def apply_translation(self, *args):
if self.view and self.level:
rmatrix = np.eye(4)
r = rotation_matrix((self.model.angle_z.get() * np.pi / 180,
self.model.angle_y.get() * np.pi / 180,
self.model.angle_x.get() * np.pi / 180))
rmatrix[:3, :3] = r[::-1, ::-1]
cmatrix = np.array([
self.model.center_x.get() / self.level,
self.model.center_y.get() / self.level,
self.model.center_z.get() / self.level
])
tmatrix = np.array([
self.model.offset_x.get() / self.level,
self.model.offset_y.get() / self.level,
self.model.offset_z.get() / self.level
])
#
# The last of 4 columns of the affine transform is the
# translation. The translation is the rotated center minus the
# offset plus the center, not rotated.
#
rmatrix[3, :3] = rmatrix[:3, :3].dot(tmatrix - cmatrix) + cmatrix
rotate_transform = MatrixTransform(rmatrix)
self.translation_frame.transform = rotate_transform
self.center_frame.transform = MatrixTransform(
np.array([[1, 0, 0, cmatrix[0]], [0, 1, 0, cmatrix[1]],
[0, 0, 1, cmatrix[2]], [0, 0, 0, 1]]))
self.scene.update()
def as_matrix_transform(transform):
"""
Simplify a transform to a single matrix transform, which makes it a lot
faster to compute transformations.
Raises a TypeError if the transform cannot be simplified.
"""
if isinstance(transform, ChainTransform):
matrix = np.identity(4)
for tr in transform.transforms:
# We need to do the matrix multiplication manually because VisPy
# somehow doesn't mutliply matrices if there is a perspective
# component. The equation below looks like it's the wrong way
# around, but the VisPy matrices are transposed.
matrix = np.matmul(as_matrix_transform(tr).matrix, matrix)
return MatrixTransform(matrix)
elif isinstance(transform, InverseTransform):
matrix = as_matrix_transform(transform._inverse)
return MatrixTransform(matrix.inv_matrix)
elif isinstance(transform, NullTransform):
return MatrixTransform()
elif isinstance(transform, STTransform):
return transform.as_matrix()
elif isinstance(transform, MatrixTransform):
return transform
else:
raise TypeError("Could not simplify transform of type {0}".format(
type(transform)))
def __init__(self):
vispy.app.Canvas.__init__(self, keys='interactive', size=(800, 800))
# Create 4 copies of an image to be displayed with different transforms
image = get_image()
self.images = [visuals.ImageVisual(image, method='impostor')
for i in range(4)]
# Transform all images to a standard size / location (because
# get_image() might return unexpected sizes)
s = 100. / max(self.images[0].size)
tx = 0.5 * (100 - (self.images[0].size[0] * s))
ty = 0.5 * (100 - (self.images[0].size[1] * s))
base_tr = STTransform(scale=(s, s), translate=(tx, ty))
self.images[0].transform = (STTransform(scale=(30, 30),
translate=(600, 600)) *
SineTransform() *
STTransform(scale=(0.1, 0.1),
translate=(-5, -5)) *
base_tr)
tr = MatrixTransform()
tr.rotate(40, (0, 0, 1))
tr.rotate(30, (1, 0, 0))
tr.translate((0, -20, -60))
p = MatrixTransform()
p.set_perspective(0.5, 1, 0.1, 1000)
tr = p * tr
tr1 = (STTransform(translate=(200, 600)) *
tr *
STTransform(translate=(-50, -50)) *
base_tr)
self.images[1].transform = tr1
tr2 = (STTransform(scale=(3, -100), translate=(200, 50)) *
LogTransform((0, 2, 0)) *
STTransform(scale=(1, -0.01), translate=(-50, 1.1)) *
base_tr)
self.images[2].transform = tr2
tr3 = (STTransform(scale=(400, 400), translate=(570, 400)) *
PolarTransform() *
STTransform(scale=(np.pi/150, -0.005),
translate=(-3.3*np.pi/4., 0.7)) *
base_tr)
self.images[3].transform = tr3
text = visuals.TextVisual(
text=['logarithmic', 'polar', 'perspective', 'custom (sine)'],
pos=[(100, 20), (500, 20), (100, 410), (500, 410)],
color='k', font_size=16)
self.visuals = self.images + [text]
self.show()
def _niimg_rot():
"""Get rotation trnasformations of each slice."""
# Sagittal
sg_rot = MatrixTransform()
sg_rot.rotate(90., (0, 0, 1))
sg_rot.rotate(180., (0, 1, 0))
# Coronal
cr_rot = MatrixTransform()
cr_rot.rotate(90., (0, 0, 1))
cr_rot.rotate(180., (0, 1, 0))
# Axial
ax_rot = MatrixTransform()
ax_rot.rotate(180., (1, 0, 0))
return sg_rot, cr_rot, ax_rot
def __init__(self, _model: AtlasSectionViewModel):
self._model = _model
self._model.register(self.update)
self._canvas = SceneCanvas()
self._viewbox = ViewBox(parent=self._canvas.scene)
self._canvas.central_widget.add_widget(self._viewbox)
self._viewbox.camera = TurntableCamera(
interactive=False,
fov=0, # Makes it an ortho camera.
azimuth=0,
elevation=90,
)
self._slice = Image(cmap='grays', parent=self._viewbox.scene)
self._slice.transform = MatrixTransform()
self._slice.set_data(self._model.atlas_section_image)
self._slice.clim = self._model.clim
self._viewbox.camera.center = self._model.camera_center
self._viewbox.camera.scale_factor = self._viewbox.camera.scale_factor
self._vertical_line = InfiniteLine(pos=0,
vertical=True,
parent=self._viewbox.scene)
self._horizontal_line = InfiniteLine(pos=0,
vertical=False,
parent=self._viewbox.scene)
self._canvas.events.mouse_press.connect(self.mouse_press)
self._canvas.events.mouse_move.connect(self.mouse_move)
self._vertical_line.set_data(color=self._model.vertical_line_color)
self._horizontal_line.set_data(color=self._model.horizontal_line_color)
def axis_visual(scale=1.0, parent=None):
"""
Returns a :class:`vispy.scene.visuals.XYZAxis` class instance using given
scale.
Parameters
----------
scale : numeric, optional
Axis visual scale.
parent : Node, optional
Parent of the axis visual in the `SceneGraph`.
Returns
-------
XYZAxis
Axis visual.
"""
axis = XYZAxis(parent=parent)
transform = MatrixTransform()
transform.scale((scale, scale, scale))
axis.transform = transform
return axis
def _createShapeNode(self, shape):
shapeType = shape.getType()
if shapeType == dynamics.SphereShape.getStaticType():
self.shapeNode = SphereShapeNode(shape, parent=self)
elif shapeType == dynamics.BoxShape.getStaticType():
self.shapeNode = BoxShapeNode(shape, parent=self)
# elif shapeType == dynamics.EllipsoidShape.getStaticType():
# print(shapeType)
elif shapeType == dynamics.CylinderShape.getStaticType():
self.shapeNode = CylinderShapeNode(shape, parent=self)
elif shapeType == dynamics.CapsuleShape.getStaticType():
self.shapeNode = CapsuleShapeNode(shape, parent=self)
# elif shapeType == dynamics.ConeShape.getStaticType():
# print(shapeType)
# elif shapeType == dynamics.PlaneShape.getStaticType():
# print(shapeType)
# elif shapeType == dynamics.MultiSphereConvexHullShape.getStaticType():
# print(shapeType)
elif shapeType == dynamics.MeshShape.getStaticType():
self.shapeNode = MeshShapeNode(shape, parent=self)
# elif shapeType == dynamics.SoftMeshShape.getStaticType():
# print(shapeType)
# elif shapeType == dynamics.LineSegmentShape.getStaticType():
# print(shapeType)
else:
print(
"{} is an unsupported shape type. Ping JS to implement this.")
if self.shapeNode is None:
return
self.shapeNode.transform = MatrixTransform()
def __init__(self, source=None, **kwargs):
super(PolarImage, self).__init__(**kwargs)
self.unfreeze()
# source should be an object, which contains information about
# a specific radar source
self.source = source
# source should contain the radar coordinates in some usable format
# here I assume offset from lower left (0,0)
if source is not None:
xoff = source['X']
yoff = source['Y']
else:
xoff = 0
yoff = 0
# this takes the image sizes and uses it for transformation
self.theta = self._data.shape[0]
self.range = self._data.shape[1]
# PTransform takes care of making PPI from data array
# rot rotates the ppi 180 deg (image origin is upper left)
# the translation moves the image to centere the ppi
rot = MatrixTransform()
rot.rotate(180, (0, 0, 1))
self.transform = (
STTransform(translate=(self.range + xoff, self.range + yoff, 0)) *
rot * PTransform())
self.freeze()
def load_maze(self, maze_file, mirror=True, maze_coord_file=None):
self.maze = Maze(maze_file, maze_coord_file) #color='gray'
self.scale_factor = 100
self.origin = -np.array(self.maze.coord['Origin']).astype(
np.float32) * self.scale_factor
self.origin_hd = np.arctan2(-self.origin[1],
self.origin[0]) / np.pi * 180
self.border = np.array(self.maze.coord['border']).astype(np.float32)
self.x_range = (self.origin[0] + self.border[0] * self.scale_factor,
self.origin[0] + self.border[2] * self.scale_factor)
self.y_range = (self.origin[1] + self.border[1] * self.scale_factor,
self.origin[1] + self.border[3] * self.scale_factor)
self._arrow_len = (self.x_range[1] - self.x_range[0]) / 10
# self.marker.move(self.origin[:2])
# self.current_pos = self.origin[:2]
### MatrixTransform perform Affine Transform
transform = MatrixTransform()
# transform.rotate(angle=90, axis=(1, 0, 0)) # rotate around x-axis for 90, the maze lay down
if mirror:
self.mirror = True
transform.matrix[:,
2] = -transform.matrix[:,
2] # reflection matrix, mirror image on x-y plane
transform.scale(
scale=4 *
[self.scale_factor]) # scale at all 4 dim for scale_factor
transform.translate(pos=self.origin) # translate to origin
self.maze.transform = transform
self.view.add(self.maze)
self.set_range()
print('Origin:', self.origin)
print('border:', self.border)
def on_atlas_update(self, volume: ndarray, transform: ndarray):
self._atlas_volume.set_data(volume,
clim=(np.min(volume), np.max(volume)))
self._atlas_volume.transform = MatrixTransform(transform.T)
self._viewbox.camera.center = (0, 0, 0)
self._viewbox.camera.scale_factor = transform[0, 0] * volume.shape[0]
self._canvas.update()
def __init__(self):
app.Canvas.__init__(self, keys='interactive', size=(800, 550))
vertices, faces, outline = create_box(width=1, height=1, depth=1,
width_segments=4,
height_segments=8,
depth_segments=16)
self.box = visuals.BoxVisual(width=1, height=1, depth=1,
width_segments=4,
height_segments=8,
depth_segments=16,
vertex_colors=vertices['color'],
edge_color='b')
self.theta = 0
self.phi = 0
self.transform = MatrixTransform()
self.box.transform = self.transform
self.show()
self.timer = app.Timer(connect=self.rotate)
self.timer.start(0.016)
def __init__(self,
keys='interactive',
size=(640, 480),
show=True,
**kwargs):
super().__init__(keys=keys, size=size, show=show, **kwargs)
self.unfreeze()
self._viewbox = self.central_widget.add_view(camera='turntable')
self._baseAxis = visuals.XYZAxis(parent=self._viewbox.scene, width=5)
self._gridLines = visuals.GridLines()
self._viewbox.add(self._gridLines)
self._cubeAxis = visuals.XYZAxis(parent=self._viewbox.scene, width=5)
Plot3D = scene.visuals.create_visual_node(LinePlotVisual)
self._plot = Plot3D(([0], [0], [0]),
width=3.0,
color='y',
edge_color='w',
symbol='x',
face_color=(0.2, 0.2, 1, 0.8),
parent=self._viewbox.scene)
self._xPos = np.array([0], dtype=np.float32)
self._yPos = np.array([0], dtype=np.float32)
self._zPos = np.array([0], dtype=np.float32)
self._cube = visuals.Cube(parent=self._viewbox.scene,
color=(0.5, 0.5, 1, 0.5),
edge_color=(0.6, 0.2, 0.8, 1))
self._transform = MatrixTransform()
self._cube.transform = self._transform
self._cubeAxis.transform = self._transform
self.freeze()
def __init__(self):
app.Canvas.__init__(self, keys='interactive', size=(800, 550))
self.meshes = []
self.rotation = MatrixTransform()
# Generate some data to work with
global mdata
mdata = create_sphere(20, 40, 1.0)
# Mesh with pre-indexed vertices, uniform color
self.meshes.append(visuals.MeshVisual(meshdata=mdata, color='b'))
# Mesh with pre-indexed vertices, per-face color
# Because vertices are pre-indexed, we get a different color
# every time a vertex is visited, resulting in sharp color
# differences between edges.
verts = mdata.get_vertices(indexed='faces')
nf = verts.size // 9
fcolor = np.ones((nf, 3, 4), dtype=np.float32)
fcolor[..., 0] = np.linspace(1, 0, nf)[:, np.newaxis]
fcolor[..., 1] = np.random.normal(size=nf)[:, np.newaxis]
fcolor[..., 2] = np.linspace(0, 1, nf)[:, np.newaxis]
mesh = visuals.MeshVisual(vertices=verts, face_colors=fcolor)
self.meshes.append(mesh)
# Mesh with unindexed vertices, per-vertex color
# Because vertices are unindexed, we get the same color
# every time a vertex is visited, resulting in no color differences
# between edges.
verts = mdata.get_vertices()
faces = mdata.get_faces()
nv = verts.size // 3
vcolor = np.ones((nv, 4), dtype=np.float32)
vcolor[:, 0] = np.linspace(1, 0, nv)
vcolor[:, 1] = np.random.normal(size=nv)
vcolor[:, 2] = np.linspace(0, 1, nv)
self.meshes.append(visuals.MeshVisual(verts, faces, vcolor))
self.meshes.append(
visuals.MeshVisual(verts, faces, vcolor, shading='flat'))
self.meshes.append(
visuals.MeshVisual(verts, faces, vcolor, shading='smooth'))
# Lay out meshes in a grid
grid = (3, 3)
s = 300. / max(grid)
for i, mesh in enumerate(self.meshes):
x = 800. * (i % grid[0]) / grid[0] + 400. / grid[0] - 2
y = 800. * (i // grid[1]) / grid[1] + 400. / grid[1] + 2
transform = ChainTransform([
STTransform(translate=(x, y), scale=(s, s, s)), self.rotation
])
mesh.transform = transform
mesh.transforms.scene_transform = STTransform(scale=(1, 1, 0.01))
self.show()
self.timer = app.Timer(connect=self.rotate)
self.timer.start(0.016)
def _colorbar_for_surf(colormap, limits):
colorbar = ColorBar(colormap, 'top', (50, 10), clim=limits)
tr = MatrixTransform()
tr.rotate(-90, (0, 1, 0))
tr.translate((0, -100, 50))
colorbar.transform = tr
return colorbar
def plot_line_vispy(points,
clf=True,
tube_radius=1.,
colour=None,
zero_centroid=True,
closed=False,
mus=None,
cmap=None,
tube_points=8,
**kwargs):
# Add an extra point to fix tube drawing bug
last_tangent = points[-1] - points[-2]
points = n.vstack([points, points[-1] + 0.0001 * last_tangent])
ensure_vispy_canvas()
if clf:
clear_vispy_canvas()
canvas = vispy_canvas
from vispy import app, scene, color
if isinstance(cmap, str):
from matplotlib.cm import get_cmap
mpl_cmap = get_cmap(cmap)
cmap = lambda v: n.array(mpl_cmap(v))
cmap = cmap or (lambda c: hsv_to_rgb(c, 1, 1))
if colour is None:
colours = n.linspace(0, 1, len(points))
colours = n.array([cmap(c) for c in colours])
else:
colours = color.ColorArray(colour)
if mus is not None:
colours = n.array([hsv_to_rgb(c, 1, 1) for c in mus])
l = scene.visuals.Tube(points,
color=colours,
shading='smooth',
radius=tube_radius,
tube_points=tube_points,
closed=closed)
canvas.view.add(l)
# canvas.view.camera = 'arcball'
canvas.view.camera = scene.ArcballCamera(fov=30,
distance=7.5 *
n.max(n.abs(points)))
#canvas.view.camera = scene.TurntableCamera(fov=30)
if zero_centroid:
l.transform = MatrixTransform()
# l.transform = scene.transforms.AffineTransform()
l.transform.translate(-1 * n.average(points, axis=0))
canvas.show()
# import ipdb
# ipdb.set_trace()
return canvas
def _master_transform(self):
"""vispy.visuals.transforms.MatrixTransform:
Central node's firstmost transform.
"""
# whenever a new parent is set, the transform is reset
# to a NullTransform so we reset it here
if not isinstance(self.node.transform, MatrixTransform):
self.node.transform = MatrixTransform()
return self.node.transform
def updateSlice(self,cutAt):
self.sectionTo = cutAt
self.volume.set_data(self.vol_data[:,0:self.sectionTo,:])
self.section2D = self.vol_data[:,self.sectionTo,:]
self.plane.set_data(self.section2D)
self.plane.transform = MatrixTransform()
self.plane.transform.rotate(90, (1,0,0))
self.plane.transform.translate((0,self.sectionTo,0))
def __init__(self, state_vec, p):
self.state_vec = state_vec
self.n = 0
self.n_max = len(state_vec)
self.p = p
self.radius = p/6.0
self.rot = MatrixTransform()
self.v_orient = None
self.x = 0.
self.y = 0.
self.z = 0.
def __init__(self, view, face_color, state_vec, orient_vec):
super(mbVector, self).__init__(10,
10,
0.05,
1.,
0.1,
0.25,
color=face_color,
shading="smooth",
parent=view)
self.unfreeze()
self.n = 0
self.n_max = len(state_vec)
self.trafo = MatrixTransform()
self.state_vec = state_vec
self.orient_vec = orient_vec
def plot_lines_vispy(lines,
clf=True,
tube_radius=1.,
colours=None,
zero_centroid=True,
tube_points=8,
closed=False,
**kwargs):
ensure_vispy_canvas()
if clf:
clear_vispy_canvas()
canvas = vispy_canvas
from vispy import app, scene, color
if not isinstance(tube_radius, list):
tube_radius = [tube_radius for _ in range(len(lines))]
if colours is None:
colours = ['purple' for line in lines]
tubes = []
for colour, points, radius in zip(colours, lines, tube_radius):
l = scene.visuals.Tube(points,
color=colour,
shading='smooth',
radius=radius,
closed=closed,
tube_points=tube_points)
tubes.append(l)
from .visualcollection import MeshCollection
collection = MeshCollection(tubes)
canvas.view.add(collection)
canvas.view.camera = 'arcball'
canvas.view.camera.fov = 30
# canvas.view.camera = scene.TurntableCamera(
# fov=90, up='z', distance=1.2*n.max(n.max(
# points, axis=0)))
if zero_centroid:
l.transform = MatrixTransform()
# l.transform = scene.transforms.AffineTransform()
l.transform.translate(-1 * n.average(points, axis=0))
canvas.show()
return canvas
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 __init__(self,
size=(500, 10),
cmap='grays',
clim=None,
label_str="Colorbar",
label_color='black',
label_size=12,
tick_size=10,
border_width=1.0,
border_color='black',
visible=True,
parent=None):
assert clim is not None, 'clim must be specified explicitly.'
# Create a scene.visuals.Image (without parent by default).
scene.visuals.Image.__init__(self,
parent=None,
interpolation='nearest',
method='auto')
self.unfreeze()
self.visible = visible
self.canvas_size = None # will be set when parent is linked
# Record the important drawing parameters.
self.pos = (0, 0)
self.bar_size = size # tuple
self.cmap = get_colormap(cmap) # vispy Colormap
self.clim = clim # tuple
# Record the styling parameters.
self.label_str = label_str
self.label_color = label_color
self.label_size = label_size
self.tick_size = tick_size
self.border_width = border_width
self.border_color = border_color
# Draw colorbar using Matplotlib.
self.set_data(self._draw_colorbar())
# Give a Matrix transform to self in order to move around canvas.
self.transform = MatrixTransform()
self.freeze()
def __init__(self,
loc=(80, 72),
size=60,
seismic_coord_system=True,
width=2,
antialias=True,
visible=True,
parent=None):
# Create a scene.visuals.XYZAxis (without parent by default).
scene.visuals.XYZAxis.__init__(self,
parent=parent,
width=width,
antialias=antialias)
self.interactive = True
self.unfreeze()
self.visible = visible
self.canvas_size = None # will be set when parent is linked
# Determine the size and position.
self.loc = loc
self.size = size
# z-axis down seismic coordinate system, or z-axis up normal system.
self.seismic_coord_system = seismic_coord_system
# The selection highlight (a Ellipse visual with transparent color).
# The circle is centered on the axis legend.
self.highlight = scene.visuals.Ellipse(
parent=parent,
center=self.loc,
radius=self.size,
color=(1, 1, 0, 0.5)) # transparent yellow color
self.highlight.visible = False # only show when selected
# Set the anchor point (2D screen coordinates). The mouse will
# drag the axis by anchor point to move around the screen.
self.anchor = None # None by default
self.offset = np.array([0, 0])
# The axis legend is rotated to align with the parent camera. Then put
# the legend to specified location and scale up to desired size.
# The location is computed from the top-left corner.
self.transform = MatrixTransform()
self.freeze()
def array_to_stt(arr):
"""Turn a 4x4 array into a scale and translate matrix transformation.
Parameters
----------
arr : array_like
A 4x4 array.
Returns
-------
transform : VisPy.transform
The VisPy transformation.
"""
arr[-1, 0:-1] = arr[0:-1, -1]
arr[0:-1, -1] = 0.
transform = MatrixTransform(arr)
# transform.scale(np.diag(arr)[0:-1])
# transform.translate(arr[0:-1, -1])
return transform
def __init__(self):
app.Canvas.__init__(self, keys='interactive', size=(800, 800))
# Define several Line visuals that use the same position data
# but have different colors and transformations
colors = [color, (1, 0, 0, 1), (0, 1, 0, 1), (0, 0, 1, 1),
(1, 1, 0, 1), (1, 1, 1, 1)]
self.lines = [visuals.LineVisual(pos=pos, color=colors[i])
for i in range(6)]
center = STTransform(translate=(400, 400))
self.lines[0].transform = center
self.lines[1].transform = (center *
STTransform(scale=(1, 0.1, 1)))
self.lines[2].transform = (center *
STTransform(translate=(200, 200, 0)) *
STTransform(scale=(0.3, 0.5, 1)))
self.lines[3].transform = (center *
STTransform(translate=(-200, -200, 0),
scale=(200, 1)) *
LogTransform(base=(10, 0, 0)) *
STTransform(translate=(1, 0, 0)))
self.lines[4].transform = MatrixTransform()
self.lines[4].transform.rotate(45, (0, 0, 1))
self.lines[4].transform.scale((0.3, 0.3, 1))
self.lines[4].transform.translate((200, 200, 0))
self.lines[5].transform = (STTransform(translate=(200, 600, 0),
scale=(5, 5)) *
PolarTransform() *
LogTransform(base=(2, 0, 0)) *
STTransform(scale=(0.01, 0.1),
translate=(4, 20)))
self.show()
def _updateShapeData(self, firstTime):
if firstTime:
assimpMatrix = self.assimpNode.contents.mTransformation
self.transform = MatrixTransform() # TODO(JS): Necessary?
self.transform.matrix = _fromAssimpMatrixToNumpyMatrix(
assimpMatrix)
for mesh in self.assimpNode.meshes:
self.assimpMeshNodes += [
AssimpMeshNode(assimpMesh=mesh,
assimpScene=self.assimpScene,
parent=self)
]
for child in self.assimpNode.children:
self.assimpChildNodes += [
AssimpNodeNode(child,
assimpScene=self.assimpScene,
parent=self)
]
else:
for assimpChildNode in self.assimpChildNodes:
assimpChildNode.refresh()
def array_to_stt(arr):
"""Turn a (4, 4) array into a scale and translate matrix transformation.
Parameters
----------
arr : array_like
A (4, 4) array.
Returns
-------
transform : VisPy.transform
The VisPy transformation.
"""
assert isinstance(arr, np.ndarray) and arr.shape == (4, 4)
_arr = arr.copy()
_arr[-1, 0:-1] = _arr[0:-1, -1]
_arr[0:-1, -1] = 0.
transform = MatrixTransform(_arr)
# transform.scale(np.diag(_arr)[0:-1])
# transform.translate(_arr[0:-1, -1])
return transform
def _niimg_mat(hdr, idx):
"""Get the transformation of a single slice.
Parameters
----------
hdr : array_like
The (4, 4) transformation array.
idx : tuple
Slices indicies.
Returns
-------
tf : MatrixTransform
Image transformation.
"""
hdr_mat = np.array(hdr.matrix).copy().T
mat = np.identity(4, dtype=np.float32)
to_idx = [[idx[0]], [idx[1]]], [idx[0], idx[1]]
mat[[[0], [1]], [0, 1]] = hdr_mat[to_idx]
mat[[0, 1], -1] = hdr_mat[[idx[0], idx[1]], -1]
return MatrixTransform(mat.T)
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, exp_df_path, trial_df_path, rig_leds_path):
exp_df = pd.read_pickle(exp_df_path)
trial_df = pd.read_pickle(trial_df_path)
self.df = exp_df.join(trial_df.drop('block', axis=1),
on='trial_number')
self.rig_leds = np.load(rig_leds_path)
self.precalculate_data()
verts, faces, normals, nothin = vispy.io.read_mesh(
os.path.join(fh.PACKAGE_DIR, '../datafiles', 'head.obj'))
verts = np.einsum('ni,ji->nj', (verts - verts.mean(axis=0)),
fh.from_yawpitchroll(180, 90, 0))
#verts = verts - verts.mean(axis=0)
# add SceneCanvas first to create QApplication object before widget
self.vispy_canvas = vispy.scene.SceneCanvas(create_native=True,
vsync=True,
show=True,
bgcolor=(0.2, 0.2, 0.2, 0))
super(ExperimentVisualization, self).__init__()
#self.setAttribute(Qt.WA_TranslucentBackground)
self.timer = vispy.app.Timer(1 / 30,
start=False,
connect=self.advance_frame)
self.n_trials = len(self.df)
self.current_trial = 0
self.i_frame = 0
self.current_row = self.df.iloc[self.current_trial]
self.current_R_helmet = None
self.current_gaze_normals = None
self.current_ref_points = None
self.vispy_view = self.vispy_canvas.central_widget.add_view()
self.vispy_view.camera = 'turntable'
self.vispy_view.camera.center = self.rig_leds[127, :] + (
self.rig_leds[0, :] - self.rig_leds[127, :]) + (
self.rig_leds[254, :] - self.rig_leds[127, :])
self.vispy_view.camera.fov = 40
self.vispy_view.camera.distance = 1500
self.main_layout = QtWidgets.QVBoxLayout()
self.setLayout(self.main_layout)
self.frame_slider = QtWidgets.QSlider(Qt.Horizontal)
self.frame_slider.setMinimum(0)
self.frame_slider.valueChanged.connect(self.on_slider_change)
self.trial_picker = QtWidgets.QSpinBox()
self.trial_picker.setMaximum(self.n_trials)
self.trial_picker.valueChanged.connect(self.on_picker_change)
self.trial_changed.connect(self.load_trial)
self.frame_changed.connect(self.load_frame)
self.picker_slider_layout = QtWidgets.QHBoxLayout()
self.main_layout.addWidget(self.vispy_canvas.native)
self.main_layout.addLayout(self.picker_slider_layout)
self.animation_button = QtWidgets.QPushButton('Start Animation')
self.picker_slider_layout.addWidget(self.animation_button)
self.animation_button.clicked.connect(self.toggle_animation)
self.frame_label = QtWidgets.QLabel('Frame')
self.picker_slider_layout.addWidget(self.frame_label)
self.picker_slider_layout.addWidget(self.frame_slider)
self.picker_slider_layout.addWidget(QtWidgets.QLabel('Trial'))
self.picker_slider_layout.addWidget(self.trial_picker)
self.rig_vis = visuals.Markers()
self.rig_vis.set_gl_state(depth_test=False)
self.rig_vis.antialias = 0
self.vispy_view.add(self.rig_vis)
self.helmet_vis = visuals.Markers()
self.vispy_view.add(self.helmet_vis)
self.gaze_vis = visuals.Line()
self.vispy_view.add(self.gaze_vis)
self.head_mesh = visuals.Mesh(vertices=verts,
shading='smooth',
faces=faces,
mode='triangles',
color=(0.5, 0.55, 0.7))
self.head_mesh.shininess = 0
self.head_mesh.light_dir = [0, 1, 1]
# self.head_mesh.light_color = np.array((1, 1, 0.95)) * 0.8
self.head_mesh.ambient_light_color = np.array((0.98, 0.98, 1)) * 0.2
self.head_mesh.attach(Alpha(0.3))
self.head_mesh.set_gl_state(depth_test=True, cull_face=True)
self.head_mesh_transform = MatrixTransform()
self.head_mesh.transform = self.head_mesh_transform
self.vispy_view.add(self.head_mesh)
self.trial_changed.emit(0)
self.frame_changed.emit(0)
self.show()
vispy.app.run()