def surf_regular():
"""Now visualize the data as done in mlab.
"""
w = WarpScalar()
mayavi.add_filter(w)
o = Outline()
s = Surface()
mayavi.add_module(o)
mayavi.add_module(s)
def glyph():
"""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 VTK scene.
mayavi.new_scene()
# Read a VTK (old style) data file.
r = VTKXMLFileReader()
r.initialize(join(dirname(enthought.mayavi.__file__),
'examples', 'data', 'fire_ug.vtu'))
mayavi.add_source(r)
# Create an outline and a vector cut plane.
mayavi.add_module(Outline())
v = VectorCutPlane()
mayavi.add_module(v)
v.glyph.color_mode = 'color_by_scalar'
# Now mask the points and show glyphs (we could also use
# Vectors but glyphs are a bit more generic)
m = MaskPoints()
m.filter.set(on_ratio=10, random_mode=True)
mayavi.add_filter(m)
g = Glyph()
mayavi.add_module(g)
# Note that this adds the module to the filtered output.
g.glyph.scale_mode = 'scale_by_vector'
# Use arrows to view the scalars.
g.glyph.glyph_source = g.glyph.glyph_list[1]
def streamline():
"""Sets up the mayavi pipeline for the visualization.
"""
# Create an outline for the data.
o = Outline()
mayavi.add_module(o)
s = Streamline(streamline_type='tube')
mayavi.add_module(s)
s.stream_tracer.integration_direction = 'both'
s.seed.widget.center = 3.5, 0.625, 1.25
s.module_manager.scalar_lut_manager.show_scalar_bar = True
i = IsoSurface()
mayavi.add_module(i)
i.contour.contours[0] = 550
i.actor.property.opacity = 0.5
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 generate_mayavi_line_plot(self, srcid_sciclasses_list,
use_linfit_segments=False,
enable_mayavi2_interactive_gui=False):
""" Generate a Mayavi mlab 3D plot which summarizes iterative
classification of a TUTOR source over the number of epochs
used/added.
"""
# TODO: I would like to plot each sci class a different color
# - I should have each science class re-use a single number/color
# - I should label which science class by color, as Y axis labels
# TODO: I will need to insert a 0 point onto arrays (for s[0]?)
if enable_mayavi2_interactive_gui:
from enthought.mayavi.scripts import mayavi2
mayavi2.standalone(globals())
from enthought.mayavi import mlab
# scalar cut plane plotting module stuff:
import enthought.mayavi
from enthought.mayavi.modules.scalar_cut_plane import ScalarCutPlane
epoch_ids = [0] # x
class_groups = [0] # y
probs = [0] # z
styles = [0] # numbers used for coloring & glyph sizes
used_final_classes = []
i_srcid = 0
for final_class in self.pars['interested_sci_classes']:
if not finalclass_ordered_dict.has_key(final_class):
continue # skip this science class since nothing to plot
else:
used_final_classes.append(final_class)
srcid_sciclasses_list = finalclass_ordered_dict[final_class]
for src_id,sci_classes in srcid_sciclasses_list:
print 'src_id:', src_id, '\t', final_class
sci_classes.generate_linearfit_endpoints_segments()
i = 0
for class_name,class_dict in sci_classes.class_dict.iteritems():
class_style = self.sciclass_style_dict[class_name]
if use_linfit_segments:
for segment_dict in class_dict['linfit_segments']:
epoch_ids.extend([segment_dict['epoch_ids'][0]])
class_groups.extend([i_srcid])
probs.extend([0])
styles.extend([0])
epoch_ids.extend(segment_dict['epoch_ids'])
class_groups.extend([i_srcid]*len(segment_dict['epoch_ids']))
probs.extend(segment_dict['probs'])
styles.extend([class_style]*len(segment_dict['epoch_ids']))
epoch_ids.extend([segment_dict['epoch_ids'][-1]])
class_groups.extend([i_srcid])
probs.extend([0])
styles.extend([0])
else:
epoch_ids.extend([class_dict['epoch_ids'][0]])
class_groups.extend([i_srcid])
probs.extend([0])
styles.extend([0])
epoch_ids.extend(class_dict['epoch_ids'])
class_groups.extend([i_srcid]*len(class_dict['epoch_ids']))
probs.extend(class_dict['probs'])
styles.extend([class_style]*len(class_dict['epoch_ids']))
epoch_ids.extend([class_dict['epoch_ids'][-1]])
class_groups.extend([i_srcid])
probs.extend([0])
styles.extend([0])
i += 1
i_srcid += 3 # Y spacing between srcids within a science-class
i_srcid += 20 # Y spacing between science-class groups
mlab.plot3d(numpy.array(epoch_ids),
numpy.array(class_groups),
numpy.array(probs)*100.0,
numpy.array(styles),
colormap="Paired",
tube_radius=1)
# extent=[0,600,
# 0,i_srcid,
# 15, 110])
mlab.axes(xlabel='N of epochs',
ylabel='science class',
zlabel='% Prob.')#,
# DEBUG/UPGRADE: These seem to trigger some bug about Actor methods:
# extent=[0,600,
# 0,i_srcid,
# -10, 110])
title_str = "num_srcids=%d probability_cut=%0.2lf factor_threshold=%0.2lf bin_size=%d poly_order=%d" % (\
self.pars['num_srcids_to_retrieve_plot'],
self.pars['sciclass_probability_cut'],
self.pars['polyfit_factor_threshold'],
self.pars['polyfit_bin_size'],
self.pars['polyfit_poly_order'])
##### TITLE:
# The 'z' is a flag in Mayavi2 v3.1.0 documentation:
#mlab.text(0.01, 0.97, title_str, width=1.0, name='title', z=0.0)
mlab.text(0.01, 0.97, title_str, width=1.0, name='title')
##### SCIENCE CLASS LABELS:
# TODO: Eventually I would like the class labels to be colored and
# placed on the y axis, but this requires:
# 1) later mayavi version to allow 3D text positioning
# 2) ability to match text color to the line color-map.
if 1:
used_final_classes.reverse()
y = 0.95
for class_name in used_final_classes:
class_str = "%2d %s" %(len(finalclass_ordered_dict[class_name]),
class_name)
mlab.text(0.85, y, class_str, width=0.095*(len(class_str)/20.0))
y -= 0.018
##### Add a x-axis plane (I can't figure out code to make it opaque)
if 0:
cp = ScalarCutPlane()
mayavi.add_module(cp)
cp.implicit_plane._hideshow() # this un-displays the plane
cp.implicit_plane.normal = 0,0,1
cp.implicit_plane.origin = 150,168,15
#cp.implicit_plane.position= 0.15 # feature not available yet
print '##### cp:'
cp.print_traits()
print '##### cp.implicit_plane:'
cp.implicit_plane.print_traits()
print '##### cp.implicit_plane._HideShowAction:'
cp.implicit_plane._HideShowAction.print_traits()
##### Camera position:
if enable_mayavi2_interactive_gui:
camera_distance = 600
else:
camera_distance = 1200
enthought.mayavi.tools.camera.view(azimuth=50,
elevation=70, # 0:looking down to -z
distance=camera_distance,
focalpoint=(100,(i_srcid*0.4),50))
#enthought.mayavi.mlab.show_pipeline() # this introspecive feature is not available in current mayavi version.
#####If no Mayavi2 GUI, we allow user to resize image before saving file
if not enable_mayavi2_interactive_gui:
print 'Please resize window & Press a Key.'
import curses
stdscr = curses.initscr()
while 1:
c = stdscr.getch()
break
curses.endwin()
##### Save figure:
img_fpath ="/tmp/%s%s.png" %(title_str.replace('=','').replace(' ','_'),
self.pars['save_plot_image_suffix'])
if os.path.exists(img_fpath):
os.system('rm ' + img_fpath)
mlab.savefig(img_fpath)#, size=(500,500))#, dpi=200) #size flag doesn't do anything
print "Saved:", img_fpath
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()
r.initialize(join(dirname(enthought.mayavi.__file__),
'examples', 'data', 'heart.vtk'))
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