def __init__(self, id, display, steps_mesh, patch_id, color=None):
"""
Constructor
"""
self.id = id
self.display = display
self.steps_mesh = steps_mesh
if not color:
color = [random.random(), random.random(), random.random(), 0.3]
tmpatch = sgeom.castToTmPatch(steps_mesh.getPatch(patch_id))
self.bound_max = [v * display.scale for v in tmpatch.getBoundMax()]
self.bound_min = [v * display.scale for v in tmpatch.getBoundMin()]
patch_surface = tmpatch.getAllTriIndices()
patch_surface = np.array(patch_surface, dtype=INDEX_DTYPE)
v_set_size = steps_mesh.getTriVerticesSetSizeNP(patch_surface)
tris_data = np.zeros(patch_surface.size * 3, dtype=INDEX_DTYPE)
v_set = np.zeros(v_set_size, dtype=INDEX_DTYPE)
verts_data = np.zeros(v_set_size * 3)
steps_mesh.getTriVerticesMappingSetNP(patch_surface, tris_data, v_set)
steps_mesh.getBatchVerticesNP(v_set, verts_data)
verts_data *= display.scale
tris_data.shape = -1, 3
verts_data.shape = -1, 3
mesh_data = gl.MeshData(vertexes=verts_data, faces=tris_data)
gl.GLMeshItem.__init__(self,
meshdata=mesh_data,
smooth=False,
computeNormals=True,
shader='balloon',
glOptions='additive')
self.setColor(color)
display.addItem(self)
def highlightPatch(mesh, patch_id, tri_proxy):
"""
Highlight the STEPS compartment.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* patch_id Name of the patch
* tri_proxy Triangle element proxy generated by STEPS mesh importing function
Return:
None
"""
patch = sgeom.castToTmPatch(mesh.getPatch(patch_id))
data = patch.getAllTriIndices()
highlightSTEPSTris(data, tri_proxy)
def __init__(self,
plot,
mesh,
sim,
patch_id,
spec_id,
axis="x",
nbins=20,
y_range=None,
**kwargs):
self.plot = plot
self.mesh = mesh
self.sim = sim
self.patch_id = patch_id
self.spec_id = spec_id
self.nbins = nbins
if y_range != None:
self.plot.setYRange(y_range[0], y_range[1])
tmpatch = sgeom.castToTmPatch(mesh.getPatch(patch_id))
self.tris = tmpatch.getAllTriIndices()
self.axis = 0
if axis == "x":
self.axis = 0
plot.setLabel('bottom', 'X Coordinate', units='m')
elif axis == "y":
self.axis = 1
plot.setLabel('bottom', 'Y Coordinate', units='m')
elif axis == "z":
self.axis = 2
plot.setLabel('bottom', 'Z Coordinate', units='m')
self.bound_max = tmpatch.getBoundMax()[self.axis]
self.bound_min = tmpatch.getBoundMin()[self.axis]
bins = np.linspace(self.bound_min, self.bound_max, nbins + 1)
centers = [mesh.getTriBarycenter(t)[self.axis] for t in self.tris]
self.belongs = np.digitize(centers, bins)
self.bin_data = []
for b in range(nbins):
self.bin_data.append(bins[b])
self.bin_data.append(bins[b + 1])
data = np.zeros(nbins + 1)
for t in range(len(self.tris)):
data[self.belongs[t] - 1] += sim.getTriCount(
self.tris[t], self.spec_id)
y_data = []
for b in range(nbins):
y_data.append(data[b])
y_data.append(data[b])
self.curve = plot.plot(self.bin_data, y_data, fillLevel=-0.3, **kwargs)
def __init__(self,
id,
display,
mesh,
sim,
patch_id,
specs_colors,
spec_size=0.1):
"""
Constructor.
"""
self.patch_id = patch_id
tris = sgeom.castToTmPatch(mesh.getPatch(patch_id)).getAllTriIndices()
VisualTrisChannel.__init__(self, id, display, mesh, sim, tris,
specs_colors, spec_size)
def __init__(self, id, display, steps_mesh, comp_id, color=None):
"""
Constructor
"""
self.id = id
self.display = display
self.steps_mesh = steps_mesh
if not color:
color = [random.random(), random.random(), random.random(), 0.3]
tmcomp = sgeom.castToTmComp(steps_mesh.getComp(comp_id))
self.bound_max = [v * display.scale for v in tmcomp.getBoundMax()]
self.bound_min = [v * display.scale for v in tmcomp.getBoundMin()]
ipatches = set(tmcomp.getIPatches())
opatches = set(tmcomp.getOPatches())
patches = ipatches.union(opatches)
surface_tris = smeshctrl.findSurfTrisInComp(steps_mesh, tmcomp)
for p in patches:
surface_tris.extend(sgeom.castToTmPatch(p).getAllTriIndices())
surface_tris = np.array(surface_tris, dtype=INDEX_DTYPE)
v_set_size = steps_mesh.getTriVerticesSetSizeNP(surface_tris)
tris_data = np.zeros(surface_tris.size * 3, dtype=INDEX_DTYPE)
v_set = np.zeros(v_set_size, dtype=INDEX_DTYPE)
verts_data = np.zeros(v_set_size * 3)
steps_mesh.getTriVerticesMappingSetNP(surface_tris, tris_data, v_set)
steps_mesh.getBatchVerticesNP(v_set, verts_data)
verts_data *= display.scale
tris_data.shape = -1, 3
verts_data.shape = -1, 3
mesh_data = gl.MeshData(vertexes=verts_data, faces=tris_data)
gl.GLMeshItem.__init__(self,
meshdata=mesh_data,
smooth=False,
computeNormals=True,
shader='balloon',
glOptions='additive')
self.setColor(color)
display.addItem(self)
def __init__(self,
id,
display,
mesh,
sim,
patch_id,
spec_id,
spec_color=None,
spec_size=0.2,
max_nspec=100000,
max_density=1000e12,
auto_adjust=True):
"""
Constructor.
"""
self.patch_id = patch_id
tris = sgeom.castToTmPatch(mesh.getPatch(patch_id)).getAllTriIndices()
VisualTrisSpec.__init__(self, id, display, mesh, sim, tris, spec_id,
spec_color, spec_size, max_nspec, max_density,
auto_adjust)