def test_drr_registration():
import numpy as np
from PIL import Image
from camera import Camera
from raybox import RayBox
from drr_set import DrrSet
from drr_registration import DrrRegistration
from utils import read_rho, str_to_mat
xray1 = Image.open('Test_Data/Sawbones_L2L3/0.bmp').convert('L')
xray2 = Image.open('Test_Data/Sawbones_L2L3/90.bmp').convert('L')
xray1 = np.array(xray1).astype(np.float32)
xray2 = np.array(xray2).astype(np.float32)
xray1 = (xray1-xray1.min())/(xray1.max()-xray1.min())
xray2 = (xray2-xray2.min())/(xray2.max()-xray2.min())
m1 = str_to_mat('[-0.785341, -0.068020, -0.615313, -5.901115; 0.559239, 0.348323, -0.752279, -4.000824; 0.265498, -0.934903, -0.235514, -663.099792]')
m2 = str_to_mat('[-0.214846, 0.964454, 0.153853, 12.792526; 0.557581, 0.250463, -0.791436, -6.176056; -0.801838, -0.084251, -0.591572, -627.625305]')
k1 = str_to_mat('[3510.918213, 0.000000, 368.718994; 0.000000, 3511.775635, 398.527802; 0.000000, 0.000000, 1.000000]')
k2 = str_to_mat('[3533.860352, 0.000000, 391.703888; 0.000000, 3534.903809, 395.485229; 0.000000, 0.000000, 1.000000]')
cam1, cam2 = Camera(m1, k1), Camera(m2, k2)
raybox = RayBox('cpu')
rho, sp = read_rho('Test_Data/Sawbones_L2L3/sawbones.nii.gz')
raybox.set_rho(rho, sp)
drr_set = DrrSet(cam1, cam2, raybox)
drr_registration = DrrRegistration(xray1, xray2, drr_set)
res = drr_registration.register(np.array([-98.92, -106.0, -185.0, -35.0, 25.0, 175]))
print(res)
def init_cams_from_path(self, fpaths):
cams = []
for fpath in fpaths:
with open(fpath) as f:
s = f.read()
m = str_to_mat(re.search('[Mm]\s*=\s*\[(.*)\]', s).group(1))
k = str_to_mat(re.search('[Kk]\s*=\s*\[(.*)\]', s).group(1))
h = int(re.search('[Hh]\s*=\s*([0-9]+)', s).group(1))
w = int(re.search('[Ww]\s*=\s*([0-9]+)', s).group(1))
cams.append(Camera(m=m, k=k, h=h, w=w))
# TODO: Add to drr_set
self.drr_set.set_cams(*cams)
print('Set cams')
def test_camera_set_tfm_fixed():
import time
from camera import Camera
from camera_set import CameraSet
from utils import str_to_mat
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
m1 = str_to_mat('[-0.785341, -0.068020, -0.615313, -5.901115; 0.559239, 0.348323, -0.752279, -4.000824; 0.265498, -0.934903, -0.235514, -663.099792]')
m2 = str_to_mat('[-0.214846, 0.964454, 0.153853, 12.792526; 0.557581, 0.250463, -0.791436, -6.176056; -0.801838, -0.084251, -0.591572, -627.625305]')
k1 = str_to_mat('[3510.918213, 0.000000, 368.718994; 0.000000, 3511.775635, 398.527802; 0.000000, 0.000000, 1.000000]')
k2 = str_to_mat('[3533.860352, 0.000000, 391.703888; 0.000000, 3534.903809, 395.485229; 0.000000, 0.000000, 1.000000]')
cam1 = Camera(m=m1, k=k1)
cam2 = Camera(m=m2, k=k2)
camset = CameraSet(cam1, cam2)
center = camset.center
# Z rotations, i.e PSI from 0 to 360 degrees
plt.ion()
fig = plt.figure()
ax = fig.gca(projection='3d')
for rz in range(-180, 180, 5):
params = [0, 0, 0, 0, 0, rz]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Z rotation')
r = camset.tfm[:3, :3]
u, v ,w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
ax.plot3D([center[0], center[0] + u[0]],
[center[1], center[1] + u[1]],
[center[2], center[2] + u[2]],
color='red')
ax.plot3D([center[0], center[0] + v[0]],
[center[1], center[1] + v[1]],
[center[2], center[2] + v[2]],
color='green')
ax.plot3D([center[0], center[0] + w[0]],
[center[1], center[1] + w[1]],
[center[2], center[2] + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for ry in range(-180, 180, 5):
params = [0, 0, 0, 0, ry, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Y rotation')
r = camset.tfm[:3, :3]
u, v ,w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
ax.plot3D([center[0], center[0] + u[0]],
[center[1], center[1] + u[1]],
[center[2], center[2] + u[2]],
color='red')
ax.plot3D([center[0], center[0] + v[0]],
[center[1], center[1] + v[1]],
[center[2], center[2] + v[2]],
color='green')
ax.plot3D([center[0], center[0] + w[0]],
[center[1], center[1] + w[1]],
[center[2], center[2] + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for rx in range(-180, 180, 5):
params = [0, 0, 0, rx, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'X rotation')
r = camset.tfm[:3, :3]
u, v ,w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
ax.plot3D([center[0], center[0] + u[0]],
[center[1], center[1] + u[1]],
[center[2], center[2] + u[2]],
color='red')
ax.plot3D([center[0], center[0] + v[0]],
[center[1], center[1] + v[1]],
[center[2], center[2] + v[2]],
color='green')
ax.plot3D([center[0], center[0] + w[0]],
[center[1], center[1] + w[1]],
[center[2], center[2] + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for tx in range(-100, 100, 5):
params = [tx, 0, 0, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
r = camset.tfm[:3, :3]
u, v, w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
tx, ty, tz = camset.tfm[:3, 3]
ax.text(center[0] + tx, center[1] + ty, center[2] + tz, 'X translation')
ax.plot3D([center[0] + tx, center[0] + tx + u[0]],
[center[1] + ty, center[1] + ty + u[1]],
[center[2] + tz, center[2] + tz + u[2]],
color='red')
ax.plot3D([center[0] + tx, center[0] + tx + v[0]],
[center[1] + ty, center[1] + ty + v[1]],
[center[2] + tz, center[2] + tz + v[2]],
color='green')
ax.plot3D([center[0] + tx, center[0] + tx + w[0]],
[center[1] + ty, center[1] + ty + w[1]],
[center[2] + tz, center[2] + tz + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for ty in range(-100, 100, 5):
params = [0, ty, 0, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
r = camset.tfm[:3, :3]
u, v, w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
tx, ty, tz = camset.tfm[:3, 3]
ax.text(center[0] + tx, center[1] + ty, center[2] + tz, 'Y translation')
ax.plot3D([center[0] + tx, center[0] + tx + u[0]],
[center[1] + ty, center[1] + ty + u[1]],
[center[2] + tz, center[2] + tz + u[2]],
color='red')
ax.plot3D([center[0] + tx, center[0] + tx + v[0]],
[center[1] + ty, center[1] + ty + v[1]],
[center[2] + tz, center[2] + tz + v[2]],
color='green')
ax.plot3D([center[0] + tx, center[0] + tx + w[0]],
[center[1] + ty, center[1] + ty + w[1]],
[center[2] + tz, center[2] + tz + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for tz in range(-100, 100, 5):
params = [0, 0, tz, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot_fixed(fig, ax, '1')
cam2._make_cam_plot_fixed(fig, ax, '2')
r = camset.tfm[:3, :3]
u, v, w = 100*r[0, :], 100*r[1, :], 100*r[2, :]
tx, ty, tz = camset.tfm[:3, 3]
ax.text(center[0] + tx, center[1] + ty, center[2] + tz, 'Z translation')
ax.plot3D([center[0] + tx, center[0] + tx + u[0]],
[center[1] + ty, center[1] + ty + u[1]],
[center[2] + tz, center[2] + tz + u[2]],
color='red')
ax.plot3D([center[0] + tx, center[0] + tx + v[0]],
[center[1] + ty, center[1] + ty + v[1]],
[center[2] + tz, center[2] + tz + v[2]],
color='green')
ax.plot3D([center[0] + tx, center[0] + tx + w[0]],
[center[1] + ty, center[1] + ty + w[1]],
[center[2] + tz, center[2] + tz + w[2]],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
def test_camera_set_tfm():
import time
import numpy as np
from camera import Camera
from camera_set import CameraSet
from utils import str_to_mat
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
m1 = str_to_mat('[-0.785341, -0.068020, -0.615313, -5.901115; 0.559239, 0.348323, -0.752279, -4.000824; 0.265498, -0.934903, -0.235514, -663.099792]')
m2 = str_to_mat('[-0.214846, 0.964454, 0.153853, 12.792526; 0.557581, 0.250463, -0.791436, -6.176056; -0.801838, -0.084251, -0.591572, -627.625305]')
k1 = str_to_mat('[3510.918213, 0.000000, 368.718994; 0.000000, 3511.775635, 398.527802; 0.000000, 0.000000, 1.000000]')
k2 = str_to_mat('[3533.860352, 0.000000, 391.703888; 0.000000, 3534.903809, 395.485229; 0.000000, 0.000000, 1.000000]')
cam1 = Camera(m=m1, k=k1)
cam2 = Camera(m=m2, k=k2)
camset = CameraSet(cam1, cam2)
center = camset.center
# Z rotations, i.e PSI from 0 to 360 degrees
plt.ion()
fig = plt.figure()
ax = fig.gca(projection='3d')
for rz in range(-180, 180, 5):
params = [0, 0, 0, 0, 0, rz]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Z rotation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
p1 = cam1.pos
p2 = cam2.pos
c = camset.center
verts = [c-(p1+p2), c-(p1-p2), c+(p1+p2), c+(p1-p2)]
verts = [list(map(lambda x: x.tolist(), verts))]
parallelogram = Poly3DCollection(verts)
ax.add_collection3d(parallelogram, zs='z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for ry in range(-180, 180, 5):
params = [0, 0, 0, 0, ry, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Y rotation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
p1 = cam1.pos
p2 = cam2.pos
c = camset.center
verts = [c-(p1+p2), c-(p1-p2), c+(p1+p2), c+(p1-p2)]
verts = [list(map(lambda x: x.tolist(), verts))]
parallelogram = Poly3DCollection(verts)
ax.add_collection3d(parallelogram, zs='z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for rx in range(-180, 180, 5):
params = [0, 0, 0, rx, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'X rotation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
p1 = cam1.pos
p2 = cam2.pos
c = camset.center
verts = [c-(p1+p2), c-(p1-p2), c+(p1+p2), c+(p1-p2)]
verts = [list(map(lambda x: x.tolist(), verts))]
parallelogram = Poly3DCollection(verts)
ax.add_collection3d(parallelogram, zs='z')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.001)
ax.clear()
for tx in range(-100, 100, 5):
params = [tx, 0, 0, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'X translation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
c = camset.center
t_c = np.linalg.inv(camset.tfm).dot(c.tolist() + [1])[:3]
ax.plot3D([t_c[0]], [t_c[1]], [t_c[2]], marker='*', color='red')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.01)
ax.clear()
for ty in range(-100, 100, 5):
params = [0, ty, 0, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Y translation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
c = camset.center
t_c = np.linalg.inv(camset.tfm).dot(c.tolist() + [1])[:3]
ax.plot3D([t_c[0]], [t_c[1]], [t_c[2]], marker='*', color='red')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.01)
ax.clear()
for tz in range(-100, 100, 5):
params = [0, 0, tz, 0, 0, 0]
camset.set_tfm_params(*params)
cam1._make_cam_plot(fig, ax, '1')
cam2._make_cam_plot(fig, ax, '2')
ax.text(center[0], center[1], center[2], 'Z translation')
ax.plot3D([center[0], center[0] + 100],
[center[1], center[1] + 0],
[center[2], center[2] + 0],
color='red')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 100],
[center[2], center[2] + 0],
color='green')
ax.plot3D([center[0], center[0] + 0],
[center[1], center[1] + 0],
[center[2], center[2] + 100],
color='blue')
ax.set_xlim3d(center[0] - 600, center[0] + 600)
ax.set_ylim3d(center[1] - 600, center[1] + 600)
ax.set_zlim3d(center[2] - 600, center[2] + 600)
c = camset.center
t_c = np.linalg.inv(camset.tfm).dot(c.tolist() + [1])[:3]
ax.plot3D([t_c[0]], [t_c[1]], [t_c[2]], marker='*', color='red')
fig.canvas.draw()
fig.canvas.flush_events()
plt.pause(0.01)
ax.clear()
def patch_to_pts(patch):
if patch is not '':
patch = str_to_mat(patch).T
return np.vstack((patch, np.ones((1, patch.shape[1]))))
else:
return None
help='Second params file')
parser.add_argument('--drr_dir', type=str, required=True,
help='Directory with DRRs')
parser.add_argument('--prefix', type=str, default='',
help='Prefix for images')
parser.add_argument('--patch', type=str, default='',
help='3D Patch to project on 2D')
parser.add_argument('--carm_dir', type=str, required=True,
help='Directory with Carm images')
parser.add_argument('--results_dir', type=str, required=True,
help='Results dir')
args = parser.parse_args()
camera_set = CameraSet()
with open(args.camera1, 'r') as f:
s = f.read()
m1 = str_to_mat(re.search('[Mm]\s*=\s*\[(.*)\]', s).group(1))
k1 = str_to_mat(re.search('[Kk]\s*=\s*\[(.*)\]', s).group(1))
h1 = int(re.search('[Hh]\s*=\s*([0-9]+)', s).group(1))
w1 = int(re.search('[Ww]\s*=\s*([0-9]+)', s).group(1))
cam1 = Camera(m=m1, k=k1, h=h1, w=w1)
with open(args.camera2, 'r') as f:
s = f.read()
m2 = str_to_mat(re.search('[Mm]\s*=\s*\[(.*)\]', s).group(1))
k2 = str_to_mat(re.search('[Kk]\s*=\s*\[(.*)\]', s).group(1))
h2 = int(re.search('[Hh]\s*=\s*([0-9]+)', s).group(1))
w2 = int(re.search('[Ww]\s*=\s*([0-9]+)', s).group(1))
cam2 = Camera(m=m2, k=k2, h=h2, w=w2)
with open(args.camera3, 'r') as f:
s = f.read()
m3 = str_to_mat(re.search('[Mm]\s*=\s*\[(.*)\]', s).group(1))
k3 = str_to_mat(re.search('[Kk]\s*=\s*\[(.*)\]', s).group(1))