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