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John Biddiscombe CSCS Swiss National Supercomputing Centre 03/06/2008 Working with Time in ParaView.

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Presentation on theme: "John Biddiscombe CSCS Swiss National Supercomputing Centre 03/06/2008 Working with Time in ParaView."— Presentation transcript:

1 John Biddiscombe CSCS Swiss National Supercomputing Centre 03/06/2008 Working with Time in ParaView

2 Contents Data Formats for time-dependent data Overview of GUI controls Animation Controls Connection between GUI and internals Comparative Visualization mode Temporal Pipeline Overview Time Dependent Filters (vtkTemporalXXX) Manipulating Time in Filters (C++ code)… Gotchas & Bugs Future Plans

3 Data Import

4 Formats Supported Exodus (used by several US research facilities) vtkPVDReader (vtk XML Collection) filename.pvd + Filename-00.vtu/vti/vtp etc vtkFileSeriesReader vtkXML * Reader PolyData, UnstructuredGrid, StructuredGrid, ImageData, RectilinearGrid, Multiblock, Heirarchical etc. Legacy VTK files with 001, 002, 003 filenames Ensight (case files, ASCII/Binary data) OpenFOAM, SpyPlot, Phasta, STL, MFIX (untested by me) Xdmf (extensible data model format) XML light data with geometry/time information inside Hdf5 – heavy – big data containing scalars/fields (CSCS) custom readers include netCDF, H5Part (from CSCS web site)

5 Vtk (XML based) file format VTK Collection - Easy to create by hand if necessary A General purpose holder for vtk XML files of all types vtu=unstructured, vtp=polydata, vtr=rectilinear, vti=imagedata Each individual file can be binary/text, compressed or not The VTK Collection is in fact a generic holder for MultiBlock composite datasets which can store time information too. The vtkXMLReader family is responsible for loading this kind of data. User can use vtkXML_xxx_Writer to write N time steps of any kind of data and then add a little XML meta data to describe it. Caveat : pvd time collections are not working well in parallel (NxM split of blocks)

6 .pvd versus File List.pvd collection is a true Time compatible holder for data Time steps can be specified with real time values Dont need to be contiguous or equally spaced FileSeriesReader : Selecting *.vtu/p/i/etc simple but efficient way of loading time series One step per file Cant specify true time values vtkFileSeriesReader is clever Load one – get one Load *.ext, get time series No C++ changes required to reader

7 vtkFileSeriesReader : make reader time aware <FileSeriesReaderProxy name="XMLUnstructuredGridReader" class="vtkFileSeriesReader" label="XML Unstructured Grid reader" file_name_method="SetFileName"> <Documentation short_help=blah blah long_help=ditto"> The XML Unstructured Grid reader reads the VTK XML unstructured grid data file format. The standard extension is.vtu. This reader also supports file series.

8 FileSeriesReader (slide 2) Put details of your existing reader in ExposedProperties <Proxy name="Reader" proxygroup="internal_sources" proxyname="XMLUnstructuredGridReaderCore">

9 FileSeriesReader (slide 3) <StringVectorProperty name="FileName" clean_command="RemoveAllFileNames" command="AddFileName" animateable="0" number_of_elements="0" repeat_command="1"> The list of files to be read by the reader. If more than 1 file is specified, the reader will switch to file series mode in which it will pretend that it can support time and provide 1 file per time step.

10 FileSeriesReader (slide 4) The part which makes it time aware <DoubleVectorProperty name="TimestepValues" information_only="1"> Available timestep values.

11 Old and New Time in ParaView In PV2.x Time was generally animated by changing the TimeStep value of a reader (or filter sometimes). In PV3.x Time is an information variable/object passed down the pipeline which makes it possible for filters to modify time before passing it to their source. For this reason, the GUI sets the time inside the Rendering/Mapping code and not via a TimeStep variable. Some older (custom) readers may still have a TimeStep variable, but this is being phased out and its use is not encouraged – unless you are trying to do something a bit special (see later slides).

12 Reader XML <DoubleVectorProperty name="TimestepValues" information_only="1"> Available timestep values. For any reader If you omit this (this is all you need in the XML) Then you wont see the time information. It connects the TIME_STEPS key to the GUI

13 The old method (xml for reference) <IntVectorProperty name="TimeStep" command="SetTimeStep" number_of_elements="1" default_values="0" animateable="0" information_property="TimestepValues"> Set the current timestep. And for convenience we usually provided a GetTimestepValues(vector)

14 C++ Reader : RequestInformation Scan files/data structures and build a list/vector/array of times Set TIME_STEPS for discrete time data (most readers really) outInfo->Set( vtkStreamingDemandDrivenPipeline::TIME_STEPS(), &this->TimeStepValues[0], this->TimeStepValues.size()); Set TIME_RANGE if continuous, but can also be set for discrete double timeRange[2]; timeRange[0] = this->TimeStepValues.front(); timeRange[1] = this->TimeStepValues.back(); outInfo->Set( vtkStreamingDemandDrivenPipeline::TIME_RANGE(), timeRange, 2);

15 C++ Reader : RequestData Find the correct time step (index into array of step values) if ( outInfo->Has(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEPS())) { // usually only one actual step requested double requestedTimeValue = outInfo- >Get(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEPS())[0]; this->ActualTimeStep = vtkstd::find_if( this->TimeStepValues.begin(), this->TimeStepValues.end(), vtkstd::bind2nd( WithinTolerance( ), requestedTimeValue )) - this->TimeStepValues.begin(); }

16 C++ Reader : RequestData Time stamp the output DataObject using DATA_TIME_STEPS output->GetInformation()->Set(vtkDataObject::DATA_TIME_STEPS(), &requestedTimeValue, 1); Nothing bad happens if you dont – But filters which use the time information wont get what they need. vtkTemporalPathLineFilter builds lists of data times for each frame and joins the dots. You can read the UPDATE_TIME_STEPS key, but it might not be the same, and is strictly only present during RequestUpdateExtent

17 GUI Controls Animating with Time

18 Animation GUI Controls Time value displayed in toolbar – Time step mode – user can change step Sequence mode – user can change time freely VCR style toolbar has play controls (play, step forward/back, jump to start/end) Data with Time support shows the timesteps in the information tab. (Lacks ability to click on timestep and jump to it) Animation control has settings for time stepping and keyframes Abort button to stop movie generation not obvious

19 Time Modes in Animation Inspector Snap to TimeSteps When you click play the animation will begin at whatever time step you are on and continue until it either reaches the end (or is stopped manually). When stopped the animation will continue from where it left off if restarted. Each frame played represents a single time step of the input data There is no need to set any keyframes or specify any particular property to animate. The Track selection is used to select or create keyframes

20 Time Modes in Animation Inspector Snap to TimeSteps : * * * Warning * * * When dataset 1 is loaded it may have time values 0, 1, 2, 3, …..N When dataset 2 is loaded it may have time values 0.5, 1.5, 2.5, 3.5, …..M Playing an animation in Snap To TimeSteps mode will traverse ALL KNOWN Timesteps – which means 0, 0.5, 1, 1.5, 2, 2.5 …..max(M,N) This can cause unexpected results! Future time support should allow you to Snap to active pipeline steps so that only the times exported for a particular dataset/filter will be traversed. (In development). Fix : Use Sequence mode and lock the start and end times to prevent changes

21 Time Modes in Animation Inspector Sequence Mode The start and end times correspond to the max and min values of time in the data you loaded. If you manually change the start/end times you can Lock the new times – this prevents them being reset to the default start/end times if new data is loaded. Animation will now ignore the Time steps present in the data and use interval=(end/start)/(numFrames-1) This is frequently NOT WHAT YOU WANT

22 Time Modes in Animation Inspector Worked example interval=(end/start)/(numFrames-1) 60.001424 - 50.001424 = 10 Num Frames = 10 We should get our original time steps back (1s per step) In fact we get 10/(numFrames-1) = 1.11111111s/frame Need to use 11 frames to get 0,1,2,3,4,5,6,7,8,9,10 Note : In the some versions of PV3 selecting time values which are not exactly the same as those present will produce no update. It should snap to the nearest time step, but does not. See SnapToTimeSteps for a fix.

23 Time Modes in Animation Inspector Real Time Animates using the Wall time Not always useful for the majority of filters/data sources that we use Useful to animate as fast as we can if data was stored with time representing a real clock value and we wish to play back data in real time. In this mode not all times may be displayed. Some will be skipped or some may be on screen for ages. Could also be very handy for integrating generators of data (eg sensor equipment) into the gui and displaying the real time update of the sensor (no examples of this yet though)

24 Comparative visualization

25 Comparative View Inspector Allows MxN array of views on the same data Allows a variable to be changed along the X axis. Wrong - limitation used to be that time must be between 0.0-1.0 for the view to operate Solution : TemporalShiftScale with 1/N scale factor (or use Normalize flag set if present in CVS)

26 Same Data at multiple T Uses Time steps of selected object Avoid mismatched time display in same window. FilmStrip uses X Comparative : X&Y Works, but patience required

27 Comparative viz Summary Much easier than Creating multiple windows manually Setting up Shift/Scale Instantiating Pipelines Setting view/display properties Can also use other plot styles.

28 Time Dependent Algorithms/Filters Pipeline Introduction

29 The pipeline is demand driven with data flowing downstream Information flowing up and down stream In PV3 Time is part of the Information flow. Data source filter(s) Display/GUI Renderer Data Information UPDATE_TIME_STEPS

30 How does it work How does the pipeline actually fit together All filters are connected together by Executives which receive information from downstream (and upstream) and decide Are the data inputs valid Are the data outputs valid Is everything else valid Has anything changed since I last updated In PV3 Time is passed as information and the executives can LOOP portions of the pipeline over multiple time steps This means that filters can request multiple time steps This enables us to implement Time Dependent Algorithms

31 Pipeline Looping vtkTemporalDataSet When the pipeline is looped to generate multiple time steps, the executive generates a dataset collection The collection is passed to the temporal algorithm The algorithm can request any number of time steps But usually 2 (linear interpolation) In order to make looping work, some information keys are used internally

32 Information Keys During Updates, the pipeline makes 4 request passes… DataObject, Information, UpdateExtent, Data Keys exported by time aware sources TIME_RANGE (continuous), TIME_STEPS (discrete) Time aware reader will declare N steps 0.0, 0.1, 0.2…..etc Keys used during requests UPDATE_TIME_STEPS (Filter says I want these) Interpolator says I need times 0.1 and 0.2 for example Keys set during execution DATA_TIME_STEPS (Source says I made these) Data generator says I generated times 0.1 and 0.2 Keys used internally by executives REQUIRES_TIME_DOWNSTREAM (looping will be needed) CONTINE_EXECUTING (multiple passes inside algorithm)

33 Time Dependent Algorithms/Filters Interpolation

34 (Linear) Interpolation vtkTemporalInterpolator Linearly interpolates between 2 time steps When Time T.5 is requested it requests times T and T+1 2 Modes of Operation Continuous Discrete Continuous Mode DiscreteTimeStepInterval=0.0 Filter generates no TIME_STEPS on output – just a TIME_RANGE GUI can request any time between min/max Discrete Mode DiscreteTimeStepInterval>0 Filter generates (max-min)/DiscreteTimeStepInterval steps GUI sees discrete data with new TIME_STEPS values

35 (Linear) Interpolation Continuous mode Input data (left) has N discrete time steps Output data (right) has no time steps It does report a TIME_RANGE So the GUI knows that any time between min/max can be requested

36 Interpolation – Continuous mode Data Courtesy : David Graham, Plymouth UK.

37 (Linear) Interpolation Discrete mode Example : DiscreteTimeStepInterval=0.01 New time steps are generated and the output data looks like it has 10x as many time steps. Note that no interpolation of the data has been performed yet, only when something is actually rendered/requested will the interpolation take place.

38 Interpolation – Discrete mode

39 (Linear) Interpolation What can be interpolated Any Dataset which does not change topology between time steps Point positions are interpolated Connectivity (cells are copied) Point Data is interpolated Cell Data is interpolated ImageData/PolyData/Rectilinear/Unstructured All can be interpolated if cell connectivity and number of cells remains the same MultiBlock/MultiGroup/Heirarchical/AMR If the tree structure remains the same between time steps and the individual leaves satisfy above conditions Other interpolation methods could be added

40 Discrete mode Given an input with N time steps, but a few are accidentally missing (lost of never generated) Set DiscreteTimeStep Interval to the original time step size (say 0.1 or 0.01 etc) Data saved every Nth frame to save IO time. Output now seems to be exactly the same as the input – except that the steps that were missing from the input are recreated using interpolation when requested on the output Animate using Snap To TimeSteps mode Animation will look like intended original Fixing Problems with the interpolator

41 Problem Fixing Example (Interpolation) Before Missing data, low sampling Problems for particle tracer After Lovely

42 Temporal DataSet Cache

43 Interpolation – Use a cache If animation from 0->t is performed using a TemporalInterpolator, the interpolator will request 2 time steps each time it updates Interpolating at 0.1 spacing between 2 steps causes Step 0 + Step 1 : Output Step 0.1 Step 0 + Step 1 : Output Step 0.2 Each step N times! Step 0 + Step 1 : Output Step 0.3 Use a TemporalDataSetCache to store 2 timesteps and prevent this repeated re-execution of the pipeline Data source (time aware) TemporalDataSet Cache Display/GUI Renderer Interpolator

44 Branching Time – Use a cache Its not just the filter delivering the data at T, but the whole upstream pipeline that is protected… Consider the case where a pipeline branches and different T values are requested. The cache prevents updates from one section propagating too far upstream and forcing the other branch to be re-executed needlessly. Simple filter(s) (no special time requirements) Temporal DataSetCache TemporalFilter (requires multiple time steps, e.g.. Particle tracer) TemporalShiftScale (modifies time values) Display/GUI Renderer Data source (time aware)

45 Branching Time – Caution in the GUI When different values to T are visible/manipulated Only display the leaf nodes of the pipeline Rendering intermediate portions can trigger unwanted/confusing updates Simple filter(s) (no special time requirements) Temporal DataSetCache TemporalFilter (requires multiple time steps, e.g.. Particle tracer) TemporalShiftScale (modifies time values) Display/GUI Renderer Data source (time aware) UPDATE_TIME_STEPS Display/GUI Renderer UPDATE_TIME_STEPS

46 Multiple Inputs Related Cautionary Note #1

47 Time dependent filters with multiple inputs Trigger updates on all inputs Particle Tracer is one example Multiple Inputs Temporal DataSetCache Particle Tracer Display/GUI Renderer Data source (time aware) UPDATE_TIME_STEPS Slice – Seed Points (for example) Avoid this. Save Seeds if possible

48 Temporal Snap to TimeSteps

49 SnapToTimeSteps Example Data source (time aware) TemporalDataSet Cache Display/GUI Renderer Interpolator Snap To TimeStep Time To Text

50 Time Display Side note Source : Time Source Takes time from the UPDATE_TIME_STEPS Actually it takes it directly from the view which is responsible for setting the key on the filter/output Filter->Temporal->Annotate Time Takes its time from DATA_TIME_STEPS Which is the actual time step output from the filter The two might not always be the same (snap to timestep for example)

51 Time Shifting

52 Temporal Shift Scale Changes time between the input and output of a filter Can be used to compare the same data at 2 different values of T (though the comparative viz view is easier to use in some ways) Invaluable for combining different datasets with different T values See example pipeline below T out = PreShift + T in *Scale + PostShift NB. +ve PostShift produces +ve delay of output time seems the wrong way around but time 0 is now time N, so it takes N seconds to get to it

53 Temporal Shift Scale Pre-Shift = -50.0014 Scale = 1/10 Post-Shift = 3 Before 50-0014 - 60.0014 After 3.0 – 4.0

54 Developer Tip : Hiding bad time data In RequestData if (outInfo->Has(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEPS())) { double requestedTimeValue = outInfo-> Get(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEPS())[0]; if (requestedTimeValue TimeStepValues.front() || requestedTimeValue>this->TimeStepValues.back()) { this->TimeOutOfRange = 1; } output->GetInformation()->Set(vtkDataObject::DATA_TIME_STEPS(), &requestedTimeValue, 1); } … if (this->TimeOutOfRange && this->MaskOutOfTimeRangeOutput) { // don't do anything, just return success return 1; }

55 Developer Tip : Normalize Time In RequestInformation if (this->NormalizeToUnitTime && this->TimeStepValues.size()>0) { double t1 = this->TimeStepValues.front(); double t2 = this->TimeStepValues.back(); double t3 = (t2-t1)>0 ? (1.0/(t2-t1)) : 1.0; for (unsigned int i=0; i TimeStepValues.size(); i++) { double t = this->TimeStepValues[i]; this->TimeStepValues[i] = t3*(t-t1); } Then everything comes out {0,1} Feature might be available in ShiftScale. Regional Variations

56 Comparative Vis (using Time shift) Time shift + Interpolation + Trails 3 time dependent features in 1 go

57 Temporal Shift Scale Periodic Mode : Turns N time steps spanning t time units into N*T steps spanning T*t units Periodic End Correction If simulation steps are {0,1,2…N-1} and {N-1} is identical to {0} Periodic end correction OFF = {0,1,2…N-1,1,2,3..N-1} Otherwise {0,1,2…N-1,1,2,3..N-1} causes duplicated step If simulation steps are {0,1,2…N-1} and {N-1} is different from {0} Periodic end correction On Otherwise {0,1,2…N-1,0,2,3..N-1} causes duplicated step

58 Periodic example 2 Separate Datasets one 40 steps one 80 steps Duration 1s (approx) Need 5+hours 80*3600*5 = 1.44E6 Tried 10,000 Periods in ParaView (1 day?) Need a better model!

59 Particle Tracer Pipeline (one nasty example) DataSet 1 Temporal Cache Particle Tracer Interpolate PathLines DataSet 2Shift Scale Temporal Cache Seeds 1 GUI Seeds 2

60 Periodic Time + Resampling + Time Shift

61 Side Note : XML for Temporal Support <SourceProxy name="TemporalSnapToTimeStep" class="vtkTemporalSnapToTimeStep" label="Temporal Snap-to-Time-Step"> Will change in future : no way of saying : DataType : PolyData : Temporal_required

62 Particle Tracer TemporalStreamTracer

63 Particle Tracing All Inputs must have same vector field Multiple Multiblock Inputs supported (Temporal Required) Meshes can be dynamic Parallel operation If input dataset has N time steps Particle tracer will generate N-1 output steps Output step 0 time value corresponds to input step {0,1} time Nothing can be generated until 1 time period has passed Seed points are supplied as separate inputs Use SetTimeStep to combat odd time input combinations

64 Request Update Extent for (int i=0; i<numInputs; i++) { vtkInformation *inInfo = inputVector[0]->GetInformationObject(i); // our output timestep T is timestep T+1 in the source // so output inputTimeSteps[T], inputTimeSteps[T+1] inInfo-> Set(vtkStreamingDemandDrivenPipeline::UPDATE_TIME_STEPS(), &this->InputTimeValues[this->ActualTimeStep], 2); vtkDebugMacro(<< "requested 2 time values : " InputTimeValues[this->ActualTimeStep] << " " InputTimeValues[this->ActualTimeStep+1]); }

65 Particle Tracing (setup example) Source (seedpoints) LineSource 100 points Time Step resolution Leave as 1 – this can be used to scale time if the input time was not stored correctly (e.g. it goes 0…N but should be 0.1 0.2 0.3 etc) Time Step (output index) Set to zero initially – this will request steps, (0,1) from the input and the time actually corresponds to T=1 (but it will be the 0 th step on the output)

66 Particle Tracing Force re-injection every 1 or 2 time steps Particles will be injected at the seed points every N steps Input vectors Usually a velocity field, but could be another Initial Integration step Used by Runge-Kutta integration to make incremental velocity field approximations Can be smaller but 0.25 usually OK Static Seeds - Static Mesh Force optimizations GEOMETRY_NOT_MODIFIED (work in progress)

67 Particle Tracing Ignore pipeline time This is very important – the particle tracer generates less output steps than the input (-1) and so we cannot (yet) use the default animation controls due to bug mentioned earlier. NB. This works now, but the comment is useful We therefore instruct the particle tracer to ignore pipeline time and instead animate the Timestep property from 0 to N-2 (if the input has N steps, the Particle tracer has N-1 steps output, so we go from 0 to N-2 to get the correct number) Particle filename (not shown) An option to store particles to disk will be included at a future date.

68 Side Note : Ignore Pipeline Time if (this->IgnorePipelineTime) { if (this->TimeStep OutputTimeValues.size()) { requestedTimeValue = this->OutputTimeValues[this->TimeStep]; } else { requestedTimeValue = this->OutputTimeValues.back(); } this->ActualTimeStep = this->TimeStep; vtkDebugMacro(<< "SetTimeStep : requestedTimeValue << requestedTimeValue << " ActualTimeStep " ActualTimeStep); } else { the usual stuff to get requested time }

69 Particle Tracing To generate animation of particles Use Sequence Mode Animation Use N-1 Frames (because there will be N-1 steps generated – this data had 51 steps on the input indexed as 0-50), so we use 50 frames for output Create a Keyframe on ParticleTracer TimeStep. Set Keyframe index 0 Time to start time = 0.0 here Value to TimeStep 0 Set Keyframe index 1 Time to end time = 7.99 in this example Value to 49 (last index = 51-2) Animation can now be played/saved as movie

70 Francis Turbine

71 PathLineFilter

72 Pathline Filter Connects to output of Particle tracer Can be used on any dataset with points (not just particles) Now supports selection of subset But needs to be updated to use vtkSelection type Uses Ids from selection dataset to choose points for line construction Is not strictly a vtkTemporalXXX filter because it does not loop time Listents to DATE_TIME_STEPS on input and builds list from that See other slides for example of usage

73 Plotting Data over Time

74 Plotting of data over Time Iterative operation Extract one or more variables at a point or region over time GUI not driving the iteration process Filter manually sets CONTINUE_EXECUTING Exodus Data supports FAST_PATH_FOR_TEMPORAL_DATA And uses FAST_PATH_OBJECT_TYPE, (POINT, CELL, EDGE, FACE) FAST_PATH_ID_TYPE, (INDEX, GLOBAL) FAST_PATH_OBJECT_ID, (vtkIdType) vtkSelections ? For future use?

75 03/06/2008 Temporal Statistics

76 Computes Mean Min Max Standard Deviation More can be added Can take time!

77 03/06/2008 Selection+Time

78 Selection over time The same procedure can be used to query a particle over all available time Extract Selection over time filter builds a spreadsheet of values for the selected IDs over all time steps NB: Cant set a sub region of time using the animation controls yet, but this feature will be coming Selection tutorial should cover possible types Cell/Point/Global IDs can be used here 03/06/2008

79 Plot Selection over time 03/06/2008 Which Point to display Which field(s)

80 Plot Selection over Time

81 03/06/2008 Animations with Non simple time

82 How to animate a slice on a time-dependent dataset Problem When I try to animate, time changes as well as the slice I cant set time start/end to constants and then animate slice alone ParaView hangs because of zero increment Trying to fool it with tiny increments is not safe. Show animation viewer and double click time track Now animate the slice or other property using sequence mode And keyframes to suit.

83 Demo 1 How to animate a slice, and then animate the data? Double click on these tracks

84 Setup a slice keyframe Create Slice offset keyframe Animate a slice 50 frames one way 50 frames back again Note that extents are +/- 1.5 = 3 Check values when adding keyframes

85 Change the Time track itself Double click Time track Time is variable It has its own keyframes Fix time from frames 1-50 Animate time from 50 to 50+60

86 Sequence mode coordination Make sure the Animation inspector has the same information as the animation viewer And….the keyframes When you add/remove them, or adjust the start/end time, they get rescaled Could do with a locking keyframe time option here The time here should be thought of as frames

87 Demo 2 Fixed, forward and reverse time in one animation Animation (frame) time View (data) time We need tracks per dataset – to combine different sources

88 Animate Camera from Python phi = range(0, 360) for i in phi: view.CameraPosition = [2400*math.cos(i*math.pi*2.0/360), 2400*math.sin(i*math.pi*2.0/360), 300] view.StillRender() imgfile = "/path/to/snapshot.%03d.png" % i view.WriteImage(imgfile, "vtkPNGWriter", 1) To be Continued Python versions of TimeAnimationCue, Scene, View Exercise for the reader (Utkarsh) : recreate fancy time animations in Python

89 Conclusion Few Time dependent filters in ParaView so far But … Already powerful tool for animations/analysis Animation improvements and time step handling will make it hard to beat in terms of features and flexibility

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