.z'] = oz
colours = dlg.getColour()
oldC = self.pipeline.colourFilter.currentColour
ims = []
for c in colours:
self.pipeline.colourFilter.setColour(c)
ims.append(np.atleast_3d(self.genIm(dlg, imb, mdh)))
im = GeneratedImage(ims,imb, pixelSize, dlg.getZSliceThickness(), colours, mdh = mdh)
imfc = ViewIm3D(im, mode='visGUI', title='Generated %s - %3.1fnm bins' % (self.name, pixelSize), glCanvas=self.visFr.glCanvas, parent=self.mainWind)
#imfc = imageView.MultiChannelImageViewFrame(self.visFr, self.visFr.glCanvas, im, title='Generated %s - %3.1fnm bins' % (self.name, pixelSize))
#self.visFr.generatedImages.append(imfc)
#imfc.Show()
self.pipeline.colourFilter.setColour(oldC)
else:
imfc = None
dlg.Destroy()
return imfc
def RefreshView(self):
if not self.pipeline.ready:
return #get out of here
if len(self.pipeline['x']) == 0:
wx.MessageBox('No data points - try adjusting the filter',
"len(filter['x']) ==0")
return
if self.glCanvas.init == 0: #glcanvas is not initialised
return
bCurr = wx.BusyCursor()
if self.pipeline.objects == None:
# if 'bObjMeasure' in dir(self):
# self.bObjMeasure.Enable(False)
self.objectMeasures = None
if not self.rav == None: #remove previous event viewer
i = 0
found = False
while not found and i < self.notebook.GetPageCount():
if self.notebook.GetPage(i) == self.rav:
self.notebook.DeletePage(i)
found = True
else:
i += 1
self.rav = None
if self.viewMode == 'points':
self.glCanvas.setPoints(self.pipeline['x'], self.pipeline['y'],
self.pointColour())
if 'glCanvas3D' in dir(self):
self.glCanvas3D.setPoints(self.pipeline['x'],
self.pipeline['y'],
self.pipeline['z'],
self.pointColour())
self.glCanvas3D.setCLim(self.glCanvas.clim, (-5e5, -5e5))
elif self.viewMode == 'tracks':
self.glCanvas.setTracks(self.pipeline['x'], self.pipeline['y'],
self.pipeline['clumpIndex'],
self.pointColour())
elif self.viewMode == 'triangles':
self.glCanvas.setTriang(self.pipeline.getTriangles())
elif self.viewMode == 'voronoi':
status = statusLog.StatusLogger("Generating Voronoi Diagram ... ")
self.glCanvas.setVoronoi(self.pipeline.getTriangles())
elif self.viewMode == 'quads':
if self.pipeline.Quads == None:
status = statusLog.StatusLogger("Generating QuadTree ...")
self.pipeline.GenQuads()
self.glCanvas.setQuads(self.pipeline.Quads)
elif self.viewMode == 'interp_triangles':
self.glCanvas.setIntTriang(self.pipeline.getTriangles(),
self.pointColour())
elif self.viewMode == 'blobs':
if self.pipeline.objects == None:
#check to see that we don't have too many points
if len(self.pipeline['x']) > 1e5:
goAhead = wx.MessageBox(
'You have %d events in the selected ROI;\nThis could take a LONG time ...'
% len(self.pipeline['x']),
'Continue with blob detection',
wx.YES_NO | wx.ICON_EXCLAMATION)
if not goAhead == wx.YES:
return
self.glCanvas.setBlobs(*self.pipeline.getBlobs())
self.objCInd = self.glCanvas.c
self.displayPane.hlCLim.SetData(self.glCanvas.c, self.glCanvas.clim[0],
self.glCanvas.clim[1])
if not self.colp == None and self.colp.IsShown():
self.colp.refresh()
#self.sh.shell.user_ns.update(self.__dict__)
wx.EndBusyCursor()