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_data(fname):
"""Given a VTK file name `fname`, this creates a mayavi2 reader
for it and adds it to the pipeline. It returns the reader
created.
"""
# 'mayavi' is always defined on the interpreter.
mayavi.new_scene()
d = VTKFileReader()
d.initialize(fname)
mayavi.add_source(d)
return d
def setup_data(fname):
"""Given a VTK file name `fname`, this creates a mayavi2 reader
for it and adds it to the pipeline. It returns the reader
created.
"""
# 'mayavi' is always defined on the interpreter.
mayavi.new_scene()
d = VTKFileReader()
d.initialize(fname)
mayavi.add_source(d)
return d
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_source(self, fname):
"""Given a VTK file name `fname`, this creates a mayavi2 reader
for it and adds it to the pipeline. It returns the reader
created.
"""
if fname is None:
return None
source = VTKFileReader()
source.initialize(fname)
mlab.pipeline.add_dataset(source)
return source
def setup_source(self, fname):
"""Given a VTK file name `fname`, this creates a mayavi2 reader
for it and adds it to the pipeline. It returns the reader
created.
"""
if fname is None:
return None
source = VTKFileReader()
source.initialize(fname)
mlab.pipeline.add_dataset(source)
return source
def do(self):
script = self.script
############################################################
# Create a new scene and set up the visualization.
scene = self.new_scene()
# Read a VTK (old style) data file.
source = VTKFileReader()
source.initialize(get_example_data('heart.vtk'))
script.add_source(source)
script.add_module(Surface())
# In order to test the restoration of visualization properly
# we should modify the camera
view(130., 44., 65., [14., 14., 14.])
############################################################
# Test if saving a visualization and restoring it works.
# Save visualization.
f = BytesIO()
f.name = abspath('test.mv2') # We simulate a file.
script.save_visualization(f)
f.seek(0) # So we can read this saved data.
# This is the old camera state
old_camera_state = get_state(scene.scene.camera)
# Remove existing scene.
engine = script.engine
engine.close_scene(scene)
# Load visualization
script.load_visualization(f)
scene = engine.current_scene
# Now do the check.
new_camera_state = get_state(scene.scene.camera)
for attr, new_value in new_camera_state.items():
if attr.startswith("_"):
continue
new_value = array(new_value)
old_value = array(old_camera_state[attr])
assert (new_value == old_value).all()
def postprocessing(self):
import mayavi, vtk, os
from mayavi import mlab
mlab.init_notebook()
from mayavi.sources.vtk_xml_file_reader import VTKXMLFileReader
from mayavi.sources.vrml_importer import VRMLImporter
from mayavi.modules.outline import Outline
from mayavi.modules.streamline import Streamline
from mayavi.modules.iso_surface import IsoSurface
from mayavi.sources.vtk_file_reader import VTKFileReader
print('Mayavi {}, {}, DISPLAY {}'.format(mayavi.__version__, vtk.vtkVersion.GetVTKSourceVersion(), os.environ['DISPLAY']))
# fetch the results
fname='Composition_00010000.vtk'
oc_proj_base = self.wJobPath.value.strip(' /')
oc=DavProxy()
oc.set_token()
oc.get(oc_proj_base + '/OP/VTK/'+fname, './' + fname)
# run mlab pipeline
mlab.clf() # clear figure
r = VTKFileReader()
r.initialize(fname)
r.point_scalars_name = 'TotalComposition_Li'
scp=mlab.pipeline.scalar_cut_plane(r, view_controls=False,plane_orientation='y_axes')
scpx=mlab.pipeline.scalar_cut_plane(r, view_controls=False,plane_orientation='x_axes')
mlab.pipeline.outline(r)
col_cp=mlab.scalarbar(scp, title='C(Li)', orientation='vertical')
return mlab.gcf() # plot
def contour():
mayavi.new_scene()
r = VTKFileReader()
r.initialize('heart.vtk')
mayavi.add_source(r)
o = Outline()
mayavi.add_module(o)
gp = GridPlane()
mayavi.add_module(gp)
gp = GridPlane()
mayavi.add_module(gp)
gp.grid_plane.axis = 'y'
gp = GridPlane()
mayavi.add_module(gp)
gp.grid_plane.axis = 'z'
cgp = ContourGridPlane()
mayavi.add_module(cgp)
cgp.grid_plane.position = 15
cgp = ContourGridPlane()
mayavi.add_module(cgp)
cgp.grid_plane.axis = 'y'
cgp.grid_plane.position = 15
cgp.contour.filled_contours = True
iso = IsoSurface(compute_normals=True)
mayavi.add_module(iso)
iso.contour.contours = [220.0]
cp = ScalarCutPlane()
mayavi.add_module(cp)
cp.implicit_plane.normal = 0, 0, 1
def setup_data(fname):
mayavi.new_scene()
d = VTKFileReader()
d.initialize(fname)
mayavi.add_source(d)
return d
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
def do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.grid_plane import GridPlane
############################################################
# 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 three simple grid plane modules.
# First normal to 'x' axis.
gp1 = GridPlane()
script.add_module(gp1)
# Second normal to 'y' axis.
gp2 = GridPlane()
# We'll test how robust things are by setting attributes
# *before* we add it to the scene.
gp2.grid_plane.axis = 'y'
gp2.grid_plane.position = 16
script.add_module(gp2)
# Third normal to 'z' axis.
gp3 = GridPlane()
script.add_module(gp3)
gp3.grid_plane.axis = 'z'
gp3.grid_plane.position = 6
for gp in (gp1, gp2, gp3):
gp.actor.property.set(ambient=1.0)
# 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 = BytesIO()
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 deepcopied.
# Pop the source object.
source = s.children.pop()
# Add it back to see if that works without error.
s.children.append(source)
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
self.check()
def do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.contour_grid_plane \
import ContourGridPlane
from 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()
class TestVTKFileReader(unittest.TestCase):
def setUp(self):
# Read a VTK data file.
self.src = VTKFileReader()
def tearDown(self):
"""For necessary clean up, automatically called by TestCase
after the test methods have been invoked"""
self.src = None
return
def check(self, n_points, n_cells):
"""Do the actual testing."""
output = self.src.outputs[0]
self.assertEqual(output.number_of_points, n_points)
self.assertEqual(output.number_of_cells, n_cells)
def test_structured_points_file(self):
self.src.initialize(get_example_data("texThres2.vtk"))
self.check(128, 127)
def test_rectiliner_grid_file(self):
self.src.initialize(get_example_data("RectGrid2.vtk"))
self.check(17061, 14720)
def test_polydata_file(self):
self.src.initialize(get_example_data("polyEx.vtk"))
self.check(8, 6)
def test_structured_grid_file(self):
self.src.initialize(get_example_data("SampleStructGrid.vtk"))
self.check(24000, 21489)
def test_unstructured_grid_file(self):
self.src.initialize(get_example_data("uGridEx.vtk"))
self.check(27, 12)
def test_field_file(self):
self.src.initialize(get_example_data("fieldfile.vtk"))
self.check(18, 3)
def read(self, fname, split=True, *args):
""" read a vtk file """
from mayavi.sources.vtk_file_reader import VTKFileReader
my_reader = VTKFileReader()
return generic_vtk_read(my_reader, fname, split=split)
def do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.grid_plane import GridPlane
############################################################
# 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 three simple grid plane modules.
# First normal to 'x' axis.
gp1 = GridPlane()
script.add_module(gp1)
# Second normal to 'y' axis.
gp2 = GridPlane()
# We'll test how robust things are by setting attributes
# *before* we add it to the scene.
gp2.grid_plane.axis = 'y'
gp2.grid_plane.position = 16
script.add_module(gp2)
# Third normal to 'z' axis.
gp3 = GridPlane()
script.add_module(gp3)
gp3.grid_plane.axis = 'z'
gp3.grid_plane.position = 6
for gp in (gp1, gp2, gp3):
gp.actor.property.set(ambient=1.0)
# 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 deepcopied.
# Pop the source object.
source = s.children.pop()
# Add it back to see if that works without error.
s.children.append(source)
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
self.check()
def setUp(self):
# Read a VTK data file.
self.src = VTKFileReader()
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
def do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.contour_grid_plane \
import ContourGridPlane
from 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()
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()
import os
from mayavi.core.api import Engine
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.surface import Surface
vtkFile = 'flow.vtk'
# Create the MayaVi engine and start it.
engine = Engine()
engine.start()
scene = engine.new_scene()
# Read in VTK file and add as source
reader = VTKFileReader()
reader.initialize(vtkFile)
engine.add_source(reader)
# Add Surface Module
surface = Surface()
engine.add_module(surface)
# Move the camera
scene.scene.camera.elevation(-70)
# Save scene to image file
scene.scene.save_png('image.png')
# Create a GUI instance and start the event loop.
# This stops the window from closing
from enthought.pyface.api import GUI
gui = GUI()
import numpy as np
from mayavi.api import Engine
from mayavi.sources.vtk_file_reader import VTKFileReader
# In[2]:
e = Engine()
e.start()
# In[3]:
s = e.new_scene()
# In[4]:
r = VTKFileReader()
# In[5]:
r.initialize('heart.vtk')
e.add_source(r)
# In[6]:
from mayavi.modules import api
# In[7]:
o = api.Outline()
# In[8]:
def do_profile(self):
############################################################
# Imports.
############################################################
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.contour_grid_plane \
import ContourGridPlane
from 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()
s.render()
# Remove existing scene.
engine = script.engine
engine.close_scene(s)
def do_profile(self):
############################################################
# Imports.
############################################################
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.outline import Outline
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.contour_grid_plane \
import ContourGridPlane
from 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()
s.render()
# Remove existing scene.
engine = script.engine
engine.close_scene(s)
import os
from mayavi.core.api import Engine
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.modules.surface import Surface
vtkFile_l = 'lh.vtk'
vtkFile_r = 'rh.vtk'
# Create the MayaVi engine and start it.
engine = Engine()
engine.start()
scene = engine.new_scene()
# Read in VTK file and add as source
reader1 = VTKFileReader()
reader1.initialize(vtkFile_l)
engine.add_source(reader1)
# Add Surface Module
surface = Surface()
engine.add_module(surface)
# Move the camera
scene.scene.camera.elevation(90)
scene.scene.camera.azimuth(-180)
# Save scene to image file
scene.scene.save_png('image.png')
# Create a GUI instance and start the event loop.
class TestVTKFileReader(unittest.TestCase):
def setUp(self):
# Read a VTK data file.
self.src = VTKFileReader()
def tearDown(self):
"""For necessary clean up, automatically called by TestCase
after the test methods have been invoked"""
self.src = None
return
def check(self, n_points, n_cells):
"""Do the actual testing."""
output = self.src.outputs[0]
self.assertEqual(output.number_of_points, n_points)
self.assertEqual(output.number_of_cells, n_cells)
def test_structured_points_file(self):
self.src.initialize(get_example_data('texThres2.vtk'))
self.check(128, 127)
def test_rectiliner_grid_file(self):
self.src.initialize(get_example_data('RectGrid2.vtk'))
self.check(17061, 14720)
def test_polydata_file(self):
self.src.initialize(get_example_data('polyEx.vtk'))
self.check(8, 6)
def test_structured_grid_file(self):
self.src.initialize(get_example_data('SampleStructGrid.vtk'))
self.check(24000, 21489)
@unittest.skipIf(vtk_major_version == 5 and vtk_minor_version < 10,
"This test is probably broken in VTK < 5.10")
def test_unstructured_grid_file(self):
self.src.initialize(get_example_data('UGridEx.vtk'))
self.check(27, 12)
def test_field_file(self):
self.src.initialize(get_example_data('fieldfile.vtk'))
self.check(18, 3)
def do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.vtk_file_reader import VTKFileReader
from mayavi.filters.contour import Contour
from mayavi.filters.optional import Optional
from mayavi.filters.collection import Collection
from mayavi.filters.api import PolyDataNormals
from mayavi.modules.api import Surface
############################################################
# 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)
c = Contour()
# `name` is used for the notebook tabs.
n = PolyDataNormals(name='Normals')
o = Optional(filter=n, label_text='Compute normals')
coll = Collection(filters=[c, o], name='IsoSurface')
script.add_filter(coll)
s = Surface()
script.add_module(s)
########################################
# do the testing.
def check(coll):
"""Check if test status is OK given the collection."""
c, o = coll.filters
c = c.filter
n = o.filter
assert coll.outputs[0].point_data.scalars.range == (127.5, 127.5)
# Adding a contour should create the appropriate output in
# the collection.
c.contours.append(200)
assert coll.outputs[0].point_data.scalars.range == (127.5, 200.0)
# the collection's output should be that of the normals.
assert coll.outputs[0] is n.outputs[0]
# disable the optional filter and check.
o.enabled = False
assert 'disabled' in o.name
assert coll.outputs[0] is c.outputs[0]
# Set back everything to original state.
c.contours.pop()
o.enabled = True
assert coll.outputs[0].point_data.scalars.range == (127.5, 127.5)
assert coll.outputs[0] is n.outputs[0]
assert 'disabled' not in o.name
check(coll)
############################################################
# 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
# Now do the check.
coll = s.children[0].children[0]
check(coll)
############################################################
# 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 do the check.
coll = s.children[0].children[0]
check(coll)
# 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
# Now do the check.
coll = s.children[0].children[0]
check(coll)
import os from mayavi.core.api import Engine from mayavi.sources.vtk_file_reader import VTKFileReader from mayavi.modules.surface import Surface vtkFile_l = '/Users/richad/bin/lh.vtk' vtkFile_r = '/Users/richad/bin/rh.vtk' # Create the MayaVi engine and start it. engine = Engine() engine.start() #scene = engine.new_scene() # Read in VTK file and add as source surface1 = Surface() reader1 = VTKFileReader() reader1.initialize(vtkFile_l) engine.add_source(reader1) engine.add_filter(surface1, reader1) surface2 = Surface() reader2 = VTKFileReader() reader2.initialize(vtkFile_r) engine.add_source(reader2) engine.add_filter(surface2, reader2) #import networkx as nx import numpy as np #import pickle as pk #import matplotlib.pyplot as plt #import bct from mayavi import mlab
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()
