def __init__(self, viewer, parent=None, order=0):
self._viewer = viewer
self._data = np.array([
[0, 0, -1],
[1, 0, -1],
[0, -5, -1],
[0, 5, -1],
[1, -5, -1],
[1, 5, -1],
])
self._default_color = np.array([1, 0, 1, 1])
self._target_length = 150
self._scale = 1
self._quantity = None
self._unit_reg = None
self.node = Line(connect='segments',
method='gl',
parent=parent,
width=3)
self.node.order = order
self.node.transform = STTransform()
# In order for the text to always appear centered on the scale bar,
# the text node should use the line node as the parent.
self.text_node = Text(pos=[0.5, -1], parent=self.node)
self.text_node.order = order
self.text_node.transform = STTransform()
self.text_node.font_size = 10
self.text_node.anchors = ("center", "center")
self.text_node.text = f"{1}px"
# Note:
# There are issues on MacOS + GitHub action about destroyed
# C/C++ object during test if those don't get disconnected.
def set_none():
self.node._set_canvas(None)
self.text_node._set_canvas(None)
# the two canvas are not the same object, better be safe.
self.node.canvas._backend.destroyed.connect(set_none)
self.text_node.canvas._backend.destroyed.connect(set_none)
assert self.node.canvas is self.text_node.canvas
# End Note
self._viewer.events.theme.connect(self._on_data_change)
self._viewer.scale_bar.events.visible.connect(self._on_visible_change)
self._viewer.scale_bar.events.colored.connect(self._on_data_change)
self._viewer.scale_bar.events.ticks.connect(self._on_data_change)
self._viewer.scale_bar.events.position.connect(
self._on_position_change)
self._viewer.camera.events.zoom.connect(self._on_zoom_change)
self._viewer.scale_bar.events.font_size.connect(self._on_text_change)
self._viewer.scale_bar.events.unit.connect(self._on_dimension_change)
self._on_visible_change(None)
self._on_data_change(None)
self._on_dimension_change(None)
self._on_position_change(None)
def __init__(self, viewer, parent=None, order=0):
self._viewer = viewer
# Load logo and make grayscale
logopath = join(dirname(__file__), '..', 'resources', 'logo.png')
logo = imread(logopath)
self._logo_raw = logo
self._logo_border = np.all(logo[..., :3] == [38, 40, 61], axis=2)
self._logo = np.zeros(logo.shape)
self.node = ImageNode(parent=parent)
self.node.order = order
self.node.cmap = 'grays'
self.node.transform = STTransform()
self.text_node = Text(pos=[0, 0],
parent=parent,
method='gpu',
bold=False)
self.text_node.order = order
self.text_node.transform = STTransform()
self.text_node.anchors = ('left', 'center')
self.text_node.text = ('to add data:\n'
' - drag and drop file(s) here\n'
' - select File > Open from the menu\n'
' - call a viewer.add_* method')
self.text_node.color = np.divide(
str_to_rgb(darken(self._viewer.palette['foreground'], 30)), 255)
self._on_palette_change(None)
self._on_visible_change(None)
self._on_canvas_change(None)
def attach(self, viewer, view, canvas, parent=None, order=0):
super().attach(viewer, view, canvas, parent, order)
self.rect_node = Compound(
[Line(connect='segments', method='gl', width=4)],
parent=parent,
)
self.rect_node.transform = STTransform()
self.rect_node.order = order
self.handle_node = Compound(
[Line(connect='segments', method='gl', width=2)],
parent=parent,
)
self.handle_node.transform = STTransform()
self.handle_node.order = order
self._nodes = [self.rect_node, self.handle_node]
canvas.connect(self.on_mouse_press)
canvas.connect(self.on_mouse_move)
canvas.connect(self.on_mouse_release)
self._viewer.camera.events.zoom.connect(self._on_zoom_change)
self._viewer.dims.events.ndisplay.connect(self._on_data_change)
self._on_zoom_change(None)
self._on_data_change(None)
self._update_position()
self._update_size()
def test_mesh_shading_filter(shading):
size = (45, 40)
with TestingCanvas(size=size, bgcolor="k") as c:
v = c.central_widget.add_view(border_width=0)
# Create visual
mdata = create_sphere(20, 40, radius=20)
mesh = scene.visuals.Mesh(meshdata=mdata,
shading=shading,
color=(0.1, 0.3, 0.7, 0.9))
v.add(mesh)
from vispy.visuals.transforms import STTransform
mesh.transform = STTransform(translate=(20, 20))
mesh.transforms.scene_transform = STTransform(scale=(1, 1, 0.01))
rendered = c.render()[..., 0] # R channel only
if shading in ("flat", "smooth"):
# there should be a gradient, not solid colors
assert np.unique(rendered).size >= 28
# sphere/circle starts "dark" on the left and gets brighter
# then hits a bright spot and decreases after
invest_row = rendered[23].astype(np.float64)
# overall, we should be increasing brightness up to a "bright spot"
assert (np.diff(invest_row[:29]) >= -1).all()
else:
assert np.unique(rendered).size == 2
def __init__(self, texture, pos):
self.vshader = Function("""
void line_of_sight() {
vec4 polar_pos = $transform(vec4($pos, 1));
if( polar_pos.x > 0.999 ) {
polar_pos.x = 0.001;
}
vec4 c = texture2D($texture, vec2(polar_pos.x, 0.5));
float depth = c.r;
if( polar_pos.y > depth+0.5 ) {
$mask = vec3(0.5, 0.5, 1); // out-of-sight objects turn blue
}
else {
$mask = vec3(1, 1, 1);
}
}
""")
self.fshader = Function("""
void apply_texture_mask() {
gl_FragColor *= vec4($mask,1);
}
""")
self.center = STTransform()
self.transform = STTransform(
scale=(0.5 / np.pi, 1, 0),
translate=(0.5, 0, 0)) * PolarTransform().inverse * self.center
self.vshader['pos'] = pos
self.vshader['transform'] = self.transform
self.vshader['texture'] = texture
self.vshader['mask'] = Varying('mask', dtype='vec3')
self.fshader['mask'] = self.vshader['mask']
def __define_eyeballs(self):
lsphere = visuals.Sphere(radius=0.024, method='ico', color='red')
rsphere = visuals.Sphere(radius=0.024, method='ico', color='green')
lsphere.transform = STTransform(translate=self.leyeball)
rsphere.transform = STTransform(translate=self.reyeball)
self.view.add(lsphere)
self.view.add(rsphere)
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 test_transforms():
# test transform mapping between nodes
root = Node()
n1 = Node(parent=root)
n2 = Node(parent=n1)
n3 = Node(parent=root)
n4 = Node(parent=n3)
n1.transform = STTransform(scale=(0.1, 0.1), translate=(7, 6))
n2.transform = STTransform(scale=(0.2, 0.3), translate=(5, 4))
n3.transform = STTransform(scale=(0.4, 0.5), translate=(3, 2))
n4.transform = STTransform(scale=(0.6, 0.7), translate=(1, 0))
assert np.allclose(n1.transform.map((0, 0))[:2], (7, 6))
assert np.allclose(n1.node_transform(root).map((0, 0))[:2], (7, 6))
assert np.allclose(n2.transform.map((0, 0))[:2], (5, 4))
assert np.allclose(n2.node_transform(root).map((0, 0))[:2],
(5*0.1+7, 4*0.1+6))
assert np.allclose(root.node_transform(n1).map((0, 0))[:2],
(-7/0.1, -6/0.1))
assert np.allclose(root.node_transform(n2).map((0, 0))[:2],
((-7/0.1-5)/0.2, (-6/0.1-4)/0.3))
# just check that we can assemble transforms correctly mapping across the
# scenegraph
assert n2.node_path(n4) == ([n2, n1, root], [n3, n4])
assert n4.node_path(n2) == ([n4, n3, root], [n1, n2])
assert n2.node_path(root) == ([n2, n1, root], [])
assert root.node_path(n4) == ([root], [n3, n4])
assert n2.node_path_transforms(n4) == [n4.transform.inverse,
n3.transform.inverse,
n1.transform, n2.transform]
assert n4.node_path_transforms(n2) == [n2.transform.inverse,
n1.transform.inverse,
n3.transform, n4.transform]
pts = np.array([[0, 0], [1, 1], [-56.3, 800.2]])
assert np.all(n2.node_transform(n1).map(pts) == n2.transform.map(pts))
assert np.all(n2.node_transform(root).map(pts) ==
n1.transform.map(n2.transform.map(pts)))
assert np.all(n1.node_transform(n3).map(pts) ==
n3.transform.inverse.map(n1.transform.map(pts)))
assert np.all(n2.node_transform(n3).map(pts) ==
n3.transform.inverse.map(
n1.transform.map(n2.transform.map(pts))))
assert np.all(n2.node_transform(n4).map(pts) ==
n4.transform.inverse.map(n3.transform.inverse.map(
n1.transform.map(n2.transform.map(pts)))))
# test transforms still work after reparenting
n3.parent = n1
assert np.all(n2.node_transform(n4).map(pts) == n4.transform.inverse.map(
n3.transform.inverse.map(n2.transform.map(pts))))
# test transform simplification
assert np.all(n2.node_transform(n4).map(pts) ==
n2.node_transform(n4).simplified.map(pts))
def update(ev):
global x1, y1, z1, x2, y2, z2
sphere1.transform = STTransform(translate=[x1, y1, z1])
sphere3.transform = STTransform(translate=[x2, y2, z2])
y1 -= 0.4
z2 -= 0.4
view.camera.fov = view.camera.fov + 1
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 __init__(self, texture, transform, scale):
self.fshader = Function("""
void apply_texture_mask() {
vec4 tex_pos = $transform(gl_FragCoord);
tex_pos /= tex_pos.w;
vec4 mask = texture2D($texture, tex_pos.xy);
mask.w = 1.0;
gl_FragColor = gl_FragColor * mask;
}
""")
self.fshader['texture'] = texture
self.scale_tr = STTransform(scale=scale) * STTransform(translate=(0.5,
0.5))
self.fshader['transform'] = self.scale_tr * transform
def __init__(self):
vispy.app.Canvas.__init__(self, keys='interactive', size=(800, 800))
self.images = [visuals.ImageVisual(image, method='impostor')
for i in range(4)]
self.images[0].transform = (STTransform(scale=(30, 30),
translate=(600, 600)) *
SineTransform() *
STTransform(scale=(0.1, 0.1),
translate=(-5, -5)))
tr = AffineTransform()
tr.rotate(30, (0, 0, 1))
tr.scale((3, 3))
self.images[1].transform = (STTransform(translate=(200, 600)) *
tr *
STTransform(translate=(-50, -50)))
self.images[2].transform = (STTransform(scale=(3, -150),
translate=(200, 100)) *
LogTransform((0, 2, 0)) *
STTransform(scale=(1, -0.01),
translate=(-50, 1.3)))
self.images[3].transform = (STTransform(scale=(400, 400),
translate=(600, 300)) *
PolarTransform() *
STTransform(scale=(np.pi/200, 0.005),
translate=(-3*np.pi/4., 0.1)))
for img in self.images:
img.tr_sys = TransformSystem(self)
img.tr_sys.visual_to_document = img.transform
self.show()
def test_canvas_render(blend_func):
"""Test rendering a canvas to an array.
Different blending functions are used to test what various Visuals may
produce without actually using different types of Visuals.
"""
with Canvas(size=(125, 125), show=True, title='run') as c:
im1 = np.zeros((100, 100, 4)).astype(np.float32)
im1[:, :, 0] = 1
im1[:, :, 3] = 1
im2 = np.zeros((50, 50, 4)).astype(np.float32)
im2[:, :, 1] = 1
im2[:, :, 3] = 0.4
# Create the image
image1 = ImageVisual(im1)
image1.transform = STTransform(translate=(20, 20, 0))
image1.transforms.configure(canvas=c, viewport=(0, 0, 125, 125))
image2 = ImageVisual(im2)
image2.transform = STTransform(translate=(0, 0, -1))
image2.transforms.configure(canvas=c, viewport=(0, 0, 125, 125))
if blend_func:
image1.set_gl_state(preset='translucent', blend_func=blend_func)
image2.set_gl_state(preset='translucent', blend_func=blend_func)
@c.events.draw.connect
def on_draw(ev):
gloo.clear('black')
gloo.set_viewport(0, 0, *c.physical_size)
image1.draw()
image2.draw()
rgba_result = c.render()
rgb_result = c.render(alpha=False)
# the results should be the same except for alpha
np.testing.assert_allclose(rgba_result[..., :3], rgb_result)
# the image should have something drawn in it
assert not np.allclose(rgba_result[..., :3], 0)
# the alpha should not be completely transparent
assert not np.allclose(rgba_result[..., 3], 0)
if blend_func is None or 'one' in blend_func:
# no transparency
np.testing.assert_allclose(rgba_result[..., 3], 255)
else:
# the alpha should have some transparency
assert (rgba_result[..., 3] != 255).any()
def __init__(self, scene, los_tex, size, supersample=4):
vert = """
#version 120
attribute vec2 pos;
varying vec2 v_pos;
void main(void) {
gl_Position = vec4(pos, 0, 1);
v_pos = $transform(gl_Position).xy;
}
"""
frag = """
#version 120
varying vec2 v_pos;
uniform sampler2D los_tex;
void main(void) {
vec2 polar_pos = $transform(vec4(v_pos, 0, 1)).xy;
float los_depth = texture2D(los_tex, vec2(polar_pos.x, 0.5)).r;
float diff = (los_depth+1 - polar_pos.y);
gl_FragColor = vec4(diff, diff, diff, 1);
}
"""
self.scene = scene
self.size = (size[0] * supersample, size[1] * supersample)
self.vertices = np.array(
[[-1, -1], [1, -1], [-1, 1], [-1, 1], [1, -1], [1, 1]],
dtype='float32')
self.program = ModularProgram(vert, frag)
self.program['pos'] = self.vertices
self.program['los_tex'] = los_tex
self.program.vert['transform'] = STTransform(
scale=(size[1] / 2., size[0] / 2.)) * STTransform(translate=(1, 1))
self.center = STTransform()
self.program.frag['transform'] = STTransform(
scale=(0.5 / np.pi, 1, 1),
translate=(0.5, 0, 0)) * PolarTransform().inverse * self.center
self.tex = vispy.gloo.Texture2D(shape=self.size + (4, ),
format='rgba',
interpolation='linear')
self.fbo = vispy.gloo.FrameBuffer(color=self.tex,
depth=vispy.gloo.RenderBuffer(
self.size))
def create_cities(self):
# initialize city markers
self.markers = Markers(parent=self.view.scene)
# move z-direction a bit negative (means nearer to the viewer)
self.markers.transform = STTransform(translate=(0, 0, -10))
cities = utils.get_cities_coords()
cnameList = []
ccoordList = []
for k, v in cities.items():
cnameList.append(k)
ccoordList.append(v)
ccoord = np.vstack(ccoordList)
ccoord = utils.wgs84_to_radolan(ccoord)
pos_scene = np.zeros((ccoord.shape[0], 2), dtype=np.float32)
pos_scene[:] = ccoord - self.r0
# initialize Markers
self.markers.set_data(pos=pos_scene,
symbol="disc",
edge_color="blue",
face_color='red',
size=10)
# initialize Markertext
self.text = Text(text=cnameList,
pos=pos_scene,
font_size=15,
anchor_x='right',
anchor_y='top',
parent=self.view.scene)
def create_marker(self, id, pos, name):
marker = Markers(parent=self.view.scene)
marker.transform = STTransform(translate=(0, 0, -10))
marker.interactive = True
# add id
marker.unfreeze()
marker.id = id
marker.freeze()
marker.set_data(pos=pos[np.newaxis],
symbol="disc",
edge_color="blue",
face_color='red',
size=10)
# initialize Markertext
text = Text(text=name,
pos=pos,
font_size=15,
anchor_x='right',
anchor_y='top',
parent=self.view.scene)
return marker, text
def load_cue(self, cue_file, cue_name=None):
_cue = Cue(cue_file)
_cue.name = cue_name
self.cues[cue_name] = _cue
self.cues[cue_name].center = self.maze.coord[cue_name]
self.cues[cue_name].origin = self.origin
self.cues[cue_name].transform = STTransform()
self.cues[cue_name].scale(100)
self.cues[cue_name].pos = [0, 0, self.cues[cue_name].center[-1]]
self.view.add(self.cues[cue_name])
self.cues_height[cue_name] = self.cues[cue_name].center[
-1] # jovian will use this papameter
@_cue.connect
def on_move(target_item, target_pos):
if hasattr(self, 'jov'):
self.jov.teleport(prefix='model',
target_pos=target_pos,
target_item=target_item)
else:
_cue_default_offset = self.cues[
target_item]._xy_center * self.cues[
target_item]._scale_factor
self.cues[
target_item]._transform.translate = self._to_jovian_coord(
target_pos).astype(np.float32) - _cue_default_offset
def _create_image_chunk(self, chunk: ChunkData):
"""Add a new chunk.
Parameters
----------
chunk : ChunkData
The data used to create the new chunk.
"""
image_chunk = ImageChunk()
data = self._outline_chunk(chunk.data)
# Parent VispyImageLayer will process the data then set it.
self._set_node_data(image_chunk.node, data)
# Make the new ImageChunk a child positioned with us.
image_chunk.node.parent = self.node
pos = [chunk.pos[0] * 1024, chunk.pos[1] * 1024]
size = chunk.size * 16
# pos = [512, 0]
# size = 7
# print(pos, size)
image_chunk.node.transform = STTransform(translate=pos,
scale=[size, size])
return image_chunk
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 _niimg_norm(sh, diag, translate):
"""Normalize the volume between (0., 1.)."""
# Compute normalization ratio
ratio = np.abs(diag) * sh
sgn = np.sign(diag)
# Get scale and translate
sc = 1. / ratio
tr = -(translate + np.array([0., 0, 0])) / ratio
# Define transformations of each slice
sg_norm = STTransform(scale=(sc[1], sc[2], 1.),
translate=(tr[1], tr[2], 1.))
cr_norm = STTransform(scale=(sc[0], sc[2], 1.),
translate=(sgn[0] * tr[0], tr[2], 1.))
ax_norm = STTransform(scale=(sc[1], sc[0], 1.),
translate=(tr[1], sgn[0] * tr[0], 1.))
return sg_norm, cr_norm, ax_norm
def __init__(self, **kwargs):
super(RadolanCanvas, self).__init__(keys='interactive', **kwargs)
# set size ov Canvas
self.size = 450, 450
# unfreeze needed to add more elements
self.unfreeze()
# add grid central widget
self.grid = self.central_widget.add_grid()
# add view to grid
self.view = self.grid.add_view(row=0, col=0)
self.view.border_color = (0.5, 0.5, 0.5, 1)
# add signal emitters
self.mouse_moved = EventEmitter(source=self, type="mouse_moved")
# block double clicks
self.events.mouse_double_click.block()
# initialize empty RADOLAN image
img_data = np.zeros((900, 900))
# initialize colormap, we take cubehelix for now
# this is the most nice colormap for radar in vispy
cmap = 'cubehelix'
# initialize Image Visual with img_data
# add to view
self.image = Image(
img_data,
method='subdivide',
#interpolation='bicubic',
cmap=cmap,
parent=self.view.scene)
# add transform to Image
# (mostly positioning within canvas)
self.image.transform = STTransform(translate=(0, 0, 0))
# get radolan ll point coodinate into self.r0
self.r0 = utils.get_radolan_origin()
# create cities (Markers and Text Visuals
self.create_cities()
# create PanZoomCamera
self.cam = PanZoomCamera(name="PanZoom",
rect=Rect(0, 0, 900, 900),
aspect=1,
parent=self.view.scene)
self.view.camera = self.cam
self._mouse_position = None
self.freeze()
# print FPS to console, vispy SceneCanvas internal function
self.measure_fps()
def smooth_3d(vol, smooth_factor=3, correct=True):
"""Smooth a 3-D volume.
Parameters
----------
vol : array_like
The volume of shape (N, M, P)
smooth_factor : int | 3
The smoothing factor.
Returns
-------
vol_smooth : array_like
The smooth volume with the same shape as vol.
"""
tf = NullTransform()
# No smoothing :
if (not isinstance(smooth_factor, int)) or (smooth_factor < 3):
return vol, tf
# Smoothing array :
sz = np.full((3, ), smooth_factor, dtype=int)
smooth = np.ones([smooth_factor] * 3) / np.prod(sz)
# Apply smoothing :
sm = fftconvolve(vol, smooth, mode='same')
if correct:
# Get the shape of the vol and the one with 'full' convolution :
vx, vy, vz = vol.shape
vcx, vcy, vcz = np.array([vx, vy, vz]) + smooth_factor - 1
# Define transform :
sc = [vx / vcx, vy / vcy, vz / vcz]
tr = .5 * np.array([smooth_factor] * 3)
tf = STTransform(scale=sc, translate=tr)
return sm, tf
def __init__(self):
app.Canvas.__init__(self,
title='Arrows example',
keys='interactive',
size=(1050, 650))
line1 = curves.curve4_bezier((10.0, 0.0), (50, -190), (350, 190),
(390, 0.0))
arrows1 = np.array([line1[-2], line1[-1]]).reshape((1, 4))
line2 = curves.curve4_bezier((10.0, 0.0), (190, -190), (210, 190),
(390, 0.0))
arrows2 = np.array([line2[1], line2[0], line2[-2], line2[-1]]).reshape(
(2, 4))
line3 = curves.curve3_bezier((10.0, 0.0), (50, 190), (390, 0.0))
arrows3 = np.array([line3[-2], line3[-1]]).reshape((1, 4))
arrow_types = ["curved", "stealth", "inhibitor_round", "angle_60"]
self.lines = []
for i, arrow_type in enumerate(arrow_types):
arrows = [
visuals.ArrowVisual(line1,
color='w',
width=6,
method='agg',
arrows=arrows1,
arrow_type=arrow_type,
arrow_size=30.0),
visuals.ArrowVisual(line2,
color='w',
width=2,
method='agg',
arrows=arrows2,
arrow_type=arrow_type,
arrow_size=5.0),
visuals.ArrowVisual(line3,
color='w',
width=4,
method='agg',
arrows=arrows3,
arrow_type=arrow_type,
arrow_size=10.0)
]
# Translate each line visual downwards
for j, visual in enumerate(arrows):
x = 50 + (i * 250)
y = 100 + (200 * j)
visual.transform = STTransform(translate=[x, y],
scale=(0.5, 1.0))
visual.events.update.connect(lambda event: self.update())
self.lines.extend(arrows)
self.show()
class Canvas(app.Canvas):
def __init__(self):
app.Canvas.__init__(self, keys='interactive')
ps = self.pixel_scale
n = 10000
pos = 0.25 * np.random.randn(n, 2).astype(np.float32)
color = np.random.uniform(0, 1, (n, 3)).astype(np.float32)
size = np.random.uniform(2 * ps, 12 * ps, (n, 1)).astype(np.float32)
self.points = MarkerVisual(pos=pos, color=color, size=size)
self.panzoom = STTransform(scale=(1, 0.2), translate=(0, 500))
w2 = (self.size[0] / 2, self.size[1] / 2)
self.transform = ChainTransform([
self.panzoom,
STTransform(scale=w2, translate=w2),
LogTransform(base=(0, 2, 0))
])
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
gloo.set_state(blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'))
def on_mouse_move(self, event):
if event.is_dragging:
dxy = event.pos - event.last_event.pos
button = event.press_event.button
if button == 1:
self.panzoom.move(dxy)
elif button == 2:
center = event.press_event.pos
self.panzoom.zoom(np.exp(dxy * (0.01, -0.01)), center)
self.update()
def on_resize(self, event):
self.width, self.height = event.size
gloo.set_viewport(0, 0, self.width, self.height)
def on_draw(self, event):
gloo.clear()
self.points.draw(self.tr_sys)
def test_mesh_wireframe_filter():
size = (45, 40)
with TestingCanvas(size=size, bgcolor="k") as c:
v = c.central_widget.add_view(border_width=0)
# Create visual
mdata = create_sphere(20, 40, radius=20)
mesh = scene.visuals.Mesh(meshdata=mdata,
shading=None,
color=(0.1, 0.3, 0.7, 0.9))
wireframe_filter = WireframeFilter(color='red')
mesh.attach(wireframe_filter)
v.add(mesh)
from vispy.visuals.transforms import STTransform
mesh.transform = STTransform(translate=(20, 20))
mesh.transforms.scene_transform = STTransform(scale=(1, 1, 0.01))
rendered_with_wf = c.render()
assert np.unique(rendered_with_wf[..., 0]).size >= 50
wireframe_filter.enabled = False
rendered_wo_wf = c.render()
# the result should be completely different
# assert not allclose
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_wf, rendered_wo_wf)
wireframe_filter.enabled = True
wireframe_filter.wireframe_only = True
rendered_with_wf_only = c.render()
# the result should be different from the two cases above
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_wf_only, rendered_with_wf)
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_wf_only, rendered_wo_wf)
wireframe_filter.enabled = True
wireframe_filter.wireframe_only = False
wireframe_filter.faces_only = True
rendered_with_faces_only = c.render()
# the result should be different from the cases above
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_faces_only, rendered_with_wf)
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_faces_only, rendered_wo_wf)
pytest.raises(AssertionError, np.testing.assert_allclose,
rendered_with_faces_only, rendered_with_wf_only)
def draw_scene(self):
self.fixed_frame = scene.node.Node(self.view.scene)
self.fixed_frame.transform = STTransform(
translate=(-self.moving_volume.shape[2] // 2,
-self.moving_volume.shape[1] // 2, -500))
fixed_volume = scene.visuals.Volume(
self.fixed_volume,
parent=self.fixed_frame,
threshold=self.model.fixed_display_threshold.get(),
emulate_texture=False)
fixed_volume.cmap = TranslucentFixedColormap()
fixed_volume.method = VOLUME_RENDERING_METHOD
#
# The transformation is done as follows:
#
# The translation frame handles the offset
#
# The centering frame picks the center of the moving frame
#
# The rotation frame rotates about the center
#
# The uncentering frame readjusts the coordinates so that 0, 0 is
# placed away from the center.
#
self.translation_frame = scene.node.Node(self.fixed_frame)
moving_volume = scene.visuals.Volume(
self.moving_volume,
parent=self.translation_frame,
threshold=self.model.moving_display_threshold.get(),
emulate_texture=False)
moving_volume.cmap = TranslucentMovingColormap()
moving_volume.method = VOLUME_RENDERING_METHOD
self.camera = scene.cameras.TurntableCamera(
parent=self.view.scene,
fov=60.,
elevation=self.fixed_volume.shape[2] // 2,
name="Turntable")
self.view.camera = self.camera
self.center_frame = scene.node.Node(parent=self.view)
self.axis = scene.visuals.XYZAxis(parent=self.center_frame)
axis_t = STTransform(scale=(50, 50, 50, 1))
self.axis.transform = axis_t.as_matrix()
self.apply_translation()
self.scene.events.mouse_move.connect(self.on_mouse_move)
class Canvas(app.Canvas):
def __init__(self):
app.Canvas.__init__(self, keys='interactive')
n = 10000
pos = 0.25 * np.random.randn(n, 2).astype(np.float32)
color = np.random.uniform(0, 1, (n, 3)).astype(np.float32)
size = np.random.uniform(2, 12, (n, 1)).astype(np.float32)
self.points = MarkerVisual(pos=pos, color=color, size=size)
self.panzoom = STTransform(scale=(1, 0.2), translate=(0, 500))
w2 = (self.size[0]/2, self.size[1]/2)
self.transform = ChainTransform([self.panzoom,
STTransform(scale=w2, translate=w2),
LogTransform(base=(0, 2, 0))])
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
def on_initialize(self, event):
gloo.set_state(blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'))
def on_mouse_move(self, event):
if event.is_dragging:
dxy = event.pos - event.last_event.pos
button = event.press_event.button
if button == 1:
self.panzoom.move(dxy)
elif button == 2:
center = event.press_event.pos
self.panzoom.zoom(np.exp(dxy * (0.01, -0.01)), center)
self.update()
def on_resize(self, event):
self.width, self.height = event.size
gloo.set_viewport(0, 0, self.width, self.height)
def on_draw(self, event):
gloo.clear()
self.points.draw(self.tr_sys)
def __init__(self):
app.Canvas.__init__(self, keys='interactive')
n = 10000
pos = 0.25 * np.random.randn(n, 2).astype(np.float32)
color = np.random.uniform(0, 1, (n, 3)).astype(np.float32)
size = np.random.uniform(2, 12, (n, 1)).astype(np.float32)
self.points = MarkerVisual(pos=pos, color=color, size=size)
self.panzoom = STTransform(scale=(1, 0.2), translate=(0, 500))
w2 = (self.size[0]/2, self.size[1]/2)
self.transform = ChainTransform([self.panzoom,
STTransform(scale=w2, translate=w2),
LogTransform(base=(0, 2, 0))])
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
def __init__(self):
app.Canvas.__init__(self, keys='interactive', size=(800, 800))
# Create several visuals demonstrating different features of Line
self.lines = [
# agg-method lines:
# per-vertex color
visuals.LineVisual(pos=pos, color=color, method='agg'),
# solid
visuals.LineVisual(pos=pos, color=(0, 0.5, 0.3, 1), method='agg'),
# wide
visuals.LineVisual(pos=pos, color=color, width=5, method='agg'),
# GL-method lines:
visuals.LineVisual(pos=pos, color=color, method='gl'),
visuals.LineVisual(pos=pos, color=(0, 0.5, 0.3, 1), method='gl'),
visuals.LineVisual(pos=pos, color=color, width=5, method='gl'),
# GL-method: "connect" not available in AGG method yet
# only connect alternate vert pairs
visuals.LineVisual(pos=pos,
color=(0, 0.5, 0.3, 1),
connect='segments',
method='gl'),
# connect specific pairs
visuals.LineVisual(pos=pos,
color=(0, 0.5, 0.3, 1),
connect=connect,
method='gl'),
]
counts = [0, 0]
for i, line in enumerate(self.lines):
# arrange lines in a grid
tidx = (line.method == 'agg')
x = 400 * tidx
y = 140 * (counts[tidx] + 1)
counts[tidx] += 1
line.transform = STTransform(translate=[x, y])
# redraw the canvas if any visuals request an update
line.events.update.connect(lambda evt: self.update())
self.texts = [
visuals.TextVisual('GL',
bold=True,
font_size=24,
color='w',
pos=(200, 40)),
visuals.TextVisual('Agg',
bold=True,
font_size=24,
color='w',
pos=(600, 40))
]
for text in self.texts:
text.transform = NullTransform()
self.visuals = self.lines + self.texts
self.show()
def _master_transform(self):
"""vispy.visuals.transforms.STTransform:
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, STTransform):
self.node.transform = STTransform()
return self.node.transform
def test_histogram():
"""Test histogram visual"""
size = (200, 100)
with TestingCanvas(size=size, bgcolor='w') as c:
np.random.seed(2397)
data = np.random.normal(size=100)
hist = Histogram(data, bins=20, color='k', parent=c.scene)
hist.transform = STTransform((size[0] // 10, -size[1] // 20, 1),
(100, size[1]))
assert_image_approved(c.render(), "visuals/histogram.png")
def __init__(self):
app.Canvas.__init__(self, keys="interactive")
ps = self.pixel_scale
n = 10000
pos = 0.25 * np.random.randn(n, 2).astype(np.float32)
color = np.random.uniform(0, 1, (n, 3)).astype(np.float32)
size = np.random.uniform(2 * ps, 12 * ps, (n, 1)).astype(np.float32)
self.points = MarkerVisual(pos=pos, color=color, size=size)
self.panzoom = STTransform(scale=(1, 0.2), translate=(0, 500))
w2 = (self.size[0] / 2, self.size[1] / 2)
self.transform = ChainTransform(
[self.panzoom, STTransform(scale=w2, translate=w2), LogTransform(base=(0, 2, 0))]
)
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
gloo.set_state(blend=True, blend_func=("src_alpha", "one_minus_src_alpha"))
def __init__(self):
QtCore.QObject.__init__(self)
app.Canvas.__init__(self, keys='interactive', resizable=False)
ps = self.pixel_scale
self.roi_visuals = []
self.current_roi = None
self.finished = False
self.drawing_roi = False
self.markers = []
self.panzoom = STTransform(scale=(1, 1), translate=(0, 0))
self.transform = ChainTransform([self.panzoom,
STTransform(scale=[1, 1], translate=[1,1]),
LogTransform(base=(0, 0, 0))])
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
gloo.set_state(blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'))
self.timer = app.Timer('auto', connect=self.on_timer, start=True)
class Canvas(QtCore.QObject, app.Canvas):
roiCreated = Signal(object)
roiDeleted = Signal(object)
def __init__(self):
QtCore.QObject.__init__(self)
app.Canvas.__init__(self, keys='interactive', resizable=False)
ps = self.pixel_scale
self.roi_visuals = []
self.current_roi = None
self.finished = False
self.drawing_roi = False
self.markers = []
self.panzoom = STTransform(scale=(1, 1), translate=(0, 0))
self.transform = ChainTransform([self.panzoom,
STTransform(scale=[1, 1], translate=[1,1]),
LogTransform(base=(0, 0, 0))])
self.tr_sys = TransformSystem(self)
self.tr_sys.visual_to_document = self.transform
gloo.set_state(blend=True,
blend_func=('src_alpha', 'one_minus_src_alpha'))
self.timer = app.Timer('auto', connect=self.on_timer, start=True)
#self.native.setFixedSize(800, 600)
def on_timer(self, event):
self.update()
def on_mouse_release(self, event):
if event.button == 2 and self.drawing_roi:
self.drawing_roi = False
self.current_roi.draw_finished()
self.roi_visuals.append(self.current_roi)
self.current_roi.menu.addAction(QtGui.QAction('Export ROIs', self.current_roi.menu, triggered=lambda : save_file_gui(self.export_rois, prompt='Export ROIs to text file', filetypes='Text Files (*.txt)')))
self.current_roi.menu.addAction(QtGui.QAction('Import ROIs', self.current_roi.menu, triggered=lambda : open_file_gui(self.import_rois, prompt='Import ROIs from text file', filetypes='Text Files (*.txt)')))
self.current_roi.select()
self.roiCreated.emit(self.current_roi)
elif any([roi.hover for roi in self.roi_visuals]) and event.button == 2 and not self.drawing_roi and event.last_event.type == 'mouse_press':
self.current_roi.contextMenuEvent(self.native.mapToGlobal(QtCore.QPoint(*event.pos)))
for roi in self.roi_visuals:
if roi.selected:
roi.finish_translate()
def export_rois(self, fname):
roi_strs = [repr(roi) for roi in self.roi_visuals]
with open(fname, 'w') as outf:
outf.write('\n'.join(roi_strs))
def import_rois(self, fname):
rois = ROIVisual.importROIs(fname)
for roi in rois:
while roi.id in [r.id for r in self.roi_visuals]:
roi.setId(roi.id + 1)
self.roi_visuals.append(roi)
def translatedPoint(self, pos):
return np.array([(pos[0] - self.panzoom.translate[0]) / self.panzoom.scale[0], (pos[1] - self.panzoom.translate[1]) / self.panzoom.scale[1]])
def on_mouse_press(self, event):
if self.drawing_roi:
return
if 'Control' in event.modifiers:
for roi in self.roi_visuals:
if roi.contains(self.translatedPoint(event.pos)):
if roi.selected:
roi.deselect()
else:
roi.select()
else:
self.current_roi = None
for roi in self.roi_visuals:
if roi.mouseIsOver(self.translatedPoint(event.pos)):
self.current_roi = roi
roi.select()
else:
roi.deselect()
def on_key_press(self, event):
if event.key == 'a' and 'Control' in event.modifiers:
for roi in self.roi_visuals:
roi.select()
elif event.key == 'Delete':
for roi in self.roi_visuals[:]:
if roi.selected:
self.delete_roi(roi)
def remove_roi(self, roi):
if self.current_roi == roi:
self.current_roi = None
self.roi_visuals.remove(roi)
self.roiDeleted.emit(roi)
def on_mouse_move(self, event):
pos = self.translatedPoint(event.pos)
for roi in self.roi_visuals:
if not self.drawing_roi:
if roi.mouseIsOver(pos):
self.current_roi = roi
if event.is_dragging:
dxy = self.translatedPoint(event.pos) - self.translatedPoint(event.last_event.pos)
button = event.press_event.button
if button == 1:
self.panzoom.move(event.pos - event.last_event.pos)
elif button == 2:
if not self.drawing_roi and any([roi.mouseIsOver(pos) for roi in self.roi_visuals]):
for roi in self.roi_visuals:
if roi.selected:
roi.translate(dxy)
elif self.drawing_roi == True:
self.current_roi.extend(pos)
else:
for roi in self.roi_visuals:
roi.deselect()
new_id = 1
while new_id in [roi.id for roi in self.roi_visuals]:
new_id += 1
self.current_roi = ROIVisual(new_id, pos)
self.drawing_roi = True
self.update()
def on_mouse_wheel(self, event):
center = event.pos
dz = event.delta[1]
self.panzoom.zoom(np.exp(np.array([.1, .1]) * dz), center)
def on_resize(self, event):
self.width, self.height = event.size
gloo.set_viewport(0, 0, self.width, self.height)
def on_draw(self, event):
gloo.clear()
for ch in self.markers:
ch.draw(self.tr_sys)
for roi in self.roi_visuals:
roi.draw(self.tr_sys)
if self.current_roi != None:
self.current_roi.draw(self.tr_sys)
volume1.transform = scene.STTransform(translate=(64, 64, 0))
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
# create colormaps that work well for translucent and additive volume rendering
class TransFire(BaseColormap):
glsl_map = """
vec4 translucent_fire(float t) {
return vec4(pow(t, 0.5), t, t*t, max(0, t*1.05 - 0.05));
}
"""
class TransGrays(BaseColormap):
glsl_map = """
def __init__(self, canvas=None, aspect=None, **kwargs):
self._aspect = aspect
self.attach(canvas)
STTransform.__init__(self, **kwargs)
