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 __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 __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()