def save(self, filename, binary=True):
"""Write a ``MultiBlock`` dataset to disk.
Written file may be an ASCII or binary vtm file.
Parameters
----------
filename : str
Filename of mesh to be written. File type is inferred from
the extension of the filename unless overridden with
ftype. Can be one of the following types (.vtm or .vtmb)
binary : bool, optional
Writes the file as binary when True and ASCII when False.
Notes
-----
Binary files write much faster than ASCII and have a smaller
file size.
"""
filename = os.path.abspath(os.path.expanduser(filename))
ext = pyvista.get_ext(filename)
if ext in ['.vtm', '.vtmb']:
writer = vtk.vtkXMLMultiBlockDataWriter()
else:
raise Exception('File extension must be either "vtm" or "vtmb"')
writer.SetFileName(filename)
writer.SetInputDataObject(self)
if binary:
writer.SetDataModeToBinary()
else:
writer.SetDataModeToAscii()
writer.Write()
return
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, npy, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Actor): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if ".vtk" in fr:
writer = vtk.vtkPolyDataWriter()
elif ".ply" in fr:
writer = vtk.vtkPLYWriter()
pscal = obj.GetPointData().GetScalars()
if not pscal:
pscal = obj.GetCellData().GetScalars()
if pscal and pscal.GetName():
writer.SetArrayName(pscal.GetName())
#writer.SetColorMode(0)
lut = objct.GetMapper().GetLookupTable()
if lut:
writer.SetLookupTable(lut)
elif ".stl" in fr:
writer = vtk.vtkSTLWriter()
elif ".obj" in fr:
writer = vtk.vtkOBJWriter()
elif ".vtp" in fr:
writer = vtk.vtkXMLPolyDataWriter()
elif ".vtm" in fr:
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif ".xyz" in fr:
writer = vtk.vtkSimplePointsWriter()
elif ".facet" in fr:
writer = vtk.vtkFacetWriter()
elif ".tif" in fr:
writer = vtk.vtkTIFFWriter()
writer.SetFileDimensionality(len(obj.GetDimensions()))
elif ".vti" in fr:
writer = vtk.vtkXMLImageDataWriter()
elif ".mhd" in fr:
writer = vtk.vtkMetaImageWriter()
elif ".nii" in fr:
writer = vtk.vtkNIFTIImageWriter()
elif ".png" in fr:
writer = vtk.vtkPNGWriter()
elif ".jpg" in fr:
writer = vtk.vtkJPEGWriter()
elif ".bmp" in fr:
writer = vtk.vtkBMPWriter()
elif ".npy" in fr:
if utils.isSequence(objct):
objslist = objct
else:
objslist = [objct]
dicts2save = []
for obj in objslist:
dicts2save.append( _np_dump(obj) )
np.save(fileoutput, dicts2save)
return dicts2save
elif ".xml" in fr: # write tetrahedral dolfin xml
vertices = objct.coordinates().astype(str)
faces = np.array(objct.faces()).astype(str)
ncoords = vertices.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
if len(faces[0]) == 4:# write tetrahedral mesh
ntets = faces.shape[0]
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'" z="'+z+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="'+str(i)
+ '" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'" v3="'+v3+'"/>\n')
elif len(faces[0]) == 3:# write triangle mesh
ntri = faces.shape[0]
outF.write(' <mesh celltype="triangle" dim="2">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, dummy_z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntri) + '">\n')
for i in range(ntri):
v0, v1, v2 = faces[i]
outF.write(' <triangle index="'+str(i)+'" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format", fileoutput, "file not saved.", c="r")
return objct
try:
if hasattr(writer, 'SetFileTypeToBinary'):
if binary:
writer.SetFileTypeToBinary()
else:
writer.SetFileTypeToASCII()
writer.SetInputData(obj)
writer.SetFileName(fileoutput)
writer.Write()
colors.printc("~save Saved file: " + fileoutput, c="g")
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
def testRead(self):
ents = Read(self.filename)
self.model = smtk.model.Model(ents[0])
#Verify that the model is marked as discrete
self.assertEqual(
self.model.geometryStyle(), smtk.model.DISCRETE,
'Expected discrete model, got {gs}'.format(gs=self.model.geometryStyle()))
#Verify that the file contains the proper number of groups.
subgroups = self.model.groups()
numGroups = len(subgroups)
self.assertEqual(numGroups, 3, 'Expected 3 groups, found %d' % numGroups)
numSubGroupsExpected = [1, 7, 3]
allgroups = []
for i in range(len(numSubGroupsExpected)):
numSubGroups = len(subgroups[i].members())
self.assertEqual(numSubGroupsExpected[i], numSubGroups,
'Expected {e} groups, found {a}'.format(e=numSubGroupsExpected[i], a=numSubGroups))
allgroups += subgroups[i].members()
#Verify that the group names match those from the Exodus file.
nameset = {
'Unnamed block ID: 1 Type: HEX8': '#5a5255',
'Unnamed set ID: 1': '#ae5a41',
'Unnamed set ID: 2': '#559e83',
'Unnamed set ID: 3': '#c3cb71',
'Unnamed set ID: 4': '#1b85b8',
'Unnamed set ID: 5': '#cb2c31',
'Unnamed set ID: 6': '#8b1ec4',
'Unnamed set ID: 7': '#ff6700'
}
self.assertTrue(all([x.name() in nameset for x in allgroups]),
'Not all group names recognized.')
# Verify that no groups which are not in the list above are present.
groupnames = [x.name() for x in allgroups]
self.assertTrue(all([x in groupnames for x in nameset]),
'Some expected group names not present.')
# Count the number of each *type* of group (node, face, volume)
#print '\n'.join([str((x.name(), x.flagSummary())) for x in allgroups])
grouptypes = [x.flagSummary() for x in allgroups]
gtc = {x:grouptypes.count(x) for x in grouptypes}
expectedgrouptypecounts = {
'boundary group (0-d entities)': 3,
'boundary group (0,1,2-d entities)': 7,
'domain group (3-d entities)': 1
}
for entry in gtc.items():
print '%40s: %d' % entry
self.assertEqual(gtc, expectedgrouptypecounts,
'At least one group was of the wrong type.')
if self.haveVTK() and self.haveVTKExtension():
# Render groups with colors:
for grp in allgroups:
color = self.hex2rgb(nameset[grp.name()])
SetEntityProperty(grp, 'color', as_float=color)
# The element block should not be shown as it is coincident with some
# of the side sets and throws off baseline images. Remove its tessellation.
if grp.name() == 'Unnamed block ID: 1 Type: HEX8':
grp.setTessellation(smtk.model.Tessellation())
self.startRenderTest()
mbs, filt, mapper, actor = self.addModelToScene(self.model)
self.renderer.SetBackground(1,1,1)
cam = self.renderer.GetActiveCamera()
cam.SetFocalPoint(0., 0., 0.)
cam.SetPosition(19,17,-43)
cam.SetViewUp(-0.891963, -0.122107, -0.435306)
self.renderer.ResetCamera()
self.renderWindow.Render()
import vtk
#wri = vtk.vtkCompositeDataWriter()
#wri.SetInputData(mbs.GetOutputDataObject(0))
#wri.SetFileName('/tmp/foofar.vtk')
#wri.Write()
## wri = vtk.vtkXMLDataSetWriter()
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetDataModeToAscii()
wri.SetInputData(mbs.GetOutputDataObject(0))
wri.SetFileName('/tmp/foofar.vtm')
wri.Write()
try:
self.assertImageMatch(['baselines', 'exodus', 'disk_out_ref.png'])
finally:
self.interact()
else:
self.assertFalse(
self.haveVTKExtension(),
'Could not import vtk. Python path is {pp}'.format(pp=sys.path))
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, npy, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Mesh): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if fr.endswith(".vtk"):
writer = vtk.vtkPolyDataWriter()
elif fr.endswith(".ply"):
writer = vtk.vtkPLYWriter()
pscal = obj.GetPointData().GetScalars()
if not pscal:
pscal = obj.GetCellData().GetScalars()
if pscal and pscal.GetName():
writer.SetArrayName(pscal.GetName())
#writer.SetColorMode(0)
lut = objct.GetMapper().GetLookupTable()
if lut:
writer.SetLookupTable(lut)
elif fr.endswith(".stl"):
writer = vtk.vtkSTLWriter()
elif fr.endswith(".vtp"):
writer = vtk.vtkXMLPolyDataWriter()
elif fr.endswith(".vtm"):
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
if isinstance(ob, Mesh): # picks transformation
ob = ob.polydata(True)
elif isinstance(ob, (vtk.vtkActor, vtk.vtkVolume)):
ob = ob.GetMapper().GetInput()
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif fr.endswith(".xyz"):
writer = vtk.vtkSimplePointsWriter()
elif fr.endswith(".facet"):
writer = vtk.vtkFacetWriter()
elif fr.endswith(".tif"):
writer = vtk.vtkTIFFWriter()
writer.SetFileDimensionality(len(obj.GetDimensions()))
elif fr.endswith(".vti"):
writer = vtk.vtkXMLImageDataWriter()
elif fr.endswith(".mhd"):
writer = vtk.vtkMetaImageWriter()
elif fr.endswith(".nii"):
writer = vtk.vtkNIFTIImageWriter()
elif fr.endswith(".png"):
writer = vtk.vtkPNGWriter()
elif fr.endswith(".jpg"):
writer = vtk.vtkJPEGWriter()
elif fr.endswith(".bmp"):
writer = vtk.vtkBMPWriter()
elif fr.endswith(".npy"):
if utils.isSequence(objct):
objslist = objct
else:
objslist = [objct]
dicts2save = []
for obj in objslist:
dicts2save.append( _np_dump(obj) )
np.save(fileoutput, dicts2save)
return dicts2save
elif fr.endswith(".obj"):
outF = open(fileoutput, "w")
outF.write('# OBJ file format with ext .obj\n')
outF.write('# File Created by vtkplotter\n')
cobjct = objct.clone().clean()
for p in cobjct.points():
outF.write('v '+ str(p[0]) +" "+ str(p[1])+" "+ str(p[2])+'\n')
for vn in cobjct.normals(cells=False):
outF.write('vn '+str(vn[0])+" "+str(vn[1])+" "+str(vn[2])+'\n')
#pdata = cobjct.polydata().GetPointData().GetScalars()
#if pdata:
# ndata = vtk_to_numpy(pdata)
# for vd in ndata:
# outF.write('vp '+ str(vd) +'\n')
#ptxt = cobjct.polydata().GetPointData().GetTCoords() # not working
#if ptxt:
# ntxt = vtk_to_numpy(ptxt)
# print(len(cobjct.faces()), cobjct.points().shape, ntxt.shape)
# for vt in ntxt:
# outF.write('vt '+ str(vt[0]) +" "+ str(vt[1])+ ' 0\n')
for f in cobjct.faces():
fs = ''
for fi in f:
fs += " "+str(fi+1)
outF.write('f' + fs + '\n')
#ldata = cobjct.polydata().GetLines().GetData()
#print(cobjct.polydata().GetLines())
#if ldata:
# ndata = vtk_to_numpy(ldata)
# print(ndata)
# for l in ndata:
# ls = ''
# for li in l:
# ls += str(li+1)+" "
# outF.write('l '+ ls + '\n')
outF.close()
return objct
elif fr.endswith(".xml"): # write tetrahedral dolfin xml
vertices = objct.points().astype(str)
faces = np.array(objct.faces()).astype(str)
ncoords = vertices.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
if len(faces[0]) == 4:# write tetrahedral mesh
ntets = faces.shape[0]
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'" z="'+z+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="'+str(i)
+ '" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'" v3="'+v3+'"/>\n')
elif len(faces[0]) == 3:# write triangle mesh
ntri = faces.shape[0]
outF.write(' <mesh celltype="triangle" dim="2">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, dummy_z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntri) + '">\n')
for i in range(ntri):
v0, v1, v2 = faces[i]
outF.write(' <triangle index="'+str(i)+'" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format", fileoutput, "file not saved.", c="r")
return objct
try:
if hasattr(writer, 'SetFileTypeToBinary'):
if binary:
writer.SetFileTypeToBinary()
else:
writer.SetFileTypeToASCII()
writer.SetInputData(obj)
writer.SetFileName(fileoutput)
writer.Write()
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Actor): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if ".vtk" in fr:
w = vtk.vtkPolyDataWriter()
elif ".ply" in fr:
w = vtk.vtkPLYWriter()
elif ".stl" in fr:
w = vtk.vtkSTLWriter()
elif ".vtp" in fr:
w = vtk.vtkXMLPolyDataWriter()
elif ".vtm" in fr:
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif ".xyz" in fr:
w = vtk.vtkSimplePointsWriter()
elif ".facet" in fr:
w = vtk.vtkFacetWriter()
elif ".tif" in fr:
w = vtk.vtkTIFFWriter()
w.SetFileDimensionality(len(obj.GetDimensions()))
elif ".vti" in fr:
w = vtk.vtkXMLImageDataWriter()
elif ".mhd" in fr:
w = vtk.vtkMetaImageWriter()
elif ".png" in fr:
w = vtk.vtkPNGWriter()
elif ".jpg" in fr:
w = vtk.vtkJPEGWriter()
elif ".bmp" in fr:
w = vtk.vtkBMPWriter()
elif ".xml" in fr: # write tetrahedral dolfin xml
vertices = obj.coordinates()
faces = obj.cells()
ncoords = vertices.shape[0]
ntets = faces.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="' + str(i) + '" x="' + str(x) +
'" y="' + str(y) + '" z="' + str(z) + '"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="' + str(i) + '" v0="' +
str(v0) + '" v1="' + str(v1) + '" v2="' + str(v2) +
'" v3="' + str(v3) + '"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format",
fileoutput,
"file not saved.",
c="r")
return objct
try:
if hasattr(w, 'SetFileTypeToBinary'):
if binary:
w.SetFileTypeToBinary()
else:
w.SetFileTypeToASCII()
w.SetInputData(obj)
w.SetFileName(fileoutput)
w.Write()
colors.printc("~save Saved file: " + fileoutput, c="g")
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
def main(file_, o):
"""Main program"""
sp = StatePoint(file_)
sp.read_results()
validate_options(sp, o)
if o.list:
print_available(sp)
return
if o.vtk:
if not o.output[-4:] == ".vtm": o.output += ".vtm"
else:
if not o.output[-5:] == ".silo": o.output += ".silo"
if o.vtk:
try:
import vtk
except:
print('The vtk python bindings do not appear to be installed properly.\n'
'On Ubuntu: sudo apt-get install python-vtk\n'
'See: http://www.vtk.org/')
return
else:
try:
import silomesh
except:
print('The silomesh package does not appear to be installed properly.\n'
'See: https://github.com/nhorelik/silomesh/')
return
if o.vtk:
blocks = vtk.vtkMultiBlockDataSet()
blocks.SetNumberOfBlocks(5)
block_idx = 0
else:
silomesh.init_silo(o.output)
# Tally loop #################################################################
for tally in sp.tallies:
# skip non-mesh tallies or non-user-specified tallies
if o.tallies and not tally.id in o.tallies: continue
if not 'mesh' in tally.filters: continue
print("Processing Tally {}...".format(tally.id))
# extract filter options and mesh parameters for this tally
filtercombos = get_filter_combos(tally)
meshparms = get_mesh_parms(sp, tally)
nx,ny,nz = meshparms[:3]
ll = meshparms[3:6]
ur = meshparms[6:9]
if o.vtk:
ww = [(u-l)/n for u,l,n in zip(ur,ll,(nx,ny,nz))]
grid = grid = vtk.vtkImageData()
grid.SetDimensions(nx+1,ny+1,nz+1)
grid.SetOrigin(*ll)
grid.SetSpacing(*ww)
else:
silomesh.init_mesh('Tally_{}'.format(tally.id), *meshparms)
# Score loop ###############################################################
for sid,score in enumerate(tally.scores):
# skip non-user-specified scrores for this tally
if o.scores and tally.id in o.scores and not sid in o.scores[tally.id]:
continue
# Filter loop ############################################################
for filterspec in filtercombos:
# skip non-user-specified filter bins
skip = False
if o.filters and tally.id in o.filters:
for filter_,bin in filterspec[1:]:
if filter_ in o.filters[tally.id] and \
not bin in o.filters[tally.id][filter_]:
skip = True
break
if skip: continue
# find and sanitize the variable name for this score
varname = get_sanitized_filterspec_name(tally, score, filterspec)
if o.vtk:
vtkdata = vtk.vtkDoubleArray()
vtkdata.SetName(varname)
dataforvtk = {}
else:
silomesh.init_var(varname)
lbl = "\t Score {}.{} {}:\t\t{}".format(tally.id, sid+1, score, varname)
# Mesh fill loop #######################################################
for x in range(1,nx+1):
sys.stdout.write(lbl+" {0}%\r".format(int(x/nx*100)))
sys.stdout.flush()
for y in range(1,ny+1):
for z in range(1,nz+1):
filterspec[0][1] = (x,y,z)
val = sp.get_value(tally.id-1, filterspec, sid)[o.valerr]
if o.vtk:
# vtk cells go z, y, x, so we store it now and enter it later
i = (z-1)*nx*ny + (y-1)*nx + x-1
dataforvtk[i] = float(val)
else:
silomesh.set_value(float(val), x, y, z)
# end mesh fill loop
print()
if o.vtk:
for i in range(nx*ny*nz):
vtkdata.InsertNextValue(dataforvtk[i])
grid.GetCellData().AddArray(vtkdata)
del vtkdata
else:
silomesh.finalize_var()
# end filter loop
# end score loop
if o.vtk:
blocks.SetBlock(block_idx, grid)
block_idx += 1
else:
silomesh.finalize_mesh()
# end tally loop
if o.vtk:
writer = vtk.vtkXMLMultiBlockDataWriter()
writer.SetFileName(o.output)
writer.SetInput(blocks)
writer.Write()
else:
silomesh.finalize_silo()
def testRead(self):
ents = Read(self.filename)
self.model = smtk.model.Model(ents[0])
#Verify that the model is marked as discrete
self.assertEqual(
self.model.geometryStyle(), smtk.model.DISCRETE,
'Expected discrete model, got {gs}'.format(
gs=self.model.geometryStyle()))
#Verify that the file contains the proper number of groups.
subgroups = self.model.groups()
numGroups = len(subgroups)
self.assertEqual(numGroups, 3,
'Expected 3 groups, found %d' % numGroups)
numSubGroupsExpected = [1, 7, 3]
allgroups = []
for i in range(len(numSubGroupsExpected)):
numSubGroups = len(subgroups[i].members())
self.assertEqual(
numSubGroupsExpected[i], numSubGroups,
'Expected {e} groups, found {a}'.format(
e=numSubGroupsExpected[i], a=numSubGroups))
allgroups += subgroups[i].members()
#Verify that the group names match those from the Exodus file.
nameset = {
'Unnamed block ID: 1 Type: HEX8': '#5a5255',
'Unnamed set ID: 1': '#ae5a41',
'Unnamed set ID: 2': '#559e83',
'Unnamed set ID: 3': '#c3cb71',
'Unnamed set ID: 4': '#1b85b8',
'Unnamed set ID: 5': '#cb2c31',
'Unnamed set ID: 6': '#8b1ec4',
'Unnamed set ID: 7': '#ff6700'
}
self.assertTrue(all([x.name() in nameset for x in allgroups]),
'Not all group names recognized.')
# Verify that no groups which are not in the list above are present.
groupnames = [x.name() for x in allgroups]
self.assertTrue(all([x in groupnames for x in nameset]),
'Some expected group names not present.')
# Count the number of each *type* of group (node, face, volume)
#print '\n'.join([str((x.name(), x.flagSummary())) for x in allgroups])
grouptypes = [x.flagSummary() for x in allgroups]
gtc = {x: grouptypes.count(x) for x in grouptypes}
expectedgrouptypecounts = {
'boundary group (0-d entities)': 3,
'boundary group (0,1,2-d entities)': 7,
'domain group (3-d entities)': 1
}
for entry in gtc.items():
print '%40s: %d' % entry
self.assertEqual(gtc, expectedgrouptypecounts,
'At least one group was of the wrong type.')
if self.haveVTK() and self.haveVTKExtension():
# Render groups with colors:
for grp in allgroups:
color = self.hex2rgb(nameset[grp.name()])
SetEntityProperty(grp, 'color', as_float=color)
# The element block should not be shown as it is coincident with some
# of the side sets and throws off baseline images. Remove its tessellation.
if grp.name() == 'Unnamed block ID: 1 Type: HEX8':
grp.setTessellation(smtk.model.Tessellation())
self.startRenderTest()
mbs, filt, mapper, actor = self.addModelToScene(self.model)
self.renderer.SetBackground(1, 1, 1)
cam = self.renderer.GetActiveCamera()
cam.SetFocalPoint(0., 0., 0.)
cam.SetPosition(19, 17, -43)
cam.SetViewUp(-0.891963, -0.122107, -0.435306)
self.renderer.ResetCamera()
self.renderWindow.Render()
import vtk
#wri = vtk.vtkCompositeDataWriter()
#wri.SetInputData(mbs.GetOutputDataObject(0))
#wri.SetFileName('/tmp/foofar.vtk')
#wri.Write()
## wri = vtk.vtkXMLDataSetWriter()
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetDataModeToAscii()
wri.SetInputData(mbs.GetOutputDataObject(0))
wri.SetFileName('/tmp/foofar.vtm')
wri.Write()
try:
self.assertImageMatch(
['baselines', 'exodus', 'disk_out_ref.png'])
finally:
self.interact()
else:
self.assertFalse(
self.haveVTKExtension(),
'Could not import vtk. Python path is {pp}'.format(
pp=sys.path))
def main():
parser = create_parser()
args = parser.parse_args()
config = config_to_dict(args.config)
try:
casePath = config["case"]
seedPatchName = config["patch"]
nSamples = int(config["nSamples"])
writePath = config["file"]
except KeyError:
print("ERROR: required parameter not specified in config file.")
raise
try:
debug = bool(int(config["debug"]))
except KeyError:
debug = False
pass
try:
time = float(config["time"])
except KeyError:
time = None
pass
try:
dry = bool(int(config["dry"]))
except KeyError:
dry = False
pass
try:
slow = bool(int(config["slow"]))
except KeyError:
slow = False
print("Will use slow averaging")
pass
try:
patchAlgorithm = str(config["patchalg"])
except KeyError:
patchAlgorithm = "cut"
print("Will use plane cuts for averaging patch data")
pass
if debug:
print("The debug switch is on")
print("")
print("The case path is "+casePath)
print("The name of the seed patch is "+seedPatchName)
print("The number of samples to be taken along z is "+str(nSamples))
print("The produced filename will be "+writePath)
# Case reader
print("Reading")
reader = read(casePath, time, debug)
# Writer
writer = vtk.vtkXMLMultiBlockDataWriter()
writer.SetFileName(writePath)
caseData = reader.GetOutput()
internalBlock = caseData.GetBlock(0)
bounds = internalBlock.GetBounds()
patchBlocks = caseData.GetBlock(1)
seedPatchBlock = patchBlocks.GetBlock(get_block_index(patchBlocks,
seedPatchName))
# The polyData for the 2d fields, copied from the seed patch
internalData = vtk.vtkPolyData()
internalData.ShallowCopy(seedPatchBlock)
internalData.BuildLinks()
print("Sampling and averaging internal field")
zero_out_arrays(internalData)
if slow:
average_internal_field_data(internalBlock, internalData, nSamples, debug, dry)
else:
new_average_internal_field_data(internalBlock, internalData, nSamples, debug, dry)
print("Creating boundary polyData")
boundaryData = create_boundary_polydata(patchBlocks, internalData, bounds, debug)
print("Averaging data for patches")
average_patch_data(caseData, boundaryData, nSamples, bounds, patchAlgorithm, debug)
add_boundary_names_to_fielddata(internalData, boundaryData)
print("Marking boundary cells.")
mark_boundary_cells(internalData, boundaryData, debug)
print("Assembling multi-block structure")
multiBlock = assemble_multiblock(internalData, boundaryData)
print("Writing")
writer.SetInputData(multiBlock)
writer.Write()
else:
usage()
exit(1)
transforms = dict()
transformers = dict()
data_connectors_v = dict()
data_connectors_t = dict()
data_connectors_d = dict()
big_data_source = vtk.vtkMultiBlockDataGroupFilter()
add_compatiblity_methods(big_data_source)
big_data_writer = vtk.vtkXMLMultiBlockDataWriter()
add_compatiblity_methods(big_data_writer)
contactors = dict()
offsets = dict()
vtkmath = vtk.vtkMath()
class Quaternion():
def __init__(self, *args):
self._data = vtk.vtkQuaternion[float](*args)
def __mul__(self, q):
r = Quaternion()
g.Update()
mb = g.GetOutputDataObject(0)
a = vtk.vtkFloatArray()
a.SetName("foo")
a.SetNumberOfTuples(1)
a.SetValue(0, 10)
mb.GetFieldData().AddArray(a)
file_root = VTK_TEMP_DIR + '/testxml'
file0 = file_root + ".vtm"
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(file0)
wri.Write()
read = vtk.vtkXMLMultiBlockDataReader()
read.SetFileName(file0)
read.Update()
output = read.GetOutputDataObject(0)
assert(output.GetFieldData().GetArray("foo"))
assert(output.GetFieldData().GetArray("foo").GetValue(0) == 10)
os.remove(file0)
os.remove(file_root + "/testxml_0.vti")
os.rmdir(file_root)
def beam_to_vtk(filename, output = 'beam', option_ISO = False, option_NOT_ISO = False, option_primaries = False, option_secondaries = False):
file = uproot4.open(filename)
evt = file.get('Event')
partID_tracks = evt.arrays(['Trajectory.partID'], library='np')['Trajectory.partID']
s_tracks = evt.arrays(['Trajectory.S'], library='np')['Trajectory.S']
tracks = evt.arrays(['Trajectory.XYZ'], library='np')['Trajectory.XYZ']
mb = _vtk.vtkMultiBlockDataSet()
mb.SetNumberOfBlocks(len(tracks))
colors = _vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
red = [255, 0, 0]
green = [0, 255, 0]
blue = [0, 0, 255]
mbIndex = 0
for i in range(len(tracks)):
for j in range(len(tracks[i])):
run = False
if option_ISO and j == 0 and s_tracks[i].tolist()[j][-1] > 15.42:
run = True
if option_NOT_ISO and j == 0 and s_tracks[i].tolist()[j][-1] < 15.42:
run = True
if option_primaries and j == 0:
run = True
if option_secondaries and j != 0:
run = True
if partID_tracks[i][j] == 2212:
color = blue
elif partID_tracks[i][j] == 2112:
color = green
else:
run = False
if run:
steps = tracks[i].tolist()[j]
lines = _vtk.vtkCellArray()
pts = _vtk.vtkPoints()
line0 = _vtk.vtkLine()
line1 = _vtk.vtkLine()
pts.InsertNextPoint([steps[0].member('fX'), steps[0].member('fY'), steps[0].member('fZ')])
line0.GetPointIds().SetId(0, 0)
for k in range(1, len(steps) - 1):
if k % 2 == 0:
lines.InsertNextCell(line0)
colors.InsertNextTuple(color)
line0 = _vtk.vtkLine()
if k % 2 == 1 and k != 1:
lines.InsertNextCell(line1)
colors.InsertNextTuple(color)
line1 = _vtk.vtkLine()
pts.InsertNextPoint([steps[k].member('fX'), steps[k].member('fY'), steps[k].member('fZ')])
line0.GetPointIds().SetId(k % 2, k)
line1.GetPointIds().SetId((k - 1) % 2, k)
# Create a polydata to store everything in
linesPolyData = _vtk.vtkPolyData()
# Add the points to the dataset
linesPolyData.SetPoints(pts)
# Add the lines to the dataset
linesPolyData.SetLines(lines)
# Color the lines
# colors.InsertNextTuple(color)
linesPolyData.GetCellData().SetScalars(colors)
mb.SetBlock(mbIndex, linesPolyData)
mbIndex += 1
print(f"Progress: {i / len(tracks) * 100}%")
writer = _vtk.vtkXMLMultiBlockDataWriter()
writer.SetDataModeToAscii()
writer.SetInputData(mb)
print(f"Trying to write file {output}.vtm")
writer.SetFileName(f"{output}.vtm")
writer.Write()
g.Update()
mb = g.GetOutputDataObject(0)
a = vtk.vtkFloatArray()
a.SetName("foo")
a.SetNumberOfTuples(1)
a.SetValue(0, 10)
mb.GetFieldData().AddArray(a)
file_root = VTK_TEMP_DIR + '/testxml'
file0 = file_root + ".vtm"
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(file0)
wri.Write()
read = vtk.vtkXMLMultiBlockDataReader()
read.SetFileName(file0)
read.Update()
output = read.GetOutputDataObject(0)
assert (output.GetFieldData().GetArray("foo"))
assert (output.GetFieldData().GetArray("foo").GetValue(0) == 10)
os.remove(file0)
os.remove(file_root + "/testxml_0.vti")
os.rmdir(file_root)
