def view_data(filename, fieldName='x-velocity'):
"""Visualize a 3D numpy array in mayavi2.
"""
# 'mayavi' is always defined on the interpreter.
mayavi.new_scene()
# Make the data and add it to the pipeline.
data = read_data(filename, fieldName)
src = ArraySource(transpose_input_array=False)
src.scalar_data = data
mayavi.add_source(src)
# Visualize the data.
o = Outline()
mayavi.add_module(o)
ipw = ImagePlaneWidget()
mayavi.add_module(ipw)
ipw.module_manager.scalar_lut_manager.show_scalar_bar = True
ipw.module_manager.scalar_lut_manager.data_name = fieldName
ipw_y = ImagePlaneWidget()
mayavi.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
ipw_z = ImagePlaneWidget()
mayavi.add_module(ipw_z)
ipw_z.ipw.plane_orientation = 'z_axes'
def _view_data_fired(self):
mayavi = self.get_mayavi()
from mayavi.modules.outline import Outline
from mayavi.modules.image_plane_widget import ImagePlaneWidget
# Visualize the data.
o = Outline()
mayavi.add_module(o)
ipw = ImagePlaneWidget()
mayavi.add_module(ipw)
ipw.module_manager.scalar_lut_manager.show_scalar_bar = True
ipw_y = ImagePlaneWidget()
mayavi.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
def setUp(self):
# Create dataset with multiple scalars.
arr1 = zeros(27, 'f')
for n in range(27):
arr1[n] = (1+float(n))/10.0
arr2 = (arr1 + 1).astype('d')
arr3 = arr1 + 2.0*(0.5 - random.random(27))
arr3 = arr3.astype('f')
p = tvtk.ImageData(dimensions=[3,3,3],spacing=[1,1,1],
scalar_type='int')
p.point_data.scalars = arr1
p.point_data.scalars.name = 'first'
j2 = p.point_data.add_array(arr2)
p.point_data.get_array(j2).name='second'
j3 = p.point_data.add_array(arr3)
p.point_data.get_array(j3).name='third'
p.update()
self.img = p
self.first = arr1
self.second = arr2
self.third = arr3
# Setup the mayavi pipeline.
e = NullEngine()
e.start()
e.new_scene()
self.e = e
src = VTKDataSource(data=p)
e.add_source(src)
self.src = src
ipw = ImagePlaneWidget()
e.add_module(ipw)
self.ipw = ipw
def view():
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.outline import Outline
from mayavi.modules.image_plane_widget import ImagePlaneWidget
mayavi.new_scene()
src = VTKDataSource(data=spoints)
mayavi.add_source(src)
mayavi.add_module(Outline())
mayavi.add_module(ImagePlaneWidget())
def view_numpy():
"""Example showing how to view a 3D numpy array in mayavi2.
"""
# 'mayavi' is always defined on the interpreter.
mayavi.new_scene()
# Make the data and add it to the pipeline.
data = make_data()
src = ArraySource(transpose_input_array=False)
src.scalar_data = data
mayavi.add_source(src)
# Visualize the data.
o = Outline()
mayavi.add_module(o)
ipw = ImagePlaneWidget()
mayavi.add_module(ipw)
ipw.module_manager.scalar_lut_manager.show_scalar_bar = True
ipw_y = ImagePlaneWidget()
mayavi.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
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'
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.
d = ArraySource()
sc = self.make_data()
d.scalar_data = sc
e.add_source(d)
# Create an outline for the data.
o = Outline()
e.add_module(o)
# ImagePlaneWidgets for the scalars
ipw = ImagePlaneWidget()
e.add_module(ipw)
ipw_y = ImagePlaneWidget()
e.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
ipw_z = ImagePlaneWidget()
e.add_module(ipw_z)
ipw_z.ipw.plane_orientation = 'z_axes'
self.scene = e.current_scene
return
def view_data(data):
"""Example showing how to view a 3D numpy array in mayavi2.
"""
def set_labelE(ind):
return '{0:.0f} eV'.format(source.energies[ind])
def move_view(obj, evt):
labelE.text = set_labelE(ipwX.ipw.slice_index)
pos = labelE.position
labelE.position = ipwX.ipw.slice_index * src.spacing[0] + 1,\
pos[1], pos[2]
labelE.vector_text.update()
def set_lut(ipw):
lutM = ipw.module_manager.scalar_lut_manager
# lutM.show_scalar_bar = True
# lutM.number_of_labels = 9
lutM.lut.scale = 'log10'
lutM.lut.range = [dataMax * vmin, dataMax]
lutM.lut_mode = 'hot'
@animate()
def anim(data, ipwX):
scene.scene.off_screen_rendering = True
scene.scene.anti_aliasing_frames = 0
for i in range(0, data.shape[0], 1):
ipwX.ipw.slice_index = i
move_view(None, None)
if saveName is not None:
scene.scene.save('{0}{1:04d}.png'.format(saveName, i))
yield
# 'mayavi' is always defined on the interpreter.
scene = mayavi.new_scene() # analysis:ignore
scene.scene.background = (0, 0, 0)
print(source.prefix_save_name())
src = ArraySource(transpose_input_array=True)
sh = data.shape
# print(sh)
if 'xrt' in source.prefix_save_name() or\
'srw' in source.prefix_save_name():
src.scalar_data = data[:, :sh[1] // 2 + 1, :sh[2] // 2 + 1].copy()
else:
src.scalar_data = data[:, ::-1, ::-1].copy()
# src.spacing = np.array([-0.05, 1, 1])
# src.spacing = np.array([-0.25, 1, 1])
src.spacing = np.array([-0.25, 0.25, 0.25])
mayavi.add_source(src) # analysis:ignore
# Visualize the data.
# o = Outline()
# mayavi.add_module(o)
ipwY = ImagePlaneWidget()
mayavi.add_module(ipwY) # analysis:ignore
ipwY.ipw.plane_orientation = 'y_axes' # our x-axis
ipwY.ipw.slice_index = int(data.shape[1] - 1)
# if 'xrt' in source.prefix_save_name():
# ipwY.ipw.slice_index /= int(2)
ipwY.ipw.left_button_action = 0
set_lut(ipwY)
if isZplane:
ipwZ = ImagePlaneWidget()
mayavi.add_module(ipwZ) # analysis:ignore
ipwZ.ipw.plane_orientation = 'z_axes' # our z-axis
ipwZ.ipw.slice_index = int(data.shape[2] - 1)
# if 'xrt' in source.prefix_save_name():
# ipwZ.ipw.slice_index /= int(2)
ipwZ.ipw.left_button_action = 0
if 'xrt' in source.prefix_save_name() or\
'srw' in source.prefix_save_name():
pass
else:
data = np.concatenate((data[:, :0:-1, :], data), axis=1)
data = np.concatenate((data[:, :, :0:-1], data), axis=2)
sh = data.shape
print(sh)
src = ArraySource(transpose_input_array=True)
src.scalar_data = data.copy()
# src.spacing = np.array([-0.05, 1, 1])
# src.spacing = np.array([-0.25, 1, 1])
src.spacing = np.array([-0.25, 0.25, 0.25])
mayavi.add_source(src) # analysis:ignore
ipwX = ImagePlaneWidget()
mayavi.add_module(ipwX) # analysis:ignore
ipwX.ipw.plane_orientation = 'x_axes' # energy
set_lut(ipwX)
ipwX.ipw.add_observer('WindowLevelEvent', move_view)
ipwX.ipw.add_observer('StartInteractionEvent', move_view)
ipwX.ipw.add_observer('EndInteractionEvent', move_view)
labelE = Text3D()
mayavi.add_module(labelE) # analysis:ignore
labelE.position = (1, data.shape[1] * 0.73 * src.spacing[1],
data.shape[2] * 0.85 * src.spacing[2])
labelE.orientation = 90, 0, 90
labelE.text = 'Energy'
labelE.scale = 3, 3, 1
labelE.actor.property.color = 0, 1, 1
labelE.orient_to_camera = False
labelE.text = set_labelE(0)
view(45, 70, 200)
wantToAnimate = True
if wantToAnimate:
anim(data, ipwX)
else:
ipwX.ipw.slice_index = data.shape[0] - 1
move_view(None, None)
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 do(self):
############################################################
# Imports.
script = self.script
from mayavi.sources.array_source import ArraySource
from mayavi.modules.outline import Outline
from mayavi.modules.image_plane_widget import ImagePlaneWidget
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
sc = self.make_data()
d.scalar_data = sc
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# ImagePlaneWidgets for the scalars
ipw = ImagePlaneWidget()
script.add_module(ipw)
ipw_y = ImagePlaneWidget()
script.add_module(ipw_y)
ipw_y.ipw.plane_orientation = 'y_axes'
ipw_z = ImagePlaneWidget()
script.add_module(ipw_z)
ipw_z.ipw.plane_orientation = 'z_axes'
# Set the scene to a suitable view.
self.set_view(s)
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
# Set the scene to a suitable view.
self.set_view(s)
self.check()
############################################################
# Test if the MayaVi2 visualization can be deepcopied.
# Pop the source object.
sources = s.children
s.children = []
# Add it back to see if that works without error.
s.children.extend(sources)
self.set_view(s)
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.
sources1 = copy.deepcopy(sources)
s.children[:] = sources
self.set_view(s)
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
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