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()