def _fetchTransformStack( self ): # connect to the database connectString = r"Provider=Microsoft.Jet.OLEDB.4.0;Data Source=" + self._config.databaseFile + ";" try: connection = adodbapi.connect( connectString ) except adodbapi.Error: raise IOError, "Could not open database." # try to figure out reconstruction ID from recontruction name print "NAME: " + self._config.reconstructionName cursor = connection.cursor() cursor.execute( "SELECT id FROM reconstruction WHERE name=?", [ self._config.reconstructionName ] ) row = cursor.fetchone() if row == None: raise IOError, "Reconstruction not found." print "reconstructionID: %i" % row[ 0 ] # build transformStack cursor.execute( "SELECT angle, centerx, centery, tx, ty FROM centeredRigid2DTransform WHERE reconstruction_id=? ORDER BY seq_nr", [ row[ 0 ] ] ) for row in cursor.fetchall(): trfm = itk.itkCenteredRigid2DTransform_New() params = trfm.GetParameters() for i in range(0,5): params.SetElement( i, row[ i ] ) trfm.SetParameters( params ) self._transformStack.append( trfm ) cursor.close() connection.close()
def _fetchTransformStack(self):
# connect to the database
connectString = r"Provider=Microsoft.Jet.OLEDB.4.0;Data Source=" + self._config.databaseFile + ";"
try:
connection = adodbapi.connect(connectString)
except adodbapi.Error:
raise IOError, "Could not open database."
# try to figure out reconstruction ID from recontruction name
print "NAME: " + self._config.reconstructionName
cursor = connection.cursor()
cursor.execute("SELECT id FROM reconstruction WHERE name=?", [self._config.reconstructionName])
row = cursor.fetchone()
if row == None:
raise IOError, "Reconstruction not found."
print "reconstructionID: %i" % row[0]
# build transformStack
cursor.execute(
"SELECT angle, centerx, centery, tx, ty FROM centeredRigid2DTransform WHERE reconstruction_id=? ORDER BY seq_nr",
[row[0]],
)
for row in cursor.fetchall():
trfm = itk.itkCenteredRigid2DTransform_New()
params = trfm.GetParameters()
for i in range(0, 5):
params.SetElement(i, row[i])
trfm.SetParameters(params)
self._transformStack.append(trfm)
cursor.close()
connection.close()
def _createPipelines(self):
"""Setup all necessary logic to transform, combine and convert all
input images.
Call this ONLY if things have changed, i.e. when
your change observer is called or if the transform2D input ports
are changed.
"""
if not self._imageStack or not self._transformStack:
self._destroyPipelines()
# in this case, we should break down the pipeline
return
# take care of all inputs
self._imageAppend.RemoveAllInputs()
#totalTrfm = itk.itkEuler2DTransform_New()
totalTrfm = itk.itkCenteredRigid2DTransform_New()
totalTrfm.SetIdentity()
prevImage = self._imageStack[0]
for trfm, img, i in zip(self._transformStack,
self._imageStack,
range(len(self._imageStack))):
# accumulate with our totalTransform
totalTrfm.Compose(trfm.GetPointer(), 0)
# make a copy of the totalTransform that we can use on
# THIS image
# copyTotalTrfm = itk.itkEuler2DTransform_New()
copyTotalTrfm = itk.itkCenteredRigid2DTransform_New()
# this is a really kludge way to copy the total transform,
# as concatenation doesn't update the Parameters member, so
# getting and setting parameters is not the way to go
copyTotalTrfm.SetIdentity()
copyTotalTrfm.Compose(totalTrfm.GetPointer(),0)
# this SHOULD have worked
#pda = totalTrfm.GetParameters()
#copyTotalTrfm.SetParameters(pda)
# this actually increases the ref count of the transform!
# resampler
resampler = itk.itkResampleImageFilterF2F2_New()
resampler.SetTransform(copyTotalTrfm.GetPointer())
resampler.SetInput(img)
region = prevImage.GetLargestPossibleRegion()
resampler.SetSize(region.GetSize())
resampler.SetOutputSpacing(prevImage.GetSpacing())
resampler.SetOutputOrigin(prevImage.GetOrigin())
resampler.SetDefaultPixelValue(0)
# set up all the
rescaler = itk.itkRescaleIntensityImageFilterF2US2_New()
rescaler.SetOutputMinimum(0)
rescaler.SetOutputMaximum(65535)
rescaler.SetInput(resampler.GetOutput())
print "Resampling image %d" % (i,)
rescaler.Update() # give ITK a chance to complain
itkExporter = itk.itkVTKImageExportUS2_New()
itkExporter.SetInput(rescaler.GetOutput())
# this is so the ref keeps hanging around
self._itkExporterStack.append(itkExporter)
vtkImporter = vtk.vtkImageImport()
CVIPy.ConnectITKUS2ToVTK(itkExporter.GetPointer(),
vtkImporter)
# FIXME KLUDGE: we ignore image 0 (this is for joris)
# if i > 0:
# self._imageAppend.AddInput(vtkImporter.GetOutput())
# setup the previous Image for the next loop
prevImage = img
def _createPipelines(self):
"""Setup all necessary logic to transform, combine and convert all
input images.
Call this ONLY if things have changed, i.e. when
your change observer is called or if the transform2D input ports
are changed.
"""
if not self._imageStack or not self._transformStack:
self._destroyPipelines()
# in this case, we should break down the pipeline
return
# take care of all inputs
self._imageAppend.RemoveAllInputs()
#totalTrfm = itk.itkEuler2DTransform_New()
totalTrfm = itk.itkCenteredRigid2DTransform_New()
totalTrfm.SetIdentity()
prevImage = self._imageStack[0]
for trfm, img, i in zip(self._transformStack, self._imageStack,
range(len(self._imageStack))):
# accumulate with our totalTransform
totalTrfm.Compose(trfm.GetPointer(), 0)
# make a copy of the totalTransform that we can use on
# THIS image
# copyTotalTrfm = itk.itkEuler2DTransform_New()
copyTotalTrfm = itk.itkCenteredRigid2DTransform_New()
# this is a really kludge way to copy the total transform,
# as concatenation doesn't update the Parameters member, so
# getting and setting parameters is not the way to go
copyTotalTrfm.SetIdentity()
copyTotalTrfm.Compose(totalTrfm.GetPointer(), 0)
# this SHOULD have worked
#pda = totalTrfm.GetParameters()
#copyTotalTrfm.SetParameters(pda)
# this actually increases the ref count of the transform!
# resampler
resampler = itk.itkResampleImageFilterF2F2_New()
resampler.SetTransform(copyTotalTrfm.GetPointer())
resampler.SetInput(img)
region = prevImage.GetLargestPossibleRegion()
resampler.SetSize(region.GetSize())
resampler.SetOutputSpacing(prevImage.GetSpacing())
resampler.SetOutputOrigin(prevImage.GetOrigin())
resampler.SetDefaultPixelValue(0)
# set up all the
rescaler = itk.itkRescaleIntensityImageFilterF2US2_New()
rescaler.SetOutputMinimum(0)
rescaler.SetOutputMaximum(65535)
rescaler.SetInput(resampler.GetOutput())
print "Resampling image %d" % (i, )
rescaler.Update() # give ITK a chance to complain
itkExporter = itk.itkVTKImageExportUS2_New()
itkExporter.SetInput(rescaler.GetOutput())
# this is so the ref keeps hanging around
self._itkExporterStack.append(itkExporter)
vtkImporter = vtk.vtkImageImport()
CVIPy.ConnectITKUS2ToVTK(itkExporter.GetPointer(), vtkImporter)
# FIXME KLUDGE: we ignore image 0 (this is for joris)
# if i > 0:
# self._imageAppend.AddInput(vtkImporter.GetOutput())
# setup the previous Image for the next loop
prevImage = img
