def new_axis(fig=None):
from mayavi.modules.axes import Axes
from mayavi.tools.engine_manager import get_engine, engine_manager
from mayavi.tools.figure import gcf
scene = gcf()
if fig is None:
engine = get_engine()
else:
engine = engine_manager.find_figure_engine(fig)
engine.current_scene = fig
if scene.scene is not None:
scene.scene.disable_render = True
parent = engine.current_object
# Try to find an existing module, if not add one to the pipeline
if parent == None:
target = scene
else:
target = parent
ax = Axes()
engine.add_module(ax, obj=parent)
if scene.scene is not None:
scene.scene.disable_render = False
return ax
def view_mlab():
engine = mayavi.mlab.get_engine()
from mayavi.modules.axes import Axes
axes = Axes()
axes.name = 'Axes'
axes.axes.fly_mode = 'none'
axes.axes.number_of_labels = 8
axes.axes.font_factor = 0.5
#module_manager = self.__module_manager()
# Add the label / marker:
engine.add_filter(axes)
from mayavi.modules.outline import Outline
outline = Outline()
outline.name = 'Outline'
engine.add_filter(outline)
mayavi.mlab.show()
def setUp(self):
"""Initial setting up of test fixture, automatically called by
TestCase before any other test method is invoked"""
e = NullEngine()
# Uncomment to see visualization for debugging etc.
#e = Engine()
e.start()
s = e.new_scene()
self.e = e
self.s = s
############################################################
# Create a new scene and set up the visualization.
#Make the grid
grid = self.make_grid4scatter()
e.add_source(grid)
eg = ExtractGrid()
e.add_filter(eg)
nb_ticks = 6
eg.x_ratio = eg.y_ratio = eg.z_ratio = 100 / (nb_ticks - 1) / 2
gpx = GridPlane()
e.add_module(gpx)
gpx.grid_plane.axis = 'x'
gpy = GridPlane()
e.add_module(gpy)
gpy.grid_plane.axis = 'y'
gpz = GridPlane()
e.add_module(gpz)
gpz.grid_plane.axis = 'z'
#Add the scatter
d = VTKDataSource()
d.data = self.make_scatter()
e.add_source(d)
if is_old_pipeline():
a = Axes()
e.add_module(a)
a.axes.number_of_labels = nb_ticks
self.eg = eg
self.gpx = gpx
self.gpy = gpy
self.gpz = gpz
self.scene = e.current_scene
return
def _annotateScene(self):
script = self.script
# Domain (axes and outline)
script.add_source(VTKDataSource(data=vtk_geometry.domain()))
script.engine.current_object.name = "Domain"
outline = Outline()
script.add_module(outline)
outline.actor.property.opacity = 0.2
axes = Axes()
axes.axes.x_label = "X"
axes.axes.y_label = "Y"
axes.axes.z_label = "Z"
axes.axes.label_format = "%-0.1f"
script.add_module(axes)
return
def _show_data(self):
if self.source is not None:
return
mayavi = self.get_mayavi()
if mayavi.engine.current_scene is None:
mayavi.new_scene()
from mayavi.sources.array_source import ArraySource
vol = self.volume
origin = vol[::2]
spacing = (vol[1::2] - origin)/(self.dimensions -1)
src = ArraySource(transpose_input_array=False,
scalar_data=self.data,
origin=origin,
spacing=spacing)
self.source = src
mayavi.add_source(src)
from mayavi.modules.outline import Outline
from mayavi.modules.image_plane_widget import ImagePlaneWidget
from mayavi.modules.axes import Axes
# Visualize the data.
o = Outline()
mayavi.add_module(o)
a = Axes()
mayavi.add_module(a)
self._ipw1 = ipw = ImagePlaneWidget()
mayavi.add_module(ipw)
ipw.module_manager.scalar_lut_manager.show_scalar_bar = True
self._ipw2 = ipw_y = ImagePlaneWidget()
mayavi.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
self._ipw3 = ipw_z = ImagePlaneWidget()
mayavi.add_module(ipw_z)
ipw_z.ipw.plane_orientation = 'z_axes'
outline1.actor.mapper.scalar_range = array([0., 1.]) outline1.outline_mode = 'full' outline1.actor.property.specular_color = (0.0, 0.0, 0.0) outline1.actor.property.diffuse_color = (0.0, 0.0, 0.0) outline1.actor.property.ambient_color = (0.0, 0.0, 0.0) outline1.actor.property.color = (0.0, 0.0, 0.0) outline1.actor.property.line_width = 4. outline1.actor.property.line_width = 4. #scene.scene.background = (0.7529411764705882, 0.7529411764705882, 0.7529411764705882) scene.scene.background = (1.0, 1.0, 1.0) scene.scene.jpeg_quality = 100 from mayavi.modules.axes import Axes axes = Axes() engine.add_module(axes, obj=None) axes.axes.x_label = 'i' axes.axes.y_label = 'j' axes.axes.z_label = 'k' axes.axes.label_format = '' axes.property.display_location = 'background' scene.scene.isometric_view() camera_light = engine.scenes[0].scene.light_manager.lights[0] camera_light.activate = True camera_light.azimuth = -20.0 camera_light.elevation = 35.0 camera_light.color = (1.0, 0.0, 1.0)
def __generate_velocity_grid(self, cellid, iso_surface=False):
"""Generates a velocity grid from a given spatial cell id
:param cellid: The spatial cell's ID
:param iso_surface: If true, plots the iso surface
"""
# Create nodes
# Get velocity blocks and avgs:
blocksAndAvgs = self.vlsvReader.read_blocks(cellid)
if len(blocksAndAvgs) == 0:
print "CELL " + str(cellid) + " HAS NO VELOCITY BLOCK"
return False
# Create a new scene
self.__engine.new_scene()
mayavi.mlab.set_engine(self.__engine) # CONTINUE
# Create a new figure
figure = mayavi.mlab.gcf(engine=self.__engine)
figure.scene.disable_render = True
blocks = blocksAndAvgs[0]
avgs = blocksAndAvgs[1]
# Get nodes:
nodesAndKeys = self.vlsvReader.construct_velocity_cell_nodes(blocks)
# Create an unstructured grid:
points = nodesAndKeys[0]
tets = nodesAndKeys[1]
tet_type = tvtk.Voxel().cell_type # VTK_VOXEL
ug = tvtk.UnstructuredGrid(points=points)
# Set up the cells
ug.set_cells(tet_type, tets)
# Input data
values = np.ravel(avgs)
ug.cell_data.scalars = values
ug.cell_data.scalars.name = "avgs"
# Plot B if possible:
# Read B vector and plot it:
if self.vlsvReader.check_variable("B") == True:
B = self.vlsvReader.read_variable(name="B", cellids=cellid)
elif self.vlsvReader.check_variable("B_vol") == True:
B = self.vlsvReader.read_variable(name="B_vol", cellids=cellid)
else:
B = self.vlsvReader.read_variable(name="background_B", cellids=cellid) + self.vlsvReader.read_variable(
name="perturbed_B", cellids=cellid
)
points2 = np.array([[0, 0, 0]])
ug2 = tvtk.UnstructuredGrid(points=points2)
ug2.point_data.vectors = [B / np.linalg.norm(B)]
ug2.point_data.vectors.name = "B_vector"
# src2 = VTKDataSource(data = ug2)
d2 = mayavi.mlab.pipeline.add_dataset(ug2)
# mayavi.mlab.add_module(Vectors())
vec = mayavi.mlab.pipeline.vectors(d2)
vec.glyph.mask_input_points = True
vec.glyph.glyph.scale_factor = 1e6
vec.glyph.glyph_source.glyph_source.center = [0, 0, 0]
# Visualize
d = mayavi.mlab.pipeline.add_dataset(ug)
if iso_surface == False:
iso = mayavi.mlab.pipeline.surface(d)
else:
ptdata = mayavi.mlab.pipeline.cell_to_point_data(d)
iso = mayavi.mlab.pipeline.iso_surface(ptdata, contours=[1e-15, 1e-14, 1e-12], opacity=0.3)
figure.scene.disable_render = False
self.__unstructured_figures.append(figure)
# Name the figure
figure.name = (
str(cellid)
+ ", "
+ self.variable_plotted
+ " = "
+ str(self.vlsvReader.read_variable(self.variable_plotted, cellids=cellid))
)
from mayavi.modules.axes import Axes
axes = Axes()
axes.name = "Axes"
axes.axes.fly_mode = "none"
axes.axes.number_of_labels = 8
axes.axes.font_factor = 0.5
# module_manager = self.__module_manager()
# Add the label / marker:
self.__engine.add_filter(axes)
from mayavi.modules.outline import Outline
outline = Outline()
outline.name = "Outline"
self.__engine.add_filter(outline)
return True
def run(self):
"""This is executed once the application GUI has started.
*Make sure all other MayaVi specific imports are made here!*
"""
# Various imports to do different things.
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.axes import Axes
from mayavi.modules.grid_plane import GridPlane
from mayavi.modules.image_plane_widget import ImagePlaneWidget
from mayavi.modules.text import Text
from mayavi.modules.contour_grid_plane import ContourGridPlane
from mayavi.modules.iso_surface import IsoSurface
script = self.script
# Create a new scene.
script.new_scene()
# Read a VTK (old style) data file.
r = VTKFileReader()
r.initialize(join(get_data_dir(abspath(__file__)), 'heart.vtk'))
script.add_source(r)
# Put up some text.
t = Text(text='MayaVi rules!',
x_position=0.2,
y_position=0.9,
width=0.8)
t.property.color = 1, 1, 0 # Bright yellow, yeah!
script.add_module(t)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# Create an axes for the data.
a = Axes()
script.add_module(a)
# Create three simple grid plane modules.
# First normal to 'x' axis.
gp = GridPlane()
script.add_module(gp)
# Second normal to 'y' axis.
gp = GridPlane()
gp.grid_plane.axis = 'y'
script.add_module(gp)
# Third normal to 'z' axis.
gp = GridPlane()
script.add_module(gp)
gp.grid_plane.axis = 'z'
# Create one ImagePlaneWidget.
ipw = ImagePlaneWidget()
script.add_module(ipw)
# Set the position to the middle of the data.
ipw.ipw.slice_position = 16
# Create one ContourGridPlane normal to the 'x' axis.
cgp = ContourGridPlane()
script.add_module(cgp)
# Set the position to the middle of the data.
cgp.grid_plane.axis = 'y'
cgp.grid_plane.position = 15
# An isosurface module.
iso = IsoSurface(compute_normals=True)
script.add_module(iso)
iso.contour.contours = [200.0]
# Set the view.
s = script.engine.current_scene
cam = s.scene.camera
cam.azimuth(45)
cam.elevation(15)
s.render()
def plot(filename, number_bins=6):
"""Plot the cubes from a file.
The cubes are stratified into number_bins norm bins. The
transparency of the cubes is set depending on which norm bin the
cube is in.
"""
re_matrix_A = re.compile("^\s*Matrix A$")
re_matrix_B = re.compile("^\s*Matrix B$")
re_matrix_C = re.compile("^\s*Matrix C$")
re_product_space = re.compile("^\s*Product Space$")
fd = open(filename)
(block_size, A_i, A_j, A_width_i, A_width_j,
A_norm) = read_squares(fd, re_matrix_A, end=re_matrix_B)
(block_size, B_i, B_j, B_width_i, B_width_j,
B_norm) = read_squares(fd, re_matrix_B, end=re_matrix_C)
(block_size, C_i, C_j, C_width_i, C_width_j,
C_norm) = read_squares(fd, re_matrix_C, end=re_product_space)
(prod_i, prod_j, prod_k, prod_width_i, prod_width_j, prod_width_k,
prod_norm) = read_cubes(fd, re_product_space)
# Get the current figure.
figure = mlab.gcf()
# Get the engine.
engine = mlab.get_engine()
# Clean the figure.
mlab.clf()
# Turn off rendering (for performance).
figure.scene.disable_render = True
# Tune background color.
figure.scene.background = (1., 1., 1.)
# Stratify matrix squares.
(norms_stratified, A_i_stratified, A_j_stratified, A_width_i_stratified,
A_width_j_stratified) = stratify(number_bins, A_norm, A_i, A_j, A_width_i,
A_width_j)
# Add matrices.
print("Plotting matrix A")
for i in range(number_bins):
if len(A_i_stratified[i]) > 0:
points = mlab.points3d(A_i_stratified[i],
[1 for j in range(len(A_i_stratified[i]))],
A_j_stratified[i],
mode='cube',
color=(0.0, 0.5019607843137255,
0.5019607843137255),
scale_factor=1,
opacity=0.5 * (i + 1) / float(number_bins))
points.glyph.glyph_source.glyph_source.x_length = block_size
points.glyph.glyph_source.glyph_source.y_length = 0
points.glyph.glyph_source.glyph_source.z_length = block_size
(norms_stratified, B_i_stratified, B_j_stratified, B_width_i_stratified,
B_width_j_stratified) = stratify(number_bins, B_norm, B_i, B_j, B_width_i,
B_width_j)
# Add matrices.
print("Plotting matrix B")
for i in range(number_bins):
if len(B_i_stratified[i]) > 0:
points = mlab.points3d([1 for j in range(len(B_i_stratified[i]))],
B_j_stratified[i],
B_i_stratified[i],
mode='cube',
color=(0.5019607843137255, 0.0, 0.0),
scale_factor=1,
opacity=0.5 * (i + 1) / float(number_bins))
points.glyph.glyph_source.glyph_source.x_length = 0
points.glyph.glyph_source.glyph_source.y_length = block_size
points.glyph.glyph_source.glyph_source.z_length = block_size
(norms_stratified, C_i_stratified, C_j_stratified, C_width_i_stratified,
C_width_j_stratified) = stratify(number_bins, C_norm, C_i, C_j, C_width_i,
C_width_j)
# Add matrices.
print("Plotting matrix C")
for i in range(number_bins):
if len(C_i_stratified[i]) > 0:
points = mlab.points3d(C_i_stratified[i],
C_j_stratified[i],
[1 for j in range(len(C_i_stratified[i]))],
mode='cube',
color=(0.5019607843137255, 0.0,
0.5019607843137255),
scale_factor=1,
opacity=0.5 * (i + 1) / float(number_bins))
points.glyph.glyph_source.glyph_source.x_length = block_size
points.glyph.glyph_source.glyph_source.y_length = block_size
points.glyph.glyph_source.glyph_source.z_length = 0
# Stratify cubes by norm.
(norms_stratified, prod_i_stratified, prod_j_stratified,
prod_k_stratified) = stratify(number_bins, prod_norm, prod_i, prod_j,
prod_k)
# Add cubes.
print("Plotting product cubes")
for i in range(number_bins):
if len(prod_i_stratified[i]) > 0:
points = mlab.points3d(prod_i_stratified[i],
prod_j_stratified[i],
prod_k_stratified[i],
mode='cube',
color=(0.2, .2, .2),
scale_factor=1,
opacity=0.75 * (i + 1) / float(number_bins))
points.glyph.glyph_source.glyph_source.x_length = block_size
points.glyph.glyph_source.glyph_source.y_length = block_size
points.glyph.glyph_source.glyph_source.z_length = block_size
i_max = max(numpy.amax(prod_i), numpy.amax(prod_j),
numpy.amax(prod_k)) + block_size / 2
print("i_max = {:e}".format(i_max))
# Insert fake invisible data-set for axes.
mlab.points3d([1, i_max], [1, i_max], [1, i_max],
mode='cube',
scale_factor=0)
#mlab.axes(xlabel="i", ylabel="j", zlabel="k", extent=[1, xmax, 1, xmax, 1, xmax])
# Box around the whole thing.
mlab.outline(extent=[1, i_max, 1, i_max, 1, i_max])
outline = engine.scenes[0].children[-1].children[0].children[1]
outline.actor.property.color = (0, 0, 0)
outline.actor.property.line_width = 2
# Add axes.
from mayavi.modules.axes import Axes
axes = Axes()
engine.add_module(axes, obj=None)
axes.axes.label_format = '%-3.0f'
axes.axes.width = 2
axes.axes.x_label = 'i'
axes.axes.y_label = 'j'
axes.axes.z_label = 'k'
axes.label_text_property.color = (0, 0, 0)
axes.label_text_property.opacity = 0.0
axes.label_text_property.shadow = True
axes.label_text_property.shadow_offset = numpy.array([1, -1])
axes.property.color = (0, 0, 0)
axes.property.display_location = 'background'
axes.title_text_property.color = (0, 0, 0)
axes.title_text_property.shadow_offset = numpy.array([1, -1])
figure.scene.disable_render = False
figure.scene.camera.compute_view_plane_normal()
import os.path
#-------------------------------------------------------------------------------------------------------
#./spammsand_invsqrt 33_x8_11_S.mm 1.d-1 1.d-3 1.d-1 1.d-1 D U R b=16
# figure.scene.isometric_view()
# png_filename = os.path.splitext(filename)[0] + "_isov.png"
# print("Saving image to " + png_filename)
# figure.scene.save(png_filename,size=(1024,1024))
# figure.scene.camera.position = [2381.7518163797836, 2526.3678093421449, 2530.13269951962]
# figure.scene.camera.focal_point = [440.00000000000028, 440.0000000000029, 439.99999999999733]
# figure.scene.camera.view_angle = 30.0
# figure.scene.camera.view_up = [-0.4189314063923294, -0.41776697205346547, 0.80620545383879905]
# figure.scene.camera.clipping_range = [1986.7866107311997, 5491.0522577990569]
# figure.scene.camera.compute_view_plane_normal()
# figure.scene.render()
# png_filename = os.path.splitext(filename)[0] + "_cant_x.png"
# print("Saving image to " + png_filename)
# figure.scene.save(png_filename,size=(1024,1024))
#./spammsand_invsqrt water_500_to_6-311gss.mm 1.d-2 1.d-4 1.d-1 0.d0 D U R
figure.scene.camera.position = [
35816.735234550884, 38331.094829602851, 41443.525860211055
]
figure.scene.camera.focal_point = [
2614.1156973829502, 2621.6382407405645, -241.34477379674968
]
figure.scene.camera.view_angle = 30.0
figure.scene.camera.view_up = [
-0.45361775222697864, -0.4654155004102597, 0.76001272807921516
]
figure.scene.camera.clipping_range = [
26313.825398895184, 87716.669164634935
]
figure.scene.camera.compute_view_plane_normal()
figure.scene.render()
png_filename = os.path.splitext(filename)[0] + "_cant_x.png"
print("Saving image to " + png_filename)
figure.scene.save(png_filename, size=(768, 768))
def generate_custom_velocity_grid( vlsvReader, blocks_and_values, iso_surface=False ):
'''Generates a velocity grid from a given spatial cell id
:param vlsvReader: Some vlsv reader with a file open
:param velocity_cell_map: Given velocity cell ids and values in python dict() format (see read_velocity_cells function in vlsvReader)
:param iso_surface: If true, plots the iso surface
# Example usage:
import pytools as pt
#vlsvReader = pt.vlsvfile.VlsvReader("example.vlsv")
cellid = 1111
velocity_cell_map = vlsvReader.read_velocity_cells(cellid)
velocity_cell_ids = velocity_cell_map.keys()
velocity_cell_values = velocity_cell_map.values()
velocity_cell_map[velocity_cell_ids[10]] = 3e-7
generate_custom_velocity_grid( vlsvReader, velocity_cell_map )
'''
# Create nodes
# Get velocity blocks and avgs:
# Get helper function:
blocksAndAvgs = blocks_and_values
if len(blocksAndAvgs) == 0:
print "CELL " + str(cellid) + " HAS NO VELOCITY BLOCK"
return False
# Create a new scene
#engine.new_scene()
#mayavi.mlab.set_engine(engine)
# Create a new figure
#figure = mayavi.mlab.clf()
#figure.scene.disable_render = True
blocks = blocksAndAvgs[0]
avgs = blocksAndAvgs[1]
# Get nodes:
nodesAndKeys = vlsvReader.construct_velocity_cell_nodes(blocks)
# Create an unstructured grid:
points = nodesAndKeys[0]
tets = nodesAndKeys[1]
tet_type=tvtk.Voxel().cell_type#VTK_VOXEL
ug=tvtk.UnstructuredGrid(points=points)
# Set up the cells
ug.set_cells(tet_type,tets)
# Input data
values=np.ravel(avgs)
ug.cell_data.scalars=values
ug.cell_data.scalars.name='avgs'
#figure.scene.disable_render = False
d = mayavi.mlab.pipeline.add_dataset(ug)
if iso_surface == False:
iso = mayavi.mlab.pipeline.surface(d)
else:
ptdata = mayavi.mlab.pipeline.cell_to_point_data(d)
iso = mayavi.mlab.pipeline.iso_surface(ptdata, contours=[1e-15,1e-14,1e-12], opacity=0.3)
engine = mayavi.mlab.get_engine()
from mayavi.modules.axes import Axes
axes = Axes()
axes.name = 'Axes'
axes.axes.fly_mode = 'none'
axes.axes.number_of_labels = 8
axes.axes.font_factor = 0.5
#module_manager = self.__module_manager()
# Add the label / marker:
engine.add_filter( axes )
from mayavi.modules.outline import Outline
outline = Outline()
outline.name = 'Outline'
engine.add_filter( outline )
mayavi.mlab.show()
def __generate_velocity_grid(self, cellid, iso_surface=False):
'''Generates a velocity grid from a given spatial cell id
:param cellid: The spatial cell's ID
:param iso_surface: If true, plots the iso surface
'''
# Create nodes
# Get velocity blocks and avgs:
blocksAndAvgs = self.vlsvReader.read_blocks(cellid)
if len(blocksAndAvgs) == 0:
print "CELL " + str(cellid) + " HAS NO VELOCITY BLOCK"
return False
# Create a new scene
self.__engine.new_scene()
mayavi.mlab.set_engine(self.__engine) #CONTINUE
# Create a new figure
figure = mayavi.mlab.gcf(engine=self.__engine)
figure.scene.disable_render = True
blocks = blocksAndAvgs[0]
avgs = blocksAndAvgs[1]
# Get nodes:
nodesAndKeys = self.vlsvReader.construct_velocity_cell_nodes(blocks)
# Create an unstructured grid:
points = nodesAndKeys[0]
tets = nodesAndKeys[1]
tet_type = tvtk.Voxel().cell_type #VTK_VOXEL
ug = tvtk.UnstructuredGrid(points=points)
# Set up the cells
ug.set_cells(tet_type, tets)
# Input data
values = np.ravel(avgs)
ug.cell_data.scalars = values
ug.cell_data.scalars.name = 'avgs'
# Plot B if possible:
# Read B vector and plot it:
if self.vlsvReader.check_variable("B") == True:
B = self.vlsvReader.read_variable(name="B", cellids=cellid)
elif self.vlsvReader.check_variable("B_vol") == True:
B = self.vlsvReader.read_variable(name="B_vol", cellids=cellid)
else:
B = self.vlsvReader.read_variable(
name="background_B",
cellids=cellid) + self.vlsvReader.read_variable(
name="perturbed_B", cellids=cellid)
points2 = np.array([[0, 0, 0]])
ug2 = tvtk.UnstructuredGrid(points=points2)
ug2.point_data.vectors = [B / np.linalg.norm(B)]
ug2.point_data.vectors.name = 'B_vector'
#src2 = VTKDataSource(data = ug2)
d2 = mayavi.mlab.pipeline.add_dataset(ug2)
#mayavi.mlab.add_module(Vectors())
vec = mayavi.mlab.pipeline.vectors(d2)
vec.glyph.mask_input_points = True
vec.glyph.glyph.scale_factor = 1e6
vec.glyph.glyph_source.glyph_source.center = [0, 0, 0]
# Visualize
d = mayavi.mlab.pipeline.add_dataset(ug)
if iso_surface == False:
iso = mayavi.mlab.pipeline.surface(d)
else:
ptdata = mayavi.mlab.pipeline.cell_to_point_data(d)
iso = mayavi.mlab.pipeline.iso_surface(
ptdata, contours=[1e-15, 1e-14, 1e-12], opacity=0.3)
figure.scene.disable_render = False
self.__unstructured_figures.append(figure)
# Name the figure
figure.name = str(cellid) + ", " + self.variable_plotted + " = " + str(
self.vlsvReader.read_variable(self.variable_plotted,
cellids=cellid))
from mayavi.modules.axes import Axes
axes = Axes()
axes.name = 'Axes'
axes.axes.fly_mode = 'none'
axes.axes.number_of_labels = 8
axes.axes.font_factor = 0.5
#module_manager = self.__module_manager()
# Add the label / marker:
self.__engine.add_filter(axes)
from mayavi.modules.outline import Outline
outline = Outline()
outline.name = 'Outline'
self.__engine.add_filter(outline)
return True
def generate_custom_velocity_grid(vlsvReader,
blocks_and_values,
iso_surface=False):
'''Generates a velocity grid from a given spatial cell id
:param vlsvReader: Some vlsv reader with a file open
:param velocity_cell_map: Given velocity cell ids and values in python dict() format (see read_velocity_cells function in vlsvReader)
:param iso_surface: If true, plots the iso surface
# Example usage:
import pytools as pt
#vlsvReader = pt.vlsvfile.VlsvReader("example.vlsv")
cellid = 1111
velocity_cell_map = vlsvReader.read_velocity_cells(cellid)
velocity_cell_ids = velocity_cell_map.keys()
velocity_cell_values = velocity_cell_map.values()
velocity_cell_map[velocity_cell_ids[10]] = 3e-7
generate_custom_velocity_grid( vlsvReader, velocity_cell_map )
'''
# Create nodes
# Get velocity blocks and avgs:
# Get helper function:
blocksAndAvgs = blocks_and_values
if len(blocksAndAvgs) == 0:
print("CELL " + str(cellid) + " HAS NO VELOCITY BLOCK")
return False
# Create a new scene
#engine.new_scene()
#mayavi.mlab.set_engine(engine)
# Create a new figure
#figure = mayavi.mlab.clf()
#figure.scene.disable_render = True
blocks = blocksAndAvgs[0]
avgs = blocksAndAvgs[1]
# Get nodes:
nodesAndKeys = vlsvReader.construct_velocity_cell_nodes(blocks)
# Create an unstructured grid:
points = nodesAndKeys[0]
tets = nodesAndKeys[1]
tet_type = tvtk.Voxel().cell_type #VTK_VOXEL
ug = tvtk.UnstructuredGrid(points=points)
# Set up the cells
ug.set_cells(tet_type, tets)
# Input data
values = np.ravel(avgs)
ug.cell_data.scalars = values
ug.cell_data.scalars.name = 'avgs'
#figure.scene.disable_render = False
d = mayavi.mlab.pipeline.add_dataset(ug)
if iso_surface == False:
iso = mayavi.mlab.pipeline.surface(d)
else:
ptdata = mayavi.mlab.pipeline.cell_to_point_data(d)
iso = mayavi.mlab.pipeline.iso_surface(ptdata,
contours=[1e-15, 1e-14, 1e-12],
opacity=0.3)
engine = mayavi.mlab.get_engine()
from mayavi.modules.axes import Axes
axes = Axes()
axes.name = 'Axes'
axes.axes.fly_mode = 'none'
axes.axes.number_of_labels = 8
axes.axes.font_factor = 0.5
#module_manager = self.__module_manager()
# Add the label / marker:
engine.add_filter(axes)
from mayavi.modules.outline import Outline
outline = Outline()
outline.name = 'Outline'
engine.add_filter(outline)
mayavi.mlab.show()
def run(self):
"""This is executed once the application GUI has started.
*Make sure all other MayaVi specific imports are made here!*
"""
# Various imports to do different things.
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.axes import Axes
from mayavi.modules.grid_plane import GridPlane
from mayavi.modules.image_plane_widget import ImagePlaneWidget
from mayavi.modules.text import Text
script = self.script
# Create a new scene.
script.new_scene()
# Read a VTK (old style) data file.
r = VTKFileReader()
r.initialize(
join(get_data_dir(dirname(abspath(__file__))), 'heart.vtk'))
script.add_source(r)
# Put up some text.
t = Text(text='MayaVi rules!',
x_position=0.2,
y_position=0.9,
width=0.8)
t.property.color = 1, 1, 0 # Bright yellow, yeah!
script.add_module(t)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# Create an axes for the data.
a = Axes()
script.add_module(a)
# Create an orientation axes for the scene. This only works with
# VTK-4.5 and above which is why we have the try block.
try:
from mayavi.modules.orientation_axes import OrientationAxes
except ImportError:
pass
else:
a = OrientationAxes()
a.marker.set_viewport(0.0, 0.8, 0.2, 1.0)
script.add_module(a)
# Create three simple grid plane modules.
# First normal to 'x' axis.
gp = GridPlane()
script.add_module(gp)
# Second normal to 'y' axis.
gp = GridPlane()
gp.grid_plane.axis = 'y'
script.add_module(gp)
# Third normal to 'z' axis.
gp = GridPlane()
script.add_module(gp)
gp.grid_plane.axis = 'z'
# Create one ImagePlaneWidget.
ipw = ImagePlaneWidget()
script.add_module(ipw)
# Set the position to the middle of the data.
ipw.ipw.slice_position = 16
