def isosurf_builtin(self, event=None):
from PYME.experimental import isosurface
from PYME.LMVis import gl_render3D_shaders as glrender
from PYME.LMVis.layers.mesh import TriangleRenderLayer
glcanvas = new_mesh_viewer() #glrender.showGLFrame()
glcanvas.layer_data = {}
for i in range(self.image.data.shape[3]):
isolevel = self.do.Offs[i] + .5 / self.do.Gains[i]
T = isosurface.isosurface(self.image.data[:, :, :, i].astype('f'),
isolevel=isolevel,
voxel_size=self.image.voxelsize,
origin=self.image.origin)
glcanvas.layer_data[self.image.names[i]] = T
layer = TriangleRenderLayer(
glcanvas.layer_data,
dsname=self.image.names[i],
method='shaded',
context=glcanvas.gl_context,
cmap=['C', 'M', 'Y', 'R', 'G', 'B'][i % 6],
#normal_mode='Per face', #use face normals rather than vertex normals, as there is currently a bug in computation of vertex normals
)
glcanvas.add_layer(layer)
layer.engine._outlines = False
layer.show_lut = False
self.canvases.append(glcanvas)
glcanvas.displayMode = '3D'
glcanvas.fit_bbox()
glcanvas.Refresh()
def gen_isosurface(visFr):
from PYME.LMVis.layers.mesh import TriangleRenderLayer
from PYME.recipes.surface_fitting import DualMarchingCubes
oc_name = gen_octree_from_points(visFr)
surf_name, surf_count = visFr.pipeline.new_ds_name('surf',
return_count=True)
recipe = visFr.pipeline.recipe
dmc = DualMarchingCubes(recipe,
invalidate_parent=False,
input=oc_name,
output=surf_name)
if dmc.configure_traits(kind='modal'):
recipe.add_module(dmc)
recipe.execute()
print('Isosurface generated, adding layer')
layer = TriangleRenderLayer(visFr.pipeline,
dsname=surf_name,
method='shaded',
cmap=['C', 'M', 'Y', 'R', 'G',
'B'][surf_count % 6])
visFr.add_layer(layer)
dmc._invalidate_parent = True
print('Isosurface layer added')
def gen_isosurface_from_tesselation(visFr):
from PYME.LMVis.layers.mesh import TriangleRenderLayer
from PYME.recipes.surface_fitting import MarchingTetrahedra
surf_count = 0
oc_name = 'delaunay%d' % surf_count
surf_name, surf_count = visFr.pipeline.new_ds_name('surf')
recipe = visFr.pipeline.recipe
mt = MarchingTetrahedra(recipe,
invalidate_parent=False,
input=oc_name,
output=surf_name)
if mt.configure_traits(kind='modal'):
recipe.add_module(mt)
recipe.execute()
print('Isosurface generated, adding layer')
layer = TriangleRenderLayer(visFr.pipeline,
dsname=surf_name,
method='shaded',
cmap=['C', 'M', 'Y', 'R', 'G',
'B'][surf_count % 6])
visFr.add_layer(layer)
mt._invalidate_parent = True
print('Isosurface layer added')
def open_surface(visFr):
import wx
# from PYME.experimental import triangle_mesh
from PYME.experimental import _triangle_mesh as triangle_mesh
from PYME.LMVis.layers.mesh import TriangleRenderLayer
filename = wx.FileSelector(
"Choose a file to open",
default_extension='stl',
wildcard='STL mesh (*.stl)|*.stl|PLY mesh (*.ply)|*.ply')
#print filename
if not filename == '':
surf_count = 0
surf_name = 'surf%d' % surf_count
while surf_name in visFr.pipeline.dataSources.keys():
surf_count += 1
surf_name = 'surf%d' % surf_count
ext = filename.split('.')[-1]
if ext == 'stl':
visFr.pipeline.dataSources[
surf_name] = triangle_mesh.TriangleMesh.from_stl(filename)
elif ext == 'ply':
visFr.pipeline.dataSources[
surf_name] = triangle_mesh.TriangleMesh.from_ply(filename)
else:
raise ValueError('Invalid file extension .' + str(ext))
layer = TriangleRenderLayer(visFr.pipeline,
dsname=surf_name,
method='shaded')
visFr.add_layer(layer)
def gen_isosurface_from_tesselation(visFr):
from PYME.LMVis.layers.mesh import TriangleRenderLayer
from PYME.recipes.surface_fitting import DelaunayMarchingTetrahedra
if 'delaunay0' not in visFr.pipeline.dataSources.keys():
del_name = add_tesselation(visFr)
else:
_, c = visFr.pipeline.new_ds_name('delaunay', return_count=True)
del_name = 'delaunay{}'.format(c-1)
if 'dn' not in visFr.pipeline.dataSources[del_name].keys():
# visFr.pipeline.selectDataSource(del_name)
estimate_density(visFr)
surf_name, surf_count = visFr.pipeline.new_ds_name('surf', return_count=True)
recipe = visFr.pipeline.recipe
mt = DelaunayMarchingTetrahedra(recipe, invalidate_parent=False, input=del_name, output=surf_name)
if mt.configure_traits(kind='modal'):
recipe.add_modules_and_execute([mt,])
print('Isosurface generated, adding layer')
layer = TriangleRenderLayer(visFr.pipeline, dsname=surf_name, method='shaded', cmap = ['C', 'M', 'Y', 'R', 'G', 'B'][surf_count % 6])
visFr.add_layer(layer)
mt._invalidate_parent = True
print('Isosurface layer added')
def add_tesselation_layer(visFr):
from PYME.LMVis.layers.mesh import TriangleRenderLayer
surf_name = add_tesselation(visFr)
if surf_name is not None:
layer = TriangleRenderLayer(visFr.pipeline, dsname=surf_name, method='flat',
cmap='hot')
visFr.add_layer(layer)
print('Tesselation layer added')
def OnLoadHarmonicRepresentation(self, wx_event):
import wx
from PYME.IO import tabular, FileUtils
from PYME.Analysis.points.spherical_harmonics import scaled_shell_from_hdf
import PYME.experimental._triangle_mesh as triangle_mesh
from PYME.LMVis.layers.mesh import TriangleRenderLayer
fdialog = wx.FileDialog(
None,
'Load Spherical Harmonic Representation',
wildcard='Harmonic shell (*.hdf)|*.hdf',
style=wx.FD_OPEN,
defaultDir=FileUtils.nameUtils.genShiftFieldDirectoryPath())
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
path = fdialog.GetPath()
fdialog.Destroy()
else:
fdialog.Destroy()
return
shell = scaled_shell_from_hdf(path)
points = tabular.MappingFilter(self.pipeline.selectedDataSource)
separations, closest_points = shell.distance_to_shell(
(points['x'], points['y'], points['z']), d_angles=self.d_angle)
self._shells.append(shell)
shell_number = len(self._shells)
points.addColumn('distance_to_loaded_shell%d' % shell_number,
separations)
points.addColumn(
'inside_shell%d' % shell_number,
shell.check_inside(points['x'], points['y'], points['z']))
self.pipeline.addDataSource('shell%d_mapped' % shell_number, points)
self.pipeline.selectDataSource('shell%d_mapped' % shell_number)
v, f = shell.get_mesh_vertices_faces(self.d_angle)
surf = triangle_mesh.TriangleMesh(v, f)
self.pipeline.dataSources['shell_surface'] = surf
layer = TriangleRenderLayer(self.pipeline,
dsname='shell_surface',
method='shaded',
cmap='C')
self.vis_frame.add_layer(layer)
self.vis_frame.RefreshView()
def OnCalcHarmonicRepresentation(self, wx_event):
from PYME.recipes import surface_fitting
import PYME.experimental._triangle_mesh as triangle_mesh
from PYME.LMVis.layers.mesh import TriangleRenderLayer
recipe = self.pipeline.recipe
shell_maker = surface_fitting.SphericalHarmonicShell(
recipe,
input_name=self.pipeline.selectedDataSourceKey,
output_name='harmonic_shell')
if shell_maker.configure_traits(kind='modal'):
recipe.add_modules_and_execute([
shell_maker,
])
shell = recipe.namespace['harmonic_shell']
shell_mapped = recipe.namespace['shell_mapped']
self._shells.append(shell)
self.pipeline.addDataSource('shell_mapped', shell_mapped)
self.pipeline.selectDataSource('shell_mapped')
# Add a surface rendering
v, f = shell.get_mesh_vertices_faces(self.d_angle)
surf = triangle_mesh.TriangleMesh(v, f)
self.pipeline.dataSources['shell_surface'] = surf
layer = TriangleRenderLayer(self.pipeline,
dsname='shell_surface',
method='shaded',
cmap='C')
self.vis_frame.add_layer(layer)
self.vis_frame.RefreshView()