def addCylinder(x, y, i):
#print (i, x, y)
fibre_label = "fibre" + str(i)
core_label = "core" + str(i)
gvxr.makeCylinder(fibre_label, 50, 815, fiber_radius, "micrometer")
gvxr.makeCylinder(core_label, 50, 815, core_radius, "micrometer")
gvxr.setLocalTransformationMatrix(
fibre_label, [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1])
gvxr.setLocalTransformationMatrix(
core_label, [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1])
gvxr.translateNode(fibre_label, y, 0, x, "micrometer")
gvxr.translateNode(core_label, y, 0, x, "micrometer")
gvxr.applyCurrentLocalTransformation(fibre_label)
gvxr.applyCurrentLocalTransformation(core_label)
# Fiber
gvxr.setCompound(fibre_label, fiber_material)
gvxr.setDensity(fibre_label, fiber_density, "g.cm-3")
gvxr.setLinearAttenuationCoefficient(fibre_label, fiber_mu, "cm-1")
# Core
gvxr.setElement(core_label, core_material)
gvxr.setLinearAttenuationCoefficient(core_label, core_mu, "cm-1")
gvxr.addMesh("fiber_geometry", fibre_label)
gvxr.addMesh("core_geometry", core_label)
def setCylinders(apGeneSet):
gvxr.removePolygonMeshesFromXRayRenderer()
gvxr.removePolygonMeshesFromSceneGraph()
number_of_cylinders = round(len(apGeneSet) / 2)
gvxr.emptyMesh("fiber_geometry", "root")
gvxr.emptyMesh("core_geometry", "root")
for i in range(number_of_cylinders):
x = g_matrix_x + (apGeneSet[i * 2 + 0] - 0.5) * max(
g_matrix_width, g_matrix_height) * 1.25
y = g_matrix_y + (apGeneSet[i * 2 + 1] - 0.5) * max(
g_matrix_width, g_matrix_height) * 1.25
# There is no activation_set, use all the individuals
if type(activation_set) == type(None):
#print(i+1, '/', number_of_cylinders, [apGeneSet[i * 2 + 0], apGeneSet[i * 2 + 1]])
addCylinder(x, y, i)
# There is an activation_set
else:
# Only use the active individuals
if activation_set[i] == True:
addCylinder(x, y, i)
else:
print('\t', i, " is deactivated ")
# Matrix
resetMatrix()
#gvxr.subtractMesh("Matrix", "fiber_geometry")
gvxr.setMixture("Matrix", matrix_material)
gvxr.setDensity("Matrix", matrix_density, "g.cm-3")
gvxr.saveSTLfile("Matrix")
gvxr.setLinearAttenuationCoefficient("Matrix", matrix_mu, "cm-1")
# Fiber
#gvxr.subtractMesh("fiber_geometry", "core_geometry")
gvxr.setCompound("fiber_geometry", fiber_material)
gvxr.setDensity("fiber_geometry", fiber_density, "g.cm-3")
gvxr.setLinearAttenuationCoefficient("fiber_geometry", fiber_mu, "cm-1")
# Core
gvxr.setElement("core_geometry", core_material)
gvxr.setLinearAttenuationCoefficient("core_geometry", core_mu, "cm-1")
#gvxr.addPolygonMeshAsOuterSurface("Matrix");
#gvxr.addPolygonMeshAsOuterSurface("fiber_geometry");
#gvxr.addPolygonMeshAsInnerSurface("fiber_geometry");
gvxr.addPolygonMeshAsInnerSurface("core_geometry")
def OnDoubleClick(self, event):
self.OnSingleClick(event)
text = self.tree.item(self.selected_item,"text");
if text == "root":
print ("Ignore root")
elif text == "":
print ("Ignore empty name")
else:
print("you clicked on ", text)
material_selection = MaterialSelection.MaterialSelection(self.root, text, gvxr.getMaterialLabel(text), gvxr.getDensity(text));
child_children = gvxr.getNumberOfChildren(text);
if material_selection.cancel == False:
global x_ray_image;
# Element
if material_selection.materialType.get() == 0:
gvxr.setElement(text, material_selection.element_name.get());
gvxr.setDensity(text, float(material_selection.density.get()), "g/cm3");
# Mixture
elif material_selection.materialType.get() == 1:
gvxr.setMixture(text, material_selection.mixture.get());
gvxr.setDensity(text, float(material_selection.density.get()), "g/cm3");
# Compound
elif material_selection.materialType.get() == 2:
gvxr.setCompound(text, material_selection.compound.get());
gvxr.setDensity(text, float(material_selection.density.get()), "g/cm3");
# Hounsfield unit
elif material_selection.materialType.get() == 3:
gvxr.setHU(text, material_selection.hounsfield_value.get());
# Mass attenuation coefficient
elif material_selection.materialType.get() == 4:
gvxr.setDensity(text, float(material_selection.density.get()), "g/cm3");
print("?");
# Linear attenuation coefficient
elif material_selection.materialType.get() == 5:
gvxr.setDensity(text, float(material_selection.density.get()), "g/cm3");
print("?");
self.tree.item(self.selected_item, values=(str(child_children), gvxr.getMaterialLabel(text), str(gvxr.getDensity(text))))
x_ray_image = gvxr.computeXRayImage();
gvxr.displayScene()
self.xray_vis.draw(x_ray_image);
def setXRayEnvironment():
gvxr.createWindow()
gvxr.setWindowSize(512, 512)
#gvxr.usePointSource();
gvxr.setMonoChromatic(80, "keV", 1000)
gvxr.setDetectorUpVector(0, 0, -1)
gvxr.setDetectorNumberOfPixels(768, 1024)
gvxr.setDetectorPixelSize(0.5, 0.5, "mm")
# 5 dpi
setXRayParameters(10.0, 100.0)
gvxr.loadSceneGraph("./hand.dae", "m")
node_label_set = []
node_label_set.append('root')
# The list is not empty
while (len(node_label_set)):
# Get the last node
last_node = node_label_set[-1]
# Initialise the material properties
# print("Set ", label, "'s Hounsfield unit");
# gvxr.setHU(label, 1000)
Z = gvxr.getElementAtomicNumber("H")
gvxr.setElement(last_node, gvxr.getElementName(Z))
# Change the node colour to a random colour
gvxr.setColour(last_node, random.uniform(0, 1), random.uniform(0, 1),
random.uniform(0, 1), 1.0)
# Remove it from the list
node_label_set.pop()
# Add its Children
for i in range(gvxr.getNumberOfChildren(last_node)):
node_label_set.append(gvxr.getChildLabel(last_node, i))
gvxr.moveToCentre('root')
gvxr.disableArtefactFiltering()
gvxr.rotateNode('root', -90, 1, 0, 0)
def createTarget():
global target
target_SOD = 100
target_SDD = 140
target_angles_pa = [
0, 20, 0, -10, 0, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]
target = []
target.append(target_SOD)
target.append(target_SDD)
for i in range(len(target_angles_pa)):
target.append(target_angles_pa[i])
gvxr.createWindow()
gvxr.setWindowSize(512, 512)
#gvxr.usePointSource();
gvxr.setMonoChromatic(80, "keV", 1000)
gvxr.setDetectorUpVector(0, 0, -1)
gvxr.setDetectorNumberOfPixels(1536, 1536)
gvxr.setDetectorPixelSize(0.5, 0.5, "mm")
# 5 dpi
setXRayParameters(target_SOD, target_SDD)
gvxr.loadSceneGraph("./hand.dae", "m")
node_label_set = []
node_label_set.append('root')
# The list is not empty
while (len(node_label_set)):
# Get the last node
last_node = node_label_set[-1]
# Initialise the material properties
# print("Set ", label, "'s Hounsfield unit");
# gvxr.setHU(label, 1000)
Z = gvxr.getElementAtomicNumber("H")
gvxr.setElement(last_node, gvxr.getElementName(Z))
# Change the node colour to a random colour
gvxr.setColour(last_node, random.uniform(0, 1), random.uniform(0, 1),
random.uniform(0, 1), 1.0)
# Remove it from the list
node_label_set.pop()
# Add its Children
for i in range(gvxr.getNumberOfChildren(last_node)):
node_label_set.append(gvxr.getChildLabel(last_node, i))
gvxr.moveToCentre('root')
gvxr.disableArtefactFiltering()
target_image = bone_rotation(target_angles_pa)
plt.imsave("./posterior-anterior/RMSE/target.png",
target_image,
cmap='Greys_r')
return target_image, target
def main(argv):
global x_ray_image
parser = argparse.ArgumentParser()
parser.add_argument(
"-input",
type=str,
help=
"Input file (see http://assimp.sourceforge.net/main_features_formats.html for a list of supported file formats)"
)
parser.add_argument(
"-unit",
type=str,
help="Unit of length corresponding to the input",
choices=["um", "mm", "cm", "dm", "m", "dam", "hm", "km"])
args = parser.parse_args()
if args.input and args.unit:
# Create an OpenGL context
print("Create an OpenGL context")
gvxr.createWindow()
gvxr.setWindowSize(512, 512)
# Set up the beam
print("Set up the beam")
gvxr.setSourcePosition(100.0, 0.0, 0.0, "cm")
gvxr.usePointSource()
#gvxr.useParallelBeam();
gvxr.setMonoChromatic(0.08, "MeV", 1)
# Set up the detector
print("Set up the detector")
gvxr.setDetectorPosition(-40.0, 0.0, 0.0, "cm")
gvxr.setDetectorUpVector(0, 0, -1)
gvxr.setDetectorNumberOfPixels(1024, 1024)
gvxr.setDetectorPixelSize(0.5, 0.5, "mm")
# Load the data
print("Load the data")
gvxr.loadSceneGraph(args.input, args.unit)
gvxr.disableArtefactFiltering()
#gvxr.loadMeshFile("chest", "./HVPTest/chest2.obj", "mm");
#gvxr.invertNormalVectors("armR");
#gvxr.invertNormalVectors("chest");
node_label_set = []
node_label_set.append('root')
# The list is not empty
while (len(node_label_set)):
# Get the last node
last_node = node_label_set[-1]
# Initialise the material properties
#print("Set ", label, "'s Hounsfield unit");
#gvxr.setHU(label, 1000)
Z = gvxr.getElementAtomicNumber("H")
gvxr.setElement(last_node, gvxr.getElementName(Z))
# Change the node colour to a random colour
gvxr.setColour(last_node, random.uniform(0, 1),
random.uniform(0, 1), random.uniform(0, 1), 1.0)
# Remove it from the list
node_label_set.pop()
# Add its Children
for i in range(gvxr.getNumberOfChildren(last_node)):
node_label_set.append(gvxr.getChildLabel(last_node, i))
'''
for label in gvxr.getMeshLabelSet():
print("Move ", label, " to the centre");
#gvxr.moveToCentre(label);
#print("Move the mesh to the center");
#gvxr.moveToCenter(label);
#gvxr.invertNormalVectors(label);
'''
#gvxr.moveToCentre();
gvxr.moveToCentre('root')
# Compute an X-ray image
#print("Compute an X-ray image");
#gvxr.disableArtefactFiltering();
#gvxr.enableArtefactFilteringOnGPU();
# Not working anymore gvxr.enableArtefactFilteringOnGPU();
# Not working anymore gvxr.enableArtefactFilteringOnCPU();
x_ray_image = np.array(gvxr.computeXRayImage())
'''x_ray_image -= 0.0799;
x_ray_image /= 0.08 - 0.0799;
plt.ioff();
plt.imshow(x_ray_image, cmap="gray");
plt.show()
'''
#gvxr.setShiftFilter(-0.0786232874);
#gvxr.setScaleFilter(726.368958);
gvxr.displayScene()
app = App.App(0.08)
def poserior_anterior(angles):
node_label_set = []
node_label_set.append('root')
# The list is not empty
while (len(node_label_set)):
# Get the last node
node = node_label_set[-1]
# Initialise the material properties
Z = gvxr.getElementAtomicNumber("H")
gvxr.setElement(node, gvxr.getElementName(Z))
# Change the node colour to a random colour
gvxr.setColour(node, random.uniform(0, 1), random.uniform(0, 1),
random.uniform(0, 1), 1.0)
# Remove it from the list
node_label_set.pop()
# Add its Children
for i in range(gvxr.getNumberOfChildren(node)):
node_label_set.append(gvxr.getChildLabel(node, i))
if node == 'root':
gvxr.rotateNode(node, angles[0], 1, 0, 0)
gvxr.rotateNode(node, angles[1], 0, 1, 0)
if node == 'node-Thu_Meta':
gvxr.rotateNode(node, angles[2], 1, 0, 0)
gvxr.rotateNode(node, angles[3], 0, 1, 0)
if node == 'node-Thu_Prox':
gvxr.rotateNode(node, angles[4], 1, 0, 0)
gvxr.rotateNode(node, angles[5], 0, 1, 0)
if node == 'node-Thu_Dist':
gvxr.rotateNode(node, angles[6], 1, 0, 0)
gvxr.rotateNode(node, angles[7], 0, 1, 0)
if node == 'node-Lit_Meta':
gvxr.rotateNode(node, angles[8], 1, 0, 0)
gvxr.rotateNode(node, angles[9], 0, 1, 0)
if node == 'node-Lit_Prox':
gvxr.rotateNode(node, angles[10], 1, 0, 0)
gvxr.rotateNode(node, angles[11], 0, 1, 0)
if node == 'node-Lit_Midd':
gvxr.rotateNode(node, angles[12], 1, 0, 0)
gvxr.rotateNode(node, angles[13], 0, 1, 0)
if node == 'node-Lit_Dist':
gvxr.rotateNode(node, angles[14], 1, 0, 0)
gvxr.rotateNode(node, angles[15], 0, 1, 0)
if node == 'node-Thi_Meta':
gvxr.rotateNode(node, angles[16], 1, 0, 0)
gvxr.rotateNode(node, angles[17], 0, 1, 0)
if node == 'node-Thi_Prox':
gvxr.rotateNode(node, angles[18], 1, 0, 0)
gvxr.rotateNode(node, angles[19], 0, 1, 0)
if node == 'node-Thi_Midd':
gvxr.rotateNode(node, angles[20], 1, 0, 0)
gvxr.rotateNode(node, angles[21], 0, 1, 0)
if node == 'node-Thi_Dist':
gvxr.rotateNode(node, angles[22], 1, 0, 0)
gvxr.rotateNode(node, angles[23], 0, 1, 0)
if node == 'node-Mid_Meta':
gvxr.rotateNode(node, angles[24], 1, 0, 0)
gvxr.rotateNode(node, angles[25], 0, 1, 0)
if node == 'node-Mid_Prox':
gvxr.rotateNode(node, angles[26], 1, 0, 0)
gvxr.rotateNode(node, angles[27], 0, 1, 0)
if node == 'node-Mid_Midd':
gvxr.rotateNode(node, angles[28], 1, 0, 0)
gvxr.rotateNode(node, angles[29], 0, 1, 0)
if node == 'node-Mid_Dist':
gvxr.rotateNode(node, angles[30], 1, 0, 0)
gvxr.rotateNode(node, angles[31], 0, 1, 0)
if node == 'node-Ind_Meta':
gvxr.rotateNode(node, angles[32], 1, 0, 0)
gvxr.rotateNode(node, angles[33], 0, 1, 0)
if node == 'node-Ind_Prox':
gvxr.rotateNode(node, angles[34], 1, 0, 0)
gvxr.rotateNode(node, angles[35], 0, 1, 0)
if node == 'node-Ind_Midd':
gvxr.rotateNode(node, angles[36], 1, 0, 0)
gvxr.rotateNode(node, angles[37], 0, 1, 0)
if node == 'node-Ind_Dist':
gvxr.rotateNode(node, angles[0], 1, 0, 0)
gvxr.rotateNode(node, angles[0], 0, 1, 0)
x_ray_image = gvxr.computeXRayImage()
image = np.array(x_ray_image)
return image