def onCentrar(self):
volumenCentrar = self.imagenSelector.currentNode()
lm = slicer.app.layoutManager()
origenVolumen = volumenCentrar.GetOrigin()
volumeLogic = slicer.vtkSlicerVolumesLogic()
origenCentro = [0, 0, 0]
volumeLogic.GetVolumeCenteredOrigin(volumenCentrar, origenCentro)
traslacion = [0, 0, 0]
volumenCentrar.SetOrigin(origenCentro)
lm.resetSliceViews()
for i in range(3):
traslacion[i] = origenCentro[i] - origenVolumen[i]
T = slicer.vtkMRMLTransformNode()
I = slicer.vtkMRMLTransformNode()
transmatrix = vtk.vtkMatrix4x4()
transform = vtk.vtkTransform()
T.SetAndObserveTransformToParent(transform)
T.SetName('centrarTransformacionSeeg')
I.SetName('CentrarTInversaSeeg')
transmatrix.DeepCopy((1, 0, 0, traslacion[0], 0, 1, 0, traslacion[1],
0, 0, 1, traslacion[2], 0, 0, 0, 1))
transform.SetMatrix(transmatrix)
inv = transform.GetInverse()
I.SetAndObserveTransformToParent(inv)
slicer.mrmlScene.AddNode(T)
slicer.mrmlScene.AddNode(I)
def build_xml_scene(self, nodeName):
'''
obs - list of slicer objects
file - filepath to write the xml
builds the XML scene of all object in self.SlicerSelectedModelsList
'''
x_scene = Element('scene')
s_scene = slicer.mrmlScene
if slicer.util.getNode(nodeName) is not None:
model = slicer.util.getNode(nodeName)
try:
transform = slicer.util.getNode(model.GetName()+'_trans')
except slicer.util.MRMLNodeNotFoundException:
transform = None
if not transform:
transform = slicer.vtkMRMLTransformNode()
transform.SetName(model.GetName()+'_trans')
s_scene.AddNode(transform)
model.SetAndObserveTransformNodeID(transform.GetID())
xob = SubElement(x_scene, 'b_object')
xob.set('name', model.GetName())
my_matrix = transform.GetMatrixTransformFromParent()
xmlmx = self.matrix_to_xml_element(slicer.util.arrayFromVTKMatrix(my_matrix))
xob.extend([xmlmx])
return x_scene
def generate3DVisualisationNode(self,
polydata,
name,
color=(1, 1, 1),
initial_pos_x=0):
#create Model Node
shape_node = slicer.vtkMRMLModelNode()
shape_node.SetAndObservePolyData(polydata)
shape_node.SetName(name)
#create display node
model_display = slicer.vtkMRMLModelDisplayNode()
model_display.SetColor(color[0], color[1], color[2])
model_display.AutoScalarRangeOff()
model_display.SetScene(slicer.mrmlScene)
model_display.SetName("Display " + name)
#create transform node
transform = vtk.vtkTransform()
transform.Translate(initial_pos_x, 0, 0)
transform_node = slicer.vtkMRMLTransformNode()
transform_node.SetName("Translation " + name)
transform_node.SetAndObserveTransformToParent(transform)
#Add Nodes to Slicer
slicer.mrmlScene.AddNode(transform_node)
slicer.mrmlScene.AddNode(model_display)
slicer.mrmlScene.AddNode(shape_node)
#Link nodes
shape_node.SetAndObserveTransformNodeID(transform_node.GetID())
shape_node.SetAndObserveDisplayNodeID(model_display.GetID())
def CreateNewTransform(self, trial_num, numSamp):
transformNode = slicer.vtkMRMLTransformNode()
slicer.mrmlScene.AddNode(transformNode)
transformNode.CreateDefaultStorageNode()
transform_name = 'Transform_trial_'+str(trial_num)+'_nsamp_'+str(numSamp)
transformNode.SetName(transform_name)
return transformNode
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
slicer.mrmlScene.Clear(0)
self.transformNode1 = slicer.vtkMRMLTransformNode()
self.transformNode1.SetName("Transform 1")
slicer.mrmlScene.AddNode(self.transformNode1)
self.transformNode2 = slicer.vtkMRMLTransformNode()
self.transformNode2.SetName("Transform 2")
slicer.mrmlScene.AddNode(self.transformNode2)
self.transformNode3 = slicer.vtkMRMLTransformNode()
self.transformNode3.SetName("Transform 3")
slicer.mrmlScene.AddNode(self.transformNode3)
self.delayMs = 700
def update_scene(self, xml):
if not self.watching: return
try: #any better ideas??
tree = ET.ElementTree(ET.fromstring(xml))
except:
return
x_scene = tree.getroot()
s_scene = slicer.mrmlScene
#scene = slicer.mrmlScene
for b_ob in x_scene:
#get the name of blender object
name = b_ob.get('name')
xml_mx = b_ob.find('matrix')
try:
slicer_model = slicer.util.getNode(name)
except slicer.util.MRMLNodeNotFoundException:
slicer_model = None
return
#if not slicer_model:
#try to get transform node
try:
transform = slicer.util.getNode(name+'_trans')
except slicer.util.MRMLNodeNotFoundException:
transform = None
if not transform:
transform = slicer.vtkMRMLTransformNode()
transform.SetName(name+'_trans')
s_scene.AddNode(transform)
slicer_model.SetAndObserveTransformNodeID(transform.GetID())
#set the elements of transform form the matrix
#my_matrix = vtk.vtkMatrix4x4()
my_matrix = transform.GetMatrixTransformFromParent()
for i in range(0,4):
for j in range(0,4):
my_matrix.SetElement(i,j,float(xml_mx[i][j].text))
#update object location in scene
transform.SetAndObserveMatrixTransformToParent(my_matrix)
#update color
if b_ob.find("material"):
mat_color = b_ob.find('material')
slicer_model.GetDisplayNode().SetColor(float(mat_color.find('r').text), float(mat_color.find('g').text), float(mat_color.find('b').text))
def onHelloWorldButtonClicked(self):
#find the temp directory
self_dir = os.path.dirname(os.path.abspath(__file__))
tmp_dir = os.path.join(self_dir, "tmp")
print(tmp_dir)
if not os.path.exists(tmp_dir):
print('there is no temporary directory')
print('there needs to be a folder named "tmp"')
print('it should be in same folder with this script')
print('this script is located here')
print(self_dir)
return
scene_file = os.path.join(tmp_dir, "blend_to_slicer.xml")
print(scene_file)
if not os.path.exists(scene_file):
print('NO XML FILE IN THE TEMP DIRECOTRY')
print("Export scene from Blender")
print("it needs to be stored in the following directory")
print(tmp_dir)
return
my_file = open(scene_file)
tree = ET.parse(my_file)
x_scene = tree.getroot()
my_file.close()
s_scene = slicer.mrmlScene
#scene = slicer.mrmlScene
for b_ob in x_scene:
#get the name of blender object
name = b_ob.get('name')
#check if there is the same sicer model in the scene
slicer_model = slicer.util.getNode(name)
if not slicer_model:
ob_file = os.path.join(tmp_dir, name + ".ply")
if os.path.exists(ob_file):
print(name + ' loading model from .ply')
ret = slicer.util.loadModel(ob_file)
if not ret:
print('could not load the ply model')
slicer_model = slicer.util.getNode(name)
if not slicer_model: continue
disp_node = slicer_model.GetDisplayNode()
disp_node.SetSliceIntersectionVisibility(True)
disp_node.SetSliceIntersectionThickness(2)
mat = b_ob.find('material')
if mat is not None:
r, g, b = mat.find('r').text, mat.find(
'g').text, mat.find('b').text
disp_node.SetColor(float(r), float(g), float(b))
else:
continue
else:
print(name + ' model exists in scene already')
xml_mx = b_ob.find('matrix')
#try to get transform node
transform = slicer.util.getNode(name + '_trans')
if not transform:
transform = slicer.vtkMRMLTransformNode()
transform.SetName(name + '_trans')
s_scene.AddNode(transform)
slicer_model.SetAndObserveTransformNodeID(transform.GetID())
#set the elements of transform form the matrix
#my_matrix = vtk.vtkMatrix4x4()
my_matrix = transform.GetMatrixTransformFromParent()
for i in range(0, 4):
for j in range(0, 4):
my_matrix.SetElement(i, j, float(xml_mx[i][j].text))
#update object location in scene
transform.SetAndObserveMatrixTransformToParent(my_matrix)
def do_correctionsClicked(self):
# Copy and paste into Slicer Python interactor
# Drag visible fiducials to deform transform
# Scale defines how large cube will be created
# numPerEdge defines how many fiducials to put on each edge of the cube
size = 0
scalex = 10.0
scaley = 10.0
scalez = 10.0
numPerEdge = size / 10
# Create the FROM fiducial list, and hide it so it doesn't change with mouse interactions
slicer.mrmlScene.AddNode(self.toFids)
self.toFids.Copy(self.fromFids)
self.toFids.SetName('toFids')
self.toFids.GetDisplayNode().SetVisibility(True)
# Create the transform node to hold the deformable transformation later
try:
slicer.mrmlScene.RemoveNode(slicer.util.getNode("TpsTransform"))
tNode = slicer.vtkMRMLTransformNode()
tNode.SetName('TpsTransform')
slicer.mrmlScene.AddNode(tNode)
except:
print("creating new TpsTransform")
tNode = slicer.vtkMRMLTransformNode()
tNode.SetName('TpsTransform')
slicer.mrmlScene.AddNode(tNode)
# Function that will be called whenever a TO fiducial moves and the transform needs an update
def updateTpsTransform(caller, eventid):
numPerEdge = self.fromFids.GetNumberOfFiducials()
if numPerEdge != self.toFids.GetNumberOfFiducials():
print
'Error: Fiducial numbers are not equal!'
return
fp = vtk.vtkPoints()
tp = vtk.vtkPoints()
f = [0, 0, 0]
t = [0, 0, 0]
for i in range(numPerEdge):
self.fromFids.GetNthFiducialPosition(i, f)
self.toFids.GetNthFiducialPosition(i, t)
fp.InsertNextPoint(f)
tp.InsertNextPoint(t)
tps = vtk.vtkThinPlateSplineTransform()
tps.SetSourceLandmarks(fp)
tps.SetTargetLandmarks(tp)
tps.SetBasisToR()
tNode.SetAndObserveTransformToParent(tps)
self.toFids.AddObserver(vtk.vtkCommand.ModifiedEvent,
updateTpsTransform)
# A ROI annotation defines the region where the transform will be visualized
roi = self.inputSelector1.currentNode()
slicer.mrmlScene.AddNode(roi)
roi.SetDisplayVisibility(True)
# Set up transform visualization as gridlines
tNode.CreateDefaultDisplayNodes()
d = tNode.GetDisplayNode()
d.SetAndObserveRegionNode(roi)
d.SetVisualizationMode(
slicer.vtkMRMLTransformDisplayNode.VIS_MODE_GRID)
d.SetVisibility(False)
roi.SetAndObserveTransformNodeID(tNode.GetID())
TransformNode = self.inputSelector4.currentNode()
tNode.SetAndObserveTransformNodeID(TransformNode.GetID())