def put_axes(view):
size = 20
domain_x = (118.34 - size / 2, 118.34 + size / 2)
domain_y = (117.69 - size / 2, 117.69 + size / 2)
xax = scene.Axis(pos=[[-0.5, -0.5], [0.5, -0.5]],
domain=domain_x,
tick_direction=(0, -1),
font_size=16,
axis_color='white',
tick_color='white',
text_color='white',
parent=view)
xax.transform = scene.STTransform(translate=(0, 0, -0.2))
yax = scene.Axis(pos=[[-0.5, -0.5], [-0.5, 0.5]],
domain=domain_y,
tick_direction=(-1, 0),
font_size=16,
axis_color='white',
tick_color='white',
text_color='white',
parent=view)
yax.transform = scene.STTransform(translate=(0, 0, -0.2))
def Vispy(matrice):
def normalize(x, cmin=None, cmax=None, clip=True):
"""Normalize an array from the range [cmin, cmax] to [0,1],
with optional clipping."""
if not isinstance(x, np.ndarray):
x = np.array(x)
if cmin is None:
cmin = x.min()
if cmax is None:
cmax = x.max()
if cmin == cmax:
return .5 * np.ones(x.shape)
else:
cmin, cmax = float(cmin), float(cmax)
y = (x - cmin) * 1. / (cmax - cmin)
if clip:
y = np.clip(y, 0., 1.)
return y
canvas = scene.SceneCanvas(keys='interactive', bgcolor='w')
view = canvas.central_widget.add_view()
view.camera = scene.TurntableCamera(up='z', fov=60)
matrice = (matrice + 1) * 127
# Simple surface plot example
# x, y values are not specified, so assumed to be 0:50
couleurs = normalize(CMAPGRAD)
couleurs = np.flip(couleurs, 0)
p1 = scene.visuals.SurfacePlot(z=matrice)
#couleurs[0]
p1.transform = scene.transforms.MatrixTransform()
p1.transform.scale([1/100, 1/100, 4/100])
p1.transform.translate([0, 0, 0])
view.add(p1)
p1._update_data()
# p1._update_data() # cheating.
cf = scene.filters.ZColormapFilter(vs.color.Colormap(couleurs, interpolation='linear'), zrange=(matrice.max(), matrice.min()))
p1.attach(cf)
xax = scene.Axis(pos=[[-0.5, -0.5], [0.5, -0.5]], tick_direction=(0, -1),
font_size=16, axis_color='k', tick_color='k', text_color='k',
parent=view.scene)
xax.transform = scene.STTransform(translate=(0, 0, -0.2))
yax = scene.Axis(pos=[[-0.5, -0.5], [-0.5, 0.5]], tick_direction=(-1, 0),
font_size=16, axis_color='k', tick_color='k', text_color='k',
parent=view.scene)
yax.transform = scene.STTransform(translate=(0, 0, -0.2))
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=view.scene)
canvas.show()
app.run()
def test_perspective_render():
with TestingCanvas(size=(120, 200)) as canvas:
grid = canvas.central_widget.add_grid()
imdata = io.load_crate().astype('float32') / 255
views = []
images = []
for i, imethod in enumerate(['impostor', 'subdivide']):
v = grid.add_view(row=i, col=0, border_color='white')
v.camera = 'turntable'
v.camera.fov = 50
v.camera.distance = 30
views.append(v)
image = scene.visuals.Image(imdata, method=imethod, grid=(4, 4))
image.transform = scene.STTransform(translate=(-12.8, -12.8),
scale=(0.1, 0.1))
v.add(image)
images.append(image)
image = canvas.render()
canvas.close()
# Allow many pixels to differ by a small amount--texture sampling and
# exact triangle position will differ across platforms. However a
# change in perspective or in the widget borders should trigger a
# failure.
assert_image_approved(image,
'scene/cameras/perspective_test.png',
'perspective test 1: 2 identical views with '
'correct perspective',
px_threshold=20,
px_count=60,
max_px_diff=200)
def test_panzoom_center():
with TestingCanvas(size=(120, 200)) as canvas:
grid = canvas.central_widget.add_grid()
imdata = io.load_crate().astype('float32') / 255
v = grid.add_view(row=0, col=0)
v.camera = 'panzoom'
image = scene.visuals.Image(imdata)
image.transform = scene.STTransform(translate=(-12.8, -12.8),
scale=(0.1, 0.1))
v.add(image)
result1 = canvas.render()[..., :3]
assert v.camera.center == (0.5, 0.5, 0)
v.camera.center = (-12.8, -12.8, 0)
result2 = canvas.render()[..., :3]
assert not np.allclose(result1, result2)
# we moved to the lower-left corner of the image that means only the
# upper-right quadrant should have data, the rest is black background
np.testing.assert_allclose(result2[100:, :], 0)
np.testing.assert_allclose(result2[:, :60], 0)
assert not np.allclose(result2[:100, 60:], 0)
assert v.camera.center == (-12.8, -12.8, 0)
def set_values(self,vol_array):
#Calculate center and range
self.calc_bounds()
# Flip axes on volume array
vol_flipped = np.flipud(np.swapaxes(vol_array,0,2))
# Draw volumetric plot
self._volume=scene.visuals.Volume(vol_flipped,clim=self._clim)
self._nx,self._ny,self._nz = vol_array.shape
self._volume.transform = scene.STTransform(
# Off centered but in bounds
translate=(self._xlim[0]+self._xr/(2*self._nx),
self._ylim[0]+self._yr/(2*self._ny),
self._zlim[0]+self._zr/(2*self._nz)),
scale=(self._xr/self._nx,self._yr/self._ny,self._zr/self._nz))
# Centered and out of bounds?
#translate=(self._xlim[0]-self._xr/(self._nx-1),
# self._ylim[0]-self._yr/(self._ny-1),
# self._zlim[0]-self._zr/(self._nz-1)),
#scale=(self._xr/(self._nx-1),
# self._yr/(self._ny-1),
# self._zr/(self._nz-1)))
self._volume.cmap = colormap.CubeHelixColormap(reverse=True)
self._volume.method = 'mip'
def preview_shifts(a, b, shifts):
canvas = scene.SceneCanvas(keys="interactive")
canvas.size = 1024, 1024
canvas.show()
# create view box
vb_xy = scene.widgets.ViewBox(border_color="white", parent=canvas.scene)
vb_xz = scene.widgets.ViewBox(border_color="white", parent=canvas.scene)
vb_yz = scene.widgets.ViewBox(border_color="white", parent=canvas.scene)
vbs = vb_xy, vb_xz, vb_yz
# put them in a grid
grid = canvas.central_widget.add_grid()
grid.padding = 6
grid.add_widget(vb_xy, 0, 0)
grid.add_widget(vb_xz, 1, 0)
grid.add_widget(vb_yz, 0, 1)
# genereate colormap
n_colors = 128
alphas = np.linspace(0.0, 1.0, n_colors)
color_red = np.c_[np.ones((n_colors, )),
np.zeros((n_colors, )),
np.zeros((n_colors)), alphas]
cmap_red = Colormap(color_red)
color_blue = np.c_[np.zeros((n_colors)),
np.zeros((n_colors, )),
np.ones((n_colors, )), alphas]
cmap_blue = Colormap(color_blue)
# build shifts for mips
sz, sy, sx = shifts
nz, ny, nx = a.shape
shifts = ((sx, sy), (sx, sz), (sy, sz))
print(shifts)
# create visuals
i = 0
for im, cm in zip((a, b), (cmap_red, cmap_blue)):
mips = [im.max(axis=axis) for axis in range(3)]
for vb, mip, shift in zip(vbs, mips, shifts):
image = scene.visuals.Image(mip, cmap=cm, parent=vb.scene)
image.set_gl_state("translucent", depth_test=False)
# apply transformation
if i > 0:
image.transform = scene.STTransform(translate=shift)
else:
i += 1
# assign cameras
for vb in vbs:
vb.camera = scene.PanZoomCamera(aspect=1)
vb.camera.set_range()
vb.camera.flip = (0, 1, 0)
app.run()
def __init__(self, keys='interactive'):
super(DemoScene, self).__init__()
# Layout and canvas creation
box = QtGui.QVBoxLayout(self)
self.resize(500, 500)
self.setLayout(box)
self.canvas = scene.SceneCanvas(keys=keys)
box.addWidget(self.canvas.native)
# Camera
self.view = self.canvas.central_widget.add_view()
self.view.camera = scene.cameras.TurntableCamera(elevation=25,
azimuth=20,
distance=2.0,
center=(0, 0, 0))
# Data
fitsdata = pyfits.open('l1448_13co.fits')
vol1 = np.nan_to_num(fitsdata[0].data)
self.vol_data = vol1
"""
The transpose here and after is for solving the coordinate mismatch between volume visual input data and its
rendering result. The rendered volume shown on 2D screen, or 'what we see', is through displaying transform
(self.tr here) of 'transposed input data', thus we use 'transpose' to enable our selection focusing on 'what
we see' on the screen rather than the real input data of volume.
"""
new_pos = np.transpose(vol1)
# TODO: replace the min&max threshold with real settings in Glue UI
min_threshold = np.min(self.vol_data)
max_threshold = np.max(self.vol_data)
self.pos_data = np.argwhere(
new_pos >= min_threshold) # get voxel positions
grays = get_translucent_cmap(1, 1, 1)
self.volume_pool = [(vol1, (1, 6), grays)]
self.volume = MultiVolume(self.volume_pool)
self.trans = [
-vol1.shape[2] / 2., -vol1.shape[1] / 2., -vol1.shape[0] / 2.
]
self.volume.transform = scene.STTransform(translate=self.trans)
self.view.add(self.volume)
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=self.view.scene)
self.selection = SelectionCommon(canvas=self.canvas,
view=self.view,
vol_data=self.vol_data,
volume=self.volume,
volume_pool=self.volume_pool,
pos_data=self.pos_data)
def __init__(self, parent=None):
super(VispyWidget, self).__init__(parent=parent)
# Prepare Vispy canvas. We set the depth_size to 24 to avoid issues
# with isosurfaces on MacOS X
self.canvas = scene.SceneCanvas(keys='interactive',
show=False,
config={'depth_size': 24})
# Set up a viewbox
self.view = self.canvas.central_widget.add_view()
self.view.parent = self.canvas.scene
# Set whether we are emulating a 3D texture. This needs to be enabled
# as a workaround on Windows otherwise VisPy crashes.
self.emulate_texture = (sys.platform == 'win32'
and sys.version_info[0] < 3)
self.scene_transform = scene.STTransform()
self.limit_transforms = {}
# Add a 3D cube to show us the unit cube. The 1.001 factor is to make
# sure that the grid lines are not 'hidden' by volume renderings on the
# front side due to numerical precision.
vertices, filled_indices, outline_indices = create_cube()
self.axis = scene.visuals.Mesh(vertices['position'],
outline_indices,
color=(1, 1, 1),
mode='lines')
self.axis.transform = self.scene_transform
self.view.add(self.axis)
# Create a turntable camera. For now, this is the only camerate type
# we support, but if we support more in future, we should implement
# that here
# Remove the fov=60 here to solve the mismatch of selection problem
# self.view.camera = scene.cameras.TurntableCamera(parent=self.view.scene, distance=2)
self.view.camera = scene.cameras.TurntableCamera(
parent=self.view.scene, distance=2.0)
# Add the native canvas widget to this widget
layout = QtGui.QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self.canvas.native)
self.setLayout(layout)
# We need to call render here otherwise we'll later encounter an OpenGL
# program validation error.
self.canvas.render()
# Set up callbacks
add_callback(self, 'visible_axes', nonpartial(self._toggle_axes))
def test_3d_axis_visual():
canvas = scene.SceneCanvas(keys=None, size=(800, 600), show=True)
view = canvas.central_widget.add_view()
scene_transform = scene.STTransform()
view.camera = scene.cameras.TurntableCamera(parent=view.scene,
fov=0.,
distance=4.0)
AxesVisual3D(view=view, axis_color='red', transform=scene_transform)
canvas.native.show()
canvas.native.close()
def setVolume(self, vol=None, path=None, sliceobj=None):
if path is not None and vol is None:
if '*' in path:
vol = loader.loadimageseries(path)
elif os.path.splitext(path)[-1] == '.npy':
vol = loader.loadimage(path)
else:
vol = loader.loadtiffstack(path)
elif vol is None:
vol = self.vol
if vol is None:
return
self.vol = vol
if slice is not None:
def intify(a):
if a is not None: return int(a)
sliceobj = [
slice(intify(s.start), intify(s.stop), intify(s.step))
for s in sliceobj
]
slicevol = self.vol[sliceobj]
else:
slicevol = self.vol
# Set whether we are emulating a 3D texture
emulate_texture = False
# Create the volume visuals
if self.volume is None:
self.volume = scene.visuals.Volume(slicevol,
parent=self.view.scene,
emulate_texture=emulate_texture)
self.volume.method = 'translucent'
else:
self.volume.set_data(slicevol)
self.volume._create_vertex_data(
) #TODO: Try using this instead of slicing array?
# Translate the volume into the center of the view (axes are in strange order for unkown )
scale = 3 * (2.0 / self.vol.shape[1], )
translate = map(lambda x: -scale[0] * x / 2, reversed(vol.shape))
self.volume.transform = scene.STTransform(translate=translate,
scale=scale)
def __init__(self, parent=None, viewer_state=None):
# Prepare Vispy canvas. We set the depth_size to 24 to avoid issues
# with isosurfaces on MacOS X
self.canvas = scene.SceneCanvas(keys=None, show=False,
config={'depth_size': 24},
bgcolor=rgb(settings.BACKGROUND_COLOR))
# Set up a viewbox
self.view = self.canvas.central_widget.add_view()
self.view.parent = self.canvas.scene
# Set whether we are emulating a 3D texture. This needs to be enabled
# as a workaround on Windows otherwise VisPy crashes.
self.emulate_texture = (sys.platform == 'win32' and
sys.version_info[0] < 3)
self.scene_transform = scene.STTransform()
self.limit_transforms = {}
fc = rgb(settings.FOREGROUND_COLOR)
self.axis = AxesVisual3D(axis_color=fc, tick_color=fc, text_color=fc,
tick_width=1, minor_tick_length=2,
major_tick_length=4, axis_width=0,
tick_label_margin=10, axis_label_margin=25,
tick_font_size=6, axis_font_size=8,
view=self.view,
transform=self.scene_transform)
# Create a turntable camera. For now, this is the only camerate type
# we support, but if we support more in future, we should implement
# that here
# Orthographic perspective view as default
self.view.camera = scene.cameras.TurntableCamera(parent=self.view.scene,
fov=0., distance=4.0)
# We need to call render here otherwise we'll later encounter an OpenGL
# program validation error.
# self.canvas.render()
self.viewer_state = viewer_state
try:
self.viewer_state.add_callback('*', self._update_from_state, as_kwargs=True)
except TypeError: # glue-core >= 0.11
self.viewer_state.add_global_callback(self._update_from_state)
self._update_from_state(force=True)
def __init__(self):
scene.SceneCanvas.__init__(self, keys='interactive', size=(960, 960), show=True, bgcolor='black', title='MRI', vsync=False)
self.unfreeze()
self.view = self.central_widget.add_view()
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_thumbnail.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_scoreMap_2.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_scoreMap_1.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_scoreMap_9.npz')['arr_0']
# self.vol_data = self.vol_data / self.vol_data.max()
# self.vol_data[self.vol_data < .5] = 0
self.vol_data = bp.unpack_ndarray_file('/home/yuncong/CSHL_volumes/volume_MD589_annotation.bp')
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_annotationAllClasses.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_labelmap.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD594_predMap.npz')['arr_0']
# self.vol_data = np.load('/home/yuncong/CSHL_volumes/volume_MD589_predMap.npz')['arr_0']
self.vol_data = self.vol_data[::2,::2,::2].astype(np.float)/9.
# self.vol_data = np.flipud(np.rollaxis(self.vol_data, 1))
# self.sectionTo = 150
self.sectionTo = 50
colors = np.loadtxt('/home/yuncong/Brain/visualization/100colors.txt')
# self.volume = scene.visuals.Volume(self.vol_data[:,0:self.sectionTo,:], parent=self.view.scene, cmap=get_colormap('coolwarm'))
self.volume = scene.visuals.Volume(self.vol_data[:,0:self.sectionTo,:], parent=self.view.scene, method='mip', cmap=Colormap([(0,0,0),(0,1,0), (1,0,0), (0,1,0), (0,0,1), (1,1,0),
(0,1,1), (1,1,0),(1,0.5,0),(0,0.5,0),(0,0,1)], interpolation='linear'))
self.volume.transform = scene.STTransform(translate=(0,0,0))
CMAP = self.volume.cmap
self.section2D = self.vol_data[:,self.sectionTo,:]
self.plane = scene.visuals.Image(self.section2D, parent=self.view.scene, cmap=CMAP, relative_step_size=1.5)
# self.plane.transform = scene.STTransform(translate=(0,self.sectionTo,0))
# self.plane.transform = scene.STTransform(translate=(0,0,0))
self.plane.transform = MatrixTransform()
self.plane.transform.rotate(90, (1,0,0))
self.plane.transform.translate((0,self.sectionTo,0))
self.plane.attach(BlackToAlpha())
self.view.camera = scene.cameras.ArcballCamera(parent=self.view.scene)
def set_values(self,vol_array):
#Calculate center and range
self.calc_bounds()
# Flip axes on volume array
vol_flipped = np.flipud(np.swapaxes(vol_array,0,2))
# Draw volumetric plot
self._volume=scene.visuals.Volume(vol_flipped)
self._nx,self._ny,self._nz = vol_array.shape
self._volume.transform = scene.STTransform(
#translate=(-self._nx/2,-self._ny/2,-self._nz/2),
translate=((1-self._nx)/2,(1-self._nz)/2,0),
scale=(self._xr/self._nx,self._yr/self._ny,self._zr/self._nz))
self._volume.cmap = colormap.CubeHelixColormap()
self._volume.method = 'mip'
def setData(self, data):
if data is None: return
data = np.nan_to_num(data)
self.data = data
# Create the volume visuals
if self.volume is not None:
self.volume.set_data(data)
self.volume._create_vertex_data(
) # TODO: Try using this instead of slicing array?
# Translate the volume into the center of the view (axes are in strange order for unkown )
scale = 3 * (2.0 / self.data.shape[1], )
translate = list(
map(lambda x: -scale[0] * x / 2, reversed(data.shape)))
self.volume.transform = scene.STTransform(translate=translate,
scale=scale)
self.update()
def __init__(self):
scene.SceneCanvas.__init__(self,
keys='interactive',
size=(960, 960),
show=True,
bgcolor='black',
title='MRI',
vsync=False)
self.unfreeze()
self.view = self.central_widget.add_view()
self.vol_data = np.load(
'/home/yuncong/CSHL_volumes/volume_MD589_thumbnail.npz')['arr_0']
# self.vol_data = np.flipud(np.rollaxis(self.vol_data, 1))
self.sectionTo = 150
self.volume = scene.visuals.Volume(self.vol_data[:,
0:self.sectionTo, :],
parent=self.view.scene)
self.volume.transform = scene.STTransform(translate=(0, 0, 0))
CMAP = self.volume.cmap
self.section2D = self.vol_data[:, self.sectionTo, :]
self.plane = scene.visuals.Image(self.section2D,
parent=self.view.scene,
cmap=CMAP,
relative_step_size=1.5)
# self.plane.transform = scene.STTransform(translate=(0,self.sectionTo,0))
# self.plane.transform = scene.STTransform(translate=(0,0,0))
self.plane.transform = MatrixTransform()
self.plane.transform.rotate(90, (1, 0, 0))
self.plane.transform.translate((0, self.sectionTo, 0))
self.plane.attach(BlackToAlpha())
self.view.camera = scene.cameras.ArcballCamera(parent=self.view.scene)
def __init__(self, keys='interactive'):
super(DemoScene, self).__init__()
# Layout and canvas creation
box = QtGui.QVBoxLayout(self)
self.resize(800, 600)
self.setLayout(box)
self.canvas = scene.SceneCanvas(keys=keys)
box.addWidget(self.canvas.native)
# Connect events
self.canvas.events.mouse_press.connect(self.on_mouse_press)
self.canvas.events.mouse_release.connect(self.on_mouse_release)
self.canvas.events.mouse_move.connect(self.on_mouse_move)
self.canvas.events.key_press.connect(self.on_key_press)
# Setup some defaults
self.mesh = None
self.selected = []
self.white = (1.0, 1.0, 1.0, 1.0)
self.black = (0.0, 0.0, 0.0, 0.0)
# Camera
self.view = self.canvas.central_widget.add_view()
self.view.camera = scene.cameras.TurntableCamera(elevation=90,
azimuth=0,
fov=60,
center=(0, 0, 0))
# Data
fitsdata = fits.open('l1448_13co.fits')
self.vol_data = np.nan_to_num(fitsdata[0].data)
"""
The transpose here and after is for solving the coordinate mismatch between volume visual input data and its
rendering result. The rendered volume shown on 2D screen, or 'what we see', is through displaying transform
(self.tr here) of 'transposed input data', thus we use 'transpose' to enable our selection focusing on 'what
we see' on the screen rather than the real input data of volume.
"""
new_pos = np.transpose(self.vol_data)
# TODO: replace the min&max threshold with real settings in Glue UI
self.pos_data = np.indices(self.vol_data.shape).reshape(
3, -1).transpose()
grays = get_translucent_cmap(1, 1, 1)
self.volume_pool = [(self.vol_data, (1, 6), grays)]
self.volume = MultiVolume(self.volume_pool)
self.trans = [
-self.vol_data.shape[2] / 2., -self.vol_data.shape[1] / 2.,
-self.vol_data.shape[0] / 2.
]
self.volume.transform = scene.STTransform(translate=self.trans)
self.view.add(self.volume)
self.tr = self.volume.get_transform(map_from='visual', map_to='canvas')
# create a volume for showing the selected part
self.volume1 = scene.visuals.Volume(self.vol_data,
clim=(4, 6),
parent=self.view.scene)
self.volume1.transform = scene.STTransform(translate=self.trans)
self.volume1.visible = False
# Add a text instruction
self.text = scene.visuals.Text('',
color='white',
pos=(self.canvas.size[0] / 4.0, 20),
parent=self.canvas.scene)
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=self.view.scene)
# Set up for lasso drawing
self.line_pos = []
self.line = scene.visuals.Line(color='yellow',
method='gl',
parent=self.canvas.scene)
# Selection
self.selection_flag = False
self.selection_pool = {
'1': 'lasso',
'2': 'rectangle',
'3': 'ellipse',
'4': 'pick',
'5': 'floodfill'
}
self.selection_id = '1' # default as 1
self.selection_origin = (0, 0)
def preview_volume(vols, shifts=None):
canvas = scene.SceneCanvas(keys="interactive")
canvas.size = 1024, 1024
canvas.show()
# create view box
view = canvas.central_widget.add_view()
# genereate colormap
"""
n_colors = 256
alphas = np.linspace(0.0, 1.0, n_colors)
color = np.c_[
alphas, alphas, alphas, alphas
]
cmap = Colormap(color)
"""
from utoolbox.data.io.amira import AmiraColormap
color = AmiraColormap("volrenGlow.am")
color = np.array(color)
color[0, :] = 0
color[:, 3] /= 100
cmap = Colormap(color)
for i, vol in enumerate(vols):
volume = scene.visuals.Volume(vol,
cmap=cmap,
parent=view.scene,
emulate_texture=False)
volume.method = "translucent"
volume.transform = scene.STTransform(scale=(2, 2, 5.5))
volume.set_gl_state("translucent", depth_test=False)
if shifts:
volume.transform = scene.STTransform(translate=shifts[i])
# assign camera
camera = scene.cameras.TurntableCamera(parent=view.scene,
fov=60.0,
name="Arcball",
elevation=30.0)
view.camera = camera
view.camera.flip = (False, True, True)
view.camera.reset()
# axis
axis = scene.visuals.XYZAxis(parent=view)
s = STTransform(translate=(50, 50), scale=(50, 50, 50, 1))
affine = s.as_matrix()
axis.transform = affine
# link with camera
@canvas.events.mouse_move.connect
def on_mouse_move(event):
if event.button == 1 and event.is_dragging:
axis.transform.reset()
axis.transform.rotate(camera.roll, (0, 0, 1))
axis.transform.rotate(camera.elevation, (1, 0, 0))
axis.transform.rotate(camera.azimuth, (0, 1, 0))
axis.transform.scale((50, 50, 0.001))
axis.transform.translate((50.0, 50.0))
axis.update()
# render rotation movie
"""
n_steps = 240
axis = [0, 0, 0]
logger.debug(".. rendering")
step_angle = 360.0 / n_steps
writer = imageio.get_writer("t1-head_split_rotate.mp4", fps=24)
for i in range(n_steps):
im = canvas.render()
writer.append_data(im)
view.camera.transform.rotate(step_angle, axis)
writer.close()
"""
app.run()
trans = (-(xmax - xmin) / 2.0, -(ymax - ymin) / 2.0, -(zmax - zmin) / 2.0)
# Create a canvas with a 3D viewport
canvas = scene.SceneCanvas(keys='interactive',
config={'depth_size': 24},
bgcolor='white')
view = canvas.central_widget.add_view()
surface = scene.visuals.Isosurface(density,
level=density.max() / 2.,
shading=None,
color=(0.5, 0.6, 1, 0.5),
parent=view.scene)
# surface.transform = scene.transforms.STTransform(translate=(-len(X)/2., -len(Y)/2., -len(Z)/2.))
surface.set_gl_state(depth_test=True, cull_face=True)
surface.transform = scene.STTransform(translate=trans)
surface2 = scene.visuals.Isosurface(density,
level=density.max() / 4.,
shading=None,
color=(1, 0, 0, 0.1),
parent=view.scene)
# surface2.transform = scene.transforms.STTransform(translate=(-s[0]/2., -s[1]/2., -s[2]/2.))
surface2.set_gl_state(depth_test=True, cull_face=True)
surface2.transform = scene.STTransform(translate=trans)
# Add a 3D scatter plot
scat_visual = scene.visuals.Markers()
scat_visual.set_data(P,
symbol='disc',
edge_color=None,
def on_key_press(event):
if event.text == 's':
global still_num
# Stop preexisting animation
fade_out.stop()
usr_message.text = 'Saved still image'
usr_message.color = (1, 1, 1, 0)
# Write screen to .png
still = canvas.render()
still_name = str(seq) + "_" + str(still_num) + ".png"
io.write_png(still_name, still)
still_num = still_num + 1
# Display and fade saved message
fade_out.start()
if event.text == 'e':
global load_data
# Stop preexisting animation
fade_out.stop()
usr_message.color = (1, 1, 1, 0)
if load_data == None:
global fractal_data
# export data created in this program
file_name = "3D_Fractal_" + seq + "_steps" + str(steps)
np.save(file_name, fractal_data, allow_pickle=False)
# set user message
usr_message.text = 'Exported fractal'
else:
# set user message
usr_message.text = 'Cannot export data loaded into program'
# display user message
fade_out.start()
if event.text == 'l':
global volume, loaded_data_later
loaded_data_later = True
# Stop preexisting animation
fade_out.stop()
usr_message.color = (1, 1, 1, 0)
# open file dialog to select load data
root = tk.Tk()
root.withdraw()
load_data = filedialog.askopenfilename()
# make sure file extension is .npy
file_ext = load_data[len(load_data) - 3:]
if file_ext != 'npy':
usr_message.text = 'Can only load .npy files'
else:
usr_message.text = 'Fractal loaded'
# load fractal data
fractal_data = np.load(load_data)
# normalize data and get color map
fractal_3D, chaotic_boundary = normalize(fractal_data, 0.0)
fractal_map = getfractalcolormap(chaotic_boundary)
# erase old volume
volume.parent = None
# make new volume from normalized fractal data
volume = scene.visuals.Volume(fractal_3D,
clim=(0, 1),
method='translucent',
parent=view.scene,
threshold=0.225,
cmap=fractal_map,
emulate_texture=False)
volume.transform = scene.STTransform(translate=(-steps // 2,
-steps // 2,
-steps // 2))
# display user message
fade_out.start()
oranges = np.array([1, 0.5, 0, 0.5])
# Combine data
combined_data = np.zeros(data.shape + (4, ))
combined_data += data[:, :, :, np.newaxis] / 6. * grays
combined_data += subset1[:, :, :, np.newaxis] / 4. * reds
combined_data += subset2[:, :, :, np.newaxis] / 4. * greens
combined_data += subset3[:, :, :, np.newaxis] / 4. * blues
combined_data += subset4[:, :, :, np.newaxis] / 4. * oranges
combined_data /= 5.
combined_data = np.clip(combined_data, 0, 1)
volume1 = RGBAVolume(combined_data, parent=view.scene)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
view.camera = scene.cameras.TurntableCamera(parent=view.scene,
fov=60.,
name='Turntable')
canvas.update()
#
# # create colormaps that work well for translucent and additive volume rendering
#
#
# # for testing performance
# # @canvas.connect
# # def on_draw(ev):
# # canvas.update()
#
# Create some visuals to show
# AK: Ideally, we could just create one visual that is present in all
# scenes, but that results in flicker for the PanZoomCamera, I suspect
# due to errors in transform caching.
im1 = io.load_crate().astype('float32') / 255
#image1 = scene.visuals.Image(im1, grid=(20, 20), parent=scenes)
for par in scenes:
image = scene.visuals.Image(im1, grid=(20, 20), parent=par)
#vol1 = np.load(io.load_data_file('volume/stent.npz'))['arr_0']
#volume1 = scene.visuals.Volume(vol1, parent=scenes)
#volume1.transform = scene.STTransform(translate=(0, 0, 10))
# Assign cameras
vb1.camera = scene.BaseCamera()
vb2.camera = scene.PanZoomCamera()
vb3.camera = scene.TurntableCamera()
vb4.camera = scene.FlyCamera()
# If True, show a cuboid at each camera
if False:
cube = scene.visuals.Cube((3, 3, 5))
cube.transform = scene.STTransform(translate=(0, 0, 6))
for vb in (vb1, vb2, vb3, vb4):
vb.camera.parents = scenes
cube.add_parent(vb.camera)
if __name__ == '__main__':
if sys.flags.interactive != 1:
app.run()
sur_scale = [(xmax - xmin) / 50., (ymax - ymin) / 50., (zmax - zmin) / 50.]
# Create a canvas with a 3D viewport
canvas = scene.SceneCanvas(keys='interactive',
config={'depth_size': 24},
bgcolor='white')
view = canvas.central_widget.add_view()
surface = scene.visuals.Isosurface(density,
level=density.max() / 2.,
shading=None,
color=(0.5, 0.6, 1, 0.5),
parent=view.scene)
# surface.transform = scene.transforms.STTransform(translate=(-len(X)/2., -len(Y)/2., -len(Z)/2.))
surface.set_gl_state(depth_test=True, cull_face=True)
surface.transform = scene.STTransform(translate=trans, scale=sur_scale)
surface2 = scene.visuals.Isosurface(density,
level=density.max() / 4.,
shading=None,
color=(1, 0, 0, 0.1),
parent=view.scene)
# surface2.transform = scene.transforms.STTransform(translate=(-s[0]/2., -s[1]/2., -s[2]/2.))
surface2.set_gl_state(depth_test=True, cull_face=True)
surface2.transform = scene.STTransform(translate=trans, scale=sur_scale)
# Add a 3D scatter plot
scat_visual = scene.visuals.Markers()
scat_visual.set_data(P,
symbol='disc',
edge_color=None,
# Prepare canvas
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
canvas.measure_fps()
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Set whether we are emulating a 3D texture
emulate_texture = False
# Create the volume visuals, only one is visible
volume1 = scene.visuals.Volume(vol1,
parent=view.scene,
threshold=0.225,
emulate_texture=emulate_texture)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
with open('kelp_pickle/PP_3d.pickle', 'rb') as inFile:
myVol = pickle.load(inFile)
myVol = np.flipud(np.rollaxis(myVol, 2))
volume2 = scene.visuals.Volume(myVol,
parent=view.scene,
threshold=0.2,
emulate_texture=emulate_texture)
volume1.visible = False
nx, ny, nz = myVol.shape
volume2.transform = scene.STTransform(translate=(-nx / 4, -ny / 2, -nz / 2))
# Create three cameras (Fly, Turntable and Arcball)
fov = 60
cam1 = scene.cameras.FlyCamera(parent=view.scene, fov=fov, name='Fly')
cam2 = scene.cameras.TurntableCamera(parent=view.scene,
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
camera = scene.cameras.ArcballCamera(parent=view.scene,
fov=60,
scale_factor=steps * 3,
center=(0, 0, 0))
view.camera = camera
# Create the volume
volume = scene.visuals.Volume(fractal_3D,
clim=(0, 1),
method='translucent',
parent=view.scene,
threshold=0.225,
emulate_texture=False)
volume.transform = scene.STTransform(translate=(-steps // 2, -steps // 2,
-steps // 2))
# Creating color map to display fractal
fractal_colors = [(1, 0, 1, .5), (0, 0, 1, .5), (.1, .8, .8, .3),
(.1, 1, .1, .3), (1, 1, 0, .2), (1, 0, 0, .1),
(0, 1, 1, (1 - chaotic_boundary) / 7),
(0, 1, .8, (1 - chaotic_boundary) / 8), (0, 0, 0, 0),
(0, 0, 0, 0)]
color_control_pts = [
0, (0.6 * chaotic_boundary), (0.7 * chaotic_boundary),
(0.8 * chaotic_boundary), (0.9 * chaotic_boundary),
(0.95 * chaotic_boundary), (0.97 * chaotic_boundary),
(0.99 * chaotic_boundary), chaotic_boundary, chaotic_boundary, 1.0
]
fractal_map = Colormap(fractal_colors,
xax.stretch = (1, 0.05)
grid.add_widget(xax, 1, 1)
xax.link_view(view)
N = 4900
M = 2000
cols = int(N**0.5)
view.camera.rect = (0, 0, cols, N / cols)
lines = scene.ScrollingLines(n_lines=N,
line_size=M,
columns=cols,
dx=0.8 / M,
cell_size=(1, 8),
parent=view.scene)
lines.transform = scene.STTransform(scale=(1, 1 / 8.))
def update(ev):
m = 50
data = np.random.normal(size=(N, m), scale=0.3)
data[data > 1] += 4
lines.roll_data(data)
canvas.context.flush() # prevent memory leak when minimized
timer = app.Timer(connect=update, interval=0)
timer.start()
if __name__ == '__main__':
import sys
# Prepare canvas
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Create the visuals
vol = np.load(io.load_data_file('volume/stent.npz'))['arr_0']
volume = scene.visuals.Volume(vol, parent=view.scene, threshold=0.225)
np.random.seed(1)
points = np.random.rand(100, 3) * (128, 128, 128)
markers = scene.visuals.Markers(pos=points, parent=view.scene)
# add a transform to markers, to show clipping is in scene coordinates
markers.transform = scene.STTransform(translate=(0, 0, 128))
# Create the clipping planes filter for the markers (Volume has its own clipping logic)
clipper = PlanesClipper()
# and attach it to the markers
markers.attach(clipper)
# Create and set the camera
fov = 60.
cam = scene.cameras.TurntableCamera(parent=view.scene,
fov=fov,
name='Turntable')
view.camera = cam
# since volume data is in 'zyx' coordinates, we have to reverse the coordinates
# we use as a center
def __init__(self, vol1_path, vol2_path):
vol1_path = vol1_path
vol2_path = vol2_path
vol1 = load_numpy_array(vol1_path)
if vol2_path is not None:
vol2 = load_numpy_array(vol2_path)
canvas = scene.SceneCanvas(keys='interactive',
size=(800, 600),
show=True)
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Set whether we are emulating a 3D texture
emulate_texture = False
# Create the volume visuals, only one is visible
volume1 = scene.visuals.Volume(vol1,
parent=view.scene,
threshold=0.225,
emulate_texture=emulate_texture)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
if vol2_path is not None:
volume2 = scene.visuals.Volume(vol2,
parent=view.scene,
threshold=0.2,
emulate_texture=emulate_texture)
volume2.visible = False
# Create three cameras (Fly, Turntable and Arcball)
fov = 60.
cam1 = scene.cameras.FlyCamera(parent=view.scene, fov=fov, name='Fly')
cam2 = scene.cameras.TurntableCamera(parent=view.scene,
fov=fov,
name='Turntable')
cam3 = scene.cameras.ArcballCamera(parent=view.scene,
fov=fov,
name='Arcball')
view.camera = cam2 # Select turntable at first
# Create an XYZaxis visual
axis = scene.visuals.XYZAxis(parent=view)
s = STTransform(translate=(50, 50), scale=(50, 50, 50, 1))
affine = s.as_matrix()
axis.transform = affine
# Implement axis connection with cam2
@canvas.events.mouse_move.connect
def on_mouse_move(event):
if event.button == 1 and event.is_dragging:
axis.transform.reset()
axis.transform.rotate(cam2.roll, (0, 0, 1))
axis.transform.rotate(cam2.elevation, (1, 0, 0))
axis.transform.rotate(cam2.azimuth, (0, 1, 0))
axis.transform.scale((50, 50, 0.001))
axis.transform.translate((50., 50.))
axis.update()
# Implement key presses
@canvas.events.key_press.connect
def on_key_press(event):
global opaque_cmap, translucent_cmap
if event.text == '1':
cam_toggle = {cam1: cam2, cam2: cam3, cam3: cam1}
view.camera = cam_toggle.get(view.camera, cam2)
print(view.camera.name + ' camera')
if view.camera is cam2:
axis.visible = True
else:
axis.visible = False
elif event.text == '2':
methods = ['mip', 'translucent', 'iso', 'additive']
method = methods[(methods.index(volume1.method) + 1) % 4]
print("Volume render method: %s" % method)
cmap = \
opaque_cmap if method in ['mip', 'iso'] else \
translucent_cmap
volume1.method = method
volume1.cmap = cmap
if vol2_path is not None:
volume2.method = method
volume2.cmap = cmap
elif event.text == '3':
volume1.visible = not volume1.visible
volume2.visible = not volume1.visible
elif event.text == '4':
if volume1.method in ['mip', 'iso']:
cmap = opaque_cmap = next(opaque_cmaps)
else:
cmap = translucent_cmap = next(translucent_cmaps)
volume1.cmap = cmap
if vol2_path is not None:
volume2.cmap = cmap
elif event.text == '0':
cam1.set_range()
cam3.set_range()
elif event.text != '' and event.text in '[]':
s = -0.025 if event.text == '[' else 0.025
volume1.threshold += s
if vol2_path is not None:
volume2.threshold += s
if volume1.visible:
th = volume1.threshold
if vol2_path is not None:
th = volume2.threshold
print("Isosurface threshold: %0.3f" % th)
# Prepare canvas
canvas = scene.SceneCanvas(keys='interactive', size=(800, 600), show=True)
#canvas.measure_fps()
# Set up a viewbox to display the image with interactive pan/zoom
view = canvas.central_widget.add_view()
# Set whether we are emulating a 3D texture
emulate_texture = False
# Create the volume visual
vol = scene.visuals.Volume(vol,
parent=view.scene,
threshold=0.225,
emulate_texture=emulate_texture)
vol.transform = scene.STTransform(scale=(1, 1, z_stretch))
# Create two cameras (1 for firstperson, 3 for 3d person)
fov = 60.
cam1 = scene.cameras.FlyCamera(parent=view.scene, fov=fov, name='Fly')
cam2 = scene.cameras.TurntableCamera(parent=view.scene,
fov=fov,
name='Turntable')
cam3 = scene.cameras.ArcballCamera(parent=view.scene, fov=fov, name='Arcball')
view.camera = cam2 # Select turntable at first
# create colormaps that work well for translucent and additive volume rendering
class TransFire(BaseColormap):
glsl_map = """
vec4 translucent_fire(float t) {
p1.transform.translate([-0.5, -0.5, 0])
view.add(p1)
# p1._update_data() # cheating.
# cf = scene.filters.ZColormapFilter('fire', zrange=(z.max(), z.min()))
# p1.attach(cf)
xax = scene.Axis(pos=[[-0.5, -0.5], [0.5, -0.5]],
tick_direction=(0, -1),
font_size=16,
axis_color='k',
tick_color='k',
text_color='k',
parent=view.scene)
xax.transform = scene.STTransform(translate=(0, 0, -0.2))
yax = scene.Axis(pos=[[-0.5, -0.5], [-0.5, 0.5]],
tick_direction=(-1, 0),
font_size=16,
axis_color='k',
tick_color='k',
text_color='k',
parent=view.scene)
yax.transform = scene.STTransform(translate=(0, 0, -0.2))
# Add a 3D axis to keep us oriented
axis = scene.visuals.XYZAxis(parent=view.scene)
if __name__ == '__main__':
canvas.show()
imdata = io.load_crate().astype('float32') / 255
views = []
images = []
for i in range(2):
for j in range(2):
v = grid.add_view(row=i, col=j, border_color='white')
v.camera = 'turntable'
v.camera.fov = 50
v.camera.distance = 30
#v.camera = 'panzoom'
#v.camera.aspect = 1
views.append(v)
image = scene.visuals.Image(imdata, method='impostor', grid=(4, 4))
image.transform = scene.STTransform(translate=(-12.8, -12.8),
scale=(0.1, 0.1))
v.add(image)
images.append(image)
@canvas.connect
def on_key_press(ev):
if ev.key.name == '1':
print("Image method: impostor")
for im in images:
im.method = 'impostor'
elif ev.key.name == '2':
print("Image method: subdivide")
for im in images:
im.method = 'subdivide'
elif ev.key.name == '3':