User Manual
Contents
1. The following pictures about the Raycasting 1 2 Renderer are showing a part of the Teddybear data set which is marked inverse in this figure This data set has an overall resolution of 128x128x62 Voxel All time information correspond to a calculation on a Pentium4 2 66GHz the output resolution at which the following images were rendered and used in this document is 640x480 f P eo 3 Figure 6 3 Image see Figure 6 2 rendered using Raycasting 1 with an integration step size of 1 The calculation took 35s Figure 6 4 Image see Figure 6 2 rendered using Raycasting with an integration step size of 1 2 The calculation took 70s Figure 6 5 Image see Figure 6 2 rendered using Raycasting 1 with an integration step size of 1 8 The calculation took 270s D A color Z A exp extinction u djs d 6 1 0 l 0 Dif fuse normal LightDirection LightColor DiffuseColor 7 6 2 Specular normal Z LightDirection amp lossiness z LightColor SpecularColor 2 6 3 color Emissivity 7 Diffuse Specular 6 4 For actual calculation we integrate from the back to the front with a specified step size The exponential function is approximated by a first order taylor series One step of the integration then looks like this when starting with loo O I color 1 ertiction I_ oa a 6 2 1 Improvements Pre Integrated Integration The idea to use pre integration c2. hee l Figure 4 2 A maximum in the histogramm anything useful Figure 4 3 Having assigned an opaque material to the surrounding voxels a in tik mi ee iB Figure 4 4 Different areas in the histogramm sometimes produce similar results _ Figure 4 5 Result with some more transfer function elements The blue surface is a bit transparent you can look throught it This image was rendered using the Raycasting2 renderer with a step size of 1 4 5 Preferences With Edit Preferences in the main menu see chapter 3 2 you can open the preferences dialog to configure vvis Your settings are saved to a file called vvis conf It is saved into your home directory 5 1 Texture method At texture method tab the texture method renderer can be configured le Preferences Texture method Raycasting Display Texture Sizes Specify texture sizes as power of 2 6 i 256 Pixel y g if 256 Pixel Slices How many textures should be drawn behind each other Speci as power of 2 g 256 Textures You can specify the texture size of the textures and the number of textures to be drawn behind each other The texture method renderer requires both numbers to be a power of 2 Therefore you can specify the exponent to a base of 2 The resulting texture size respectivly slices is displayed right of the
3. User Manual development of VVIS application Tobias Eberle lt tobias eberle mx de gt Johannes Lampel lt johannes lampel net gt development of Qt GUI version Stefan Becker lt stefan becker urz uni hd de gt Ronald lt rlautens x urz uni heidelberg de gt Practical Course Of Dr Susanne Kromker IWR University of Heidelberg Germany 2006 Inhaltsverzeichnis Ve HUVEC CUCU OI gic cease scxstesetscet rad ips ainsstanse sen a alunos a eae 2 ZFC IIIS IM CN E E E A E E E ede edaedeareaervient 3 WN ae T A O E A 4 MAC an maa sees Raa LN Rah oat oa Shee Monat htm aa ce aac aaah ae Ned 4 LINUX fassaascicstan aatieteavensaaaacavacnaane aan esirialniormanmats ES 4 se n 11 9 6 1 Sete nn fe eee 5 3 2 Description of the main MENU ccccccceceseeceeeceseeeeeeeeeteeeseeeeueeeseceueeeeetseetaeenseeaeeeanes 5 3 3 The rendered volume display ssrcsirisirs tinio tadien a a Tea 6 ROUN Gannett gras ee ears ae eae ieee ele hee og hai 6 Z OON Nese cette sta yac aeyascs yetucntys tesa aia sade easesaeis E paoas ec caneeioakeeee 6 4 Transter FUNCION EGITO s sornioasirenni n a A au tans useniRaanee end E aaa gneaaNS 8 4 1 Whats a TPANSTED FUNCUON sic siccisciavnevasicpnnacaianvidsianewa fevenearawaxhssxtedudsevnauadieraravenetevaadann 8 A Z WN OC RAIN Ss hatets aga maceatart cents tants a A a sonondete eee a ease 8 4 2 1 Density against gradient length ccccceccsecceecceeeeeeeceeceeessesaeeseeesaeeeeeseeesaees 8
4. a 2 OOR I eee a eee eee eT eee eRe Ce Peer ere ey ee Peer a Pee ere eerie ete 9 4 3 Transfer function ClEMEMS vensicussinesniasioiwedimarensdotivniemedboreinmieeiatwebiavtoumsauneennebel 10 7a lB FLV ane ener nee on en a ee Pe ee on me 10 74 Ie L Manuara 1 Aen ne een rer ee te ne a ee ee a 10 71 Tee i If GF r gt an re Pe O ee eer ete ene eee ce 10 7 AOE pene cn een en en E eo ee Pee eee Ne ee ee ee 11 Aoo EA egsa a EAEE EEE 11 APD INC INOW nucia na aaa nue tun bop a awe 11 A o NO a E earaaeansen uameneanes 11 4 3 8 Enabling disabling element ccccccecccescccececeeeeeeeeseeeceueeseessueeeueesaeessaeees 12 4 4 Hints for Classification of a new Volume Data Set ccccecccecceeeceeeeeteeeseeeeeeees 12 FPFE O S O O RTE oe 16 co eal Texure me Noanne a nn ee nee eee 16 OZ RAYC SUN Grea teeta ce eae E eects enum daetatceind ie aentacenn elnaandaadvalutabentass 17 IDISA Gere ee tee eee eee ener ee eee en ee ee eee 18 GV OLUIME FR CMOS CIS aian T carktaien eee twata daa Rnegncaunausaeahernnts 19 60 1 Texture Rendel aise 2634 sexsacesed aA 19 6 1 1 Pre Integrated Texture RENCEeSe l ccccccccecceseceeeceeeceeeeeeeceeccuesaeeseeesaeeseeees 19 O22 TRAY CASING a dareutene tae ice eaten eves ived Senceaatcetiansearauaiuetinetaas sete souan tania steataneraetetey 20 118 016 2 19 heen eee hee ee ene ee ene ae eee mene tare ene ee ere ee eee ree 29 1 Introduction vvis is designed to re
5. The raycasting renderers can only provide interactive refresh rates at low resolutions like 64x64 on current hardware But they are capable of creating images with high resolution and random sizes The data provided throught the transfer function is fully used with exception of the pre integrated volume renderer In all renderers we are often in between the positions of different density values In such cases the density values are trilinear interpolated except in the preview mode of the raycasting renderers which gain their main speedup by not interpolating the voxel data The preview mode is enabled when you hold down the mouse button and rotate the volume 6 1 Texture Renderer The Texture Renderer produces images of the volume data by creating a stack of RGBA textures Those textures are then drawn on several planes The colors used in the texture are defined by the emissivity of the transfer function as well as the transparency Since you won t see much of this texture stack from positions which are near to the planes the textures are drawn onto a total of 3 stacks for each viewing direction one are created Two of them are displayed their selection depends on the viewing direction The stack whose planes are the most perpendicular to the viewing direction is not displayed The order in which the textures are drawn is also depending on the direction of view 6 1 1 Pre Integrated Texture Renderer Between two planes which are mapped onto t
6. for better image quality for usual voxel data sets and transfer functions a step size of 1 should be ok Bigger step sizes still work but complete surfaces seen with a lower step size might have jagged edges or be broken down to several parts with the new configuration Using a integration step size half as big as before will result in a twice as long calculation time An integration step size of 1 means that the step size is the same as the size of one voxel in the data set along the X axis 9 3 Display At this tab display options can be configured Texture method Rapcasting Display Brightness Default brightness 53 Default brightness You can specify the brightness that is used by default It is used at vvis startup 6 Volume Renderers vvis provides different types of volume rendering methods Each of them has advantages and disadvantages therefore it is useful to know how they work Summarizing one can say that the texture method and especially shear warp are the way to go when creating a new transfer function and you want to test how a new element added there affects the rendered images The texture method provides a smoothly rotating view of the volume and the related emissivity values without caring much about absorbitivity and completely ignoring light properties Shear Warp is a bit slower but is capable of calculating light effects and absorbtivity but the resolution is depending on the voxel data size
7. to use intermediate slices and then use trilinear interpolation to be able to render thin parts of the volume correctly This would then be rather a shear warp variant of the raycasting algorithms but the main intention for viewing rays shear volume slices project ie le warp image plane Figure 6 6 Idea of the Shear Warp Algorithm image taken from 1 implementing this algorithm was to have a fast and sufficient quality renderer for previewing the transfer functions The speedup of this algorithm is a result of the fact that complete axis aligned voxel planes can be processed one after another This is positive in terms of cache usage but primarily it allows us creating run length encoded tables based on a volume which is already classified by a transfer function The areas in which we only have transparent and non emissive transfer function elements can be skipped during rendering For the teddy image for example only 18 of the total voxels had to be processed the rest was saved due to run length encoding Often the percentage of voxels not being transparent is even lower you can look up the actual value in the log which is created when the renderer prepares the data Figure 6 7 Output of Shear Warp Renderer Calculation took 140ms on a Pentium4 2 66Ghz the original image size was 256x256 pixel this is a 147x106 pixel big part of it Preparing the RLE tables took 420ms on the same system
8. which was only depending on density values Therefore they only needed to store a 2 dimensional field or a 3 dimensional field if different step sizes have to be available Since our implementation also uses the gradient lengths for selecting a transfer function element at least a 4 dimensional lookup table would have been necessary Together with a sufficient quantization this table would have been really big therefore we decided to see what happens if we create a table only relying on the density values1 This precalculated table is used in the Pre Int Raycaster and can be used in the Pre Int Texture Renderer A variant of this is the second raycaster Here no table is precomputed but similar calculations are done during rendering For each density value inside the region defined by end and start value the related transferfunction elements are used to calculate a mean value also linearly interpolating the gradient lengths This calculations are relatively fast and the result for similar rendering times look smoother for this method compare figure 6 4 and 6 8 We ran a test using a 2 dimensional hash table for the density values and then adding integrated values together with the gradient lengths of start and end point to lists Two gradient lengths were said to be equal if their absolute difference was smaller than one for testing purposes During rendering there were a lot of hits in our cache but this did not result in a performan
9. 2 Manual apply By default every change of the transfer function results in a recomputation of the computation that has to be done before displaying the first frame If you want to make a set of changes this is annoying and wastes your time To get rid of this feature enable manual checkbox Doing so you have to click on Apply each time you want your changes be applied 4 3 3 Create To create new transfer function elements use the mouse to select a region of the histgram Move the mouse to the position to start at press the left mouse button and leaved it pressed move the mouse to stop position and release the mouse button The Material Editor opens showing you your selected area You can make some settings for the new element Click on OK for creating the element or on Cancel for not creating it 4 3 4 Order The order of the transfer function elements is important if they overlap The renderer uses the first one that fits The transfer function element list shows the elements in the current order Use the buttons Up and Down to change it 4 3 5 Edit If you want to edit an element select it and click on Edit The material editor opens By Material Editor Description Density From O47 To 0 50 Gradient Length From 5 00 To 65 00 Ernissivity TO Change Color Absorotryity 0 55 Diffuse 5 Specular Specular highlights 30 00 ea You can specify a description d
10. Figure 6 8 Image see Figure 6 2 rendered using Raycasting 2 with an integration step size of 1 The calculation took 80s LJA Figure 6 9 Image see Figure 6 2 rendered using Raycasting 2 with an integration step size of 1 2 The calculation took 160s Figure 6 10 Image see Figure 6 2 rendered using Raycasting 2 with an integration step size of 1 4 The calculation took 315s Bibliography 1 2 3 4 9 Philippe Lacroute Marc Levoy Fast Volume Rendering Using a Shear Warp Factorization of the Viewing Transformation http www graphics stanford edu papers lacroute thesis Jon Sweeney Klaus Mueller Shear Warp Deluxe The Shear Warp Algorithm Revisited http www cs sunysb edu mueller papers vissymFinal pdf Klaus Engel Martin Kraus Thomas Ertl High Quality Pre Integrated Volume rendering Using Hardware Accelerated Pixel Shading http wwwvis informatik uni stuttgart de engel pre integrated Christof Rezk Salama Klaus Engel Fernando Vega Higuera The OpenQVis Project http openqvis sf net Various Authors Slides for talks on Siggraph http www cs utah edu jmk sigg crs 02 courses 0067 html
11. ame from a paper about using hardwareaccelerated pixel shading 3 Their aim was to run the integration on a graphics chip and to avoid effects due to transfer functions which would need a very high sampling rate The assumption here was that the density values between 2 subsequent points of our integration changes linearly Thus all combinations for a given step size can be calculated before displaying the volume during the rendering itself just a simple lookup has to be done which can even be done with the limited capabilities of programmable graphics hardware The calculations currently used are the following when i and j are the density values while s and t are the corresponding gradient lengths of the start and end point Lookup ignoring the gradient lengths used in Pre Int Raycaster lookupE missivityi Emissivity Ai 1 A j dA 6 6 J0 Calculation using the gradient lengths used Pre Int Texture Renderer and the Raycaster 2 and accordingly for the other data provided by the transfer function pl intEmissivity i j s t Emissivity Ai 1 A j As 1 A t dA 6 7 Jo This is just calculating the mean value Also obeying absorption when calculating diffuse specular and emissive material properties resulted in artefacts while rendering The used code is still implemented as mode 5 and 6 in the Prelntegrator class In the paper mentioned above they obviously used a one dimensional transfer function
12. an open and close the transfer function editor 4 1 What is a Transfer Function The data to be visualized by this program are density values on a rectangular grid Drawing each of those voxels directly as some different shaded black and white transparent cubes might be possible but this approach already fails if the data source produces density values around the object we want to look at which are not transparent Therefore this step has to be configurable This is done by a so called transfer function which assigns values needed for the display algorithms see 6 Volume Renderers to each of the voxels The transfer functions used in vwvis consist of one or more transfer function elements Those elements specify the emissive diffuse and specular color the glossiness and absorbtivity for voxels inside a range of density values and gradient lengths 4 2 Histograms A histogram shows how often a certain voxel configuration exists in the currently loaded volume There are two different histograms available Density against gradient length and density only The values at the current mouse position are displayed on the right below the histogram 4 2 1 Density against gradient length The gradient length is displayed at the x axis the density at the y axis Each point of the histogram is displayed in 256 gray values The darker a value is the more often it occures The origin is at the lower left Existing transfer function elements are displayed
13. arp Renderer see 6 3 is the best choice here After changing the transfer function it needs some time for precalculating but then you can examine the result at suitable refresh rates To get a rough idea of the volume data just create a transfer function element which covers all or almost all density values but which only covers higher gradient lengths And already specify the lighting properties like diffuse and specular color to have a better impression of the object Figure 4 1 Then take a look at the histogramm and mark a part which looks promising for example a irregular part or a part of a geometric figure which looks interesting Figure 4 2 Note that empty space around the actual object also created entries on the history table This part of the data is often located on the left bottom part of the histogram Figure 4 3 Sometimes even different areas on the histogramm might produce similar looking results In this case mainly the gradient lengths are different therefore the red transfer function element is rather describing an outer isosurface of the objects whereas the blue one describes rather describes an isosurface just a little bit more inside When rendering this with a raycaster you might get problems when the step size is that big that there are pixels where the red transfer function element has been hit and others where the blue one has been hit Therefore it might be better to remove one of them or merge them Figure 4 4
14. as colored boxes using the emissivity color If an element is selected a black border is displayed around the box The Density is mapped linearly and the gradient length is mapped via the square root onto the square since there are usually more interesting areas at the lower gradient lengths in the histogram The brightness of each point on the histogram is proportional to the logarithm of the probability White represents a zero probability black maximum probability density 4 i gradient length 4 2 2 Density The histogram shows how often a density value occures in the volume data Below the histogram the existing transfer function elements are displayed as little boxes The selected one is drawn with a black border 4 3 Transfer function elements ivanster Function Editor axi Density against gradient length Density denzity gradient length To create a new segment use the mouse to select a region Density Description Density from Density to Gradient from Gradient D4 05 207 Edit ik 0 57 MeL ote ii 0 08 0 3 CEs pen Save Save Ag _ manual Apply 4 3 1 Display All transfer function elements are displayed in the list below the histogram If you choose one element there it is highlighted in the histogram For instance in the picture above the green transfer function element is selected The list shows a description whether it is enabled and the ranges of the element 4 3
15. ce boost it slowed the rendering process even down by 10 The main reason for this was probably the size of the stored data which easily reached 100MB when rendering a 1024x768 image and therewith the bad CPU cache usage for those operations Only applying this caching for regions on the histogram with high densities and calculating other values directly anyway or resorting the used STL vectors so that more used data would be faster to access has not been tested since it did not looked promising 6 3 Shear Warp The idea of the shear warp algorithm is to factorize the view matrix into a shear and a warp transformation A shear transformation of the original volume data is performed then this data is projected perpendicular to the sheared planes onto the so called intermediate image This intermediate image is then warped and we get the final output see figure 6 6 In contrast to the raycasting renderer this is an object based algorithm since we loop through the elements of our volume This is the reason that the output size of the shear warp renderer is directly coupled to the volume size On the other side in the image based renderers like the raycaster one pixel of the final image is calculated after another and within this process the related data from the volume is gathered When performing the shear operation the voxel data is not interpolated We implemented this once but we encoutered a lot of flickering when rotating maybe one would have
16. e to convert them first using File Convert After choosing a file some calculations are done Converting volume data from one file format to another Please follow the instructions of the wizard Displays resolution and slice thickness of loaded voxel data Saves the volume as currently displayed as tiff image close vvis Opens or closes the transfer function editor This editor is descripted in detail in chapter 4 Opens a preferences dialog where you can configure vvis See chapter 5 for details Chooses the renderer used for displaying the volume The differences between the renderes are described in chapter 6 Opens a dialog to input a number between 0 and 255 to use a new brightness Increments the brightness by 10 steps Decrements the brightness by 10 steps Dialog showing some information about wis 3 3 The rendered volume display Rotating the volume Press the left mouse button and move the mouse around to rotate the volume In the preferences see chapter 5 you can specify a lower texture size for the raycasting renderers used while rotating to get higher frame rates Zooming Press the right mouse button and move the mouse fore and back BP aTi JoB Fie Edit Renderer Display Help Figure 3 2 Main window showing volume data using the raycasting 2 renderer 4 Transfer Function Editor With Edit Transfer function in the main menu see chapter 3 2 you c
17. ensity and gradient length range emissivity diffuse and specular light and absorbtivity The sphere on the left side shows a preview of the light colors and absorbtivity 4 3 6 Remove Transfer function elements can be deleted by selecting one and clicking on Delete With Clear you can delete all elements 4 3 7 Save You can save your created transfer function elements by clicking on Save or Save As The elements are saved to a XML file which can also be edited by hand With Open you can load an existing transfer function file 4 3 8 Enabling disabling elements Transfer function elements can be en disabled individually by clicking on the checkbox in the list To enable or disable all elements right click on the list and choose the appropriate menuitem from the displayed contextmenu 4 4 Hints for Classification of a new Volume Data Set le Figure 4 1 Getting a rough idea of the volume data First of all it is very useful to Know what the data is all about what we are aiming at to display We need to orientate ourself we need to know where is up where is down where we can find the main features we want to show Here it is often useful to create a simple transfer function then take a look what is already displayed and then continue to the details To do so select a renderer which is running fast enough on your system and which creates images showing enough details In most cases the Shear W
18. entry With greater texture sizes or more slices the quality gets better but the computation lasts longer All the computation is done before displaying the first frame that is that you have to wait longer to see the volume but rotating and zooming is not effected Exceeding your graphic card s onboard memory will result in a drastic performance loss so keep in mind how much memory one texture needs All textures used here are RGBA textures i e they need 4 byte for each texel thus 256 256x256 textures need 64MB The texture renderer often draws 2 stacks of textures therefore this might be the upper limit for using the texture renderer on a 128MB graphics card 5 2 Raycasting At this tab the raycasting renderer Raycasting 1 2 and with pre integration can be configured By Preferences Texture method FRapcasting Display Texture Sizes In pinels ole w ale Texture Sizes while rotating ou can choose texture sizes that are used for better user interaction while rotating the volume In pixels it she we Integration step size 0 125 You can specify the texture sizes in pixels The computation of the textures is done each frame Therefore you can specify a lower texture size used while rotating the volume to get higher frame rates During rotation the renderer is also in a preview mode which disables any interpolation during the calculations to speed up the image generation The integration step size can be lowered
19. he textures there might be imporant information especially if we have a transfer function with steep slopes which would require high resolution sampling For each viewing direction along the coordinate axis one could integrate between the texture planes using trinlinear interpolation and store the information on the textures But since a table with the pre integrated transfer function already existed this was a test if this might also improve the image quality of the textur renderer For the lookup table one value on a plane and a value at the same position on the plane on the plane s neighbour are taken and used for the table lookup see pre int raycasting 6 2 1 The used assumption here is that we are looking almost perpendicular onto the planes Using this lookup tables has the same disadvantages as described in the part about pre integrated raycasting you have to neglect the information about the gradient length when using the transfer function To avoid this the pre int lookup table class provides an integration function which also interpolates between given gradient lengths not only density values This cannot be stored in a lookup table this calculations have to be done when the textures are generated thus there is no speedup as with the lookup table compared to the normal texture renderer during texture generation Figure 6 1 Example showing the difference between the normal texture renderer on the left and the integrating texture
20. nder 3D scalar fields i e volume data collected by medical applications It can handle several file formats like the format of the University of Erlangen used by openavis nttp openqvis sf net and the format of the University of Heidelberg used by the non Opensource program Vrend It can produce such files from a series of TIFF images To display the volume different algorithms are available texture method texture method using pre integration raycasting raycasting using pre integration and shear warp 2 Requirements To compile vvis the following requirements have to met for the different platforms WIN e qt 4 1 1 at least e OpenGL e libtiff http www libtiff org MAC e qt 4 1 1 at least e libtiff http www libtiff org LINUX e qt 4 1 1 at least e libtiff http www libtiff org 3 Main window 3 1 The window Bates aax Fie Edit Renderer Display Help welcome to QT yis Figure 3 1 This is the window you see after vvis has started At the logo position in the middle the volume is displayed 3 2 Description of the main menu File Edit Renderer Display Help Open Convert Information Save screenshot Quit Transfer function Preferences Set Brightness Increment Brightness Decrement Brightness About Opens a file containing volume data Currently OpenQVis and Vrend file format is supported If you want to use several tiff filles you hav
21. renderer also interpolating the gradient lengths on the right One can see that the surface of the bonsai tree trunk is renderer more smoothly using the integration This image was taken from a position 30 degree off a primary axis The function used in the pre int class provides a method of calculating which is mainly a computation of a mean value for the properties described by the transfer function In this case this simplification even has an advantage since this computation does not depend on permutations of the start and end values Therefore the same textures can be used for looking at the volume from opposite directions The code of the renderer provides both methods the slow one obeying gradient length information is currently used in the GUI 6 2 Raycasting Raycasting works by integrating a number of lines throught the volume The intensity seen in the final result is dependent on the absorbtivity of the material assigned to the voxels its emissivity and its behaviour when light is shed on it All these properties are again defined by the transfer function The integral looks like this for directional light specified by LightDirection and LightColor a parametrization of our line x a function to get the normal of the related isosurface from the voxel data normal x and the results of the transfer function Emissivity x DiffuseColor x SpecularColor x and Glossiness x By we mean component wise multiplication Figure 6 2
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