def execute_module(self):
# get the vtkDICOMVolumeReader to try and execute
self._reader.Update()
# now get some metadata out and insert it in our output stream
# first determine axis labels based on IOP ####################
iop = self._reader.GetImageOrientationPatient()
row = iop[0:3]
col = iop[3:6]
# the cross product (plane normal) based on the row and col will
# also be in the LPH coordinate system
norm = [0,0,0]
vtk.vtkMath.Cross(row, col, norm)
xl = misc_utils.major_axis_from_iop_cosine(row)
yl = misc_utils.major_axis_from_iop_cosine(col)
zl = misc_utils.major_axis_from_iop_cosine(norm)
lut = {'L' : 0, 'R' : 1, 'P' : 2, 'A' : 3, 'F' : 4, 'H' : 5}
if xl and yl and zl:
# add this data as a vtkFieldData
fd = self._reader.GetOutput().GetFieldData()
axis_labels_array = vtk.vtkIntArray()
axis_labels_array.SetName('axis_labels_array')
for l in xl + yl + zl:
axis_labels_array.InsertNextValue(lut[l])
fd.AddArray(axis_labels_array)
def execute_module(self):
# get the vtkDICOMVolumeReader to try and execute
self._reader.Update()
# now get some metadata out and insert it in our output stream
# first determine axis labels based on IOP ####################
iop = self._reader.GetImageOrientationPatient()
row = iop[0:3]
col = iop[3:6]
# the cross product (plane normal) based on the row and col will
# also be in the LPH coordinate system
norm = [0, 0, 0]
vtk.vtkMath.Cross(row, col, norm)
xl = misc_utils.major_axis_from_iop_cosine(row)
yl = misc_utils.major_axis_from_iop_cosine(col)
zl = misc_utils.major_axis_from_iop_cosine(norm)
lut = {'L': 0, 'R': 1, 'P': 2, 'A': 3, 'F': 4, 'H': 5}
if xl and yl and zl:
# add this data as a vtkFieldData
fd = self._reader.GetOutput().GetFieldData()
axis_labels_array = vtk.vtkIntArray()
axis_labels_array.SetName('axis_labels_array')
for l in xl + yl + zl:
axis_labels_array.InsertNextValue(lut[l])
fd.AddArray(axis_labels_array)
def _update_image(self, gdcm_reader):
"""Given a vtkGDCMImageReader instance that has read the given
file, update the image viewer.
"""
r = gdcm_reader
self._image_viewer.SetInput(r.GetOutput())
#if r.GetNumberOfOverlays():
# self._image_viewer.AddInput(r.GetOverlay(0))
# now make the nice text overlay thingies!
# DirectionCosines: first two columns are X and Y in the LPH
# coordinate system
dc = r.GetDirectionCosines()
x_cosine = \
dc.GetElement(0,0), dc.GetElement(1,0), dc.GetElement(2,0)
lph = misc_utils.major_axis_from_iop_cosine(x_cosine)
if lph:
self._image_viewer.xl_text_actor.SetInput(lph[0])
self._image_viewer.xr_text_actor.SetInput(lph[1])
else:
self._image_viewer.xl_text_actor.SetInput('X')
self._image_viewer.xr_text_actor.SetInput('X')
y_cosine = \
dc.GetElement(0,1), dc.GetElement(1,1), dc.GetElement(2,1)
lph = misc_utils.major_axis_from_iop_cosine(y_cosine)
if lph:
if r.GetFileLowerLeft():
# no swap
b = lph[0]
t = lph[1]
else:
# we have to swap these around because VTK has the
# convention of image origin at the upper left and GDCM
# dutifully swaps the images when loading to follow this
# convention. Direction cosines (IOP) is not swapped, so
# we have to compensate here.
b = lph[1]
t = lph[0]
self._image_viewer.yb_text_actor.SetInput(b)
self._image_viewer.yt_text_actor.SetInput(t)
else:
self._image_viewer.yb_text_actor.SetInput('X')
self._image_viewer.yt_text_actor.SetInput('X')
mip = r.GetMedicalImageProperties()
d = r.GetOutput().GetDimensions()
ul = self._image_viewer.ul_text_actor
ul.imsize = (d[0], d[1])
ul.imnum = mip.GetImageNumber() # string
ul.frnum = self._image_viewer.GetSlice()
self._update_image_ul_text()
ur = self._image_viewer.ur_text_actor
ur.SetInput('%s\n%s\n%s\n%s' % (
mip.GetPatientName(),
mip.GetPatientID(),
mip.GetStudyDescription(),
mip.GetSeriesDescription()))
br = self._image_viewer.br_text_actor
br.SetInput('DeVIDE\nTU Delft')
# we have a new image in the image_viewer, so we have to reset
# the camera so that the image is visible.
if not self._config.lock_pz:
self._reset_image_pz()
# also reset window level
if not self._config.lock_wl:
self._reset_image_wl()
self._image_viewer.Render()
def execute_module(self):
# have to cast to normal strings (from unicode)
filenames = [str(i) for i in self._config.dicom_filenames]
# make sure all is zeroed.
self._reader.SetFileName(None)
self._reader.SetFileNames(None)
# we only sort and derive slice-based spacing if there are
# more than 1 filenames
if len(filenames) > 1:
sorter = gdcm.IPPSorter()
sorter.SetComputeZSpacing(True)
sorter.SetZSpacingTolerance(1e-2)
ret = sorter.Sort(filenames)
alpha_sorted = False
if not ret:
if self._config.robust_spacing:
self._module_manager.log_warning(
'Could not sort DICOM filenames by IPP. Doing alphabetical sorting.')
filenames.sort()
alpha_sorted = True
else:
raise RuntimeError(
'Could not sort DICOM filenames before loading.')
if sorter.GetZSpacing() == 0.0 and not alpha_sorted:
msg = 'DICOM IPP sorting yielded incorrect results.'
raise RuntimeError(msg)
# then give the reader the sorted list of files
sa = vtk.vtkStringArray()
if alpha_sorted:
flist = filenames
else:
flist = sorter.GetFilenames()
for fn in flist:
sa.InsertNextValue(fn)
self._reader.SetFileNames(sa)
elif len(filenames) == 1:
self._reader.SetFileName(filenames[0])
else:
raise RuntimeError(
'No DICOM filenames to read.')
# now do the actual reading
self._reader.Update()
# see what the reader thinks the spacing is
spacing = list(self._reader.GetDataSpacing())
if len(filenames) > 1 and not alpha_sorted:
# after the reader has done its thing,
# impose derived spacing on the vtkImageChangeInformation
# (by default it takes the SpacingBetweenSlices, which is
# not always correct)
spacing[2] = sorter.GetZSpacing()
# single or multiple filenames, we have to set the correct
# output spacing on the image change information
print "SPACING: ", spacing
self._ici.SetOutputSpacing(spacing)
self._ici.Update()
# integrate DirectionCosines into output data ###############
# DirectionCosines: first two columns are X and Y in the LPH
# coordinate system
dc = self._reader.GetDirectionCosines()
x_cosine = \
dc.GetElement(0,0), dc.GetElement(1,0), dc.GetElement(2,0)
y_cosine = \
dc.GetElement(0,1), dc.GetElement(1,1), dc.GetElement(2,1)
# calculate plane normal (z axis) in LPH coordinate system by taking the cross product
norm = [0,0,0]
vtk.vtkMath.Cross(x_cosine, y_cosine, norm)
xl = misc_utils.major_axis_from_iop_cosine(x_cosine)
yl = misc_utils.major_axis_from_iop_cosine(y_cosine)
# vtkGDCMImageReader swaps the y (to fit the VTK convention),
# but does not flip the DirectionCosines here, so we do that.
# (only if the reader is flipping)
if yl and not self._reader.GetFileLowerLeft():
yl = tuple((yl[1], yl[0]))
zl = misc_utils.major_axis_from_iop_cosine(norm)
lut = {'L' : 0, 'R' : 1, 'P' : 2, 'A' : 3, 'F' : 4, 'H' : 5}
if xl and yl and zl:
# add this data as a vtkFieldData
fd = self._ici.GetOutput().GetFieldData()
axis_labels_array = vtk.vtkIntArray()
axis_labels_array.SetName('axis_labels_array')
for l in xl + yl + zl:
axis_labels_array.InsertNextValue(lut[l])
fd.AddArray(axis_labels_array)
def _update_image(self, gdcm_reader):
"""Given a vtkGDCMImageReader instance that has read the given
file, update the image viewer.
"""
r = gdcm_reader
self._image_viewer.SetInput(r.GetOutput())
#if r.GetNumberOfOverlays():
# self._image_viewer.AddInput(r.GetOverlay(0))
# now make the nice text overlay thingies!
# DirectionCosines: first two columns are X and Y in the LPH
# coordinate system
dc = r.GetDirectionCosines()
x_cosine = \
dc.GetElement(0,0), dc.GetElement(1,0), dc.GetElement(2,0)
lph = misc_utils.major_axis_from_iop_cosine(x_cosine)
if lph:
self._image_viewer.xl_text_actor.SetInput(lph[0])
self._image_viewer.xr_text_actor.SetInput(lph[1])
else:
self._image_viewer.xl_text_actor.SetInput('X')
self._image_viewer.xr_text_actor.SetInput('X')
y_cosine = \
dc.GetElement(0,1), dc.GetElement(1,1), dc.GetElement(2,1)
lph = misc_utils.major_axis_from_iop_cosine(y_cosine)
if lph:
if r.GetFileLowerLeft():
# no swap
b = lph[0]
t = lph[1]
else:
# we have to swap these around because VTK has the
# convention of image origin at the upper left and GDCM
# dutifully swaps the images when loading to follow this
# convention. Direction cosines (IOP) is not swapped, so
# we have to compensate here.
b = lph[1]
t = lph[0]
self._image_viewer.yb_text_actor.SetInput(b)
self._image_viewer.yt_text_actor.SetInput(t)
else:
self._image_viewer.yb_text_actor.SetInput('X')
self._image_viewer.yt_text_actor.SetInput('X')
mip = r.GetMedicalImageProperties()
d = r.GetOutput().GetDimensions()
ul = self._image_viewer.ul_text_actor
ul.imsize = (d[0], d[1])
ul.imnum = mip.GetImageNumber() # string
ul.frnum = self._image_viewer.GetSlice()
self._update_image_ul_text()
ur = self._image_viewer.ur_text_actor
ur.SetInput('%s\n%s\n%s\n%s' %
(mip.GetPatientName(), mip.GetPatientID(),
mip.GetStudyDescription(), mip.GetSeriesDescription()))
br = self._image_viewer.br_text_actor
br.SetInput('DeVIDE\nTU Delft')
# we have a new image in the image_viewer, so we have to reset
# the camera so that the image is visible.
if not self._config.lock_pz:
self._reset_image_pz()
# also reset window level
if not self._config.lock_wl:
self._reset_image_wl()
self._image_viewer.Render()
