new examples

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 = {}
@@ -180,6 +184,7 @@
     display_settings=display_settings)
 Fig.show()
 
+# Plot Gaussian Curvature
 mesh_data['title'] = 'example_mesh.gii Gaussian Curvature'
 intensity_data['values'] = gaussian_curv
 display_settings['colorbar_label'] = 'Gaussian Curvature'
@@ -189,6 +194,7 @@
     display_settings=display_settings)
 Fig.show()
 
+# Plot Shape Index
 mesh_data['title'] = 'example_mesh.gii Shape Index'
 intensity_data['values'] = shapeIndex
 display_settings['colorbar_label'] = 'Shape Index'
@@ -198,6 +204,7 @@
     display_settings=display_settings)
 Fig.show()
 
+# Plot Curvedness
 mesh_data['title'] = 'example_mesh.gii Curvedness'
 intensity_data['values'] = curvedness
 display_settings['colorbar_label'] = 'Curvedness'
@@ -207,6 +214,7 @@
     display_settings=display_settings)
 Fig.show()
 
+# Plot Quadric K Mean Absolute Change
 mesh_data['vertices'] = quadric.vertices
 mesh_data['faces'] = quadric.faces
 mesh_data['title'] = 'Quadric K Mean Absolute Change'
@@ -218,6 +226,7 @@
     display_settings=display_settings)
 Fig.show()
 
+# 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'
@@ -227,7 +236,8 @@
     display_settings=display_settings)
 Fig.show()
 
-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(

examples/example_distortion.py

@@ -52,13 +52,65 @@
 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.mes3d_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+Fig.show()
+
 # ############################################################################
 # # 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
+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_s.faces
+mesh_data['title'] = 'example_mesh.gii Smoothed Mesh'
+intensity_data = None
+Fig = splt.mes3d_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+Fig.show()

examples/example_texture.py

@@ -80,6 +80,6 @@
     intensity_data,
     display_settings,
 )
-
+fig.show()
 #os.makedirs(PATH, exist_ok=True)
 #fig.write_image(SAVE_DIR, width=1600, height=900)

examples/example_topology.py

@@ -92,13 +92,81 @@
 print(mesh.is_watertight)
 print(mesh_closed.is_watertight)
 
+
+print('close mesh')
+broken_vertices_mesh_closed = stop.broken_vertices(mesh_closed)
+print(np.count_nonzero(broken_vertices_mesh_closed))
+print('open mesh')
+broken_vertices_open_mesh = stop.broken_vertices(open_mesh)
+print(np.count_nonzero(broken_vertices_open_mesh))
+
 #############################################################################
-# VISUALIZATION USING EXTERNAL TOOLS
+# VISUALIZATION USING INTERNAL TOOLS
 #############################################################################
-# import slam.plot as splt
-# from vispy.scene import Line
-# from visbrain.objects import VispyObj, SourceObj
-#
+
+import slam.plot as splt
+
+vertices = mesh_closed.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 Mean Curvature
+display_settings = {}
+display_settings['colorbar_label'] = 'Broken Vertices'
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = mesh_closed.faces
+mesh_data['title'] = 'Mesh Close'
+intensity_data = {}
+intensity_data['values'] = broken_vertices_mesh_closed
+intensity_data["mode"] = "vertex"
+Fig = splt.mes3d_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+Fig.show()
+
+
+
+vertices = open_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 = {}
+display_settings['colorbar_label'] = 'Broken Vertices'
+mesh_data = {}
+mesh_data['vertices'] = vertices_translate
+mesh_data['faces'] = open_mesh.faces
+mesh_data['title'] = 'Mesh Close'
+intensity_data = {}
+intensity_data['values'] = broken_vertices_open_mesh
+intensity_data["mode"] = "vertex"
+Fig = splt.mes3d_projection(
+    mesh_data=mesh_data,
+    intensity_data=intensity_data,
+    display_settings=display_settings)
+Fig.show()
 # ###############################################################################
 # # show the result
 # # WARNING : BrainObj should be added first before
@@ -222,9 +290,3 @@
 # visb_sc5 = splt.visbrain_plot(mesh=mesh_closed, caption="closed mesh")
 # visb_sc5.preview()
 
-print('close mesh')
-broken_vertices = stop.broken_vertices(mesh_closed)
-print(np.count_nonzero(broken_vertices))
-print('open mesh')
-broken_vertices = stop.broken_vertices(open_mesh)
-print(np.count_nonzero(broken_vertices))

examples/example_vertex_voronoi.py

@@ -36,9 +36,11 @@
 print(vert_vor.shape)
 print(np.sum(vert_vor) - mesh.area)
 
+
 #############################################################################
-# VISUALIZATION USING EXTERNAL TOOLS
+# VISUALIZATION USING INTERNAL TOOLS
 #############################################################################
+
 import slam.plot as splt
 ###############################################################################
 # Visualization

slam/plot.py

@@ -143,4 +143,4 @@ def mes3d_projection(mesh_data, intensity_data=None, display_settings=None):
         },
     )
 
-    return fig
+    return fig