def initXRaySimulator():
########################
# Set up the beam
print("Set up the beam")
gvxr.setSourcePosition(
distance_source_detector_in_m - distance_object_detector_in_m, 0.0,
0.0, "mm")
gvxr.usePointSource()
gvxr.useParallelBeam()
for energy, percentage in energy_spectrum_in_keV:
gvxr.addEnergyBinToSpectrum(energy, "keV", percentage)
# Set up the detector
print("Set up the detector")
gvxr.setDetectorPosition(-distance_object_detector_in_m, 0.0, 0.0, "m")
gvxr.setDetectorUpVector(0, 1, 0)
gvxr.setDetectorNumberOfPixels(detector_width_in_pixels,
detector_height_in_pixels)
gvxr.setDetectorPixelSize(pixel_size_in_micrometer,
pixel_size_in_micrometer, "micrometer")
global angular_step
angular_step = angular_span_in_degrees / number_of_projections
print("Number of projections: ", str(number_of_projections))
print("angular_span_in_degrees: ", str(angular_span_in_degrees))
print("angular_step: ", str(angular_step))
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)
# 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.usePointSource();
#gvxr.useParallelBeam();
gvxr.setMonoChromatic(0.08, "MeV", 1000);
# Set up the detector
print("Set up the detector");
gvxr.setDetectorUpVector(0, 0, -1);
gvxr.setDetectorNumberOfPixels(1024, 1536);
gvxr.setDetectorPixelSize(0.5, 0.5, "mm");
setXRayParameters(ground_truth_SOD, ground_truth_SDD);
# Load the data
print("Load the data");
gvxr.loadSceneGraph("/home/ti/Documents/gvxr-python3-gui/hand.dae", "m");
gvxr.moveToCentre('root');
gvxr.disableArtefactFiltering();
# Compute groud truth x-ray image
ground_truth_image = poserior_anterior(ground_truth_angles);
plt.imsave("ground-truth.png", ground_truth_image);
# Compute optimisation
image = random_search();
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)
min_corner[2] + (max_corner[2] - min_corner[2]) / 2.0
]
# Set up the beam
print("Set up the beam")
gvxr.setSourcePosition(centre[0], centre[1], centre[2] - 10.0, "cm")
gvxr.usePointSource()
#gvxr.useParallelBeam();
gvxr.setMonoChromatic(0.08, "MeV", 1000)
# Set up the detector
print("Set up the detector")
gvxr.setDetectorPosition(centre[0], centre[1], centre[2] + 10.0, "cm")
gvxr.setDetectorUpVector(0, -1, 0)
gvxr.setDetectorNumberOfPixels(640, 320)
gvxr.setDetectorPixelSize(0.125, 0.125, "mm")
# Compute an X-ray image
print("Compute an X-ray image")
gvxr.disableArtefactFiltering()
# Not working anymore gvxr.enableArtefactFilteringOnGPU();
# Not working anymore gvxr.enableArtefactFilteringOnCPU();
x_ray_image = gvxr.computeXRayImage()
# Save the last image into a file
print("Save the last image into a file")
gvxr.saveLastXRayImage()
gvxr.saveLastLBuffer()
# Display the image with Matplotlib
if use_matplotlib: