def __init__(self):
self.fig = mlab.figure()
self.scene = self.fig.scene
src = ArraySource(transpose_input_array=False)
src.scalar_data = np.random.randn(10,10,10)
src.origin = [-50,-50,-50]
src.spacing = [10,10,10]
mlab.pipeline.image_plane_widget(src, figure=self.fig)
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, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
e.add_source(d)
# Create an outline for the data.
o = Outline()
e.add_module(o)
# View the data.
st = Streamline()
e.add_module(st)
widget = st.seed.widget
widget.set(radius=1.0,
center=(-4.0, -4.0, -4.0),
theta_resolution=4,
phi_resolution=4)
st = Streamline(streamline_type='ribbon')
seed = st.seed
seed.widget = seed.widget_list[1]
e.add_module(st)
seed.widget.set(point1=(-5.0, -4.5, -4.0), point2=(-5.0, -4.5, 4.0))
st.ribbon_filter.width = 0.25
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[2]
e.add_module(st)
seed.widget.set(center=(-5.0, 1.5, -2.5))
st.tube_filter.radius = 0.15
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[3]
e.add_module(st)
seed.widget.position = (-5.0, 3.75, 3.75)
st.tube_filter.radius = 0.2
self.st = st
self.scene = e.current_scene
return
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, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
e.add_source(d)
# Create an outline for the data.
o = Outline()
e.add_module(o)
# View the data.
st = Streamline()
e.add_module(st)
widget = st.seed.widget
widget.set(radius=1.0, center=(-4.0, -4.0, -4.0),
theta_resolution=4, phi_resolution=4)
st = Streamline(streamline_type='ribbon')
seed = st.seed
seed.widget = seed.widget_list[1]
e.add_module(st)
seed.widget.set(point1=(-5.0, -4.5, -4.0), point2=(-5.0, -4.5, 4.0))
st.ribbon_filter.width = 0.25
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[2]
e.add_module(st)
seed.widget.set(center=(-5.0, 1.5, -2.5))
st.tube_filter.radius = 0.15
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[3]
e.add_module(st)
seed.widget.position=(-5.0, 3.75, 3.75)
st.tube_filter.radius = 0.2
self.st = st
self.scene = e.current_scene
return
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, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
e.add_source(d)
# Create an outline for the data.
o = Outline()
e.add_module(o)
# Glyphs for the scalars
g = Glyph()
e.add_module(g)
g.glyph.glyph_source.glyph_position = 'center'
g.glyph.glyph.vector_mode = 'use_normal'
g.glyph.glyph.scale_factor = 0.5
g.actor.property.line_width = 1.0
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_position = 'tail'
gs.glyph_source = gs.glyph_list[1]
e.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, 3, 0))
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_source = gs.glyph_list[2]
gs.glyph_position = 'head'
e.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, -2, 0))
self.g=g
self.v=v
self.scene = e.current_scene
return
def view_numpy():
if 0:
"""Example showing how to view a 3D numpy array in mayavi2.
"""
# 'mayavi' is always defined on the interpreter.
mayavi.new_scene()
#print mayavi.new_scene()
print mayavi.new_scene.__doc__
print type(mayavi)
print type(mayavi.get_active_window())
# 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'
# # Create the data.
# from numpy import pi, sin, cos, mgrid
# dphi, dtheta = pi/250.0, pi/250.0
# [phi,theta] = mgrid[0:pi+dphi*1.5:dphi,0:2*pi+dtheta*1.5:dtheta]
# m0 = 4; m1 = 3; m2 = 2; m3 = 3; m4 = 6; m5 = 2; m6 = 6; m7 = 4;
# r = sin(m0*phi)**m1 + cos(m2*phi)**m3 + sin(m4*theta)**m5 + cos(m6*theta)**m7
# x = r*sin(phi)*cos(theta)
# y = r*cos(phi)
# z = r*sin(phi)*sin(theta)
#
# # View it.
# from enthought.mayavi import mlab
# s = mlab.mesh(x, y, z)
# #mlab.show()
my_test_molecule()
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 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 _create_data_fired(self):
mayavi = self.get_mayavi()
from enthought.mayavi.sources.array_source import ArraySource
s = self._make_data()
src = ArraySource(transpose_input_array=False, scalar_data=s)
self.source = src
mayavi.add_source(src)
def _mk_image_data(self):
""" Creates an ImageData VTK data set and the associated ArraySource
using the factory's attributes.
"""
self._mayavi_source = ArraySource(transpose_input_array=True,
scalar_data=self.scalar_data,
origin=[0., 0., 0],
spacing=[1, 1, 1])
self._vtk_source = self._mayavi_source.image_data
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 reset(self, **traits):
"""Creates the dataset afresh or resets existing data source."""
# First set the attributes without really doing anything since
# the notification handlers are not called.
self.set(trait_change_notify=False, **traits)
vectors = self.vectors
scalars = self.scalars
x, y, z = [np.atleast_3d(a) for a in self.x, self.y, self.z]
u, v, w = self.u, self.v, self.w
if 'vectors' in traits:
u=vectors[:,0].ravel()
v=vectors[:,1].ravel()
w=vectors[:,2].ravel()
self.set(u=u,v=v,w=w,trait_change_notify=False)
else:
if u is not None and len(u) > 0:
#vectors = np.concatenate([u[..., np.newaxis],
# v[..., np.newaxis],
# w[..., np.newaxis] ],
# axis=3)
vectors = np.c_[u.ravel(), v.ravel(),
w.ravel()].ravel()
vectors.shape = (u.shape[0] , u.shape[1], w.shape[2], 3)
self.set(vectors=vectors, trait_change_notify=False)
if vectors is not None and len(vectors) > 0 and scalars is not None:
assert len(scalars) == len(vectors)
if x.shape[0] <= 1:
dx = 1
else:
dx = x[1, 0, 0] - x[0, 0, 0]
if y.shape[1] <= 1:
dy = 1
else:
dy = y[0, 1, 0] - y[0, 0, 0]
if z.shape[2] <= 1:
dz = 1
else:
dz = z[0, 0, 1] - z[0, 0, 0]
if self.m_data is None:
ds = ArraySource(transpose_input_array=True)
else:
ds = self.m_data
old_scalar = ds.scalar_data
ds.set(vector_data=vectors,
origin=[x.min(), y.min(), z.min()],
spacing=[dx, dy, dz],
scalar_data=scalars)
if scalars is old_scalar:
ds._scalar_data_changed(scalars)
self.dataset = ds.image_data
self.m_data = ds
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)
self.t = Text3D()
e.add_module(self.t)
self.scene = e.current_scene
return
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 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 reset(self, **traits):
"""Creates the dataset afresh or resets existing data source."""
# First set the attributes without really doing anything since
# the notification handlers are not called.
self.set(trait_change_notify=False, **traits)
x, y, mask = self.x, self.y, self.mask
scalars = self.scalars
# We may have used this without specifying x and y at all in
# which case we set them from the shape of scalars.
nx, ny = scalars.shape
#Build X and Y from shape of Scalars if they are none
if x is None and y is None:
x, y = np.mgrid[-nx/2.:nx/2, -ny/2.:ny/2]
if mask is not None and len(mask) > 0:
scalars[mask.astype('bool')] = np.nan
# The NaN trick only works with floats.
scalars = scalars.astype('float')
self.set(scalars=scalars, trait_change_notify=False)
z = np.array([0])
self.set(x=x, y=y, z=z, trait_change_notify=False)
# Do some magic to extract the first row/column, independently of
# the shape of x and y
x = np.atleast_2d(x.squeeze().T)[0, :].squeeze()
y = np.atleast_2d(y.squeeze())[0, :].squeeze()
if x.ndim == 0:
dx = 1
else:
dx = x[1] - x[0]
if y.ndim == 0:
dy = 1
else:
dy = y[1] - y[0]
if self.m_data is None:
ds = ArraySource(transpose_input_array=True)
else:
ds = self.m_data
old_scalar = ds.scalar_data
ds.set(origin=[x.min(), y.min(), 0],
spacing=[dx, dy, 1],
scalar_data=scalars)
if old_scalar is scalars:
ds._scalar_data_changed(scalars)
self.dataset = ds.image_data
self.m_data = ds
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 enthought.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 enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.image_plane_widget import ImagePlaneWidget
from enthought.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'
data.buf.shape = (data.nx, data.ny, data.nz) max_ib=numpy.argmax(data.buf) ix,iy,iz=data.get_ix_iy_iz(max_ib) # 'mayavi' is always defined on the interpreter. e = OffScreenEngine() #e = Engine() e.start() win = e.new_scene(magnification=1) win.scene.isometric_view() # Make the data and add it to the pipeline. src = ArraySource(transpose_input_array=True) src.scalar_data = data.buf src.spacing=(data.dx, data.dy, -data.dz) src.origin=(data.x_orig, data.y_orig, -data.z_orig) #print src.all_trait_names() # e.add_source(src) # Visualize the data. # o = Outline() # e.add_module(o) # lut=e.scenes[0].children[0].children[0].scalar_lut_manager # lut.data_range=[-1,600] # lut.show_legend = True # lut.data_name = 'Stack'
def add_cortical_surf(self):
# lifted from Gael Varoquax
# this is fairly brittle-- don't know what will result if
# the brain is not skull-stripped
# brain_image is (currently) a copy of the integer indices
# (not the "real valued" scalars)
brain_image = self.master_src.blender.main.image_arr.copy()
np.putmask(brain_image, brain_image>255, 0)
# since this is skull stripped from BET, the boundary will be
# wherever the image drops off to 0
arr = ndimage.gaussian_filter(
(brain_image > 0).astype('d'), 6
)
mask = ndimage.binary_fill_holes(arr > .5)
# iterations x voxel size ~= erosion depth??
mask = ndimage.binary_erosion(mask, iterations=5)
arr_blurred = ndimage.gaussian_filter(
mask.astype('d'), 2
)
# This AA filter will rather dangle off the pipeline..
# it will be the "source" of the ProbeFilter, but we want
# to keep it pipeline-enabled so that we can dynamically
# change colors
point_scalars = surf_to_component[self.surface_component]
surf_colors = mlab.pipeline.set_active_attribute(
self.master_src, point_scalars=point_scalars
)
# Now, make a new ArraySource with the attributes copied
# from master_src
anat_blurred = ArraySource(transpose_input_array=False)
anat_blurred.scalar_data = arr_blurred
anat_blurred.scalar_name = 'blurred'
anat_blurred.origin = self.master_src.data.origin
anat_blurred.spacing = self.master_src.data.spacing
anat_blurred = mlab.pipeline.add_dataset(anat_blurred)
## anat_blurred.update_pipeline()
contour = mlab.pipeline.contour(anat_blurred)
decimated = mlab.pipeline.decimate_pro(contour)
extracted = mlab.pipeline.user_defined(
decimated, filter=self.poly_extractor
)
sampler = tvtk.ProbeFilter()
sampler.source = surf_colors.outputs[0]
surf_points = mlab.pipeline.user_defined(extracted, filter=sampler)
self.cortical_surf = mlab.pipeline.surface(
surf_points,
opacity=.95
)
self.cortical_surf.actor.property.backface_culling = True
self.bcontour = contour
self.surf_colors = surf_colors
def do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.glyph import Glyph
from enthought.mayavi.modules.vector_cut_plane import VectorCutPlane
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
sc, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# Glyphs for the scalars
g = Glyph()
script.add_module(g)
g.glyph.glyph_source.glyph_position = 'center'
g.glyph.glyph.vector_mode = 'use_normal'
g.glyph.glyph.scale_factor = 0.5
g.actor.property.line_width = 1.0
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_position = 'tail'
gs.glyph_source = gs.glyph_list[1]
script.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, 3, 0))
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_source = gs.glyph_list[2]
gs.glyph_position = 'head'
script.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, -2, 0))
# Set the scene to a suitable view.
self.set_view(s)
self.check()
############################################################
# Test if the modules respond correctly when the components
# are changed.
g.actor = g.actor.__class__()
glyph = g.glyph
g.glyph = glyph.__class__()
g.glyph = glyph
glyph = v.glyph
v.glyph = glyph.__class__()
v.glyph = glyph
v.actor = v.actor.__class__()
v.cutter = v.cutter.__class__()
ip = v.implicit_plane
v.implicit_plane = ip.__class__()
v.implicit_plane = ip
s.render()
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
# 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 setUp(self):
"""Initial setting up of test fixture, automatically called by TestCase before any other test method is invoked"""
d = ArraySource()
self.data = d
def plot_slice_mayavi(dat_filename,output_file,hyp_x,hyp_y,hyp_z,search_grid_file_name,max_stack_value):
base_path=os.getenv('WAVELOC_PATH')
lib_path="%s/lib"%base_path
# grid geometry
hdr_file=lib_path + os.sep + search_grid_file_name
# detection
detection=50
# stations
stations_file="%s/coord_stations_piton"%lib_path
sta=StationList()
sta.read_from_file(stations_file)
# create the object to contain the stations
pd = tvtk.PolyData()
pd.points = [[s.x/1000.0, s.y/1000.0, -s.elev/1000.0] for s in sta.stations.values()]
# create the object to contain the stations
try:
pd_hyp = tvtk.PolyData()
pd_hyp.points=[[hyp_x,hyp_y,hyp_z]]
except TypeError:
pass
# read the dat file
print dat_filename
data=QDGrid()
data.read_NLL_hdr_file(hdr_file)
data.buf=numpy.fromfile(dat_filename, dtype=numpy.int16)
max_ib=numpy.argmax(data.buf)
print max_ib
max_val=data.buf[max_ib]
ix,iy,iz=data.get_ix_iy_iz(max_ib)
#data.buf=numpy.array(data.buf, dtype=numpy.float)
data.buf.shape = (data.nx, data.ny, data.nz)
# 'mayavi' is always defined on the interpreter.
e = OffScreenEngine()
#e = Engine()
e.start()
win = e.new_scene(magnification=1)
e.current_scene.scene.off_screen_rendering = True
win.scene.isometric_view()
# Make the data and add it to the pipeline.
src = ArraySource(transpose_input_array=True)
src.scalar_data = data.buf
src.spacing=(data.dx, data.dy, -data.dz)
src.origin=(data.x_orig, data.y_orig, -data.z_orig)
e.add_source(src)
# Visualize the data.
o = Outline()
e.add_module(o)
lut=e.scenes[0].children[0].children[0].scalar_lut_manager
lut.data_range=[-1,max_stack_value]
lut.show_legend = True
lut.data_name = 'Stack'
# Create one ContourGridPlane normal to the 'x' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the position to the middle of the data.
if max_val > detection:
cgp.grid_plane.position = ix
else:
cgp.grid_plane.position = data.nx/2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output=cgp.grid_plane.outputs[0]
x_data=numpy.array(output.point_data.scalars.to_array())
# Another with filled contours normal to 'y' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'y'
if max_val > detection:
cgp.grid_plane.position = iy
else:
cgp.grid_plane.position = data.ny/2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output=cgp.grid_plane.outputs[0]
y_data=numpy.array(output.point_data.scalars.to_array())
# Another with filled contours normal to 'z' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'z'
if max_val > detection:
cgp.grid_plane.position = iz
else:
cgp.grid_plane.position = data.nz/2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output=cgp.grid_plane.outputs[0]
z_data=numpy.array(output.point_data.scalars.to_array())
a=Axes()
e.add_module(a)
d=VTKDataSource()
d.data=pd
e.add_source(d)
g=Glyph()
e.add_module(g)
g.glyph.glyph_source.glyph_source=g.glyph.glyph_source.glyph_list[4]
g.glyph.glyph_source.glyph_source.radius=0.1
d=VTKDataSource()
d.data=pd_hyp
e.add_source(d)
g=Glyph()
e.add_module(g)
g.glyph.glyph_source.glyph_source=g.glyph.glyph_source.glyph_list[4]
g.glyph.glyph_source.glyph_source.radius=0.5
g.actor.property.color=(0.0,0.0,0.0)
#view(azimuth=-60,elevation=60,distance=120)
win.scene.save(output_file,size=(800,800))
e.stop()
del win
del e
return (x_data, y_data, z_data)
def do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.surface import Surface
from enthought.mayavi.modules.vectors import Vectors
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
self.check_input_validation(d)
sc, vec = self.make_2d_data()
d.origin = (-1, -1, 0)
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# View the data.
s = Surface()
script.add_module(s)
v = Vectors()
script.add_module(v)
# Add a 3D data source
d = ArraySource()
sc, vec = self.make_3d_data()
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# View a slice.
s = Surface()
script.add_module(s)
v = Vectors()
script.add_module(v)
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
self.check()
############################################################
# Test if saving a visualization and restoring it works.
bg = s.scene.background
# 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
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
s.scene.background = bg
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)
s.scene.reset_zoom()
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
s.scene.reset_zoom()
self.check()
def plot_slice_mayavi(dat_filename, output_file, hyp_x, hyp_y, hyp_z,
search_grid_file_name, max_stack_value):
base_path = os.getenv('WAVELOC_PATH')
lib_path = "%s/lib" % base_path
# grid geometry
hdr_file = lib_path + os.sep + search_grid_file_name
# detection
detection = 50
# stations
stations_file = "%s/coord_stations_piton" % lib_path
sta = StationList()
sta.read_from_file(stations_file)
# create the object to contain the stations
pd = tvtk.PolyData()
pd.points = [[s.x / 1000.0, s.y / 1000.0, -s.elev / 1000.0]
for s in sta.stations.values()]
# create the object to contain the stations
try:
pd_hyp = tvtk.PolyData()
pd_hyp.points = [[hyp_x, hyp_y, hyp_z]]
except TypeError:
pass
# read the dat file
print dat_filename
data = QDGrid()
data.read_NLL_hdr_file(hdr_file)
data.buf = numpy.fromfile(dat_filename, dtype=numpy.int16)
max_ib = numpy.argmax(data.buf)
print max_ib
max_val = data.buf[max_ib]
ix, iy, iz = data.get_ix_iy_iz(max_ib)
#data.buf=numpy.array(data.buf, dtype=numpy.float)
data.buf.shape = (data.nx, data.ny, data.nz)
# 'mayavi' is always defined on the interpreter.
e = OffScreenEngine()
#e = Engine()
e.start()
win = e.new_scene(magnification=1)
e.current_scene.scene.off_screen_rendering = True
win.scene.isometric_view()
# Make the data and add it to the pipeline.
src = ArraySource(transpose_input_array=True)
src.scalar_data = data.buf
src.spacing = (data.dx, data.dy, -data.dz)
src.origin = (data.x_orig, data.y_orig, -data.z_orig)
e.add_source(src)
# Visualize the data.
o = Outline()
e.add_module(o)
lut = e.scenes[0].children[0].children[0].scalar_lut_manager
lut.data_range = [-1, max_stack_value]
lut.show_legend = True
lut.data_name = 'Stack'
# Create one ContourGridPlane normal to the 'x' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the position to the middle of the data.
if max_val > detection:
cgp.grid_plane.position = ix
else:
cgp.grid_plane.position = data.nx / 2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output = cgp.grid_plane.outputs[0]
x_data = numpy.array(output.point_data.scalars.to_array())
# Another with filled contours normal to 'y' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'y'
if max_val > detection:
cgp.grid_plane.position = iy
else:
cgp.grid_plane.position = data.ny / 2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output = cgp.grid_plane.outputs[0]
y_data = numpy.array(output.point_data.scalars.to_array())
# Another with filled contours normal to 'z' axis.
cgp = ContourGridPlane()
e.add_module(cgp)
# Set the axis and position to the middle of the data.
cgp.grid_plane.axis = 'z'
if max_val > detection:
cgp.grid_plane.position = iz
else:
cgp.grid_plane.position = data.nz / 2
cgp.contour.filled_contours = True
cgp.actor.property.opacity = 0.6
output = cgp.grid_plane.outputs[0]
z_data = numpy.array(output.point_data.scalars.to_array())
a = Axes()
e.add_module(a)
d = VTKDataSource()
d.data = pd
e.add_source(d)
g = Glyph()
e.add_module(g)
g.glyph.glyph_source.glyph_source = g.glyph.glyph_source.glyph_list[4]
g.glyph.glyph_source.glyph_source.radius = 0.1
d = VTKDataSource()
d.data = pd_hyp
e.add_source(d)
g = Glyph()
e.add_module(g)
g.glyph.glyph_source.glyph_source = g.glyph.glyph_source.glyph_list[4]
g.glyph.glyph_source.glyph_source.radius = 0.5
g.actor.property.color = (0.0, 0.0, 0.0)
#view(azimuth=-60,elevation=60,distance=120)
win.scene.save(output_file, size=(800, 800))
e.stop()
del win
del e
return (x_data, y_data, z_data)
def make_src(self, nan=False):
data = np.empty((3, 3, 3))
if nan:
data[0] = np.nan
data.flat[:] = np.arange(data.size)
return ArraySource(scalar_data=data)
def do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.streamline import Streamline
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
sc, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# View the data.
st = Streamline()
script.add_module(st)
widget = st.seed.widget
widget.set(radius=1.0,
center=(-4.0, -4.0, -4.0),
theta_resolution=4,
phi_resolution=4)
st = Streamline(streamline_type='ribbon')
seed = st.seed
seed.widget = seed.widget_list[1]
script.add_module(st)
seed.widget.set(point1=(-5.0, -4.5, -4.0), point2=(-5.0, -4.5, 4.0))
st.ribbon_filter.width = 0.25
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[2]
script.add_module(st)
seed.widget.set(center=(-5.0, 1.5, -2.5))
st.tube_filter.radius = 0.15
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[3]
script.add_module(st)
seed.widget.position = (-5.0, 3.75, 3.75)
st.tube_filter.radius = 0.2
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
s.render()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
############################################################
# Test if the modules respond correctly when the components
# are changed.
tf = st.tube_filter
st.tube_filter = tf.__class__()
st.tube_filter = tf
st.ribbon_filter = st.ribbon_filter.__class__()
seed = st.seed
st.seed = seed.__class__()
st.seed = seed
st.actor = st.actor.__class__()
tracer = st.stream_tracer
st.stream_tracer = tracer.__class__()
st.stream_tracer = tracer
s.render()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
s.render()
############################################################
# Test if saving a visualization and restoring it works.
bg = s.scene.background
# 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
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
s.render()
s.scene.background = bg
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
############################################################
# 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)
s.scene.reset_zoom()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
# 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
s.scene.reset_zoom()
self.compare_image(s, 'images/test_streamline.png')
def do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.streamline import Streamline
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
sc, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# View the data.
st = Streamline()
script.add_module(st)
widget = st.seed.widget
widget.set(radius=1.0, center=(-4.0, -4.0, -4.0),
theta_resolution=4, phi_resolution=4)
st = Streamline(streamline_type='ribbon')
seed = st.seed
seed.widget = seed.widget_list[1]
script.add_module(st)
seed.widget.set(point1=(-5.0, -4.5, -4.0), point2=(-5.0, -4.5, 4.0))
st.ribbon_filter.width = 0.25
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[2]
script.add_module(st)
seed.widget.set(center=(-5.0, 1.5, -2.5))
st.tube_filter.radius = 0.15
st = Streamline(streamline_type='tube')
seed = st.seed
seed.widget = seed.widget_list[3]
script.add_module(st)
seed.widget.position=(-5.0, 3.75, 3.75)
st.tube_filter.radius = 0.2
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
s.render()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
############################################################
# Test if the modules respond correctly when the components
# are changed.
tf = st.tube_filter
st.tube_filter = tf.__class__()
st.tube_filter = tf
st.ribbon_filter = st.ribbon_filter.__class__()
seed = st.seed
st.seed = seed.__class__()
st.seed = seed
st.actor = st.actor.__class__()
tracer = st.stream_tracer
st.stream_tracer = tracer.__class__()
st.stream_tracer = tracer
s.render()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
s.render()
############################################################
# Test if saving a visualization and restoring it works.
bg = s.scene.background
# 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
# Set the scene to a suitable view.
s.scene.z_plus_view()
c = s.scene.camera
c.azimuth(-30)
c.elevation(30)
s.render()
s.scene.background = bg
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
############################################################
# 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)
s.scene.reset_zoom()
# Now compare the image.
self.compare_image(s, 'images/test_streamline.png')
# 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
s.scene.reset_zoom()
self.compare_image(s, 'images/test_streamline.png')
ny = 100 nz = 60 # Import Array # electrostatics information data = numpy.loadtxt(field) row1 = data[:,3] # Adjust the shape of the data plotdata = row1.reshape((nx,ny)) src1 = ArraySource(transpose_input_array=True) src1.name = u'Daten' src1.scalar_data = plotdata mayavi.add_source(src1) # ------------------------------------------- #array_source = engine.scenes[0].children[0] #engine.add_filter(<enthought.mayavi.modules.iso_surface.IsoSurface object at 0xa1a8059c>, array_source) # ------------------------------------------- #from enthought.mayavi.tools.show import show #show() iso_surface = IsoSurface() array_source = engine.scenes[0].children[0] engine.add_filter(iso_surface, array_source)
Lx = 1
Ly = 1
Lz = 1
x, y, z = ogrid[0:Lx:(Nx+1)*1j,0:Ly:(Ny+1)*1j,0:Lz:(Nz+1)*1j]
# Strictly speaking, H is the magnetic field of the "transverse electric" eigenmode m=n=p=1
# of a rectangular resonator cavity, with dimensions Lx, Ly, Lz
Hx = sin(x*pi/Lx)*cos(y*pi/Ly)*cos(z*pi/Lz)
Hy = cos(x*pi/Lx)*sin(y*pi/Ly)*cos(z*pi/Lz)
Hz = cos(x*pi/Lx)*cos(y*pi/Ly)*sin(z*pi/Lz)
Hv_scal = sqrt(Hx**2 + Hy**2 + Hz**2)
# We want to load a scalars data (Hv_scal) as magnitude of a given 3D vector (Hv = {Hx, Hy, Hz})
# Hv_scal is a 3D scalars data, Hv is a 4D scalars data
src = ArraySource()
src.scalar_data = Hv_scal # load scalars data
# To load vectors data
# src.vector_data = Hv
# <markdowncell>
# Loading data from file using FileReader methods
# -----------------------------------------------
#
# To load a VTK data file, say heart.vtk file in mayavi/examples/data/
# directory, simply type:
#
# <codecell>
data.buf = numpy.fromfile(data_file, dtype=numpy.int16)
data.buf = numpy.array(data.buf, dtype=numpy.float)
print data.buf.min(), data.buf.max()
data.buf.shape = (data.nx, data.ny, data.nz)
max_ib = numpy.argmax(data.buf)
ix, iy, iz = data.get_ix_iy_iz(max_ib)
# 'mayavi' is always defined on the interpreter.
e = OffScreenEngine()
#e = Engine()
e.start()
win = e.new_scene(magnification=1)
win.scene.isometric_view()
# Make the data and add it to the pipeline.
src = ArraySource(transpose_input_array=True)
src.scalar_data = data.buf
src.spacing = (data.dx, data.dy, -data.dz)
src.origin = (data.x_orig, data.y_orig, -data.z_orig)
#print src.all_trait_names()
# e.add_source(src)
# Visualize the data.
# o = Outline()
# e.add_module(o)
# lut=e.scenes[0].children[0].children[0].scalar_lut_manager
# lut.data_range=[-1,600]
# lut.show_legend = True
# lut.data_name = 'Stack'
def do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.glyph import Glyph
from enthought.mayavi.modules.vector_cut_plane import VectorCutPlane
############################################################
# Create a new scene and set up the visualization.
s = self.new_scene()
d = ArraySource()
sc, vec = self.make_data()
d.origin = (-5, -5, -5)
d.scalar_data = sc
d.vector_data = vec
script.add_source(d)
# Create an outline for the data.
o = Outline()
script.add_module(o)
# Glyphs for the scalars
g = Glyph()
script.add_module(g)
g.glyph.glyph_source.glyph_position = 'center'
g.glyph.glyph.vector_mode = 'use_normal'
g.glyph.glyph.scale_factor = 0.5
g.actor.property.line_width = 1.0
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_position = 'tail'
gs.glyph_source = gs.glyph_list[1]
script.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, 3, 0))
v = VectorCutPlane()
glyph = v.glyph
gs = glyph.glyph_source
gs.glyph_source = gs.glyph_list[2]
gs.glyph_position = 'head'
script.add_module(v)
v.implicit_plane.set(normal=(0, 1, 0), origin=(0, -2, 0))
# Set the scene to a suitable view.
self.set_view(s)
self.check()
############################################################
# Test if the modules respond correctly when the components
# are changed.
g.actor = g.actor.__class__()
glyph = g.glyph
g.glyph = glyph.__class__()
g.glyph = glyph
glyph = v.glyph
v.glyph = glyph.__class__()
v.glyph = glyph
v.actor = v.actor.__class__()
v.cutter = v.cutter.__class__()
ip = v.implicit_plane
v.implicit_plane = ip.__class__()
v.implicit_plane = ip
s.render()
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
# 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 do(self):
############################################################
# Imports.
script = self.script
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.modules.outline import Outline
from enthought.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 = 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
# 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()