Voluviz - FFI rapporter - Forsvarets forskningsinstitutt
Contents
1. 25i X Center 127 127 TT ee Y Center 63 191 127 25 2 Center 127 127 Figure 1 9 Loading the selected subset 9 Select a subset of the original volume by using the subset dialog box see figure 1 8 10 Press the apply button see figure 1 9 11 Repeat until satisfied 14 2 TECHNICAL MANUAL 2 1 Introduction VoluViz is a direct volume rendering application based on SGI Volumizer 2 and OpenGL Trolltech s Qt GUI library is used to create the user interface Note that Qt only exists in a 32 bit configuration therefore VoluViz must be compiled as a 32 bit application Due to limitations in the HDF4 file format the size of the volume texture can not exceed 2GB The src docs directory contains documentation generated by Doxygen 1 in several formats html TeX etc 2 2 Prerequisites The following software must be installed on your system OpenGL SGI OpenGL Volumizer 2 4 tested with version 2 2 Qt 3 tested with version 2 3 1 HDF4 2 C compiler and gmake 2 3 Compiling and Running the Application To compile the application go to the VoluViz root directory and type gmake Modification of the Makefile might be necessary depending on where the prerequisite packages are located To run the application enter the following command o voluviz filename hdf 2 4 Program Components VoluViz consists of the following m2. 1 on page 20 for further details CONTENTS 1 1 USER MANUAL Introduction 12 Functionality 1 2 1 Using the mouse 122 File menu 1 2 3 Edit menu 124 View menu 1 3 Color editor 1 4 Example 2 TECHNICAL MANUAL 2 1 Introduction 2 2 Prerequisites 2 3 Compiling and running the application 2 4 Program components 2 5 The main Qt GUI application 2 6 The renderer 2 7 File and dataset handling 2 8 The color table editor 2 9 Misc dialogs and support code 2 10 Future work APPENDIX A 1 Volume file format A 2 VoluViz Color File format VVCF Distribution list Page COCOONNN N 14 14 14 14 14 15 15 17 17 18 19 20 20 25 VOLUVIZ 1 0 REPORT 1 USER MANUAL 1 11 Introduction VoluViz is a volume rendering application designed for viewing three dimensional volume data It supports interactive viewing of large e g 5123 or greater datasets VoluViz has many features including trilinear interpolation interactive color table both RGBA and HSVA picking of subsets clip planes and visualization of two fields Currently VoluViz is restricted to handle data defined on uniform grids Due to the use of SGI s OpenGL Volumizer 2 4 Voluviz only runs on SGI hardware with support for 3D texture mapping and color tables for example the Onyx 3200 To run the application enter the following command voluviz filename hdf If 1t is necessary to compile VoluViz instructions can be found in section 2 3 on
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4. page 14 1 2 Functionality VoluViz is a GUI Graphical User Interface application and commands are accessed via the menu system see figure 1 1 1 2 1 Using the mouse To rotate the volume press and hold the left mouse button while moving the mouse To move the volume press and hold the middle mouse button while moving the mouse To zoom in and out press and hold the middle and left mouse buttons while moving the mouse backwards and forwards 1 2 2 File menu Open loads a HDF volume file The user must then use the subset dialog to set the desired view volume and press apply to render the volume Hotkey Ctrl 0 Quit quits the VoluViz application Hotkey Ctrl 0 Figure 1 1 The VoluViz GUI with a sample dataset loaded 1 2 3 Edit menu Background sets the background color This can be a single color a vertical gradient between two colors a gradient between four colors defined at the corners of the screen The colors are chosen by entering a string of color names e g black white See the Qt documentation 3 for the Q Color class under setNamedColor for a list of valid colors Color editor opens the Color editor See section 1 3 for information on using the Color editor Hotkey Ctrl C Subset re displays the subset dialog box Use the subset dialog box to specify the volume to be rendered Hotkey Ctrl S Sampling rate sets the number of slices that are used to render t
5. FFI RAPPORT VOLUVIZ 1 0 REPORT GAARDER Trond HELGELAND Anders FFI RAPPORT 2002 03449 FFIBM 820 170 VOLUVIZ 1 0 REPORT GAARDER Trond HELGELAND Anders FFI RAPPORT 2002 03449 FORSVARETS FORSKNINGSINSTITUTT Norwegian Defence Research Establishment P O Box 25 NO 2027 Kjeller Norway Approved Kjeller 2 September 2002 Bjarne Haugstad Director of Research FORSVARETS FORSKNINGSINSTITUTT FFI UNCLASSIFIED Norwegian Defence Research Establishment P O BOX 25 SECURITY CLASSIFICATION OF THIS PAGE N0 2027 KJELLER NORWAY when data entered REPORT DOCUMENTATION PAGE PUBL REPORT NUMBER SECURITY CLASSIFICATION 3 NUMBER OF FFI RAPPORT 2002 03449 UNCLASSIFIED PAGES PROJECT REFERENCE DECLASSIFICATION DOW NGRADING SCHEDULE 25 FFIBM 820 170 TITLE VOLUVIZ 1 0 REPORT NAMES OF AUTHOR S IN FULL surname first GAARDER Trond HELGELAND Anders DISTRIBUTION STATEMENT Approved for public release Distribution unlimited Offentlig tilgjengelig INDEXING TERMS IN ENGLISH IN NORWEGIAN a VoluViz VoluViz b Visualization Visualisering c Direct volume rendering Direkte volumrendering a Volumizer 2 Volumizer 2 e THESAURUS REFERENCE 8 ABSTRACT VoluViz is a direct volume rendering application based on SGI s OpenGL Volumizer 2 and OpenGL and is designed for interactive viewing of three dimensional volume data Its features include trilinear interpolaion interactive color table both RGBA and HSVA picking o
6. ain components The main Qt GUI application The renderer 15 File and dataset handling The color table editor Misc dialogs and support code 2 5 The main Qt GUI application The main Ot GUI application handles the user interaction and controls the other VoluViz components The following files are included in the main Ot GUI application component main cpp VoluViz h VoluViz cpp 2 6 The renderer The renderer draws the volume data and other graphical elements It also handles mouse manipulation of the scene and clip plane translating rotating scaling The following files are included in the renderer component Viewer h Viewer cpp The Viewer class is the heart of VoluViz It renders the volume and geometry as well as supporting geometry like bounding boxes and axes SGI s Volumizer 2 API is used to render the volume while the rest of the rendering code is standard OpenGL For an overview of the Volumizer 2 rendering process see 4 Currently the VoluViz renderer uses the vzTMLUTShader to render the volume and uses the vzBlock to define the volume geometry Future extensions might include using more advanced geometries e g unstructured tetrahedral meshes All OpenGL code is located in classes that inherit from QGL Widget 3 Such a class must re implement the three virtual functions initializeGL paintGL and resizeGL The Viewer class inherits from QGL Widget and is defined in Viewer
7. ble and a zoomable detailed view 10 The color space combo box allows you to choose between HSVA and RGBA color spaces The channel views shows the color table for each color component The channels will be hue saturation value and alpha or red green blue and alpha depending on the chosen color space To modify the color table the user inserts and manipulates a number of knots in the desired channel view To insert a knot press the middle mouse button To move an existing knot move the mouse over the desired knot and while pressing the left mouse button drag the knot to its new position To delete a knot move the mouse over the desired knot and press the the right mouse button Each channel has an interpolation mode linear spline or gauss that determines the interpolation funtion between knots The exact operation of the color table depends on the data set being viewed Voluviz supports the following texture types One component texture contains only one component per voxel In this case all four channels use those values as indices Two component texture contains two components per voxel e g two field vizualisation the first component maps to the HSV RGB channels while the second component maps to the alpha channel Four component texture contains four components per voxel and maps these to the RGBA channels respectively The HSVA color space does not work very well in this scenario See the sec
8. f subsets clip planes and visualization of two fields The report is in two parts The first part gives a description of the functionality of VoluViz and treats common usage patterns The second part is a technical manual discussing implementation issues and program structure Possible future extensions are also discussed AUTHORIZED BY POSITION This page only 2 September 2002 Bjarne Haugstad Director of Research UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE when data entered ISBN 82 464 0669 8 PREFACE About this report This report is divided into two parts The first part gives a description of the functionality of VoluViz and treats common usage patterns The second part is a technical manual discussing implementation issues and program structure Possible future extensions are also discussed Audience of this report The first part is written for users of the VoluViz application The focus is on learning to use the application not on technical details No previous experience is needed The second part is intended for advanced users and developers interested in the internals of the VoluViz application and class library Experience with C Qt OpenGL and Volumizer 2 is recommended Some familiarity with volume visualization principles is also useful Note on datasets The VoluViz application reads volume datasets stored in HDF4 2 files There are some restrictions on the format of these files See Appendix A
9. h The vzBlock object represents a simple axis aligned cube By default the extents of the cube are set to 0 0 0 and 1 1 1 16 class Viewer public QGL Widget t Q OBJECT must include this if you use Ot signals slots public Viewer QWidget parent const char name virtual Viewer void protected No copying allowed Viewer const Viewer amp c m_vsctrl 0 0 m_vscClipPlane 0 0 No assignment allowed Viewer amp operator const Viewer amp rhs return this void initializeGL void void resizeGL int w int h void paintGL void The VoluViz rendering code is mostly located in the paintGL function This function renders the scene and is called whenever the widget is redrawn void Viewer paintGL t Set Background if m_dataset NULL return Transform to viewport and move the volume to center Draw ROI box if m_drawROlbox drawROlbox Draw axis if m_axisActive 17 drawAxis Clip Plane if m_clipPlaneActive setClipPlane SE E ke ag RR elskede se leke se elskede 3K K see se FK K FK 3K 2K 3K 2K 3k K K 3K K 3K KK FK K FK 3K KK 3K K K K A fF Additional geometry in physical coordinates can be inserted here SE E ke K 2 2 k k k k kk k k k k k lekke K 2h K 3K aK k see K 3K K FK ske se see K 3K K 3K RT FK K RI TR K K K K K K K K A Transform the volume to physical coordinates if m_boundingBoxActive drawBoundingb
10. he volume If the reduced checkbox is checked the number of slices are reduced during user manipulation of the volume moving rotating scaling etc This decreases the rendering workload and increases the interactivity of the application Hotkey Ctrl R 1 2 4 View menu Axis displays the coordinates of the volume along the x y and z axis Hotkey Ctrl A Bounding box displays an axis aligned bounding box surrounding the volume Hotkey Ctrl B Clip plane enables the clip plane The volume on one side of the plane is displayed while the other side is clipped The clip plane can be manipulated using the mouse in conjunction with the keyboard To rotate the clip plane press Shift and hold the left mouse button while moving the mouse To slide the clip plane along the plane normal press Shift and hold the middle mouse button while moving the mouse The clip plane can be aligned with the x y and z axis by pressing Shift X Shift Y and Shift Z respectively Pressing one of these combinations twice in a row flips the clip plane 180 degrees so that the visible portion of the volume becomes invisble clipped and vice versa To reset the clip plane to the initial configuration press Shift R Hotkey Ctrl P 1 3 Color editor Figure 1 2 The VoluViz color table editor The VoluViz Color editor is divided into three main parts see figure 1 2 The combined section include a global view of the color ta
11. l ChannelEditors into one combined lookup table that is then passed to the renderer as an array of floats in the range 0 1 on the form R G B A R G B The size of the lookup table array is currently 4 256 2 9 Misc dialogs and support code This category includes many support classes that are used by the VoluViz application The following files are included in the Misc dialogs and support code component Subset h Subset cpp StringDialog h StringDialog cpp rotation vector3 h rotation vector3 cpp rotation matrix3 h 19 rotation matrix3 cpp rotation matrix4 h rotation matrix4 cpp rotation quaternion h rotation quaternion cpp rotation transform h rotation transform cpp rotation Ball h rotation Ball cpp rotation VSController h rotation VSController cpp Subset and StringDialog are Qt widgets used by the main application The VSController class is a virtual trackball 5 used to rotate the volume and clip plane in the viewer The rest of the files in the rotation subdirectory are support files for VSController 2 10 Future work VoluViz should be extended to use more of the advanced features in Volumizer 2 In particular VoluViz should support data in formats other than vzBlock It may also be desirable to support different Volumizer 2 shaders other than vzTMLUTShader Possible formats and shader classes are listed in 4 Volumizer 2 supports several diffe
12. nds on the value of colormaptype 24 References 1 Doxygen webpage http www doxygen org 2 HDF webpage http hdf ncsa uiuc edu 3 Qt webpage http www trolltech com 4 K JONES OpenGL Volumizer 2 Programmer s Guide Silicon Graphics http www sgi com software volumizer documents html 5 K SHOEMAKE ARCBALL A user interface for specifying three dimensinal orientation using a mouse In Proceedings of Graphics Interface 92 pages 151 156 May 1992 25 2 11 DISTRIBUTION LIST FFIBM Dato 2 september 2002 RAPPORTTYPE KRYSS AV RAPPORTNR REFERANSE RAPPORTENS DATO RAPP notar er 2002 03449 FFIBM 820 170 2 september 2002 ANTALL EKS ANTALL SIDER UTSTEDT Unclassified 30 25 RAPPORTENS TITTEL FORFATTER E VOLUVIZ 1 0 REPORT GAARDER Trond HELGELAND Anders FORDELING GODKJENT AV FORSKNINGSSJEF FORDELING GODKJENT AV AVDELINGSSJEF Bjarne Haugstad Jan Ivar Botnan EKSTERN FORDELING INTERN FORDELING ANTALL EKSNR TIL www ffi no Adm direkt r stabssjef FFIE FFISYS FFIBM FFIN Forfattereksemplerer Restopplag til FFI Bibl ELEKTRONISK FORDELING FFI veven yvind Andreassen FFIBM OyA Thor Gjesdal FFIBM ThG Jan Olav Langseth FFIBM JOL Atle Ommundsen FFIBM AOm B Anders P Reif FFIBM BRe Carl Erik Wasberg FFIBM CEW FFI K1 Retningslinjer for fordeling og forsendelse er gitt i Oraklet Bind I Bestemmelser om publikasjoner for Forsvarets forskningsinstitutt pkt 2 og 5
13. nnel MG struct VVCF CHANNEL HEADER Interpolation mode used by the channel vvInterpolation interpolation Number of points knots in the channel unsigned int numpoints 22 111 VoluViz Color table file Format header This struct defines the VoluViz Color table file Format vvcf This struct is designed to be read from and written to file using binary read write functions for example fstream read and fstream write or the C standard library struct VVCF_HEADER Magic number unsigned short magic 1 Version number unsigned short version RGBA or HSVA colorspace vvColorSpace colorspace 111 Type of colormap note Only VVCF_RGBA is supported in this version vvColorMapType colormaptype Component type Anote Only VVCF_UNSIGNED_BYTE is supported in this version 7 vvComponentType comptype Number of entries int the color map unsigned int numindices 23 A vvcf file consists of a VVCF_HEADER one or more VVCF CHANNEL HEADERs depending on the value of colormaptype and a number of control points A control point consists of an integer index and a floating point value After the last VVCF_CHANNEL_HEADER the control points are stored as a block of numpoints indices and then a block of numpoints values Finally a block containing the entries in the lookup table is stored This block consists of numindices tuples The size of these tuples depe
14. ote that the SDS containing the coordinate data must be the first SDS in the HDF file The HDFLoader cpp file contains the VoluViz volume file loading code A 2 VoluViz Color table file Format VVCF The VoluViz Color table file Format vvcf is defined in the VVColorFile h located in the src color directory The latest version version 2 is included here Magic number for identifying vvcf files const unsigned short VVCF_MAGICNUMBER 0x00008365 Version number for this file format const unsigned short VVCF_VERSION 0x00000002 Identifies either a RGBA or a HSVA colorspace enum vvColorSpace VVCF_CS_RGBA VVCF_CS_HSVA Identifies a colormap type Identifies a LUMINANCE one channel LUMINANCE ALPHA two channels or RGBA four channels colormap Currently Volu Viz only supports uniform grids 21 enum vvColorMapType VVCF_RGBA VVCFLUMINANCE ALPHA VVCF_LUMINANCE Identifies component type enum vvComponentType VVCF_UNSIGNED_BYTE VVCF_UNSIGNED_SHORT VVCF_UNSIGNED_INT VVCF_FLOAT VVCF_BYTE VVCF_SHORT VVCF_INT Identifies method of interpolation Values are interpolated from knots using this interpolation method enum vvinterpolation VVCF INTER LINEAR VVCF INTER SPLINES VVCF_INTER_GAUSSIAN VVCF INTER PAINT VVCF INTER COUNT ie 111 VoluViz Color table file Format channel header JE Carries metadata for one cha
15. ox J Render the volume data renderVolumeData 2 7 File and dataset handling The File and dataset handling controls the loading of the HDF files and creates the textures vzParameterVolumeTexture 4 The following files are included in the File and dataset handling component HDFLoader h HDFLoader cpp Dataset h Dataset cpp 2 8 The color table editor The color table editor serves as the user interface to the underlying Volumizer 2 lookup table It consists of a Qt widget and assorted helper classes The following files are included in the color table editor component color CEditor h 18 color CEditor cpp color ChannelEditor h color ChannelEditor cpp color TFChannel h color TFChannel cpp color TFControlPoint h color TFControlPoint cpp color V VColorFile h CEditor is the main user interface and consists of several Qt widgets and six ChannelEditor widgets Four of these represent each of the HSVA RGBA channels while the remaining two show the combined lookup table Each of these ChannelEditors contain a TFChannel object that keeps track of the control points TFControlPoint and interpolation mode The TF classes were borrowed from a Volumizer 2 sample application original source in Volumizer2 src tfeditor The CEditor class is able to load and save the lookup table in VoluViz Color table file Format vvcf see appendix A 2 page 20 The CEditor class combines the individua
16. rent texture types byte short float etc while VoluViz only supports unsigned byte textures VoluViz should take advantage of the possibilities present in Volumizer 2 and support several texture types Lookup tables are currently restricted to 256 entries Volumizer 2 is capable of handling larger lookup tables so this limit should be removed Users should be able to create animations movies of their VoluViz sessions and take snapshots for presentation purposes An effort to integrate volume and geometric shapes using Coin has started VoluViz should support the HDFS file format in addition to HDFA For a list of known bugs and possible future extensions see the todo file in the VoluViz root directory 20 A APPENDIX A 1 Volume file format VoluViz loads files in the HDF4 2 file format developed by NCSA The HDF4 library comes with its own routines for handling HDF files VoluViz uses HDF4 Scientific Data Sets SD APD to open and read files A Scientific Data Set SDS is a group of data structures used to store and describe multidimensional arrays of scientific data A HDF file can contain several Scientific Data Sets A VoluViz HDF file contains at least one SDS containing byte data luminance Multi field data sets contain additional SDSs e g luminance alpha They may also contain a SDS describing the domain coordinates The coordinate type uniform unstructured etc is stored in a SD attribute called coord_type N
17. tion on vzParameterLookupTable and vzParameter VolumeTexture in 4 Note that all VoluViz color tables have 256 entries This is due to the fact that VoluViz only supports unsigned byte textures The Color editor also supports saving and loading of color tables Load and save functionality can be accessed from the Color editor file menu 1 4 Example This is a step by step example of using VoluViz to view a volumetric data set using most of the features present in VoluViz 1 Open a data set by choosing File Open see figure 1 3 11 25 X Center 127 127 X Size 1 256 FE AL Y Center 127 127 Y Size 1 256 25 Z Center 127 127 Z Size 1 256 Figure 1 4 Volume loaded and ready Press the apply button in the subset dialog box to load and render the volume see figure 1 4 Open the Color editor by choosing Edit Color editor Create a suitable color table using the Color editor see figure 1 5 Enable the clip plane by choosing View Clip plane see figure 1 6 Choose View gt Bounding box to display an axis aligned boundig box around the volume Position the volume using the mouse see figure 1 7 Change the background using Edit Background 12 Ele Edit View Figure 1 7 Positioning the volume X Center 127 127 X Size 1 255 ud Y Center 63 191 Y Size 1 256 Z Center 127 127 Z Size 1 256
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