examples

examples/example_basics.py

@@ -161,5 +161,3 @@
     mesh.bounding_cylinder.volume,
     mesh.bounding_sphere.volume,
 )
-
-

examples/example_curvature.py

@@ -146,9 +146,11 @@
 )
 angular_error_1 = 180 * angular_error_1 / np.pi
 
+
 #############################################################################
-# VISUALIZATION USING EXTERNAL TOOLS
+# VISUALIZATION USING INTERNAL TOOLS
 #############################################################################
+
 import slam.plot as splt
 
 vertices = mesh.vertices
@@ -161,10 +163,12 @@
                   [0, np.cos(theta), -np.sin(theta)],
                   [0, np.sin(theta),  np.cos(theta)]])
 vertices_translate = np.dot(rot_x, vertices_translate.T).T
-rot_z = np.array([[np.cos(theta), -np.sin(theta),0],
-                  [np.sin(theta),  np.cos(theta),0],
-                  [0, 0, 1],])
+rot_z = np.array([[np.cos(theta), -np.sin(theta), 0],
+                  [np.sin(theta),  np.cos(theta), 0],
+                  [0, 0, 1], ])
 vertices_translate = np.dot(rot_z, vertices_translate.T).T
+
+# Plot Mean Curvature
 display_settings = {}
 display_settings['colorbar_label'] = 'Mean Curvature'
 mesh_data = {}
@@ -174,70 +178,76 @@
 intensity_data = {}
 intensity_data['values'] = mean_curv
 intensity_data["mode"] = "vertex"
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_1.png")
 
+# Plot Gaussian Curvature
 mesh_data['title'] = 'example_mesh.gii Gaussian Curvature'
 intensity_data['values'] = gaussian_curv
 display_settings['colorbar_label'] = 'Gaussian Curvature'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_2.png")
 
+# Plot Shape Index
 mesh_data['title'] = 'example_mesh.gii Shape Index'
 intensity_data['values'] = shapeIndex
 display_settings['colorbar_label'] = 'Shape Index'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_3.png")
 
+# Plot Curvedness
 mesh_data['title'] = 'example_mesh.gii Curvedness'
 intensity_data['values'] = curvedness
 display_settings['colorbar_label'] = 'Curvedness'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_4.png")
 
+# Plot Quadric K Mean Absolute Change
 mesh_data['vertices'] = quadric.vertices
 mesh_data['faces'] = quadric.faces
 mesh_data['title'] = 'Quadric K Mean Absolute Change'
 intensity_data['values'] = k_mean_absolute_change
 display_settings['colorbar_label'] = 'K Mean Absolute Change'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_5.png")
 
+# Plot Quadric Angular Error 0
 mesh_data['title'] = 'Quadric Angular Error 0'
 intensity_data['values'] = angular_error_0
 display_settings['colorbar_label'] = 'Angular Error 0'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
 Fig.write_image("example_curvature_6.png")
 
-mesh_data['title'] = ('Quadric Angular Error 1')
+# Plot Quadric Angular Error 1
+mesh_data['title'] = 'Quadric Angular Error 1'
 intensity_data['values'] = angular_error_1
 display_settings['colorbar_label'] = 'Angular Error 1'
-Fig = splt.mes3d_projection(
+Fig = splt.mesh_projection(
     mesh_data=mesh_data,
     intensity_data=intensity_data,
     display_settings=display_settings)
-#Fig.show()
+# Fig.show()
 Fig.write_image("example_curvature_7.png")

examples/example_differential_geometry.py

@@ -21,7 +21,7 @@
 # importation of slam modules
 import slam.io as sio
 import slam.differential_geometry as sdg
-
+import numpy as np
 ###############################################################################
 # loading an examplar mesh and corresponding texture
 mesh_file = "../examples/data/example_mesh.gii"
@@ -52,37 +52,56 @@
 print(norm_grad)
 
 #############################################################################
-# VISUALIZATION USING EXTERNAL TOOLS
+# VISUALIZATION USING INTERNAL TOOLS
 #############################################################################
-# # import visbrain # visu using visbrain
-# visb_sc = splt.visbrain_plot(
-#     mesh=mesh,
-#     tex=tex.darray[0],
-#     caption="mesh with curvature", cblabel="curvature"
-# )
-# visb_sc.preview()
-# ###############################################################################
-# # show the smoothed mesh
-# visb_sc = splt.visbrain_plot(
-# mesh=s_mesh,
-# caption="smoothed mesh"
-# )
-# visb_sc.preview()
-# ###############################################################################
-# # show the norm of the gradient of the curvature
-# visb_sc = splt.visbrain_plot(
-#     mesh=mesh,
-#     tex=norm_grad,
-#     caption="norm of the gradient of curvature",
-#     cblabel="gradient magnitude",
-# )
-# visb_sc.preview()
-# ###############################################################################
-# # show the depth potential function
-# visb_sc = splt.visbrain_plot(
-#     mesh=mesh,
-#     tex=dpf[0],
-#     caption="depth potential function",
-#     cblabel="dpf"
-# )
-# visb_sc.preview()
+
+import slam.plot as splt
+
+vertices = mesh.vertices
+# center the vertices
+vertices = vertices - np.mean(vertices, axis=0)
+vertices_translate = np.copy(vertices)
+# rotate the vertices
+theta = np.pi / 2
+rot_x = np.array([[1, 0, 0],
+                  [0, np.cos(theta), -np.sin(theta)],
+                  [0, np.sin(theta),  np.cos(theta)]])
+vertices_translate = np.dot(rot_x, vertices_translate.T).T
+rot_z = np.array([[np.cos(theta), -np.sin(theta), 0],
+                  [np.sin(theta),  np.cos(theta), 0],
+                  [0, 0, 1], ])
+vertices_translate = np.dot(rot_z, vertices_translate.T).T
+
+# Plot Original Mesh
+display_settings = {}
+display_settings['colorbar_label'] = 'Curvature'
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = mesh.faces
+mesh_data['title'] = 'example_mesh.gii Mean Curvature'
+intensity_data = {}
+intensity_data['values'] = tex.darray[0]
+intensity_data["mode"] = "vertex"
+Fig = splt.mesh_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+# Fig.show()
+Fig.write_image("example_differential_geometry_1.png")
+
+# Show the Norm of the Gradient of the Curvature
+display_settings = {}
+display_settings['colorbar_label'] = 'Gradient Magnitude'
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = mesh.faces
+mesh_data['title'] = 'example_mesh.gii Norm of the Gradient of Curvature'
+intensity_data = {}
+intensity_data['values'] = norm_grad
+intensity_data["mode"] = "vertex"
+Fig = splt.mesh_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+# Fig.show()
+Fig.write_image("example_differential_geometry_2.png")

examples/example_distortion.py

@@ -52,13 +52,61 @@
 edge_diff = sdst.edge_length_difference(mesh, mesh_s)
 edge_diff
 
+
 #############################################################################
-# VISUALIZATION USING EXTERNAL TOOLS
+# VISUALIZATION USING INTERNAL TOOLS
 #############################################################################
+
+import slam.plot as splt
+
 # # Visualization of the original mesh
-# visb_sc = splt.visbrain_plot(mesh=mesh, caption="original mesh")
-# visb_sc.preview()
+vertices = mesh.vertices
+# center the vertices
+vertices = vertices - np.mean(vertices, axis=0)
+vertices_translate = np.copy(vertices)
+# rotate the vertices
+theta = np.pi / 2
+rot_x = np.array([[1, 0, 0],
+                  [0, np.cos(theta), -np.sin(theta)],
+                  [0, np.sin(theta),  np.cos(theta)]])
+vertices_translate = np.dot(rot_x, vertices_translate.T).T
+rot_z = np.array([[np.cos(theta), -np.sin(theta), 0],
+                  [np.sin(theta),  np.cos(theta), 0],
+                  [0, 0, 1],])
+vertices_translate = np.dot(rot_z, vertices_translate.T).T
+display_settings = {}
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = mesh.faces
+mesh_data['title'] = 'example_mesh.gii Original Mesh'
+intensity_data = None
+Fig = splt.mesh_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+# Fig.show()
+Fig.write_image("example_distortion_1.png")
+
 # ############################################################################
 # # Visualization of the smoothed mesh
-# visb_sc = splt.visbrain_plot(mesh=mesh_s, caption="smoothed mesh")
-# visb_sc.preview()
+
+vertices = mesh_s.vertices
+# center the vertices
+vertices = vertices - np.mean(vertices, axis=0)
+vertices_translate = np.copy(vertices)
+# rotate the vertices
+vertices_translate = np.dot(rot_x, vertices_translate.T).T
+vertices_translate = np.dot(rot_z, vertices_translate.T).T
+
+display_settings = {}
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = mesh_s.faces
+mesh_data['title'] = 'example_mesh.gii Smoothed Mesh'
+intensity_data = None
+Fig = splt.mesh_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+# Fig.show()
+Fig.write_image("example_distortion_2.png")