def createGlyph(self, input, type='Box', factor=0.1, mode="All Points"):
"""Create a new 'Glyph'
"""
glyph = pv.Glyph(Input=input, GlyphType=type)
glyph.OrientationArray = ['POINTS', 'No orientation array']
glyph.ScaleArray = ['POINTS', '{}'.format(input.ResultArrayName)]
glyph.ScaleFactor = factor
glyph.GlyphTransform = 'Transform2'
glyph.GlyphMode = mode
return glyph
def makeGlyph(vtuIn,
RenderViewIn,
scale=40.0,
color=[1.0, 0.0, 0.0]): # create a new 'Glyph'
# create a new 'Glyph'
glyph1 = pvs.Glyph(Input=vtuIn, GlyphType='Arrow')
glyph1.Vectors = ['POINTS', 'Curvature']
glyph1.ScaleMode = 'vector'
glyph1.ScaleFactor = scale
glyph1.GlyphMode = 'All Points'
glyph1Display = pvs.Show(glyph1, RenderViewIn)
glyph1Display.DiffuseColor = color
def main():
import paraview.simple as para
version_major = para.servermanager.vtkSMProxyManager.GetVersionMajor()
source = para.GetActiveSource()
renderView1 = para.GetRenderView()
atoms = para.Glyph(
Input=source,
GlyphType='Sphere',
Scalars='radii',
ScaleMode='scalar',
)
para.RenameSource('Atoms', atoms)
atomsDisplay = para.Show(atoms, renderView1)
if version_major <= 4:
atoms.SetScaleFactor = 0.8
atomicnumbers_PVLookupTable = para.GetLookupTableForArray(
'atomic numbers', 1)
atomsDisplay.ColorArrayName = ('POINT_DATA', 'atomic numbers')
atomsDisplay.LookupTable = atomicnumbers_PVLookupTable
else:
atoms.ScaleFactor = 0.8
para.ColorBy(atomsDisplay, 'atomic numbers')
atomsDisplay.SetScalarBarVisibility(renderView1, True)
para.Render()
# create a new 'Table To Points'
tableToPoints1 = pv.TableToPoints(Input=hitsCsv)
tableToPoints1.XColumn = 'X'
tableToPoints1.YColumn = 'Y'
tableToPoints1.ZColumn = 'Z'
# find view
renderView1 = pv.FindViewOrCreate('RenderView1', viewtype='RenderView')
# set active view
pv.SetActiveView(renderView1)
# create a new 'Glyph'
# sphere
glyph1 = pv.Glyph(Input=tableToPoints1, GlyphType='Sphere')
glyph1.Scalars = ['POINTS', 'Q']
glyph1.ScaleMode = 'scalar'
glyph1.ScaleFactor = scaleFactor
glyph1.GlyphMode = 'All Points'
#glyph1.GlyphType.ThetaResolution = 8
#glyph1.GlyphType.PhiResolution = 8
# get color transfer function/color map for args.colourColumn
cLUT = pv.GetColorTransferFunction(args.colourColumn)
nc = vtk.vtkNamedColors()
rgb = [0. for i in range(3)]
if args.colourColumn == 'Q':
cLUT.ApplyPreset("Plasma (matplotlib)")
else:
nc.GetColorRGB("Magenta", rgb)
class Pipeline:
grid = coprocessor.CreateProducer(datadescription, 'input')
# Normalise radius - simplifies creating glyphs
normalise = pvs.Calculator(Input=grid)
normalise.CoordinateResults = 1
normalise.Function = 'coords/%i' % sphere_radius
# Visualise velocity field using arrows
glyph = pvs.Glyph(Input=normalise, GlyphType='Arrow')
glyph.Scalars = ['POINTS', 'None']
glyph.Vectors = ['CELLS', 'u']
glyph.ScaleFactor = 0.2
glyph.GlyphTransform = 'Transform2'
glyph.GlyphType.TipResolution = 12
glyph.GlyphType.TipRadius = 0.05
glyph.GlyphType.ShaftRadius = 0.015
# Create a new 'Render View'
renderView = pvs.CreateView('RenderView')
renderView.ViewSize = [1500, 768]
renderView.AxesGrid = 'GridAxes3DActor'
renderView.StereoType = 0
renderView.CameraPosition = [-5, -2, 4]
renderView.CameraViewUp = [0.5, 0.3, 0.8]
renderView.CameraParallelScale = 1.7
renderView.Background = [0.32, 0.34, 0.43]
# Register the view with coprocessor
# and provide it with information such as the filename to use,
# how frequently to write the images, etc.
coprocessor.RegisterView(renderView,
filename='velocity_field_%t.png',
freq=1,
fittoscreen=1,
magnification=1,
width=800,
height=800,
cinema={})
renderView.ViewTime = datadescription.GetTime()
# Create colour transfer function for velocity field
uLUT = pvs.GetColorTransferFunction('u')
uLUT.RGBPoints = [
1.7, 0.23, 0.30, 0.75, 20.9, 0.87, 0.87, 0.87, 40.0, 0.71,
0.016, 0.15
]
uLUT.ScalarRangeInitialized = 1.0
# Show velocity field magnitude
velocitymagDisplay = pvs.Show(normalise, renderView)
velocitymagDisplay.Representation = 'Surface'
velocitymagDisplay.ColorArrayName = ['CELLS', 'u']
velocitymagDisplay.LookupTable = uLUT
# Show colour legend
uLUTColorBar = pvs.GetScalarBar(uLUT, renderView)
uLUTColorBar.Title = 'u'
uLUTColorBar.ComponentTitle = 'Magnitude'
velocitymagDisplay.SetScalarBarVisibility(renderView, True)
# Show velocity field glyphs
glyphDisplay = pvs.Show(glyph, renderView)
glyphDisplay.Representation = 'Surface'
glyphDisplay.ColorArrayName = [None, '']
def batchVis(c1File,particleFile,step,saveAs):
"""Renders a bijel top down view in paraview and saves a screenshot."""
import paraview.simple as pv
# visualize a vtk file
c1 = pv.LegacyVTKReader(FileNames=c1File)
p = pv.LegacyVTKReader(FileNames=particleFile)
renderView1 = pv.GetActiveViewOrCreate('RenderView')
renderView1.ViewSize = [1298, 860]
renderView1.Background = [1.0, 1.0, 1.0]
renderView1.InteractionMode = '2D'
pDisplay = pv.Show(p, renderView1)
c1Display = pv.Show(c1, renderView1)
# create particle glyphs
glyph = pv.Glyph(Input=p,GlyphType="Sphere")
glyph.ScaleFactor = 1.0
glyph.GlyphMode = 'All Points'
glyph.GlyphType.Radius = 1.0
glyph.GlyphType.ThetaResolution = 20
glyph.GlyphType.PhiResolution = 20
glyph.Scalars = ['POINTS','radius']
glyph.Vectors = ['POINTS','None']
glyph.ScaleMode = 'scalar'
# show data in view
glyphDisplay = pv.Show(glyph, renderView1)
pv.ColorBy(glyphDisplay, None)
pv.SetActiveSource(c1)
pv.ColorBy(c1Display, ('POINTS', 'c1'))
c1Display.RescaleTransferFunctionToDataRange(True)
c1Display.SetRepresentationType('Volume')
# make box outline
# box = pv.Box()
# box.XLength = 128.0
# box.YLength = 128.0
# box.ZLength = 64.0
# box.Center = [64.0, 64.0, 32.0]
# boxDisplay = pv.Show(box, renderView1)
# boxDisplay.SetRepresentationType('Outline')
# boxDisplay.AmbientColor = [0.0, 0.0, 0.0]
# set coloring of c1
c1LUT = pv.GetColorTransferFunction('c1')
c1LUT.RGBPoints = [0.006000000052154064, 0.231373, 0.298039, 0.752941, 0.5120000033639371, 0.865003, 0.865003, 0.865003, 1.0180000066757202, 0.705882, 0.0156863, 0.14902]
c1LUT.ColorSpace = 'Diverging'
c1LUT.BelowRangeColor = [0.0, 0.0, 0.0]
c1LUT.AboveRangeColor = [1.0, 1.0, 1.0]
c1LUT.NanColor = [1.0, 1.0, 0.0]
c1LUT.Discretize = 1
c1LUT.NumberOfTableValues = 256
c1LUT.ScalarRangeInitialized = 1.0
c1LUT.AllowDuplicateScalars = 1
c1PWF = pv.GetOpacityTransferFunction('c1')
c1PWF.Points = [0.0, 0.05, 0.5, 0.0, 0.3, 0.05, 0.5, 0.0, 0.4, 0.5, 0.5, 0.0, 0.6, 0.5, 0.5, 0.0, 0.7, 0.05, 0.5, 0.0, 1., 0.05, 0.5, 0.0]
# annotate time step in rendering
# text = pv.Text
# text.Text = 'Step '+str(step)
# textDisplay = pv.Show(text,renderView1)
# textDisplay.Color = [0.0, 0.0, 0.0]
# textDisplay.WindowLocation = 'UpperCenter'
# reset view to fit data
renderView1.ResetCamera()
# pv.Render()
# save screen shot
viewLayout1 = pv.GetLayout()
print(saveAs)
pv.SaveScreenshot(saveAs, layout=viewLayout1, magnification=1, quality=100)
# clean up
# pv.Delete(box)
pv.Delete(glyph)
pv.Delete(p)
pv.Delete(c1)
del c1
del p
del glyph
class Pipeline:
# Create data source "input" (provides simulation fields)
simData = coprocessor.CreateProducer(datadescription, "input")
# Write VTK output if requested
if writeVtkOutput:
fullWriter = pvs.XMLHierarchicalBoxDataWriter(
Input=simData, DataMode="Appended", CompressorType="ZLib")
# Set freq=1 to ensure that output is written whenever the pipeline runs
coprocessor.RegisterWriter(fullWriter,
filename='bg_out_%t.vth',
freq=1)
# Create a new render view to generate images
renderView = pvs.CreateView('RenderView')
renderView.ViewSize = [1500, 768]
renderView.InteractionMode = '2D'
renderView.AxesGrid = 'GridAxes3DActor'
renderView.CenterOfRotation = [2.8, 1.7, 0.0]
renderView.StereoType = 0
renderView.CameraPosition = [2.8, 1.7, 10000.0]
renderView.CameraFocalPoint = [2.8, 1.7, 0.0]
renderView.CameraParallelScale = 3.386
renderView.Background = [0.32, 0.34, 0.43]
renderView.ViewTime = datadescription.GetTime()
# Show simulation time with 1 digit after decimal point
annotateTime = pvs.AnnotateTime()
annotateTime.Format = 'time: %.1f'
timeDisplay = pvs.Show(annotateTime, renderView)
# Combine uu and vv components into velocity vector field
calculatorVelField = pvs.Calculator(Input=simData)
calculatorVelField.AttributeType = 'Cell Data'
calculatorVelField.ResultArrayName = 'velocity'
calculatorVelField.Function = 'uu*iHat+vv*jHat'
# Compute velocity field magnitudes
calculatorVelMag = pvs.Calculator(Input=calculatorVelField)
calculatorVelMag.AttributeType = 'Cell Data'
calculatorVelMag.ResultArrayName = 'mag'
calculatorVelMag.Function = 'mag(velocity)'
# Remove cells with vanishing velocity magnitude
velMagThreshold = pvs.Threshold(calculatorVelMag)
velMagThreshold.Scalars = ['CELLS', 'mag']
velMagThreshold.ThresholdRange = [1.0e-6, 1.0e30]
# Visualise remaining velocity vector field using arrows with fixed length
# and skipping cells to avoid crowding
glyphs = pvs.Glyph(Input=velMagThreshold, GlyphType='Arrow')
glyphs.Vectors = ['CELLS', 'velocity']
glyphs.ScaleFactor = 0.2
glyphs.GlyphMode = 'Every Nth Point'
glyphs.Stride = 100
glyphs.GlyphTransform = 'Transform2'
# Register the view with coprocessor and provide it with information such as
# the filename to use. Set freq=1 to ensure that images are rendered whenever
# the pipeline runs
coprocessor.RegisterView(renderView,
filename='bg_out_%t.png',
freq=1,
fittoscreen=0,
magnification=1,
width=1500,
height=768,
cinema={})
# Create colour transfer function for field
LUT = pvs.GetColorTransferFunction('hh')
LUT.RGBPoints = [
9.355e-05, 0.231, 0.298, 0.753, 0.0674, 0.865, 0.865, 0.865,
0.135, 0.706, 0.0157, 0.149
]
LUT.ScalarRangeInitialized = 1.0
# Render data field and colour by field value using lookup table
fieldDisplay = pvs.Show(simData, renderView)
fieldDisplay.Representation = 'Surface'
fieldDisplay.ColorArrayName = ['CELLS', 'hh']
fieldDisplay.LookupTable = LUT
# Add velocity field visualisation
velfieldDisplay = pvs.Show(glyphs, renderView)
def render_frames(
scene,
frames_dir=None,
frame_window=None,
render_missing_frames=False,
save_state_to_file=None,
no_render=False,
show_preview=False,
show_progress=False,
job_id=None,
):
# Validate scene
if scene["View"]["ViewSize"][0] % 16 != 0:
logger.warning(
"The view width should be a multiple of 16 to be compatible with"
" QuickTime.")
if scene["View"]["ViewSize"][1] % 2 != 0:
logger.warning(
"The view height should be even to be compatible with QuickTime.")
render_start_time = time.time()
# Setup layout
layout = pv.CreateLayout("Layout")
# Setup view
if "Background" in scene["View"]:
bg_config = scene["View"]["Background"]
del scene["View"]["Background"]
if isinstance(bg_config, list):
if isinstance(bg_config[0], list):
assert len(bg_config) == 2, (
"When 'Background' is a list of colors, it must have 2"
" entries.")
bg_config = dict(
BackgroundColorMode="Gradient",
Background=parse_as.color(bg_config[0]),
Background2=parse_as.color(bg_config[1]),
)
else:
bg_config = dict(
BackgroundColorMode="Single Color",
Background=parse_as.color(bg_config),
)
bg_config["UseColorPaletteForBackground"] = 0
scene["View"].update(bg_config)
bg_config = None
else:
bg_config = None
view = pv.CreateRenderView(**scene["View"])
pv.AssignViewToLayout(view=view, layout=layout, hint=0)
# Set spherical background texture
if bg_config is not None:
bg_config["BackgroundColorMode"] = "Texture"
skybox_datasource = bg_config["Datasource"]
del bg_config["Datasource"]
background_texture = pvserver.rendering.ImageTexture(
FileName=parse_as.path(scene["Datasources"][skybox_datasource]))
background_sphere = pv.Sphere(Radius=bg_config["Radius"],
ThetaResolution=100,
PhiResolution=100)
background_texture_map = pv.TextureMaptoSphere(Input=background_sphere)
pv.Show(
background_texture_map,
view,
Texture=background_texture,
BackfaceRepresentation="Cull Frontface",
Ambient=1.0,
)
# Load the waveform data file
waveform_h5file, waveform_subfile = parse_as.file_and_subfile(
scene["Datasources"]["Waveform"])
waveform_data = WaveformDataReader(FileName=waveform_h5file,
Subfile=waveform_subfile)
pv.UpdatePipeline()
# Generate volume data from the waveform. Also sets the available time range.
# TODO: Pull KeepEveryNthTimestep out of datasource
waveform_to_volume_configs = scene["WaveformToVolume"]
if isinstance(waveform_to_volume_configs, dict):
waveform_to_volume_configs = [{
"Object": waveform_to_volume_configs,
}]
if "VolumeRepresentation" in scene:
waveform_to_volume_configs[0]["VolumeRepresentation"] = scene[
"VolumeRepresentation"]
waveform_to_volume_objects = []
for waveform_to_volume_config in waveform_to_volume_configs:
volume_data = WaveformToVolume(
WaveformData=waveform_data,
SwshCacheDirectory=parse_as.path(
scene["Datasources"]["SwshCache"]),
**waveform_to_volume_config["Object"],
)
if "Modes" in waveform_to_volume_config["Object"]:
volume_data.Modes = waveform_to_volume_config["Object"]["Modes"]
if "Polarizations" in waveform_to_volume_config["Object"]:
volume_data.Polarizations = waveform_to_volume_config["Object"][
"Polarizations"]
waveform_to_volume_objects.append(volume_data)
# Compute timing and frames information
time_range_in_M = (
volume_data.TimestepValues[0],
volume_data.TimestepValues[-1],
)
logger.debug(f"Full available data time range: {time_range_in_M} (in M)")
if "FreezeTime" in scene["Animation"]:
frozen_time = scene["Animation"]["FreezeTime"]
logger.info(f"Freezing time at {frozen_time}.")
view.ViewTime = frozen_time
animation = None
else:
if "Crop" in scene["Animation"]:
time_range_in_M = scene["Animation"]["Crop"]
logger.debug(f"Cropping time range to {time_range_in_M} (in M).")
animation_speed = scene["Animation"]["Speed"]
frame_rate = scene["Animation"]["FrameRate"]
num_frames = animate.num_frames(
max_animation_length=time_range_in_M[1] - time_range_in_M[0],
animation_speed=animation_speed,
frame_rate=frame_rate,
)
animation_length_in_seconds = num_frames / frame_rate
animation_length_in_M = animation_length_in_seconds * animation_speed
time_per_frame_in_M = animation_length_in_M / num_frames
logger.info(f"Rendering {animation_length_in_seconds:.2f}s movie with"
f" {num_frames} frames ({frame_rate} FPS or"
f" {animation_speed:.2e} M/s or"
f" {time_per_frame_in_M:.2e} M/frame)...")
if frame_window is not None:
animation_window_num_frames = frame_window[1] - frame_window[0]
animation_window_time_range = (
time_range_in_M[0] + frame_window[0] * time_per_frame_in_M,
time_range_in_M[0] +
(frame_window[1] - 1) * time_per_frame_in_M,
)
logger.info(
f"Restricting rendering to {animation_window_num_frames} frames"
f" (numbers {frame_window[0]} to {frame_window[1] - 1}).")
else:
animation_window_num_frames = num_frames
animation_window_time_range = time_range_in_M
frame_window = (0, num_frames)
# Setup animation so that sources can retrieve the `UPDATE_TIME_STEP`
animation = pv.GetAnimationScene()
# animation.UpdateAnimationUsingDataTimeSteps()
# Since the data can be evaluated at arbitrary times we define the time steps
# here by setting the number of frames within the full range
animation.PlayMode = "Sequence"
animation.StartTime = animation_window_time_range[0]
animation.EndTime = animation_window_time_range[1]
animation.NumberOfFrames = animation_window_num_frames
logger.debug(
f"Animating from scene time {animation.StartTime} to"
f" {animation.EndTime} in {animation.NumberOfFrames} frames.")
def scene_time_from_real(real_time):
return (real_time / animation_length_in_seconds *
animation_length_in_M)
# For some reason the keyframe time for animations is expected to be within
# (0, 1) so we need to transform back and forth from this "normalized" time
def scene_time_from_normalized(normalized_time):
return animation.StartTime + normalized_time * (
animation.EndTime - animation.StartTime)
def normalized_time_from_scene(scene_time):
return (scene_time - animation.StartTime) / (animation.EndTime -
animation.StartTime)
# Setup progress measuring already here so volume data computing for
# initial frame is measured
if show_progress and not no_render:
logging.getLogger().handlers = [TqdmLoggingHandler()]
animation_window_frame_range = tqdm.trange(
animation_window_num_frames,
desc="Rendering",
unit="frame",
miniters=1,
position=job_id,
)
else:
animation_window_frame_range = range(animation_window_num_frames)
# Set the initial time step
animation.GoToFirst()
# Display the volume data. This will trigger computing the volume data at the
# current time step.
for volume_data, waveform_to_volume_config in zip(
waveform_to_volume_objects, waveform_to_volume_configs):
vol_repr = (waveform_to_volume_config["VolumeRepresentation"]
if "VolumeRepresentation" in waveform_to_volume_config else
{})
volume_color_by = config_color.extract_color_by(vol_repr)
if (vol_repr["VolumeRenderingMode"] == "GPU Based"
and len(volume_color_by) > 2):
logger.warning(
"The 'GPU Based' volume renderer doesn't support multiple"
" components.")
volume = pv.Show(volume_data, view, **vol_repr)
pv.ColorBy(volume, value=volume_color_by)
if "Slices" in scene:
for slice_config in scene["Slices"]:
slice_obj_config = slice_config.get("Object", {})
slice = pv.Slice(Input=volume_data)
slice.SliceType = "Plane"
slice.SliceOffsetValues = [0.0]
slice.SliceType.Origin = slice_obj_config.get(
"Origin", [0.0, 0.0, -0.3])
slice.SliceType.Normal = slice_obj_config.get(
"Normal", [0.0, 0.0, 1.0])
slice_rep = pv.Show(slice, view,
**slice_config.get("Representation", {}))
pv.ColorBy(slice_rep, value=volume_color_by)
# Display the time
if "TimeAnnotation" in scene:
time_annotation = pv.AnnotateTimeFilter(volume_data,
**scene["TimeAnnotation"])
pv.Show(time_annotation, view, **scene["TimeAnnotationRepresentation"])
# Add spheres
if "Spheres" in scene:
for sphere_config in scene["Spheres"]:
sphere = pv.Sphere(**sphere_config["Object"])
pv.Show(sphere, view, **sphere_config["Representation"])
# Add trajectories and objects that follow them
if "Trajectories" in scene:
for trajectory_config in scene["Trajectories"]:
trajectory_name = trajectory_config["Name"]
radial_scale = (trajectory_config["RadialScale"]
if "RadialScale" in trajectory_config else 1.0)
# Load the trajectory data
traj_data_reader = TrajectoryDataReader(
RadialScale=radial_scale,
**scene["Datasources"]["Trajectories"][trajectory_name],
)
# Make sure the data is loaded so we can retrieve timesteps.
# TODO: This should be fixed in `TrajectoryDataReader` by
# communicating time range info down the pipeline, but we had issues
# with that (see also `WaveformDataReader`).
traj_data_reader.UpdatePipeline()
if "Objects" in trajectory_config:
with animate.restore_animation_state(animation):
follow_traj = FollowTrajectory(
TrajectoryData=traj_data_reader)
for traj_obj_config in trajectory_config["Objects"]:
for traj_obj_key in traj_obj_config:
if traj_obj_key in [
"Representation",
"Visibility",
"TimeShift",
"Glyph",
]:
continue
traj_obj_type = getattr(pv, traj_obj_key)
traj_obj_glyph = traj_obj_type(
**traj_obj_config[traj_obj_key])
follow_traj.UpdatePipeline()
traj_obj = pv.Glyph(Input=follow_traj,
GlyphType=traj_obj_glyph)
# Can't set this in the constructor for some reason
traj_obj.ScaleFactor = 1.0
for glyph_property in (traj_obj_config["Glyph"] if "Glyph"
in traj_obj_config else []):
setattr(
traj_obj,
glyph_property,
traj_obj_config["Glyph"][glyph_property],
)
traj_obj.UpdatePipeline()
if "TimeShift" in traj_obj_config:
traj_obj = animate.apply_time_shift(
traj_obj, traj_obj_config["TimeShift"])
pv.Show(traj_obj, view,
**traj_obj_config["Representation"])
if "Visibility" in traj_obj_config:
animate.apply_visibility(
traj_obj,
traj_obj_config["Visibility"],
normalized_time_from_scene,
scene_time_from_real,
)
if "Tail" in trajectory_config:
with animate.restore_animation_state(animation):
traj_tail = TrajectoryTail(TrajectoryData=traj_data_reader)
if "TimeShift" in trajectory_config:
traj_tail = animate.apply_time_shift(
traj_tail, trajectory_config["TimeShift"])
tail_config = trajectory_config["Tail"]
traj_color_by = config_color.extract_color_by(tail_config)
if "Visibility" in tail_config:
tail_visibility_config = tail_config["Visibility"]
del tail_config["Visibility"]
else:
tail_visibility_config = None
tail_rep = pv.Show(traj_tail, view, **tail_config)
pv.ColorBy(tail_rep, value=traj_color_by)
if tail_visibility_config is not None:
animate.apply_visibility(
traj_tail,
tail_visibility_config,
normalized_time_from_scene=normalized_time_from_scene,
scene_time_from_real=scene_time_from_real,
)
if "Move" in trajectory_config:
move_config = trajectory_config["Move"]
logger.debug(
f"Animating '{move_config['guiName']}' along trajectory.")
with h5py.File(trajectory_file, "r") as traj_data_file:
trajectory_data = np.array(
traj_data_file[trajectory_subfile])
if radial_scale != 1.0:
trajectory_data[:, 1:] *= radial_scale
logger.debug(f"Trajectory data shape: {trajectory_data.shape}")
animate.follow_path(
gui_name=move_config["guiName"],
trajectory_data=trajectory_data,
num_keyframes=move_config["NumKeyframes"],
scene_time_range=time_range_in_M,
normalized_time_from_scene=normalized_time_from_scene,
)
# Add non-spherical horizon shapes (instead of spherical objects following
# trajectories)
if "Horizons" in scene:
for horizon_config in scene["Horizons"]:
with animate.restore_animation_state(animation):
horizon = pv.PVDReader(FileName=scene["Datasources"]
["Horizons"][horizon_config["Name"]])
if horizon_config.get("InterpolateTime", False):
horizon = pv.TemporalInterpolator(
Input=horizon, DiscreteTimeStepInterval=0)
if "TimeShift" in horizon_config:
horizon = animate.apply_time_shift(horizon,
horizon_config["TimeShift"],
animation)
# Try to make horizon surfaces smooth. At low angular resoluton
# they still show artifacts, so perhaps more can be done.
horizon = pv.ExtractSurface(Input=horizon)
horizon = pv.GenerateSurfaceNormals(Input=horizon)
horizon_rep_config = horizon_config.get("Representation", {})
if "Representation" not in horizon_rep_config:
horizon_rep_config["Representation"] = "Surface"
if "AmbientColor" not in horizon_rep_config:
horizon_rep_config["AmbientColor"] = [0.0, 0.0, 0.0]
if "DiffuseColor" not in horizon_rep_config:
horizon_rep_config["DiffuseColor"] = [0.0, 0.0, 0.0]
if "Specular" not in horizon_rep_config:
horizon_rep_config["Specular"] = 0.2
if "SpecularPower" not in horizon_rep_config:
horizon_rep_config["SpecularPower"] = 10
if "SpecularColor" not in horizon_rep_config:
horizon_rep_config["SpecularColor"] = [1.0, 1.0, 1.0]
if "ColorBy" in horizon_rep_config:
horizon_color_by = config_color.extract_color_by(
horizon_rep_config)
else:
horizon_color_by = None
horizon_rep = pv.Show(horizon, view, **horizon_rep_config)
if horizon_color_by is not None:
pv.ColorBy(horizon_rep, value=horizon_color_by)
# Animate visibility
if "Visibility" in horizon_config:
animate.apply_visibility(
horizon,
horizon_config["Visibility"],
normalized_time_from_scene=normalized_time_from_scene,
scene_time_from_real=scene_time_from_real,
)
if "Contours" in horizon_config:
for contour_config in horizon_config["Contours"]:
contour = pv.Contour(Input=horizon,
**contour_config["Object"])
contour_rep = pv.Show(contour, view,
**contour_config["Representation"])
pv.ColorBy(contour_rep, None)
if "Visibility" in horizon_config:
animate.apply_visibility(
contour,
horizon_config["Visibility"],
normalized_time_from_scene=
normalized_time_from_scene,
scene_time_from_real=scene_time_from_real,
)
# Configure transfer functions
if "TransferFunctions" in scene:
for tf_config in scene["TransferFunctions"]:
colored_field = tf_config["Field"]
transfer_fctn = pv.GetColorTransferFunction(colored_field)
opacity_fctn = pv.GetOpacityTransferFunction(colored_field)
tf.configure_transfer_function(transfer_fctn, opacity_fctn,
tf_config["TransferFunction"])
# Save state file before configuring camera keyframes.
# TODO: Make camera keyframes work with statefile
if save_state_to_file is not None:
pv.SaveState(save_state_to_file + ".pvsm")
# Camera shots
# TODO: Make this work with freezing time while the camera is swinging
if animation is None:
for i, shot in enumerate(scene["CameraShots"]):
if (i == len(scene["CameraShots"]) - 1 or
(shot["Time"] if "Time" in shot else 0.0) >= view.ViewTime):
camera_motion.apply(shot)
break
else:
camera_motion.apply_swings(
scene["CameraShots"],
scene_time_range=time_range_in_M,
scene_time_from_real=scene_time_from_real,
normalized_time_from_scene=normalized_time_from_scene,
)
# Report time
if animation is not None:
report_time_cue = pv.PythonAnimationCue()
report_time_cue.Script = """
def start_cue(self): pass
def tick(self):
import paraview.simple as pv
import logging
logger = logging.getLogger('Animation')
scene_time = pv.GetActiveView().ViewTime
logger.info(f"Scene time: {scene_time}")
def end_cue(self): pass
"""
animation.Cues.append(report_time_cue)
if show_preview and animation is not None:
animation.PlayMode = "Real Time"
animation.Duration = 10
animation.Play()
animation.PlayMode = "Sequence"
if no_render:
logger.info("No rendering requested. Total time:"
f" {time.time() - render_start_time:.2f}s")
return
if frames_dir is None:
raise RuntimeError("Trying to render but `frames_dir` is not set.")
if os.path.exists(frames_dir):
logger.warning(
f"Output directory '{frames_dir}' exists, files may be overwritten."
)
else:
os.makedirs(frames_dir)
if animation is None:
pv.Render()
pv.SaveScreenshot(os.path.join(frames_dir, "frame.png"))
else:
# Iterate over frames manually to support filling in missing frames.
# If `pv.SaveAnimation` would support that, here's how it could be
# invoked:
# pv.SaveAnimation(
# os.path.join(frames_dir, 'frame.png'),
# view,
# animation,
# FrameWindow=frame_window,
# SuffixFormat='.%06d')
# Note that `FrameWindow` appears to be buggy, so we set up the
# `animation` according to the `frame_window` above so the frame files
# are numberd correctly.
for animation_window_frame_i in animation_window_frame_range:
frame_i = frame_window[0] + animation_window_frame_i
frame_file = os.path.join(frames_dir, f"frame.{frame_i:06d}.png")
if render_missing_frames and os.path.exists(frame_file):
continue
logger.debug(f"Rendering frame {frame_i}...")
animation.AnimationTime = (
animation.StartTime +
time_per_frame_in_M * animation_window_frame_i)
pv.Render()
pv.SaveScreenshot(frame_file)
logger.info(f"Rendered frame {frame_i}.")
logger.info(
f"Rendering done. Total time: {time.time() - render_start_time:.2f}s")
def pvd_to_mp4(sim_dir,
path_to_movies,
movie_name='movie',
representation='Surface',
num_regions=0):
###############################
# Validate directory and data #
###############################
if not (os.path.isdir(sim_dir)):
raise Exception('pvd_to_mp4: Invalid simulation directory')
if not (os.path.isdir(path_to_movies)):
raise Exception('pvd_to_mp4: Invalid movie directory')
if representation not in ['Surface', 'Points']:
raise Exception(
'pvd_to_mp4: Representation must be either Surface or Points')
if num_regions not in [0, 9]:
raise Exception(
'pvd_to_mp4: Currently there is only support for 9 node regions')
# sim_id = os.path.basename(os.path.normpath(sim_dir))
possible_data_directories = []
for directory in os.listdir(sim_dir):
if directory.startswith('results_from_time'):
possible_data_directories.append(os.path.join(sim_dir, directory))
if len(possible_data_directories) == 0:
raise Exception(
'pvd_to_mp4: Could not find a "results_from_time_X" directory')
# The last directory alphabetically will be the one after any initial relaxation simulation
data_directory = sorted(possible_data_directories)[-1]
# Get the location of the pvd file
pvd_file = os.path.join(data_directory, 'results.pvd')
if not (os.path.isfile(pvd_file)):
raise Exception('pvd_to_mp4: Could not find a pvd data file')
if os.path.getsize(pvd_file) < 1024:
raise Exception(
'pvd_to_mp4: pvd file exists but is < 1kb. Presumably simulation failed to finish as expected.'
)
full_movie_path = os.path.join(path_to_movies,
movie_name + '_' + representation + '.mp4')
##################################
# Set up scene with box and data #
##################################
# Get active view. This is the ParaView default view - blue background with cross hairs and orientation axes
render_view = pv.GetActiveViewOrCreate('RenderView')
# Change parameters to be how we want them for output
render_view.ViewSize = [1600, 900] # Size of output (pixels)
render_view.CenterAxesVisibility = 0 # Remove cross hairs
render_view.OrientationAxesVisibility = 0 # Remove orientation axes
render_view.Background = [0.5, 0.5,
0.5] # Set background colour to 50% grey
# Create a unit square (a 3D Box with ZLength set to zero)
unit_square = pv.Box()
unit_square.ZLength = 0.0
unit_square.YLength = 9.0 / 16.0
unit_square.Center = [0.5, 0.5, 0.0]
# Show the box in the current render view, and colour it black
unit_square_display = pv.Show(unit_square, render_view)
unit_square_display.DiffuseColor = [0.0, 0.0, 0.0]
# Read the relevant pvd file from the Chaste output
results_pvd = pv.PVDReader(FileName=pvd_file)
# Show the data in the current render view as a surface
results_pvd_display = pv.Show(results_pvd, render_view)
results_pvd_display.Representation = representation
if representation == 'Points' and num_regions == 9:
pv.ColorBy(results_pvd_display, ('POINTS', 'Node Regions'))
node_regions_lut = pv.GetColorTransferFunction('NodeRegions')
# Each four digits are: data value, r, g, b (colour)
node_regions_lut.RGBPoints = [
0.0,
1.00,
0.00,
0.00, # LEFT_APICAL_REGION, red
1.0,
1.00,
0.00,
0.00, # RIGHT_APICAL_REGION, red
2.0,
1.00,
0.00,
1.00, # LEFT_PERIAPICAL_REGION, purple
3.0,
1.00,
0.00,
1.00, # RIGHT_PERIAPICAL_REGION, purple
4.0,
0.00,
0.00,
1.00, # LEFT_LATERAL_REGION, blue
5.0,
0.00,
0.00,
1.00, # RIGHT_LATERAL_REGION, blue
6.0,
1.00,
1.00,
1.00, # LEFT_BASAL_REGION, white
7.0,
1.00,
1.00,
1.00, # RIGHT_BASAL_REGION, white
8.0,
1.00,
1.00,
1.00
] # LAMINA_REGION, white
cell_regions_lut = pv.GetColorTransferFunction('CellRegions')
cell_regions_lut.RGBPoints = [
-1.0,
0.0,
0.00,
0.00, # basal lamina, black
0.0,
0.00,
0.00,
1.00, # left region, blue
1.0,
1.00,
1.00,
1.00, # centre_region, white
2.0,
1.00,
0.00,
0.00
] # right_region, red
# Glyphs for cell region
cell_glyphs = pv.Glyph(Input=results_pvd, GlyphType='2D Glyph')
cell_glyphs.Scalars = ['CELLS', 'Cell Regions']
cell_glyphs.ScaleFactor = 0.01
cell_glyphs.GlyphMode = 'All Points'
cell_glyphs.GlyphType.GlyphType = 'Diamond'
cell_glyphs.GlyphType.Filled = 1
cell_glyphs.GlyphTransform.Scale = [1.0, 2.0, 1.0]
cell_glyphs_display = pv.Show(cell_glyphs, render_view)
cell_glyphs_display.Opacity = 0.5
# Glyphs for node region
node_glyphs = pv.Glyph(Input=results_pvd, GlyphType='2D Glyph')
node_glyphs.Scalars = ['POINTS', 'Node Regions']
node_glyphs.ScaleFactor = 0.002
node_glyphs.GlyphMode = 'All Points'
node_glyphs.GlyphType.GlyphType = 'Circle'
node_glyphs.GlyphType.Filled = 1
pv.Show(node_glyphs, render_view)
###################################
# Put the camera where we want it #
###################################
# This happens after all calls to Show, as Show may do some automatic camera re-setting
render_view.InteractionMode = '2D'
render_view.CameraPosition = [0.5, 0.5, 1.0]
render_view.CameraFocalPoint = [0.5, 0.5, 0.0]
# This parameter sets the 'zoom' and needs fine-tuning by the aspect ratio
render_view.CameraParallelScale = 0.5 * 9.0 / 16.0
##################################
# Set up and write the animation #
##################################
# Get an animation scene, which has parameters we need to change before output
animation_scene = pv.GetAnimationScene()
# Get a list of time step values from the pvd file. Typically this will look like [t_0, t1, t2, ..., t_end]
time_step_info = results_pvd.TimestepValues
num_time_steps = len(time_step_info)
# Set the animation parameters
animation_scene.NumberOfFrames = num_time_steps # If num frames != num time steps, some interpolation will be used
animation_scene.StartTime = time_step_info[
0] # Usually t_0, the first entry in time_step_info
animation_scene.EndTime = time_step_info[
-1] # Usually t_end, the final entry in time_step_info
# Write the animation as a series of uncompressed png files, with no magnification
pv.WriteAnimation(sim_dir + 'results_' + representation + '.png',
Magnification=1,
Compression=False)
# Raise exception if the png files are not generated as expected
if not (os.path.isfile(sim_dir + 'results_' + representation +
'.0000.png')):
raise Exception('pvd_to_mp4: png sequence not exported as expected')
#######################################
# Convert from png to mp4 and tidy up #
#######################################
# Ubuntu 14.04 (trusty) came bundled with avconv instead of ffmpeg, but they're nearly the same software
# so we don't have to change the command other than the name of the video converter to use
if platform.linux_distribution()[2] == 'trusty':
video_converter = 'avconv'
else:
video_converter = 'ffmpeg'
# Set how long you want the video to be (in seconds), and set the frame rate accordingly
video_duration = 15.0
frame_rate = str(num_time_steps / video_duration)
# Send the system command to run avconv/ffmpeg. Parameters:
# -v 0 Suppress console output so as not to clutter the terminal
# -r frame_rate Set the frame rate calculated above
# -f image2 Set the convert format (image sequence to video)
# -i dir/results.%04d.png Input expected as dir/results.####.png, the output from WriteAnimation above
# -c:v h264 Video codec to use is h264
# -crf 0 Set video quality: 0 best, 51 worst (https://trac.ffmpeg.org/wiki/Encode/H.264)
# -y dir/movie.mp4 Output directory and name
os.system(video_converter + ' -v 0 -r ' + frame_rate + ' -f image2 -i ' +
sim_dir + 'results_' + representation +
'.%04d.png -c:v h264 -crf 0 -y ' + full_movie_path)
# Raise exception if the mp4 file is not generated as expected
if not (os.path.isfile(full_movie_path)):
raise Exception('pvd_to_mp4: mp4 not generated as expected')
# Raise exception if the mp4 file file is created but is smaller than 1kb - ffmpeg sometimes
# generates an empty file even if an error occurs
if os.path.getsize(full_movie_path) < 1024:
raise Exception('pvd_to_mp4: mp4 not generated as expected')
# Clean up the png files created by WriteAnimation
os.system('rm ' + sim_dir + '*.png')
class Pipeline:
grid = coprocessor.CreateProducer(datadescription, 'input')
# Simulation domain outline
outline = pvs.Outline(Input=grid)
# Horizontal slice at the bottom
slice = pvs.Slice(Input=grid)
slice.SliceType = 'Plane'
slice.SliceOffsetValues = [0.0]
slice.SliceType.Origin = [0.0, 0.0, 101.94]
slice.SliceType.Normal = [0.0, 0.0, 1.0]
slice.Triangulatetheslice = False
# Glyphs for representing velocity field
glyph = pvs.Glyph(Input=grid, GlyphType='Arrow')
glyph.Vectors = ['CELLS', 'u']
glyph.ScaleMode = 'vector'
glyph.ScaleFactor = 0.01
glyph.GlyphMode = 'Every Nth Point'
glyph.Stride = 200
# Create a new render view
renderView = pvs.CreateView('RenderView')
renderView.ViewSize = [800, 400]
renderView.InteractionMode = '2D'
renderView.AxesGrid = 'GridAxes3DActor'
renderView.CenterOfRotation = [0.18, 0.0, 102]
renderView.StereoType = 0
renderView.CameraPosition = [-3.4, -6.8, 107]
renderView.CameraFocalPoint = [-0.27, -0.41, 102]
renderView.CameraViewUp = [0.057, 0.49, 0.87]
renderView.CameraParallelScale = 1.0
renderView.Background = [0.32, 0.34, 0.43]
# Register the view with coprocessor
coprocessor.RegisterView(renderView,
filename='image_%t.png',
freq=1,
fittoscreen=0,
magnification=1,
width=800,
height=400,
cinema={})
renderView.ViewTime = datadescription.GetTime()
# Get color transfer function/color map for field rho
rhoLUT = pvs.GetColorTransferFunction('rho')
rhoLUT.RGBPoints = [
1.17, 0.231, 0.298, 0.752, 1.33, 0.865, 0.865, 0.865, 1.49,
0.706, 0.0157, 0.149
]
rhoLUT.ScalarRangeInitialized = 1.0
# Show slice
sliceDisplay = pvs.Show(slice, renderView)
sliceDisplay.Representation = 'Surface With Edges'
sliceDisplay.ColorArrayName = ['CELLS', 'rho']
sliceDisplay.LookupTable = rhoLUT
sliceDisplay.ScaleFactor = 0.628
sliceDisplay.SelectScaleArray = 'None'
sliceDisplay.GlyphType = 'Arrow'
sliceDisplay.GlyphTableIndexArray = 'None'
sliceDisplay.DataAxesGrid = 'GridAxesRepresentation'
sliceDisplay.PolarAxes = 'PolarAxesRepresentation'
sliceDisplay.GaussianRadius = 0.314
sliceDisplay.SetScaleArray = [None, '']
sliceDisplay.ScaleTransferFunction = 'PiecewiseFunction'
sliceDisplay.OpacityArray = [None, '']
sliceDisplay.OpacityTransferFunction = 'PiecewiseFunction'
# Show color legend
sliceDisplay.SetScalarBarVisibility(renderView, True)
# Show glyph
glyphDisplay = pvs.Show(glyph, renderView)
# Show outline
outlineDisplay = pvs.Show(outline, renderView)
# Get color legend/bar for rhoLUT in view renderView
rhoLUTColorBar = pvs.GetScalarBar(rhoLUT, renderView)
rhoLUTColorBar.WindowLocation = 'LowerRightCorner'
rhoLUTColorBar.Title = 'rho'
rhoLUTColorBar.ComponentTitle = ''
def __init__(self, filepath='.'):
self.filepath = filepath
self.time = 0.0
self.surfaceColorMode = 0 # Local range
self.subSurfaceColorMode = 0 # Local range
# Surface View
self.viewSurface = simple.CreateRenderView(True)
self.viewSurface.EnableRenderOnInteraction = 0
self.viewSurface.OrientationAxesVisibility = 0
self.viewSurface.Background = [0.9, 0.9, 0.9]
self.viewSurface.InteractionMode = '2D'
self.viewSurface.CameraParallelProjection = 1
# SubSurface view
self.viewSubSurface = simple.CreateRenderView(True)
self.viewSubSurface.EnableRenderOnInteraction = 0
self.viewSubSurface.OrientationAxesVisibility = 0
self.viewSubSurface.Background = [0.9, 0.9, 0.9]
self.viewSubSurface.InteractionMode = '2D'
self.viewSubSurface.CameraParallelProjection = 1
# Read dataset
self.reader = simple.ParFlowReader(FileName=filepath, DeflectTerrain=1)
self.readerSurface = simple.OutputPort(self.reader, 1)
self.readerSubSurface = simple.OutputPort(self.reader, 0)
# Water table depth
self.waterTableDepth = simple.WaterTableDepth(
Subsurface=self.readerSubSurface, Surface=self.readerSurface)
self.cellCenter = simple.CellCenters(Input=self.waterTableDepth)
self.wtdVectCalc = simple.Calculator(Input=self.cellCenter)
self.wtdVectCalc.ResultArrayName = 'wtdVect'
self.wtdVectCalc.Function = 'iHat + jHat + kHat * water table depth'
self.waterTableDepthGlyph = simple.Glyph(
Input=self.wtdVectCalc,
GlyphType='Cylinder',
ScaleFactor=500,
GlyphMode='All Points',
GlyphTransform='Transform2',
ScaleArray=['POINTS', 'wtdVect'],
VectorScaleMode='Scale by Components',
)
self.waterTableDepthGlyph.GlyphTransform.Rotate = [90.0, 0.0, 0.0]
self.waterTableDepthGlyph.GlyphType.Resolution = 12
self.waterTableDepthGlyph.GlyphType.Radius = 0.25
self.waterTableRepresentation = simple.Show(self.waterTableDepthGlyph,
self.viewSubSurface)
self.waterTableRepresentation.Visibility = 0
# Water balance
self.waterBalance = simple.WaterBalance(
Subsurface=self.readerSubSurface, Surface=self.readerSurface)
self.waterBalanceOverTime = simple.PlotGlobalVariablesOverTime(
Input=self.waterBalance)
# Surface representation
self.surfaceRepresentation = simple.Show(self.readerSurface,
self.viewSurface)
self.surfaceRepresentation.SetScalarBarVisibility(
self.viewSurface, True)
# SubSurface representation + slice extract
self.reader.UpdatePipeline()
self.voi = self.reader.GetClientSideObject().GetOutputDataObject(
0).GetExtent()
self.extractSubset = simple.ExtractSubset(Input=self.readerSubSurface)
self.subSurfaceRepresentation = simple.Show(self.extractSubset,
self.viewSubSurface)
self.subSurfaceRepresentation.Representation = 'Surface'
# Reset camera + center of rotation
simple.Render(self.viewSurface)
simple.ResetCamera(self.viewSurface)
self.viewSurface.CenterOfRotation = self.viewSurface.CameraFocalPoint
simple.Render(self.viewSubSurface)
simple.ResetCamera(self.viewSubSurface)
self.viewSubSurface.CenterOfRotation = self.viewSubSurface.CameraFocalPoint
# Time management
self.animationScene = simple.GetAnimationScene()
self.animationScene.UpdateAnimationUsingDataTimeSteps()
