def close_all():
"""Close all visvis windows."""
vv.closeAll()
# Get image
im1 = vv.imread('astronaut.png')[:, :, 1].astype('float32')
im1 = pirt.diffuse(im1, 1)[::2, ::2] / 255.0
# Deform image
scale = im1.shape[0] * 0.4
rd = pirt.create_random_deformation(im1, 40, 40, mapping='backward', seed=1001)
im2 = rd.apply_deformation(im1)
# Add noise
im1 += np.random.normal(0, 0.1, im1.shape)
im2 += np.random.normal(0, 0.1, im1.shape)
# Get figure
vv.closeAll()
fig = vv.figure(1)
vv.clf()
fig.position = 200, 100, 900, 500
# Init registration
reg = pirt.GravityRegistration(im1, im2)
# reg = pirt.DiffeomorphicDemonsRegistration(im1, im2)
# reg = pirt.ElastixRegistration(im1, im2)
if isinstance(reg, pirt.DiffeomorphicDemonsRegistration):
reg.params.speed_factor = 2
reg.params.noise_factor = 0.1
reg.params.mapping = 'backward'
reg.params.scale_sampling = 16
reg.params.final_grid_sampling = 35
def select_stent(volnr, params=None):
"""
This functions calls the stent extration function. It contains seed points
for each dataset
"""
if params is None:
params = getDefaultParams()
ssdf._stent_tracking_params = params
if volnr == 1:
#vol 1
vol, sampling, origin = load_volume(1)
seed_points = Pointset(3)
seed_points.Append(60, 110, 133)
seed_points.Append(100, 75, 150)
seed_points.Append(160, 70, 148)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 2:
#vol 2
vol, sampling, origin = load_volume(2)
seed_points = Pointset(3)
seed_points.Append(60, 175, 155)
seed_points.Append(100, 150, 170)
seed_points.Append(165, 140, 167)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 3:
#vol 3
vol, sampling, origin = load_volume(3)
seed_points = Pointset(3)
seed_points.Append(47, 160, 140)
seed_points.Append(80, 145, 130)
seed_points.Append(130, 130, 128)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 4:
#vol 4
vol, sampling, origin = load_volume(4)
seed_points = Pointset(3)
seed_points.Append(40, 160, 160)
seed_points.Append(140, 145, 135)
seed_points.Append(150, 150, 150)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 5:
#vol 5
vol, sampling, origin = load_volume(5)
seed_points = Pointset(3)
seed_points.Append(34, 150, 170)
seed_points.Append(60, 135, 180)
seed_points.Append(130, 140, 180)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 6:
#vol 6
vol, sampling, origin = load_volume(6)
seed_points = Pointset(3)
seed_points.Append(40, 170, 175)
seed_points.Append(70, 160, 180)
seed_points.Append(140, 142, 168)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 7:
#vol 7
vol, sampling, origin = load_volume(7)
seed_points = Pointset(3)
seed_points.Append(40, 180, 160)
seed_points.Append(110, 160, 160)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 8:
#vol 8
vol, sampling, origin = load_volume(8)
seed_points = Pointset(3)
seed_points.Append(60, 130, 190)
seed_points.Append(80, 110, 180)
seed_points.Append(120, 112, 140)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 18:
#vol 18
vol, sampling, origin = load_volume(18)
seed_points = Pointset(3)
seed_points.Append(70, 170, 140)
seed_points.Append(135, 150, 160)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
else:
raise ValueError('Invalid volnr')
plot = True
if plot:
points = Pointset(3)
for i in range(len(node_points_stent)):
points.Append(node_points_stent[i][2], node_points_stent[i][1],
node_points_stent[i][0])
points_2 = Pointset(3)
for i in range(len(stent_points_stent)):
points_2.Append(stent_points_stent[i][2], stent_points_stent[i][1],
stent_points_stent[i][0])
vv.closeAll()
vv.volshow(vol)
vv.plot(points_2, ls='', ms='.', mc='g', mw=4, alpha=0.5)
vv.plot(points, ls='', ms='.', mc='b', mw=4, alpha=0.9)
graph = from_nodes_to_graph(node_points_stent)
return graph
def save_3D_gradient_images(save_path, data, name):
""" Makes an avi of the volume rendered gradient specified by the name
parameter using visvis
"""
#load all of the volumes into memory
vols = []
#setup the visvis setup to capture all of the images
f = vv.clf()
a = vv.gca()
m = vv.MotionDataContainer(a, interval = 500)
#loop over all the times
times = data.get_times()
mn = 1000000000000
mx = -1
#get the min and max range over which to scale the image set
for i in range(0, len(times)):
#load the volume
vol = data.get_gradient_at_time(times[i], name).C
#get the min and max of these to save
mx = max(np.max(vol), mx)
mn = min(np.min(vol), mn)
#delete the loaded volume for memory issues
del vol
#now take screen shots of these images
for i in range(0, len(times)):
#load the volume
vol = data.get_gradient_at_time(times[i], name).C
print(vol.shape)
#draw it
t = vv.volshow(vol)
t.colormap = vv.CM_HOT
t.renderstyle = 'iso'
t.parent = m
#set the camera filed of view
a.camera.fov = 60
a.camera.elevation = 30
a.camera.zoom = 0.01
#set the limits to the min and max
t.clim = (mn, mx)
#Force the axis to draw now
a.Draw()
f.DrawNow()
t_m.sleep(1)
#get the zero padded time
s = ZeroPad(times[-1], times[i])
#create the save file path
file_path = save_path + name + "_" + s + ".jpeg"
#Now get the screenshot
vv.screenshot(file_path)
#load this image using PIL, append a color bar showing the min and max
ss = Image.open(file_path)
w, h = ss.size
#make a new font
font = ImageFont.truetype("arial.ttf", 24)
color_bar = draw_color_bar(mn, mx, 50, int(.99*h), font)
#get the colorbar dimension
w1, h1 = color_bar.size
#make a new image
ht = max(h, h1)
im_final = Image.new("RGB", (w + w1 + 10, ht), "white")
#paste the other images on to this
im_final.paste(color_bar, (w + 10, 0))
im_final.paste(ss, (0, 0))
#Now finally draw the time and the text on top of this
draw = ImageDraw.Draw(im_final)
#get the text to draw
txt = "Species: " + name + " Time: " + repr(times[i])
#gte the position
pos = (25, 20)
draw.text(pos, txt, font = font, fill = (0,0,0))
#save the final file
im_final.save(file_path)
#close all the figures
vv.closeAll()
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein
#
# Visvis is distributed under the terms of the (new) BSD License.
# The full license can be found in 'license.txt'.
import visvis as vv
def closeAll():
""" closeAll()
Closes all figures.
"""
for fig in [fig for fig in vv.BaseFigure._figures.values()]:
fig.Destroy()
if __name__ == '__main__':
import time
# Create figures
vv.figure()
vv.figure()
vv.processEvents(); vv.processEvents()
time.sleep(1.0)
# Close all
vv.closeAll()
def closeAll():
vv.closeAll()
