Zindaiji 3 ver 1.071


Zindaiji 3 is a visualization application for particle simulation data. Zindaiji is named after a location name near NAOJ mitaka campus.
The aim of Zindaiji 3 is

Currently, I have working for the base functions for the second aim ... ; )

Well, you want to visualize volume data?

Features of Zindaiji

In Zindaiji 3, comparing to the prevous version, I have improved (or be trying to improve) following features.

Zindaiji 3 uses OpenGL and its Shader Language. PCs with fast graphic board are recommended. Old PCs with OpenGL version 1.5 or before would not work. OpenGL ver 3.0 or later is recommended.

Many functions does not work on Intel CPU Graphics. As for 3D Graphics, AMD APU looks better choice, at least for now.



2012/01/15 ver0.30
2012/01/19 ver0.32
2012/01/31 ver0.35
2012/02/13 ver0.37
2012/02/27 ver0.40
2012/03/17 ver0.42
2012/04/04 ver0.45
2012/04/22 ver0.47
2012/04/24 ver0.48
2012/05/15 ver0.50
2012/05/31 ver0.52
2012/06/25 ver0.54
2012/07/06 ver0.56
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2012/08/06 ver0.60
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2014/02/06 ver0.83
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2015/03/23 ver0.97
2015/04/06 ver0.975
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2015/06/08 ver0.985
2015/07/09 ver0.99
2015/08/24 ver0.995
2015/11/09 ver1.00
2015/12/28 ver1.01
2016/01/29 ver1.02
2016/02/29 ver1.03
2016/04/04 ver1.04
2016/05/09 ver1.05
2016/08/08 ver1.06
2016/10/31 ver1.07

2017/02/21 ver 1.071


version 1.071
I found .zip for 1.07 is broken. I replaced the file with 1.071(2017/02/21)

Zindaiji3MacOSX072.zip(ver0.74 and later is not yet)

Source File



Decompress the downloaded file and set the entire folder to any folder under your control. Since some configure files are saved at the folder with the executable files, please do not set them to a folder where you have limited permittions, such as system folder.
Zindaiji 3 does not touch the registry, so that you can uninstall by simply removing the folder.

Linux version requires installation of wxWidget-gtk, Lua and OpenEXR (2.0 or later). In ubuntu, these libraries can be installed via synaptic.

Currently, only 32 bit version exists for MacOS X. In Mac OS X version, you must execute ./Zindaiji3Mac.app/Contents/MacOS/Zindaiji3Mac in command line from terminal at the appropriate directory. (I'm just a new comer to Mac world, and I don't know how to make it executable by double clicking... It seems that wxWidgets 2.9 supports Mac OS X 64bit version. I must upgrade wxWidgets in near future...)

Since Zindaiji 3 is on the first stage of the developping, I expect many bugs are hidden in it. If you are kind enough, you can report them in my blog, though it is written in Japanese...


About comipilation from source codes.

for Linux (Ubuntu)

for Windows


1. Preview

2. Data Loading

Data Loader Dialog Loading HDF5 Decompess TOKI Compression

Loading PDC Loading .bphys Scripting for data making

3. Main Menu

Save Image Sequence Data Exporter Dialog Pov-Ray Rendering Configure

View and Camera Configure Light Source Editor

Color Curve Editor Texture Setting

Stereogram Configure Scene Config Preference Dialog

4. Visualization Parameters

Texture Setting Display Option Objects and Pseudo-Objects

5. Filter Panel

Boolean Filtering Periodic
Box Culling Information
Object Text Stick Grid Locus
Databox Copybox Fog BG Analytics

6. Camera Path

7. Timeline Editor

Key Frame Time Remap Marker Parent-Child relation Graph Editor

8. Expression

Editor Making Data Tables for Lua

9. Animation

10. PovRay Rendering

11. Tips for Handling Large Data

12. Known Problems and FAQ



The largest panel in default state is the preview panel, where the visualized images are shown. By default a grid, a camera, light sources, and a pivot (sky blue cross mark) are shown.

In Zindaiji, you can rotate the scene as you are rolling "trackball". Rotation is assigned to left button of the mouse by default. The center of the rotation is the pivot. Ctrl + left mouse button works as innertial gyration. Gyration would continue after you release the mouse.

Also, zooming is assigned to middle button and mouse wheel. For a mouse without middle button, Alt + left mouse button works as if it were middle mouse button.

Panning is assigned to Shift+Ctrl+left mouse button. Note that when the preview panel is panned, the center of the rotation (pivot) also moves.

Panning moves the location of the pivot.

Dragging an Item

You can select and/or move items (camera and lightsources) in Preview Panel.
In default, selection is attributed to Shift+right mouse button, and moving selected item is attributed to Shift+left mouse button.
In bottom-left corner, there are buttons for translate, rotate and scaling. Shortcut key 'T', 'R' and 'S' are assined respectively.

When an item is selected, guide arrows/rings are displayed. By directly dragging them with Shift+left mouse button, you can move it along x/y/z axis. In translation mode, you can move the item along the plane perpendicular to the view when dragging elsewhere. You can use short cut key "X", "Y", and "Z" to set the move mode along x/y/z axis.

Configuration of the mouse setting is in Preference Dialog.

You can transform items by keyboad input. For example, "tx0.5+enter" would move selected item 0.5 for x direction.


The pull-down at top-left corner is a selector for the point of view. "Free" view is default one, which you can navigate as described above. "Cam0" is a view connected to the camera path. When you change the frames for timeline, the point of view automatically follows the camera path.
Other views are along the line of axis.

These views can be selected by short cut keys 0(Free), 1, 3, 7, and ctrl-1, ctrl-3, ctrl-7.

Toggle of perspective and orthographic is 5. Fisheye and Panorama views are valid in "Free" mode.

When this check box is checked, pivot automatically follows the camera anchor.

MEMO Panel

Selecting MEMO for the point of view, a special panel for text input opens.
Use this text for memorandum of any sort. The text in this panel would be saved in project fils.

2. Data Loading

Open Data Loader Dialog from menu or Alt-Ctrl-O.

Basically, sequantial binary or ascii files can be read.
The format of file can be edited to some extent. in the dialog

As special formats, HDF5 file and Maya or Blender particle system cache file can be read.



Open or save a project file. The extention of the project file is .zjp or .zjp.gz.

To load particle data, this menu opens a Data Loader Dialog.

Save a image shown on the screen. When multiple panels are displayed, image on the top-left panel would be saved. To save image sequence, this menu opens a Save Image Sequence Dialog.

Snapshot image is simply captured from the panel, so that the image size is automatically given.
If you want to get images with arbitray size (upto 4096), save image using Save Image Sequence Dialog.

Also, you can copy snapshot image to clipboard.

Export data or other informations. Currently particle data exportion is implemented. With export, can convert data from Ascii format to Binary format, for faster loading in future use.
You can configure the format by Data Exporter Dialog.

Closes the scene.

Quit Zindaiji 3


Undo and Redo.

Copy and Paste. Keyframes in Timeline, or Filters can be handled.

Selection of keyframes in Timeline.

Change the current frame numerically. Also, You can set the current frame numerically by text controls at Timeline Editor.

Toggle Time Remap mode. Time Remap controls the time of data sequence as a parameter.

Release the memory used for particle data.


Filters do some manipulations to the data. You can apply multiple filters.
Detailed parameters of filters would be shown on Filter Panel.


You can export scene files for rendering with Pov-Ray. Though it take much longer time, Pov-Ray can make ray-traced photo realistic images. Note that all features in Zindaiji3 can be exported for Pov-Ray. Only objects with surface, like shperes or sticks, can be rendered.

Open a Dialog for Pov-Ray rendering configure.

Export scene file(s), or render these files using Pov-Ray.


Zindaiji can show multiple preview panels up to 4. This menu set the number of the preview panel.

Extra panel is a window with a single preview panel, which floats over the main window.
The panel can be maximized by "Alt+Enter". Thus, if the scene is not so heavy, you can play the scene with "SPACE" key in full screen mode.
If you do so, hiding data in main window would improve the performance.


Open a View And Camera Config Dialog. The dialog provides the way to configure the setting about view and camera path.

Open a Light Source Editor. In Zindaiji3, you can set up to 7 light sources.

Open a Color Curve Editor.

Open a Texture Setting.

Open a Stereogram Config Dialog.

Open a editor for periodic boundary. The setting is used in Data Loader, Copybox Filter and Periodic Filter.

Open a dialog that shows log message.

To configure the parameters such as total length of the scene, open a Scene Dialog.

Open a Preference Dialog. The dialog provides the way to edit the parameter such as mouse configure etc.

Lua Script

Configure external table files that can be refered from Lua script for expression. See this page for detail.



This panel gives settings for visualization parameter of each particle. Attrib0-3 corresponds to particles with TYPE0-3. Zindaiji can handle up to 4 types of particles.

Zindaiji draws particles as one of the following.

Billboad is a translucent square polygon looking at the camere direction, textured with a image like gas cloud. One can represent pseudo-continuous gas with many billboard particles. This method is especially good for visualization of SPH simulation.

Quality parameter determines the number of polygons in drawing a sphere. In billboard mode, objects look to camera position precisely in higher quality mode (slower). Use middle or better parameter in Fisheye rendering mode.

Simultaneously drawing sphere (object) and billbaord, you can add simple effect of glare or gaseous impression to objects.

Choose the modes for rendering objects. In AlphaBlending mode, a translucent particles (partially) hide the colors behind. This is good for a situation such that a gas cloud hide the light from the stars behind.

In Additive mode, a color of particles are just added to the canvas. This is good to show simple density distribution, or some light-emitting particles like stars.

Also, you can select a shader by the right hand side combobox. This function is valid only for displaying spheres.
"Original" uses is default openGL rendering pipeline.
Note that the location of highlight is calculated approximately, so that this mode is not good for fish-eye rendering.

In "Gouroud" mode, the color is calculated at each vertex of polygons, like original pipeline. The rule for coloring is somewhat different. Note that a "star" appears at the border of polygons.
In "Phong" mode, the color is calculated for each pixels, so that the seam between polygons disappers.

You can render a image like illustration with "Toon" shader.
You can set parameters for two toon shading methd, painting black surfaces near rectangular to the ray, or drawing outlines.

Later method is useful for 3D object composed of triangular polygons only with correct normal information.

"Scatter" shader is for billbaord. It enlighen or darken particles according to the relative direction of light and camera position.
The parameter just right of color button determine the effect of scattering. Minus value is forward scattering dominating, and plus value is backward scattering dominatiing.

"Alpha Clip" shader is for billbaord. Useful with pseudo-sphere or pseudo-object.
This shader discard pixels with alpha values less than some threshold. With this process, you can omit Z-sort in some cases. Without clipping, a nearby billboard drawed first may hide other particles even in transparent region. To prevent this artifact to occur without clipping, you must do Z-sort.

This method is valid only if texture has only fully transparent region and fully opaque region. You must use Z-sort for textures with semi-transparent region.

Clipping threshold can be set in Texture setting dialog.

"Normal map" shader represents direction of normal vector relative to the camera by color components.
Using normal map, an approximate lighting is implemented in pseudo sphere or pseudo object mode.

This parameter determine whether to use the radius parameter of each particls to display a sphere or billboard, or just use constant value (1). These values are multiplied by the value Radius Factor.

This parameter determine the opacity of the particles. Alpha 0 means entirely transparent object. If this parameter is set to constant, all particles has the same opacity determined by the Alpha Factor.

When this is set Depend on R (power -2), the opacity depends on particle radius square inversely. This is good to represent SPH simulations, because the density depends on R-3, while the length of the light path which travel through the particle depends on R, the absorotion of the light roughtly depends on R-2. In this case, Opacity is set to Max[Amax, (R/Rbase)2], where Rbase and Amax are set at Base/Max line.

To implement more complex functions for alpha value, use expression.

Setting a color of particles (billboard or point). An icon at the left side of the color button allows you to toggle color-curve and constant color mode. Cliking the button shows a color selection daialog, or Color Curve Editor, according to the mode.

Setting a color of particles (sphere). Three colors are ambient, diffuse, and specular colors respectively. Ambient color is a color which can be seen even at the opposite side of the light source. At the near side to the light source, diffuse and specular color are added to the ambient color according to the angles between the sphere, light source, and the camera.

Material color is also able to be edited by Color Curve Editor.

Texture Setting

To configure parameters about texture (for GL or PovRay) and shader, open texture setting dialog.

Particle attribute is linked to texture setting dialog by selecting particle attribute tab.

Draw Option

This panel provides the setting of parameters concerning the valance between the quality and speed of the display. Display particles in downsized number. In order to not largely change the impression of the image, sizes and opacity of the remained particles are automatically enhanced in according to the downsize number.

When drawing translucent objects, one must draw from far objects to the near objects sequentially, because the apparent color of nearer objects depend on the color of the distant objects. This option determine whether to do the z sort. If you do not use translucent, or draw objects in additive mode, you can omit the z-sort process.

When "random" is set, the order of displaying particles would be shuffled randomly.

When multiple types of particles exists, changing openGL status from one fitted to a particles to another one fitted to another particle takes large time.
When this option is set to "Use Attrib0 Only", Zindaiji displays all particles as Type0, and omit most of status changing process of OpenGL, making the drawaing considerably fast.

If there is no type information, you can classify particles with Expression.

Using shadow volume method, you can render with shadow for sphere particles.
Shadowing greatly improve the reality of the scene, while it considerably lengthen the rendering time.

The speed of the rendering depends on the number and total area of "shadow polygons".

Smaller values for length makes rendering faster, but it should not smaller than the scale of the target objects. By choosing "Show Shadow" mode, the shadow polygons are displayed explicitly.

You can turning on and off shadowing for individual light in Light Source Editor.

These parameters determine the quality and length of the shadow polygon.
In the terms of rendering speed, length value should be as small as possible.


You can display time and color curve infor mation as legends on preview panel. The position of them can be selected by pull down menu.
You can edit prefix strings and fontstle and size by Time and Time Style pull down menus.

The four check-boxies represents color curve from attribute 0 to attribute 3.

Alpha components are represented by background checker-board pattern. Simple color cuver without transparency information can be selectable. (Select "Hide Alpha" on pull down menu.)

You can show or hide tics on the color curve.

*Known problem* number on the tics may be trimmed. This should be remended in future.


Zindaiji3 uses 16bit FBO Objects for rendering, so that the image in the memory has more information than the image shown on the 8bit image on the monitor.
Level and gamma parameters determine how 16bit FBO images are mapped to the 8bit image.
Note that only 8bit image saving is supported in current Zindaiji 3.

You can also adjust the color of the image on the monitor with Hue and Saturation sliders.


You can see the particle information in Info tab. This is especially useful when checking whether your data is correctly loaded.


Parameters of filters are shown in Filter Panel. Multiple filters can be shown in the panel sequentially. By clicking the topmost button of each filter, you can collapse of expand each panel.
Several Filteres would be implemented and they would classified to Boolean, Objects, or some other categolies.

T, R, S in the panel represents Translate, Rotate, and Scale.


Boolean Filter screens out particles out of some defined regions. You can display cross-sectional view using these filters.

Filtering Filter screens out particles according to its index. It would be helpful for seeing some limited number of particles.

Periodic Filter wraps particles outside of the boundary box.

Box Culling Filter screens out particles out of sight. This makes rendering faster, but comes with some overhead

Information Filter shows index or ID of each particle.


Object Filter sets primitive objects to the scene.

Text Filter sets text objects to the scene.

Stick Filter shows sticks between particles. Use with data of molecuar dynamics, for example.

Grid Filter sets coordinate grid to the scene.

Locus Filter shows locus of selected particles.


Databox Filter moves, rotates, or scales the coordinate system of the data.
We expect this filter make it much easier to make a scene with a rotating data, instead of making camera circulate around the data.

Copybox Filter copies data along the arbitrary directions.
Suitable for visualize data with periodic boundary condition, like moleculars in crystal.

Fog Filter enables fog effects, which modify the color of particles according to their distance to the camera.
Currently, fog works only in phong and original OpenGL rendering.

BG Filter show a large sphere with background images, starfield and color curve. Analtics Filter shows a result of arbitrary analytical script.


View And Camera Config

View 0-3 corresponds to the 4 Prview Panels respectively. Translate and Rotate in View Settings represents the position and Euler rotation angle of the very point of view which is used to display the preview panel.
On the other hand, those in Camera Setting represent the position and angle of the camera at current frame in the camera path.

You can edit the camerapath with Timeline Editor. When you set the display mode as Cam0, the view automatically follows the camerapath.

The check box "Look Anchor" determines whether to force the camera to track the anchor point, which is initially set at the origin. This mode works well when you want to follow the some moving phenomena in the data, thoush you must handle the anchor by hands. (Import of parameters from some text file is a good idea. It would be implemented in future).

Editing Camerapath

Three "Se Key" buttons at the left-bottom corner have important function for camerapath editing.

"POS" sets a keyframe to the camerapath at the current position of the view.
"POS+ROT" sets keyframes on both position and rotation.

In many cases, what you have to do is just determine the best layout on preview window, and just press the buttons.
Perhaps, using "POS+ROT" button is better for editting a fly-through path, while using "POS" button is good for editting a path looking around the anchor with "Look Anchor" checking.

"Anc" sets a keyframe to the position of the anchor. In this case, the position of the "pivot" is copied to the position of the anchor.



The red line represents the current frame. You can control current frame and range of working area using the sliders.
With text control boxes at the left of main slider, you can set current frame numerically.
Green boxes represent frames that the data is already stored on the memory.


At the default, time dependency is set to be OFF, and the parameter is constant at all frames.
To toggle time dependency to be ON, click icon.
Time dependent paramers can be edited in the timeline editor. You can set keyframes in the timeline, and parameters are automatically interpolated between keyframes.

Insert and removal of keyframes can be done from right mouse button menu, or check box at the left side.

For multidimentional parameters, such as 3-dimentional positions, each components can be edited separately.
Toggle "Link" button to edit parameters individually.

Also, you can edit the key frame numerically by calling input dialog, by double clicking on the key, or from right mouse button menu.

Following types of interpolations are implemented.


In HERMITE(AUTO) mode, the parameters are interpolated using cubic function. The velocity at the key frame is automatically calculated using previous and next keyframes.
In HERMITE(SEMIAUTO) mode, you can set the "Ease" parameter, which is multiplied to the velocity at the key frame.
When this parameter is setted to 0, the parameter gradually approaches to the key value with decreasing velocity, which goes to 0 at the time of key frame.
This feature allows you to make motion with ease-in and ease-out effects.

Snapshot Button

You can take contemporal snapshot and show it on screen by buttons.

Useful for comparing snapshots with different visualizing parameters, or different frame.
This feature skips re-rendering and just shows image on memory. Thus, it can be useful in heavy scenes.

Shy Button

You can hide unnecessary paramters from TIMELINE EDITOR using shy button . When Kilroy mark on the each parameter and global Kilroy mark on the upper left are both ON (i.e. Mr. Kilroy is hiding), the marked parameters will be hidden.
If you want to reappear them, turn global Kilroy mark OFF.

Time Remap

If Time Remap mode is turned on by Edit(&E) menu, you can control the time as one of parameters.
*note* This is an experimental feature, and some bugs exist in preload and memory release algorithm.

Assuming you have data sequence with 100 files.
If you want the scene wait 50 frames at the initial and final state, set the length of the scene to 200, and set keyframes of time remap 0 at 0 frame, 0 at 50 frame, 99 at 149 frame and 99 at 199 frame.


You can set markers on the part that shows frame numbers. Select Add Marker from right-click menu.
The markers can be moved by mouse. It can show tag characters from A to D.

Parent-Child reration

From right-click menu in TL editor, you can select parent object.

Child object follows the movings of the parent object. Note that rotation is not implemented in the parent-child relationship

Graph Editor

You can see the increase or decrease of parameter graphically and handle key frame in Graph Editor. You can set the range of view numerically, or by mouse-wheel or by panning (Shift + Ctrl + left mouse button).


You can use expression in timeline parameter and some other features.

An equal icon is for validating expression, and a notebook and pencil icon button opens expression editor.

When expression is validated, Zindaiji 3 uses value returned from expression.
For example, using expression that returns x+t,y,z for camera position makes camera moving linearly.

As another sample, the right hand image shows how to classify particles with expression. Particles with index >= 512 is classified as type 1, while others are classified as type 0.

Zindaiji 3 uses Lua library for expression. See Documentations for Lua for details.

Data Making by Expression

The first aim of Zindaiji is to visualize external particle data. However yo u can construct data itself by using expression.
For example, you can construct something like rotating particle disk by a pure script.

To modify data after reading, you must configure "Post Process" in Data Loader Dialog.

When you construct data without reading external data files, push "Execute Script Only" button instead of "Open File Sequence".

Scripting for Data Modification or Construction


You can refer external table files from Lua script for expression.

To register external table files, open a dialog for Tables for Lua.


The buttons at the bottom control the current time.
You can easily understand meanings of the buttons.

By setting stepping parameter larger than 1, frames would be omit in animation.
With stepping 2, frame 0, 2, 4, 6, .... would be rendered.
This feature would work well when editing scenes with large data where loading and displaying takes seconds.

"Interval" represents interpolation steps between frames. For example, when setting interval 5 in a scene with 10 timestep data, total 50 pictures would be saved when exporting image sequences.
The data between each time step would be interpolated according to the rule that was configured in Data Loader Dialog.

"Prefetch" determines the ranges for data prefetch.
If you set the "prefetch" to be 3, data would be loaded in advence up to 3 frames ahead of the current frame.
The prefetch loading is done by another thread(s), so that the fall in the performance is small. With proper settings, prefetch can be much help for reduction of the waiting time in editing or rendering.

10. PovRay Rendering

You can export scene files for rendering with Pov-Ray. Though it take much longer time, Pov-Ray can make ray-traced photo realistic images. Note that all features in Zindaiji3 can be exported for Pov-Ray. Only objects with surface, like shperes or sticks, can be rendered.

See Dialog for PovRay rendering configure for details.


In handling large data, long rendering time makes manipulation troublesome.
When "Auto Abort" is ON, rendering would be aborted in 1 second, making manipulation much easier. (you can handle downsize slider now!)

Of course, check it off when trying final rendering.

Also, clicking red cross button forces to abort rendering.
(Exactly speaking, if mouse left button is downed on red cross button. This is because checking process for mouse clicking in OS is postponded during redering process...)

Windows Time Out

If an application does not response for 5 seconds, windows OS gray out the windows. This effect interferes rendering process. To avoid having the windows ghosting effect, you have to change timeout value in registry.

Please google about timeout. Be careful when editing registry.


On PC with Intel HD Graphics etc. (typically, non-graphic-oriented note PC), only black window may appear. This is because these graphics does not implement 16bit (or 8bit FBO). Set FBO configure in View and Camera Configure to be "Direct Draw".

On some graphic system, refresh of window may have trouble.
This phenomenon may be improved by setting of "Refresh type" in Preference Dialog.

In Ubuntu OS, the number that a process can open have a limitation in default state. Zindaiji3 uses many icon file and library files, and may biolate this limitaion. If this happens, a error occurs that says too many files are opened.
Informations about how to fix this problem can be obtaioned in WWW. (I do not describe details here). Try it please.

Radeon sereies on Linux OS may have errors with some shader rendering. As a symptomatic treatment, make shader setting to be off in Preference.

Zindaiji3 uses OpenEXR library.

Part of this work (HDF5 File Reader, Quad-buffering Stereo, etc. ) is supported by NIFS/NINS under the project of Formation of International Scientific Base and Network.
Part of this work (Stochastic transparency, etc.) is supported by Kyoto University, Institute for the Promotion of Excellence in Highter Education Visualization Laboratory.

inserted by FC2 system