bgcolor=(1, 1, 1),
fgcolor=(0.5, 0.5, 0.5))
quiver = mlab.quiver3d(ccx,
ccy,
ccz,
eigVecs4D[:, :, 0, 0].ravel(),
eigVecs4D[:, :, 0, 1].ravel(),
eigVecs4D[:, :, 0, 2].ravel(),
scalars=eigVals3D[:, :, 0].ravel(),
mask_points=150,
scale_mode='scalar',
colormap='plasma',
opacity=1)
# mlab.outline()
# Added axis
engine.add_filter(axes, quiver)
quiver.glyph.color_mode = 'color_by_scalar'
quiver.glyph.glyph_source.glyph_source.glyph_type = 'dash'
scene = engine.scenes[0]
scene.scene.jpeg_quality = 100
scene.scene.anti_aliasing_frames = 20
# Axis related settings
axes.axes.x_label = 'x [m]'
axes.axes.y_label = 'y [m]'
axes.axes.z_label = 'z [m]'
axes.title_text_property.bold, axes.label_text_property.bold = False, False
axes.label_text_property.italic = False
axes.title_text_property.font_family = 'times'
# Axis texts scales to fit in the viewport?
axes.axes.scaling = False
# Text color
2. - (np.minimum(pts[::interval, 2], 5000) / float(
(-pts[:, 2]).max())) / 1000.,
scale_factor=10.,
colormap='Blues')
'''3'''
pts = np.array([x for x in pts3 if x[2] > -93500])
ptsViz2 = mlab.points3d(pts[::interval, 0],
pts[::interval, 1],
pts[::interval, 2],
2. - (np.minimum(pts[::interval, 2], 5000) / float(
(-pts[:, 2]).max())) / 1000.,
scale_factor=10.,
colormap='PuOr')
transform_data = TransformData()
engine.add_filter(transform_data, engine.scenes[0].children[1])
transform_data.children = [engine.scenes[0].children[1].children[0]]
# engine.scenes[0].children[1].children[0]=[]
transform_data.transform.matrix.__setstate__({
'elements': [
0.9553782053802112, -0.09691967661345026, 0.27903236545178867,
-392.81878278215254, 0.09283849668727677, 0.9952919671849423,
0.02783726980083738, 231.6724797545669, -0.2804166511056782,
-0.0006901755293638524, 0.9598781305147085, -118.84124965680712, 0.0,
0.0, 0.0, 1.0
]
})
transform_data.widget.set_transform(transform_data.transform)
transform_data.filter.update()
transform_data.widget.enabled = False
figure = mlab.figure(1, bgcolor=(0,0,0), fgcolor=(1,1,1))
mlab.clf()
figure.scene.disable_render = True
interval = 15
'''2'''
pts = np.array([x for x in pts2 if x[2] > -93500])
ptsViz1 = mlab.points3d(pts[::interval,0], pts[::interval,1], pts[::interval,2], 2.-(np.minimum(pts[::interval,2], 5000)/float((-pts[:,2]).max()))/1000., scale_factor=10., colormap='Blues')
'''3'''
pts = np.array([x for x in pts3 if x[2] > -93500])
ptsViz2 = mlab.points3d(pts[::interval,0], pts[::interval,1], pts[::interval,2], 2.-(np.minimum(pts[::interval,2], 5000)/float((-pts[:,2]).max()))/1000., scale_factor=10., colormap='PuOr')
transform_data = TransformData()
engine.add_filter(transform_data, engine.scenes[0].children[1])
transform_data.children = [engine.scenes[0].children[1].children[0]]
# engine.scenes[0].children[1].children[0]=[]
transform_data.transform.matrix.__setstate__({'elements': [0.9553782053802112, -0.09691967661345026, 0.27903236545178867, -392.81878278215254, 0.09283849668727677, 0.9952919671849423, 0.02783726980083738, 231.6724797545669, -0.2804166511056782, -0.0006901755293638524, 0.9598781305147085, -118.84124965680712, 0.0, 0.0, 0.0, 1.0]})
transform_data.widget.set_transform(transform_data.transform)
transform_data.filter.update()
transform_data.widget.enabled = False
'''1'''
pts = np.array([x for x in pts1 if x[2] > -93500])
ptsViz1 = mlab.points3d(pts[::interval,0], pts[::interval,1], pts[::interval,2], 2.-(np.minimum(pts[::interval,2], 5000)/float((-pts[:,2]).max()))/1000., scale_factor=10., colormap='summer')
mlab.view(azimuth=0, elevation=0, distance=3000., focalpoint=(0,0,0), figure=figure)#, reset_roll=False)
figure.scene.disable_render = False
transform_data2 = TransformData()
# Recorded script from Mayavi2
from numpy import array
from mayavi import mlab
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# -------------------------------------------
vtk_file_reader = engine.open('/home/dori/develop/pySAM/vtk/_55_1.11595_1.70081e-05.vtk')
from mayavi.modules.surface import Surface
surface = Surface()
engine.add_filter(surface, vtk_file_reader)
mlab.savefig('scene.png')
engine.add_module(module_manager3, obj=None) module_manager3.scalar_lut_manager.reverse_lut = True module_manager3.scalar_lut_manager.reverse_lut = False module_manager3.scalar_lut_manager.reverse_lut = True module_manager3.scalar_lut_manager.reverse_lut = False array_source2 = engine.scenes[0].children[2] array_source2.children[1:2] = [] module_manager4 = ModuleManager() engine.add_module(module_manager4, obj=None) array_source = engine.scenes[0].children[0] array_source.children[1:2] = [] from mayavi.modules.axes import Axes axes = Axes() module_manager = engine.scenes[0].children[0].children[0] engine.add_filter(axes, module_manager) scene.scene.camera.position = [437.19923996106922, -121.22299589742653, 164.6998334377177] scene.scene.camera.focal_point = [64.5, 64.5, 64.5] scene.scene.camera.view_angle = 30.0 scene.scene.camera.view_up = [-0.4727384608678496, -0.60095494152678108, 0.64449321631095513] scene.scene.camera.clipping_range = [228.1627604400266, 681.25637670357492] scene.scene.camera.compute_view_plane_normal() scene.scene.render() from mayavi.modules.surface import Surface surface = Surface() engine.add_filter(surface, module_manager) scene.scene.camera.position = [457.54060862037477, 151.6004944233332, -81.685995020579185] scene.scene.camera.focal_point = [64.5, 64.5, 64.5] scene.scene.camera.view_angle = 30.0 scene.scene.camera.view_up = [0.37956817215096489, -0.70260197392637047, 0.60189572927936885] scene.scene.camera.clipping_range = [237.76612866853119, 669.16771468729144]
# Recorded script from Mayavi2
from numpy import array
from mayavi import mlab
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# -------------------------------------------
scene = engine.scenes[0]
vtk_file_reader = engine.open(u'out.vtk', scene)
from mayavi.modules.surface import Surface
surface = Surface()
engine.add_filter(surface, vtk_file_reader)
from mayavi.modules.iso_surface import IsoSurface
iso_surface1 = IsoSurface()
vtk_file_reader = engine.scenes[0].children[0]
engine.add_filter(iso_surface1, vtk_file_reader)
scene.scene.x_minus_view()
hand=mlab.gcf(engine)
mlab.figure(hand,bgcolor=(1,1,1))
surface.actor.property.opacity = 0.78
scene.scene.save(u'out.png')
def view(prefix, name):
"""
construct a generic visualization of base mesh, refined mesh,
and potential/field/pseudopotential data in mayavi2
requires running within mayavi2 or ipython with threads or
something like::
from pyface.api import GUI
GUI().start_event_loop()
in your script to interact with it.
this is from a simplified macro recorded in mayavi2
"""
"""
wwc 11/23/2018
In both python 2.7 and 3.5, this 3D visualization with mayavi
works in Linux, but it's not compatible with X11 remote forwarding.
Install mayavi through conda channel "menpo" in python 3.5 or just
see environment setup of "ele35" in README. However, I haven't
found a mayavi version for python 3.6.
"""
import mayavi
try:
from mayavi.api import Engine
engine = Engine()
engine.start()
except AttributeError: # NameError:
engine = mayavi.engine
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
base_mesh_name = "%s_mesh.vtk" % prefix
if os.access(base_mesh_name, os.R_OK):
base_mesh = engine.open(base_mesh_name)
surface = Surface()
engine.add_filter(surface, base_mesh)
surface.actor.property.representation = 'wireframe'
surface.actor.property.line_width = 1
mesh_name = "%s_%s_mesh.vtk" % (prefix, name)
if os.access(mesh_name, os.R_OK):
mesh = engine.open(mesh_name)
mesh.cell_scalars_name = 'charge'
surface = Surface()
engine.add_filter(surface, mesh)
module_manager = mesh.children[0]
module_manager.scalar_lut_manager.lut_mode = 'RdBu'
module_manager.scalar_lut_manager.use_default_range = False
r = np.fabs(module_manager.scalar_lut_manager.data_range).max()
module_manager.scalar_lut_manager.data_range = [-r, r]
surface.actor.property.backface_culling = True
data_name = "%s_%s.vtk" % (prefix, name)
if os.access(data_name, os.R_OK):
data = engine.open(data_name)
if "pseudo_potential" in data._point_scalars_list:
data.point_scalars_name = "pseudo_potential"
else:
data.point_scalars_name = "potential"
iso_surface = IsoSurface()
engine.add_filter(iso_surface, data)
module_manager = data.children[0]
module_manager.scalar_lut_manager.lut_mode = 'Greys'
iso_surface.contour.auto_contours = True
iso_surface.contour.number_of_contours = 5
try:
iso_surface.contour.maximum_contour = 1e-2
except:
pass
scene.scene.isometric_view()
scene.scene.render()
engine.add_module(module_manager3, obj=None)
module_manager3.scalar_lut_manager.reverse_lut = True
module_manager3.scalar_lut_manager.reverse_lut = False
module_manager3.scalar_lut_manager.reverse_lut = True
module_manager3.scalar_lut_manager.reverse_lut = False
array_source2 = engine.scenes[0].children[2]
array_source2.children[1:2] = []
module_manager4 = ModuleManager()
engine.add_module(module_manager4, obj=None)
array_source = engine.scenes[0].children[0]
array_source.children[1:2] = []
from mayavi.modules.axes import Axes
axes = Axes()
module_manager = engine.scenes[0].children[0].children[0]
engine.add_filter(axes, module_manager)
scene.scene.camera.position = [
437.19923996106922, -121.22299589742653, 164.6998334377177
]
scene.scene.camera.focal_point = [64.5, 64.5, 64.5]
scene.scene.camera.view_angle = 30.0
scene.scene.camera.view_up = [
-0.4727384608678496, -0.60095494152678108, 0.64449321631095513
]
scene.scene.camera.clipping_range = [228.1627604400266, 681.25637670357492]
scene.scene.camera.compute_view_plane_normal()
scene.scene.render()
from mayavi.modules.surface import Surface
surface = Surface()
engine.add_filter(surface, module_manager)
scene.scene.camera.position = [
from mayavi.api import Engine
from mayavi.modules.streamline import Streamline
from mayavi.tools.show import show
try:
engine = mayavi.engine
except NameError:
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
vtk_file_reader = engine.open(sys.argv[1])
axes = Axes()
engine.add_filter(axes, vtk_file_reader)
streamline = Streamline()
engine.add_filter(streamline, vtk_file_reader)
streamline.seed.widget.center = array([0.0, 12.0, 12.0])
streamline.seed.widget.center = array([0.0, 12.0, 12.0])
streamline.seed.widget.handle_direction = array([1.0, 0.0, 0.0])
streamline.seed.widget.enabled = False
streamline1 = Streamline()
engine.add_filter(streamline1, vtk_file_reader)
streamline1.seed.widget = streamline1.seed.widget_list[2]
streamline1.seed.widget.center = array([30.0, 12.0, 12.0])
streamline1.seed.widget.enabled = False
streamline1.seed.widget.center = array([30.0, 12.0, 12.0])
streamline1.seed.widget.interactor = None
streamline1.seed.widget.center = array([39.0, 12.0, 12.0])
def view(prefix, name):
"""
construct a generic visualization of base mesh, refined mesh,
and potential/field/pseudopotential data in mayavi2
requires running within mayavi2 or ipython with threads or
something like::
from pyface.api import GUI
GUI().start_event_loop()
in your script to interact with it.
this is from a simplified macro recorded in mayavi2
"""
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
base_mesh_name = "%s_mesh.vtk" % prefix
if os.access(base_mesh_name, os.R_OK):
base_mesh = engine.open(base_mesh_name)
surface = Surface()
engine.add_filter(surface, base_mesh)
surface.actor.property.representation = 'wireframe'
surface.actor.property.line_width = 1
mesh_name = "%s_%s_mesh.vtk" % (prefix, name)
if os.access(mesh_name, os.R_OK):
mesh = engine.open(mesh_name)
mesh.cell_scalars_name = 'charge'
surface = Surface()
engine.add_filter(surface, mesh)
module_manager = mesh.children[0]
module_manager.scalar_lut_manager.lut_mode = 'RdBu'
module_manager.scalar_lut_manager.use_default_range = False
r = np.fabs(module_manager.scalar_lut_manager.data_range).max()
module_manager.scalar_lut_manager.data_range = [-r, r]
surface.actor.property.backface_culling = True
data_name = "%s_%s.vtk" % (prefix, name)
if os.access(data_name, os.R_OK):
data = engine.open(data_name)
if "pseudo_potential" in data._point_scalars_list:
data.point_scalars_name = "pseudo_potential"
else:
data.point_scalars_name = "potential"
iso_surface = IsoSurface()
engine.add_filter(iso_surface, data)
module_manager = data.children[0]
module_manager.scalar_lut_manager.lut_mode = 'Greys'
iso_surface.contour.auto_contours = True
iso_surface.contour.number_of_contours = 5
try:
iso_surface.contour.maximum_contour = 1e-2
except:
pass
scene.scene.isometric_view()
scene.scene.render()
from numpy import array
from mayavi.modules.axes import Axes
from mayavi.api import Engine
from mayavi.modules.surface import Surface
from mayavi.tools.show import show
try:
engine = mayavi.engine
except NameError:
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
vtk_file_reader = engine.open(sys.argv[1], scene)
axes = Axes()
axes.property.color = (0.0, 0.0, 0.0)
engine.add_filter(axes, vtk_file_reader)
surface = Surface()
engine.add_filter(surface, vtk_file_reader)
scene.scene.background = (1.0, 1.0, 1.0)
scene.scene.foreground = (0.0, 0.0, 0.0)
surface.contour.contours = [1.5]
surface.actor.mapper.progress = 1.0
surface.actor.mapper.scalar_range = array([ 0., 3.])
surface.enable_contours = True
show()