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vtk_overlay_window.py
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vtk_overlay_window.py
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# -*- coding: utf-8 -*-
# pylint: disable=too-many-instance-attributes, no-name-in-module
# pylint:disable=super-with-arguments, too-many-arguments, line-too-long
"""
Module to provide a set of VTK renderers that can be used to create an Augmented Reality viewer.
Expected usage:
::
window = VTKOverlayWindow()
window.add_vtk_models(list) # list of VTK models
window.add_vtk_actor(actor) # or individual actor
window.set_camera_matrix(ndarray) # Set 3x3 ndarray of OpenCV camera intrinsic matrix.
while True:
image = # acquire np.ndarray image some how, e.g. from webcam or USB source.
window.set_video_image(image)
window.set_camera_pose(camera_to_world) # set 4x4 ndarray
"""
import logging
import cv2
import numpy as np
import sksurgerycore.utilities.validate_matrix as vm
import vtk
from PySide6.QtWidgets import QSizePolicy
from vtk.util.numpy_support import vtk_to_numpy
from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
import sksurgeryvtk.camera.vtk_camera_model as cm
import sksurgeryvtk.utils.matrix_utils as mu
LOGGER = logging.getLogger(__name__)
class VTKOverlayWindow(QVTKRenderWindowInteractor):
"""
Sets up a VTK Overlay Window that can be used to
overlay multiple VTK models on a video stream. Internally, the Window
has 5 renderers, 0=backmost, 5=frontmost.
# Level 0: Video
# Level 1: VTK rendered models - e.g. internal anatomy
# Level 2: Video
# Level 3: VTK rendered models - e.g. external anatomy
# Level 4: VTK rendered text annotations.
The video channels should be RGBA. You can choose in the constructor
whether the video should go to Level 0 or Level 2.
If you put video in the Level 0, and overlay models in Level 1, you get a simple overlay
which may be suitable for things like overlaying calibration points on chessboards,
but you will get poor visual coherence for medical AR, as the bright colours of a synthetic overlay
will always make the model appear in front of the video, even when you dial back the opacity of the model.
If you put the video in Level 2, it would obscure the rendered models in Level 1.
But you can apply a mask to the alpha channel setting the alpha to either 0 or 255.
If the mask contains say a circle, it will have the effect of showing the video when the
alpha channel is 255 and the rendering behind when the alpha channel is 0. So, you can
use this to peek inside an organ by rendering the video in Level 2 with a mask creating a hole,
and the internal anatomy in Level 1. Then you put the external anatomy, e.g. liver surface in Level 3.
:param offscreen: Enable/Disable offscreen rendering.
:param camera_matrix: Camera extrinsics matrix.
:param clipping_range: Near/Far clipping range.
:param zbuffer: If True, will only render zbuffer of main renderer.
:param opencv_style: If True, adopts OpenCV camera convention, otherwise OpenGL.
:param init_pose: If True, will initialise the camera pose to identity.
:param reset_camera: If True, resets camera when a new model is added.
:param init_widget: If True we will call self.Initialize and self.Start
as part of the init function. Set to false if you're on Linux.
:param video_in_level_0: If true, will add video to level 0, fully opaque, no masking.
:param video_in_level_2: If true, will add video to level 1. If level_2_video_mask is present, will mask alpha channel.
"""
def __init__(
self,
offscreen=False,
camera_matrix=None,
clipping_range=(1, 1000),
zbuffer=False,
opencv_style=True,
init_pose=False,
reset_camera=True,
init_widget=True,
video_in_level_0=True, # For backwards compatibility, prior to 3rd Feb 2024.
video_in_level_2=False, # For backwards compatibility, prior to 3rd Feb 2024.
level_2_video_mask=None, # For masking in level 3
):
"""
Constructs a new VTKOverlayWindow.
"""
super(VTKOverlayWindow, self).__init__()
# Take and cache/store constructor arguments.
if offscreen:
self.GetRenderWindow().SetOffScreenRendering(1)
else:
self.GetRenderWindow().SetOffScreenRendering(0)
self.camera_matrix = camera_matrix
self.clipping_range = clipping_range
self.zbuffer = zbuffer
self.opencv_style = opencv_style
self.reset_camera = reset_camera
self.video_in_level_0 = video_in_level_0
self.video_in_level_2 = video_in_level_2
self.level_2_video_mask = level_2_video_mask
# Some default reference data, or member variables.
self.aspect_ratio = 1
self.camera_to_world = np.eye(4)
self.rgb_input = np.ones((400, 400, 3), dtype=np.uint8)
self.rgb_frame = None
self.rgba_frame = None
self.screen = None
# VTK objects initialised later
self.output = None
self.output_halved = None
self.vtk_image = None
self.vtk_array = None
self.interactor = None
# Setup an image importer to import the RGB video image.
# Until the image is set, we use the default one created above.
self.rgb_image_extent = (
0,
self.rgb_input.shape[1] - 1,
0,
self.rgb_input.shape[0] - 1,
0,
self.rgb_input.shape[2] - 1,
)
self.rgb_image_importer = vtk.vtkImageImport()
self.rgb_image_importer.SetDataScalarTypeToUnsignedChar()
self.rgb_image_importer.SetNumberOfScalarComponents(3)
self.rgb_image_importer.SetDataExtent(self.rgb_image_extent)
self.rgb_image_importer.SetWholeExtent(self.rgb_image_extent)
# Setup an image importer to import the RGBA video image.
# Until the image is set, we use the default one created above.
self.rgba_image_extent = (
0,
self.rgb_input.shape[1] - 1,
0,
self.rgb_input.shape[0] - 1,
0,
self.rgb_input.shape[2],
)
self.rgba_image_importer = vtk.vtkImageImport()
self.rgba_image_importer.SetDataScalarTypeToUnsignedChar()
self.rgba_image_importer.SetNumberOfScalarComponents(4)
self.rgba_image_importer.SetDataExtent(self.rgba_image_extent)
self.rgba_image_importer.SetWholeExtent(self.rgba_image_extent)
# Enable VTK Depth peeling settings for render window.
self.GetRenderWindow().AlphaBitPlanesOn()
self.GetRenderWindow().SetMultiSamples(0)
# Five layers used, see class level docstring.
self.GetRenderWindow().SetNumberOfLayers(5)
# Create and setup Level 0 (video) renderer.
self.level_0_image_actor = vtk.vtkImageActor()
self.level_0_image_actor.SetInputData(self.rgb_image_importer.GetOutput())
self.level_0_image_actor.VisibilityOff()
self.level_0_renderer = vtk.vtkRenderer()
self.level_0_renderer.SetLayer(0)
self.level_0_renderer.InteractiveOff()
self.level_0_renderer.AddActor(self.level_0_image_actor)
self.level_0_camera = self.level_0_renderer.GetActiveCamera()
self.level_0_camera.ParallelProjectionOn()
# Create and setup Level 1 (VTK scene) renderer.
self.level_1_renderer = vtk.vtkRenderer()
self.level_1_renderer.SetLayer(1)
self.level_1_renderer.LightFollowCameraOn()
self.level_1_renderer.UseDepthPeelingOn()
self.level_1_renderer.SetMaximumNumberOfPeels(100)
self.level_1_renderer.SetOcclusionRatio(0.1)
# Create and setup Level 2 (masked video) renderer.
self.level_2_image_actor = vtk.vtkImageActor()
self.level_2_image_actor.SetInputData(self.rgba_image_importer.GetOutput())
self.level_2_image_actor.VisibilityOff()
self.level_2_renderer = vtk.vtkRenderer()
self.level_2_renderer.SetLayer(2)
self.level_2_renderer.InteractiveOff()
self.level_2_renderer.AddActor(self.level_2_image_actor)
self.level_2_camera = self.level_2_renderer.GetActiveCamera()
self.level_2_camera.ParallelProjectionOn()
# Create and setup Level 3 (VTK scene) renderer.
self.level_3_renderer = vtk.vtkRenderer()
self.level_3_renderer.SetLayer(3)
self.level_3_renderer.LightFollowCameraOn()
self.level_3_renderer.UseDepthPeelingOn()
self.level_3_renderer.SetMaximumNumberOfPeels(100)
self.level_3_renderer.SetOcclusionRatio(0.1)
# Create and setup Level 4 (Overlay's, like text annotations) renderer.
self.level_4_renderer = vtk.vtkRenderer()
self.level_4_renderer.SetLayer(4)
self.level_4_renderer.LightFollowCameraOn()
# Use this to ensure the video is setup correctly at construction.
self.set_video_image(self.rgb_input)
# Setup the general interactor style. See VTK docs for alternatives.
self.interactor = vtk.vtkInteractorStyleTrackballCamera()
self.SetInteractorStyle(self.interactor)
# Hook VTK world up to window
# The ordering of these statements is important. If we want the
# be able to move the camera around the foreground (or move the)
# foreground objects using RenderWindowInteractor, the foreground
# should be added last.
if not self.zbuffer:
self.GetRenderWindow().AddRenderer(self.level_0_renderer)
self.GetRenderWindow().AddRenderer(self.level_1_renderer)
self.GetRenderWindow().AddRenderer(self.level_2_renderer)
self.GetRenderWindow().AddRenderer(self.level_3_renderer)
self.GetRenderWindow().AddRenderer(self.level_4_renderer)
else:
self.GetRenderWindow().AddRenderer(self.level_1_renderer)
# Set Qt Size Policy
self.size_policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setSizePolicy(self.size_policy)
# Set default position to origin.
if init_pose:
default_pose = np.eye(4)
self.set_camera_pose(default_pose)
# Startup the widget
if init_widget:
self.Initialize() # Allows the interactor to initialize itself.
self.Start() # Start the event loop.
else:
print(
"\nYou've elected to initialize the VTKOverlayWindow(),",
"be sure to do it in your calling function.",
)
def closeEvent(self, evt):
super().closeEvent(evt)
self.Finalize()
def set_video_image(self, input_image):
"""
Sets the video image that is used for the background.
See also constructor args video_in_level_0 and video_in_level_2 which controls
in which layer(s) the video image ends up.
"""
if not isinstance(input_image, np.ndarray):
raise TypeError("Input is not an np.ndarray")
if len(input_image.shape) != 3:
raise ValueError("Input image should be 3 channel, i.e. RGB.")
# Note: We will assume that any video comming in is 3 channel, BGR.
# But layer 2 will use RGBA as we need the alpha channel.
if (
self.video_in_level_0 and self.rgb_input.shape != input_image.shape
): # i.e. if the size has changed.
self.level_0_image_actor.VisibilityOn()
self.rgb_image_extent = (
0,
input_image.shape[1] - 1,
0,
input_image.shape[0] - 1,
0,
input_image.shape[2] - 1,
)
self.rgb_image_importer.SetDataExtent(self.rgb_image_extent)
self.rgb_image_importer.SetWholeExtent(self.rgb_image_extent)
if (
self.video_in_level_2 and self.rgb_input.shape != input_image.shape
): # i.e. if the size has changed.
self.level_2_image_actor.VisibilityOn()
self.rgba_image_extent = (
0,
self.input_image.shape[1] - 1,
0,
self.input_image.shape[0] - 1,
0,
self.input_image.shape[2],
)
self.rgba_image_importer.SetDataExtent(self.rgba_image_extent)
self.rgba_image_importer.SetWholeExtent(self.rgba_image_extent)
if self.video_in_level_0 or self.video_in_level_2:
self.__update_video_image_cameras()
self.__update_projection_matrices()
if self.video_in_level_0:
self.rgb_input = input_image
self.rgb_frame = np.copy(self.rgb_input[:, :, ::-1])
self.rgb_image_importer.SetImportVoidPointer(self.rgb_frame.data)
self.rgb_image_importer.SetDataExtent(self.rgb_image_extent)
self.rgb_image_importer.SetWholeExtent(self.rgb_image_extent)
self.rgb_image_importer.Modified()
self.rgb_image_importer.Update()
if self.video_in_level_2:
self.rgb_input = input_image
self.rgba_frame = 255 * np.ones(
(
input_image.shape[0],
input_image.shape[1],
input_image.shape[2],
),
dtype=np.uint8,
)
self.rgba_frame[:, :, 0:3] = self.rgb_input
self.rgba_image_importer.SetImportVoidPointer(self.rgba_frame.data)
self.rgba_image_importer.SetDataExtent(self.image_extent)
self.rgba_image_importer.SetWholeExtent(self.image_extent)
self.rgba_image_importer.Modified()
self.rgba_image_importer.Update()
def __update_video_image_camera(self, camera, image_extent):
"""
Internal method to position a renderers camera to face a video image,
and to maximise the view of the image in the viewport.
"""
origin = (0, 0, 0)
spacing = (1, 1, 1)
# Works out the number of millimetres to the centre of the image.
x_c = origin[0] + 0.5 * (image_extent[0] + image_extent[1]) * spacing[0]
y_c = origin[1] + 0.5 * (image_extent[2] + image_extent[3]) * spacing[1]
# Works out the total size of the image in millimetres.
i_w = (image_extent[1] - image_extent[0] + 1) * spacing[0]
i_h = (image_extent[3] - image_extent[2] + 1) * spacing[1]
# Works out the ratio of required size to actual size.
w_r = i_w / self.width()
h_r = i_h / self.height()
# Then you adjust scale differently depending on whether the
# screen is predominantly wider than your image, or taller.
if w_r > h_r:
scale = 0.5 * i_w * (self.height() / self.width())
else:
scale = 0.5 * i_h
camera.SetFocalPoint(x_c, y_c, 0.0)
camera.SetPosition(x_c, y_c, -1000)
camera.SetViewUp(0.0, -1.0, 0.0)
camera.SetClippingRange(990, 1010)
camera.SetParallelProjection(True)
camera.SetParallelScale(scale)
def __update_video_image_cameras(self):
"""
Position the background renderer camera, so that the video image
is maximised and centralised in the screen.
"""
if self.video_in_level_0:
self.__update_video_image_camera(
self.level_0_renderer.GetActiveCamera(), self.rgb_image_extent
)
if self.video_in_level_2:
self.__update_video_image_camera(
self.level_2_renderer.GetActiveCamera(), self.rgba_image_extent
)
def __update_projection_matrix(self, renderer, camera, input_image):
"""
If a camera_matrix is available, then we are using a calibrated camera.
This method recomputes the projection matrix, dependent on window size.
"""
opengl_mat = None
vtk_mat = None
if self.camera_matrix is not None:
if input_image is None:
raise ValueError("Camera matrix is provided, but no image.")
opengl_mat, vtk_mat = cm.set_camera_intrinsics(
renderer,
camera,
input_image.shape[1],
input_image.shape[0],
self.camera_matrix[0][0],
self.camera_matrix[1][1],
self.camera_matrix[0][2],
self.camera_matrix[1][2],
self.clipping_range[0],
self.clipping_range[1],
)
vpx, vpy, vpw, vph = cm.compute_scissor(
self.width(),
self.height(),
input_image.shape[1],
input_image.shape[0],
self.aspect_ratio,
)
x_min, y_min, x_max, y_max = cm.compute_viewport(
self.width(), self.height(), vpx, vpy, vpw, vph
)
renderer.SetViewport(x_min, y_min, x_max, y_max)
vtk_rect = vtk.vtkRecti(vpx, vpy, vpw, vph)
camera.SetUseScissor(True)
camera.SetScissorRect(vtk_rect)
return opengl_mat, vtk_mat
def __update_projection_matrices(self):
"""
If a camera_matrix is available, then we are using a calibrated camera.
This method recomputes the projection matrix, dependent on window size.
"""
renderer = self.get_foreground_renderer(layer=1)
opengl_mat, vtk_mat = self.__update_projection_matrix(
renderer,
renderer.GetActiveCamera(),
self.rgb_input,
)
renderer = self.get_foreground_renderer(layer=3)
opengl_mat, vtk_mat = self.__update_projection_matrix(
renderer,
renderer.GetActiveCamera(),
self.rgb_input,
)
return opengl_mat, vtk_mat
def resizeEvent(self, ev):
"""
Ensures that when the window is resized, the background renderer
will correctly reposition the camera such that the image fully
fills the screen, and if the foreground renderer is calibrated,
also updates the projection matrix.
:param ev: Event
"""
super(VTKOverlayWindow, self).resizeEvent(ev)
self.__update_video_image_cameras()
self.__update_projection_matrices()
self.Render()
def set_camera_matrix(self, camera_matrix):
"""
Sets the camera projection matrix from a numpy 3x3 array.
:param camera_matrix: numpy 3x3 ndarray containing fx, fy, cx, cy
"""
vm.validate_camera_matrix(camera_matrix)
self.camera_matrix = camera_matrix
opengl_mat, vtk_mat = self.__update_projection_matrices()
self.Render()
return opengl_mat, vtk_mat
def set_camera_pose(self, camera_to_world):
"""
Sets the camera position and orientation, from a numpy 4x4 array.
:param camera_to_world: camera_to_world transform.
"""
vm.validate_rigid_matrix(camera_to_world)
self.camera_to_world = camera_to_world
vtk_mat = mu.create_vtk_matrix_from_numpy(camera_to_world)
cm.set_camera_pose(
self.level_1_renderer.GetActiveCamera(), vtk_mat, self.opencv_style
)
cm.set_camera_pose(
self.level_3_renderer.GetActiveCamera(), vtk_mat, self.opencv_style
)
self.Render()
def add_vtk_models(self, models, layer=1):
"""
Add VTK models to a renderer.
Here, a 'VTK model' is any object that has an attribute called actor
that is a vtkActor.
:param models: list of VTK models.
:param layer: Render layer to add to, default 1 (forground)
"""
if layer == 0:
raise ValueError("You shouldn't add actors to the background video.")
if layer == 1:
renderer = self.level_1_renderer
elif layer == 2:
raise ValueError("You shouldn't add actors to the midground video.")
elif layer == 3:
renderer = self.level_3_renderer
elif layer == 4:
renderer = self.level_4_renderer
else:
raise ValueError("Invalid layer specified")
for model in models:
renderer.AddActor(model.actor)
if model.get_outline():
renderer.AddActor(model.get_outline_actor(renderer.GetActiveCamera()))
if self.reset_camera:
renderer.ResetCamera()
def add_vtk_actor(self, actor, layer=1):
"""
Add a vtkActor directly.
:param actor: vtkActor
:param layer: Render layer to add to, default 1 (foreground)
"""
if layer == 0:
raise ValueError("You shouldn't add actors to the background video.")
if layer == 1:
renderer = self.level_1_renderer
elif layer == 2:
raise ValueError("You shouldn't add actors to the midground video.")
elif layer == 3:
renderer = self.level_3_renderer
elif layer == 4:
renderer = self.level_4_renderer
else:
raise ValueError("Invalid layer specified")
renderer.AddActor(actor)
if self.reset_camera:
renderer.ResetCamera()
def get_background_renderer(self):
"""
Returns one of the background video layers, depending on
the constructor arguments. So, either level 0 or 2.
"""
if self.video_in_level_0:
return self.level_0_renderer
if self.video_in_level_2:
return self.level_2_renderer
raise ValueError("Didn't find background renderer.")
def get_foreground_renderer(self, layer=1):
"""
Returns the foreground vtkRenderer. For legacy compatibility,
this will assume layer 1, like this class was pre-Feb 3rd 2024.
:return: vtkRenderer
"""
if layer == 0:
raise ValueError("Layer 0 is not a foreground renderer.")
if layer == 1:
return self.level_1_renderer
if layer == 2:
raise ValueError("Layer 2 is not a foreground renderer.")
if layer == 3:
return self.level_3_renderer
if layer == 4:
return self.level_4_renderer
raise ValueError(f"Invalid layer specification:{layer}")
def get_foreground_camera(self, layer=1):
"""
Returns the camera for the foreground vtkRenderer. For legacy compatibility,
this will assume layer 1, like this class was pre-Feb 3rd 2024.
:returns: vtkCamera
"""
renderer = self.get_foreground_renderer(layer)
return renderer.GetActiveCamera()
def set_foreground_camera(self, camera, layer=1):
"""
Set the foreground camera to track the view in another window. For legacy compatibility,
this will assume layer 1, like this class was pre-Feb 3rd 2024.
"""
renderer = self.get_foreground_renderer(layer)
renderer.SetActiveCamera(camera)
def get_overlay_renderer(self):
"""
This returns the top-most layer, where you might put text annotations for example.
"""
return self.level_4_renderer
def set_screen(self, screen):
"""
Link the widget with a particular screen.
This is necessary when we have multi-monitor setups.
:param screen: QScreen object.
"""
self.screen = screen
self.move(screen.geometry().x(), screen.geometry().y())
def set_stereo_left(self):
"""
Set the render window to left stereo view.
"""
self._RenderWindow.SetStereoTypeToLeft()
def set_stereo_right(self):
"""
Set the render window to right stereo view.
"""
self._RenderWindow.SetStereoTypeToRight()
def convert_scene_to_numpy_array(self):
"""
Convert the current window view to a numpy array.
:return output: Scene as numpy array
"""
vtk_win_to_img_filter = vtk.vtkWindowToImageFilter()
vtk_win_to_img_filter.SetInput(self.GetRenderWindow())
if not self.zbuffer:
vtk_win_to_img_filter.SetInputBufferTypeToRGB()
vtk_win_to_img_filter.Update()
self.vtk_image = vtk_win_to_img_filter.GetOutput()
else:
vtk_win_to_img_filter.SetInputBufferTypeToZBuffer()
vtk_scale = vtk.vtkImageShiftScale()
vtk_scale.SetInputConnection(vtk_win_to_img_filter.GetOutputPort())
vtk_scale.SetOutputScalarTypeToUnsignedChar()
vtk_scale.SetShift(0)
vtk_scale.SetScale(-255)
vtk_scale.Update()
self.vtk_image = vtk_scale.GetOutput()
width, height, _ = self.vtk_image.GetDimensions()
self.vtk_array = self.vtk_image.GetPointData().GetScalars()
number_of_components = self.vtk_array.GetNumberOfComponents()
np_array = vtk_to_numpy(self.vtk_array).reshape(
height, width, number_of_components
)
self.output = cv2.flip(np_array, flipCode=0)
return self.output
def save_scene_to_file(self, file_name):
"""
Save's the current screen to file.
VTK works in RGB, but OpenCV assumes BGR, so swap the colour
space before saving to file.
:param file_name: must be compatible with cv2.imwrite()
"""
self.convert_scene_to_numpy_array()
self.output = cv2.cvtColor(self.output, cv2.COLOR_RGB2BGR)
cv2.imwrite(file_name, self.output)
def get_camera_state(self, layer=1):
"""
Get all the necessary variables to allow the camera
view to be restored. For legacy compatibility,
this will assume layer 1, like this class was pre-Feb 3rd 2024.
"""
# pylint: disable=unused-variable, eval-used
renderer = self.get_foreground_renderer(layer)
camera = renderer.GetActiveCamera()
camera_properties = {}
properties_to_save = [
"Position",
"FocalPoint",
"ViewUp",
"ViewAngle",
"ParallelProjection",
"ParallelScale",
"ClippingRange",
"EyeAngle",
"EyeSeparation",
"UseOffAxisProjection",
]
for camera_property in properties_to_save:
# eval will run commands of the form
# 'camera.GetPosition()', 'camera.GetFocalPoint()' for each property
property_value = eval("camera.Get" + camera_property + "()")
camera_properties[camera_property] = property_value
return camera_properties
def set_camera_state(self, camera_properties, layer=1):
"""
Set the camera properties to a particular view poisition/angle etc. For legacy compatibility,
this will assume layer 1, like this class was pre-Feb 3rd 2024.
"""
# pylint: disable=unused-variable, eval-used
renderer = self.get_foreground_renderer(layer)
camera = renderer.GetActiveCamera()
for camera_property, value in camera_properties.items():
# eval statements 'camera.SetPosition(position)',
# 'camera.SetFocalPoint(focalpoint) etc.
eval("camera.Set" + camera_property + "(" + str(value) + ")")