def __init__(self):
self._imageTransform = None
self._stencil = None
self._voiExtent = None
self._voiPolyData = None
# create a statistics object
self._imageStats = _MicroView.vtkImageStatistics()
self._imageStats.SetProgressText("Calculating image stats...")
self._imageStats.AddObserver(
'ProgressEvent', self.HandleVTKProgressEvent)
# parameters to be calculated
self._meanValue = None
self._stdDeviation = None
self._total = None
self._voxelCount = None
self._histogram = None
self._threshold = None
self._binSize = 1
def __init__(self):
self._imageTransform = None
self._stencil = None
self._voiExtent = None
self._voiPolyData = None
# create a statistics object
self._imageStats = _MicroView.vtkImageStatistics()
self._imageStats.SetProgressText("Calculating image stats...")
self._imageStats.AddObserver('ProgressEvent',
self.HandleVTKProgressEvent)
# parameters to be calculated
self._meanValue = None
self._stdDeviation = None
self._total = None
self._voxelCount = None
self._histogram = None
self._threshold = None
self._binSize = 1
def BMDAnalysis(self):
with wx.BusyCursor():
state = self._app_states[self._current_image_index]
imageStats2 = _MicroView.vtkImageStatistics()
imageStats2.SetInputConnection(
component.getUtility(ICurrentImage).GetOutputPort())
# VTK-6
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
imageStats2.SetStencilData(self.__stencil_data)
else:
imageStats2.SetStencil(self.__stencil_data)
imageStats2.SetWaterValue(float(state.WaterADU))
imageStats2.SetBoneValue(int(state.BoneADU))
imageStats2.SetLowerExclusionValue(int(state.LowerExclusion))
imageStats2.SetUpperExclusionValue(int(state.UpperExclusion))
imageStats2.SetBVFThreshold(float(state.threshold))
imageStats2.SetProgressText('BMD Analysis...')
imageStats2.AddObserver('ProgressEvent',
self.HandleVTKProgressEvent)
imageStats2.Update()
# Mean and Standard Deviation
self.Mean = imageStats2.GetMean()[0]
self.StdDev = imageStats2.GetStandardDeviation()[0]
# self.MeanResultLabel.configure(text="%0.2f" % self.Mean)
# self.StdDevResultLabel.configure(text="%0.2f" % self.StdDev)
# BMD
self.BMD = imageStats2.GetBMD()
self.BMC = imageStats2.GetBoneMass()
self.Volume = imageStats2.GetVolume() * 1000.0 # we use mm^3 here
self.Voxels = imageStats2.GetVoxelCount()
self.ThresholdedBMD = imageStats2.GetThresholdedBMD()
self.ThresholdedBMC = imageStats2.GetThresholdedBoneMass()
# BVF
self.BVF = 0.0
try:
self.BVF = imageStats2.GetBoneVoxelCount() / float(
imageStats2.GetVoxelCount())
except:
pass
del imageStats2
out = StringIO.StringIO()
out.write("\n==============\n")
out.write("= BMD Analysis\n")
out.write("==============\n")
out.write(" Mean: %10.4f\n" % (self.Mean, ))
out.write(" Standard Deviation: %10.4f\n" % (self.StdDev, ))
out.write(" Total Volume: %10.4f (mm^3)\n" % (self.Volume, ))
out.write(" Bone Volume: %10.4f (mm^3)\n" %
(self.Volume * self.BVF, ))
out.write(" Voxel: %d\n" % self.Voxels)
if int(state.BoneADU) == 0:
out.write(
" Bone mineral content (mg): Error, No BoneHU for image.\n"
)
out.write(" BMD (mg/cc): Error, No BoneHU for image.\n")
out.write(
" Tissue mineral density (mg/cc): Error, No BoneHU for image.\n"
)
else:
out.write(" Bone mineral content (mg): %10.4f\n" % (self.BMC))
out.write(" BMD (mg/cc): %10.4f\n" % (self.BMD))
out.write(" Tissue mineral content (mg): %10.4f\n" %
(self.ThresholdedBMC))
out.write(" Tissue mineral density (mg/cc): %10.4f\n" %
(self.ThresholdedBMD))
out.write(" BVF: %10.4f\n" % self.BVF)
out.write('\n')
self._BMDOutStr = out.getvalue()
out.close()
self._ResultsDict['BMDMean'] = self.Mean
self._ResultsDict['BMDStdDev'] = self.StdDev
self._ResultsDict['BMDVolume'] = self.Volume
self._ResultsDict['BMDBoneVolume'] = self.Volume * self.BVF
self._ResultsDict['BMDVoxels'] = self.Voxels
self._ResultsDict['BMDBVF'] = self.BVF
if int(state.BoneADU) > 0:
self._ResultsDict['BMDBMC'] = self.BMC
self._ResultsDict['BMDBMD'] = self.BMD
self._ResultsDict['BMDTMC'] = self.ThresholdedBMC
self._ResultsDict['BMDTMD'] = self.ThresholdedBMD
event.notify(ProgressEvent("BMD Analysis... Done.", 1.0))
# return status
return 0
def BMDAnalysis(self):
with wx.BusyCursor():
state = self._app_states[self._current_image_index]
imageStats2 = _MicroView.vtkImageStatistics()
imageStats2.SetInputConnection(component.getUtility(
ICurrentImage).GetOutputPort())
# VTK-6
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
imageStats2.SetStencilData(self.__stencil_data)
else:
imageStats2.SetStencil(self.__stencil_data)
imageStats2.SetWaterValue(float(state.WaterADU))
imageStats2.SetBoneValue(int(state.BoneADU))
imageStats2.SetLowerExclusionValue(int(state.LowerExclusion))
imageStats2.SetUpperExclusionValue(int(state.UpperExclusion))
imageStats2.SetBVFThreshold(float(state.threshold))
imageStats2.SetProgressText('BMD Analysis...')
imageStats2.AddObserver(
'ProgressEvent', self.HandleVTKProgressEvent)
imageStats2.Update()
# Mean and Standard Deviation
self.Mean = imageStats2.GetMean()[0]
self.StdDev = imageStats2.GetStandardDeviation()[0]
# self.MeanResultLabel.configure(text="%0.2f" % self.Mean)
# self.StdDevResultLabel.configure(text="%0.2f" % self.StdDev)
# BMD
self.BMD = imageStats2.GetBMD()
self.BMC = imageStats2.GetBoneMass()
self.Volume = imageStats2.GetVolume() * 1000.0 # we use mm^3 here
self.Voxels = imageStats2.GetVoxelCount()
self.ThresholdedBMD = imageStats2.GetThresholdedBMD()
self.ThresholdedBMC = imageStats2.GetThresholdedBoneMass()
# BVF
self.BVF = 0.0
try:
self.BVF = imageStats2.GetBoneVoxelCount() / float(
imageStats2.GetVoxelCount())
except:
pass
del imageStats2
out = StringIO.StringIO()
out.write("\n==============\n")
out.write("= BMD Analysis\n")
out.write("==============\n")
out.write(" Mean: %10.4f\n" % (self.Mean,))
out.write(" Standard Deviation: %10.4f\n" % (self.StdDev,))
out.write(" Total Volume: %10.4f (mm^3)\n" % (self.Volume,))
out.write(" Bone Volume: %10.4f (mm^3)\n" % (
self.Volume * self.BVF,))
out.write(" Voxel: %d\n" % self.Voxels)
if int(state.BoneADU) == 0:
out.write(
" Bone mineral content (mg): Error, No BoneHU for image.\n")
out.write(" BMD (mg/cc): Error, No BoneHU for image.\n")
out.write(
" Tissue mineral density (mg/cc): Error, No BoneHU for image.\n")
else:
out.write(" Bone mineral content (mg): %10.4f\n" % (
self.BMC))
out.write(" BMD (mg/cc): %10.4f\n" % (self.BMD))
out.write(" Tissue mineral content (mg): %10.4f\n" % (
self.ThresholdedBMC))
out.write(" Tissue mineral density (mg/cc): %10.4f\n" % (
self.ThresholdedBMD))
out.write(" BVF: %10.4f\n" % self.BVF)
out.write('\n')
self._BMDOutStr = out.getvalue()
out.close()
self._ResultsDict['BMDMean'] = self.Mean
self._ResultsDict['BMDStdDev'] = self.StdDev
self._ResultsDict['BMDVolume'] = self.Volume
self._ResultsDict['BMDBoneVolume'] = self.Volume * self.BVF
self._ResultsDict['BMDVoxels'] = self.Voxels
self._ResultsDict['BMDBVF'] = self.BVF
if int(state.BoneADU) > 0:
self._ResultsDict['BMDBMC'] = self.BMC
self._ResultsDict['BMDBMD'] = self.BMD
self._ResultsDict['BMDTMC'] = self.ThresholdedBMC
self._ResultsDict['BMDTMD'] = self.ThresholdedBMD
event.notify(ProgressEvent("BMD Analysis... Done.", 1.0))
# return status
return 0