def get_resampled_stack(self,
resampling_grid=None,
spacing=None,
interpolator="Linear",
default_pixel_value=0.0,
filename=None):
if (resampling_grid is None and spacing is None) or \
(resampling_grid is not None and spacing is not None):
raise IOError(
"Either 'resampling_grid' or 'spacing' must be specified")
# Get SimpleITK-interpolator
try:
interpolator_str = interpolator
interpolator = eval("sitk.sitk" + interpolator_str)
except:
raise ValueError("Error: interpolator is not known. "
"Must fit sitk.InterpolatorEnum format. "
"Possible examples include "
"'NearestNeighbor', 'Linear', or 'BSpline'.")
if resampling_grid is not None:
resampled_stack_sitk = sitk.Resample(self.sitk, resampling_grid,
sitk.Euler3DTransform(),
interpolator,
default_pixel_value,
self.sitk.GetPixelIDValue())
resampled_stack_sitk_mask = sitk.Resample(
self.sitk_mask, resampling_grid, sitk.Euler3DTransform(),
sitk.sitkNearestNeighbor, 0, self.sitk_mask.GetPixelIDValue())
else:
resampler = simplereg.resampler.Resampler
resampled_stack_sitk = resampler.get_resampled_image_sitk(
image_sitk=self.sitk,
spacing=spacing,
interpolator=interpolator,
padding=default_pixel_value,
add_to_grid_unit="mm",
)
resampled_stack_sitk_mask = resampler.get_resampled_image_sitk(
image_sitk=self.sitk_mask,
spacing=spacing,
interpolator=sitk.sitkNearestNeighbor,
padding=0,
add_to_grid_unit="mm",
)
# Create Stack instance
if filename is None:
filename = self._filename + "_" + interpolator_str
stack = self.from_sitk_image(
image_sitk=resampled_stack_sitk,
slice_thickness=resampled_stack_sitk.GetSpacing()[-1],
filename=filename,
image_sitk_mask=resampled_stack_sitk_mask,
)
return stack
def get_isotropically_resampled_stack(self,
resolution=None,
interpolator="Linear",
extra_frame=0,
filename=None,
mask_dilation_radius=0,
mask_dilation_kernel="Ball"):
# Choose interpolator
try:
interpolator_str = interpolator
interpolator = eval("sitk.sitk" + interpolator_str)
except:
raise ValueError("Error: interpolator is not known")
if resolution is None:
spacing = self.sitk.GetSpacing()[0]
else:
spacing = resolution
# Resample image and its mask to isotropic grid
resampler = simplereg.resampler.Resampler
isotropic_resampled_stack_sitk = resampler.get_resampled_image_sitk(
image_sitk=self.sitk,
spacing=spacing,
interpolator=interpolator,
padding=0.0,
add_to_grid=extra_frame,
add_to_grid_unit="mm",
)
isotropic_resampled_stack_sitk_mask = resampler.get_resampled_image_sitk(
image_sitk=self.sitk_mask,
spacing=spacing,
interpolator=sitk.sitkNearestNeighbor,
padding=0,
add_to_grid=extra_frame,
add_to_grid_unit="mm",
)
if mask_dilation_radius > 0:
dilater = sitk.BinaryDilateImageFilter()
dilater.SetKernelType(eval("sitk.sitk" + mask_dilation_kernel))
dilater.SetKernelRadius(mask_dilation_radius)
isotropic_resampled_stack_sitk_mask = dilater.Execute(
isotropic_resampled_stack_sitk_mask)
# Create Stack instance
if filename is None:
filename = self._filename + "_" + interpolator_str + "Iso"
stack = self.from_sitk_image(
image_sitk=isotropic_resampled_stack_sitk,
filename=filename,
slice_thickness=isotropic_resampled_stack_sitk.GetSpacing()[-1],
image_sitk_mask=isotropic_resampled_stack_sitk_mask,
)
return stack