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compute_error.py
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compute_error.py
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import os
import re
import argparse
import numpy as np
import matplotlib.pyplot as plt
from camera import Camera
from camera_set import CameraSet
from utils import str_to_mat
def to_grayscale(img):
if len(img.shape) == 2:
return img
elif len(img.shape) == 3:
return img[..., :3].mean(2)
else:
raise ValueError()
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
def get_projected_patch(p, x):
# xs are columns of x
if x is None:
return None
y = p.dot(x)
y = y[:2, :]/y[2, :]
return np.hstack((y, y[:, 0].reshape(-1, 1)))
def plot_drr(bg, ol, fids1, fids2, alpha=0.5, patch=None):
fig, ax = plt.subplots()
ax.imshow(bg, origin='lower', alpha=1)
ax.imshow(1-ol, cmap='copper', origin='lower', alpha=alpha)
ax.set_xticks([])
ax.set_yticks([])
# color = list(map(lambda x: to_rgba(x, 1), ['#FF0000', '#00FF00', '#0000FF', '#00FFFF', '#FFFF00', '#FF00FF']))
# ax.scatter(fids1[0, :], fids1[1, :], marker='*', color='red', label='C-Arm markers')
# ax.scatter(fids2[0, :], fids2[1, :], marker='*', color='blue', label='CT markers')
if patch is not None:
ax.plot(patch[0, :], patch[1, :], marker='*', linestyle='-.', color='chartreuse')
ax.legend(fancybox=True, framealpha=0.25, fontsize=10, borderpad=0.5)
return fig, ax
def get_rms_err(x):
return np.sqrt((np.linalg.norm(x, ord=2, axis=0)**2).mean())
def get_rigid_rms(x, y):
x_c = x - np.mean(x, 1, keepdims=True)
y_c = y - np.mean(y, 1, keepdims=True)
s = np.dot(x_c, y_c.T)
u, _, vh = np.linalg.svd(s)
r = np.dot(vh.T, u.T)
t = np.mean(y, 1, keepdims=True) - np.dot(r, np.mean(x, 1, keepdims=True))
x_tfmd = np.dot(r, x) + t
return get_rms_err(x_tfmd - y)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--camera1', type=str, required=True,
help='Camera 1 file')
parser.add_argument('--camera2', type=str, required=True,
help='Camera 2 file')
parser.add_argument('--camera3', type=str, required=True,
help='Camera 3 file')
parser.add_argument('--camera4', type=str, required=True,
help='Camera 4 file')
parser.add_argument('--fids1', type=str, required=True,
help='First fiducials file')
parser.add_argument('--fids2', type=str, required=True,
help='Second fiducials file')
parser.add_argument('--params_carm', type=str, default='',
help='First params file')
parser.add_argument('--params_drr', type=str, required=True,
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))
h3 = int(re.search('[Hh]\s*=\s*([0-9]+)', s).group(1))
w3 = int(re.search('[Ww]\s*=\s*([0-9]+)', s).group(1))
cam3 = Camera(m=m3, k=k3, h=h3, w=w3)
with open(args.camera4, 'r') as f:
s = f.read()
m4 = str_to_mat(re.search('[Mm]\s*=\s*\[(.*)\]', s).group(1))
k4 = str_to_mat(re.search('[Kk]\s*=\s*\[(.*)\]', s).group(1))
h4 = int(re.search('[Hh]\s*=\s*([0-9]+)', s).group(1))
w4 = int(re.search('[Ww]\s*=\s*([0-9]+)', s).group(1))
cam4 = Camera(m=m4, k=k4, h=h4, w=w4)
camera_set.set_cams(*[cam1, cam2, cam3, cam4])
if len(args.params_carm) > 0:
with open(args.params_carm, 'r') as f:
s = f.read()
tx = float(re.search('Tx\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
ty = float(re.search('Ty\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
tz = float(re.search('Tz\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
rx = float(re.search('Rx\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
ry = float(re.search('Ry\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
rz = float(re.search('Rz\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
params_carm = [tx, ty, tz, rx, ry, rz]
else:
params_carm = [0, 0, 0, 0, 0, 0]
camera_set.set_tfm_params(*params_carm)
tfm1 = camera_set.tfm
with open(args.params_drr, 'r') as f:
s = f.read()
tx = float(re.search('Tx\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
ty = float(re.search('Ty\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
tz = float(re.search('Tz\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
rx = float(re.search('Rx\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
ry = float(re.search('Ry\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
rz = float(re.search('Rz\s*=\s*([-+]?[0-9]*\.?[0-9]*)', s).group(1))
params_drr = [tx, ty, tz, rx, ry, rz]
camera_set.set_tfm_params(*params_drr)
tfm2 = camera_set.tfm
with open(args.fids1, 'r') as f:
s = f.read()
fids1 = np.array(list(map(lambda x: list(map(float, x.split(','))), s.strip().split('\n')))).T
fids1 = np.vstack((fids1, np.ones(fids1.shape[1])))
with open(args.fids2, 'r') as f:
s = f.read()
fids2 = np.array(list(map(lambda x: list(map(float, x.split(','))), s.strip().split('\n')))).T
fids2 = np.vstack((fids2, np.ones(fids2.shape[1])))
fids1_tfmd = np.dot(tfm1, fids1)
fids1_tfmd = fids1_tfmd[:3, :]/fids1_tfmd[3, :]
fids2_tfmd = np.dot(tfm2, fids2)
fids2_tfmd = fids2_tfmd[:3, :]/fids2_tfmd[3, :]
errs = fids2_tfmd - fids1_tfmd
rms_3d = get_rms_err(errs)
rms_3d_svd = get_rigid_rms(fids1[:3, :], fids2[:3, :])
# Ground truth fiducials
camera_set.set_tfm_params(*params_carm)
fids1_tfmd2d1 = camera_set.cams[0].p.dot(fids1)
fids1_tfmd2d1 = fids1_tfmd2d1[:2, :]/fids1_tfmd2d1[2, :]
fids1_tfmd2d2 = camera_set.cams[1].p.dot(fids1)
fids1_tfmd2d2 = fids1_tfmd2d2[:2, :]/fids1_tfmd2d2[2, :]
fids1_tfmd2d3 = camera_set.cams[2].p.dot(fids1)
fids1_tfmd2d3 = fids1_tfmd2d3[:2, :]/fids1_tfmd2d3[2, :]
fids1_tfmd2d4 = camera_set.cams[3].p.dot(fids1)
fids1_tfmd2d4 = fids1_tfmd2d4[:2, :]/fids1_tfmd2d4[2, :]
# Synthetic CT fiducials
camera_set.set_tfm_params(*params_drr)
fids2_tfmd2d1 = camera_set.cams[0].p.dot(fids2)
fids2_tfmd2d1 = fids2_tfmd2d1[:2, :]/fids2_tfmd2d1[2, :]
fids2_tfmd2d2 = camera_set.cams[1].p.dot(fids2)
fids2_tfmd2d2 = fids2_tfmd2d2[:2, :]/fids2_tfmd2d2[2, :]
fids2_tfmd2d3 = camera_set.cams[2].p.dot(fids2)
fids2_tfmd2d3 = fids2_tfmd2d3[:2, :]/fids2_tfmd2d3[2, :]
fids2_tfmd2d4 = camera_set.cams[3].p.dot(fids2)
fids2_tfmd2d4 = fids2_tfmd2d4[:2, :]/fids2_tfmd2d4[2, :]
rms_2d_1 = get_rms_err(fids1_tfmd2d1 - fids2_tfmd2d1)
rms_2d_2 = get_rms_err(fids1_tfmd2d2 - fids2_tfmd2d2)
rms_2d_3 = get_rms_err(fids1_tfmd2d3 - fids2_tfmd2d3)
rms_2d_4 = get_rms_err(fids1_tfmd2d4 - fids2_tfmd2d4)
# MRI patch
patch = patch_to_pts(args.patch)
patch_proj1 = get_projected_patch(camera_set.cams[0].p, patch)
patch_proj2 = get_projected_patch(camera_set.cams[1].p, patch)
patch_proj3 = get_projected_patch(camera_set.cams[2].p, patch)
patch_proj4 = get_projected_patch(camera_set.cams[3].p, patch)
# Find cam1 and cam2 images of synthetic CT and real CT, blend, draw markers
c_arms = sorted([os.path.join(args.carm_dir, x) for x in os.listdir(args.carm_dir) if x.startswith(args.prefix) and x.endswith('.png')])
drrs = sorted([os.path.join(args.drr_dir, x) for x in os.listdir(args.drr_dir) if x.startswith(args.prefix) and x.endswith('.png')])
# im11 = to_grayscale(plt.imread(c_arms[0]))
# im12 = to_grayscale(plt.imread(c_arms[1]))
# im13 = to_grayscale(plt.imread(c_arms[2]))
# im14 = to_grayscale(plt.imread(c_arms[3]))
im11 = plt.imread(c_arms[0])
im12 = plt.imread(c_arms[1])
im13 = plt.imread(c_arms[2])
im14 = plt.imread(c_arms[3])
im21 = to_grayscale(plt.imread(drrs[0]))
im22 = to_grayscale(plt.imread(drrs[1]))
im23 = to_grayscale(plt.imread(drrs[2]))
im24 = to_grayscale(plt.imread(drrs[3]))
fig1, ax1 = plot_drr(im11, im21, fids1_tfmd2d1, fids2_tfmd2d1, patch=patch_proj1)
fig2, ax2 = plot_drr(im12, im22, fids1_tfmd2d2, fids2_tfmd2d2, patch=patch_proj2)
fig3, ax3 = plot_drr(im13, im23, fids1_tfmd2d3, fids2_tfmd2d3, patch=patch_proj3)
fig4, ax4 = plot_drr(im14, im24, fids1_tfmd2d4, fids2_tfmd2d4, patch=patch_proj4)
fig1.savefig(
os.path.join(args.results_dir, os.path.basename(args.params_drr).split('.')[0] + '_drr1.png'),
bbox_inches='tight', pad_inches=0, transparent=True, dpi=100
)
fig2.savefig(
os.path.join(args.results_dir, os.path.basename(args.params_drr).split('.')[0] + '_drr2.png'),
bbox_inches='tight', pad_inches=0, transparent=True, dpi=100
)
fig3.savefig(
os.path.join(args.results_dir, os.path.basename(args.params_drr).split('.')[0] + '_drr3.png'),
bbox_inches='tight', pad_inches=0, transparent=True, dpi=100
)
fig4.savefig(
os.path.join(args.results_dir, os.path.basename(args.params_drr).split('.')[0] + '_drr4.png'),
bbox_inches='tight', pad_inches=0, transparent=True, dpi=100
)
np.set_printoptions(precision=2)
print('{:.2f}, {:.2f}, {:.2f}, {:.2f}, {:.2f}, {:.2f}'.format(rms_3d_svd, rms_3d, rms_2d_1, rms_2d_2, rms_2d_3, rms_2d_4))