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="Windbarb plot", keys="interactive",
size=(830, 430))
self.windbarb_length = 25
self.grid_spacing = 50
self.grid_coords = None
self.line_vertices = None
self.last_mouse = (0, 0)
self.generate_grid()
direction_vectors = (self.grid_coords - self.last_mouse).astype(
np.float32)
direction_vectors[:] /= 10
direction_vectors[:, 1] *= -1
self.visual = WindbarbVisual(pos=self.grid_coords,
wind=direction_vectors,
trig=False,
edge_color='black',
face_color='black',
size=self.windbarb_length)
self.visual.events.update.connect(lambda evt: self.update())
self.visual.transform = NullTransform()
self.show()
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 __init__(self):
app.Canvas.__init__(self,
title='Bezier lines example',
keys='interactive',
size=(400, 750))
self.lines = [
visuals.LineVisual(curves.curve4_bezier((10, 0), (50, -190),
(350, 190), (390, 0)),
color='w',
width=2,
method='agg'),
visuals.LineVisual(curves.curve4_bezier((10, 0), (190, -190),
(210, 190), (390, 0)),
color='w',
width=2,
method='agg'),
visuals.LineVisual(curves.curve3_bezier((10, 0), (30, 200),
(390, 0)),
color='w',
width=2,
method='agg')
]
# Translate each line visual downwards
for i, line in enumerate(self.lines):
x = 0
y = 200 * (i + 1)
line.transform = STTransform(translate=[x, y])
self.texts = [
visuals.TextVisual('Third order curve',
bold=True,
color='w',
font_size=14,
pos=(200, 75)),
visuals.TextVisual('Quadratic curve',
bold=True,
color='w',
font_size=14,
pos=(200, 525)),
]
for text in self.texts:
text.transform = NullTransform()
self.visuals = self.lines + self.texts
self.show()
def __init__(self,
atlas,
sprite_size=(16, 16),
point_cs='pixel',
method=None):
if method is None:
if 'GL_GEOMETRY_SHADER' in vispy.gloo.gl.__dict__:
method = 'geometry'
else:
method = 'point_sprite'
self.method = method
self.point_cs = point_cs
self.atlas = atlas
self.atlas.atlas_changed.connect(self._atlas_changed)
self.position = np.empty((0, 3), dtype='float32')
self.sprite = np.empty((0, ), dtype='uint32')
self.sprite_size = sprite_size
self.fgcolor = np.empty((0, 4), dtype='float32')
self.bgcolor = np.empty((0, 4), dtype='float32')
self._atlas_tex = vispy.gloo.Texture2D(shape=(1, 1, 4),
format='rgba',
interpolation='nearest')
self._atlas_map_tex = vispy.gloo.Texture1D(shape=(1, 4),
format='rgba',
internalformat='rgba32f',
interpolation='nearest')
self._need_data_upload = False
self._need_atlas_upload = True
self._null_transform = NullTransform()
if method == 'point_sprite':
shaders = self.vertex_shader_2, self.fragment_shader_2
elif method == 'geometry':
shaders = self.vertex_shader_3, self.fragment_shader_3, self.geometry_shader_3
else:
raise ValueError('method must be "point_sprite" or "geometry"')
vispy.visuals.Visual.__init__(self, *shaders)
self._draw_mode = 'points'
self.shared_program['position'] = vispy.gloo.VertexBuffer()
self.shared_program['sprite'] = vispy.gloo.VertexBuffer()
self.shared_program['fgcolor'] = vispy.gloo.VertexBuffer()
self.shared_program['bgcolor'] = vispy.gloo.VertexBuffer()
self.update_gl_state(depth_test=True)
def __init__(self):
app.Canvas.__init__(self, size=(800, 600), keys="interactive")
self.bars = []
self.bars.append(get_left_orientation_bar())
self.bars.append(get_right_orientation_bar())
self.bars.append(get_top_orientation_bar())
self.bars.append(get_bottom_orientation_bar())
# construct a default transform that does identity scaling
# and does not translate the coordinates
transform = NullTransform()
self.transform_sys = TransformSystem(self)
self.transform_sys.visual_to_document = transform
self.show()
def __init__(self):
app.Canvas.__init__(self, size=(800, 600), keys="interactive")
img_data = get_mandlebrot_escape_values(600, 400)
self.image = ImageVisual(img_data, cmap=colormap)
image_transform = STTransform(scale=(1.3, 1.3), translate=(100, 0))
self.image_transform_sys = TransformSystem(self)
self.image_transform_sys.visual_to_document = image_transform
self.vertical_bar = get_vertical_bar()
# construct a default transform that does identity scaling
# and does not translate the coordinates
colorbar_transform = NullTransform()
self.colorbar_transform_sys = TransformSystem(self)
self.colorbar_transform_sys.visual_to_document = colorbar_transform
self.show()
def __init__(self):
app.Canvas.__init__(self,
title="Quiver plot",
keys="interactive",
size=(830, 430))
self.arrow_length = 20
self.grid_coords = None
self.line_vertices = None
self.last_mouse = (0, 0)
self.generate_grid()
self.visual = visuals.ArrowVisual(color='white',
connect='segments',
arrow_size=8)
self.visual.events.update.connect(lambda evt: self.update())
self.visual.transform = NullTransform()
self.show()
def __init__(self, bounds=(0, 0, 1, 1), transform=None):
self.bounds = bounds # (x, y, w, h)
if transform is None:
transform = NullTransform()
self._transform = None
self.transform = transform
def __init__(
self,
data=None,
method='auto',
grid=(1, 1),
cmap='viridis',
clim='auto',
gamma=1.0,
interpolation='nearest',
**kwargs,
):
self._data = None
self._gamma = gamma
# load 'float packed rgba8' interpolation kernel
# to load float interpolation kernel use
# `load_spatial_filters(packed=False)`
kernel, self._interpolation_names = load_spatial_filters()
self._kerneltex = Texture2D(kernel, interpolation='nearest')
# The unpacking can be debugged by changing "spatial-filters.frag"
# to have the "unpack" function just return the .r component. That
# combined with using the below as the _kerneltex allows debugging
# of the pipeline
# self._kerneltex = Texture2D(kernel, interpolation='linear',
# internalformat='r32f')
# create interpolation shader functions for available
# interpolations
fun = [
Function(_interpolation_template % n)
for n in self._interpolation_names
]
self._interpolation_names = [
n.lower() for n in self._interpolation_names
]
self._interpolation_fun = dict(zip(self._interpolation_names, fun))
self._interpolation_names.sort()
self._interpolation_names = tuple(self._interpolation_names)
# overwrite "nearest" and "bilinear" spatial-filters
# with "hardware" interpolation _data_lookup_fn
self._interpolation_fun['nearest'] = Function(_texture_lookup)
self._interpolation_fun['bilinear'] = Function(_texture_lookup)
if interpolation not in self._interpolation_names:
raise ValueError("interpolation must be one of %s" %
', '.join(self._interpolation_names))
self._interpolation = interpolation
# check texture interpolation
if self._interpolation == 'bilinear':
texture_interpolation = 'linear'
else:
texture_interpolation = 'nearest'
self._method = method
self._grid = grid
self._texture_limits = None
self._need_texture_upload = True
self._need_vertex_update = True
self._need_colortransform_update = True
self._need_interpolation_update = True
self._texture = Texture2D(np.zeros((1, 1, 4)),
interpolation=texture_interpolation)
self._subdiv_position = VertexBuffer()
self._subdiv_texcoord = VertexBuffer()
# impostor quad covers entire viewport
vertices = np.array(
[[-1, -1], [1, -1], [1, 1], [-1, -1], [1, 1], [-1, 1]],
dtype=np.float32,
)
self._impostor_coords = VertexBuffer(vertices)
self._null_tr = NullTransform()
self._init_view(self)
super(ImageVisual, self).__init__(vcode=VERT_SHADER, fcode=FRAG_SHADER)
self.set_gl_state('translucent', cull_face=False)
self._draw_mode = 'triangles'
# define _data_lookup_fn as None, will be setup in
# self._build_interpolation()
self._data_lookup_fn = None
self.clim = clim
self.cmap = cmap
if data is not None:
self.set_data(data)
self.freeze()
def __init__(self, data_arrays, origin_x, origin_y, cell_width, cell_height,
shape=None,
tile_shape=(DEFAULT_TILE_HEIGHT, DEFAULT_TILE_WIDTH),
texture_shape=(DEFAULT_TEXTURE_HEIGHT, DEFAULT_TEXTURE_WIDTH),
wrap_lon=False,
cmap='viridis', method='tiled', clim='auto', gamma=None,
interpolation='nearest', **kwargs):
# projection properties to be filled in later
self.cell_width = None
self.cell_height = None
self.origin_x = None
self.origin_y = None
self.shape = None
if method != 'tiled':
raise ValueError("Only 'tiled' method is currently supported")
method = 'subdivide'
grid = (1, 1)
# visual nodes already have names, so be careful
if not hasattr(self, "name"):
self.name = kwargs.get("name", None)
self._viewable_mesh_mask = None
self._ref1 = None
self._ref2 = None
self.texture_shape = texture_shape
self.tile_shape = tile_shape
self.num_tex_tiles = self.texture_shape[0] * self.texture_shape[1]
self._stride = 0 # Current stride is None when we are showing the overview
self._latest_tile_box = None
self.wrap_lon = wrap_lon
self._tiles = {}
# What tiles have we used and can we use (each texture uses the same 'state')
self.texture_state = TextureTileState(self.num_tex_tiles)
self.set_channels(data_arrays, shape=shape,
cell_width=cell_width, cell_height=cell_height,
origin_x=origin_x, origin_y=origin_y)
self.ndim = len(self.shape) or [x for x in data_arrays if x is not None][0].ndim
self.num_channels = len(data_arrays)
# load 'float packed rgba8' interpolation kernel
# to load float interpolation kernel use
# `load_spatial_filters(packed=False)`
kernel, self._interpolation_names = load_spatial_filters()
self._kerneltex = Texture2D(kernel, interpolation='nearest')
# The unpacking can be debugged by changing "spatial-filters.frag"
# to have the "unpack" function just return the .r component. That
# combined with using the below as the _kerneltex allows debugging
# of the pipeline
# self._kerneltex = Texture2D(kernel, interpolation='linear',
# internalformat='r32f')
# create interpolation shader functions for available
# interpolations
fun = [Function(_interpolation_template % n)
for n in self._interpolation_names]
self._interpolation_names = [n.lower()
for n in self._interpolation_names]
self._interpolation_fun = dict(zip(self._interpolation_names, fun))
self._interpolation_names.sort()
self._interpolation_names = tuple(self._interpolation_names)
# overwrite "nearest" and "bilinear" spatial-filters
# with "hardware" interpolation _data_lookup_fn
self._interpolation_fun['nearest'] = Function(_texture_lookup)
self._interpolation_fun['bilinear'] = Function(_texture_lookup)
if interpolation not in self._interpolation_names:
raise ValueError("interpolation must be one of %s" %
', '.join(self._interpolation_names))
self._interpolation = interpolation
# check texture interpolation
if self._interpolation == 'bilinear':
texture_interpolation = 'linear'
else:
texture_interpolation = 'nearest'
self._method = method
self._grid = grid
self._need_texture_upload = True
self._need_vertex_update = True
self._need_colortransform_update = False
self._need_interpolation_update = True
self._textures = [TextureAtlas2D(self.texture_shape, tile_shape=self.tile_shape,
interpolation=texture_interpolation,
format="LUMINANCE", internalformat="R32F",
) for i in range(self.num_channels)
]
self._subdiv_position = VertexBuffer()
self._subdiv_texcoord = VertexBuffer()
# impostor quad covers entire viewport
vertices = np.array([[-1, -1], [1, -1], [1, 1],
[-1, -1], [1, 1], [-1, 1]],
dtype=np.float32)
self._impostor_coords = VertexBuffer(vertices)
self._null_tr = NullTransform()
self._init_view(self)
if self.VERT_SHADER is None or self.FRAG_SHADER is None:
raise RuntimeError("No shader specified for this subclass")
super(ImageVisual, self).__init__(vcode=self.VERT_SHADER, fcode=self.FRAG_SHADER)
self.set_gl_state('translucent', cull_face=False)
self._draw_mode = 'triangles'
# define _data_lookup_fn as None, will be setup in
# self._build_interpolation()
self._data_lookup_fns = [Function(_rgb_texture_lookup) for i in range(self.num_channels)]
if isinstance(clim, str):
if clim != 'auto':
raise ValueError("C-limits can only be 'auto' or 2 floats for each provided channel")
clim = [clim] * self.num_channels
if not isinstance(cmap, (tuple, list)):
cmap = [cmap] * self.num_channels
assert (len(clim) == self.num_channels)
assert (len(cmap) == self.num_channels)
_clim = []
_cmap = []
for idx in range(self.num_channels):
cl = clim[idx]
if cl == 'auto':
_clim.append((np.nanmin(data_arrays[idx]), np.nanmax(data_arrays[idx])))
elif cl is None:
# Color limits don't matter (either empty channel array or other)
_clim.append((0., 1.))
elif isinstance(cl, tuple) and len(cl) == 2:
_clim.append(cl)
else:
raise ValueError("C-limits must be a 2-element tuple or the string 'auto' for each channel provided")
cm = cmap[idx]
_cmap.append(cm)
self.clim = _clim
self._texture_LUT = None
self.gamma = gamma if gamma is not None else (1.,) * self.num_channels
# only set colormap if it isn't None
# (useful when a subclass's shader doesn't expect a colormap)
if _cmap[0] is not None:
self.cmap = _cmap[0]
self.overview_info = None
self.init_overview(data_arrays)
self.freeze()
def __init__(self, data, origin_x, origin_y, cell_width, cell_height,
shape=None,
tile_shape=(DEFAULT_TILE_HEIGHT, DEFAULT_TILE_WIDTH),
texture_shape=(DEFAULT_TEXTURE_HEIGHT, DEFAULT_TEXTURE_WIDTH),
wrap_lon=False, projection=DEFAULT_PROJECTION,
cmap='viridis', method='tiled', clim='auto', gamma=1.,
interpolation='nearest', **kwargs):
if method != 'tiled':
raise ValueError("Only 'tiled' method is currently supported")
method = 'subdivide'
grid = (1, 1)
# visual nodes already have names, so be careful
if not hasattr(self, "name"):
self.name = kwargs.get("name", None)
self._viewable_mesh_mask = None
self._ref1 = None
self._ref2 = None
self.origin_x = origin_x
self.origin_y = origin_y
self.cell_width = cell_width
self.cell_height = cell_height # Note: cell_height is usually negative
self.texture_shape = texture_shape
self.tile_shape = tile_shape
self.num_tex_tiles = self.texture_shape[0] * self.texture_shape[1]
self._stride = (0, 0) # Current stride is None when we are showing the overview
self._latest_tile_box = None
self.wrap_lon = wrap_lon
self._tiles = {}
assert (shape or data is not None), "`data` or `shape` must be provided"
self.shape = shape or data.shape
self.ndim = len(self.shape) or data.ndim
# Where does this image lie in this lonely world
self.calc = TileCalculator(
self.name,
self.shape,
Point(x=self.origin_x, y=self.origin_y),
Resolution(dy=abs(self.cell_height), dx=abs(self.cell_width)),
self.tile_shape,
self.texture_shape,
wrap_lon=self.wrap_lon,
projection=projection,
)
# What tiles have we used and can we use
self.texture_state = TextureTileState(self.num_tex_tiles)
# load 'float packed rgba8' interpolation kernel
# to load float interpolation kernel use
# `load_spatial_filters(packed=False)`
kernel, self._interpolation_names = load_spatial_filters()
self._kerneltex = Texture2D(kernel, interpolation='nearest')
# The unpacking can be debugged by changing "spatial-filters.frag"
# to have the "unpack" function just return the .r component. That
# combined with using the below as the _kerneltex allows debugging
# of the pipeline
# self._kerneltex = Texture2D(kernel, interpolation='linear',
# internalformat='r32f')
# create interpolation shader functions for available
# interpolations
fun = [Function(_interpolation_template % n)
for n in self._interpolation_names]
self._interpolation_names = [n.lower()
for n in self._interpolation_names]
self._interpolation_fun = dict(zip(self._interpolation_names, fun))
self._interpolation_names.sort()
self._interpolation_names = tuple(self._interpolation_names)
# overwrite "nearest" and "bilinear" spatial-filters
# with "hardware" interpolation _data_lookup_fn
self._interpolation_fun['nearest'] = Function(_texture_lookup)
self._interpolation_fun['bilinear'] = Function(_texture_lookup)
if interpolation not in self._interpolation_names:
raise ValueError("interpolation must be one of %s" %
', '.join(self._interpolation_names))
self._interpolation = interpolation
# check texture interpolation
if self._interpolation == 'bilinear':
texture_interpolation = 'linear'
else:
texture_interpolation = 'nearest'
self._method = method
self._grid = grid
self._need_texture_upload = True
self._need_vertex_update = True
self._need_colortransform_update = True
self._need_interpolation_update = True
self._texture = TextureAtlas2D(self.texture_shape, tile_shape=self.tile_shape,
interpolation=texture_interpolation,
format="LUMINANCE", internalformat="R32F",
)
self._subdiv_position = VertexBuffer()
self._subdiv_texcoord = VertexBuffer()
# impostor quad covers entire viewport
vertices = np.array([[-1, -1], [1, -1], [1, 1],
[-1, -1], [1, 1], [-1, 1]],
dtype=np.float32)
self._impostor_coords = VertexBuffer(vertices)
self._null_tr = NullTransform()
self._init_view(self)
super(ImageVisual, self).__init__(vcode=VERT_SHADER, fcode=FRAG_SHADER)
self.set_gl_state('translucent', cull_face=False)
self._draw_mode = 'triangles'
# define _data_lookup_fn as None, will be setup in
# self._build_interpolation()
self._data_lookup_fn = None
self.gamma = gamma
self.clim = clim if clim != 'auto' else (np.nanmin(data), np.nanmax(data))
self._texture_LUT = None
self.cmap = cmap
self.overview_info = None
self.init_overview(data)
# self.transform = PROJ4Transform(projection, inverse=True)
self.freeze()
def return_node(self, node: ImageVisual) -> None:
"""Return a node that's no number being used."""
if node is not None:
node.parent = None # Remove from the Scene Graph.
node.transform = NullTransform()
self.nodes.append(node)
