def test_gui(self):
pp = Pointset(3)
pp.append(0, 0, 0)
pp.append(0, 1, 0)
pp.append(1, 2, 0)
pp.append(0, 2, 1)
# Create all solids
vv.solidBox((0, 0, 0))
sphere = vv.solidSphere((3, 0, 0))
cone = vv.solidCone((6, 0, 0))
# a cone with 4 faces is a pyramid
pyramid = vv.solidCone((9, 0, 0), N=4)
vv.solidCylinder((0, 3, 0), (1, 1, 2))
ring = vv.solidRing((3, 3, 0))
vv.solidTeapot((6, 3, 0))
vv.solidLine(pp+Point(9, 3, 0), radius=0.2)
# Make the ring green
ring.faceColor = 'g'
# Make the sphere dull
sphere.specular = 0
sphere.diffuse = 0.4
# Show lines in yellow pyramid
pyramid.faceColor = 'r'
pyramid.edgeShading = 'plain'
# Colormap example
N = cone._vertices.shape[0]
cone.SetValues(np.linspace(0, 1, N))
cone.colormap = vv.CM_JET
def on_key(event):
"""KEY commands for user interaction
UP/DOWN = show/hide nodes
ENTER = show edge and attribute values [select 2 nodes]
DELETE = remove edge [select 2 nodes]
CTRL = replace intially created ringparts
ESCAPE = FINISH: refine, smooth
"""
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_ENTER:
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c, ct, p, l = _utils_GUI.get_edge_attributes(model, select1, select2)
# visualize edge and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
_utils_GUI.set_edge_labels(t1,t2,t3,ct,c,l)
a = vv.gca()
view = a.GetView()
pp = Pointset(p) # visvis meshes do not work with PointSet
line = vv.solidLine(pp, radius = 0.2)
line.faceColor = 'y'
a.SetView(view)
if event.key == vv.KEY_DELETE:
# remove edge
assert len(selected_nodes) == 2
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c, ct, p, l = _utils_GUI.get_edge_attributes(model, select1, select2)
model.remove_edge(select1, select2)
# visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
_utils_GUI.set_edge_labels(t1,t2,t3,ct,c,l)
a = vv.gca()
view = a.GetView()
pp = Pointset(p)
line = vv.solidLine(pp, radius = 0.2)
line.faceColor = 'r'
a.SetView(view)
if event.key == vv.KEY_CONTROL:
# replace intially created ringparts
ringparts(ringpart=ringpart)
figparts()
def show(items, normals=None):
"""Function that shows a mesh object.
"""
for item in items:
vv.clf()
# convert to visvis.Mesh class
new_normals = []
new_vertices = []
for k, v in item.vertices.iteritems():
new_normals.append(item.normal(k))
new_vertices.append(v)
mesh = item.to_visvis_mesh()
mesh.SetVertices(new_vertices)
mesh.SetNormals(new_normals)
mesh.faceColor = 'y'
mesh.edgeShading = 'plain'
mesh.edgeColor = (0, 0, 1)
axes = vv.gca()
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.SetLimits()
if normals is not None:
for normal in normals:
sl = solidLine(normal, 0.15)
sl.faceColor = 'r'
# Show title and enter main loop
vv.title('Show')
app = vv.use()
app.Run()
def show(self):
for projection_name in self.rsa_assessment.projection_list():
rsa_projection = self.rsa_assessment.projection(projection_name)
# projection = self.assessment.projection(i)
# projector = self.projectors[i]
self.plot_image_data(rsa_projection.image,
rsa_projection.t,
sampling=0.1)
for image_segment_name in rsa_projection.image_segment_list():
try:
rsa_image_segment = rsa_projection.image_segment(
image_segment_name)
except NotImplementedError:
continue
for line in rsa_projection.segment_point_lines(
rsa_image_segment):
ps = vv.Pointset(3)
ps.append(*list(line.a[:3]))
ps.append(*list(line.b[:3]))
vl = vv.solidLine(ps, radius=self.lineSize, N=self.lineN)
vl.faceColor = self.lineColor
for scene_segment_name in self.rsa_assessment.scene_segment_list():
try:
scene_segment = self.rsa_assessment.scene_segment(
scene_segment_name)
except NotImplementedError:
continue
scene_segment.match_crossing_lines()
for i in range(len(scene_segment.points)):
vs = vv.solidSphere(translation=tuple(
scene_segment.points[i][:3]),
scaling=([self.pointSize] * 3),
N=self.sphereN,
M=self.sphereM)
vs.faceColor = self.pointColor
# Enter main loop
app = vv.use()
app.Run()
def vis_spared_edges(graph, radius=0.6, axes=None):
""" in step 3 with anacondaRing, prune_redundant spares strong triangle edges.
visualize with a model
"""
from visvis import Pointset
if graph is None:
return
if axes is None:
a = vv.gca()
else:
axes.MakeCurrent()
a = vv.gca()
for (n1, n2) in graph.edges():
if graph.node[n1].get('spared', False) and \
graph.node[n2].get('spared', False):
p = graph.edge[n1][n2]['path']
pp = Pointset(p)
line = vv.solidLine(pp, radius=radius)
line.faceColor = 'y'
vv.figure()
a = vv.gca()
# Define points for the line
pp = Pointset(3)
pp.append(0,0,0); pp.append(0,1,0); pp.append(1,2,0); pp.append(0,2,1)
# Create all solids
box = vv.solidBox((0,0,0))
sphere = vv.solidSphere((3,0,0))
cone = vv.solidCone((6,0,0))
pyramid = vv.solidCone((9,0,0), N=4) # a cone with 4 faces is a pyramid
cylinder = vv.solidCylinder((0,3,0),(1,1,2))
ring = vv.solidRing((3,3,0))
teapot = vv.solidTeapot((6,3,0))
line = vv.solidLine(pp+Point(9,3,0), radius = 0.2)
# Let's put a face on that cylinder
# This works because 2D texture coordinates are automatically generated for
# the sphere, cone, cylinder and ring.
im = vv.imread('astronaut.png')
cylinder.SetTexture(im)
# Make the ring green
ring.faceColor = 'g'
# Make the sphere dull
sphere.specular = 0
sphere.diffuse = 0.4
# Show lines in yellow pyramid
def plot3d(self,
img,
bodies={
'pose3d': np.empty((0, 13, 3)),
'pose2d': np.empty((0, 13, 2))
},
hands={
'pose3d': np.empty((0, 21, 3)),
'pose2d': np.empty((0, 21, 2))
},
faces={
'pose3d': np.empty((0, 84, 3)),
'pose2d': np.empty((0, 84, 2))
},
body_with_wrists=[],
body_with_head=[],
interactive=False):
"""
:param img: a HxWx3 numpy array
:param bodies: dictionnaroes with 'pose3d' (resp 'pose2d') with the body 3D (resp 2D) pose
:param faces: same with face pose
:param hands: same with hand pose
:param body_with_wrists: list with for each body, a tuple (left_hand_id, right_hand_id) of the index of the hand detection attached to this body detection (-1 if none) for left and right hands
:parma body_with_head: list with for each body, the index of the face detection attached to this body detection (-1 if none)
:param interactive: whether to open the viewer in an interactive manner or not
"""
# body pose do not use the same coordinate systems
bodies['pose3d'][:, :, 0] *= -1
bodies['pose3d'][:, :, 1] *= -1
# Compute 3D scaled representation of each part, stored in "points3d"
hands, bodies, faces = [copy.copy(s) for s in (hands, bodies, faces)]
parts = (hands, bodies, faces)
for part in parts:
part['points3d'] = np.zeros_like(part['pose3d'])
for part_idx in range(len(part['pose3d'])):
points3d = scale_orthographic(part['pose3d'][part_idx],
part['pose2d'][part_idx])
part['points3d'][part_idx] = points3d
# Various display tricks to make the 3D visualization of full-body nice
# (1) for faces, add a Z offset to faces to align them with the body
for body_id, face_id in enumerate(body_with_head):
if face_id != -1:
z_offset = bodies['points3d'][body_id, 12, 2] - np.mean(
faces['points3d'][face_id, :, 2])
faces['points3d'][face_id, :, 2] += z_offset
# (2) for hands, add a 3D offset to put them at the wrist location
for body_id, (lwrist_id, rwrist_id) in enumerate(body_with_wrists):
if lwrist_id != -1:
hands['points3d'][lwrist_id, :, :] = bodies['points3d'][
body_id, 7, :] - hands['points3d'][lwrist_id, 0, :]
if rwrist_id != -1:
hands['points3d'][rwrist_id, :, :] = bodies['points3d'][
body_id, 6, :] - hands['points3d'][rwrist_id, 0, :]
img = np.asarray(img)
height, width = img.shape[:2]
fig = vv.figure(1)
fig.Clear()
fig._SetPosition(0, 0, self.figsize[0], self.figsize[1])
if not interactive:
fig._enableUserInteraction = False
axes = vv.gca()
# Hide axis
axes.axis.visible = False
scaling_factor = 1.0 / height
# Camera interaction is not intuitive along z axis
# We reference every object to a parent frame that is rotated to circumvent the issue
ref_frame = vv.Wobject(axes)
ref_frame.transformations.append(vv.Transform_Rotate(-90, 1, 0, 0))
ref_frame.transformations.append(
vv.Transform_Translate(-0.5 * width * scaling_factor, -0.5, 0))
# Draw image
if self.display2d:
# Display pose in 2D
img = visu.visualize_bodyhandface2d(img,
dict_poses2d={
'body': bodies['pose2d'],
'hand': hands['pose2d'],
'face': faces['pose2d']
},
lw=2,
max_padding=0,
bgr=False)
XX, YY = np.meshgrid([0, width * scaling_factor], [0, 1])
img_z_offset = 0.5
ZZ = img_z_offset * np.ones(XX.shape)
# Draw image
embedded_img = vv.surf(XX, YY, ZZ, img)
embedded_img.parent = ref_frame
embedded_img.ambientAndDiffuse = 1.0
# Draw a grid on the bottom floor to get a sense of depth
XX, ZZ = np.meshgrid(
np.linspace(0, width * scaling_factor, 10),
img_z_offset - np.linspace(0, width * scaling_factor, 10))
YY = np.ones_like(XX)
grid3d = vv.surf(XX, YY, ZZ)
grid3d.parent = ref_frame
grid3d.edgeColor = (0.1, 0.1, 0.1, 1.0)
grid3d.edgeShading = 'plain'
grid3d.faceShading = None
# Draw pose
for part in parts:
for part_idx in range(len(part['points3d'])):
points3d = part['points3d'][part_idx] * scaling_factor
# Draw bones
J = len(points3d)
is_body = (J == 13)
ignore_neck = False if not is_body else body_with_head[
part_idx] != -1
bones, bonecolors, pltcolors = visu._get_bones_and_colors(
J, ignore_neck=ignore_neck)
for (kpt_id1, kpt_id2), color in zip(bones, bonecolors):
color = color[2], color[1], color[0] # BGR vs RGB
p1 = visu._get_xyz(points3d, kpt_id1)
p2 = visu._get_xyz(points3d, kpt_id2)
pointset = vv.Pointset(3)
pointset.append(p1)
pointset.append(p2)
# Draw bones as solid capsules
bone_radius = 0.005
line = vv.solidLine(pointset, radius=bone_radius)
line.faceColor = color
line.ambientAndDiffuse = 1.0
line.parent = ref_frame
# Draw keypoints, except for faces
if J != 84:
keypoints_to_plot = points3d
if ignore_neck:
# for a nicer display, ignore head keypoint
keypoints_to_plot = keypoints_to_plot[:12, :]
# Use solid spheres
for i in range(len(keypoints_to_plot)):
kpt_wobject = vv.solidSphere(
translation=keypoints_to_plot[i, :].tolist(),
scaling=1.5 * bone_radius)
kpt_wobject.faceColor = (255, 0, 0)
kpt_wobject.ambientAndDiffuse = 1.0
kpt_wobject.parent = ref_frame
# Use just an ambient lighting
axes.light0.ambient = 0.8
axes.light0.diffuse = 0.2
axes.light0.specular = 0.0
cam = vv.cameras.ThreeDCamera()
axes.camera = cam
#z axis
cam.azimuth = -45
cam.elevation = 20
cam.roll = 0
# Orthographic camera
cam.fov = 0
if self.camera_zoom is None:
cam.zoom *= 1.3 # Zoom a bit more
else:
cam.zoom = self.camera_zoom
if self.camera_location is not None:
cam.loc = self.camera_location
cam.SetView()
if interactive:
self.app.Run()
else:
fig._widget.update()
self.app.ProcessEvents()
img3d = vv.getframe(vv.gcf())
img3d = np.clip(img3d * 255, 0, 255).astype(np.uint8)
# Crop gray borders
img3d = img3d[10:-10, 10:-10, :]
return img3d, img
def view(mol, viewer='native'):
'''Render the molecule
The mayavi backend doesn't work under python 3. The native backend uses
visvis to render the molecule. This is very slow.
It's better to use the molecular viewer.
Args:
mol (molecule.Molecule): The molecule instance to render
viewer: The backend to use. Valid choices are 'native', 'maya'
and, 'avogadro' (default: native).
Rturns:
None
'''
# mayavi
if viewer == 'maya':
from mayavi import mlab
for atom in mol.atoms:
pts = mlab.points3d(atom.r[0], atom.r[1], atom.r[2],
scale_factor=0.75,
scale_mode='none',
resolution=20,
color=atom.color())
for i, j in mol.bonds():
mlab.plot3d([mol.atoms[i].r[0], mol.atoms[j].r[0]],
[mol.atoms[i].r[1], mol.atoms[j].r[1]],
[mol.atoms[i].r[2], mol.atoms[j].r[2]],
tube_radius=0.1,
tube_sides=20)
mlab.show()
# avogadro
if viewer == 'avogadro':
from subprocess import call
write_xyz(mol, 'avogadro.xyz')
call(['avogadro', 'avogadro.xyz'])
call(['rm', 'avogadro.xyz'])
# visvis
if viewer == 'native':
import visvis as vv
for atom in mol.atoms:
x, y, z = atom.r
at = vv.solidSphere((x, y, z), atom.radius()*0.25)
at.faceColor = atom.color()
for bond in mol.bonds():
pp = vv.Pointset(3)
pp.append(bond.atoms[0].r)
pp.append(bond.atoms[1].r)
vv.solidLine(pp, radius=0.15, N=16)
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([4, 3, 3])
x = vv.solidLine(pp, radius=0.05)
x.faceColor = 'r'
conex = vv.solidCone([4, 3, 3], scaling=[0.1, 0.1, 0.1], direction=[1, 0, 0])
conex.faceColor = 'r'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 4, 3])
y = vv.solidLine(pp, radius=0.05)
y.faceColor = 'g'
coney = vv.solidCone([3, 4, 3], scaling=[0.1, 0.1, 0.1], direction=[0, 1, 0])
coney.faceColor = 'g'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 3, 4])
z = vv.solidLine(pp, radius=0.05)
z.faceColor = 'b'
conez = vv.solidCone([3, 3, 4], scaling=[0.1, 0.1, 0.1], direction=[0, 0, 1])
conez.faceColor = 'b'
# Set axes settings
axes = vv.gca()
axes.SetLimits(rangeX=(-5, 5), rangeY=(-5, 5), rangeZ=(-5, 5))
vv.axis('off')
app = vv.use()
app.Run()
if axes is None:
axes = vv.gca()
# Create mesh object
m = vv.Mesh(axes, baseMesh)
# Adjust axes
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.cameraType = '3d'
axes.SetLimits()
# Return
axes.Draw()
return m
if __name__ == '__main__':
# Create series of points
pp = Pointset(3)
pp.append(0,1,0)
pp.append(3,2,1)
pp.append(4,5,2)
pp.append(2,3,1)
pp.append(0,4,0)
#pp.append(0,1,0) # Circular
# Make a surface-line with varying diameter
m = vv.solidLine(pp, [0.1, 0.2, 0.3, 0.1, 0.2], 8)
def on_key(event):
"""KEY commands for user interaction
'UP/DOWN = show/hide nodes'
'DELETE = remove edge [select 2 nodes] or pop node [select 1 node] '
'or remove seed in nodes1 closest to [picked point]'
'p = remove seeds posterior (y-axis) to [picked point] (use for spine seeds)'
'o = remove seeds anterior (y-axis) to [picked point]'
'i = remove seeds proximal (z-axis) to [picked point]'
'k = remove seeds distal (z-axis) to [picked point]'
'l = remove seeds left (x-axis) to [picked point]'
'j = remove seeds right (x-axis) to [picked point]'
'ALT = clean graph: remove residual clusters, pop, corner'
'PageUp= protect node closest to picked point in nodes1 axes, no pop
'n = add [picked point] (SHIFT+R-click) as seed'
'1 = redo step 1; 2 = redo step 2; 3 = redo step 3'
'z/x/a/d = axis invisible/visible/rotate'
"""
global label
global node_points
global sd
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
if 'node_points' in globals():
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
if 'node_points' in globals():
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_DELETE:
if len(selected_nodes) == 0:
# remove node closest to picked point
node = _utils_GUI.snap_picked_point_to_graph(sd._nodes1, vol, label, nodesOnly=True)
sd._nodes1.remove_node(node)
view = a1.GetView()
a1.Clear()
label = DrawModelAxes(vol, sd._nodes1, a1, clim=clim, showVol=showVol, removeStent=False)
a1.SetView(view)
if len(selected_nodes) == 2:
# remove edge
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes3.edge[select1][select2]['cost']
ct = sd._nodes3.edge[select1][select2]['ctvalue']
path = sd._nodes3.edge[select1][select2]['path']
l = stentgraph._edge_length(sd._nodes3, select1, select2)
sd._nodes3.remove_edge(select1, select2)
stentgraph.pop_nodes(sd._nodes3) # pop residual nodes
# Visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(path)
line = vv.solidLine(pp, radius = 0.2)
line.faceColor = 'r'
a3.SetView(view)
if len(selected_nodes) == 1:
# pop node
select1 = selected_nodes[0].node
stentgraph._pop_node(sd._nodes3, select1) # asserts degree == 2
selected_nodes[0].faceColor = 'w'
selected_nodes.clear()
if event.key == vv.KEY_ALT:
# ALT will FINISH model
stentgraph.prune_clusters(sd._nodes3, 3) #remove residual nodes/clusters
stentgraph.pop_nodes(sd._nodes3)
stentgraph.add_corner_nodes(sd._nodes3, th=sd._params.graph_angleVector, angTh=sd._params.graph_angleTh)
# Create mesh and visualize
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol, sd._nodes3, a3, meshColor=meshColor, clim=clim, showVol=showVol, lc='g', mw=8, lw=0.2)
# _utils_GUI.vis_spared_edges(sd._nodes3)
a3.SetView(view)
print('----DO NOT FORGET TO SAVE THE MODEL TO DISK; RUN _SAVE_SEGMENTATION----')
if event.text == 'n':
# add picked seed to nodes_1
coord2 = get_picked_seed(vol, label)
sd._nodes1.add_node(tuple(coord2))
view = a1.GetView()
point = vv.plot(coord2[0], coord2[1], coord2[2], mc= 'b', ms = 'o', mw= 8, alpha=0.5, axes=a1)
a1.SetView(view)
if event.key == vv.KEY_PAGEUP:
# protect node from pop
pickedNode = _utils_GUI.snap_picked_point_to_graph(sd._nodes1, vol, label, nodesOnly=True)
sd._nodes1.add_node(pickedNode, nopop = True)
sd._nodes2.add_node(pickedNode, nopop = True)
view = a1.GetView()
point = vv.plot(pickedNode[0], pickedNode[1], pickedNode[2], mc= 'y', ms = 'o', mw= 8, alpha=0.5, axes=a1)
a1.SetView(view)
# now rerun step 3
if event.text == 'p':
# remove false seeds posterior to picked point, e.g. for spine
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a2, label,
clim, location='posterior', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='posterior', showVol=showVol)
if event.text == 'o':
# remove seeds prox to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='anterior', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='anterior', showVol=showVol)
if event.text == 'i':
# remove seeds prox to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='proximal', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='proximal', showVol=showVol)
if event.text == 'k':
# remove seeds dist to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='distal', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='distal', showVol=showVol)
if event.text == 'l':
# remove seeds left to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='left', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='left', showVol=showVol)
if event.text == 'j':
# remove seeds right to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='right', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='right', showVol=showVol)
if event.text == '1':
# redo step1
view = a1.GetView()
a1.Clear(); a2.Clear(); a3.Clear()
sd._params = p
sd.Step1()
label = DrawModelAxes(vol, sd._nodes1, a1, clim=clim, showVol=showVol, removeStent=False) # lc, mc
a1.SetView(view)
if event.text == '2':
# redo step2
view = a2.GetView()
a2.Clear(); a3.Clear()
sd._params = p
sd.Step2()
DrawModelAxes(vol, sd._nodes2, a2, clim=clim, showVol=showVol,removeStent=False)
a2.SetView(view)
if event.text == '3':
# redo step3
view = a3.GetView()
a3.Clear()
sd._params = p
sd.Step3(cleanNodes=True)
DrawModelAxes(vol, sd._nodes3, a3, meshColor=meshColor, clim=clim, showVol=showVol,removeStent=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points, selected_nodes, pick=False)
a3.SetView(view)
def on_key(event):
"""KEY commands for user interaction
'UP/DOWN = show/hide nodes'
'DELETE = remove edge [select 2 nodes] or pop node [select 1 node] '
'or remove seed in nodes1 closest to [picked point]'
'PageDown = remove graph posterior (y-axis) to [picked point] (use for spine seeds)'
'ALT = clean graph: remove residual clusters, pop, corner'
'CTRL+SHIFT = add [picked point] (SHIFT+R-click) as seed'
"""
global label
global node_points
global sd
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_DELETE:
if len(selected_nodes) == 0:
# remove node closest to picked point
node = _utils_GUI.snap_picked_point_to_graph(sd._nodes1,
vol,
label,
nodesOnly=True)
sd._nodes1.remove_node(node)
view = a1.GetView()
a1.Clear()
label = DrawModelAxes(vol,
sd._nodes1,
a1,
clim=clim,
showVol=showVol,
removeStent=False)
a1.SetView(view)
if len(selected_nodes) == 2:
# remove edge
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes3.edge[select1][select2]['cost']
ct = sd._nodes3.edge[select1][select2]['ctvalue']
path = sd._nodes3.edge[select1][select2]['path']
l = stentgraph._edge_length(sd._nodes3, select1, select2)
sd._nodes3.remove_edge(select1, select2)
stentgraph.pop_nodes(sd._nodes3) # pop residual nodes
# Visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(path)
line = vv.solidLine(pp, radius=0.2)
line.faceColor = 'r'
# a3.SetView(view)
if len(selected_nodes) == 1:
# pop node
select1 = selected_nodes[0].node
stentgraph._pop_node(sd._nodes3, select1) # asserts degree == 2
selected_nodes[0].faceColor = 'w'
selected_nodes.clear()
if event.key == vv.KEY_ALT:
# ALT will FINISH model
stentgraph.prune_clusters(sd._nodes3,
3) #remove residual nodes/clusters
stentgraph.pop_nodes(sd._nodes3)
stentgraph.add_corner_nodes(sd._nodes3,
th=sd._params.graph_angleVector,
angTh=sd._params.graph_angleTh)
# Create mesh and visualize
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
lc='b',
mw=8,
lw=0.2)
_utils_GUI.vis_spared_edges(sd._nodes3)
a3.SetView(view)
print(
'----DO NOT FORGET TO SAVE THE MODEL TO DISK; RUN _SAVE_SEGMENTATION----'
)
if event.text == 'n':
# add picked seed to nodes_1
coord2 = get_picked_seed(vol, label)
sd._nodes1.add_node(tuple(coord2))
view = a1.GetView()
point = vv.plot(coord2[0],
coord2[1],
coord2[2],
mc='b',
ms='o',
mw=8,
alpha=0.5,
axes=a1)
a1.SetView(view)
if event.text == 'p':
# protect node from pop
pickedNode = _utils_GUI.snap_picked_point_to_graph(sd._nodes1,
vol,
label,
nodesOnly=True)
sd._nodes1.add_node(pickedNode, nopop=True)
sd._nodes2.add_node(pickedNode, nopop=True)
view = a1.GetView()
point = vv.plot(pickedNode[0],
pickedNode[1],
pickedNode[2],
mc='y',
ms='o',
mw=8,
alpha=0.5,
axes=a1)
a1.SetView(view)
# now rerun step 3
if event.key == vv.KEY_PAGEDOWN:
# remove false seeds posterior to picked point, e.g. for spine
try:
_utils_GUI.remove_nodes_by_selected_point(sd._nodes3,
vol,
a3,
label,
clim,
showVol=showVol)
except ValueError: # false nodes already cleaned by Step3
pass
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2,
vol,
a2,
label,
clim,
showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1,
vol,
a1,
label,
clim,
showVol=showVol)
if event.text == '1':
# redo step1
view = a1.GetView()
a1.Clear()
a2.Clear()
a3.Clear()
sd._params = p
sd.Step1()
label = DrawModelAxes(vol,
sd._nodes1,
a1,
clim=clim,
showVol=showVol,
removeStent=False) # lc, mc
a1.SetView(view)
if event.text == '2':
# redo step2 and 3
view = a2.GetView()
a2.Clear()
a3.Clear()
sd._params = p
sd.Step2()
sd.Step3(cleanNodes=cleanNodes)
DrawModelAxes(vol,
sd._nodes2,
a2,
clim=clim,
showVol=showVol,
removeStent=False)
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
removeStent=False)
a2.SetView(view)
if event.text == '3':
view = a3.GetView()
a3.Clear()
sd._params = p
sd.Step3(cleanNodes=cleanNodes)
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
removeStent=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
if event.text == 's':
# SAVE SEGMENTATION
# make centerline points of segmentation
paths_as_pp = points_from_edges_in_graph(sd._nodes3, type='order')
ringpoints = paths_as_pp[0].T
# Get graph model
model = sd._nodes3
seeds = sd._nodes1
Draw = sd.Draw
# Build struct
s2 = vv.ssdf.new()
# We do not need croprange, but keep for reference
s2.sampling = s.sampling
s2.origin = s.origin
s2.stenttype = s.stenttype
s2.croprange = s.croprange
for key in dir(s):
if key.startswith('meta'):
suffix = key[4:]
s2['meta' + suffix] = s['meta' + suffix]
s2.what = what
s2.params = p
s2.stentType = stentType
# Store model
s2.model = model.pack()
s2.seeds = seeds.pack()
s2.Draw = Draw
s2.ringpoints = ringpoints
#s2.mesh = ssdf.new()
# Save
savedir = select_dir(
r'C:\Users\Gebruiker\Google Drive\Afstuderen\Rings')
filename = '%s_%s_%s_%s_%s.ssdf' % (ptcode, ctcode, cropname,
'model' + what, ring)
ssdf.save(os.path.join(savedir, filename), s2)
print('saved to disk in {} as {}.'.format(savedir, filename))
vv.figure()
a = vv.gca()
# Define points for the line
pp = Pointset(3)
pp.append(0,0,0); pp.append(0,1,0); pp.append(1,2,0); pp.append(0,2,1)
# Create all solids
box = vv.solidBox((0,0,0))
sphere = vv.solidSphere((3,0,0))
cone = vv.solidCone((6,0,0))
pyramid = vv.solidCone((9,0,0), N=4) # a cone with 4 faces is a pyramid
cylinder = vv.solidCylinder((0,3,0),(1,1,2))
ring = vv.solidRing((3,3,0))
teapot = vv.solidTeapot((6,3,0))
line = vv.solidLine(pp+Point(9,3,0), radius = 0.2)
# Let's put a face on that cylinder
# This works because 2D texture coordinates are automatically generated for
# the sphere, cone, cylinder and ring.
im = vv.imread('lena.png')
cylinder.SetTexture(im)
# Make the ring green
ring.faceColor = 'g'
# Make the sphere dull
sphere.specular = 0
sphere.diffuse = 0.4
# Show lines in yellow pyramid
if axes is None:
axes = vv.gca()
# Create mesh object
m = vv.Mesh(axes, baseMesh)
# Adjust axes
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.cameraType = '3d'
axes.SetLimits()
# Return
axes.Draw()
return m
if __name__ == '__main__':
# Create series of points
pp = Pointset(3)
pp.append(0,1,0)
pp.append(3,2,1)
pp.append(4,5,2)
pp.append(2,3,1)
pp.append(0,4,0)
#pp.append(0,1,0) # Circular
# Make a surface-line with varying diameter
m = vv.solidLine(pp, [0.1, 0.2, 0.3, 0.1, 0.2], 8)
