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mks2scanner_vis.py
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mks2scanner_vis.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import numpy as np
import image_funcs as imf
import vis_funcs as vf
def main():
SHOW_WINDOW = True
SHOW_AXES = True
data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\joonas'
filenames = {'T1': 'sub-S1_ses-S8741_T1w', 'MKSS': 'markers_20210304_m1',
'ACT': 'trekkerACTlabels', 'COIL': 'magstim_fig8_coil',
'HEAD': 'head_inv', 'BRAIN': 'brain_inv', 'BRAINSIM': 'wm',
'HEADSIM': 'skin', 'MKS': 'ana_markers3'}
img_path = os.path.join(data_dir, filenames['T1'] + '.nii')
mkss_path = os.path.join(data_dir, filenames['MKS'] + '.mks')
# mkss_path = os.path.join(data_dir, filenames['MKSS'] + '.mkss')
# head_inv_path = os.path.join(data_dir, filenames['HEAD'] + '.stl')
# brain_inv_path = os.path.join(data_dir, filenames['BRAIN'] + '.stl')
head_sim_path = os.path.join(data_dir, filenames['HEADSIM'] + '.stl')
brain_sim_path = os.path.join(data_dir, filenames['BRAINSIM'] + '.stl')
coil_path = os.path.join(data_dir, filenames['COIL'] + '.stl')
coord_list, orient_list, colour_list, size_list, id_list, seed_list, tg_list = imf.load_mks(mkss_path)
n_points = coord_list.shape[0]
coord_w = np.hstack((coord_list, np.ones((n_points, 1))))
seed_w = np.hstack((seed_list, np.ones((n_points, 1))))
imagedata, affine = imf.load_image(img_path)
mri2inv_mat = imf.mri2inv(imagedata, affine)
inv2mri_mat = imf.inv2mri(imagedata, affine)
if SHOW_WINDOW:
# Create a rendering window and renderer
ren, ren_win, iren = vf.create_window()
# 0: red, 1: green, 2: blue, 3: maroon (dark red),
# 4: purple, 5: teal (petrol blue), 6: yellow, 7: orange
colours = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[0.45, 0., 0.5], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
repos = [0., 0., 0., 0., 0., 0.]
_ = vf.load_stl(head_sim_path, ren, opacity=.4, colour=[0.482, 0.627, 0.698], replace=repos, user_matrix=mri2inv_mat)
_ = vf.load_stl(head_sim_path, ren, opacity=.4, colour="SkinColor", replace=repos,
user_matrix=np.identity(4))
_ = vf.load_stl(brain_sim_path, ren, opacity=.6, colour=[1., 1., 1.], replace=repos, user_matrix=mri2inv_mat)
_ = vf.load_stl(brain_sim_path, ren, opacity=.6, colour=[1., 1., 1.], replace=repos,
user_matrix=np.identity(4))
# create fiducial markers
fids_inv_vtk = coord_w[:3, :].copy()
# from the invesalius exported fiducial markers you have to multiply the Y coordinate by -1 to
# transform to the regular 3D invesalius space where coil location is saved
fids_inv_vtk[:, 1] *= -1
fids_vis = fids_inv_vtk[:, :3]
fids_scan = inv2mri_mat @ fids_inv_vtk.T
fids_scan_vis = fids_scan.T[:3, :3]
for n in range(3):
_ = vf.add_marker(fids_scan_vis[n, :], ren, colours[n], radius=2)
for n in range(3):
_ = vf.add_marker(fids_vis[n, :], ren, colours[n], radius=2)
# --- fiducial markers
# create coil vectors
coil_pos = np.hstack((coord_w[-1, :3], orient_list[-1, :]))
coil_pos[1] *= -1
m_coil = imf.coil_transform_matrix(coil_pos)
vec_length = 75
repos_coil = [0., 0., 0., 0., 0., 90.]
# coil vectors in invesalius 3D space
p1 = m_coil[:-1, -1]
coil_dir = m_coil[:-1, 0]
coil_face = m_coil[:-1, 1]
p2_face = p1 + vec_length * coil_face
p2_dir = p1 + vec_length * coil_dir
coil_norm = np.cross(coil_dir, coil_face)
p2_norm = p1 - vec_length * coil_norm
# offset = 40
# coil_norm = coil_norm/np.linalg.norm(coil_norm)
# coord_offset_nav = p1 - offset * coil_norm
_ = vf.load_stl(coil_path, ren, opacity=.6, replace=repos_coil, colour=[1., 1., 1.], user_matrix=m_coil)
_ = vf.add_line(ren, p1, p2_dir, color=[1.0, .0, .0])
_ = vf.add_line(ren, p1, p2_face, color=[.0, 1.0, .0])
_ = vf.add_line(ren, p1, p2_norm, color=[.0, .0, 1.0])
_ = vf.add_marker(p1, ren, colours[4], radius=2)
# coil vectors in MRI space
m_coil_scan = inv2mri_mat @ m_coil
p1_scan = m_coil_scan[:-1, -1]
coil_dir_scan = m_coil_scan[:-1, 0]
coil_face_scan = m_coil_scan[:-1, 1]
p2_face_scan = p1_scan + vec_length * coil_face_scan
p2_dir_scan = p1_scan + vec_length * coil_dir_scan
coil_norm_scan = np.cross(coil_dir_scan, coil_face_scan)
p2_norm_scan = p1_scan - vec_length * coil_norm_scan
_ = vf.load_stl(coil_path, ren, opacity=.6, replace=repos_coil, colour=[1., 1., 1.], user_matrix=m_coil_scan)
_ = vf.add_line(ren, p1_scan, p2_dir_scan, color=[1.0, .0, .0])
_ = vf.add_line(ren, p1_scan, p2_face_scan, color=[.0, 1.0, .0])
_ = vf.add_line(ren, p1_scan, p2_norm_scan, color=[.0, .0, 1.0])
_ = vf.add_marker(p1_scan, ren, colours[4], radius=2)
# --- coil vectors
# seed markers
seed_3dinv = seed_w[np.newaxis, -1, :].copy()
seed_vis = seed_3dinv[0, :3]
seed_scan = inv2mri_mat @ seed_3dinv.T
seed_scan_vis = seed_scan.T[0, :3]
_ = vf.add_marker(seed_vis, ren, colours[5], radius=2)
_ = vf.add_marker(seed_scan_vis, ren, colours[6], radius=2)
# --- seed markers
# Add axes to scene origin
if SHOW_AXES:
_ = vf.add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
_ = vf.add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
_ = vf.add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Initialize window and interactor
iren.Initialize()
ren_win.Render()
iren.Start()
if __name__ == '__main__':
np.set_printoptions(suppress=True)
# np.set_printoptions(suppress=True, precision=2)
main()