def createScene(self):
# Root entity
self.rootEntity = Qt3DCore.QEntity()
# Material
self.material = Qt3DExtras.QPhongMaterial(self.rootEntity)
# Torus
self.torusEntity = Qt3DCore.QEntity(self.rootEntity)
self.torusMesh = Qt3DExtras.QTorusMesh()
self.torusMesh.setRadius(5)
self.torusMesh.setMinorRadius(1)
self.torusMesh.setRings(100)
self.torusMesh.setSlices(20)
self.torusTransform = Qt3DCore.QTransform()
self.torusTransform.setScale3D(QVector3D(1.5, 1, 0.5))
self.torusTransform.setRotation(QQuaternion.fromAxisAndAngle(QVector3D(1, 0, 0), 45))
self.torusEntity.addComponent(self.torusMesh)
self.torusEntity.addComponent(self.torusTransform)
self.torusEntity.addComponent(self.material)
# Sphere
self.sphereEntity = Qt3DCore.QEntity(self.rootEntity)
self.sphereMesh = Qt3DExtras.QSphereMesh()
self.sphereMesh.setRadius(3)
self.sphereTransform = Qt3DCore.QTransform()
self.controller = OrbitTransformController(self.sphereTransform)
self.controller.setTarget(self.sphereTransform)
self.controller.setRadius(20)
self.sphereRotateTransformAnimation = QPropertyAnimation(self.sphereTransform)
self.sphereRotateTransformAnimation.setTargetObject(self.controller)
self.sphereRotateTransformAnimation.setPropertyName(b"angle")
self.sphereRotateTransformAnimation.setStartValue(0)
self.sphereRotateTransformAnimation.setEndValue(360)
self.sphereRotateTransformAnimation.setDuration(10000)
self.sphereRotateTransformAnimation.setLoopCount(-1)
self.sphereRotateTransformAnimation.start()
self.sphereEntity.addComponent(self.sphereMesh)
self.sphereEntity.addComponent(self.sphereTransform)
self.sphereEntity.addComponent(self.material)
def __init__(self, view: Qt3DExtras.Qt3DWindow) -> None:
"""
Initialize a new instance.
Args:
view: where to render the planetary sphere.
"""
self.root_entity = Qt3DCore.QEntity()
ce = self.camera_entity = view.camera()
ce.lens().setPerspectiveProjection(45.0, 1.0, 0.1, 1000.0)
ce.setPosition(V3(0, 8, 8))
ce.setUpVector(V3(0, 1, 0))
ce.setViewCenter(V3(0, 0, 0))
self.light = Qt3DCore.QEntity(self.root_entity)
self.point_light = Qt3DRender.QPointLight(self.light)
self.point_light.setColor("white")
self.point_light.setIntensity(1.0)
self.light.addComponent(self.point_light)
# Move the light to the camera's position - on-camera 'flash'!
t = self.light_transform = Qt3DCore.QTransform(self.light)
t.setTranslation(ce.position())
self.light.addComponent(t)
self.mesh = Qt3DExtras.QSphereMesh()
self.mesh.setRings(30)
self.mesh.setSlices(30)
self.mesh.setRadius(2)
t = self.transform = Qt3DCore.QTransform()
t.setScale(1.3)
t.setTranslation(V3(0.0, 0.0, 0.0))
m = self.material = Qt3DExtras.QDiffuseSpecularMaterial()
m.setAmbient(QColor(200, 200, 255))
m.setShininess(20.0)
self.entity = Qt3DCore.QEntity(self.root_entity)
self.entity.addComponent(self.mesh)
self.entity.addComponent(self.material)
self.entity.addComponent(self.transform)
view.setRootEntity(self.root_entity)
self.entity.setEnabled(True)
def _setup_neutrons(self):
neutron_radius = 0.1
for i in range(self._num_neutrons):
mesh = Qt3DExtras.QSphereMesh(self.root_entity)
mesh.setRadius(neutron_radius)
transform = Qt3DCore.QTransform(self.root_entity)
transform.setMatrix(
self._get_sphere_transformation_matrix(
self._neutron_offsets[i]))
neutron_material = create_material(QColor("black"), QColor("grey"),
self.root_entity)
entity = create_qentity([mesh, neutron_material, transform],
self.root_entity)
self.entities.append((
entity,
self._get_sphere_transformation_matrix(
self._neutron_offsets[i]),
))
def add_sphere(self, radius, x, y, z, rings=10, slices=10):
sphereEntity = Qt3DCore.QEntity(self.rootEntity)
# Mesh
sphereMesh = Qt3DExtras.QSphereMesh()
sphereMesh.setRadius(radius)
sphereMesh.setRings(rings)
sphereMesh.setSlices(slices)
# Transforms
sphereTransform = Qt3DCore.QTransform()
sphereTransform.setTranslation(QVector3D(x, y, z))
sphereEntity.addComponent(sphereMesh)
sphereEntity.addComponent(self.material)
sphereEntity.addComponent(sphereTransform)
self.spheres.append(sphereEntity)
self.meshes.append(sphereMesh)
self.transforms.append(sphereTransform)
def createScene(self):
# Root entity
self.rootEntity = Qt3DCore.QEntity()
# Material
self.material = Qt3DExtras.QPhongMaterial(self.rootEntity)
# Torus
self.torusEntity = Qt3DCore.QEntity(self.rootEntity)
self.torusMesh = Qt3DExtras.QTorusMesh()
self.torusMesh.setRadius(5)
self.torusMesh.setMinorRadius(1)
self.torusMesh.setRings(100)
self.torusMesh.setSlices(20)
self.torusTransform = Qt3DCore.QTransform()
self.torusTransform.setScale3D(QVector3D(1.5, 1, 0.5))
self.torusTransform.setRotation(
QQuaternion.fromAxisAndAngle(QVector3D(1, 0, 0), 45))
self.torusEntity.addComponent(self.torusMesh)
self.torusEntity.addComponent(self.torusTransform)
self.torusEntity.addComponent(self.material)
# Sphere
self.sphereEntity = Qt3DCore.QEntity(self.rootEntity)
self.sphereMesh = Qt3DExtras.QSphereMesh()
self.sphereMesh.setRadius(3)
self.sphereTransform = Qt3DCore.QTransform()
self.controller = OrbitTransformController(self.sphereTransform)
self.controller.setTarget(self.sphereTransform)
self.controller.setRadius(20)
self.sphereEntity.addComponent(self.sphereMesh)
self.sphereEntity.addComponent(self.sphereTransform)
self.sphereEntity.addComponent(self.material)
def __init__(self):
super(Sphere, self).__init__()
self._type = ComponentType.Sphere
self._component = Qt3DExtras.QSphereMesh()
self._component.setRadius(5)
def __init__(self, parent, fs_subject="sample"):
super(MeshDisplayWidget, self).__init__(parent)
self.config = parent.config
self.fs_subject = fs_subject
self.view = Qt3DExtras.Qt3DWindow()
self.view.defaultFrameGraph().setClearColor(QtGui.QColor("#4d4d4f"))
self.container = QtWidgets.QWidget.createWindowContainer(self.view, self)
screen_size = self.view.screen().size()
self.container.setMinimumSize(QtCore.QSize(600, 100))
self.container.setMaximumSize(screen_size)
#h_layout = QtWidgets.QHBoxLayout(self)
#h_layout.addWidget(self.container)
self.addWidget(self.container)
self.tableView = QtWidgets.QTableView(self)
self.tableView.setObjectName("tableView")
v_layout = QtWidgets.QVBoxLayout()
v_layout.addWidget(self.tableView)
self.overlay_btn = QtWidgets.QPushButton("Update and overlay digitized points")
self.overlay_btn.clicked.connect(self.update_acquisition_overlay)
v_layout.addWidget(self.overlay_btn)
subject_name_layout = QtWidgets.QHBoxLayout()
subject_name_layout.addWidget(QtWidgets.QLabel("Subject name:"))
self.subject_name_wgt = QtWidgets.QComboBox()
subject_name_layout.addWidget(self.subject_name_wgt)
self.new_subject_wgt = QtWidgets.QPushButton("New subject")
self.new_subject_wgt.clicked.connect(self.new_subject)
subject_name_layout.addWidget(self.new_subject_wgt)
self.mute_sound_wgt = QtWidgets.QCheckBox("Mute sound")
subject_name_layout.addWidget(self.mute_sound_wgt)
v_layout.addLayout(subject_name_layout)
if "subject_dir" not in self.config["DEFAULT"]:
self.config["DEFAULT"]["subject_dir"] = str(Path(__file__).parent.absolute() / "subjects_data")
subject_dir_layout = QtWidgets.QHBoxLayout()
subject_dir_layout.addWidget(QtWidgets.QLabel("Subject dir:"))
self.subject_dir_wgt = QtWidgets.QLineEdit(self.config["DEFAULT"]["subject_dir"])
self.subject_dir_wgt.setReadOnly(False)
subject_dir_layout.addWidget(self.subject_dir_wgt)
select_subject_dir_btn = QtWidgets.QPushButton("...")
subject_dir_layout.addWidget(select_subject_dir_btn)
select_subject_dir_btn.clicked.connect(self.open_subject_dir_dlg)
v_layout.addLayout(subject_dir_layout)
self.subject_dir_wgt.textChanged.connect(self.set_subject_dir)
if not Path(self.config["DEFAULT"]["subject_dir"]).exists():
msgBox = QtWidgets.QMessageBox()
msgBox.setIcon(QtWidgets.QMessageBox.Information)
msgBox.setText(f"The chosen subject directory (i.e. {self.config['DEFAULT']['subject_dir']}) does not "
"exist. Do you want to create it or to select a new directory?")
msgBox.setWindowTitle("Non-existent subject directory")
button_create = msgBox.addButton("Create it!", QtWidgets.QMessageBox.YesRole);
msgBox.addButton("Select a different directory", QtWidgets.QMessageBox.NoRole)
msgBox.exec_()
if msgBox.clickedButton() == button_create:
Path(self.config["DEFAULT"]["subject_dir"]).mkdir(exist_ok=True, parents=True)
else:
self.open_subject_dir_dlg()
#h_layout.addLayout(v_layout)
v_layout_widget = QtWidgets.QWidget(self)
v_layout_widget.setLayout(v_layout)
self.addWidget(v_layout_widget)
self.data = QtCore.QUrl.fromLocalFile(str(Path(__file__).parent.absolute() / f"{self.fs_subject}_head.obj"))
self.root_entity = Qt3DCore.QEntity()
self.material = Qt3DExtras.QPhongMaterial()
self.material.setDiffuse(QtGui.QColor(254, 254, 254))
self.camera = self.view.camera()
self.camera.lens().setPerspectiveProjection(400.0, 16.0/9.0, 100, 1200.0)
self.camera.setPosition(QtGui.QVector3D(0, 500, 0))
self.camera.setUpVector(QtGui.QVector3D(0, 0, 1))
self.lightEntities = {}
self.lights = {}
self.lightTransforms = {}
for trans_x in [200, -200]:
for trans_y in [200, -200]:
self.lightEntities[(trans_x, trans_y)] = Qt3DCore.QEntity(self.root_entity)
self.lights[(trans_x, trans_y)] = Qt3DRender.QPointLight(self.lightEntities[(trans_x, trans_y)])
self.lights[(trans_x, trans_y)].setColor("white")
self.lights[(trans_x, trans_y)].setIntensity(0.4)
self.lightEntities[(trans_x, trans_y)].addComponent(self.lights[(trans_x, trans_y)])
self.lightTransforms[(trans_x, trans_y)] = Qt3DCore.QTransform(self.lightEntities[(trans_x, trans_y)])
self.lightTransforms[(trans_x, trans_y)].setTranslation(QtGui.QVector3D(trans_x, trans_y, 100.0))
self.lightEntities[(trans_x, trans_y)].addComponent(self.lightTransforms[(trans_x, trans_y)])
# Get co-registered head, fiducials and electrodes
data_path = Path(mne.datasets.sample.data_path())
fs_subjects_dir = data_path / 'subjects'
trans_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_raw-trans.fif'
trans = mne.read_trans(trans_fname)
montage = mne.channels.make_standard_montage('GSN-HydroCel-129')
info = mne.create_info(montage.ch_names, 100, ch_types='eeg')
raw = mne.io.RawArray(np.zeros((len(montage.ch_names), 100)), info)
raw.set_montage(montage)
eeg, fid, surf = get_aligned_artifacts(raw.info, subject=self.fs_subject, trans=trans,
subjects_dir=fs_subjects_dir, coord_frame='mri')
self.head_surf = surf
path_out = Path(str(Path(__file__).parent.absolute() / f"{self.fs_subject}_head.obj"))
if True: #not path_out.exists():
mesh = trimesh.Trimesh(surf["rr"] * 1000, surf["tris"])
open3d_mesh = open3d.geometry.TriangleMesh(vertices=open3d.utility.Vector3dVector(mesh.vertices),
triangles=open3d.utility.Vector3iVector(mesh.faces))
mesh = open3d_mesh.simplify_quadric_decimation(int(20000))
mesh = trimesh.Trimesh(np.asarray(mesh.vertices), np.asarray(mesh.triangles))
with path_out.open('w') as file_obj:
file_obj.write(trimesh.exchange.obj.export_obj(mesh))
# Head
self.data = QtCore.QUrl.fromLocalFile(str(path_out))
self.head_entity = Qt3DCore.QEntity(self.root_entity)
self.head_mesh = Qt3DRender.QMesh()
self.head_mesh.setMeshName(str(path_out))
self.head_mesh.setSource(self.data)
self.head_entity.addComponent(self.head_mesh)
self.head_entity.addComponent(self.material)
self.camController = Qt3DExtras.QOrbitCameraController(self.head_mesh)
self.camController.setCamera(self.camera)
self.camController.setLinearSpeed(self.camController.linearSpeed()*100)
self.mesh_center_of_mass = np.median(surf['rr'], 0)*1000
self.camera.setViewCenter(QtGui.QVector3D(*(self.mesh_center_of_mass)))
self.camera.viewCenterChanged.connect(self.cam_view_center_changed)
## EEG electrodes and Fiducials
self.electrode_material = Qt3DExtras.QPhongMaterial(diffuse=QtGui.QColor("#665423"))
self.fid_material = Qt3DExtras.QPhongMaterial(diffuse=QtGui.QColor("#0000FF"))
self.selected_material = Qt3DExtras.QPhongMaterial(diffuse=QtGui.QColor("#FF0000"))
self.edited_material = Qt3DExtras.QPhongMaterial(diffuse=QtGui.QColor("#FFFF00"))
self.acq_material = Qt3DExtras.QPhongMaterial(diffuse=QtGui.QColor("#00FF00"))
self.selected_item = None
self.coordinate_meshes = {}
self.coordinate_entities = {}
self.coordinate_transforms = {}
self.coordinate_materials = {}
for kind, var in zip(["fid", "elec"], [fid, eeg]):
for label, pos in var.iterrows():
pos = pos.values*1000
self.coordinate_meshes[label] = Qt3DExtras.QSphereMesh(rings=20, slices=20, radius=3)
self.coordinate_entities[label] = Qt3DCore.QEntity(self.root_entity)
self.coordinate_transforms[label] = Qt3DCore.QTransform(self.coordinate_meshes[label])
self.coordinate_transforms[label].setTranslation(QtGui.QVector3D(*pos))
self.coordinate_entities[label].addComponent(self.coordinate_meshes[label])
self.coordinate_entities[label].addComponent(self.coordinate_transforms[label])
self.acq_coordinate_meshes = {}
self.acq_coordinate_entities = {}
self.acq_coordinate_transforms = {}
self.df_montage = pd.concat([fid, eeg])
self.df_montage.columns = ["x", "y", "z"]
self.df_acq = pd.concat([self.df_montage.copy().rename(columns={"x": f"x{i+1}", "y": f"y{i+1}", "z": f"z{i+1}"})
for i in range(4)], axis=1)
model = DataFrameModel(self.df_acq)
self.tableView.setModel(model)
self.df_acq.loc[:, :] = np.nan
self.set_table_view_selection(0)
self.view.setRootEntity(self.root_entity)
self.subject_name_wgt.currentTextChanged.connect(self.load_subject)
self.update_subject_lst()