def time_fields_write_data(fname, x, y, z, time, conn, offs, ctypes, **kwargs):
""" Write data to vtk files """
pfields = kwargs.get('pointdata', None)
cfields = kwargs.get('celldata', None)
if (pfields is None and cfields is None):
raise RuntimeError("No field data given, give either "
"a point field or cell field or both.")
group = VtkGroup(fname + "/" + fname)
for i, t in enumerate(time):
if pfields is None:
pdata = None
else:
pdata = {k: pack_field(f[i, ...]) for k, f in pfields.items()}
if cfields is None:
cdata = None
else:
cdata = {k: pack_field(f[i, ...]) for k, f in cfields.items()}
unstructuredGridToVTK(fname + "/step_" + str(i),
x,
y,
z,
connectivity=conn,
offsets=offs,
cell_types=ctypes,
pointData=pdata,
cellData=cdata)
group.addFile(filepath=fname + "/step_" + str(i) + ".vtu", sim_time=t)
group.save()
def seriesVTK(ij_out):
"""
Creates a PVD file that can visualize all time steps in ParaView.
VARIABLES
---------
ij_out: Location of the VTK files from convertVTK()
"""
# Read in the VTK files made from convertVTK()
files = glob.glob('{0}/VTK/*.vti'.format(ij_out))
# Initialize the group
g = VtkGroup('{0}/VTK/timeSeries'.format(ij_out))
for vtkFile in files:
# Get time step
i = int(vtkFile.rsplit('\\vol')[-1].rsplit('.')[0])
# Calculate time step in us (10 kHz imaging)
timeStep = (i / (10E3)) * 1E6
# Add file to group
g.addFile(filepath=vtkFile, sim_time=timeStep)
# Save the group (will be a ParaView PVD file)
g.save()
def write_pvd(self):
pvd_attributes = VtkGroup(self.attributes_file_path)
for k, v in self.exported_times['attributes'].items():
pvd_attributes.addFile(k + '.vtu', sim_time=v)
pvd_attributes.save()
pvd_products = VtkGroup(self.products_file_path)
for k, v in self.exported_times['products'].items():
pvd_products.addFile(k + '.vts', sim_time=v)
pvd_products.save()
class VtkWriter():
def __init__(self, path, dim, scale):
os.makedirs(path[:path.rfind("/")], exist_ok=True)
self.path = path
self.vtk_group = VtkGroup(path)
self.spacing = scale / (dim - 1)
def record_epoch(self, epoch, sdf, grad):
out_fn = f"{self.path}_{epoch}"
imageToVTK(out_fn, [0]*3, [self.spacing]*3, pointData={"sdf" : sdf, "grad": grad})
self.vtk_group.addFile(filepath=out_fn + ".vti", sim_time=epoch)
def __exit__(self, type, value, traceback):
assert len(self._assemFiles) == len(self._blockFiles)
if len(self._assemFiles) > 1:
# multiple files need to be wrapped up into groups. VTK doesnt like having
# multiple meshes in the same group, so we write out separate Collection
# files for them
asyGroup = VtkGroup(f"{self._baseName}_asm")
for path, time in self._assemFiles:
asyGroup.addFile(filepath=path, sim_time=time)
asyGroup.save()
blockGroup = VtkGroup(f"{self._baseName}_blk")
for path, time in self._blockFiles:
blockGroup.addFile(filepath=path, sim_time=time)
blockGroup.save()
from pyevtk.hl import pointsToVTK
from pyevtk.vtk import VtkGroup
import numpy as np
g = VtkGroup("./group")
for i in range(1,nt+1):
x = np.random.rand(100)
y = np.random.rand(100)
z = np.random.rand(100)
pointsToVTK("sim"+str(i), x, y, z, {"V":(x,y,z)})
g.addFile("sim"+str(i)+".vtu", sim_time=i*l3d.dt)
g.save()
pass
wavelengths = np.arange(400, 910, 10) #nm
os.chdir(path + '3d/')
g = VtkGroup("3dscan")
#fileNames = []
for wavelength in wavelengths:
wl_ind = np.argmin(np.abs(wl - wavelength))
#gridToVTK("3d/3dscan"+str(round(wavelength)), x, y, z, cellData = {"intensity" : fgrid[wl_ind,:,:,]}, pointData = {"intensityp" : fgrid[wl_ind,:,:,]})
gridToVTK("3dscan" + str(round(wavelength)),
nx.ravel(),
ny.ravel(),
nz.ravel(),
pointData={"intensityp": fgrid[wl_ind, :, :, ]})
#gridToVTK("3d/3dscan"+str(round(wavelength)), x.ravel(), y.ravel(), z.ravel(), cellData = {"intensity" : fgrid[wl_ind,:,:,].ravel()})
g.addFile(filepath="./3dscan" + str(round(wavelength)) + '.vtr',
sim_time=round(wavelength))
#fileNames.append("3dscan" + str(round(wavelength)))
g.save()
os.chdir('..')
# import vtk_export
#
# vtk_writer = vtk_export.VTK_XML_Serial_Structured()
# wavelengths = np.arange(400,900,10) #nm
# os.chdir('3d/')
# for wavelength in wavelengths:
# wl_ind = np.argmin(np.abs(wl - wavelength))
# vtk_writer.snapshot("3dscan"+str(round(wavelength))+".vtu", gridx.ravel(), gridy.ravel(), gridz.ravel(), intensity=fgrid[wl_ind,:,:,].ravel())
# vtk_writer.writePVD("3dscan.pvd")
# os.chdir('..')
def _write_vtu_series(grid, coordinates, connectivity, data, filename_base,
last_step, is_cell_data):
steps = last_step + 1 if last_step is not None else len(data)
fn_tpl = "{}_{:08d}"
npoints = len(coordinates[0])
ncells = len(connectivity)
ref = grid.reference_element
if ref is ref is referenceelements.triangle:
points_per_cell = 3
vtk_el_type = VtkTriangle.tid
elif ref is referenceelements.square:
points_per_cell = 4
vtk_el_type = VtkQuad.tid
else:
raise NotImplementedError(
"vtk output only available for grids with triangle or rectangle reference elments"
)
connectivity = connectivity.reshape(-1)
cell_types = np.empty(ncells, dtype='uint8')
cell_types[:] = vtk_el_type
offsets = np.arange(start=points_per_cell,
stop=ncells * points_per_cell + 1,
step=points_per_cell,
dtype='int32')
group = VtkGroup(filename_base)
for i in range(steps):
fn = fn_tpl.format(filename_base, i)
vtk_data = data[i, :]
w = VtkFile(fn, VtkUnstructuredGrid)
w.openGrid()
w.openPiece(ncells=ncells, npoints=npoints)
w.openElement("Points")
w.addData("Coordinates", coordinates)
w.closeElement("Points")
w.openElement("Cells")
w.addData("connectivity", connectivity)
w.addData("offsets", offsets)
w.addData("types", cell_types)
w.closeElement("Cells")
if is_cell_data:
_addDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_addDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.closePiece()
w.closeGrid()
w.appendData(coordinates)
w.appendData(connectivity).appendData(offsets).appendData(cell_types)
if is_cell_data:
_appendDataToFile(w, cellData={"Data": vtk_data}, pointData=None)
else:
_appendDataToFile(w, cellData=None, pointData={"Data": vtk_data})
w.save()
group.addFile(filepath=fn + '.vtu', sim_time=i)
group.save()
w.addData(str(key), np.array(f[key][step]))
vx = np.array(f['u'][step])
vy = np.array(f['v'][step])
vz = np.array(f['w'][step])
w.addData("Velocity", (vx, vy, vz))
w.closeData("Point")
# Coordinates of cell vertices
w.openElement("Points")
w.addData("points", (X, Y, Z))
w.closeElement("Points")
w.closePiece()
w.closeGrid()
# Need to modify parameters
for key in scalar_vars:
w.appendData(data=np.array(f[key][step]))
w.appendData(data=(vx, vy, vz))
w.appendData((X, Y, Z))
w.save()
print("file: " + filename + " added")
g = VtkGroup(new_dir + "/group")
for step in times:
g.addFile(filepath=new_data + '/' + str(step) + '.vts',
sim_time=float(step))
g.save()
print("group file: group.pvd added")
# * *
# * 2. Redistributions in binary form must reproduce the above copyright notice, *
# * this list of conditions and the following disclaimer in the documentation *
# * and/or other materials provided with the distribution. *
# * *
# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
# ***********************************************************************************
# **************************************************************
# * Example of how to create a VTK group to visualize time *
# * dependent data. *
# **************************************************************
from pyevtk.vtk import VtkGroup
g = VtkGroup("./group")
g.addFile(filepath="sim0000.vtu", sim_time=0.0)
g.addFile(filepath="sim0001.vtu", sim_time=1.0)
g.addFile(filepath="sim0002.vtu", sim_time=2.0)
g.addFile(filepath="sim0003.vtu", sim_time=3.0)
g.save()
def build_particle_file(fname_in, fname_outbase, ignore_xtime):
"""
Take existing netCDF4 input f_in and produce
vtu files for f_outbase with all the particle data
Phillip Wolfram
LANL
07/15/2014
"""
# initialize the starting points
fullpath = fname_in.split(os.sep)
# don't want to place this in starting directory
g = VtkGroup(fname_outbase + '_' + os.path.splitext(fullpath[-1])[0])
# open the database
f_in = netCDF4.Dataset(fname_in, 'r')
# num particles and data frames
Ntime = len(f_in.dimensions['Time'])
# initialize empty dictionary
particleData = dict()
for t in np.arange(Ntime):
# get the points locations
x = f_in.variables['xParticle'][t]
y = f_in.variables['yParticle'][t]
z = f_in.variables['zParticle'][t]
print(f'{t+1}/{Ntime}...')
particleType = f_in.variables['xParticle'].dimensions
particleTypeStatic = f_in.variables['indexToParticleID'].dimensions
# get particle data
particleData.clear()
coordinateVars = ['xParticle', 'yParticle', 'zParticle']
nonCoords = [i for i in f_in.variables if i not in coordinateVars]
for v in nonCoords:
dim = f_in.variables[v].dimensions
if dim == particleType:
particleData[str(v)] = cleanup(f_in.variables[v][t])
if dim == particleTypeStatic:
particleData[str(v)] = cleanup(f_in.variables[v][:])
if (ignore_xtime) or ('xtime' not in f_in.variables):
# Set time to a simple index.
time = 2 * t
else:
# Set decimal time similar to that in `paraview_vtk_extractor` so
# that the `annotate_date` macro from MPAS-Tools can be used.
xtime = f_in.variables['xtime'][t].tostring().decode('utf-8') \
.strip()
date = datetime(int(xtime[0:4]), int(xtime[5:7]), int(xtime[8:10]),
int(xtime[11:13]), int(xtime[14:16]),
int(xtime[17:19]))
time = date2num(
date, units='days since 0000-01-01', calendar='noleap') / 365
# file name
f_out = f'{fname_outbase}_{os.path.splitext(fullpath[-1])[0]}_{str(t)}'
# output file
pointsToVTK(f_out, x, y, z, data=particleData)
# make sure the file is added to the time vector
g.addFile(filepath=f_out + '.vtu', sim_time=time)
# save the animation file
g.save()
from pyevtk.hl import pointsToVTK
from pyevtk.vtk import VtkGroup
import numpy as np
g = VtkGroup("./group")
for i in range(1, nt + 1):
x = np.random.rand(100)
y = np.random.rand(100)
z = np.random.rand(100)
pointsToVTK("sim" + str(i), x, y, z, {"V": (x, y, z)})
g.addFile("sim" + str(i) + ".vtu", sim_time=i * l3d.dt)
g.save()