Roi from model bounds

[amymmorton]

A start to the subvolume 3d registration testing, implements the roi generation from model bounds

TO DO:
iterate on all Models | load from file

[amymmorton]

@sbelsk You can take this and help iterate on it or make another from scratch

TO DO:

• load stl from file- iterate for all Model nodes
• use CropVolume

   /// Perform non-interpolated (voxel-based) cropping.
   /// If limitToInputExtent is set to true (default) then the extent can only be smaller than the input volume.
   static int CropVoxelBased(vtkMRMLDisplayableNode* roi, vtkMRMLVolumeNode* inputVolume,
      vtkMRMLVolumeNode* outputNode, bool limitToInputExtent=true, double fillValue=0.0); 

and the generated roi to generate subvolumes

[jcfr]

Thanks @amymmorton for creating this PR along side issue #151 describing the overall workflow and providing reference to datasets 🙏

[amymmorton]

@sbelsk can you help me fix my failing precommit, Commit messages please? :(

[jcfr]

pre-commit check

The pre-commit failures have been addressed.

commit message check

The commit message check is failing because some commits start with WIP: prefix, this is described here

Addressing this could be done by using git rebase --interactive 06acebe and then editing the "faulty" commit messages. For example WIP: Initial Extension Setup -> ENH: Initial Extension Setup

[jcfr]

To address the commit message failure, the following commit title would have to be updated:

-ENH:: Crop Volumes generated from roi
+ENH: Crop Volumes generated from roi

[jcfr]

Suggested change

	def modelBounds(self, inputModel):
	inputModel: vtkMRMLModelNode
	tB = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
	inputModel.GetBounds(tB)
	# print(tB)
	# modelC = [0.0]*3
	# modelSize = [0.0]*3
	# strange that the model nodes have a getBounds- but no center and size..
	# and the roi has bno.. set Bounds- just center and size
	# numpy for array operatots:
	tnp_min = np.array([tB[0], tB[2], tB[4]])
	tnp_max = np.array([tB[1], tB[3], tB[5]])
	tnp_C = (tnp_min + tnp_max) / 2
	tnpS = tnp_min - tnp_max
	# inputModel.GetCenter(modelC)
	# inputModel.GetSize(modelSize)
	mname = inputModel.GetName()
	# use tB lims to size roi
	# Create ROI node
	modelROI = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
	modelROI.SetCenter(tnp_C.tolist())
	modelROI.SetSize(tnpS.tolist())
	modelROI.CreateDefaultDisplayNodes() # only needed for display
	roi_name = mname + "_roi"
	modelROI.SetName(roi_name)
	return modelROI
	def createROINodeFromModel(self, inputModel: vtkMRMLModelNode):
	"""
	Create an ROI node from a given model node by computing its axis-aligned bounding box.
	:param inputModel: Model node from which to derive the ROI
	:return: ROI node enclosing the input model
	"""
	# Retrieve the bounding box of the model: [xmin, xmax, ymin, ymax, zmin, zmax]
	modelBounds = [0.0] * 6
	inputModel.GetBounds(modelBounds)
	# Convert the bounding values into min/max coordinate arrays
	modelMin = np.array([modelBounds[0], modelBounds[2], modelBounds[4]])
	modelMax = np.array([modelBounds[1], modelBounds[3], modelBounds[5]])
	# Compute the center and size of the bounding box
	modelCenter = (modelMin + modelMax) / 2.0
	modelSize = modelMax - modelMin
	# Create a new ROI node centered on the model
	roiNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
	roiNode.SetName(f"{inputModel.GetName()}_roi")
	roiNode.SetCenter(modelCenter.tolist())
	roiNode.SetSize(modelSize.tolist())
	roiNode.CreateDefaultDisplayNodes() # Only needed for display
	return roiNode

[amymmorton]

Current functionality:

• stl loaded from folder
• roi generated for each model and cropped volume extracted from roi of input volume

TO DO:

• generate 3d interactive transform for "parent" model - prompt for user alignment
• apply transform to roi - extract subvolume 'target' volume
• use elastix to register
• apply output elastik tform to model (and child model)