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 test_drr_sawbones():
import numpy as np
import SimpleITK as sitk
from camera import Camera
from raybox import RayBox
import matplotlib.pyplot as plt
h = np.int32(460)
w = np.int32(460)
m = np.array([[0, 0, -1, 143],
[1, 0, 0, -96],
[0, -1, 0, -770]])
k = np.array([[1001, 0, 204.5, 0],
[0, 1001, 137.3, 0],
[0, 0, 1, 0]])
k[0,0], k[1,1] = 1.5*k[0,0], 1.5*k[1,1]
# m = np.array([[ 1. , 0. , 0. , 2. ],
# [ 0. , 0.39073113, -0.92050485, -0.64241966],
# [ 0. , 0.92050485, 0.39073113, -4.07275054],
# [ 0. , 0. , 0. , 1. ]])
rho = sitk.GetArrayFromImage(sitk.ReadImage('Test_Data/Sawbones_L2L3/sawbones.nii.gz')).transpose((1, 2, 0)).astype(np.float32)
sp = np.array([0.375, 0.375, 0.625], dtype=np.float32)[[1, 0, 2]]
n = np.array([513, 513, 456], dtype=np.int32)[[1, 0, 2]]
rho = rho[::, ::-1, ::]
#rho = np.ones((512, 512, 455))
cam1 = Camera(m, k, h=h, w=w)
cam2 = Camera(m, k, h=h, w=w)
raybox = RayBox('cpu')
raybox.set_cams(cam1, cam2)
raybox.set_rho(rho, sp)
raybox.mode = 'gpu'
raysums1, raysums2 = raybox.trace_rays()
print(raysums1.max(), raysums2.max())
plt.imsave('raysums1.png', raysums1, cmap='gray', vmin=0, vmax=1)
def test_raybox_class():
import numpy as np
from camera import Camera
from raybox import RayBox
import matplotlib.pyplot as plt
# m = np.array([[1, 0, 0, 2],
# [0, 0, -1, 1],
# [0, 1, 0, -4],
# [0, 0, 0, 1]])
m = np.array([[0, -1, 0, -1],
[0, 0, -1, 1],
[1, 0, 0, -3],
[0, 0, 0, 1]])
# m = np.array([[ 1. , 0. , 0. , 2. ],
# [ 0. , 0.39073113, -0.92050485, -0.64241966],
# [ 0. , 0.92050485, 0.39073113, -4.07275054],
# [ 0. , 0. , 0. # , 1. ]])
h = np.int32(768)
w = np.int32(768)
n = np.array([8, 8, 8], dtype=np.int32)
sp = np.array([1, 1, 1], dtype=np.float32)
k = np.array([[2*(h/2), 0, 1*(h/2), 0],
[0, 2*(w/2), 1*(w/2), 0],
[0, 0, 1, 0]])
rho = np.ones((n-1).tolist(), dtype=np.float32)
cam1 = Camera(m, k, h=h, w=w)
cam2 = Camera(m, k, h=h, w=w)
raybox = RayBox('gpu')
raybox.set_cams(cam1, cam2)
raybox.set_rho(rho, sp)
raysums1, raysums2 = raybox.trace_rays()
print(raysums1.max(), raysums2.max())
plt.imsave('raysums1.png', raysums1, cmap='gray')
def test_trace_rays():
from camera import Camera
from raybox import RayBox
import numpy as np
import matplotlib.pyplot as plt
m = np.array([[1, 0, 0, 2],
[0, 0, -1, 1],
[0, 1, 0, -4],
[0, 0, 0, 1]])
h = 8
w = 8
k = np.array([[2*(h/2), 0, 1*(h/2), 0],
[0, 2*(w/2), 1*(w/2), 0],
[0, 0, 1, 0]])
cam = Camera(m=m, k=k, h=h, w=w)
bs = np.array([-3, -2, 0])
ns = [3, 3, 3]
spacing = [1, 1, 1]
rho = np.ones((ns[0] - 1, ns[1] - 1, ns[2] - 1))
image = RayBox.trace_rays(bs, ns, spacing, rho, cam)
image = (image - image.min())/(image.max() - image.min())
def test_ray_minmax_intersec():
import numpy as np
from raybox import RayBox
from ray import Ray
raybox = RayBox([2, 0, 0], [3, 3, 3], [1, 1, 1])
i = np.array([0, -4, 0])
j = np.array([3, 0, 1])
k = np.array([4, 4/3, 4/3])
l = np.array([3, -4, 1])
m = np.array([3, 2, 1])
n = np.array([0, 0, 0])
o = np.array([1, 0, 0])
# Test 1
ray = Ray(i, j)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
np.testing.assert_almost_equal(pt1, j)
np.testing.assert_almost_equal(pt2, k)
print('Test 1 OK')
# Test 2
ray = Ray(l, j)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
np.testing.assert_almost_equal(pt1, j)
np.testing.assert_almost_equal(pt2, m)
print('Test 2 OK')
# Test 3
ray = Ray(l, n)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 3 OK')
# Test 4
ray = Ray(l, o)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 4 OK')
# Test 5
ray = Ray(i, n)
pt1, _pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 5 OK')
# Test 6
ray = Ray(i, o)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 6 OK')
# Non unit spacing
raybox = RayBox([2, 0, 0], [5, 5, 5], [0.5, 0.5, 0.5])
# Test 7
ray = Ray(i, j)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
np.testing.assert_almost_equal(pt1, j)
np.testing.assert_almost_equal(pt2, k)
print('Test 7 OK')
# Test 8
ray = Ray(l, j)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
np.testing.assert_almost_equal(pt1, j)
np.testing.assert_almost_equal(pt2, m)
print('Test 8 OK')
# Test 9
ray = Ray(l, n)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 9 OK')
# Test 10
ray = Ray(l, o)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 10 OK')
# Test 11
ray = Ray(i, n)
pt1, _pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 11 OK')
# Test 12
ray = Ray(i, o)
pt1, pt2 = raybox.get_ray_minmax_intersec(ray)
assert pt1 is None and pt2 is None
print('Test 12 OK')
def test_get_radiological_path():
import numpy as np
from raybox import RayBox
from ray import Ray
c = np.array([-3, -2, 0])
i = np.array([0, 4, 0])
j = np.array([-2, 0, 1])
k = np.array([3, 0, 0])
l = np.array([-1, -1, 1])
m = np.array([-2, 4, 1])
n = np.array([-3, -1.5, 1.5])
o = np.array([-3, -2, 1.5])
p = np.array([-2, -2, 1])
q = np.array([0, 0, 0])
r = np.array([-2, -2, 2])
s = np.array([-1.2, -2, 1.2])
t = np.array([-1.2, 0, 1])
ln = 2.12
jp = 2
jo = 2.29
lr = 1.73
tl = 1.02
sl = 1.04
rij = Ray(i, j)
rkl = Ray(k, l)
rmj = Ray(m, j)
rql = Ray(q, l)
ril = Ray(i, l)
rml = Ray(m, l)
raybox = RayBox(c, [3, 3, 3], [1, 1, 1])
alphas_rij = (1.0, 1.5, 0.5, 1.5, 1.0, 1.5, 0.0, 2.0)
alphas_rkl = (1.0, 1.5, 1.0, 1.5, -0.0, 2.0, 0.0, 2.0)
alphas_rmj = (1.0, 1.5, float("-inf"), float("inf"),
1.0, 1.5, float("-inf"), float("inf"))
alphas_rql = (1.0, 2.0, 1.0, 3.0, -0.0, 2.0, 0.0, 2.0)
alphas_ril = (1.0, 1.2, 1.0, 3.0, 0.8, 1.2, 0.0, 2.0)
alphas_rml = (0.8, 1.0, -1.0, 1.0, 0.8, 1.2, float("-inf"), float("inf"))
np.testing.assert_almost_equal(k + (alphas_rkl[0])*(l-k), l)
np.testing.assert_almost_equal(k + (alphas_rkl[1])*(l-k), n)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_rkl, rkl), ln, decimal=2)
print('Test 1 OK')
np.testing.assert_almost_equal(i + (alphas_rij[0])*(j-i), j)
np.testing.assert_almost_equal(i + (alphas_rij[1])*(j-i), o)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_rij, rij), jo, decimal=2)
print('Test 2 OK')
np.testing.assert_almost_equal(m + (alphas_rmj[0])*(j-m), j)
np.testing.assert_almost_equal(m + (alphas_rmj[1])*(j-m), p)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_rmj, rmj), jp, decimal=2)
print('Test 3 OK')
np.testing.assert_almost_equal(q + (alphas_rql[0])*(l-q), l)
np.testing.assert_almost_equal(q + (alphas_rql[1])*(l-q), r)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_rql, rql), lr, decimal=2)
print('Test 4 OK')
np.testing.assert_almost_equal(i + (alphas_ril[0])*(l-i), l)
np.testing.assert_almost_equal(i + (alphas_ril[1])*(l-i), s)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_ril, ril), sl, decimal=2)
print('Test 5 OK')
np.testing.assert_almost_equal(m + (alphas_rml[0])*(l-m), t)
np.testing.assert_almost_equal(m + (alphas_rml[1])*(l-m), l)
np.testing.assert_almost_equal(
raybox.get_radiological_path(alphas_rml, rml), tl, decimal=2)
print('Test 6 OK')
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle('DRR Viewer')
self.setMinimumSize(QtCore.QSize(800, 720))
size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
size_policy.setHeightForWidth(True)
self.setSizePolicy(size_policy)
self.central_widg = QtWidgets.QWidget(self)
# File dialog
self.file_dialog = QtWidgets.QFileDialog()
self.file_dialog.setViewMode(QtWidgets.QFileDialog.List)
self.file_dialog_out = ''
# Menu
self.menu = self.menuBar()
self.file_menu = self.menu.addMenu('File')
self.fd_in_out = {
'CT': [self.on_ct_menu, ''],
'Camera Files': [self.on_cam_menu, ''],
'C-Arm Images': [self.on_carm_menu, '']
}
for entry in ['CT', 'Camera Files', 'C-Arm Images']:
action = QtWidgets.QAction('Open {}'.format(entry), self)
action.triggered.connect(self.fd_in_out[entry][0])
self.file_menu.addAction(action)
save_drr1_action = QtWidgets.QAction('Save first DRR as ...', self)
save_drr1_action.triggered.connect(self.on_save_drr1)
self.file_menu.addAction(save_drr1_action)
save_drr2_action = QtWidgets.QAction('Save second DRR as ...', self)
save_drr2_action.triggered.connect(self.on_save_drr2)
self.file_menu.addAction(save_drr2_action)
save_params_action = QtWidgets.QAction('Save parameters as ...', self)
save_params_action.triggered.connect(self.on_save_params)
self.file_menu.addAction(save_params_action)
load_params_action = QtWidgets.QAction('Load parameters from ...',
self)
load_params_action.triggered.connect(self.on_load_params)
self.file_menu.addAction(load_params_action)
save_setup_action = QtWidgets.QAction('Save current setup as ...',
self)
save_setup_action.triggered.connect(self.on_save_setup)
self.file_menu.addAction(save_setup_action)
self.edit_menu = self.menu.addMenu('Edit')
# Status bar
self.status_bar = self.statusBar()
# Images
self.img1_widg = ImageWidget(self.central_widg)
self.img2_widg = ImageWidget(self.central_widg)
self.img3_widg = ImageWidget(self.central_widg)
self.img4_widg = ImageWidget(self.central_widg)
# Parameter widgs
self.params_widg = ParametersWidget(self.central_widg)
self.params_widg.params_edited.connect(self.on_refresh)
# Threshold widg
self.threshold_widg = ThresholdWidget(self.central_widg)
# Refresh button
self.refresh_butn = QtWidgets.QPushButton('Refresh', self)
# Recenter button
self.recenter_widg = RecenterWidget(self)
# Layout
refresh_layout = QtWidgets.QVBoxLayout()
refresh_layout.addWidget(self.refresh_butn)
refresh_layout.addWidget(self.recenter_widg)
# TODO: Add Labels (AP, LAT, left, right)
# TODO: Require at least AP and LAT
# TODO: 4x4 grid layout
left_imgs_layout = QtWidgets.QVBoxLayout()
left_imgs_layout.addWidget(self.img1_widg)
left_imgs_layout.addWidget(self.img3_widg)
right_imgs_layout = QtWidgets.QVBoxLayout()
right_imgs_layout.addWidget(self.img2_widg)
right_imgs_layout.addWidget(self.img4_widg)
# layout = QtWidgets.QGridLayout()
# layout.addLayout(left_imgs_layout, 0, 0, 1, 2)
# layout.addLayout(right_imgs_layout, 0, 3, 1, 2)
# layout.addWidget(self.threshold_widg, 0, 2, 1, 1)
# layout.addWidget(self.params_widg, 1, 0, 1, 3)
# layout.addLayout(refresh_layout, 1, 3, 1, 2)
# layout.setRowStretch(0, 1)
layout = QtWidgets.QVBoxLayout()
top_layout = QtWidgets.QHBoxLayout()
top_layout.addLayout(left_imgs_layout, 1)
top_layout.addWidget(self.threshold_widg, 0)
top_layout.addLayout(right_imgs_layout, 1)
bottom_layout = QtWidgets.QHBoxLayout()
bottom_layout.addWidget(self.params_widg, 1)
bottom_layout.addLayout(refresh_layout, 0)
layout.addLayout(top_layout, 2)
layout.addLayout(bottom_layout, 0)
self.central_widg.setLayout(layout)
self.setCentralWidget(self.central_widg)
# Focus
self.setFocusPolicy(QtCore.Qt.ClickFocus)
# Connect signals and slots
self.base_pixmap_1.connect(self.img1_widg.on_base_pixmap)
self.base_pixmap_2.connect(self.img2_widg.on_base_pixmap)
self.base_pixmap_3.connect(self.img3_widg.on_base_pixmap)
self.base_pixmap_4.connect(self.img4_widg.on_base_pixmap)
self.params_widg.alpha_slider.valueChanged.connect(
self.on_alphaslider_update)
self.refresh_butn.released.connect(self.on_refresh_btn)
self.threshold_widg.new_threshold.connect(self.on_new_threshold)
self.recenter_widg.new_center.connect(self.on_new_center)
self.alpha.connect(self.img1_widg.on_alpha)
self.alpha.connect(self.img2_widg.on_alpha)
self.alpha.connect(self.img3_widg.on_alpha)
self.alpha.connect(self.img4_widg.on_alpha)
self.drr1.connect(self.img1_widg.on_drr)
self.drr2.connect(self.img2_widg.on_drr)
self.drr3.connect(self.img3_widg.on_drr)
self.drr4.connect(self.img4_widg.on_drr)
self.img1_widg.roi_finalize.connect(self.on_roi_finalize_1)
self.img2_widg.roi_finalize.connect(self.on_roi_finalize_2)
self.img3_widg.roi_finalize.connect(self.on_roi_finalize_3)
self.img4_widg.roi_finalize.connect(self.on_roi_finalize_4)
# Logic
self.raybox = RayBox()
self.drr_set = DrrSet(self.raybox)
self.drr_registration = DrrRegistration(self.drr_set)
runoptim_action = QtWidgets.QAction('Run Optimizer', self)
runoptim_action.triggered.connect(self.on_runoptim_action)
self.edit_menu.addAction(runoptim_action)
popup_3d_action = QtWidgets.QAction('Pop up 3D visualizer', self)
self.edit_menu.addAction(popup_3d_action)
popup_3d_action.triggered.connect(self.plot_set)
gpu_mode_action = QtWidgets.QAction('GPU mode', self)
gpu_mode_action.setCheckable(True)
gpu_mode_action.toggled.connect(self.on_toggled_gpu_mode)
self.edit_menu.addAction(gpu_mode_action)
self.autorefresh = False
autorefresh_action = QtWidgets.QAction('Auto refresh', self)
autorefresh_action.setCheckable(True)
autorefresh_action.toggled.connect(self.on_autorefresh_toggle)
self.edit_menu.addAction(autorefresh_action)
roiselection_action = QtWidgets.QAction('Enable ROI selection', self)
roiselection_action.setCheckable(True)
roiselection_action.toggled.connect(self.img1_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img2_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img3_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img4_widg.on_enable_roi)
self.edit_menu.addAction(roiselection_action)
class MainWindow(QtWidgets.QMainWindow):
new_ct = QtCore.Signal(list)
input_cams_sig = QtCore.Signal(list)
base_pixmap_1 = QtCore.Signal(QtGui.QPixmap)
base_pixmap_2 = QtCore.Signal(QtGui.QPixmap)
base_pixmap_3 = QtCore.Signal(QtGui.QPixmap)
base_pixmap_4 = QtCore.Signal(QtGui.QPixmap)
drr1 = QtCore.Signal(np.ndarray)
drr2 = QtCore.Signal(np.ndarray)
drr3 = QtCore.Signal(np.ndarray)
drr4 = QtCore.Signal(np.ndarray)
alpha = QtCore.Signal(float)
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle('DRR Viewer')
self.setMinimumSize(QtCore.QSize(800, 720))
size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
size_policy.setHeightForWidth(True)
self.setSizePolicy(size_policy)
self.central_widg = QtWidgets.QWidget(self)
# File dialog
self.file_dialog = QtWidgets.QFileDialog()
self.file_dialog.setViewMode(QtWidgets.QFileDialog.List)
self.file_dialog_out = ''
# Menu
self.menu = self.menuBar()
self.file_menu = self.menu.addMenu('File')
self.fd_in_out = {
'CT': [self.on_ct_menu, ''],
'Camera Files': [self.on_cam_menu, ''],
'C-Arm Images': [self.on_carm_menu, '']
}
for entry in ['CT', 'Camera Files', 'C-Arm Images']:
action = QtWidgets.QAction('Open {}'.format(entry), self)
action.triggered.connect(self.fd_in_out[entry][0])
self.file_menu.addAction(action)
save_drr1_action = QtWidgets.QAction('Save first DRR as ...', self)
save_drr1_action.triggered.connect(self.on_save_drr1)
self.file_menu.addAction(save_drr1_action)
save_drr2_action = QtWidgets.QAction('Save second DRR as ...', self)
save_drr2_action.triggered.connect(self.on_save_drr2)
self.file_menu.addAction(save_drr2_action)
save_params_action = QtWidgets.QAction('Save parameters as ...', self)
save_params_action.triggered.connect(self.on_save_params)
self.file_menu.addAction(save_params_action)
load_params_action = QtWidgets.QAction('Load parameters from ...',
self)
load_params_action.triggered.connect(self.on_load_params)
self.file_menu.addAction(load_params_action)
save_setup_action = QtWidgets.QAction('Save current setup as ...',
self)
save_setup_action.triggered.connect(self.on_save_setup)
self.file_menu.addAction(save_setup_action)
self.edit_menu = self.menu.addMenu('Edit')
# Status bar
self.status_bar = self.statusBar()
# Images
self.img1_widg = ImageWidget(self.central_widg)
self.img2_widg = ImageWidget(self.central_widg)
self.img3_widg = ImageWidget(self.central_widg)
self.img4_widg = ImageWidget(self.central_widg)
# Parameter widgs
self.params_widg = ParametersWidget(self.central_widg)
self.params_widg.params_edited.connect(self.on_refresh)
# Threshold widg
self.threshold_widg = ThresholdWidget(self.central_widg)
# Refresh button
self.refresh_butn = QtWidgets.QPushButton('Refresh', self)
# Recenter button
self.recenter_widg = RecenterWidget(self)
# Layout
refresh_layout = QtWidgets.QVBoxLayout()
refresh_layout.addWidget(self.refresh_butn)
refresh_layout.addWidget(self.recenter_widg)
# TODO: Add Labels (AP, LAT, left, right)
# TODO: Require at least AP and LAT
# TODO: 4x4 grid layout
left_imgs_layout = QtWidgets.QVBoxLayout()
left_imgs_layout.addWidget(self.img1_widg)
left_imgs_layout.addWidget(self.img3_widg)
right_imgs_layout = QtWidgets.QVBoxLayout()
right_imgs_layout.addWidget(self.img2_widg)
right_imgs_layout.addWidget(self.img4_widg)
# layout = QtWidgets.QGridLayout()
# layout.addLayout(left_imgs_layout, 0, 0, 1, 2)
# layout.addLayout(right_imgs_layout, 0, 3, 1, 2)
# layout.addWidget(self.threshold_widg, 0, 2, 1, 1)
# layout.addWidget(self.params_widg, 1, 0, 1, 3)
# layout.addLayout(refresh_layout, 1, 3, 1, 2)
# layout.setRowStretch(0, 1)
layout = QtWidgets.QVBoxLayout()
top_layout = QtWidgets.QHBoxLayout()
top_layout.addLayout(left_imgs_layout, 1)
top_layout.addWidget(self.threshold_widg, 0)
top_layout.addLayout(right_imgs_layout, 1)
bottom_layout = QtWidgets.QHBoxLayout()
bottom_layout.addWidget(self.params_widg, 1)
bottom_layout.addLayout(refresh_layout, 0)
layout.addLayout(top_layout, 2)
layout.addLayout(bottom_layout, 0)
self.central_widg.setLayout(layout)
self.setCentralWidget(self.central_widg)
# Focus
self.setFocusPolicy(QtCore.Qt.ClickFocus)
# Connect signals and slots
self.base_pixmap_1.connect(self.img1_widg.on_base_pixmap)
self.base_pixmap_2.connect(self.img2_widg.on_base_pixmap)
self.base_pixmap_3.connect(self.img3_widg.on_base_pixmap)
self.base_pixmap_4.connect(self.img4_widg.on_base_pixmap)
self.params_widg.alpha_slider.valueChanged.connect(
self.on_alphaslider_update)
self.refresh_butn.released.connect(self.on_refresh_btn)
self.threshold_widg.new_threshold.connect(self.on_new_threshold)
self.recenter_widg.new_center.connect(self.on_new_center)
self.alpha.connect(self.img1_widg.on_alpha)
self.alpha.connect(self.img2_widg.on_alpha)
self.alpha.connect(self.img3_widg.on_alpha)
self.alpha.connect(self.img4_widg.on_alpha)
self.drr1.connect(self.img1_widg.on_drr)
self.drr2.connect(self.img2_widg.on_drr)
self.drr3.connect(self.img3_widg.on_drr)
self.drr4.connect(self.img4_widg.on_drr)
self.img1_widg.roi_finalize.connect(self.on_roi_finalize_1)
self.img2_widg.roi_finalize.connect(self.on_roi_finalize_2)
self.img3_widg.roi_finalize.connect(self.on_roi_finalize_3)
self.img4_widg.roi_finalize.connect(self.on_roi_finalize_4)
# Logic
self.raybox = RayBox()
self.drr_set = DrrSet(self.raybox)
self.drr_registration = DrrRegistration(self.drr_set)
runoptim_action = QtWidgets.QAction('Run Optimizer', self)
runoptim_action.triggered.connect(self.on_runoptim_action)
self.edit_menu.addAction(runoptim_action)
popup_3d_action = QtWidgets.QAction('Pop up 3D visualizer', self)
self.edit_menu.addAction(popup_3d_action)
popup_3d_action.triggered.connect(self.plot_set)
gpu_mode_action = QtWidgets.QAction('GPU mode', self)
gpu_mode_action.setCheckable(True)
gpu_mode_action.toggled.connect(self.on_toggled_gpu_mode)
self.edit_menu.addAction(gpu_mode_action)
self.autorefresh = False
autorefresh_action = QtWidgets.QAction('Auto refresh', self)
autorefresh_action.setCheckable(True)
autorefresh_action.toggled.connect(self.on_autorefresh_toggle)
self.edit_menu.addAction(autorefresh_action)
roiselection_action = QtWidgets.QAction('Enable ROI selection', self)
roiselection_action.setCheckable(True)
roiselection_action.toggled.connect(self.img1_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img2_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img3_widg.on_enable_roi)
roiselection_action.toggled.connect(self.img4_widg.on_enable_roi)
self.edit_menu.addAction(roiselection_action)
@QtCore.Slot(bool)
def on_autorefresh_toggle(self, checked):
if checked:
self.autorefresh = True
else:
self.autorefresh = False
@QtCore.Slot()
def on_save_setup(self):
self.file_dialog.setFileMode(QtWidgets.QFileDialog.AnyFile)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptSave)
self.file_dialog.setNameFilter('Any files (*)')
if self.file_dialog.exec_():
fpath = self.file_dialog.selectedFiles()[0]
fpath_params = '{}.txt'.format(fpath)
fpath_drr1 = '{}_drr1.png'.format(fpath)
fpath_drr2 = '{}_drr2.png'.format(fpath)
fpath_drr3 = '{}_drr3.png'.format(fpath)
fpath_drr4 = '{}_drr4.png'.format(fpath)
with open(fpath_params, 'w') as f:
params_str = 'Tx = {:.4f}\nTy = {:.4f}\nTz = {:.4f}\nRx = {:.4f}\nRy = {:.4f}\nRz = {:.4f}'.format(
self.drr_set.params[0], self.drr_set.params[1],
self.drr_set.params[2], self.drr_set.params[3],
self.drr_set.params[4], self.drr_set.params[5])
f.write(params_str)
plt.imsave(fpath_drr1,
self.img1_widg.drr,
cmap='gray',
vmin=0,
vmax=1)
plt.imsave(fpath_drr2,
self.img2_widg.drr,
cmap='gray',
vmin=0,
vmax=1)
if self.img3_widg.drr is not None:
plt.imsave(fpath_drr3,
self.img3_widg.drr,
cmap='gray',
vmin=0,
vmax=1)
if self.img4_widg.drr is not None:
plt.imsave(fpath_drr4,
self.img4_widg.drr,
cmap='gray',
vmin=0,
vmax=1)
@QtCore.Slot()
def on_save_params(self):
self.file_dialog.setFileMode(QtWidgets.QFileDialog.AnyFile)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptSave)
self.file_dialog.setNameFilter('Text Files (*.txt)')
if self.file_dialog.exec_():
fpath = self.file_dialog.selectedFiles()[0]
with open(fpath, 'w') as f:
params_str = 'Tx = {:.4f}\nTy = {:.4f}\nTz = {:.4f}\nRx = {:.4f}\nRy = {:.4f}\nRz = {:.4f}'.format(
self.drr_set.params[0], self.drr_set.params[1],
self.drr_set.params[2], self.drr_set.params[3],
self.drr_set.params[4], self.drr_set.params[5])
f.write(params_str)
@QtCore.Slot()
def on_load_params(self):
self.file_dialog.setFileMode(QtWidgets.QFileDialog.ExistingFile)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptOpen)
self.file_dialog.setNameFilter('Text Files (*.txt)')
if self.file_dialog.exec_():
fpath = self.file_dialog.selectedFiles()[0]
with open(fpath, 'r') as f:
s = f.read()
tx = float(
re.search('[Tt][Xx]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
ty = float(
re.search('[Tt][Yy]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
tz = float(
re.search('[Tt][Zz]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
rx = float(
re.search('[Rr][Xx]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
ry = float(
re.search('[Rr][Yy]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
rz = float(
re.search('[Rr][Zz]\s*=\s*([-+]?[0-9]*\.?[0-9]+)',
s).group(1))
self.params_widg.set_params(tx, ty, tz, rx, ry, rz)
@QtCore.Slot()
def on_save_drr1(self):
self.file_dialog.setFileMode(QtWidgets.QFileDialog.AnyFile)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptSave)
self.file_dialog.setNameFilter('Image Files (*.png)')
if self.file_dialog.exec_():
fpath = self.file_dialog.selectedFiles()[0]
plt.imsave(fpath, self.img1_widg.drr, cmap='gray', vmin=0, vmax=1)
@QtCore.Slot()
def on_save_drr2(self):
self.file_dialog.setFileMode(QtWidgets.QFileDialog.AnyFile)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptSave)
self.file_dialog.setNameFilter('Image Files (*.png)')
if self.file_dialog.exec_():
fpath = self.file_dialog.selectedFiles()[0]
plt.imsave(fpath, self.img2_widg.drr, cmap='gray', vmin=0, vmax=1)
@QtCore.Slot()
def on_runoptim_action(self):
params = np.array(self.params_widg.get_params())
res = self.drr_registration.register(params)
print(res)
new_params = res.x.tolist()
self.params_widg.set_params(*new_params)
self.drr_set.set_tfm_params(*new_params)
self.draw_drrs()
@QtCore.Slot(bool)
def on_toggled_gpu_mode(self, checked):
if checked:
self.raybox.mode = 'gpu'
else:
self.raybox.mode = 'cpu'
@QtCore.Slot()
def plot_set(self):
self.drr_set.plot_camera_set()
for idx, cam in enumerate(self.drr_set.cams, 1):
print('Cam', idx)
print(cam.m)
@QtCore.Slot(list)
def on_new_center(self, center):
self.drr_set.move_to(np.array(center))
self.params_widg.set_params(*(self.drr_set.params))
@QtCore.Slot(int)
def on_alphaslider_update(self, val):
alpha = val / 100
print('alpha', alpha)
self.alpha.emit(alpha)
@QtCore.Slot(float)
def on_new_threshold(self, val):
self.raybox.set_threshold(val)
@QtCore.Slot()
def on_ct_menu(self):
self.file_dialog.setNameFilter('Any files (*)')
self.file_dialog.setFileMode(QtWidgets.QFileDialog.ExistingFiles)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptOpen)
if self.file_dialog.exec_():
fpaths = self.file_dialog.selectedFiles()
self.fd_in_out['CT'][1] = fpaths
self.set_rho(fpaths)
@QtCore.Slot()
def on_cam_menu(self):
self.file_dialog.setNameFilter('Text Files (*.txt)')
self.file_dialog.setFileMode(QtWidgets.QFileDialog.ExistingFiles)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptOpen)
if self.file_dialog.exec_():
fpaths = self.file_dialog.selectedFiles()
self.fd_in_out['Camera Files'][1] = fpaths
print(fpaths)
self.init_cams_from_path(fpaths)
@QtCore.Slot()
def on_carm_menu(self):
self.file_dialog.setNameFilter('Image Files (*.png, *.bmp)')
self.file_dialog.setFileMode(QtWidgets.QFileDialog.ExistingFiles)
self.file_dialog.setAcceptMode(QtWidgets.QFileDialog.AcceptOpen)
if self.file_dialog.exec_():
fpaths = self.file_dialog.selectedFiles()
self.fd_in_out['C-Arm Images'][1] = fpaths
xrays = []
for idx, fpath in enumerate(fpaths, 1):
xrays.append(read_image_as_np(fpath))
signal = getattr(self, 'base_pixmap_{:d}'.format(idx))
signal.emit(QtGui.QPixmap(fpath))
self.drr_registration.set_xrays(*xrays)
@QtCore.Slot()
def on_refresh(self):
if self.autorefresh:
params = self.params_widg.get_params()
self.drr_set.set_tfm_params(*params)
self.draw_drrs()
@QtCore.Slot()
def on_refresh_btn(self):
params = self.params_widg.get_params()
self.drr_set.set_tfm_params(*params)
self.draw_drrs()
def draw_drrs(self):
drrs = self.raybox.trace_rays()
assert len(drrs) < 5
for idx, drr in enumerate(drrs, 1):
signal = getattr(self, 'drr{:d}'.format(idx))
signal.emit(drr)
def set_rho(self, fpaths):
rho, sp = read_rho(fpaths[0])
self.raybox.set_rho(rho, sp)
print('Set Rho')
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')
@QtCore.Slot(float, float, float, float)
def on_roi_finalize_1(self, a, b, c, d):
self.drr_registration.mask1 = (a, b, c, d)
@QtCore.Slot(float, float, float, float)
def on_roi_finalize_2(self, a, b, c, d):
self.drr_registration.mask2 = (a, b, c, d)
@QtCore.Slot(float, float, float, float)
def on_roi_finalize_3(self, a, b, c, d):
self.drr_registration.mask3 = (a, b, c, d)
@QtCore.Slot(float, float, float, float)
def on_roi_finalize_4(self, a, b, c, d):
self.drr_registration.mask4 = (a, b, c, d)