Filters
Filters are shown in side panels.
Removing or swapping filter order is in right-button mouse menu.
Most filters can be categorized for data showing and for data handling.
Several fata handling filter has effects only to preview. Not to Pov-Ray rendering image.
This is because PovRay reads .df3 files, (not filtered data in Oosawa).
To render the filtered data in Pov-Ray, you must export filterd data to .df3 file, and read that processed file afterwards.
Volume
Volume filter shows volume data, according parameter, emission, absorption, scattering.
Note that data is proccessed from top to bottom in filter order, so that swap data handling filter on the top of volume filter.
Using light and scattering (not than 0) makes PovRay to calculate self shadowing , but rendering time becomes much larger.
Note that scattering has no effects on preview. (PovRay only)
If red or yellow color is scatterd, objects beyond volume would be seen as blue or green.
If emposs shading is turned on in preview configure, shading is also enhanced in PovRay rendering mode.
Left) without emboss shading. Right) with emboss shading
Leftjwith scattering. Right) Isosurface and volume within surface.
Density always uses self data slot. You can choose other data slot for coloring.
Isosurface
This filter consruct isosurface with some critical value.
Isosurface is like empty shell in default. If you show semi-transparent isosurface, set interior solid color or volume.
As another way to fill isosurface by solid color, use fog filter targeting isosurface.
Details of Isosurface
Cross section
This filter shows cross section.
You can enhance cross section with emboss.
If you set clipping on, you can hide half side of volume beyond the cross section surface.
Also, you can make a part of cross section transparent below some critical value.
Check Clip low value in filter advanced setting.
Three-faced image
Three-face image is quite like three cross sections.
offset is a distance between projected image and volume.
Fog
Fog is a medium that emmit of absorb light. Can be used for aerial perspective.
Note that you can set fog inside isosurface.
With proper parameters, you can make the rendered image more conprehensible.
Alos, with emmiting fog, you can see volume that absorb light.
Object
Primitive
This filter set basic primitive objects like sphere or cube. Positions, rotation and scale can be handled.
Mesh
You can read mesh object with this filter. Specially formated .pov file (isosurface made by oosawa) and wavefront .obj file can be read.
Left) Primitives Right) Reading .obj file.
Text
You can set text objects on the screen.
Multilined single text objects, or multile text objects are acceptable.
If you want to show multiline texts individualy, positions and size information must be included in the text.
The format for text list is very simple ascii.
string1 | x y z | sx sy sz
string2 | x y z | sx sy sz
string3 | x y z | sx sy sz
(sx, sy, sz are scale. coordinates must be separated by space, or comma.)
Face camera checkbox makes texts to face camera.
this image shows texts that does not face camera
Dependency of size in monitor can be selected (perspective, constant, and sqrt).
*) Note that rectangular text box is filled by black color in preview. Transparent textbox is not implemented yet.
Differential Object
Differential Object is basically invisible. If it overlaps with volume, part of volume would be invisible.
In povray rendering, it also interacts with other objects.
However, in preview, it interacts with only volume.
Note that rendering quality parameter must be set quite high for volume rendering since shape of the volume becomes complicated one rather than simple box.
Copying
This filter shows copied data. Good for periodical simulation data or symmetrical data with half or quater part only.
Copyied data. (Though it is not periodical data...)
Clipping
You can show a clipped region of data. This filter targets volume or isosurface.
Note that the parameter is not based on spacial coordinate but normalized coordinate (0, 0, 0)-(1, 1, 1).
The center of volume box is at <0.5, 0.5, 0.5>.
The parameter can be edited on timeline, so that you can make slice animation.
Fix Position
This filter is for help canceling positional noise of data (or registration).
When playing with "Do Calc" on, difference between this frame and previous frame is automatically calculated and results are accumulated in memory.
When all scene is played, push "Copy Result" button and the optimized positions are copied to data box.
The registration algorithm is simple one, just searching local minimum of (dx, dy, dz) that minimalize difference between current and previous frame.
If data is noisy one, this algorithm may lead to pseudo minimum.
Sometimes, some smoothing of data improve the situation.
Level correction and Gamma Correction
This filter correct data value according to gamma curve. Note that this correction works to data itself, no to the rendered image.
IN and OUT and Gamma value is generally used ones. The last value at right of gamma is offset value of gamma curve.
The correction curve would be shown in preview preference.
This is a example of extreme correct curve.
This filter works in both preview and povray rendering.
Gauss Blur
This filter smoothes data. For triaxial blur, select ellipsoid for kernel.
Bluring is the simplest way of noise reduction, but often it is enough for grapse the general form of the data.
Note that rapidly changing data require high resolution parameter for making isosurface in povray.
Preprocessing by weak bluring often makes it easier.
Note that this filter works only in preview. Not works in Povray Renderng.
PovRay just read external .df3 file and do not modify it after reading.
Thus you must export filterd data for other .df3 files and use them for PovRay Rendering.
Be careful not to double apply blur filter to the blured data.
Also, exporting isosurface as object file and use it for povray rendering is good idea.
Inverse diffuse
Often the volume date obtained by confocal microscopy is blured in z-direction.
Assuming that these blur can be approximated by diffusion, we make a filter that apply inverse diffusion with negative diffusion coefficient.
This sample is obliquely looking a ring-like shaped data.
leftjOriginal date looks blured along z-axis.
right) Applying inverse diffuse in z-direction makes data look much better.
Note that this filter works only in preview. Not works in Povray Renderng.
Thus you must export filterd data for other .df3 files and use them for PovRay Rendering.
Data Rotate
In oosawa, cross sectional images can be made only across the x,y,z axis.
Thus, if data is not aligned well, you may not get good images.
This filter rotate data itself. Not just rotate databox, rotate data itself in the volume.
Note that this filter works only in preview. Not works in Povray Renderng.
Thus you must export filterd data for other .df3 files and use them for PovRay Rendering.
Density Curve
Making density curve between two point (in and out), and add, substruct multiply or over write on volume data.
Foe example, when some false signals comes at the edge of data, you can smoothly substruct them by this filter.
Note that this filter works only in preview. Not works in Povray Renderng.
Thus you must export filterd data for other .df3 files and use them for PovRay Rendering.
Note that rendering quality parameter must be set quite high for volume rendering since shape of the volume becomes complicated one rather than simple box.