def contour():
"""The script itself. We needn't have defined a function but
having a function makes this more reusable.
"""
# 'mayavi' is always defined on the interpreter.
# Create a new scene.
mayavi.new_scene()
# Read a VTK (old style) data file.
r = VTKFileReader()
filename = join(mayavi2.get_data_dir(dirname(abspath(__file__))),
'heart.vtk')
r.initialize(filename)
mayavi.add_source(r)
# Create an outline for the data.
o = Outline()
mayavi.add_module(o)
# Create three simple grid plane modules.
# First normal to 'x' axis.
gp = GridPlane()
mayavi.add_module(gp)
# Second normal to 'y' axis.
gp = GridPlane()
mayavi.add_module(gp)
gp.grid_plane.axis = 'y'
# Third normal to 'z' axis.
gp = GridPlane()
mayavi.add_module(gp)
gp.grid_plane.axis = 'z'
# Create one ContourGridPlane normal to the 'x' axis.
cgp = ContourGridPlane()
mayavi.add_module(cgp)
# Set the position to the middle of the data.
cgp.grid_plane.position = 15
# Another with filled contours normal to 'y' axis.
cgp = ContourGridPlane()
mayavi.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'y'
cgp.grid_plane.position = 15
cgp.contour.filled_contours = True
# An isosurface module.
iso = IsoSurface(compute_normals=True)
mayavi.add_module(iso)
iso.contour.contours = [220.0]
# An interactive scalar cut plane.
cp = ScalarCutPlane()
mayavi.add_module(cp)
cp.implicit_plane.normal = 0, 0, 1
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()
e.new_scene()
self.e = e
sgrid = datasets.generateStructuredGrid()
src = VTKDataSource(data=sgrid)
e.add_source(src)
# Create an outline for the data.
o = Outline()
e.add_module(o)
# Create one ContourGridPlane normal to the 'x' axis.
cgp1 = ContourGridPlane()
e.add_module(cgp1)
# Set the position to the middle of the data.
cgp1.grid_plane.position = 15
# Another with filled contours normal to 'y' axis.
cgp2 = ContourGridPlane()
cgp2.contour.filled_contours = True
# Set the axis and position to the middle of the data.
cgp2.grid_plane.axis = 'y'
cgp2.grid_plane.position = 15
e.add_module(cgp2)
# An isosurface module.
iso = IsoSurface(compute_normals=True)
e.add_module(iso)
iso.contour.contours = [5]
# An interactive scalar cut plane.
cp = ScalarCutPlane()
e.add_module(cp)
ip = cp.implicit_plane
ip.normal = 0, 0, 1
ip.origin = 0.5, 0.5, 1.0
# Since this is running offscreen this seems necessary.
ip.widget.origin = 0.5, 0.5, 1.0
ip.widget.enabled = False
self.scene = e.current_scene
self.cgp2 = cgp2
self.iso = iso
self.cp = cp
return
def contour(i, x):
"""The script itself. We needn't have defined a function but
having a function makes this more reusable.
"""
# 'mayavi' is always defined on the interpreter.
# Create a new scene.
mayavi.new_scene()
# Read in datacube
fd = open("output/output-cube-%.8d-%.3d" % (i, 0))
rho, rhovx, rhovz, rhovy = numpy.fromfile(file=fd,
dtype=numpy.float32).reshape(
(4, x, x, x))
src = ArraySource(transpose_input_array=False)
src.scalar_data = numpy.log10(rho).T.copy()
mayavi.add_source(src)
# Create an outline for the data.
o = Outline()
mayavi.add_module(o)
# Create one ContourGridPlane normal to the 'x' axis.
cgp = ContourGridPlane()
mayavi.add_module(cgp)
# Set the position to the middle of the data.
cgp.grid_plane.position = 0
# Another normal to 'y' axis.
cgp = ContourGridPlane()
mayavi.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'y'
cgp.grid_plane.position = 0
# Another normal to 'z' axis.
cgp = ContourGridPlane()
mayavi.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'z'
cgp.grid_plane.position = 0
# An isosurface module.
iso = IsoSurface(compute_normals=False)
mayavi.add_module(iso)
iso.contour.contours = [220.0]
# An interactive scalar cut plane.
cp = ScalarCutPlane()
mayavi.add_module(cp)
cp.implicit_plane.normal = 0, 0, 1
def streamline():
"""Sets up the mayavi pipeline for the visualization.
"""
# Create an outline for the data.
o = Outline()
mayavi.add_module(o)
s = Streamline(streamline_type='tube')
mayavi.add_module(s)
s.stream_tracer.integration_direction = 'both'
s.seed.widget.center = 3.5, 0.625, 1.25
s.module_manager.scalar_lut_manager.show_scalar_bar = True
i = IsoSurface()
mayavi.add_module(i)
i.contour.contours[0] = 550
i.actor.property.opacity = 0.5
for file0 in os.listdir('.'):
if fnmatch.fnmatch(file0, '*AMP.rec'):
filename = file0
print filename
savename = filename
##
scene1 = engine.new_scene()
scene1.scene.off_screen_rendering = True
jesse_mat_lab_coord_source1 = engine.open(filename, scene1)
##
from enthought.mayavi.modules.iso_surface import IsoSurface
iso_surface1 = IsoSurface()
engine.add_filter(iso_surface1, jesse_mat_lab_coord_source1)
iso_surface1.contour.contours[0:1] = [0.5]
##Orientation axes
orientation_axes = OrientationAxes()
engine.add_module(orientation_axes, obj=None)
orientation_axes.text_property.shadow_offset = array([1, -1])
orientation_axes.text_property.font_family = 'times'
orientation_axes.text_property.shadow_offset = array([1, -1])
orientation_axes.text_property.font_size = 15
orientation_axes.axes.axis_labels = False
##
if os.path.isdir(dir + '/pics/') == False:
os.mkdir(dir + '/pics/')
from enthought.mayavi.modules.iso_surface import IsoSurface from enthought.mayavi.filters.threshold import Threshold # <markdowncell> # then, set the threshold values: # # <codecell> thh = Threshold() script.add_filter(thh) thh.lower_threshold = 0.4 thh.upper_threshold = 0.6 isosurf = IsoSurface() thh.add_module(isosurf) isosurf.contour.contours = [0.5] isosurf.compute_normals = True isosurf.actor.property.opacity = 0.2 isosurf.module_manager.scalar_lut_manager.data_range = [0, 1] # <markdowncell> # and you're done ! # # This should look like this: # # ScriptingMayavi2(2f)Filters_attachments/filter_thrld2.png # # You can notice on the two previous figures that the Threshold module
# Using the !IsoSurface module is not more difficult. As an example, say # that we want the same result as the Surface module displays. # # <codecell> from enthought.mayavi.modules.iso_surface import IsoSurface # <markdowncell> # and # # <codecell> isosurf = IsoSurface() script.add_module(isosurf) isosurf.contour.contours = [0.1111, 0.2222, 0.3333, 0.4444, 0.5555, 0.6666, 0.7777, 0.8888] isosurf.compute_normals = True isosurf.actor.property.opacity = 0.2 isosurf.module_manager.scalar_lut_manager.data_range = [0, 1] # <markdowncell> # This yelds the same scene as previous, of course, but now, you can # control each isovalue separately. # # ScriptingMayavi2(2f)MainModules_attachments/module_isosurface.png # # The funny part is that you can set the minimum/maximum contour for # Surface or Contours for !IsoSurface in "real-time", moving the
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 enthought.mayavi.sources.vtk_file_reader import VTKFileReader
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.axes import Axes
from enthought.mayavi.modules.grid_plane import GridPlane
from enthought.mayavi.modules.image_plane_widget import ImagePlaneWidget
from enthought.mayavi.modules.text import Text
from enthought.mayavi.modules.contour_grid_plane import ContourGridPlane
from enthought.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 do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.vtk_file_reader import VTKFileReader
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.iso_surface import IsoSurface
from enthought.mayavi.modules.contour_grid_plane \
import ContourGridPlane
from enthought.mayavi.modules.scalar_cut_plane import ScalarCutPlane
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
# Read a VTK (old style) data file.
r = VTKFileReader()
r.initialize(get_example_data('heart.vtk'))
script.add_source(r)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# Create one ContourGridPlane normal to the 'x' axis.
cgp1 = ContourGridPlane()
script.add_module(cgp1)
# Set the position to the middle of the data.
cgp1.grid_plane.position = 15
# Another with filled contours normal to 'y' axis.
cgp2 = ContourGridPlane()
cgp2.contour.filled_contours = True
# Set the axis and position to the middle of the data.
cgp2.grid_plane.axis = 'y'
cgp2.grid_plane.position = 15
script.add_module(cgp2)
# An isosurface module.
iso = IsoSurface(compute_normals=True)
script.add_module(iso)
iso.contour.contours = [200.0]
# An interactive scalar cut plane.
cp = ScalarCutPlane()
script.add_module(cp)
ip = cp.implicit_plane
ip.normal = 0,0,1
ip.origin = 0,0,5
ip.widget.enabled = False
# Set the scene to an isometric view.
s.scene.isometric_view()
# Now test.
self.check()
############################################################
# Test if the modules respond correctly when the components
# are changed.
ctr = cgp2.contour
cgp2.contour = ctr.__class__()
cgp2.contour = ctr
cgp2.actor = cgp2.actor.__class__()
iso.contour = iso.contour.__class__()
iso.contour.contours = [200.0]
iso.actor = iso.actor.__class__()
iso.normals = iso.normals.__class__()
ip = cp.implicit_plane
cp.implicit_plane = cp.implicit_plane.__class__()
cp.implicit_plane = ip
ip.widget.enabled = False
cp.contour = cp.contour.__class__()
cp.cutter = cp.cutter.__class__()
cp.actor = cp.actor.__class__()
s.render()
# Now check.
self.check()
############################################################
# Test if saving a visualization and restoring it works.
# Save visualization.
f = StringIO()
f.name = abspath('test.mv2') # We simulate a file.
script.save_visualization(f)
f.seek(0) # So we can read this saved data.
# Remove existing scene.
engine = script.engine
engine.close_scene(s)
# Load visualization
script.load_visualization(f)
s = engine.current_scene
self.check()
############################################################
# Test if the MayaVi2 visualization can be deep-copied.
# Pop the source object.
source = s.children.pop()
# Add it back to see if that works without error.
s.children.append(source)
# Now set the enabled status of the widget, this is impossible
# to get correctly.
cp = source.children[0].children[-1]
cp.implicit_plane.widget.enabled = False
self.check()
# Now deepcopy the source and replace the existing one with
# the copy. This basically simulates cutting/copying the
# object from the UI via the right-click menu on the tree
# view, and pasting the copy back.
source1 = copy.deepcopy(source)
s.children[0] = source1
cp = source1.children[0].children[-1]
cp.implicit_plane.widget.enabled = False
self.check()
filename = file0
print filename
savename = filename
numb = numb + 1
jesse_mat_lab_coord_source1 = engine.open(filename)
#if os.path.isdir(dir+'/rec_movie_pics/') == False:
# os.mkdir(dir+'/rec_movie_pics/')
#filename=dir+'/rec_movie_pics/'
this_dir = dir
from enthought.mayavi.modules.iso_surface import IsoSurface
iso_surface = IsoSurface()
engine.add_filter(iso_surface, jesse_mat_lab_coord_source1)
iso_surface.contour.contours[0:1] = [thresh]
scene = engine.scenes[0]
scene.scene.render()
scene.scene.x_plus_view()
scene.scene.camera.zoom(mag)
#scene.scene.render()
## change the color bar range
if transparent != 0:
module_manager = engine.scenes[0].children[0].children[0]
module_manager.scalar_lut_manager.show_scalar_bar = True
module_manager.scalar_lut_manager.show_legend = True
module_manager.scalar_lut_manager.scalar_bar.position2 = array(
[0.17, 0.8])
module_manager.scalar_lut_manager.scalar_bar.position = array(
def do(self):
# Setup the source.
self.make_data()
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.iso_surface import IsoSurface
from enthought.mayavi.modules.contour_grid_plane \
import ContourGridPlane
from enthought.mayavi.modules.scalar_cut_plane import ScalarCutPlane
script = self.script
s = script.engine.current_scene
# Create an outline for the data.
o = Outline()
script.add_module(o)
# 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.position = 15
# Another with filled contours normal to 'y' axis.
cgp = ContourGridPlane()
cgp.contour.filled_contours = True
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'y'
cgp.grid_plane.position = 15
script.add_module(cgp)
# An isosurface module.
iso = IsoSurface(compute_normals=True)
script.add_module(iso)
iso.contour.contours = [200.0]
# An interactive scalar cut plane.
cp = ScalarCutPlane()
script.add_module(cp)
ip = cp.implicit_plane
ip.normal = 0, 0, 1
ip.origin = 0, 0, 5
ip.widget.enabled = False
# Set the scene to an isometric view.
s.scene.isometric_view()
self.check()
############################################################
# Test if saving a visualization and restoring it works.
# Save visualization.
f = StringIO()
f.name = abspath('test.mv2') # We simulate a file.
script.save_visualization(f)
f.seek(0) # So we can read this saved data.
# Remove existing scene.
engine = script.engine
engine.close_scene(s)
# Load visualization
script.load_visualization(f)
s = engine.current_scene
self.check()
############################################################
# Test if the MayaVi2 visualization can be deep-copied.
# Pop the source object.
source = s.children.pop()
# Add it back to see if that works without error.
s.children.append(source)
# Now set the enabled status of the widget, this is impossible
# to get correctly.
cp = source.children[0].children[-1]
cp.implicit_plane.widget.enabled = False
self.check()
# Now deepcopy the source and replace the existing one with
# the copy. This basically simulates cutting/copying the
# object from the UI via the right-click menu on the tree
# view, and pasting the copy back.
source1 = copy.deepcopy(source)
s.children[0] = source1
cp = source1.children[0].children[-1]
cp.implicit_plane.widget.enabled = False
self.check()