def get_scene_camera(camera, atlas):
"""
Gets a working camera.
In order these alternatives are used:
- user given camera
- atlas specific camera
- default camera
"""
if camera is None:
if atlas.default_camera is not None:
return check_camera_param(atlas.default_camera)
else:
return brainrender.CAMERA
else:
return check_camera_param(camera)
def render(self,
interactive=True,
video=False,
camera=None,
zoom=None,
**kwargs):
"""
Takes care of rendering the scene
"""
self.apply_render_style()
if not video:
if (not self.jupyter
): # cameras work differently in jupyter notebooks?
if camera is None:
camera = self.camera
if isinstance(
camera,
(str, dict)): # otherwise assume that it's vtk.camera
camera = check_camera_param(camera)
set_camera(self, camera)
if interactive:
if self.verbose and not self.jupyter:
print(brainrender.INTERACTIVE_MSG)
elif self.jupyter:
print(
"The scene is ready to render in your jupyter notebook"
)
else:
print("\n\nRendering scene.\n Press 'q' to Quit")
self._get_inset()
if zoom is None and not video:
zoom = 1.85 if brainrender.WHOLE_SCREEN else 1.5
# Make mesh labels follow the camera
if not self.jupyter:
for txt in self.actors_labels:
txt.followCamera(self.plotter.camera)
self.is_rendered = True
args_dict = dict(
interactive=interactive,
zoom=zoom,
bg=brainrender.BACKGROUND_COLOR,
axes=self.plotter.axes,
)
if video:
args_dict["offscreen"] = True
show(*self.actors, *self.actors_labels, **args_dict)
def render(self,
interactive=True,
video=False,
camera=None,
zoom=None,
**kwargs):
"""
Takes care of rendering the scene
"""
self.apply_render_style()
if not video:
if (not self.jupyter
): # cameras work differently in jupyter notebooks?
if camera is None:
camera = self.camera
if isinstance(
camera,
(str, dict)): # otherwise assume that it's vtk.camera
camera = check_camera_param(camera)
set_camera(self, camera)
if interactive and self.verbose:
if not self.jupyter:
print(
f"\n\n[{mocassin}]Rendering scene.\n Press [{orange}]'q'[/{orange}] to Quit"
)
elif self.jupyter:
print(
f"[{mocassin}]The scene is ready to render in your jupyter notebook"
)
self._get_inset()
if zoom is None and not video:
zoom = 1.2 if brainrender.WHOLE_SCREEN else 1.5
# Make mesh labels follow the camera
if not self.jupyter:
for txt in self.actors_labels:
txt.followCamera(self.plotter.camera)
self.is_rendered = True
args_dict = dict(
interactive=interactive,
zoom=zoom,
bg=brainrender.BACKGROUND_COLOR,
axes=self.plotter.axes,
)
if video:
args_dict["offscreen"] = True
if self.make_custom_axes:
self._make_custom_axes()
self.make_custom_axes = False
# Correct axes orientations
if not self._axes_order_corrected:
self._correct_axes()
show(*self.actors, *self.actors_labels, **args_dict)
def __init__(self,
brain_regions=None,
regions_aba_color=False,
neurons=None,
tracts=None,
add_root=None,
verbose=True,
jupyter=False,
display_inset=None,
base_dir=None,
camera=None,
screenshot_kwargs = {},
use_default_key_bindings=False,
title=None,
atlas=None,
atlas_kwargs=dict(),
**kwargs):
"""
Creates and manages a Plotter instance
:param brain_regions: list of brain regions acronyms to be added to the rendered scene (default value None)
:param regions_aba_color: if True, use the Allen Brain Atlas regions colors (default value None)
:param neurons: path to JSON or SWC file with data of neurons to be rendered [or list of files] (default value None)
:param tracts: list of JSON files with tractography data to be rendered (default value None)
:param add_root: if False a rendered outline of the whole brain is added to the scene (default value None)
:param verbose: if False less feedback is printed to screen (default value True)
:param display_insert: if False the inset displaying the brain's outline is not rendered (but the root is added to the scene) (default value None)
:param base_dir: path to directory to use for saving data (default value None)
:param camera: name of the camera parameters setting to use (controls the orientation of the rendered scene)
:param kwargs: can be used to pass path to individual data folders. See brainrender/Utils/paths_manager.py
:param screenshot_kwargs: pass a dictionary with keys:
- 'folder' -> str, path to folder where to save screenshots
- 'name' -> str, filename to prepend to screenshots files
- 'format' -> str, 'png', 'svg' or 'jpg'
- scale -> float, values > 1 yield higher resultion screenshots
:param use_default_key_bindings: if True the defualt keybindings from VtkPlotter are used, otherwise
a custom function that can be used to take screenshots with the parameter above.
:param title: str, if a string is passed a text is added to the top of the rendering window as a title
:param atlas: an instance of a valid Atlas class to use to fetch anatomical data for the scene. By default
if not atlas is passed the allen brain atlas for the adult mouse brain is used.
:param atlas_kwargs: dictionary used to pass extra arguments to atlas class
"""
if atlas is None:
self.atlas = ABA(base_dir=base_dir, **atlas_kwargs, **kwargs)
else:
self.atlas = atlas(base_dir=base_dir, **atlas_kwargs, **kwargs)
# Setup a few rendering options
self.verbose = verbose
self.regions_aba_color = regions_aba_color
# Infer if we are using k3d from vtkplotter.settings
if settings.notebookBackend == 'k3d':
self.jupyter = True
else:
self.jupyter = False
if display_inset is None:
self.display_inset = brainrender.DISPLAY_INSET
else:
self.display_inset = display_inset
if self.display_inset and jupyter:
print("Setting 'display_inset' to False as this feature is not available in juputer notebooks")
self.display_inset = False
if add_root is None:
add_root = brainrender.DISPLAY_ROOT
# Camera parameters
if camera is None:
if self.atlas.default_camera is not None:
self.camera = check_camera_param(self.atlas.default_camera)
else:
self.camera = brainrender.CAMERA
else:
self.camera = check_camera_param(camera)
# Set up vtkplotter plotter and actors records
if brainrender.WHOLE_SCREEN and not self.jupyter:
sz = "full"
elif brainrender.WHOLE_SCREEN and self.jupyter:
print("Setting window size to 'auto' as whole screen is not available in jupyter")
sz='auto'
else:
sz = "auto"
if brainrender.SHOW_AXES:
axes = 1
else:
axes = 0
# Create plotter
self.plotter = Plotter(axes=axes, size=sz, pos=brainrender.WINDOW_POS, title='brainrender')
self.plotter.legendBC = getColor('blackboard')
# SCreenshots and keypresses variables
self.screenshots_folder = screenshot_kwargs.pop('folder', self.atlas.output_screenshots)
self.screenshots_name = screenshot_kwargs.pop('name', brainrender.DEFAULT_SCREENSHOT_NAME)
self.screenshots_extension = screenshot_kwargs.pop('type', brainrender.DEFAULT_SCREENSHOT_TYPE)
self.screenshots_scale = screenshot_kwargs.pop('scale', brainrender.DEFAULT_SCREENSHOT_SCALE)
if not use_default_key_bindings:
self.plotter.keyPressFunction = self.keypress
self.verbose = False
if not brainrender.SCREENSHOT_TRANSPARENT_BACKGROUND:
settings.screenshotTransparentBackground = False
settings.useFXAA = True
# Prepare store for actors added to scene
self.actors = {"regions":{}, "tracts":[], "neurons":[], "root":None, "injection_sites":[],
"others":[], "labels":[],}
self._actors = None # store a copy of the actors when manipulations like slicing are done
self.store = {} # in case we need to store some data
# Add items to scene
if brain_regions is not None:
self.add_brain_regions(brain_regions)
if neurons is not None:
self.add_neurons(neurons)
if tracts is not None:
self.add_tractography(tracts)
if add_root:
self.add_root(render=True)
else:
self.root = None
if title is not None:
self.add_text(title)
# Placeholder variables
self.inset = None # the first time the scene is rendered create and store the inset here
self.is_rendered = False # keep track of if the scene has already been rendered
