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# This is a CamiTK python action
#
# Use registered (existing) SDK actions in a pipeline to
# - binarize the image using a threshold
# - reconstruct a mesh from the binary image
# - show the mesh projection in the image
# all in one go
import camitk
def init(self:camitk.Action):
self.mesh = None
return
def process(self:camitk.Action):
# get the current target
image = self.getTargets()[-1]
# get current threshold from the GUI and set the threshold property of the threshold action
currentThreshold = self.getParameterValue("Threshold")
self.thresholdAction.setParameterValue("Low Threshold", currentThreshold)
#-- 1. compute the threshold image (binary image)
self.thresholdImage = camitk.Application.applyAction("Threshold (VTK)", image)
#--2. chain this into a pipeline to obtain the reconstruction
# setup reconstruction action parameter (can also)
reconstructionAction = camitk.Application.getAction("Reconstruction")
reconstructionAction.setParameterValue("Subsample original image?", True)
self.mesh = camitk.Application.applyAction("Reconstruction", self.thresholdImage)
# Rename the output and change
self.mesh.setName(image.getName() + " mesh")
self.mesh.setColor([0.66, 0.33, 1.0, 0.3]) # you don't have to add an alpha
#--3. some cleanup: close the intermediary component (force closing = True,
# which closes the component even if it is set as modified)
if self.getParameterValue("Close Intermediate Images"):
camitk.Application.close(self.thresholdImage, True)
#--4. show the mesh projection
meshProjectionAction = camitk.Application.getAction("Mesh Projection")
# setup default mesh projection parameters
meshProjectionAction.setParameterValue("ImageComponent List", 0) # assume there the first image component is the correct one
meshProjectionAction.setParameterValue("Contour Line Width", 3)
camitk.Application.applyAction("Mesh Projection", self.mesh)
# Set the visibility boolean once everything is setup
# (this is specific to the "Mesh Projection" action logic, which requires this parameter to be set
# only after the action is applied)
meshProjectionAction.setParameterValue("Show Mesh Projection", True)
self.refreshApplication()
return True
def targetDefined(self:camitk.Action):
image = self.getTargets()[-1]
self.thresholdAction = camitk.Application.getAction("Threshold (VTK)")
# uncomment to check that the threshold action is loaded and available
# assert self.thresholdAction is not None, f"Cannot find the 'Threshold (VTK)' action. Please check your configuration"
# let the threshold action compute the low threshold value (the action computes (max-min)/2)
# from the voxels values and use it to update the GUI
self.thresholdAction.setInputComponent(image)
adjustedThreshold = self.thresholdAction.getParameterValue("Low Threshold")
self.setParameterValue("Threshold", adjustedThreshold)
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