Home

VolView 2.0 User's Guide

Contents

1. 4 8 Kl 35 nearest neighbor interpolation 35 New Window raranananranananvnnananrnnenannnnene 23 Noise Suppression Filters 56 Number of columns rows 61 Number of frames raranararannrnrnrnrnrnrnrnenr 27 Number of labels oococcccccccococononono 29 Number of eurtaces a a E 46 A E a O 70 O Oblique Probe ccccecseceeeeeeeeees 18 50 Obtaining a Trial Uicense 5 OnLine e Ee E 24 OD ACI tegen 29 35 58 OPEN ll ua 8 14 20 Open File Ward asia 14 OPEN Recent E 14 20 Open WIZ ANG EE 8 16 MENN ee 16 Orientation Marker rrrnnnnnnnnnnnnnnvannnnnnnnr 29 Sid Lal 16 64 P Page DONN sagaene 43 A e 20 A O A A 43 Piso 42 43 DAN ANS DE 11 21 67 perspective escarlata 11 21 67 physical Coordinates cceceeeeeeeeees 62 PAVSIC Al SI 64 EES tee Ee 65 Plugin Life Gy Cle EE 78 PN 14 PIN resa nende 14 Polar 68 OE A In 75 EIN ed 27 PENG N 7 PUM a EEEE E ENEA ee 20 Printing Gcreenshbots 75 9 0 5 PE 21 Probe Information 62 POCOS SD Ald E 78 Professional Mode 3 4 24 Professional Mode Features 4 progress gauge asi 11 Projection KEEN 67 Property Panels NN 18 Purchase VOIVIOW conociste 7 R RAS coordinate sevsiem 9 26 RAW DAA oster 14 16 RAM SCIAS serpet ara Se 9 58 Raw Scalars Opacity Modulated 58 VS 70 Refresh Volume Wmdow 70 Region Growimg 56 A A TE 24 Registration Ward dy Remo
2. Here is what happens when you enable this mapping At each location in the volume we have computed a gradient direction and a gradient magnitude This mapping will assign a value between 0 and 1 to each gradient magnitude This mapping is a simple ramp the mapping from the first node to the second will be a constant value usually you want this to be zero but you can increase this by moving the first node up The mapping from the second to third node is a linear ramp and all values past the third node will be mapped to 1 0 After we look up the opacity at a sample point based on scalar value using the Scalar Opacity Mapping function we then multiple this Opacity by the modulation value obtained from the Gradient Opacity Mapping function By eliminating samples with low gradient magnitude values from the image we are effectively doing an edge detection Operation during rendering This dataset was obtained by CT which tends to produce data with sharp transitions between air and soft tissue and soft tissue and bone You can see in the image on the right that the nearly constant valued region between the skin and the bone is eliminated due to the low gradient magnitudes in the area Spend some time adjusting the gradient opacity mapping and turning it on and off to get a good idea of how this mapping will affect your image Now we will adjust the color settings Start by selecting the folder icon in the Scalar Color Mapping are
3. od gt GetPointData gt GetScalars gt GetMaxId 1 od gt GetPointData gt GetScalars gt GetDataTypeSize clean up ii gt Delete ig gt Delete return 0 atic int UpdateGUI void inf vtkVVPluginInfo info vtkVVPluginInfo inf info gt OutputVolumeScalarType info gt InputVolumeScalarType info gt OutputVolumeNumberOfComponents info gt InputVolumeNumberOfComponents memcpy info gt OutputVolumeDimensions info gt InputVolumeDimensions 3 sizeof int memcpy info gt OutputVolumeSpacing info gt InputVolumeSpacing 3 sizeof float memcpy info gt OutputVolumeOrigin info gt InputVolumeOrigin 3 sizeof float return 1 tern C 1 id VV_PLUGIN_EXPORT vvVTKGradientMagnitudelnit vtkVVPluginInfo info always check the version vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUI info gt SetProperty info VVP NAME Gradient Magnitude Filter VTK info gt SetProperty info VVP GROUP Utility info gt SetProperty info VVP TERSE DOCUMENTATION Calculate the Gradient Magnitude info gt SetProperty info VVP FULL DOCUMENTATION Compute the 3D gradient magnitude of the input volume The resulting volume has the same dimensions etc as the input volume info gt SetProperty info VVP SUPPORTS IN PLACE PROCESSING 0 info gt SetProperty into VVP SUPPORTS PROCE
4. Table Of Contents algorithm 8 Now you should have working source code that you need to compile into a DLL or shared module on UNIX The plugin interface support quite complex operations and I recommend looking at some of the other plugins source code to see how they work and get ideas for what can be done SE include vtkVVPluginAPI h include lt string h gt include lt stdlib h gt include lt stdio h gt ifdef MSC VER pragma warning disable 4710 tendif template lt class IT gt TODO 1 Rename vvSampleTemplate to vv lt your_plugin gt Template void vvSampleTemplate vtkVWPluginItnfo info vtkVVProcessDataStruct pds EE Gi IT inPtr IT pds gt inData IT xoutPtr IT pds gt outData int dim info gt InputVolumeDimensions int inNumComp info gt InputVolumeNumberOfComponents int i jJ k l int abort TODO 10 Get your GUI values here loop over the slices for k 0 k lt dim 2 k update the progress status info gt UpdateProgress info float 1 0 k dim 2 Processing see if we should abort abort atoi info gt GetProperty info VVP_ABORT_PROCESSING loop over the rows and handle aborts for J 0 labore amp amp Jj lt dim 1 j loop over the columns for i 0 i lt dim 0 i loop over the components for 1 0 1 lt inNumComp 1 TODO 11 put your algorithm code he
5. To load an appearance settings file select the VolView Appearance Settings option from the Files of type menu find the file using the Open File browser and press the Open button An appearance settings file contains the parameters from the Appearance panel You can save these parameters using the Save Appearance Seitings option on the File menu It is often useful to save an appearance file when you must process multiple files of the same type in a similar way For example if you are analyzing a set of CT scans of the lungs you may find that the color and opacity mappings for one lung dataset work well for the entire set VolView supports both 3D volume and 2D series of images data sets in a variety of formats as shown below Since these data files do not contain all the information that may be necessary for accurate visualization a wizard will open to guide you through setting these values The next section will cover the wizard in more detail In order to load a 3D data file simply locate it using the Open File browser press Open then follow the instructions on the wizard To open a series of 2D data files locate any one of the files from the series and press Open VolView should automatically detect the entire set of images in the series provided that they all reside in the same directory they all have the same basic parameters such as width and height and they follow some simple naming pattern such as image 1 tif image 2 tif e
6. cceceeeeeeeeeeeeeeeeeees 25 window layout Toolbar 26 Window Menu 23 Window Level ocococcccococcccocccccconoconconono 9 X X rotation Lazimuih cece ee eeeeeeees 27 EY Axial Image se 18 XYZ coordinate system 26 X Z Frontal Image 18 Y Y rotate elevation ooococccccococococonononos 27 Y Z Sagittal Image cccceeeeeeeeee eee ees 18 Z A Ol NEE 27 ZEISS E EE 14 ZOON EE 42 43 LN Se aben 27
7. Example A C Filter This is the C code for the Utilites Boundary filter include vtkVVPluginAPI h include lt string h gt include lt stdlib h gt include lt stdio h gt define SetPixel info ptr value Switch info gt OutputVolumeScalarType case VIK_CHAR char ptr 0 char value break case VTK UNSIGNED CHAR unsigned char ptr 0 unsigned char value break case VIK SHORT short ptr 0 short value break case VTK UNSIGNED SHORT unsigned short ptr 0 unsigned short value break case MIR LONG long ptr 0 long value break case VIR UNSIGNED LONG unsigned long ptr 0 unsigned long value break case VIR INT int ptr 0 int value break case VIR UNSIGNED INT unsigned int ptr 0 unsigned int value break case VIK_FLOAT float ptr 0 float value break case VTK_DOUBLE double ptr 0 value break static int ProcessData void inf vtkVVProcessDataStruct pds vtkVVPluginiInfo info vtkVVPluginInfo inf double replacementValue atof info gt GetGUlProperty info O VVP_GUI_VALUE int dim info gt InputVolumeDimensions unsigned int rsize info gt InputVolumeScalarSize int i j k unsigned char ptr unsigned char pds gt outData for k 0 k lt dim 2 k 3 EOS APS OF Y lt dimbl Js Pt if j 0 k 0 j dim 1 1 k dim 2 1
8. Volume Display The Volume Display panel provides some basic controls that affect the display of the volume This includes the blending function used during rendering the sampling rate used for rendering the background color of the volume display window and controls for adjusting the level of detail rendering method The Window Menu The Window menu allows you to control the appearance of the application window and to create a new VolView window The appearance controls include the ability to show hide the left panel and a set of standard layout options for the display windows Note that these layout options in order from top to bottom match the layout options on the layout toolbar in order from left to right You can create custom layouts by beginning with one of these standard options then using the pulldown menu on the left side of the title bar of a display window to adjust the type of window Each of the menu items is described in more detail below Hide Show Left Panel This option will toggle the visibility of the left panel If you hide the left panel then choose a panel to display from the View menu this panel will once again be shown 1 volume The entire display area is filled with a volume display window 1 lightbox The entire display area is filled with a lightbox 1 over 3 The display area is divided so that one volume display window is over 3 image window The three image images will be the XY Axial Image window
9. You Material Properties can edit that material properties including EN FIT the ambient diffuse and specular coefficients and the specular power by Diffuse hitting the small sphere representing the Specular FT current shading parameters next to the Edit material label This will pop up the Material Properties editor with four sliders Preview Presets for these four values plus four convenient 3 presets for no shading diffuse only shading diffuse with some specular and highly specular shading An example of this interface is shown on the right Power When the Enable Shading button is off the lighting parameters in use are equivalent to full ambient with no diffuse or specular contributions The values specified here are only applicable when shading is enable Ambient is a non directional term that will uniformly increase the brightness in the image Diffuse lighting is dependent on the angle between the normal and the vector to the light source When the light is shining perpendicular to the surface it will receive the most illumination dropping off to 0 when the angle reaches 90 degrees Specular is the shiny term and is dependent on the normal direction the light vector and the viewing vector This can be thought of as a reflection of the light source in a shiny object The specular power adjusts the focus of this reflection a small power will mean an unfocused reflection such as you would see in brushed met
10. co Delete setup the input vtkImagelmport ii vtkImagelmport New ii gt SetDataExtent 0 dam 01 gt 1 0O dim 1 1 O dim 2 1 ii gt SetWholeExtent 0 dim 0 gt 1 0 dim 1 1 0 dim 2 1 ii gt SetDataScalarType info gt InputVolumeScalarType 11 gt SetNumberOfScalarComponents info gt InputVolumeNumberOfComponents ii gt SetDataOrigin info gt InputVolumeOrigin ii gt SetDataSpacing info gt InputVolumeSpacing ii gt SetImportVoidPointer pds gt inData ig gt SetInput 1i gt GetOutput get the output would be nice to have VIK write directly into the output buffer but VIK is often broken in that regard so we will try but check afterwards to see if it worked vtkImageData od ig gt GetOutput od gt UpdateInformation od gt SetExtent 0 0 0 0 0 0 91 Table Of Contents st ex VO od gt AllocateScalars int size dim 0 dim 1 pds gt NumberOfSlicesToProcess info gt InputVolumeNumberOfComponents od gt SetExtent 0 dim 0 1 O dim 1 1 pds gt StartSlice pds gt StartSlice pds gt NumberOfSlicesToProcess 1 od gt GetPointData gt GetScalars gt SetVoidArray pds gt outData size 1l run the filter od gt SetUpdateExtent od gt GetExtent od gt Update did VIK not use our memory if od gt GetScalarPointer pds gt outData memcpy pds gt outData od gt GetScalarPointer
11. interface areas Reset Interface If you would like to revert all areas back to their default positions removing the effect of all drag and drop operations on the interface press this button This option is useful when you wish to only move some areas temporarily but do not wish for this change to persists Otherwise moving an interface area to a new position will be a persistent change saved across sessions of VolView 25 Table Of Contents Toolbar Settings The Toolbar Settings area of the Application Toolbar Settings x Settings panel allows you to enable or Flatframe disable the toolbar for window layout and to 7 flat buttons control the appearance of this toolbar The upper image on the right represents the Toolbar Settings user interface while the image on the bottom shows the window layout toolbar which appears below the main menu bar when enabled Each of the three check boxes is described in more detail below IE AE ee Flat buttons Checking this option will emove the raised frame around each of the buttons in the toolbar Ivf Show window layout toolbar Flat frame Checking this option will remove the raised frame around the toolbar Show window layout toolbar The toolbar will be displayed when this box is checked otherwise it will be hidden This toolbar duplicates functionality available on the Window menu and therefore is optional Pressing a button in the toolbar will cause the display windows t
12. rather than four independent properties for example the temperature density charge and index of refraction You may load data that has up to 4 independent components You may also load data with 2 non independent components where the first is used to derive color and the second value is used to derive opacity When loading RGBA color data the data type must be unsigned char Scalar ranges The scalar range minimum and maximum values found in the dataset for each of the components will be displayed Markers 3D Cursor The 3D Cursor area on the Markers panel 3D Cursor X allows you to embed a cursor in the 3D F pisplay 3D cursor Type Cross hairs volume This interface area will appear similar to the example on the right The ex Pesiton 21 43 32 cursor will also be displayed in the three axis L R Axis Units 22 00 a aligned image windows In the image oa asis Units AAA fs windows the cursor IS an interactive annotation element 1 S Axis Units Sil 32 50 Li Two types of cursors are supported through a pulldown planes or cross hairs If Planes is selected the 3D cursor will be represented by three planes a red plane orthogonal to the X axis a green plane orthogonal to the Y axis and a blue plane orthogonal to the Z axis The position of these planes is controlled by the slider values If Cross Hairs is selected the 3D cursor will be represented by 3 lines a red line parallel to the X
13. ApplyThresholdFilterMacro COMPARISON ine e Je KS for k 0 k lt dim 2 k info gt UpdateProgress info float 1 0 k dim 2 Thresholding abort atoi info gt GetProperty info VVP_ABORT_PROCESSING for T 0r Tabort 8 7 lt dame are for i 0 i lt ne dim 0 i if ptr COMPARISON compVal ptr assignVal a info gt UpdateProgress info float 1 0 Thresholding Complete HHK a A ier HHS HI GO GP HH GF FG template lt class IT gt void vvThresholdTemplate vtkVVPluginIinfo info vtkVVProcessDataStruct pds IT IT ptr IT pds gt outData int dim info gt InputVolumeDimensions double v1 atof info gt GetGUIProperty info 1 VVP_GUI_VALUE double v2 atof info gt GetGUIProperty info 2 VVP_GUI_VALUE const char label info gt GetGUIProperty info 0 VVP_GUI_VALUE int abort 0 IT compVal IT vl IT assignVal IT v2 int nc info gt InputVolumeNumberOfComponents if strcmp label lt ETE lt EE ET E E E T lt ee Me Eg EEE 88 ApplyThresholdFilterMacro gt if strcmp label gt d ApplyThresholdFilterMacro gt static int ProcessData void inf vtkVVProcessDataStruct pds vtkVVPluginInfo into gt vtkVVPluginInfo inf switch info gt InputVolumeScalarType invoke the appropriate templated function vtkTemplateMacro3 vvThresholdTem
14. Bindings area on the Bindings panel allows you to view and modify the mouse bindings for the image display windows This interface will appear similar to the example shown on the right A set of adjustable operations are displayed as a grid covering the left middle and right mouse buttons pressed alone or in conjunction with Image Mouse Bindings x Button Only Button Shift Button Control Left WL Zoom Dan Middle Pan au wi Zoom i Right Zoom Pan WL the shift or control keys A description of each of the possible operation choices is given below W L Press the specified mouse key combination and drag to apply a window and level operation to the image Motion to the right increases the window value and to the left decreases the window value Downward motion increases the level and upward motion decreases the level These operations control brightness and contrast of the images in the image window Adjusting window and level values is linked across all image display windows Pan Press the designated mouse key combination and drag to move the image Pan operations are linked only across the lightbox views Zoom Press the mouse key combination and drag to zoom in or out Upward motion zooms in downward motion zooms out Zoom operations are linked across the three image windows Zoom operations are linked across all image display windows Image Keyboard Bindings The Image Keyboard Bindings area
15. Colors area on the Image Display panel Colors allows you to change the background color Hi Backoround E of all the image display windows There is only one button in this area which displays the current background color and shown in the example on the right When this button is pressed a color selector dialog will be displayed The appearance of this dialog will be system dependent and will look similar to the one shown below for most Windows platforms Use the color selector to choose a new background color then press OK to accept this color Note that unless you zoom out your image may fill the entire image display window and you may not see this background color This background color affects all image display windows including the three image windows the lightbox window and the oblique probe window Background Color Basic colors WI FAT BAG WI FP WPS WE A A A WS EA fete AA EER EEE ES Custom colors TERRE HANNA ei eeo w0 est Colorisolid Lum o Blue o Add to Custom Colors Probe Information The Probe Information area on the Image Probe Information Display panel provides details on the Position 18 0677 32 45 9283 microns underlying scalar value at the mouse position 17 31 44 voxels when the cursor is moved over an image ale 49 density window The appearance of this ar
16. Cropping tool 2D 3D markers Improved system performance and feedback Integrated animation tool Improved transfer function editor with more presets Oblique probe oblique image vew Automatic initial transfer function based on data Improved lighting control Redesigned user interface with customizable panels Two modes Professional and Free As of version 2 0 VolView can be used in one of two modes Free Mode or Professional Mode In Free Mode VolView has all of the basic data loading visualization and image processing functionality In Professional Mode advanced functionality such as interactive annotation animation and collaboration are added More information on these two modes is provided in the next two sections A trial license of VolView in Professional Mode is available with details on how to obtain this license provided later in this chapter This document is intended as both a tutorial and a reference guide The Quick Tutorial session will take you step by step through a typical VolView session including loading data viewing images and volumes adding annotation creating contours and applying an image processing filter This is a good place to start if you are a new VolView user The remainder of this document acts as a reference guide All users are encouraged to read the section on The User Interface as this documents many features that are new to VolView 2 0 For help on a particular setting on the interface you will find
17. Geodesic Active Contour method for segmenting a volume All the necessary preprocessing is packaged in this module This makes it a good choice when you are already familiar with the parameters settings requires for you particular data set When you are applying GeodesicActiveContour to a new data set you may want to rather go step by step using each one the individual filters Please experience first with the FastMarching modules since it is used here for preprocessing the data set before applying the GeodesicActiveContour filter Shape Detection Module ITK This module applies a Shape Detection level set method for segmenting a volume All the necessary preprocessing is packaged in this module This makes it a good choice when you are already familiar with the parameters settings requires for you particular data set When you are applying ShapeDetection to a new data set you may want to rather go step by step using each one the individual filters Please experience first with the FastMarching modules since it is used here for preprocessing the data set before applying the ShapeDetection filter Watershed Module ITK This module applies a Watershed method for segmenting a volume All the necessary preprocessing is packaged in this module This makes it a good choice when you are already familiar with the parameters settings requires for you particular data set When you are applying Watershed to a new data set you may want to rather go step b
18. about saving sessions please see the Saving Results chapter Save Appearance Settings You can save a file with the settings from the Appearance property sheet so that you may load this at a future time This includes the functions Application Settings mapping scalar value to color and opacity the function mapping gradient magnitude to opacity the weighting values for datasets with more than one component and the shading parameters These files will have an extension of vvt and can be loaded using the Open dialog For more information on saving appearance settings please refer to the Saving Results chapter Save Volume If you have modified the volume through a filtering operation or if you would like to change the format of your volume for example from DICOM to a series of jpeg files you can use the Save Volume feature For more information on this feature see the Saving Results chapter Save Screenshot This option will capture an image of all the display area and save this image to a file on your disk This image will include the image from each of the display windows in the same configuration as seen on the screen For more information on this functionality see the chapter on Saving Results Save Surfaces If you have created a surface either through a contouring operation from the Contours panel or through a filter you can save this surface using this option All surfaces will be saved into a single file and you can select f
19. appear similar to the ray cast images for a particular data set For example if you wish to generate an animation quickly it may be best to force the animation to be created with hardware acceleration rather than the more time consuming but more accurate ray casting method Include Hardware You may choose to use hardware acceleration if it is available or to turn off hardware acceleration entirely Generally this option should be left in the If Available state and a 3D texture mapping approach will be employed for interaction when supported by the graphics hardware on your system and the type of data you have loaded Currently VolView support 3D texture mapping for NVidia GeForce 3 4 or FX and for the ATI Radeon Pro 9700 This support is only available if you have data with a single component or multi component data that is not independent color alpha RGB or RGBA data Refresh Volume Window This button will redraw the volume display window This can be useful when you have changed a rendering preference such as turning off ray casting and would like to see the resulting final image Colors The Colors area on the Volume Display Loos x panel allows you to change the background background color color of the volume display window There is only one button in this area which displays the current background color and shown in the example on the right When this button is pressed a color selector dialog will be displayed The a
20. being passed as third argument of the SetProperty method should be used for the text label of the plugin in the GUI Other non GUI properties are also set with this method For example we specify whether this filter is capable of performing in place processing or not whether it allows to process data in pieces streaming or not We also provide an estimate of the memory consumption that will result from the execution of the filter This last information is provided in the form of an estimation of number of bytes to be used per voxel of the input data set Memory consumption estimation is of fundamental importance for the successful coupling between VolView and the plugin VolView will use this factor for making sure that the system has enough memory for completing the processing of the plugin and for determining if the undo information can be kept Note that this estimate is not based on the size of the final data set produced as output but on the total amount of memory required for intermediate processing In other words it should provide the peak of memory consumption during the plugin execution The initialization function in this case vvITKGradientMagnitudelnit will be called only once during the start up process of VolView The ProcessData function The ProcessData function actually performs the computations on the data The signature of this function is static int ProcessData void inf vtkVVProcessDataStruct pds where the fir
21. blending function was set to none so that only the surface contour is displayed in the volume display window The properties of the contour in 3D and 2D can be controlled within the Configure Contour area covered later in this chapter es A a D Ate WIR Level 127 5 Level 127 5 Frontal ice 00 BIR dene ETTE DR fen The Add Contour region provides the following functionality Isovalue This slider can be used to adjust the isovalue that will be used for creating a contour In addition a text entry box is used to display the isovalue and can be used to manually modify this value Component When working with more than one independent component this pulldown can be used to choose which component will be processed to generate the contour For non independent data luminance aloha and RGBA the last alpha component is always used Add Contour At Isovalue Press this button to add the contour You can remove the contour from the Configure Contour area 45 Table Of Contents Configure Contour The Configure Contour area of the Contours Configure Contour x panel is activated once a contour has been active contour created and can be used to adjust the appearance of the contour and generate isbility iv basic statistics about the contour AN color surface by scalars E example of this interface is shown on the eege O right Surface property The Configure Contour area su
22. by MetaMorph and the MetaMorph Imaging Series applications These files are a derivative of the TIFF format and typically have a stk extension Analyze Analyze files are created from the Analyze volume visualization application and will typically have a hdr extension Visualization Toolkit VTK VolView can read files written by the Visualization Toolkit This includes image data stored in the older vtk format as well as the newer vti format VolVis VolVis files are created from the VolVis volume visualization application and will typically have a slc extension BMP Images A series of Windows bitmap files can be read to form a volume The extension is typically bmp JPEG Images VolView can read a series of jpeg image files to form a volume The extension is typically jpg or jpeg PNG Images A series of PNG files can be read to form a volume The extension is typically png PNM Images VolView can read a series of pnm files to form a volume The extension of these files may be pnm pgm or ppm TIFF Images A series of TIFF images can be read to form a volume The extension is typically tif or tiff Raw Data Raw data files may be a series of 2D raw files or one 3D raw files Raw files contain a header followed by X Y C or X Y Z C in 3D data values where X Y and Z are the dimensions of the data and C is the number of components In addition to using the Open File option on the File menu to load data you
23. can also select a recently viewed file from a list using the Open Recent File option on the File menu When you load data this way the parameters that you entered previously on the Open File Wizard will be retrieve and the Open File Wizard will not be displayed If you need to change some configurable parameter in the Open File Wizard you should instead use the Open File option This option will always display the wizard even though the previous values could be retrieved from the auxiliary vvi file stored when you last opened this dataset Table Of Contents The Open Wizard The Open Wizard will guide you through setting parameters that could not be retrieve directly from the data you are opening In addition it allows you to change some automatically determined values The exact appearance and configuration of this wizard will depend on the dataset you are opening A few examples are given here to guide you through entering the values in this wizard Depending on your data you may not encounter all of these dialogs and you may encounter them in a different order than presented here When opening a series of image files the first page displayed by the Open Wizard will appear similar to the example shown below In this dialog you will see the file pattern in a Gstyle notation as well as the starting and ending image numbers You can adjust the starting and ending slice values in order to read only a subset of the data if desired P
24. center top in white italic Times Also shown in the image are a bounding box a color bar an orientation widget and a color bar Color Bar The color bar is a graphical representation of the color mapping that is currently applied to the scalars in the volume window This is an interactive annotation element There are aspects of the color bar that can be controlled with the interface such as toggling the visibility adjusting the labels a setting the title In addition there are aspects of the color bar that can be controlled interactively using the mouse in the volume display window For example you can scale the color bar switch the orientation between horizontal and vertical and adjust the placement of the color bar in the window In the example image near the end of this section you can see a color bar oriented vertically along the right side of the volume display window You can toggle the visibility of the color bar with the Display color bar toggle button By pressing the Edit button you will bring up the control panel for the color bar which will appear similar to the example shown on the Volume Color Bar E Color Bar tel Title properties Color C Font Arial iil Style IBlr s Opacity ho Label text properties Color C Fant Arial Style IBlr s Opacity 1 Maximum number of colors eu Number of labels Close Annotations right Each of the items in this control panel will be descr
25. chapters matching the tab labels with Table Of Contents sub sections matching the labeled frame around the interface elements Detailed information on each button entry slider and option can be found in these sections This documentation has been developed for VolView version 2 0 We suggest you check the VolView home page at http www kitware com products volview html for any updates news or frequently asked questions Free Mode Features VolView 2 0 can run in one of two modes Free Mode or Professional Mode You may obtain a trial license of VolView in Professional Mode once per computer Please see the section on Obtaining a Trial License for more information on how to do this If you have not yet obtained a trial license or if your license has expired VolView will run in Free Mode Although many advanced features will not be available VolView in Free Mode is still a powerful tool for volume visualization and image processing providing all the functionality necessary to perform these tasks When running VolView in Free Mode you will see the entire user interface but some regions will be locked indicating that the functionality is available only in Professional Mode A small lock icon will appear next to the label in each disabled area of the interface In Free Mode the following functionality is provided Ability to load any supported data type Appearance editor for material classification and shading Blending function
26. data is highly overlapping a voxel may be highly opaque in more than one component then using lower values on the slider will reduce the change of oversaturating the image 41 Table Of Contents Bindings Volume Mouse Bindings The Volume Mouse Bindings area on the Bindings panel allows you to view and adjust the mouse bindings for the volume window This interface will appear similar to the example shown on the right A set of adjustable operations are displayed as a grid covering the left middle and right mouse buttons pressed alone or in conjunction with the shift or control keys A description of Volume House Bindings x Button Only Button Shift Button Control Left Rotate Roll Roll Middle Pan Fly In Fly In Right Zoom Fly Out Fly Out Fly speed IS 10 00 each of the possible operation choices is given below Rotate Press the designated mouse key combination in the Volume window and drag move the mouse without releasing the button to rotate the volume and any 3D annotation For example mouse movement to the right will cause the volume to rotate around to the right Pan Press the designated mouse key combination and drag to move the volume and any 3D annotation For example mouse movement to the right will cause the volume to move to the right Zoom Press the designated mouse key combination and drag to move in closer or farther from the volum
27. gt element except that the label will be Slice Header Annotation The header annotation for the image windows functions the same as the header annotation for the volume display window Use the toggle button to turn on the header annotation and press the Edit button to bring up the header annotation dialog This dialog will allow you to set the string that you want displayed at the top of the window along with the text properties such as color font style and opacity Scale Bar The scale bar can be used to indicate scale using a small ruler drawn on the image window The scale bar in the image window behaves the same as the scale bar in the volume window You can use the toggle button to toggle the visibility of this element and you can change the color It is an interactive element that you can reposition and resize Please see the Volume Annotations section for more details Distance Measurement The distance measurement tool is a line with two spheres at the endpoints A measurement value is displayed indicating the distance between the two endpoints This is an interactive annotation element in that you can reposition the text label and you can move each endpoint or the whole measurement line For more 33 Table Of Contents 34 information on the interaction with this annotation element please see the Volume Annotations section Angle Measurement The angle measurement tool is an angle indicator two lines with three endp
28. in the Bindings panel allows you to view the keyboard shortcuts for the image display windows An example of this interface is shown on the right Each of the keyboard shortcuts are described in more detail below Keep in mind that the image window must have keyboard focus the title bar area of that window will be blue in order for the shortcuts to work Image Keyboard Bindings 4 zZ Display previous slice gt Display next slice Page Up Move backward 10 slices Page Down Move Forward 10 slices Home Display first slice End Display last slice i Reset camera and window level p Place a 3D marker on the slice m Toggle 2D marker visibility Left Arrow Display the previous slice in this image window In the lightbox this will shift all images down by one slice This shortcut will have no effect in the oblique view Right Arrow Display the next slice in this image window In the lightbox this will shift all images up by one slice This shortcut will have no effect in the oblique view Page Up Move back by 10 slices in the XY XZ or Y Z image display window In the lightbox this will move back by the number of images displayed in the lightbox For 43 Table Of Contents 44 example in a 4x3 lightbox the Page Up key will move back by 12 slices This shortcut will have no effect in the oblique view Page Down Move forward by 10 slices in the XY XZ or Y Z image display window In the lightbox this will move back by the n
29. level values You should now see an image similar to the one shown on the right In this mapping mode the scalar values are mapped through the colormap but the window level is applied to the original scalar value The result of this window level a value between 0 and 1 is multiplied by the color This tends to produce saturated colors in areas of high image intensity and black values in areas of low image intensity Step 3 Interact With The Volume Now we will focus on interaction in the volume display window At this point you should switch back the position of the Sagittal image and the volume display You can do this by selecting Volume from the pulldown menu in the large display area that is currently assigned to a Sagittal Image The Volume window should appear similar to the one shown on the right Note that the volume display window contains both the pulldown on the left for selecting window type but also a progress gauge on the right This progress gauge is used during rendering to show the progress of the displayed image In the example we see a progress bar with three distinct regions one drawn in dark blue another in light blue and one in green The blue color indicates the levels of detail that are drawn using a hardware accelerated approach The green color indicates the level of detail that is drawn using a ray casting technique This example was run on a system with a GeForce 3 graphics board allowing for hardwa
30. massar 69 EMP er 14 Seite Ein EE 53 BOUNGING BOX artis 29 C E GE 86 GEE Pile EE 88 Canny Edge Detection ITK 54 Canny Segmentation LevelSet Model ITK ET EE T 55 Check For Updates o ocococcoconccocooo 6 24 NOS EE EE 20 EE Eeer 29 68 ele EE 29 Color Mapped ScalarS oooocoococccccconcn 9 58 Color Mapped Scalars Opacity Modulated ee ee 9 58 818 01 1 Ge EE 9 COOS asados 62 Component eissien 29 35 45 Component Artbmatc 53 Component Weights cccceceeeeeeeeees 35 LGomponents raei 64 COMPO SIL ur ca 69 Compute statistics occoconococcnnonenocos 46 Seiuleif el RBE 7 24 Confidence Connected ITK 56 Configure Contour arnrnarnrrernrnavnrnaverner 46 COnN rata geed Sa 25 Connect to Remote o ococcocccccnccnconcnoo 20 76 Connected Threshold ITK 56 Connecting And Passing Control 76 Be alte LEE 45 46 74 CONTOU ele 46 CONO US E 21 Corner Anota OM 29 GOD EN 53 COD DING ua 21 48 49 50 A O 48 HA II 65 E AE ii id 8 11 14 Curvature Anisotropic Diffusion ITK 56 Curvature Flow IK 56 customer feedback oocococococononenenonononoss 6 D BC e de ERE EE 64 pala VOC E 64 DICO Mi sai ab il 14 73 DIUS Sos aras it lla 11 35 Dilate Filter VK 1 pe 56 Display 3D markerg 65 Display Windows oooooococococococococococonononos 18 8 510 ge A 21 Distance Measurement rranununnnn
31. memcpy info gt 0utputVolumeOrigin info gt InputVolumeOrigin 3 sizeof float return 1 void VV_PLUGIN_EXPORT vvBoundarylInit vtkVVPluginInfo info always check the version vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUI info gt SetProperty info VVP NAME Boundary info gt SetProperty info VVP GROUP Utility info gt SetProperty info VVP_TERSE_DOCUMENTATION Replace all boundary outside edge voxels with the specified value info gt SetProperty info VVP FULL DOCUMENTATION This filter performs a voxel replacement replacing every voxel that is a boundary voxel with the specified value Boundary voxels are the voxels that have at least one face on the boundary of the volume Put another way boundary voxels are voxels that are not fully enclosed by other voxels info gt SetProperty info VVP_SUPPORTS_IN_PLACE PROCESSING 1 info gt SetProperty info VVP_SUPPORTS_PROCESSING_PIECES Ve ek info gt SetProperty info VVP REQUIRED 7 OVERLAP ONNA info gt SetProperty info VVP_NUMBER_OF_GUI_ITEMS Ivy 87 Table Of Contents Example 2 A C Filter This is the C code for the Utilities Threshold filter include vtkVVPluginAPI h include lt string h gt include lt stdlib h gt include lt stdio h gt ifdef MSC VER pragma warning disable 4710 endif define
32. out current address is 192 168 1 79 press connect Note to connect through a firewall you Address must open ports 2255 and 2256 In addition the data ffkam 25 is not encrypted so do not send sensitive information Connect Cancel across public networks The session that makes the connection will initially have control You can see this by looking the bottom right corner of the application A connection icon will be displayed in green on the system that has control and in red on the system that is in viewing mode An example image is A VolView 2 0 Remote Connect Seles shown here for the active session LZ To pass control the user with the active session can click on the connection icon This will give control to the other session and the color of the connection icon will toggle in both sessions 76 Extending Filters With Plugins In the viewer session the entire user interface except for the Disconnect From Remove Close and Exit options on the File menu will be disabled If any of these options are selected by the viewer the two sessions will be disconnected The active session can now load a dataset Once the data is loaded in the active session it will be sent to the viewer session Any interactive performed in the active session will be reflected in the viewer session This includes direct interaction is the display windows such as rotating zooming or adjusting window level values This also include
33. settings It also SS SE provides a way to save your favorite window Pee Presets Abee level settings and restore them at a later Add Preset Remove Preset Remove All Presets time This interface appears as shown on the right The window and level settings will affect all displayed images including the three axis aligned image windows the lightbox window the oblique probe window and the display of the oblique probe in the volume window Each of the interface elements is described in more detail below Window and Level entries The entry boxes for Window and Level serve two purposes First this allows you to see the current window and level settings Typically this information is also displayed in the lower right corner of each image window but if you have turned off the corner annotation then this is the place to find the current window and level settings In addition you can change the window and level settings by typing new values in these text entry boxes The new values will take effect when you press enter in the text box or when you click on another user interface element 60 Information Window and Level are two basic values that can adjust the contrast and brightness of your image These values will depend on the underlying type of your data and how you are viewing it The default Window value will be the range of your data the largest value found in your dataset minus the smallest value found in your datas
34. the XZ Frontal Image window and the Y Z Sagittal image window from left to right 2 over 2 The same four windows will be displayed as in the above option but in a 2x2 grid of windows The volume will be on the top left with the XY Axial Image window on the top right the XZ Frontal on the bottom left and the Y Z Sagittal on the bottom right 1 over 1 Two display windows will be arranged one on top of the other with the top window being a volume display and the bottom being an XY Axial Image window 1 beside 1 Two display windows will be arranged one next to the other with the left window being a lightbox and the right window being an X Y Axial Image window 1 over 2 This layout has a volume window on the top with an XY Axial Image window on the bottom left and an X Z Frontal Image window on the bottom right 1 beside 2 This layout has a lightbox window on the left with an XY Axial Image window on the top right and an XZ Frontal Image window on the bottom right 2 over 3 Five windows are display with two on top the volume on the left and the lightbox on the right and three on the bottom the three Image windows in the same configuration as the 1 over 3 layout 3 over 3 This layout is similar to the 2 over 3 layout but now three windows are on the top the volume on the left the lightbox in the middle and the oblique probe window on the right New Window This option will open a new VolView applicati
35. the firts component of the second volume Threshold This filter performs a pixel replacement replacing pixel in the original data by a specified replacement value The pixels to be replaced are determine by comparing the original pixel value to a threshold value with a user specified comparison operation This filter operates in place and does not change the dimensions data type or spacing of the volume Gradient Magnitude Filter VTK Compute the 3D gradient magnitude of the input volume The resulting volume has the same dimensions etc as the input volume Surface Generation Filters The Surface Extraction category provides two filters for extracting surfaces one intended for smooth surfaces from binary data and the other which extracts a surface from a secondary dataset More details are provided below Anti Aliasing ITK This filter applies a level set evolution over a binary image in order to produce a smoother contour that is suitable for extracting iso surfaces The resulting contour is encoded as the zero set of the output level set The zero set will be rescaled as the mid value of the intensity range corresponding to the pixel type used This filter processes the whole image in one piece and does not change the dimensions or spacing of the volume The pixel type however is converted to unsigned 8 bits since it is enough for representing the implicit smoothed surface Isosurface VTK This filter will generate a surfac
36. then be loaded at run time into VolView For more information see both the Filters chapter and the chapter on Extending Filters With Plugins Image Display The Image Display panel provides the basic controls for adjusting the appearance of the image This includes a mapping function for displaying scalar values window level controls and probe information This panel also contains configuration controls for the lightbox and a background color selector Information The basic properties of the dataset are displayed on this panel including the number of samples along each axis the physical size and origin of the dataset the data type and number of components Markers The Markers panel includes controls for displaying and setting the properties of the 3 types of markers available in VolView This includes a 3D cursor a set of 3D markers and a 2D marker Appearance The functionality available on the Appearance panel represents the main properties that control the appearance of the volume rendered image This includes the shading parameters weighting of the various components and the functions that map scalar value to color and opacity Views And Lights This panel provides control over viewing and lighting parameters including a set of standard viewing positions the ability to choose between parallel and Application Settings perspective rendering and controls for adjusting the position color and intensity of the light source
37. to Raw Scalars except that the color value is converted into a gray scale value according to the average of the red green and blue values The window level operation is applied to this gray scale value Opacity This option is available when viewing Intensity Aloha two component non independent and RGBA data four component non independent This option is similar to Raw Scalars but displays the last component of the data the second or fourth depending on the data type This window level operation is applied to this last scalar value This is the component that is used to map the data sample to an opacity and therefore this mapping mode is known as Opacity Color Mapped Scalars The data values are passed through the transfer function assigning color and the window level is applied to this color This option is not available for RGBA data since to color values are obtained directly from the data and not through a transfer function For independent components data this mapping is applied separately to each component then combined using the weights from the Appearance panel Color Mapped Scalars Opacity Modulated This option is similar to Color Mapped Scalars except that the window level operation is performed on the component from which Information Opacity is derived rather than applying the window level directly to the color For two component non independent data this will be the second component For independent components th
38. to display the color value and interpolate between color values HSV is more natural for color definition since the spectrum of colors can be conveniently displayed on a circle Value Hue Saturation The scalar color mapping area support the same keyboard shortcuts as the scalar opacity mapping area use the n or Page Down keys to move to the next node the p or Page Up keys to move to the previous node Home for the first node End for the last node and the d or Delete keys to remove the active node In addition you cannot adjust the position of the first or last nodes nor can you delete these nodes Gradient Opacity Mapping The cradient opacity Mapping 0 00 981 50 gradient opacity mapping area is used oni s 248 95 C to assign an opacity multiplier to 5 s you to reduce the mpact regions with homogenous values and enhance the 1 areas of sharp change effectively 39 Table Of Contents performing 3D edge detection during rendering This function is always a simple ramp with four nodes similar to the scalar opacity function when in Window Level Mode An example of the gradient opacity mapping area is shown on the right Similar to the other two mappings the range of the gradient magnitude function is displayed in the upper right corner and the range bar at the bottom can be used to view a subregion of this range Regardless of the data type this range will always be positive starting from zero and w
39. with a window level applied Two other mappings are possible with this data type Color Mapped Scalars and Color Mapped Scalars Opacity Modulated Change the Mapping to Color Mapped Scalars At this point it is also useful to press the Reset button in the Window Level area You should now have an image that looks like the one shown on the right To understand where these colors come from you will need to open the Appearance panel Look at the area labeled Scalar Color Mapping You will see that a rainbow colormap has been applied to the data This color mapping will be used for volume rendering and will be used to display the images when the Image Mapper is set to a color mapped mode In this Image Mapping mode we are mapping the scalar value through the color map then applying a window level operation to the resulting color If you click on a node in this area you can slide it left 10 Application Settings or right When you release it you will see the image window update and the volume window update for the new color mapping After clicking on a node you can also change its color by clicking on a new color in the color wheel If you return to the Image Display panel this should be in the set of tabs at the top of the left panel area simply click on this tab rather than selecting the panel from the View menu you can change the Image Mapping to Color Mapped Scalar Opacity Modulated Again use the Reset button to reset the window
40. 1 waz R co 1 A twigs A Property Panels Status Bar Main Progress Gauge Main Menu Bar The menu bar provides pulldown menus along the top of the application under the following headings File Edit View Window and Help The Edit menu may not be available on all platforms The File menu provides functionality for loading and saving data printing connecting to another VolView session and exiting The functionality found in the File View Window and Help menus is described in the next sections Information on the edit copy functionality provided in the Edit menu can be found in the Saving Results chapter Toolbar The toolbar is an optional interface area directly below the main menu bar that displays pictorial representations of the different available window configurations Clicking on one of these buttons will change the set of windows in the display area The visibility and appearance of this toolbar can be controlled using the Toolbar Settings area in the Application Settings panel 18 Application Settings Property Panels The property panels are located on the left side of the window and may or may not be visible You can toggle the visibility of these panels by Hide Show Left Panel item in the Window menu You can control which panel is currently visible by selecting it from the View menu Depending on your settings on the Application Settings panel multiple panels may be displayed as tabs along the top of the property pan
41. 625 4200 academic The VolView 2 0 license includes 90 day technical support 80 day for academic discount Please see the VolView web site at http www kitware com products volview html for the latest information on licensing options and pricing Additional multi license discounts site licenses source code licenses and special product customizations are also available Please contact a Kitware representative at kitware kitware com or 518 371 3971 for more information After you purchase VolView you will receive email instructions indicating that you must provide your computer ID to register the product You can find the computer ID on the About dialog from the Help menu on the VolView menu bar After this information has been entered into the licensing database which generally takes one business day you will need to use the Registration Wizard to obtain your license Select Purchase and register the professional version from the initial page of the wizard and press Next After reviewing the instructions press Next then indicate whether your computer is connected to the Internet If your computer is connected to the Internet you can retrieve your license easily through the wizard If it is not you must use the small file icon to browse for the license file that was sent to you via email when your purchase was completed Table Of Contents Quick Tutorial Step 1 Load Data This quick tutorial will walk you through the basic ste
42. 67 Staning S lC Gn en a 27 Stalls CS aa 46 SAS E 18 SVIE eae a ee 29 SUD VOI UNINC sa 48 Super Gampimg 70 DIE e Deg 46 99 Table Of Contents Surface Generation Filters 54 Surface property acia 46 Surface Ooualtv 46 SUNACE STUE us 46 SUNA OS ara oe OF ee Cy o 74 T Technical SUPPO isc a 6 TACK REA AE 49 TRE NOT 53 TFF 14 ME 29 Title edel ee 29 A e 18 Toolbar Settings std dls 26 ele lte 25 Total surface AEA EE 46 Otal VOM EE 46 mal ICONS id 4 5 trilinear interpolatiON oocococccccococococonnnoo 35 A EE 8 U Undo Last Applied Filter 52 User Interface OUvenvlew 18 Biet ge EE 53 V ET 11 35 VIEW Men lloran 21 Views amp EIONS aia ares 67 68 Views And Lights oooococococococococncnnononoos 21 VSb ua 46 68 Visible Man EE 8 e EEN 18 46 Volume Annotations eee 29 Volume Appearance Editor 35 100 Volume Display 21 69 70 71 Volume Intormaton 64 Volume Invisible o oococococcccenocconoso 69 Volume Keyboard Bindings 42 Volume Mouse Bindings rarnrnananananennr 42 volume E D 16 VolView Appearance Settings 14 VOIVIEW SCSSION xn EE 14 VON E 14 voxel coordinates nneannannennnennennenne 62 A EE 14 AAA 91 W Ee 43 Watershed Module ITK 55 Window Level 60 Window Level Mode 35 window geometry
43. Postscript file Depending on the DPI setting the size of your data and the rendering parameters it may take several minutes to generate the postscript file During this time you must ensure that the VolView window remains open and unobscured After rendering has completed a file dialog box will pop Select a file name into which to save the Postscript file You can then go to a command prompt in a shell on your system and type you standard print command which may be lo d lt printer name gt file ps or lor P lt printer name gt file ps If you have difficulty printing your Postscript file please consult your system administrator 19 Table Of Contents Connect Sessions Collaboration Overview A new feature for VolView 2 0 is that two VolView sessions can be connected Once connected one session will be in control while the other is in viewing mode Control can be passed back and forth between sessions Data loaded in one session will be sent to the other session with any identifying information from the header removed for security purposes Any interaction performed in the session in control will be reflected in the viewer s session This functionality can be useful for telemedicine applications For example if a patient is located at a regional hospital and the nearest expert for this patient s particular injury or disease is hundreds or thousands of miles away two VolView sessions can be linked to enable to local radiolog
44. SSING PIECES WEY info gt SetProperty info VVP NUMBER OF GUI ITEMS ER ee info gt SetProperty info VVP REQUIRED 3 OVERLAP O ss 92 Extending Filters With Plugins Example 4 An ITK Filter This is the code for Surface Generation Anti Aliasing ITK include vvITKFilterModuleWithRescaling h include itkAntiAliasBinaryImageFilter h template lt class TInputPixelType gt class AntiAliasRunner public typedef TInputPixelType InputPixelType typedef itk Image lt InputPixelType 3 gt Input ImageType typedef float InternalPixelType typedef 1tk Image lt InternalPixelType 3 gt InternalImageType typedef itk AntiAliasBinaryImageFilter lt Input ImageType InternallmageType gt FilterType typedef unsigned char OutputPixelType typedef VolView Plugin FilterModuleWithRescaling lt FilterType OutputPixelType gt ModuleType public AntiAliasRunner void Execute vtkVVPluginiInfo info vtkVVProcessDataStruct pds const unsigned int maxNumberOfIterations atoi info gt GetGUlProperty info 0 VVP_GUI_VALUE const float maximumRMSError atof info gt GetGUIProperty info 1 VVP_GUI_VALUE ModuleType module module SetPluginiInfo info module SetUpdateMessage Reducing aliasing effects Set the parameters on it module GetFilter gt SetMaximumIterations maxNumberOfIterations module GetFilter gt SetMaximumRMSError maximumRMSError F module SetO
45. Simple closed surfaces After the statistics have been computed this value will indicate whether or not all of the surfaces are simple and closed Simple closed surfaces are required by the surface area and volume calculations If your surfaces are not simple and closed you can remedy this in most cases by running the Boundary filter found in the Utility category on the Filters panel Usually surfaces are not closed because they run out of the edge of the volume Setting the boundary voxels to some low value based on your scalar range will close these surfaces The boundary filter was used in the example on the right to close the surfaces Total surface area After the statistics have been computed the total surface area for the contour will be reported here if the Simple closed surfaces value is Yes Otherwise this statistic will not be available Total volume After the statistics have been computed the total volume for the contour will be reported here if the Simple closed surfaces value is Yes Otherwise this statistic will not be available Compute statistics The Compute statistics button can be pressed to compute the above four values 47 Table Of Contents Cropping Cropping The Cropping area on the Cropping panel Cropping x can be used to reduce the region of the i Enable crop volume displayed in the volume window The aren interface for this area is shown on the right a aa s This interface was captured f
46. UPPORTS IN PLACE PROCESSING 0 info gt S etProp rtyi infio VYP SUPPORTS PROCESSING PIECES TONY info gt setProperty info VVP NUMBER OF GUI ITEMS 1 1nto gt SertProperty Into VYP REOUIRED Z OVERLAP TOTI info gt SetProperty info VVP PER VOXEL MEMORY REQUIRED 8 First the macro vvPluginVersionCheck must be called in order to verify that the plugin API conforms to the current version of VolView s binary distribution When the versions do not match the plugin is not executed and an error message is reported to the user at run time Once the version number has been validated the info structure is initialized The ProcessData member of this structure is set to the pointer of the function that will perform the computation on the input data Setting the function as a function pointer allows for considerable freedom in the implementation of the function Likewise the UpdateGUI pointer in the info structure is also set to a function pointer The function SetProperty is used to define general properties of the plugin Some of these properties are displayed on the GUI as informative text For example the textual name of the plugin terse and extended documentation The properties are identified by tags This enforces further the decoupling between the internal representation of information in VolView and the 19 Table Of Contents structure of code in the plugin For example the tag VVP NAME specifies that the string
47. VolView 2 0 User s Guide Table Of Contents SE EE OVENI EW td eege a 3 MOTION 3 A O A T a AS 4 Professional Mode FEAUES Harr 4 Oblina Tra Liconsa e ree ee ener tn ee 5 TTV 6 Tecnica ee E 6 PUNASE VOL TE 7 QUICK Ge EE 8 SENT LAT Dale EE 8 EE NE MT EE eee 9 Step 3 Interact Oe RR ee En E 11 E E EE 14 kl da 14 THe Open EE 16 hat Re 18 VE Ibe tae OCW 18 Me TU EE 20 TRE VEV INA CIN UI EE 21 EVI NN 23 KN HOP On EE 24 ADDIIG ATION SES EE 25 EVERE EEE EEE EE ER sites estira 25 TOO SSUINGS E 26 PADDING ATOM EE 26 ANIMAU EE 27 AE ON SENTER 27 AMONA 29 VOLUME tee yo A aneg 29 Mage ANNONSE 33 APA ANCO RE 35 VOIUINIC Appearance ET A A A 35 MO io 42 Volume MOUSE BINANOS mias a a a is 42 Volume Keyboard BINdINGS sica nac Aa sds 42 Mage Mouse ne Dn ms oido 43 mage KeyDoardiBINdING airis is 43 Go ele 45 AO Go al ORRE EE da 45 COMM VA Ge EJ eene 46 PIN 48 ter 0 10 SEERE EE ER EN ee ren 48 ite Ee EE 49 JUS Gei 50 SI EE 52 Filler SENGS VEN EN usada ee 52 Bil Dee NN 53 SUE ENE ON ES er NNN 54 Edge DEE FER edda 54 Segmentation Level SEP ud ES GLANS 55 Segmenalon RENN GKOWING se ee ee 56 NOISE Suppression FINGIG sti tii 56 InNtensiy Transio matones tb 57 Table Of Contents Mage DENN EE 58 Made Mapping E 58 WINGOW LEV 60 MORADO ODIA SAN NE NE EN AE EE EN EE EN 61 EN 62 PODS MOE I 62 Inte deu iio eee fr 64 Volume e edu UON WEE E 64 KT EE 65 RE 65 DNS E 65 ZA AA A A a 66 VESLE HP 67 PO
48. a Select the White option to set the color to solid white Now click in the center of the editing area for the scalar color mapping to add a new white node Click on the first node on the left in order to select this node Adjust the color of this node to light brown by using the Value and Hue Saturation areas at the top of the Volume Appearance Settings area Clicking somewhere in the Hue Saturation circle will change the color of the selected node Alternatively if there is a particular Hue Saturation and Value that you would like you can manually specify this in the H S and V text entry boxes Using the first pulldown in the Scalar Color Mapping area you can change from HSV to RGB so that you may enter these values as red green and blue components instead Now you should have one light brown node to the far left a white node in the middle and a white node on the far right Click on the line very close to the light brown node to add a second light brown node You will now drag this node 2 to the right until the scalar value the first text box labeled S above is approximately 45 Drag the next white node node 3 until the scalar value is approximately 50 The interface in the Scalar Color Mapping area should appear similar to the 12 Application Settings example shown on the right If not adjust your interface until it has a similar appearance Note if you accidentally add a node you can delete it either by selecting it and pr
49. a affects all image display windows in VolView Corner Annotation The corner annotation for the image windows functions the same as the corner annotation for the volume display area Use the toggle button to turn the corner annotation on and off Use the Edit button to bring up the corner annotation dialog which will allow you to set the multi line text string to display in each corner as well as properties of this string such as color font style and opacity Keep in mind that corner annotation is automatically added to the image windows when you data is loaded The exact corner annotation is dependent on the data type but will always include the window and level values in the lower right and the image slice number in the upper left If you open the corner annotation dialog you will see these dynamic text elements already entered These items will be enclosed in lt and gt A brief description of the different dynamic annotation elements is given below lt window gt This will be replaced by the label Window and the current window value from the Window Level area on the Image Display panel lt level gt This will be replaced by the label Level and the current level value from the Window Level area on the Image Display panel lt image gt This will be replaced by the label Image and the current slice number from the slider at the bottom of this image display window lt slice gt This is identical to the lt image
50. al while a high specular power indicates a highly focused reflection indicative of a polished metal Enable Shading The Enable Shading button can be used to toggle shading Shading is enable or disabled for all components at once although it is possible to set the material properties for a particular component so that no shading is applied Ambient 1 0 Diffuse and Specular 0 0 even though shading has been enabled The first time you enable shading and the volume renders you may notice a delay while the gradient values are calculated If you have already enabled the Gradient Opacity Mapping then the gradients will have been calculated then When the gradients are calculated you will see a message in the status bar area and progress will be displayed on the main progress gauge Interactive Apply The Interactive Apply toggle button can be used to control whether or not the changes made to the mappings are displayed interactively while the change is made in the volume display window If this button is off then the volume window will only update after the change is made the mouse button is released If this button is on then Information while you reposition a node in one of the mapping functions by dragging the small circle the volume display windows will be rendering with the adjusted mapping By default this option is turned off but it can be useful while editing your mappings when you have small data or a powerful computer S
51. ameters settings requires for you particular data set When you are applying CannySegmentationLevelSet to a new data set you may want to rather go step by step using each one the individual filters Please experience first with the FastMarching modules since it is used here for preprocessing the data set before applying the CannySegmentationLevelSet filter Fast Marching ITK Fast Marcing uses a Level Set representation for propagating a front from user provided seed points A user provided speed image is used for controling the front propagation Fast Marching Module ITK This module applies a Fast Marching level set method for segmenting a volume All the necessary preprocessing is packaged in this module This makes it a good choice when you are already familiar with the parameters settings requires for you particular data set When you are applying FastMarching to a new data set you may want to rather go step by step using each one the individual filters Geodesic Active Contour ITK This module applies the Geodesic Active Contour method for segmenting a volume No preprocessing is performed here The user must provide as inputs an initial level set and the feature image which will be used to compute speeds The current image being visualized will be taken as the initial level set The speed image required as a second input can be specified by providing a file name in the GUI Geodesic Active Contour Module ITK This module applies the
52. ange the color of the light source It is recommended that you do not change the light source color In future versions when multiple light sources are supported it could be useful for generating a beautiful image for a publication or presentation where the addition of an offset light source in a different color could enhance the appearance of the image Intensity The intensity slider allows you to adjust the brightness of the light source This slider is necessary when more than one light source is enabled since you may need to decrease the intensity of each light source to avoid over saturating the image Position The position circle allows you to interactively position the light source in relation to the camera viewing position The center location indicates a light shining on the scene from behind the camera Moving the white square to the far right would cause the light to rotate around the scene until it was shining from the right It can be useful to offset the light from the camera a bit in order to enhance the structure of an object 68 Volume Display Blending Function The Blending Function area of the Volume Blending Function x Display panel appears as shown on the right None Volume Invisible and allows control over the function used to Maximum Intensity convert the 3D volume into a 2D image Each amp composite pixel on the image represents a set of voxels in the 3D volume and this blending function
53. ar value Surface style The surface style options allow you to select between drawing a solid surface representation or a wireframe representation in the wlume display window The surface often has so many small primitives that it is difficult to perceive the difference between these two styles until you zoom in closer to the surface You can use the Surface quality slider described below to reduce the primitive count and therefore decrease the density of lines in the wireframe image Surface quality The surface quality slider allows you to reduce the number of primitives in the 3D polygonal surface A quality of 1 0 indicates no reduction while a quality of 1 indicates that only 10 of the original number of primitives remain Reducing quality can be useful for improving rendering performance with large contours and reducing the number of lines in a wireframe rendering Line width The Line width slider adjust the width of the lines used to display the contour in the 2D image windows Remove Contour Pressing this button will remove the currently selected active contour Information Remove All Contours Pressing this button will remove all contours Number of surfaces After the Compute Statistics button has been pressed the number of disconnected surfaces in this iso valued contour will be reported here The statistics in the interface example above are for the contour shown to the right which has 29 disconnected surfaces
54. arameters between the VolView GUI and the plugin A plugin developer must implement a set of C Language functions that will be invoked by VolView during its interactions with the plugin The source code of the plugin is compiled and packaged in the form of a shared library No libraries from VolView are required during this process The shared library containing the plugin is finally copied into a specific directory of the VolView binary installation This particular directory is searched by VolView at start up time Any shared libraries found in this directory will be dynamically loaded The name of the library should conform to the name of the plugin initialization function The development cycle of a plugin is totally decoupled from VolView s internal code The single communication bridge between the plugins and the application is the header file defining the data and GUI structures A developer of a new plugin must simply implement the methods defined in the public header file 3 2 Defining the plugin name The plugin name will determine the name of the shared library used for deployment It will also determine the name of the initialization function For example a plugin named vvlTKGradientMagnitude will be deployed in a shared library with name libvv I TKGradientMagnitude so in Unix and vvlTKGradientMagnitude dll on MS Windows lts initialization function will be called vvITKGradientMagnitudelnit po MK VW Plein APL Wooly pew Binar
55. asting ccccsceeseeeeeeeeees 70 independent ocococococcnconoconcnnononoconcanononos 16 INTOVMANON sisi 8 21 64 initialization function ccceceeeee seen eee 78 MENS E 68 Intensity Transformation Filters 57 98 Intensity Windowing ITK 57 Interactive Apply AN 35 Interface Settings oococcccocccconcccnnnconnnnos 25 HEP JAN Ne 35 o ION 3 Inverted Cross 48 Inverted Fence smoaren na 48 oo AAA AA 76 Isolated Connected IR 56 ISOSUIMAGE VIK EE 54 SOVNE sverd 45 ME e EE 93 J PE aidan 14 K Kevboarde vesenet 21 42 43 L Eli a a aR e 29 Label text properties cceeeeeeeeeees 29 A 23 Buste EE 43 ENES E 55 level of detail arannnunnannannnnnnanvenne 11 21 Level Of Detail Options rarnrnrnanernrnnner 70 Jee ite Bei elt Tel Aase 7 Light Contour a 68 LONDON o 18 Lightbox Options EE 61 lighting parameters rrrranannrnrnrnrnrnrnenenr 21 Ene MAN as 46 DAL Lee 35 Loading Data Cverview 14 M Main Menu Bal esas 18 Main Progress Gauge rrrnnrnrnarnnvennrvennr 18 MAKES EE 21 65 66 Max lee E 29 Maximum Intensiv 69 Maximum number of colors 29 Medan ITK EE 56 Median Filter VIR 56 Medic eee 9 26 67 medical data 9 Merge Volumes arrnnnnnnvnrernrnrnrnrnenenenene 93 Metamorph Stack oooocococcocncoconcononoconnnnoss 14 A aean 21 42 43 N National Library of Medicine
56. at x Enable reformat lv Show reformat box Mouse controls Reformat Thickness 42 3 enabled or disabled with a toggle button the reformat annotation can be turned on off with a toggle button and the thickness of the slab can controlled with a slider A pulldown menu can be 49 Table Of Contents used to change the mouse action between controlling the camera the normal mode or controlling the reformat plane If thick reformatting is enabled a yellow box will appear in the Volume Display Window This box represents the reformat region of the volume and the intersection of this reformat region with the bounds of the volume Only portions of the volume lying within this yellow box will be displayed By selecting Mouse Controls Reformat you can rotate and translate the yellow box to position it over the region of interest The Thickness slider value controls how wide the yellow box is The clipping is actually performed between two parallel planes defined by the box The other four faces are drawn only for clarity but clipping is not performed against these faces When the mouse controls the reformat plane left mouse motion causes the plane to rotate and right mouse motion causes the plane to move in and out When using a parallel viewing projection the outline of the reformat will not appear to move when the reformat is moved in and out At this point it is useful to look at the intersection of the reformat plane with the v
57. ata To do this select the Application Settings panel from the View menu On this panel located the Application Area portion of the interface and select Medical You should see the three image windows labeled as Axial Frontal and Sagittal Now we will switch the position of the volume rendering and the sagittal image by selecting Sagittal Image from the pulldown menu in the upper left corner of the volume display window Your display area should now have a layout similar to the one shown in the image on the right Note that each of the image display windows has a slider along the bottom This allows you to adjust the currently displayed slice In addition a text entry box also allows you to specify this slice Try moving the slider back and forth to view the slices through the foot There are some keyboard shortcuts as well Before attempting to use the keyboard shortcuts you must ensure that this image window has keyboard focus If you click on the top bar of the window it will turn blue as it is in the image on the right indicating that this is the currently selected window Now you can use the left and right arrow keys to move back Spe See 7 WR DO and forward through slices one at a time The Page Up and Page Down keys will move back and forward by 10 slices at a time while the Home key will go to the first slice and the End key will go to the last slice Note that the slice number is reported in the text box to the righ
58. ate zooming out The interface elements specific to the Slices p Animation Settings x animation type are Number of frames ET i Animation type eh Slice type This option menu can be Sies used to choose between the three Slice type xY different major axes ees a x Starting slice This value indicates Ending slice les 28 the starting slice for the animation a SEE Ea i Bees i ee 2 Preview images will be generated using the Standard Interactivity Ending slice This value indicates the setting from the Level Of Detail Options area on the Volume Display ending slice for the animation control panel When the animation is created the best available level of detail will be used After selecting a filename you will be prompted for video compression type Not all compression types will work on your system with your current window size Microsoft Video 1 Intel Indeo R Videc R3 2 and Full Frames uncompressed will typically work Annotations Volume Annotations The Volume Annotations area of the Annotations panel provides a set of annotation elements that can be added to the volume display windows An example of this interface is shown on the right The seven different annotation elements are described in more detail below Volume Annotations W W Display corner annotation Edit Display header annotation Edit Iw Display color bar Edit E Display orientation marker Set Colo
59. axis a green line parallel to Y axis and a blue line parallel to the Z axis The lines are in the locations where the planes meet While planes are each controlled by one slider each line is controlled by the values on two sliders For example the X plane the red one is controlled by the X slider while the X line the red one is controlled by the Y and Z sliders You can change the color of each of the planes lines with the corresponding color button In the image windows the cursor can be control with the left mouse button Pressing the left mouse button over the horizontal cursor line in a window will allow you to move it up and down You can adjust the vertical cursor line left to right If you grab the cursor at the intersection of the two cursor lines you can reposition it freely within the image 3D Markers The 3D Markers area on the Markers panel p 3D Markers x volume These markers are typically used by some of the filtering methods as input seed __Addarker Removeselected Removeal points and are visible in both the volume display window and the image windows An example of this interface is shown on the right The 3D Markers area provides controls for toggling the visibility of the markers changing the color of all markers and adding and removing markers This functionality is described in more detail below Display 3D markers This toggle button controls the visibility of the 3D markers Set Color You can set t
60. below These text properties apply to all four corners of the window Max line height This value will qu control the height of a line of text If Blaue ed tu bd the text appears too big decrease Corner Annotation this number If it appears too small upper left Upper right increase it You can type the new Study 000001 John Doe value in the text box or use the eG kak s arrow tO pop up a slider Depending on the number of lines of the text and the size of your window it may be that only the lower values have any significant Max line height 0 07 gt effect on the size of the text since tproperties other constraints may limit the Color im behavior of this slider This option Family Arial is often useful when printing since Styles rlel the size of text that is appropriate S Bis for being able to read it on the Opacity 1 00 gt computer monitor may not be the ose SAA optimal size for a printout Lower left Lower right 29 Table Of Contents 30 Color This button can be used to adjust the color of the text displayed Family The font family can be selected from the pulldown menu Style The style of the text can be selected using these toggle buttons You can toggle bold italics and shadow When a button appears to be pushed in this option is selected Each of the three options can be toggles on and off independently Opacity This value adjusts the opacity of the t
61. beyond a certain limit it will jump to a new displayed distance The user interface allows you to toggle the visibility of the scale bar and to set the color of the scale bar If you move the mouse over the scale bar when VolView is idle then you will see the cursor change When the cursor is a vertical and horizontal double arrow then you can move the scale bar to a new position on the window If you move to the far left or right edges of the scale bar area the cursor will become a horizontal double arrow In this mode you can resize the width of the scale bar This resizing will not be smooth since an attempt is made to keep the displayed units in multiples of as large a value as possible given the units and the screen size Therefore you wil see the scale bar snap to a new size as you drag the mouse Bounding Box Using the Display bounding box toggle button you can toggle the visibility of a bounding box around the volume Turning this bounding box on is often useful when trying to understand the placement of some particular structure you are currently visualizing within the whole dataset It can also be useful when using the cropping functionality You can adjust the color of the bounding box A bounding box is shown in the annotation example image shown above on the right Distance Measurement The distance measurement tool is an interactive annotation element that allows you to measure the distance between any two points in the data Whe
62. box is not checked then the default size and position are used Show splash screen The splash screen showing startup progress will be displayed when VolView is launched if this button is checked Otherwise the splash screen will not be displayed and the application will appear once all initialization is complete This may require several seconds from the time you double click on the VolView icon depending on the speed of your computer and your current VolView configuration Show tooltips When the mouse cursor is held still over a user interface element for a few seconds a small yellow pop up will appear with a short usage message If this box is not checked then this functionality will be disabled Show most recent panels If this box is checked then up to four recently accessed panels will be available as tabs in the left panel When this box is not checked only the current panel and any locked panels will be displayed Enable Interface Drag amp Drop Each area on the user interface such as this Interface Settings area can be repositioned either on the same panel or on another panel To do this you simply click the left mouse over the title of the area and drag it to the new location To move the area to a new panel be sure that both panels are displayed as tabs make sure the Show most recent panels option is enabled and drop the area onto the tab of the new panel If you disable this option you will not be able to reposition the
63. calar Opacity Mapping The Scalar Opacity Mapping region allows you to control the mapping from the scalar value in the dataset to an opacity value used during rendering This function can be adjusted for example to give your volume a fuzzy cloud like appearance or a sharp surface like appearance On the right you see an example of how Scalar Opacity Mapping 0 00 2687 70 this area may look We will example E Scale 2 633 gt s 493 66 ole each portion of this editor in detail The discussion of Scalar Color Mapping and Gradient Opacity Mapping assume that you have already read this section on Scalar Opacity Mapping since many of the elements of these editors are similar On the top right corner of the editor you see the currently displayed scalar range For this data the scalar range is 0 4095 which was initially displayed by this editor Using the bar on the bottom of the editor you can control the range By dragging the rectangle on the left you can adjust the lower range value and by dragging the rectangle on the right you can adjust the upper range value The full range of the adjustment bar is the scalar range of the data reported on the Information panel In this example you can see that the upper range has been reduced by moving the right rectangle to the left You can also move the entire bar by clicking between the rectangles and dragging it to a new position Double clicking on the range bar will cause it to expa
64. ce to be found concerning the frequency with which this function should be invoked If invoked too often it will negatively impact the performance of the plugin since a considerable amount of time will be spent in GUI refreshing If not called often enough it will produce the impression that the processing is failing and the application is not responding to the user commands anymore 82 Extending Filters With Plugins A Detailed Skeleton Example This is a skeleton plugin that includes basic instructions on what you need to do to create a plugin You will want to look through vtkVVPluginAPI h as well to get a feel for how it works 1 You should save a copy of this file with the name of the plugin you want to create Say you want to create a luminance plugin then you should save this file as vvLuminance cxx or vvJohnDoeLuminance cxx in these two examples your plugin would be named Luminance or JohnDoeLuminance respectively 2 Rename a few occurances of Sample in this file to the name of your plugin Specifically look for the TODO Rename comments in the rest of this file and where you see lt your_plugin gt replace that with the name of your plugin such as Luminance This is TODO items 1 through 4 3 Update the terse and full documentation strings for your plugin This is TODO item 5 The terse documentation should be a quick one sentence description of your plugin The full documentation should be a long description of what the
65. cess the volume in place in pieces or all at once The most memory efficient option is to support processing the input volume in place but fo rthis to work your algorithm must not change the parameters of the volume see 4 because the input volume s block of memory will be used for the output volume Typically only simple algorithms can be in place The next option is in pieces This means that you will be asked to process the input volume in pieces and ProcessData will be called one time for each piece In this case the memory is not shared between the input and output so they can have different parameters The third option all at once is the simplest but consumes the most memory both the input volume and output volume must be in memory at the same time With all at once there really are no limitations so it is probably the best option for your first attempt at writing a plugin Once you have made your decision you need to specify it at TODO item 9 7 Now you can write your algorithm in the vv lt your_plugin gt Template function If you are unfamilliar with C templated functions the only real thing you need to know is that IT represents the input volumes data type e g float short etc If you have GUI items then you should get the current values of them at TOTO item 10 The we loop over all the voxels and perform an operation In this case a simple copy of the input volume to the output volume At TODO item 11 you should place your own 83
66. converts the set of voxel values into one final pixel color to display The images below represent the different blending function and the options are described in more detail below None Volume Invisible When this option is selected the volume rendering will not be displayed All annotations and surface representations will continue to be rendered This is a useful option when viewing an isosurface that is embedded within a volume or for locating 3D markers that are otherwise hidden When using this option it is often useful to turn on the bounding box annotation An example image is shown above in the center In this image we see an isovalued contour at the bone surface that is geometrically rendered The bounding box is also displayed Turning off the volume rendering allows us to clearly see the surface geometry Maximum Intensity The maximum intensity option computes the maximum scalar value of all the voxels that contribute to the pixel and displays this maximum value mapped through the scalar color and opacity transfer function and possibly modulated by the gradient opacity transfer function Shading has no effect in this mode An example image for a maximum intensity projection is shown above on the left In this image we can clearly see that the soft tissue scalar values have a higher intensity than the background voxels and the bone scalar values are the highest Although this is a very simple projection mechanism it is often favor
67. cross sessions of VolView what you add to this list will still be available next time you start VolView Add Preset When you press this button a dialog similar to the one shown o the right will appear requesting that you enter a name for this preset Type in a short descriptive name and hit enter or press the OK button This preset will be added to the pulldown menu for later selection Remove Preset Pressing this button will remove the preset indicated in the Window Level Presets pulldown menu There is no undo on this operation Remove All Presets Pressing this button will remove all Window Level presets There is no undo on this operation Lightbox Options The Lightbox Options area in the Image Lightbox Options x Display panel provides controls for the layout Number of columns 3 4 Number ofrows 3 4 and orientation of the lightbox images AN sice orientation example of this interface is shown in the l e Y slices image on the right The lightbox allows you Pek oe to view a set of consecutive images from the i Y Z slices data The interface elements in this area are described in more detail below Number of columns rows You can set the number of columns and rows to values between 1 and 5 allowing you to view up to 25 images at once 61 Table Of Contents Slice orientation You can choose to view the X Y Axial X Z Frontal or Y Z Sagittal slices of the data Colors The
68. cused reflection such as you would see in brushed metal while a high specular power indicates a highly focused reflection indicative of a polished metal Spend some time adjusting the shading parameters to understand their impact on the volume rendered image Finally we will adjust the scalar opacity Scalar Opacity Mapping O 255 mapping In this case attempt to match the DU scale 0 96667 s 31 968 oO 0 example image to the right noting that the first node has a scalar opacity value of ee approximately 0 0 the second node is 32 GI 0 the third is 35 28 the fourth is 54 28 L the fifth is 70 5 and the last node is 255 5 Once you have adjusted the opacity mapping you should have an image that appears similar to the one shown below on the right You can use the Scale slider in the Scalar Opacity Mapping area to adjust the whole mapping to be more or less opaque There are also a set of preset mappings available under the small file folder icon One of these the one used by default when the data is loaded is based on the histogram of the data There are many more features available on this Appearance panel than can be covered in a simple tutorial This panel is clearly the most complex interface in VolView 2 0 and defines the core parameters that affect the volume rendered image It is important that you spend some time becoming familiar with the use of this panel in orde
69. cute info pds break case VIR DOUBLE AntiAliasRunner lt double gt runner runner Execute info pds break default info gt SetProperty info VVP ERROR Pixel Type Unknown for the AntiAlias filter return 1 break catch itk ExceptionObject except info gt SetProperty info VVP ERROR except what return 1 return 0 static int UpdateGUI void inf vtkVVPluginInfo info vtkVVPluginInfo inf 94 info gt SetGUIProperty info 0 VVP GUI LABEL Number of Iterations Extending Filters With Plugins VVP GUI TYPE VVP GUI SCALE VVP_GUI_DEFAULT Mov VVP GUI HELP Number of times that the diffusion The more iterations the stronger the smoothing e VVP_GUI_HINTS 1 100 1 info gt SetGUIProperty info VVP_GUI_LABEL Maximum RMS Error info gt SetGUlProperty info VVP GUI TYPE VVP GUI SCALE info gt SetGUIProperty info 1 VVP GUI DEFAULT 0 05 info gt SetGUIProperty info 1 VVP GUI HELP Maximum RMS error allows This value defines the convergence criterion for the smoothing info gt SetGUIProperty info 1 VVP_ GUI_HINTS 0 001 0 1 0 001 const char stringValue info gt GetGUIProperty info 0 VVP_GUI_VALUE if stringValue info gt SetProperty info VVP_REQUIRED_Z OVERLAP 0 else info gt SetProperty info VVP_REQUIRED_Z OVERLAP stringValue info gt SetGUlProperty info 0 info gt S
70. dataset and this component is used to derive opacity through a transfer function The image on the top left shows a volume rendering of this data The next image shows Raw Scalars followed by Color Mapped Scalars on the top right On the bottom left we have opacity mapping and finally the image on the bottom right shows Color Mapped Scalars Opacity Modulated 59 Table Of Contents In this final example we have four component non independent data RGBA The first three components directly contain red green and blue color values The fourth component will be used to derive opacity through a transfer function The image on the top left below shows a volume rendering of this data The top middle image shows Raw Scalars followed by Gray Scale Scalars On the bottom left we have opacity and finally the image on the bottom right shows Raw Scalars Opacity Modulated Each mapping displays your data in a new way Keep in mind that features that may be apparent in one mapping may be entirely hidden in another so it is useful to switch between mappings to get a better understanding of your data This is especially true with the non independent data types since these mappings are the only way to visualize the different components independently Window Level The Window Level area on the Image p Window Level x Display panel allows you to view and adjust Window 1488 57 Level 949 65 Reset the current window and level
71. e Upward motion will zoom in while downward motion zooms out Roll Press the designated mouse key combination and drag to roll the image Upward motion rolls clockwise while downward motion rolls counter clockwise Fly In Press the designated mouse key combination to fly toward the volume You will fly in the direction the mouse points If the mouse is in the center this will be similar to zooming in If you move the mouse from the center you will turn in the direction of the mouse The best way to work with this mode is to point toward the location where you want to fly The speed of flight is controlled by the slider at the bottom of the Volume Mouse Operations area Fly Out Press the designated mouse key combination to fly away from the volume This is the same as the Fly In mode only zooming out instead of zooming in Volume Keyboard Bindings The Volume Keyboard Bindings area on the Bindings panel displayed the keyboard shortcuts for the volume display window An example of the interface is shown on the right Volume Keyboard Bindings x r Reset camera Currently the volume display window supports only one keyboard shortcut Pressing the r key while the volume display window has keyboard focus the title bar of the volume display window 42 Information will be blue will cause the camera to reset This is a useful shortcut when you have lost the volume during interaction Image Mouse Bindings The Image Mouse
72. e at the specified value for the second input that was specified It leave the current volume alone This allows you to display the isosurface from one volume with the volume rendering from another If the volume to be isosurfaced has more than one component then the first component will be the one isosurfaced If you want to isosurface the current volume you can use the contours page which has more options Edge Detection Filters One filter is available in the Edge Detection category The details are provided below 54 Canny Edge Detection ITK This filter applies an edge detection filter developed by Canny First it smooths the image using a discrete Gaussian filter Then it detects local maxima and marks the position of those local maxima Note that edges in the output image will be set to value 1 0 so you may need to adjust the intensity windowing parameters for visualizing the resulting edges Information Segmentation Level Sets The Segmentation category has seven algorithms based on the level sets concept More details on each of these filters are provided below Canny Segmentation LevelSet Model ITK This module applies the Canny Segmentation Level Set method for segmenting a volume A Canny edge detection filter is used to produce a set of edges that will be used to attract the zero set to them All the necessary preprocessing is packaged in this module This makes it a good choice when you are already familiar with the par
73. e data can be imported into an ITK image using the itkImportImageFilter RegionType region region SetIndex start region SetSize size Mm ImportFilt r gt SetsSp cing spacing Jy nm InportFilcer gt SetOrigian origin m ImportFilter gt SetRegion region m ImportFilter gt SetImportPointer pds gt inData totalNumberOfPixels false As The output of the import filter is then connected as the input of the ITK data pipeline and the pipeline execution can be triggered by calling Update on the last filter m_FilterA gt SetInput m ImportFilter gt GetOutput m FilterB gt SetInput m_FilterA gt GetOutput m FilterC gt SetInput m FilterB gt GetOutput m FilterD gt SetInput m FilterC gt GetOutput m FilterD gt Update Finally the output data can be copied into the pointer provided by VolView This is typically done using an ITK image iterator that will visit all the voxels outputImage m Filter gt GetOutput typedef itk ImageRegionConstIterator lt OutputImageType gt Output IteratorType OutputlteratorType ot outout Image outputImage gt GetBufferedRegion OutputPixelType outData static cast lt OutputPixelType gt pds gt o0utb ta Es ot GoToBegin while ot IsAtEnd outData ot Get ROT FFOUEDateas When memory consumption is critical it is more convenient to actually connect the output memory buffer provided by VolView to the
74. e evaluation period and for 90 days after a license purchase 30 days with the academic discount Questions must be submitted via email to support kitware com and will be answered within one business day You may send support questions after your evaluation period has expired which will be answered as time permits When sending a question to customer support please include the following information e Your name and phone number e VolView version use Help gt About to get this information e Mode free trial professional or licensed If you are reporting a bug please provide e The operating system you are using Windows 98 Windows XP Solaris HP UX Linux etc e The number of processors on your system e Video card installed e The size and type of the data you loaded 512x512x200 unsigned short data e A detailed description of the problem you encountered e The sequence of operations that caused the problem and whether it is reproducible Kitware always welcomes customer feedback If there is a particular feature that you would like to see available in VolView 2 1 please send email to support kitware com with a brief description of the functionality and how you would use it in your application area Application Settings Purchase VolView VolView 2 0 licenses may be purchased in the following configurations from the Kitware Online store 1 license for 2500 1875 academic 2 licenses for 4250 3200 academic 3 licenses for 5
75. e from an auxiliary eL file visfoot vti vvi that stores this We information Generally the vvi file is written after you have loaded a dataset so that the My Meimork Fes tips Comman 3D Fermats Ewe Zb 2 vli pic em information is retained for the next time you load it In this case the vvi file came with your VolView distribution Hit the Next button twice to load the data Mu Document This file contains the right foot from the National Library of Medicine s Visible Man dataset This is a CT dataset You can view basic information about the data by selecting the Information panel from the View menu Also be sure to select the 1 over 3 option from the Window menu to see both the volume rendering and the images at once You interface at this point should like similar to the image shown below T VolView 2 0 visfoot sti File Eck Ves Minds Help Information Image Display Volumes Display Appesrance Yoluma Information Same in Sele LOE x 247 e 200 Physical size 6695 x 233 7 x 155 mm sample eng 195 0955 L item Data origin DO O mm Deba brpa unzigned char Comporerts L Scaler rag componer L 0 to 165 CT E VolView Location off image Step 2 Interact With Images Application Settings EEK We will now explore some of the interaction possibilities in the 2D image windows First we will start by ensuring that VolView is using an RAS coordinate system for this medical d
76. e need to set to length over which to apply the opacity values in our mapping The default length will be the average spacing between your samples Increasing this length using the pop up slider will decrease the opacity of your volume since less opacity will be accumulated over the same distance while decreasing the length will increase the overall opacity The rectangular editing area displays a log based representation of the histogram of the scalar data in the background The piece wise linear function defining the opacity mapping 37 Table Of Contents 38 is displayed as a sequence of circles and lines Clicking on one of the circles will display the node number ordered left to right and will change the color from white inactive to grey active At this point the scalar opacity values associated with the node are displayed in the S and O text entry areas You can modify the values in the node either by typing in the text areas or by dragging the node Moving the node left or right will decrease or increase the scalar value moving the node down or up will decrease or increase the opacity value The motion will be constrained to keep the nodes in order node 3 must remain between nodes 2 and 4 If you use the shift key in conjunction with the mouse the motion of the node will be constrained to be entirely vertical or horizontal press the shift key after you begin dragging either vertically or horizontally to constrain to this dir
77. ea will vary depending on the type of data loaded The example shown on the top right is for 62 unsigned char data with a single component while the example shown below it is for four component dependent data Two basic pieces of information are displayed in this area the position of the cursor in 3D space and the value in the Information Probe Information x Position 217 707 167 156 098 mm 217 167 156 vowels Value 59 red 31 green 26 blue 6 hue dataset at that position The position is displayed both in physical coordinates and in voxel coordinates The physical coordinates take into account the origin and the spacing of the data whereas the voxel coordinate is simply the x y z coordinate within the 3D block of memory The data value is displayed per component of the data for both independent and non independent dataset The unit type will be displayed next to each value If a name for the unit type was not provided during data loading then unknown units will be displayed 63 Table Of Contents Information Volume Information The Volume Information area on the Volume Information x Information panel provides basic size type Size in voxels 64x 64 x 64 and units information about the currently Physical size 63 00 x 63 00 x 63 00 millimeters loaded dataset This interface May appear Sample spacing 1 00 x 1 00 x 1 00 millimeters similar to the one shown on the right Each
78. ection When a node is active you can move to the next node by pressing the n or Page Down keys on your keyboard You can move to the previous node using the p or Page Up keys The Home key will bring you to the first node while the End key will bring you to the last node Note that you cannot adjust the scalar value of the first or last nodes in the mapping these are fixes at the bounds of the scalar range To add a new node to the mapping click the left mouse button on the location where you want to add the node This will become the active node and you can adjust the values either interactively by dragging the node or with the text entry boxes for S and O To delete a node you can either drag it far below the editing box the standard dragging icon will change to a black box icon indicating that the node will be delete or you can press the Delete key or the d key on the keyboard when the node is active When in Window Level Mode only four nodes are displayed No new nodes can be added and no nodes can be deleted The scalar value horizontal position of nodes 2 and 3 can be adjusted to alter the Window and Level settings for the application In this mode these settings are tied to the ones used for the display of 2D images Adjust the Window and Level values in one of the 2D image views will alter the scalar opacity mapping In addition adjusting the position of the second and third nodes in the scalar opacity mapping will alte
79. ed by scientists who wish to see only real values from within the dataset as opposed to values derived after applying a compositing and shading step One limitation of this projection method is that in a still image it is impossible to gain depth cues and therefore structure may be difficult to discern Composite This is the default viewing mode with performs an alpha blending of all the mapped and shade scalar values contributing to the pixel Depending on your appearance settings this option may give you a translucent cloud like appearance or a shaded surface like appearance An example image for a composite projection is shown above on the left In this image we see a composite projection where shading and gradient opacity 69 Table Of Contents modulation are both utilized This leads to an image displaying the air skin transition as a translucent surface through a volume rendering rather than geometric rendering process and a solid shaded bone structure Super Sampling The Super Sampling area on the Volume Super Sampling x Display panel allows you to control the z axis by TI sampling rate used when generating the volume rendered image The interface consists of a single slider for supersampling the Z axis by a give factor which can be set to 1 2 3 or 4 This interface appears similar to the one shown on the right There are two volume rendering methods within VolView On systems that support it VolView may use t
80. eelon NPE eee de 67 Sie ee SAGER ER EEE EEE EEE EE 67 WAG IAG SOI SEERE EE EE EN 68 A E 69 BIENANG FINT SS 69 SUE SAMPING AG 70 EVER MON EE 70 EE 71 SAVIO RESUS EE 73 Saving kes EE 73 Saving VANESSA 73 SAVING Appearance SAMME Aardal 74 SAVING E lge 74 SAVN STEENS NN A A A A 74 ENE NNN 75 Prining STEENSHOS Lavrans een GASSER VS 75 Connect SES ae 76 G llaboration A RENERE 76 Connecting And Passing GOTO EEN 76 Extending FIES VIK PINS arve 78 Ex Ending Filters OVNEN EE 78 PIU EO EE 78 TAEHAIIANIZAUOM TUE iia entrar ee haa 79 The ProcessDala UNCION arsen 80 Rereshng ine E RTE 82 PDT ENE AN 83 Example EE 86 Silent SSE 88 EXample SA VR TEE 91 Example AMTK DEEN 93 NN 97 System Overview Introduction Welcome to VolView a powerful volume visualization application intended for the medical scientific and engineering communities VolView can be used to interactively visualize annotate measure Capture print and process volumetric and image data New features in VolView 2 0 include e Support for all data types unsigned char through double e Support for up to four independent components e Support for color alpha RGB and RGBA volumes e Over 30 basic and advanced image processing filters e Plug in API allows any developer to extend filtering capabilities e Collaboration between two VolView sessions e New interactive annotation widgets e Color bar scale bar orientation marker e Distance angle measurement e
81. een components The Scalar Color Mapping Scalar Opacity Mapping Gradient Opacity Mapping as well as the shading parameters set in the Material Properties dialog are per component properties that must be set independently for each component by using this option menu The Interpolation Enable Shading and Interactive Apply options as well as the Component Weights are set once for the dataset and there values will not change when adjusting the active component Table Of Contents 36 Interpolation Two interpolation options are provided nearest and linear In the process of volume rendering it is necessary to take a sample at a 3D position within the data This interpolation method determines how the scalar value is obtained at the desired x y z location from the neighboring sample values When this option is set to Nearest a nearest neighbor interpolation is employed meaning that the closest sample value is used as the value at the x y z location When this option is set to Linear a trilinear interpolation method is used to approximate he value based on the eight surrounding neighbors Generally you will want to keep this option in the Linear mode but in some applications especially with small labeled data sets it is useful to view the image without the interpolation effects Edit material The Edit material button Fe Le shows a representation of the current VolView 2 0 IronProtein vtk td material settings applied to a sphere
82. els area These will be the most recently viewed property sheets To switch between these panels simply click on the panel tab Moving the mouse to the right edge of the panel area will change the mouse to a horizontal double arrow indicating that you can resize the left panel area There is a minimum size below which you cannot resize so that interface elements will fit on the panel If you have an unusually large font you may find the need to increase the size of the panel area There are several interesting features of the property panels First you can lock a property panel in place by first clicking on the tab to make it visible if it is not already and then double clicking on the tab for this panel You will see the name of the panel change to italics indicating that it is locked on the property panels area When switching between panels using the View menu only the unlocked panels will be swapped out for the new panels If you lock all of your panels you will not be able to view any new ones until you unlock at least one Another interesting feature of the property panels is that you can close and open the areas on the panel using the small icon in the corner of the area When the area is open the icon will appear like a small X Pressing this will close the area displaying only the area title The icon in the corner will now be a small downward facing triangle Pressing this will once again open an area The areas on the panels can a
83. enabled allowing you to undo this filter operation If the data is large this option will not be available and you will have to reload the data from disk in order to undo If the filter generated a surface then the Remove Surface button will be enabled allowing you to remove the surface generated by the filter 92 Information Undo Last Applied Filter If there is enough memory and the volume was modified by the last filter applied this button will be enable Pressing it will restore the volume to the state it was in before the filter was applied Remove Surface If the previous filter generated geometric output then this button will be enabled You must remove the surface before you will be able to apply another filter There are four sources of filters in VolView 2 0 C filters C filters VTK filters and ITK filters If the name of the filter ends with ITK then this filter functionality is from the National Library of Medicine s Insight Segmentation and Registration Toolkit www itk org If the name of the filter ends with VTK then this filter functionality is from the Visualization Toolkit www vtk org Otherwise this is a C or a C filter The source code for the C C and VTK filters can be found in the VolView installation directory most likely C Program Files VolView20 in the SourceCode directory The source code for the ITK filters can be found in the InsightApplications VolviewPlugins repository More information o
84. er of a data set to view the internal structure There are six different cropping options available using the Type option menu A pictorial example is shown below followed by a description of each cropping type 48 Cross Subyolume Information Inverted Cross Off No cropping of the data is performed Slider values are ignored Subvolume The subvolume defined by the six sliders is displayed As with all cropping operations the volume will be interactively updated while the cropping sliders are moved Fence The portion of the volume that is between any pair of orthogonal clipping planes is displayed Fence is useful for moving three of the six sliders one of each X Y and Z sliders to cut out a corner of the volume Inverted Fence The inverse of the fence operation the portion of the volume that is outside of all orthogonal clipping planes is displayed Cross The portion of the volume that is between any two pair of orthogonal clipping planes is displayed Inverted Cross The inverse of the cross operation the portion of the volume that outside of at least two pair of orthogonal clipping plane is displayed Thick Reformat The Thick Reformat area on the Cropping panel provides a way to reduce the amount of volume data display in the volume window An example of this interface is shown on the right Thick reformat is the process of slicing the volume with a slab The reformat cut can be Thick Reform
85. essing the Delete key on your keyboard or by dragging it far below the editing area and releasing it So far the images we have been viewing in Scalar Color Mapping 0 255 the volume display area have been unshaded Hs A E Tail E MN e o Enable Shading button near the top of the AR i 1 Volume Appearance Settings area You can edit the material properties including the ambient diffuse and specular coefficients and the specular power by hitting the small sphere representing the current shading parameters next to the Edit material label This will pop up the Material Properties editor with four sliders for these four values plus four convenient presets for no shading diffuse only shading diffuse with some specular and highly specular shading Ambient is a non directional term that will uniformly increase the brightness in the image No shading is equivalent to full ambient with no diffuse or specular contributions Diffuse lighting is dependent on the angle between the normal and the vector to the light source When the light is shining perpendicular to the surface it will receive the most illumination dropping off to 0 when the angle reaches 90 degrees Specular is the shiny term and is dependent on the normal direction the light vector and the viewing vector This can be thought of as a reflection of the light source in a shiny object The specular power adjusts the focus of this reflection a small power will mean an unfo
86. et and the default Level will be the smallest value in the dataset plus 1 2 of the Window value These Window and Level values define a linear ramp with a modulation value of 0 0 at the smallest value in the dataset and a modulation value of 1 0 at the largest value in the dataset varying linearly in between these two endpoints You can make the image brighter or darker by adjusting the level value up or down and you can focus in on a narrower band of values improving contrast in this region by tightening the Window value In addition to adjusting these values through the user interface they can be adjusted interactively in the image window using the left mouse button this is the default setting although this binding can be altered Reset The reset button resets the Window and Level values back to the default values Pressing the r key in the image window will also reset the Window and Level values as well as the camera parameters Window Level Presets The preset pulldown e menu initially contains no entries While adjusting E VolView 2 0 Add Ed Window and Level you obtain values that you would SE A like to restore at a later time you can use the Add Preset button to add this preset It will be added to bond the pulldown list available in the Window Level OK Cancel Presets pulldown menu Simply select this item from the list in order to restore these Window and Level values These presets will be saved a
87. etGUlProperty info 0 info gt SetGUlProperty info O approximation will be computed 0 ib 1 1 info gt SetGUlProperty info info gt OutputVolumeScalarType VTK UNSIGNED CHAR info gt OutputVolumeNumberOfComponents 1 info gt OutputVolumeDimensions 0 info gt InputVolumeDimensions 0 info gt OutputVolumeDimensions l info gt InputVolumeDimensions 1 info gt OutputVolumeDimensions 2 info gt InputVolumeDimensions 2 memcpy info gt OutputVolumeSpacing info gt InputVolumeSpacing 3 sizeof float memcpy info gt OutputVolumeOrigin info gt InputVolumeOrigin 3 sizeof float return 1 extern C void VV PLUGIN EXPORT vvITKAntiAliasInit vtkVVPluginiInfo info vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUI info gt SetProperty info VVP NAME Anti Aliasing ITK info gt SetProperty info VVP GROUP Surface Generation info gt SetProperty info VVP_TERSE_DOCUMENTATION Reduction of aliasing effects info gt SetProperty info VVP_FULL DOCUMENTATION This filter applies a level set evolution over a binary image in order to produce a smoother contour that is suitable for extracting iso surfaces The resulting contour is encoded as the zero set of the output level set The zero set will be rescaled as the mid value of the intensity range corresponding to the pixel type used Th
88. ether the animation type i I 3D Views Animation type option is set to 3D View or 2 Slices Both examples are shown in this Xrotation azimuth a lo section Y rotation elevation fo Using the Animation Settings area you can Rotation roll EE lo create an AVI file that either shown a simple zoom factor 1 00 rotate zoom animation of the volume display window or a sequence of slices in one of the X Y Axial X Z Frontal or YZ Sagittal image windows The common controls are described below followed by those that are specific to each animation type Preview Create Cancel 2 Preview images will be generated using the Standard Interactivity setting from the Level Of Detail Options area on the Volume Display control panel When the animation is created the best available level of detail will be used After selecting a filename you will be prompted for a video compression type Not all compression types will work on your system The common interface elements are with your current window size Microsoft Video 1 Intel Indeo R Videc R3 2 and Full Frames uncompressed will typically work Number of frames This value specifies the number of frames in the output animation Smaller numbers will lead to faster animation creation times but a jumpier appearance Larger numbers will provide a smooth appearance but may take a while to generate and may produce large AVI files dependin
89. evel and viewing parameters When loading multiple component data more than one channel at each sample you will see a page in the Open Wizard asking you whether or not the channels are independent If these channels sampled independent properties such as temperature and velocity then the answer should be yes If these channels together form either an Intensity Alpha pair RGB or RGBA for two three or four components respectively then the answer should be no and you should not check this box The dialog will appear similar to the one shown on the right Application Settings VolView 2 0 Open Wizard Open Valores Wirard da ner eien Pepas ver fat the data samen pin SCT Streng Iefa t KAS rer ees hov Se Antares idee een fress Cour se A Volts ross uge Doten por Dee Be Oe ren roda dl do load your data Mie 22 3 ter gata Ra VER a rar da la Gr vr rt pro vda actoral mermado 61 bat Way cari lad a daa Pese ele has Fou dd Re ho ore and hen press Heal Mp G nge peras of 20 ez o E Se D Ciro the opi s VolView 2 0 Open Wizard Open Valores Wicard Apr F r Lr teg ode oder hs ia pour date ard hue tied fo esker snare enais p bo the nature of er dann Fig Piaam vent ba parte An cba pra of ar sko kuer using fe cra patee e dassi fa idin He poden Couns H Channa Area ea Pain Typa CIN as i i unsagned E bet VolView 2 0 Open Wizard Open Valores Wirard ira rs TL popen fer pos ME load
90. ext When the opacity is 1 0 the text will be fully opaque Choosing values less than 1 0 will cause the text to become translucent allowing you to see through the text Header Annotation The Display header annotation button can be used to toggle the visibility of the header annotation The header annotation is a string that is displayed along the top center of the volume display window It is best to use the header annotation only when the corner annotation is off empty in the top left and top right corners or contains only short strings Long text strings in both the upper corners of the corner annotation and the header annotation will overlap Press the Edit button to pop up the Volume Header Annotation dialog An example of this dialog is shown on the left Use the Header text entry box to enter the string 2 Volume Header Ed Header Annotation Header Header properties Color Family Arial Styles B I d Opacity 1 00 gt Close that you would like displayed on the volume window The properties of the header including the color font family style and opacity can be set See the description above for corner annotation for a definition of each of these properties An example image showing a variety of volume annotations is shown near the end of this section In this image you can see both corner annotation in the upper left and right corners in yellow Arial and header text in the
91. f volume render since it is data dependent and typically must be performed by hand In VolView there are three different mappings that impact the rendering process The Scalar Color Mapping converts the scalar data into RGB colors the Scalar Volume Appearance Settings x Component i Value Hue Saturation Interpolation Linear Edit material wa Enable Shading Interactive Apply Scalar Opacity Mapping IO 255 Ka CH Scale fi i D re Scalar Color Mapping O 255 peu A E s 6 9668 Hilo 6r sioz Vill WW HA HN ge ___ _ _u 0 63 75 Gradient Opacity Mapping om Ex ST o p Component Weights Opacity Mapping converts the scalar data into alpha values transparency and the Gradient Opacity Mapping converts the magnitude of the gradient rate of change in the scalar data into opacities The scalar color and opacity mapping are useful for classifying data values into different materials while the gradient opacity mapping is useful for enhancing edges in the data Each of the elements on the interface is described in detail below Since many of the elements are inter dependent it will be necessary to read through this entire section for a complete understanding This documentation is written with the assumption that the section will be read in its entirety Component When your data contains more than one independent component this option menu will allow you to switch betw
92. fo VVP_SUPPORTS_PROCESSING_PIECES EE info gt SetProperty info VVP NUMBER OF GUI ITEMS re 90 Extending Filters With Plugins Example 3 A VTK Filter This is the code for Utility Gradient Magnitude Filter VTK include vtkVVPluginAPI h include lt string h gt include lt stdlib h gt include vtkImagelmport h include vtkImageData h include vtkPointData h include vtkImageGradientMagnitude h include vtkCallbackCommand h extern Cc static void vvGradientMagnitudeProgress vtkObject obj unsigned long void inf void vtkNotUsed prog vtkVVPluginInfo info vtkVVPluginInfo y Lat vtkSource src vtkSource SafeDownCast obj if src info gt UpdateProgress info src gt GetProgress Computing Gradient Magnitudes check for abort src gt SetAbortExecute atoi info gt GetProperty info VVP ABORT PROCESSING static int ProcessData void inf vtkVVProcessDataStruct pds vtkVVPluginInfo info gt vtkVVPluginInfo int int dim info gt InputVolumeDimensions create a Gaussian Filter vtkImageGradientMagnitude ig vtkImageGradientMagnitude New Set the parameters on it 1g gt SetDimensionality 3 setup progress vtkCallbackCommand cc vtkCallbackCommand New cc gt SetCallback vvGradientMagnitudeProgress cc gt SetClientData inf ig gt AddObserver vtkCommand ProgressEvent cc
93. for i 0 i lt dim 0 info gt InputVolumeNumberOfComponents i SetPixel info ptr replacementValue ptr rsize else for i 0 i lt info gt InputVolumeNumberOfComponents i SetPixel info ptr replacementValue SetPixel info ptr info gt InputVolumeNumberOfComponents dim 0 1 replacementValue 86 POO OO OO GOO EO BO GPO O GP GPO GO GP OO Gl GO OO Gl PGE OP fl e Extending Filters With Plugins ptr sizes ptr ptr info gt InputVolumeNumberOfComponents rsize dame EE return 0 static int UpdateGUI void inf char tmp 1024 vtkVVPluginInfo info vtkVVPluginInfo inf info gt SetGUlProperty info 0 VVP GUI LABEL New Boundary Value info gt SetGUIProperty info 0 VVP GUI TYPE VVP GUI SCALE info gt SetGUIProperty info 0 VVP GUI DEFAULT 0 info gt SetGUlProperty info 0 VVP GUI HELP What value to set the boundary voxels to sprintf tmp ot SE 3f info gt InputVolumeScalarTypeRange 0 info gt InputVolumeScalarTypeRange 1 Ted info gt SetGUlProperty info 0 VVP GUI HINTS tmp info gt OutputVolumeScalarType info gt InputVolumeScalarType info gt OutputVolumeNumberOfComponents info gt InputVolumeNumberOfComponents memcpy info gt OutputVolumeDimensions info gt InputVolumeDimensions 3 sizeof int memcpy info gt OutputVolumeSpacing info gt InputVolumeSpacing 3 sizeof float
94. g on compression type Animation type The animation type can be set to either 3D View or Slices With 3D View you can specify rotation and zoom factors to be applied across the animation sequence For Slices you can loop through the slices in one of the three primary directions Preview The preview button will allow you to view the animation in the volume or image window For 3D View animations an interactive volume rendering rate will be used for the preview while a higher quality rendering will be used when the animation is created Create The create button will pop up a Save Animation dialog allowing you to specify the Video Compression location and file name of your animation The file Compressor HE type will be AVI and therefore the animation file Full Frames Uncompressed IAN will have an avi extension This will be added to ieee the filename if you do not enter it here Once you ve selected the file name the Video Compression dialog will be displayed allowing you to select a compressor type for this file Note that this is a standard Windows dialog which will appear similar to the one shown on the right but not every compression format will be Supported by your system Uncompressed Full Frames will always work You may need to experiment with a few of the compressed types to determine if it is supported by your system how much compression is achieved and what the best trade off is for image size vs image quality This t
95. he File menu This will pop up the Save Session dialog allowing you to specify a location and filename for the session file Session files should end ina vvs extension this extension will be Save my data to a new file then save my session added to your filename if you do not provide it Overwrite headhalf vtk then save my session Cancel Note you will be unable to save a session file if you have modified the volume data through the use of a filter and have not saved the data since there is no data on disk for the session file to reference In this case VolView will pop up a dialog similar to the one shown on the right requesting that you save the data before the session file can be created a VolView Write Error must be saved to disk before a session file can be created How would you like to proceed ap The data you loaded from headhalf vtk has been modified and Saving Volumes VolView can save volumes in a variety of formats including VTK XML format raw format or as a series of BMP TIFF JPEG PNG or PGM files You may wish to save a volume in order to change the format For example if your data is stored in raw format there are several benefits to converting to VTK XML format First the VTK XML Bivelser format is compressed which will save disk space and improve load time on large datasets Also the PPM VTK XML format has a header that stored important CADevelop information such as data dimension
96. he color of all 3D markers using this button It is useful to select a color that differs from the background color and the major colors used in the volume image display Add Marker Use the Add Marker button to add a new marker at the current 3D cursor position You can also add markers by using the keyboard shortcut p in the axis aligned image display windows You can adjust the position of a marker by dragging it either in an image display window or the volume display wndow When you select a marker with the 65 Table Of Contents left mouse button it will become the currently selected marker and will appear slightly bigger than the other markers Remove Selected Remove the currently selected marker Remove All Remove all markers 2D Marker The 2D Marker area on the Markers panel 2D Marker x allows you to turn on an overlay marker in C Dray Dmak cet Color each of the display windows The interface is l shown on the right and simply allows you to toggle these markers and adjust the color In the image windows the m key can also be used to toggle these markers When using two connected VolView sessions the 2D marker can be useful as a pointing tool This will allow you to better communicate with your remote colleague since you can say over a telephone line Here is the tumor and use the 2D marker to indicate the position Recall that mouse cursor position is independent on the two systems connected through VolVie
97. he graphics hardware to render the volume with 3D texture mapping On all systems VolView will use ray casting to create an accurate final image See the next section for more information on the various levels of detail used during rendering When using ray casting the super sample factor will control the distance between sample points along the ray A factor of 1 uses a distance that is equal to the average spacing between voxels A factor of N sets the distance between sample points to 1 N times the average spacing between voxels When a hardware method is in use this super sampling factor control the spacing between planes that are rendered with 3D texture maps to form the image The higher the super sampling factor the smoother the image will appear in ray casting Increasing the super sampling factor can help alleviate aliasing artifacts caused by high frequencies in either the volume data or the transfer functions Increasing the super sampling factor will also increase the amount of time required to create the final high resolution image Also increasing the super sampling factor may have a negative impact on the hardware accelerated rendering in that banding artifacts may appear due to insufficient frame buffer resolution for the very small opacities being accumulated Level Of Detail Options The Level Of Detail Options area on the p Level Of Detail Options x Volume Display panel can be used to adjust Standard Interactivity the re
98. ibed in more detail below Component When working with multiple component data this pulldown menu will allow you to select the component for which you wish to view the color bar Only one color bar for one component can be displayed at any time Title The color bar can be labeled This title will appear along the top of the color bar in either vertical or horizontal mode You can adjust the appearance of the title using the Title properties elements below Title properties Using this set of interface elements you can adjust the color font family style and opacity of the title of the color bar For a description of each of these elements please see the documentation for the corner text annotation above Label text properties You may used this set of interface elements to adjust the text properties including color font family style and opacity of the labels Maximum number of colors This value adjusts the number of color segments used to display the color bar A smaller number will lead to a blocky appearance in the color bar A large number will lead to a smooth appearance of the color bar but may degrade performance Number of labels The number of labels can be adjusted Bringing this number down to zero will remove all of the labels In addition to these user interface mm elements that adjust the appearance of the color bar you can reposition and resize the color bar interactively in the volume widget Move the mouse over
99. iginal position and orientation at the center of the volume 91 Table Of Contents Filters Filter Settings Overview The Filter Settings area on the Filters panel Filters Settings x provides access to powerful filtering Filter EE ul capabilities and allows for the addition of customized filters at run time An example of Replace voxels above at below the threshold value this interface for the Threshold filter is shown replace values to the right There are some elements of this TA interface that are common to all filters and Threshold val some elements that change based on the AAA NU selected filter In this section only the common elements will be described In the f rlatement Value o remaining sections of this chapter each of H the categories of filters will be described in 2 This filter performs a pixel replacement replacing pixel in the original data by a specified replacement value The pixels to be replaced are detail These categories include Utility determine by comparing the original pixel value to a threshold value Surface Generation Edge Detection with a user specified comparison operation This filter operates in Segmentation Level Sets Segmentation E not change the dimensions data type or spacing of Region Growing Noise Suppression and Intensity Transformation Apply Filter _ unde Last Applied Fitter _ Remove Surface The common elements to this interface area are the pul
100. ile using the Save Screenshot option under the File menu A screenshot is an image composed of all the image display windows currently arranged in the application First select the window arrangement you would like using the Window menu and by reassigning the content of the window using the pulldown menu in the upper left corner For example if you would like to save the lightbox image next to the volume image select the 1 beside 1 option from the Window menu then use the pulldown menu in the upper left corner of the right window to select the Volume display the left window will already contain the lightbox by default Next select the Save Screenshot option from the Edit menu A file dialog will be displayed allowing you to select the filename and type of the image file saved to disk Your options include BMP JPEG PNG PPM binary format or TIFF 74 Extending Filters With Plugins Edit Copy Screenshots VolView supports copying a screenshot to the clipboard A screenshot is an image composed of all the image display windows currently arranged in the application This functionality is only supported on the Windows platform First select the window arrangement you would like using the Window menu and by reassigning the content of the window using the pulldown menu in the upper left corner For example if you would like to save only the Axial image select either of the single layout options Volume Only or Lightbox Only then use the
101. ill be smaller than the full scalar range This is due to the fact that most gradient magnitudes will have generally low values compared to the full scalar range Initially the gradient opacity mapping will be Off shown on the first button under the label and the histogram will be absent as shown in the image at the beginning of this section You will need to turn on the gradient opacity mapping and wait for a ray cast image to be generated and therefore the gradients will be computed before the histogram of the gradient magnitudes will be displayed Alternatively if you enable shading then the gradients will be computed the direction rather than the magnitude is needed for shading but both are computed at once and the histogram will be displayed 40 Note that gradients consume memory on your computer If you have used most of the physical memory on your computer before you have turned on either shading or the gradient opacity mapping then it is likely that system performance will degrade when you turn either of these on since virtual memory will be employed The button with the file icon provides a few preset gradient magnitude functions Generally you will need to adjust this by hand since it is highly data dependent When interacting with the nodes you will notice that the first two are linked in opacity and the last two are linked in Opacity and must be 1 0 The second and third nodes can be moved horizontally to adjust the streng
102. ing Vokene af ben saler DDE pa Tage Votes man PER os crepe fri tr real ras IF pau br t Em romanen ar indep S ier Bee eech caporent ei hast Fe Cep onder sd Gite brensler funcio dk of 33 ve wm 4d ba rete Bag rn carepeorent ip repr bra ral hu menne srrserenta darm ij It eg DDE ig are nat independent hen fres pts ordered fo morse med sd OT repress Fiegen verify Hut foe sgt e cf Independent Corspzanenin ir correct Conporenta ar independent Table Of Contents The User Interface User Interface Overview The VolView user interface consists of six main regions as illustrated below This includes the Main Menu Bar the Toolbar the Property Panels the Display Windows the Status Bar and the Main Progress Gauge Note that not all of these regions will be visible at all times A detailed description of each of these regions is provided below Toolbar Main Menu Bar Display Windows VolView 2 0 FootSeries 000 jpa arms File Edit Vies Window Hee JEHESIEBEE Views B lights Cropping volume entar appeerarce Wo lame Fs Editor Desch Hi Sahra bon Inherpedaten Edt material DER l Inheracive Age Scalar Opacity Happing E DO 255 01 255 00 GL SES pa Sealir Color Mapping 0 60 2250 Hd Al Sy alaa ba fico sho wio Gradient Opacity Mapping Window 18900 Window ence RER Level 84 50 Het Bice Cie HE Je 294
103. ion is regulated by the curvature of iso contours in the image This filter processes the whole image in one piece and does not change the dimensions data type or spacing of the volume Gradient Anisotropic Diffusion ITK This filter applies an edge preserving smoothing to a volume by computing the evolution of an anisotropic diffusion partial differential equation Information Diffusion is regulated by the gradient of the image This filter processes the whole image in one piece and does not change the dimensions data type or spacing of the volume Median ITK This filters applies an intensity transform by replacing the value of every pixel with the median value of their neighborhoods The neighborhood size is defined by a radius Dilate Filter VTK This algorithm replaces a voxel with the maximum over an ellipsoidal neighborhood If the KernelSize of an axis is 1 no processing is done on that axis This filter operates in pieces and does not change the dimensions spacing etc of the volume Erode Filter VTK This algorithm replaces a voxel with the minimum over an ellipsoidal neighborhood If the KernelSize of an axis is 1 no processing is done on that axis This filter operates in pieces and does not change the dimensions spacing etc of the volume Median Filter VTK Compute a volume of the median of the neighborhoods of each voxel This filter operates in pieces and does not change the dimensions data type or s
104. is filter processes the whole image in one piece and does not change the dimensions or spacing of the volume The pixel type however iS converted to unsigned 8 bits since it is enough for representing the implicit smoothed surface info gt SetPropertyiinfo VVP SUPPORTS IN PLACE PROCESSING 0 info gt SetProperty info VVP SUPPORTS PROCESSING PIECES VOM info VVP_NUMBER_OF_GUI_ITEMS ANYS info gt SetProperty info gt SetProperty info VVP REQUIRED 7 OVERLAP MOT info gt SetProperty info VVP_PER_VOXEL_MEMORY_REQUIRED es A de 95 1 SR RE EE 23 TVOME EE 23 Moi gt EE A A 23 DESTE 2 a ae 23 A ee ee 23 VE EE 23 E EE E cece R 23 2 e EE 23 POE dere 23 lA a a N 21 66 3 NS 23 BEA A Ones 21 65 SPD MAKES it labs 21 65 3D texture MAPS aa 70 A About VolView 24 academic ee Eu EE 7 ACTIVE CONO Uy ri 46 Aere Lei EE 68 active SESSION EEN 76 AdO SONO TEEN 45 ACA WAKER cintia 65 Add Ger var 60 Ambien Eege 11 35 E 14 Maia 21 AIM Os 21 27 Animation Settings rrarnrnarnrrernrnevnrnenn 27 Animation type sa 27 el te tte eons eae nede 21 29 Anti Aliasing IR 54 APD ANC E 11 21 35 Appearance Settings occccoccocconnconnnooo 74 Application Area 9 26 67 Application Settings 9 21 25 26 AP FIG sner fee 52 AT Rade ci 70 PR TEE 27 B background color 71 BINdNGS Vase 9 21 42 43 BioRad Confocal eeng NNN NENNEN ON 14 PENN WEE 21 BIENAINg FUNCTION
105. is mapping is applied separately to each component and combined with the weights found on the Appearance panel When switching between modes keep in mind that it may be necessary to reset the Window and Level values in order to see the image You can do this either by pressing the Reset button in the Window Level area or by clicking on an image window so that it is highlighted in blue and pressing the r key Since a picture is worth a thousand words the following examples will be quite helpful in understanding the differences between these mapping modes These examples are shown for three different types of data single component data two component dependent and four component dependent For two three and four component independent the results are the same as the single component data except that the multiple results are blended together according to the weighting factors specified on the Appearance panel In this first example we have single component data The image on the left shows a volume rendering of the data The next image shows the data with a Raw Scalars mapping followed by a Color Mapped Scalars image and finally the image on the right shows an image created with Color Mapped Scalars Opacity Modulated In this next example we have two component non independent data In the first component is a simple gradient in the Y direction These values will be used to derive color In the second component is a synthesized vase
106. ist and the expert to collaborate on the review of the patient s situation For the most effective communication it is best to communicate via telephone while running the collaborative sessions of VolView Alternatively you can use a chat or meeting program such as NetMeeting to facilitate communication Please see the next section for details on how to connect two VolView sessions Connecting And Passing Control In order to connect two VolView session please follow the steps listed below Note that it will be helpful if the two users are communicating via telephone or an online chat session while the connection is made and the collaboration is performed The first step is to start VolView on the two computers If you would like to test out this functionality the two VolView sessions can both be on the same computer One of these sessions will need to connect to the other To do so you will need to know the IP address of the system to which the other VolView session will connect If you do not know the IP address of your system please contact your system administrator for this information The next step is to connect the two sessions On the VolView that will connect select the Connect To Remote option from the File menu This will pop up Connect to Remote Application the Remote Connection dialog as shown on the right Please enter the address of the second application station Enter the IP address of the other VolView session and
107. l appear different When working with four component data that is not independent it is RGBA the scalar color mapping region will be absent since the colors are directly obtained from the data Information Similar to the scalar opacity mapping region the values displayed in the upper right corner represent the range of the data and the range bar along the bottom of the editor can be used to adjust the displayed range for fine editing The active node will be larger than the others and will display its node number The text entry boxes in the upper right will reflect the scalar and color values associated with that node The scalar value is in the first text box marked S The color is displayed as either hue saturation and value H S V or red green and blue RGB depending of the setting of the first pulldown menu below the scalar color mapping label This setting HSV vs RGB will also effect the color space used to interpolate colors between nodes In the example above the color space is set to HSV and you can see in the representation of the interpolated color the color rectangle below the editing area that green is between yellow and blue In RGB color space the interpolation from yellow to blue passes through grey In addition to the color space button two other buttons are located below the scalar color mapping label The center button with a lock icon on it allows you to lock the scalar color and scalar opacity mappings toge
108. ldown to specify the filter the refresh button and the brief description at the top of the area and the long description and three buttons at the bottom of this area These are described below Filter This pulldown can be used to select the filter This is a cascading pulldown with seven categories Selecting a filter from this list will change the appearance of the interface since each filter has its own set of configurable parameters Refresh The refresh button is an icon in the shape of a circular arrow to the right of the Filter pulldown If you install a new filter plugin during application run time you must press this button in order to update the Filter pulldown with the new filter Please refer to the section on Extending Filters with Plugins for further information Brief Description Below the Filter option menu will be a one line description of the selected filter Long Description Just above the bottom three buttons will be a verbose description of the selected filter Apply Filter This button will apply the selected filter to the currently loaded data Once the filter has been applied a timer label will be added above this button indicating how long the filter required to process the data In addition an information label may also be added providing information about the execution of the filter such as how many polygons are in the generated surface If enough memory is available the Undo Last Applied Filter button will be
109. le Of Contents twice then indicate that your computer is not connected to the Internet You can then follow the instructions for manually obtaining and installing a license file Any problems encountered during registration should be reported to Kitware technical support at support kitware com or 1 518 371 3971 Check For Updates Updated versions of VolView 2 0 may be made available from time to time If you have purchased a VolView Professional Mode license you will be notified via email when new updates are available All users running the beta version of VolView 2 0 and those who have installed VolView from a CDROM are encouraged to check for updates If you are running VolView 2 0 on Windows and you have an internet connection checking for updates is quite easy Simply use the Check for Updates option on the VolView20 menu under Programs on your Start menu Alternatively you can start VolView and use the Check for Updates option on the Help menu A dialog will appear indicating either that a new version is available and it will list the release notes for this version or that you are running the latest available version If you do not have an internet connection or if you are running on Linux Unix or Mac OSX you must visit the VolView web site to check for updates The latest available version will always be indicated on http www kitware com products volview html Technical Support Customer support is provided free during th
110. lso be repositioned To move an area with one panel press the left mouse down over the title of the area drag it to a new position up or down and release the mouse Generally you should release the mouse over another area and the one you were dragging will then move below the one over which you released it To move an area to another panel you would drop the area onto the tab for the other panel both panels must be tabs in the property panels area Display Windows From one to six display windows may be visible at any time These will be located below the main menu bar and the toolbar and above the status bar and the main progress gauge If the property panels are visible they will be to the left and the display windows will be to the right There are ten basic configurations that are displayed on the toolbar pictorially and these options are duplicated in the Window menu Selecting one of these options from the toolbar or the Window menu will alter the arrangement of windows in the display area There are six different types of windows as described below Volume This is a volume rendering display of the data This window supports 3D interaction Lightbox This is an image display allowing for up to 25 consecutive images to be displayed in a grid pattern This window supports 2D interaction Oblique Probe This is the image obtained from applying an oblique probe to the volume displayed in the Volume window You can turn on the obliq
111. n VTK and ITK can be found at their respective web sites Please note that the filters described in this document are those available in the initial VolView 2 0 release More filters may be available in the version you are currently running and additional filters can be added at run time Utility Filters The filters in this category are basic utility filters for tasks such as changing the boundary values in a volume applying a threshold computing gradient magnitudes merging two volumes or cropping a volume More detailed descriptions of each of the available filters in this category are provided below Boundary This filter performs a voxel replacement replacing every voxel that is a boundary voxel with the specified value Boundary voxels are the voxels that have at least one face on the boundary of the volume Put another way boundary voxels are voxels that are not fully enclosed by other voxels Component Arithmatic This filter computes a new volume by performing an arithmatic operation on the components of the input volume While all operations will work with any input volume some make more sense than others For example computing Hue or Saturation really only makes sense with multicomponent color data and then typically with unsigned char data only The results of the calculation can replace all the components of the original volume e g create a new volume without only one component replace just the last component of the input
112. n the menu are dependent on the type of data loaded For example single component data the most common type will have only Raw Scalars Color Mapped Scalars and Color Mapped Scalars Opacity Modulated as options 58 Raw Scalars The window level operation will be performed directly on the raw scalar values found in the dataset and these resulting values will be displayed When more than one independent component is present the weighting is taken from the weighting sliders on the Appearance panel When viewing two component non independent data where the first component is used to derive color and the second is used to derive opacity this mapping displays only the first scalar component For all but color data four component non independent the resulting values will be gray scale With color data the actual RGB value found in the dataset with a window level applied is displayed This option is available will all data types Raw Scalars Opacity Modulated This option only applies to color data four component non independent In this mode the color is derived from the RGB values in the data set but the window level is applied not to the color but to the opacity alpha fourth component channel of the image The value obtained after windowing and leveling the opacity value is used to modulate the color displayed Gray Scale Scalars This option is only available for RGBA data four component non independent This option is similar
113. n you enable this tool you will see a line with two spheres at the endpoints appear within the dataset Also you will see a measurement string initially displayed in the lower left corner of the volume display window If you move the mouse over the distance measurement text you will see the horizontal and vertical double arrow indicating that you can reposition this text The line and spheres can be repositioned as well although the mouse cursor will not change when you move over these elements You can drag either of the two endpoints and reposition them anywhere within the dataset You can also drag the entire measurement tool by clicking on the line Remember your movement will be constrained by the bounds of the volume Annotations Image Annotations The Image Annotations area on the Image Annotations x Annotations panel contains the annotation Y Display corner annotation Edit elements that can be displayed in the image Display header annotation Edit windows Most of these annotation items are ce e identical to those available in the volume w Display scale bar Set Color E display window In these cases the reader is referred to the previous section on Volume e Annotations for further information ee ee W Display distance measurement An example of the Image Annotations area is shown on the right Each of the five annotation elements are described in more detail below Note that the Image Annotation are
114. nd to the full range of the data Focusing in on a smaller region of the full range can be useful when making a detailed mapping function although typically you should be able to specify you function while viewing the entire range Below the Scalar Opacity Mapping label we have two buttons and a pop up slider The first button toggles Window Level Mode When this mode is enabled the mapping will be reduced to a basic window level function The function will contain only four nodes with the first two having the same opacity value and the last two having the same opacity value A linear ramp is therefore specified between the second and third nodes More details on interacting with the nodes when in Window Level Mode is provided below The next button with a file icon on it is a pulldown menu that allows you to choose a preset opacity mapping from a list of available mappings Two of the mappings specify constant opacity functions at 0 2 or 1 0 and two represent linear ramps over the whole scalar range of the data from 0 0 to 0 2 or from 0 0 to 1 0 The default mapping is based on a histogram of the data which is displayed in the node editing area and is a linear ramp from 0 0 to 0 2 within a reduced range of the data computed using the histogram The Scale slider pop up allows you to scale the entire opacity of the mapping Since Opacity is not an instantaneous value but is defined per unit length traveled through the volume w
115. ndering rate during interaction and to Fast Sn fcr si control the different representations used for Indude the following LODs rendering the volume and looks similar to Ray Casting always the image on the right Hardware 1 Available Depending on your system configuration e VolView wil use e to lt different me Refresh volume window for rendering the volume When supported by the hardware and the type of data loaded VolView will employ a 3D texture mapping technique for accelerated rendering On all systems VolView will use a ray casting technique to produce an accurate final image Each of these methods have multiple levels of detail to produce faster images when required for interactivity By watching the progress bar on the upper right corner of the volume display window you can see the rendering method and the number of levels of detail used for generating a final image When the progress bar displays in blue a hardware accelerated technique is in use When the progress bar displays in green the image is generated with ray casting Different shades of blue and green indicate different levels of detail within a rendering method 70 Volume Display The Level Of Detail Options area has several controls that can affect the rendering method Each of these is described in more detail below Standard Interactivity This slider allows you to control the speed at which rendering occurs during interaction When
116. ne along the normal to the plane Using the left mouse button in the edge area allows you to rotate the plane around that edge s axis through the center of the plane Pressing the left mouse button in a corner area allows you to spin roll the plane around its normal Using the middle mouse button in any region of the plane provides a uniform scaling of the plane upward motion increases the size while downward motion decreases the size of the plane Pressing the right mouse button on an edge or corner area provides constrained scaling of the selected edge or two edges in the case of a corner Finally pressing the right mouse button in the center area allows you to translate the oblique plane along the two axes defined by the edges of the plane The oblique probe image can also be displayed in its own window Using the pulldown menu on one of your display windows select the Oblique Probe option from the list to view this image Window Level adjustments to this image will be reflected in the other image display windows as well as in the probe image displayed in the volume display window In the example image on the right you can see the volume display window on the left and the oblique probe image display on the right Since it is possible to lose track of the probe plane in the volume display if it is hidden by the volume or reposition far outside the volume the Reset Probe button is provided This will reset the probe plane back to the or
117. new window and level settings These values are set for the entire application window not per image window keeping all 2D views of the data synchronized Now try adjusting the window and level values using the mouse Press the left mouse button and move the cursor left to right to adjust the window value and up and down to adjust the level value You can press the Reset button in the Window Level area of the Image Display panel to reset these value In addition the r key will reset both the window level values and the display position of the image In addition to the window level functionality on the left mouse button VolView provides panning and zooming on the middle and right mouse buttons To see a list of these binding view the Bindings panel In the Image Mouse Bindings area you will see a grid of configurable mouse binding for the left middle and right mouse buttons pressed alone or in conjunction with the shift or the control keys Below this in the Image Keyboard Bindings area you will see a list of the keyboard shortcuts including those mentioned in this section Spend some time panning and zooming the image to become comfortable with this functionality Note that when you zoom the other image windows zoom as well Panning occurs independently in each image window Finally let s discuss the Image Mapping area on the Image Display panel The current mapping is set to Raw Scalars and hence you are viewing the scalar values
118. nnnnnnnnnn 29 dOS AA e a a 20 DET enee 20 75 E Edge Detection Filters ocococococooo 54 97 Table Of Contents Edit Copy Gcreenshots 75 ee E 35 Enable Shading cccccecsececeeceseeceees 35 y mA o N A E 43 ENANG Wer LS 27 Erode Fiter V TDi pias eas 56 EU AN 20 25 EXPOM DICOM patina 20 Extending Filters Overview 78 F Bu EE 29 Fast Marching IK 55 Fast Marching Module ITK 55 FN Eee 48 FIG MEN ao 20 Filter Settings Overview rrrnarnrnarnnvennr 52 A 21 53 54 55 56 57 MENA ir 76 Fer DONS ee 26 PIAL AIM E 26 Ea al gee ne eee a 42 Eege 42 Free ee 3 4 Free Mode Features ccccceeseeeeeeeeees 4 G Gaussian Smooth NIK 56 GE SIGNS E 14 FT A E N EET 70 denia 26 67 Geodesic Active Contour ITK 55 Geodesic Active Contour Module ITK 55 Gradient Anisotropic Diffusion ITK 56 Gradient Magnitude Filter VTK 53 Gradient Magnitude IIR ITK 53 Gradient Opacity Mapping 11 35 Gray ee EE 58 H hardware accCeleraton 11 70 Header Annotation ccccceeeeeeeeeeeees 29 A n 24 Hide Show Left Panel 23 A a eee 43 HSV renere See ee 35 EE EE NE NE 11 35 Image Display 9 21 58 60 61 62 Image Keyboard Bindings 9 43 Image Mappimg NN 9 58 Image Mouse Bindings ooococococoo 9 43 Include Hardware 70 Include Ray C
119. nse Leave the option selected to get a trial license and click on the Next button On the next page you will be asked if your computer is connected to the Internet Select Yes or No and press Next to continue If you selected No then you will receive instructions on alternate methods for obtaining a license Your computer ID will be displayed and you may enter this at the registration web site www kitware com VVLicense register cgi or you may email this information to support kitware com You will receive your trial license via email which you must load using the file browser button If you indicate that your computer is connected to the Internet then the next page in the Registration Wizard will give you the opportunity to enter your email address If you do enter your email address it will be used to notify you of future releases of VolView and related products Kitware values your privacy and will not distribute your email address to third parties Once your press the Next button VolView will attempt to contact the license server and install your license file If this occurs successfully you will see a message indicating this and your trial license will begin Press the Finish button to close the wizard If a connection could not be made you will see an error message This may occur if your computer is not connected to the Internet or if you use a proxy server or VPN for your connection If this error occurs please use the Back Tab
120. o be arranged as shown The buttons from left to right on the toolbar correspond to the options from top to bottom on the Window menu Application Area The Application Area user interface on the Application Area x Application Settings panel allows VolView to General be tailored for a specific application area medical The interface will appear as shown in the image on the right There are two options for the application area general or medical When a general application area is selected VolView will display the data within an XYZ coordinate system These X Y and Z labels will be used throughout the display area and the user interface for annotation labels tooltips etc When a medical application area is selected VolView will use a standard RAS coordinate system right anterior superior for displaying the data The labels Right R Left L Anterior A Posterior P Superior S and Inferior I are then used for annotation and user interface If you load a dataset which is known to be medical in nature DICOM or GESigna format for example then VolView will automatically set the application area to medical VolView will not change the application area back to general this must be manually done using this interface 26 Animation Animation Settings The Animation Settings area is the only area Animation Settings x on the Animation panel The appearance of Number of frames 10 this panel will depend on wh
121. of Data origin 1 00 1 00 1 00 milimeters the information items is described in more Data type unsigned char detail below Components 1 64 Scalar ranges component 1 0 00 to 255 00 density Size in voxels The size of the dataset is displayed as the number of sample values along the X Y and Z axes Physical size The physical size of the dataset is computed as the number of samples in a direction minus one times the spacing for that direction The subtraction of one is necessary since two voxels only span one spacing unit If a name was provided for the physical spacing unit this is displayed here as well otherwise it is listed as unknown units Sample spacing The distance between two neighboring voxels in X Y and Z is displayed here Data origin The origin of the data is the physical coordinate location of the first voxel in the dataset Data type The type of the data is the underlying storage unit for the samples This may be signed or unsigned char short or integer or it may be float or double For multiple component data all components have the same scalar type Components The number of components indicates how many unique values are stored per sample location in the volume Most volumes have just a single component If you load color data into VolView it will have 4 non independent components The designation of non independent indicates that the four values represent one quantity the color at that location
122. of the application Short messages will appear in the areas generally when VolView is performing some complex processing or when the mouse is moved over an image window Main Progress Gauge The main application progress gauge is on the bottom right of VolView During complex processing progress will be displayed in this area as a blue bar Progress for rendering will be displayed on the right side of the title bar of the volume display window The File Menu The File menu contains options that allow you to load and save data print connect to another VolView session close the window and exit the application Each of the options are described in more detail below 20 Open File This menu option will pop up the Open dialog More information on using the Open dialog can be found in the chapter on Loading Data Open Recent File A list of recently opened files will be displayed allowing you to quickly load one of these datasets If you load a file from this list you will not be prompted for information such as the name of the units the spacing and origin of the data and the acquisition order If you need to re enter this information use the Open option to load the file Save Session This menu option allows you to save the state of your VolView session so that you may open this again at a later time or share this with a colleague A session includes all of the interface settings as well as a reference to the data For more information
123. oints and a label indicating the angle between the lines Use the toggle button to turn on this annotation element You will see the two attached line segments appear on the image and the text label indicating angle in the lower left corner This is an interactive annotation element You can reposition the text by dragging it to a new location In addition you can move the entire angle measurement tool by clicking on one of the lines and dragging it within the image Clicking on an endpoint will adjust the position of this point Appearance Volume Appearance Editor The Volume Appearance Editor is the only area on the Appearance panel This area provides access to most of the parameters that affect the volume rendering A thorough understanding of the functionality presented here is recommended for creating effective visualizations An example of the interface is shown on the right The appearance of this panel will vary based on the type of data loaded This example was produced with two independent component data The controls allow you to adjust the material properties and color opacity mapping per component of your data and adjust the weights of the components Each area on the interface will be described in detail later in this section In volume rendering the appearance of the final image is heavily influenced by the functions applied to map the data into color and opacity This also happens to be the most difficult aspect o
124. olView and you wish to obtain your license About VolView This menu option will pop up a dialog containing information about the version of VolView you are running and contact information for reaching Kitware In addition your computer ID will be displayed on this dialog as well as on the registration dialog You may need this information in order to purchase VolView 24 Application Settings Interface Settings The Interface Settings area of the Application Settings panel contains a set of check boxes controlling the basic behavior of the application and will appear similar to the example shown on the right These settings are retained across sessions of VolView The individual items are described in more detail below Interface Settings Confirm on exit Save window geometry an exit Iw Show splash screen Iw Show tooltips h Show most recent panels W Enable Interface Drag amp Drop Application Settings Reset Interface Confirm on exit When this box is checked VolView will display a dialog box requiring you to confirm or cancel the operation when you exit VolView If this box is not checked then exiting VolView will cause the application to close with no opportunity to cancel the operation Save window geometry on exit When checked VolView will save the width height and position of the VolView application When restarting VolView it will appear with the same geometry as when it was last run If this
125. olume This is best accomplished when the Bounding Box annotation for the volume is turned on An example thick reformat image is shown below Oblique Probe The Oblique Probe area on the Cropping p Oblique Probe x panel allows you to view an arbitrarily W Enable oblique probe I Show scalars Set Color al oriented plane of information from within the volume The interface is shown on the right 0 Resetprbe OOOO O The oblique probe is controlled interactively from within the volume display area probe plane is shown in the volume display window In the example below you can see this plane in pink the bounding box is also being displayed in blue When showing the scalars it is often helpful to set the blending function to None on the Volume Display panel in order to avoid obscuring the view of the probe plane Turning the bounding box on on the Annotations panel is often necessary when setting the blending function to None in order to understand the placement of the plane within the bounds of the data 50 Information Window Interaction can be performed with the left middle or right mouse buttons and the operation performed depends upon where you click within the plane The plane is divided into 9 regions the center area four edge areas and four corner areas During interaction additional lines will be displayed denoting these areas Using the left mouse button in the center area allows you to translate the oblique pla
126. on window 23 Table Of Contents The Help Menu The Help menu provides access to this documentation information about the version of VolView functionality for checking for updates of VolView and access to the registration wizard Each of these options are described in more detail below OnLine Help Selecting this option will display this documentation If you are on windows this will be displayed as a compiled help file in the standard help browser On other systems this will display in html format in a web browser Check For Updates The Check For Updates option duplicates the functionality provided by the menu item of the same name under the Start gt Programs gt VolView20 system menu This option is available only on Windows platforms Use this option only if you have a network connection This will check the Kitware web site for a more recent version of VolView than the one you are currently using If a newer version is found a wizard will appear to lead you through the download install process Before beginning the installation you should exit the current session of VolView and any other sessions you may have running on your system If you do not then you will need to reboot in order for the new version to complete the installation Register Selecting this option will display the registration wizard You should use this wizard if you are obtaining a trial license of VolView 2 0 in Professional Mode or if you have purchased V
127. our data is of raw format VolView will attempt to read it with all possible readers If the data cannot be correctly recognized as a known format you will see the Open Wizard pop up requesting you to indicate that you wish to load raw data as a series of 2D files a single 3D file or to cancel this operation An example of this page is shown below If your volume of raw data is contained in one file select the single 3D file option If your data is written with one 2D slice per file select the series of 2D files option Otherwise cancel this operation Pressing the next button will display a page requesting information about the raw file as shown below On this page you will need to enter the number of columns rows and slices in the file corresponding to the X Y and Z dimensions You will also need to specify the number of channels components per sample the data type and for data types where this is necessary the byte ordering On the right side of the page you will see an image from the volume that will change as you alter the settings on this page This will help you determine if you have set all the parameters correctly If the image appears skewed you have most likely entered the columns or rows incorrectly The image on the right is interactive you can use the left mouse button to adjust window and level the middle mouse button to pan and the right mouse button to zoom Pressing the r key will reset the window l
128. output image of the last filter in the ITK pipeline This can be done by invoking the following lines of code before executing the pipeline m_FilterD gt GetOutput gt SetRegions region m_FilterD gt GetOutput gt GetPixelContainer gt SetImportPointer static cast lt OutputPixelType gt pds gt outData totalNumberOfPixels false m_Filter gt GetOutput gt Allocate The current distribution of ITK provides support for not having to write this same code for each new plugin A templated class is available for providing these basic services New plugins only need to define their own ITK pipelines and invoke the methods of the base class in the appropriate order 81 Table Of Contents Refreshing the GUI Given that the execution of most image processing algorithms take considerable time on 3D data sets it is important to provide some feedback to the user as to how the processing is progressing This also provides a chance for the user to cancel the operation if the expected total execution time is excessively long This notification can be done from within the ProcessData function by calling the UpdateProgress function of the vtkVVPluginInfo structure For example float progress 0 5 50 progress info gt UpdateProgress info progress half data set processed This function will update the progress bar on VolView s GUI and will set the last string as a message in the status bar There is a balan
129. p to 5x5 images e Interface for Window Level with configurable presets e Ability to change background colors e Advanced light control for position color intensity e Control of perspective view angle and camera reset e Advanced level of detail control for volume rendering e Create multiple isovalued contours e Export volume as DICOM e Save contours in a variety of geometric formats e Save sessions and transfer functions e Collaboration mode to connect two VolView sessions Obtaining a Trial License The first time you run VolView 2 0 the Registration Wizard should pop up This may not occur if VolView 2 0 was previously installed on this same computer You may access the wizard from the Help menu on the VolView menu bar if it does not automatically appear or if you need to alter your registration in the future The first page of the wizard will appear as shown below It is highly recommended that you obtain the trial RIES license for VolView in professional mode in order to experience the full power of this visualization and data processing system If you are connected to the A Internet the easiest way to obtain a trial license Is feet des sier wat yuten mrcha a iomse o iseit r fee rode to use this Registration Wizard If you are not on GE the Internet you can use this wizard to receive Paid el leg dei acer instructions on alternate methods for obtaining a Fun wien m Free ode trial license and to manually install this lice
130. pacing of the volume Gaussian Smooth VTK This filter smooths a volume by convolving it with a Gaussian kernel with standard deviations as specified by the user This filter operates in pieces and does not change the dimensions data type or spacing of the volume Intensity Transformation Filters The two filters in the Intensity Transformation category will adjust the pixel values in the image either according to a intensity windowing function or a Sigmoid function Further details are provided below Intensity Windowing ITK This filters applies a pixel wise intensity transform by using a IntensityWindowing function Sigmoid ITK This filters applies a pixel wise intensity transform by using a Sigmoid function 57 Table Of Contents Image Display Image Mapping The Image Mapping area on the Image image Mapping x Display panel provides control for the Mapping Raw scalars mapping of the data value to a pixel color value in the displayed image This mapping affects the display of images in the XY Axial image window the XZ Frontal image window the Y Z Sagittal image window the Lightbox image window the Oblique Probe image window and the display of the oblique probe in the volume window The interface consists of a single pulldown option menu and appears as shown on the right The Mapping pulldown menu has a subset of the following options which are described in more detail below The options included i
131. pe info gt OutputVolumeNumberOfComponents info gt InputVolumeNumberOfComponents memcpy info gt OutputVolumeDimensions info gt InputVolumeDimensions 3 sizeof int memcpy info gt OutputVolumeSpacing 1 VVP_GUI_HINTS tmp Extending Filters With Plugins 89 Table Of Contents info gt InputVolumeSpacing 3 sizeof float memcpy info gt OutputVolumeOrigin info gt InputVolumeOrigin 3 sizeof float return 1 extern cC void VV_PLUGIN_EXPORT vvThresholdInit vtkVVPluginInfo info always check the version vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUI set the properties this plugin uses info gt SetProperty info VVP NAME Threshold info gt SetProperty info VVP GROUP Utility info gt SetProperty info VVP TERSE DOCUMENTATION Replace voxels above at below the threshold value info gt SetProperty info VVP FULL DOCUMENTATION This filter performs a pixel replacement replacing pixel in the Original data by a specified replacement value The pixels to be replaced are determine by comparing the original pixel value to a threshold value with a user specified comparison operation This filter operates in place and does not change the dimensions data type or spacing of the volume info gt SetProperty info VVP_SUPPORTS_ IN PLACE PROCESSING 1 info gt SetProperty in
132. plate info static c st lt VIK TT gt 01 pds return 0 static int UpdateGUI void inf char tmp 1024 vtkVVPluginInfo info info gt SetGUIProperty info vtkVVPluginInfo inf 0 VVP GUI LABEL Replace values VVP_GUI_TYPE VVP_GUI_CHOICE VVP_GUI_DEFAULT O info gt SetGUlProperty info 0 VVP_GUI_HELP The comparison operation for a pixel info gt SetGUIProperty info 0 VVP GUI HINTS NAs VES es VVP GUI LABEL Threshold Value VVP_GUI_TYPE VVP GUI SCALE VVP GUI DEFAULT 0 VVP_GUI_HELP compare against info gt SetGUlProperty info 0 info gt SetGUlProperty info 0 info gt SetGUIProperty info info gt SetGUlProperty info info gt SetGUIProperty info info gt SetGUIProperty info The value VVP GUI LABEL Replacement Value VVP GUI TYPH VVP GUI SCALE VVP GUI DEFAULT vor info gt SetGUIProperty info 2 VVP GUI HELP The value to replace with info gt SetGUlProperty info info gt SetGUIProperty info info gt SetGUIProperty info set the range of the sliders sprintf tmp f f 3f info gt InputVolumeScalarRange 0 info gt InputVolumeScalarRange 1 LOr info gt SetGUlProperty info sprintf tmp SE Ll 3f info gt InputVolumeScalarTypeRange 0 info gt InputVolumeScalarTypeRange l LOT info gt SetGUIProperty info 2 VVP GUI HINTS tmp info gt OutputVolumeScalarType info gt InputVolumeScalarTy
133. plugin does any limitations it has and who to contact with questions 4 Inside the UpdateGUI function there is a block of code folloing TODO item 6 this code specifies the properties of the output of this plugin The implementaiton currently provided indicates that the output volume has all the same properties as the input volume Properties include the volume s dimensions spacing origin number of components per voxel and data type short int float If for example your plugin always creates floating point output then you would want to set info gt OutputVolumeScalarType VTK_FLOAT note that while we use VIK_FLOAT to indicate floating point data your plugin does not need any relationship to VTK The Visualization Toolkit itself 5 Create your GUI elements This involves two main steps First you need to determine how many GUI items you will have A GUI item can be an option menu checkbox or slider Once you have determined how many gui items you will have you need to set that value in TODO item 7 The you need to actually spcify the GUI items This is adeed to the UpdateGUI function at TODO item 8 There are a number of options here and I recommend looking at the source code to the other plugins to get an idea for how to create the GUI items 6 Now you are ready to think about how your filter will process its data There are a couple options here that you can adjust Depending on the nature of your algorithm you might be able to pro
134. plugin gt Init void VV PLUGIN EXPORT vvSamplelnit vtkVVPluginInfo info always check the version vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUT set the properties this plugin uses TODO As Rename Sample to lt your_plugin gt info gt SetProperty info VVP_NAME Sample info gt SetProperty info VVP_GROUP Utility TODO 5 update the terse and full documentation for your filter info gt SetProperty info VVP_TERSE_DOCUMENTATION Replace voxels above at below the threshold value info gt SetProperty info VVP_FULL DOCUMENTATION This filter performs a pixel replacement replacing pixel in the Original data by a specified replacement value The pixels to be replaced are determine by comparing the original pixel value to a threshold value with a user specified comparison operation This filter operates in place and does not change the dimensions data type or spacing of the volume TODO 9 set these two values to 0 or 1 based on how your plugin handles data all possible combinations of 0 and 1 are valid info gt SetProperty into MME SUPPORTS IN PLACE PROCESSING 0 info gt SetProperty info VVP_SUPPORTS_PROCESSING_PIECES TOS TODO 7 set the number of GUI items used by this plugin info gt SetProperty info VVP NUMBER OF GUI ITEMS FOT 85 Table Of Contents
135. ppearance of this dialog will be system dependent and will look similar to the one shown below for most Windows platforms Use the color selector to choose a new background color then press OK to accept this color 71 Table Of Contents 72 Background Color Basic colors WI Gey Eee WI EERE A DEES A A Gf A ee AA Ao or oa Eg Imi im Custom colors E fee Fe TETTERE EE EEE Ge Leine LUS On Colors Ke 4 Hue 1160 Red jo Sat o Green o ColorlSolid Lum o Blue o Saving Results Saving Sessions A session file is a text file that saves all of the settings in VolView and a reference to the currently loaded data If you produce a nice visualization that you would like to continue working on later you can save a session file At a later time you can open this session which will load the data and reset all the VolView parameters just as you have them when you saved the session file Also you can send a session file along with the data file remember the data is not stored in the session file only a reference to it is stored to a colleague If the data and session files are placed in the same directory on your colleagues system then VolView will automatically find the data provided the file name has not been changed If VolView cannot automatically locate the data file a file browser will be displayed allowing the user to locate the data on disk To save a session file use the Save Session option on t
136. pports the Surface style e Surface C wireframe following functionality Surface quality elt h Active Contour This pulldown allows ine width EE S 46 you to switch between the contours The isovalue is displayed on the Remove Contour option menu You can generate Rec EE ee multiple contours using the Add Contour area When you switch to a Sumber of surfaces Ge new contour the remaining elements ele closed surfaces e in this area will adjust based on the 19ta surface area Ge current properties of that contour E SE Compute statistics Visibility The visibility toggle button can be used to turn on and off the display of the contour within the volume and image windows Contour color The contour color button can be used to select a color for the contour Surface property The surface property button shows a epresentation of the current shading parameters applied to a sphere of the contour color Pressing this button will pop up the material properties editor allowing you to adjust the ambient diffuse and specular coefficients for this surface as well as the specular power Ambient is an overall brightness diffuse is a dull directional shading value a concrete appearance and specular is a shiny directional shading value a metallic appearance The specular power controls the focus of the shiny reflection brushed metal would have a low specular power while polished metal would have a high specul
137. ps of visualization and interacting with your volume data It is assumed that you will perform these steps in the order presented in this documentation Although some of the interface examples may look slightly different depending on your platform these images were captured on a Windows XP system the tutorial concepts are platform independent In this first step we will locate and load one of the example datasets that is distributed with VolView Begin by selecting the Open File option on the File menu This will pop up the file browser as shown below Using the controls provided by the dialog navigate to the place where you installed VolView On a Windows system this will most likely be C Program Files VolView20 In this directory you will find a Data directory In the Data directory will be a file called visfoot vti Click on this file and press the Open button or simply double click on the file to open it At this point the Open Wizard will pop up to RATE lead you through setting some of the Lock in E Data parameters that may not be explicitly set in 4 earl ti BB TronPratein wth the file For example with this type of data deca eer the Visualization Toolkit XML image format SE we are missing a descriptive string for the 3 measured data values and the distance unit type and we do not have any information on the orientation of the data during acquisition You will notice that values are provided in the wizard these com
138. pulldown menu in the upper left corner of this window to select the Axial Image Next select the Copy Screenshot option from the Edit menu You have now captured the image which can be pasted into other applications such as Microsoft Word or PowerPoint Printing Screenshots VolView supports sending a screenshot to a printer on Windows system or to a Postscript file on Unix systems First you must configure the windows as you would like to print them For example if you would like to print the volume display above the three image windows select the 1 over 3 option from the Window menu Note that printouts will often look better when a light or white window background is selected on the Volume Display panel and the Image Display panel Next you will need to select the quality of the print VolView supports printing at three DPI dots per inch settings You should select the DPI setting from the Page Setup menu under the File menu The available options are 100 150 and 300 DPI Higher DPI produces better images but requires more time To print the image select the Print option from the File menu On Windows systems this will bring up the standard printer selection dialog box Depending on the DPI setting the size of your data and the rendering parameters it may take several minutes to generate the image for printing During this time it is safe to hide or close the application On Unix systems the screenshot will be saved to a
139. r B Display scale bar Set Color e Corner Annotation A toggle button poe Der Set Color F is provided to turn on and off the corner annotation Depending on the type of data you loaded you may already have corner annotation visible in your volume window For example when loading some medical datasets such as DICOM the Study and Series will be displayed in the upper left corner and the Patient Name ID and Date will be displayed in the upper right corner Display distance measurement The check button can be used to toggle the visibility of the corner annotation Press the Edit button directly to the right of the Display corner annotation check button in order to control the actual text and the text properties such as font style and color Pressing the Edit button will pop up a dialog that will appear similar to the one shown on the right In this case we have loaded medical data and therefore some corner annotation was entered automatically by VolView from the header information in the file To alter the text annotation in any of the corners simply type in the text window for that corner of the window The four text entry windows which support multi line input are labelled for the four corners of the volume display window Upper left Upper right Lower left and Lower right Below these text entry areas are a set of controls that can be used to customize the appearance of the text These controls are described in more detail
140. r the Window and Level settings used to display images This mode can be quite useful when attempting to focus in on a particular scalar region for example bone in your dataset In addition to the horizontal motion of nodes 2 and 3 you can also adjust the vertical placement opacity This opacity has no meaning in the image windows and will not affect the display of the images Typically the first two nodes are left at an opacity value of 0 0 otherwise the volume image tends to become saturated and the final two nodes are adjusted to the desired opacity Scalar Color Mapping The scalar Scalar Color Mapping 0 00 4095 00 color mapping area is used to assign e 8 ESE 5 1755 00 H 0 33 5 0 70 Vi 1 00 color to each scalar value in the em DNG dataset This will allow you to for A example assign a pink color to the soft tissue values in a dataset while assigning white to the bone region An example of this interface is shown on the right gt When working with data with one component or independent components the histogram displayed in the background of the scalar color mapping will be identical to the one displayed in the scalar opacity mapping region since the same component is used to derive both When working with two component data that is not independent it is luminance alpha data the first component is used for the scalar color mapping and the second is used for the opacity mapping Hence the histograms wil
141. r to produce effective visualizations of your data Please read the Appearance chapter later in the document for more details You may also wish to consult a textbook that covers basic volume rendering if you are unfamiliar with the underlying principals One recommendation would be chapter 7 in The Visualization Toolkit An Object Orientated Approarch to 3D Graphics 3rd Edition ISBN 1 930934 07 6 Table Of Contents Loading Data Loading Data Overview Using the Open File option on the File menu you can load volumetric data as well as previously saved sessions and appearance settings files The dialog that opens when you select this option is dependent on the operating system For Windows XP the dialog will appear similar to the one shown below To load a session file select the VolView FE Session option from the Files of type menu Locks Je Dela Use the Open File dialog to browse your disk Tania for the specific file Press Open or double EE click on the session file name to load it If the BW vist 2 data referenced inside the session file cannot be found automatically another dialog will appear asking you to locate this file A session file is saved using the Save Session option on the File menu These files contain all the parameters of VolView and a pointer to the data the session file itself does not aoe contain the data G r Hr Reech Fier de Corina 30 EN a paa EH Cancai H p Elo curras rie
142. rade off is controlled with the Compression Quality slider 2 Table Of Contents During creation the images will be rendered into a memory buffer and the progress of the animation creation will be displayed on the main progress gauge in the lower right corner of the application This means that it is safe to close VolView or pop other windows on top of it this will not affect your animation The volume rendering will be performed at the best possible quality based on your settings in the Level Of Detail Options area on the Volume Display panel Cancel The cancel button can be used to cancel the preview or creation of an animation The interface elements specific to the 3D View animation type are X rotation azimuth Use this area to specify the total rotation about the X axis of the viewing coordinate system that will occur during the animation This is specified in degrees so if you want a full rotation you would enter 360 Y rotate elevation This value indicates the total rotation about the viewing coordinate Y axis that will occur during the animation Z rotation roll This value specifies the roll rotation around the viewing coordinate Z axis that will occur during the animation Zoom factor The zoom factor is a value that indicates how much you will zoom in or out during the animation The number should be close to 1 0 1 0 indicates no zoom where values above 1 0 indicate zooming in and values below 1 0 indic
143. re xoutPtr inPtr outPtr t inPtr info gt UpdateProgress info float 1 0 Processing Complete static int ProcessData void inf vtkVVProcessDataStruct pds vtkVVPluginInfo into vtkVVPluginInfo inf switch info gt InputVolumeScalarType TODO 2 Rename vvSampleTemplate to vv lt your_plugin gt Template vtkTemplateMacro3 vvSampleTemplate info pds static_cast lt VTK_TT gt 0 return 0 84 Extending Filters With Plugins this function updates the GUI elements to accomidate new data it will always get called prior to the plugin executing static int UpdateGUI void inf vtkVVPluginInfo Into vtkVVPluginInfo ant TODO 8 create your required GUI elements here TODO 6 modify the following code as required By default the output image s properties match those of the input depending on what your filter does it may need to change some of these values Ss info gt OutputVolumeScalarType info gt InputVolumeScalarType info gt OutputVolumeNumberOfComponents info gt InputVolumeNumberOfComponents memcpy info gt OutputVolumeDimensions info gt InputVolumeDimensions 3 sizeof int memcpy info gt OutputVolumeSpacing info gt InputVolumeSpacing 3 sizeof float memcpy info gt OutputVolumeOrigin info gt InputVolumeOrigin 3 sizeof float return 1 extern C TODO 3 Rename vvSampleInit to vv lt your_
144. re acceleration If your progress bar shown only shades of green then your system does not support hardware acceleration for the data type you have loaded The most common interaction methods in the volume display window are rotation panning and zooming These have been mapped to the left middle and right mouse buttons respectively Try now to interact with the volume using the mouse If you lose the volume during this interaction press the r key verifying first that the volume display window has keyboard focus to reset the camera You can also set the camera to one of the six standard directions using the Views amp Lights panel You may also wish to try switching between parallel and perspective projections Table Of Contents also available on the Views amp Lights panel to see the difference between these two projection modes Return now to the Appearance panel We will Gradient Opacity Mapping 0 42 25 now adjust the color and opacity mappings to oni 4 zl o o alter the appearance of our rendered volume Y We will first begin with turning the Gradient A Opacity Mapping on This is done by using the first pulldown menu area to change the Off to Ka 89 On Now grab the second black node from the left and drag this node down to the bottom of the editing region The interface should now look something like the image shown on the right with the volume display window appearance similar to the image shown below it
145. rection For a Medical application area these views are labeled based on 67 Table Of Contents which side of the data will be visible The panning and zooming will also be reset so that the volume is centered in the volume window and fits within the window Light Controls The Light Controls area of the Views amp Light Controls x Lights panel allows you to adjust the wht visibility position intensity and color of the light sources in the scene An example of this interface is shown on the right Color nj Intensity 1 00 In VolView 2 0 you can control only one light source so some of the settings such as the active light menu and the visibility toggle button have been disabled These features will be enabled in future releases but are included below in the description of the elements in this area Active light When multiple light sources are supported this pulldown allows you to switch between the light sources The Visibility Color and Intensity elements will update with the current values for the selected Active light The Active light will also become the selected light on the position indicator This pulldown is disabled in VolView 2 0 Visibility The visibility toggle allows you to turn on and off light sources You cannot turn off all light sources and therefore this toggle button is disabled in VolView 2 0 which supports only one light source Color The color selection button can be used to ch
146. ressing the Next button will display the volume attributes page of the wizard shown on the right below Here you can adjust the origin physical coordinate of the lower left first slice sample of the dataset and the spacing distance between neighboring samples Depending on the type of data or the existence of a previously automatically saved vvi file for this dataset there may be initial guesses in these entry boxes or the values may be the default of 0 0 0 for the origin and 1 1 1 for the spacing Pressing the Next button will display the volume units page of the wizard shown on the right below Here you can adjust the name of the distance units and the scalar value units for each component These labels will be used in various places on the user interface and in the data annotation For example the distance unit will be used for displaying measurements 20 25 millimeters and the scalar value units will be used when probing the value at 17 2 37 is 10 degrees Pressing the Next button will display the volume orientation page of the wizard shown on the next page On this page you can adjust for the layout of the data samples in the file For example if your series of images represent Sagittal images instead of the standard Axial then you would adjust these option menus to indicate this The first option menu lets you indicate which axis the image files move along and the order The second option menu allows you
147. rom Stereo Lithography STL format or VTK format Please see the Saving Results chapter for more information Export DICOM If you loaded DICOM data originally and have modified it with a filter then you can export this data back out as DICOM using this option For more information see the chapter on Saving Results Connect to Remote You can connect your VolView session to another VolView session on a different machine using this option This will allow you to pass control back and forth between the two session while keeping the visualization linked in order to facilitate communication between researchers located in remote locations For more information on this functionality please see the Connect Sessions chapter Print On Windows the Print option will open the standard system print dialog allowing you to print your image to any available printer The image will be similar to the one saved in the Save Screenshot option in that it will be a representation of what you see on your screen For more information on Printing please see the Saving Results chapter Page Setup The Page Setup option allows you to select a DPI dots per inch setting for the printed image The higher the DPI the better quality the image will have but the longer it will take to generate For further information please see the Saving Results chapter Close If you have only one VolView application window open this option will behave the same as the Exit option Othe
148. rom session of Voxel Extent X 18 to 55 Y 4 to 60 7 34 to 5 VolView in a medical application area The P au IN 3 labels would be based on X Y Z rather than L R Units 54 8 R A S if the application area had been ua general as AP Units 59 7 Cropping is the process of applying E yl fa orthogonal axis aligned cuts to the volume 1 Saat A check button is used to enable or disable cropping Control of the location of the crop is performed by adjusting the three range sliders Each range slider contains the information about the minimum and maximum range values The rectangular boxes at the end of each range can be dragged to adjust the range In addition you drag the entire range left or right by clicking on the range bar and you can expand the range bar to the full range by double clicking on the range bar When cropping is enabled an interactive cropping annotation element will be added to the three axis aligned image windows The shaded areas of the image are the areas that will be invisible in the volume display window You can adjust any of the two horizontal or vertical lines shown in the image display window by dragging them to a new location In addition you can select a crossing point of two lines to adjust both simultaneously The most basic type of cropping is the simple subvolume but there are more complex forms support that can allow you to for example remove a corn
149. rwise the close option will close only this application window Other VolView application windows that were launched using the New Window option under this Window menu will remain open Exit This option will exit this VolView session and any other VolView application windows that were launched using the New Window option under the Window menu If you have selected to confirm your exit on the Application Settings panel then a dialog will appear asking if you really want to exit Otherwise the application will close with no confirmation The View Menu The View menu contains eighteen entries that can be used to control the panel displayed on the left side of the interface These various panels contain the most of the controls for VolView including the interface for adjusting the appearance of the volume and images viewing data 21 Table Of Contents properties creating animations adding data annotations and filtering the dataset Each of the eighteen areas are described in more detail below and you can find a chapter in this documentation for each panel 22 Application Settings This panel provides controls for adjusting the appearance and behavior of the application This includes configuration items such as whether the splash screen is shown at startup whether the layout toolbar is visible and the application area Animation The Animation panel allows you to generate AVI files of basic rotations in the Volume display window or a
150. s and spacing E Develop In order to save a volume select the Save Volume G d My Computer option from the File menu The Save Volume dialog zB 34 Floppy A will appear Traverse your disk to the correct ah Eset Des E location enter the Save as type and enter a 53 Sr filename It is best to specify just the base filename S with no extension since many of the formats will GO Documents and Settings append an extension for you E E Administrator mie a gt S If your input data was DICOM then you will also have the option of saving your filtered data in ot DICOM format To do this select the Export DICOM 13 Table Of Contents option from the File menu A folder browser will appear allowing you to select the location in which to export the data The browser appearance will be platform specific and will look similar to the example on the right for Windows XP Once you locate the directory and press the OK button VolView will write the DICOM files in that directory using the same file names as the input data The header information such as patient name date and ID will be copied from the input data Saving Appearance Settings The current settings on the Appearance panel can be saved into a file which can be loaded at a later time This file is known as a VolView Appearance Settings file and is an XML based text file describing all the necessary properties to reproduce the state of the Appearance panel including
151. s and super sampling for volume rendering Filters extendable via public API Complex volume cropping Control over mapping of values for image display Interactive probing of image values 3D cursor and 3D markers Parallel and perspective projection Save volumes in any supported format e Save or print screenshots Kitware would like to thank The National Library of Medicine for their part in Supporting the development of the plug in filter capabilities This effort resulted in the release of VolView 2 0 in Free Mode to foster advanced segmentation and registration research in the medical and scientific communities Professional Mode Features VolView users may test the Professional Mode free during a trial period typically 30 days and may purchase a license for VolView 2 0 to continue using this functionality past the trial penod For information on obtaining a trial license please see the next section The last section of this chapter provides information on purchasing a VolView license Professional Mode adds many advanced features to VolView 2 0 These features include e An animation tool for basic volume image series movies e Interactive annotation elements including e Dynamic header and corner text annotation Application Settings e Color bar bounding box scale bar e Distance and angle measurement e Orientation marker e Ability to customize mouse bindings e Thick reform and oblique probing e A lightbox view with u
152. s user interface interaction such as switching the property panel displayed or changing the window configuration 17 Table Of Contents Extending Filters With Plugins Extending Filters Overview This section describes the basic steps required for writing a new plugin The example here illustrates the implementation of a simple filter having only one parameter to be set from the GUI The example assumes that the filter is written using the Insight Segmentation and Registration Toolkit ITK but should be general enough for the reader to apply to other toolkits or C C implementation as well The next section contains a detailed skeleton in C which will walk you through the steps of creating your own plugin In the following four sections actual examples are given for C C VIK and ITK These examples are filters available in VolView To install a new plugin in VolView 2 0 you would place the new dll in the Plugins directory in the installation directory For a standard Windows installation this would be c Program Files VolView20 Once you have placed the new plugin in the Plugins directory you can press the refresh button on the Filters panel to refresh the plugin interface to include this new module Plugin Life Cycle The process of developing a VolView plugin is depicted in the figure below A single public header file defines the plain GLanguage data structures used for exporting and importing data and for transferring GUI p
153. sequence of slices in an image window Annotations This panel contains a set of annotation elements for the volume and image display windows These include bounding boxes text annotation orientation markers a 3D cursor and distance and angle measurement tools Bindings The Bindings panel allows you to view the keyboard shortcuts and view and modify the mouse bindings associated with interaction in the image and volume windows For example if you prefer to rotate using the right mouse button instead of the left which is the default you can make this change on the Bindings panel Contours On this panel you can create isovalue contours These contours will be displayed in the volume and image windows In addition you can adjust properties of the contour including color and shading parameters and you can perform basic surface area and volume measurements Cropping The Cropping panel allows you to create complex axis aligned crops of the volume It also provides a thick reformat functionality thick oblique resections of the volume and an oblique probe thin cross sections with arbitrary orientation Filters This panel provides access to the plugin filters Over 30 are provided with VolView including basic utility filters such as thresholding and gradient magnitude as well as more complex ones such as techniques for level sets noise suppression and region growing New filters can be created using a publicly available API which can
154. sibility of the orientation marker and set the color Since the labels will always be drawn in black selecting a light color for this annotation element is best In addition to the user interface control you can also reposition and resize the orientation marker interactively Move the mouse cursor over this widget when VolView is in an idle state When the cursor becomes a vertical and horizontal double arrow then you can reposition the orientation marker When the cursor becomes a diagonal double arrow only in the corners of region surrounding this element then you can resize both height and width equally the orientation marker Scale Bar The scale bar is an interactive annotation element that shows a ruler indicating a specific measurement on the viewing plane This element can only be added to the scene when the camera is in a parallel projection mode see the Projection Type section in Views And Lights If you attempt to enable this annotation element while in perspective mode a dialog will pop up indicating that this is not possible The distance label shown on the scale bar will be based on the spacing on the data the zoom of the camera and the unit type specified when you loaded the data In the example we see that the scale bar shows a distance of 100 Units The label Units will be used whenever the unit distance type is unspecified As you zoom the camera the scale bar will at first zoom with the image Once it grows or shrinks
155. st argument is actually a pointer to a vtkVVPlugininfo structure that can be downcasted to it by doing veEKVYPIGGININEO Sinto rtkVVPLuginlnro jini The second argument to ProcessData is the vikVVProcessDataStruct This structure carries the information on the data set to be processed including the actual buffer of voxd data the number of voxel along each dimensions in space the voxel spacing and the voxel type among others Of particular interest in this structure are the members inData that is a pointer to the data buffer of the input data set and the outData that is a pointer to the output data set buffer The ProcessData function is expected to extract the data from the inData pointer process it and store the final results in the outData buffer The typical starting code of this function involves extracting the meta information about the data set The following code shows for example how to extract the dimensions and spacing of the data set from the vtkVVProcessDataStruct and vtkVVPluginInfo structures SizeType size IndexType start double origin 3 double spacing 3 size 0 info gt InputVolumeDimensions 0 size l info gt InputVolumeDimensions 1 size 2 pds gt NumberOfSlicesToProcess for unsigned int 150 a lt 3s7 i144 origin i spacing i start i 0 info gt InputVolumeOrigin il info gt InputVolumeSpacing il 80 Extending Filters With Plugins Using this information the imag
156. t of the slider and in the upper left corner of the image window Table Of Contents Move the slider back to some center position Use the View menu to display the Image Display panel We wil now adjust the Window and Level of the image to control the contrast and brightness Note that the current window and level settings are displayed both in the lower right corner of each image window and in the Window Level area of the Image Display panel If you recall on the Information panel we saw that the scalar range the minimum and maximum value found in the dataset is 0 to 169 therefore the initial Window is set to 169 to cover the whole range and the initial Level is set to 84 5 which is halfway between the minimum and the maximum We can adjust these values in one of two ways by manually entering new values in the Window and Level text entry boxes or by dragging the left mouse in the image display window We will first start by manually entering values that will highlight the bone Moving the mouse over the image and looking at either the status bar at the bottom of the application or the Probe Information area on the Image Display panel you can see that the scalar values in the bone region are generally at or above 77 We will emphasize this region by setting the Level to 77 and the Window to 50 Making this change should alter your image to something like the one shown on the right Note that the other two image windows also change due to the
157. tc VolView supports volume that have a data type of signed or unsigned char short or int as well as float or double These files could have 1 to 4 components per sample point For two component data this can be ather two independent components or the first component could be used to define color while the second is used to define opacity For three component data these can be three independent components or RGB For four component data these can either be four independent components or RGBA For three or four component data that is not independent the data type must be unsigned char Not all file formats support all these types of data 14 Application Settings The supported 2D and 3D data file formats are DICOM DICOM data is generated by many medical scanning devices VolView can not read all DICOM files For example if the scanning parameters such as field of view were changed during the scan VolView will be unable to read the data If the gantry was tilted during scanning VolView will be unable to read the data GE Signa GE Signa data is created by some General Electric CT and MR scanners and will typically have a mr or ct extension BioRad Confocal These files are created from a BioRad confocal microscope and will typically have a pic extension Zeiss LSM These files are created from the Zeiss microscope and typically have a lsm extension Metamorph Stack Metamorph Stack files are the output type produced
158. th of the edge detection Generally the first two nodes should be kept at 0 0 but occasionally there will be a need to set these to some small non zero value in order to de emphasize but not entirely hide the homogeneous regions of the dataset On the right you will see three images generated from the same dataset The scalar opacity mapping for all three is the Fixed 0 2 preset option The scalar color mapping for all three is the White preset option In the top image the gradient opacity mapping is off while in the other two image it is on with the first two nodes having an opacity of 0 0 This eliminates the homogeneous regions of the data highlighting the surfaces The top two images have shading off while the bottom image has shading on Note the significant image the gradient opacity mapping and shading can have on the volume rendered image Component Weights If you have more than one independent components in your dataset you will see a slider for each component at the bottom of this area These sliders allow you to adjust the contribution of each component to both the volume rendered image and the image display You can see one component by itself by setting its slider to 1 0 and all others to 0 0 If your data is in mostly separate regions a voxel will generally have a high opacity value in only one of the components then setting all sliders to 1 0 would Information produce a good image of the combined data from all channels If the
159. that the pixels in the region have intensities higher than the lower threshold The upper threshold is computed by the filter as the value that prevents the seed2 point to be included in the region of seed1 RGB Confidence Connected ITK This filter applies an region growing algorithm for segmentation The criterion for including new pixels in the region is defined by an intensity range around the mean value of the pixels existing in the region The extent of the intensity interval is computed as the product of the variance and a multiplier provided by the user The coordinates of the seed points are used as the initial position for start growing the region Noise Suppression Filters The Noise Suppression category of filters provides a set of basic filters such as median filtering and Gaussian smoothing for noise reduction Each of the eight methods provided in this category are described below 56 Curvature Anisotropic Diffusion ITK This filter applies an edge preserving smoothing to a volume by computing the evolution of an anisotropic diffusion partial differential equation Diffusion is regulated by the curvature of the image iso contours This filter processes the whole image in one piece and does not change the dimensions data type or spacing of the volume Curvature Flow ITK This filter applies an edge preserving smoothing to a volume by computing the evolution of an anisotropic diffusion partial differential equation Diffus
160. the color bar while VolView is in an idle state not currently rendering You will notice that the mouse icon changes If you are in the middle of the color bar you will see a vertical double arrow and a horizontal double arrow This indicates that using the left mouse button now will allow you to draw the color bar to a new location on the window If you move close to the top or bottom edge of the window the color bar will switch to horizontal mode If you move near the left or right edges of the window the color bar will switch to vertical mode When the mouse is near an edge of the color bar you will see a horizontal double arrow indicating that you can alter the width of the color bar a vertical double arrow indicating that you can resize the height of the color bar or a diagonal double arrow indicating that you can do both at once Orientation Marker The orientation marker is an interactive annotation element displaying the current orientation of the data using a box with labels on the sides In the example image shown on the right the Orientation marker is shown in the bottom left corner of the volume display window The application area is set to Medical and therefore 31 Table Of Contents 32 the box uses R right L left A anterior P posterior S Superior and inferior When in a general application area the letters would be X X Y Y Z and Z From the user interface you can toggle the vi
161. the shading values the interpolation type the scalar color and opacity mappings the gradient Opacity mapping and the component weights This is a good way to save a nice volume appearance before experimenting further or to save the color opacity mappings that works well with one CT dataset to try it on others To save an Appearance Settings file choose the Save Appearance Settings option from the File menu This will pop up the Save Appearance Settings dialog allowing you to specify a location and filename Appearance settings files will have an extension of vvt which will be added for you if you do not specify it with your filename Note that you should only load Appearance Settings files with data of approximately the save scalar range For example an Appearance Settings file that was saved for floating point data with a range of 3 2 to 1 7 will be meaningless if you load it while viewing an unsigned char dataset with a range of 0 to 255 Saving Surfaces The geometry that forms the isovalue contour surfaces and any geometry output by a filter can be saved into a polygonal file using the Save Surfaces option from the File menu All contours and filter output will be combined into one output file You can select the type of the output file from the choices in the Save as type pulldown menu The output type can be a VIK XML format vtp or a Stereo Lithography file stl Saving Screenshots You can save a screenshot image to a f
162. the slider is to the far left a high level of interactivity will be attempted with a goal of more than five frames per second When the slider is to the far right a target frame rate of less than one frame per second is attempted These frame rates may be achieved by making approximations that could result in images that lack sharp detail during interaction After interaction is complete the image will be generated at higher levels of detail until a full resolution image is computed depending on the other settings in this area VolView will use the interactive rendering method whenever you use the mouse to rotate pan zoom or fly in the volume window or when you adjust an interactive data annotation element The interactive rendering method will also be used when some interface elements are interactively modified For example interactive rendering is used when the cropping bounds are modified either by adjusting the sliders on the user interface or by using the mouse to adjust the cropping annotation in an image display window Include Ray Casting You may choose to always use ray casting as a level or detail or to use it only if it is necessary because hardware acceleration is not available Generally this option should be left in the Always state since the hardware accelerate volume rendering method is not guaranteed to give you a high resolution final image It is sometimes desirable to disable ray casting when the hardware accelerated images
163. ther Nodes will be added in each function so that a matching set at the same scalar value exist When these functions are locked horizontal motion changing of the scalar value of a node in one mapping is mirrored in the other Adding or deleting a node will occur in both mapping and any changes in the range display will also be reflected in both mappings The functions cannot be locked together when the scalar opacity mapping is in Window Level Mode The right button with a file icon on it contains some preset color This includes a set of solid colors a ramp from black to white and two rainbow options one that is histogram dependent and one that spans the full range Editing the nodes in the scalar color mapping is similar to editing in the scalar opacity mapping except that the nodes are constrained to a line Vertical position has no meaning Instead the color of the node is set using the Value and Hue Saturation controls from the top of the Volume Appearance Settings area An example is shown to the right The color of the active node will be displayed in this region and you can adjust the Value and Hue Saturation settings of the current node by dragging the position of the bar on the Value display and the circle on the Hue Saturation display The appearance of the Value area will be based on the current color selected in the Hue Saturation area Color is always specified in HSV color space even when an RGB color space is used
164. to specify the axis and order of the rows and the final option menu allows you to specify the axis and order of the columns If you load your data and it appears to be upside down or flipped in left right then you did not correctly specify the orientation If you are loading a series of images at 16 VolView 2 0 Open Wizard Open Valores Wirard e bere Properties Tre Be TT e td DOE Anos iranere fe each de Jn e pen ge Be lar 403 mill ba ped neh See ge remote Fen check Brant fen on fr correct partier and ree El recen 1 os ee ass mrd noir e sterling erd end ske sl ber kjeder P rura Fatterrc a filias Hira eben KE String Sine H Ernim Sea VolView 2 0 Open Wizard Open Valores Wirard dores Aires Pesa Pp al fe Oe Br o Siro het Eg red Jes ae une p Gee e origin ar spacing thant rel brt Lk reren aa Ha OF pau ieee fee origin aa Unies H al be seed pode bedt vage oP T en alk Wie i a Linea i sl e pares a EAT IN Ger 0 000 d De Spacing 3 000 D 2 000 VolView 2 0 Open Wizard Ed Open Valores Wicard Dar Lee endda pe talco ati Pepe abeto Gee the y he vill Bt e retest gt Cestance Lins fed letet Conmponent Liras degrees this point you have completely specified the parameters and the data will be loaded when you press Next or Finish If you attempt to load raw data either a series of 2D images or a 3D volume you will see some additional pages of the Open Wizard Before assuming that y
165. ue probe from the Cropping panel and adjust the placement interactively in the Volume window This window supports 2D interaction Table Of Contents X Y Axial Image This is an axis aligned slice of the data along the Z axis This window supports 2D interaction X Z Frontal Image This is an axis aligned slice of the data along the Y axis This window supports 2D interaction Y Z Sagittal Image This is an axis aligned slice of the data along the X axis This window supports 2D interaction For each of the display windows there is a pulldown menu in the upper left corner on the title bar Using this menu you can change the type of display in this area For example selecting the first Window layout option on the Window menu or the toolbar will display one Volume window Using the pulldown menu you can change this to view the Axial image in this area instead Keep in mind that you can only display each type of window once if you choose a window type that is already displayed the two windows will swap positions For example if you are viewing the Axial and Sagittal image side by side and you select Sagittal from the pulldown menu on the Axial window then the Axis and Sagittal windows will swap positions Clicking on the title bar of a window will change this title bar to blue indicating that this window currently has keyboard focus This is useful when using keyboard shortcuts Status Bar The status bar in on the bottom left
166. umber of images displayed in the lightbox This shortcut will have no effect in the oblique view Home Move to the first slice In the lightbox the image in the upper left corner will be the first slice This shortcut has no effect in the oblique view End Move to the last slice In the lightbox the image in the lower right corner will be the last slice This shortcut has no effect in the oblique view r Reset the camera and the window level values This shortcut is linked across all image view Pressing the r key in any image window will cause all image windows to reset p Add a 3D marker at the mouse cursor position This marker will appear if visible in the volume display window and all image windows and can be interactively controlled after placement by dragging to a new location m This key will toggle the visibility of the 2D marker This marker can be useful as a pointer when two sessions are connected Information Contours Add Contour The Add Contour area of the Contours panel p Add Contour X can be used to add an iso valued contour to jzovalue ME MS 28 93 VolView An example of this interface is PERES shown on the right The contour will be i displayed as a polygonal surface in the Add Contour at Isovalue volume window as well as an outline in all the image windows An example of the contour in the volume display window and the three axis aligned image windows is shown below Note that the volume
167. utputMinimum 0 module SetOutputMaximum 255 Execute the filter module ProcessData pds 5 static int ProcessData void inf vtkVVProcessDataStruct pds vtkVVPluginiInfo info vtkVVPluginInfo inf make sure there is only one component of input data if info gt InputVolumeNumberOfComponents 1 info gt SetProperty info VVP ERROR The AntiAlias filter only works with single component data return 1 try switch info gt InputVolumeScalarType case VTK CHAR AntiAliasRunner lt signed char gt runner runner Execute info pds break case VIR UNSIGNED CHAR 93 Table Of Contents AntiAliasRunner lt unsigned char gt runner runner Execute info pds break Case VIK SHORT AntiAliasRunner lt signed short gt runner runner Execute info pds break case VIR UNSIGNED SHORT AntiAliasRunner lt unsigned short gt runner runner Execute info pds break case VIR INT AntiAliasRunner lt signed int gt runner runner Execute info pds break case VTK UNSIGNED INT AntiAliasRunner lt unsigned int gt runner runner Execute info pds break case VTK LONG AntiAliasRunner lt signed long gt runner runner Execute info pds break case VIK UNSIGNED LONG AntiAliasRunner lt unsigned long gt runner runner Execute info pds break case VTK FLOAT AntiAliasRunner lt float gt runner runner Exe
168. ve Allo ci cad 65 Remove All Presets sad 60 Remove Contour EE 46 Remove Pres EE 60 Remove Selected nia ad nt 65 Remove SUM ACC sonia dai 52 A A 9 42 60 eege 35 RGB Confidence Connected ITK 56 ROM EEN e 43 Seil WE 42 A N E EE 42 S Sample pac EN 64 Sampling tale 21 A EE 11 35 Save Appearance Settings 20 Save Screenshot eee 20 Save Geseion 14 20 Save SUE sana 20 Save VOUM id 20 Save window geometry ococcccncoccnconcnconnns 25 Saving Appearance Settings 74 Saving Screenshots rrararnannrnavnrnnvarnnn 74 Saving SESSION EE 73 SAVING SUNACES ll 74 Saving VOTES ae 73 A orere 35 Scalar Color Mappmg 35 scalar Opacity Mapping ooooco 11 35 Scalar le rai 64 Cale Ba 29 Screenshots iii ia 74 75 Segmentation Level Get 55 segmentation Region Growing 56 SESSION MC tits neck a a 14 JESS ONS ae 73 SACI WEE 21 35 Shape Detection Module ITK 55 Show most recent panels rranannrnrnanerr 25 Show splash screen 25 SNOW TOO INOS EE 25 Show window layout toolbar s anasesena 26 A 57 Simple closed surfaces ooococcocococonconnnocos 46 SIZE WEE 64 Slice orientaion cece ec ee eee ee essen eeees 61 SOE LY E 27 SO AC ING EE ER In 16 64 DDC C UNAM E 11 35 specular POWET erararnrnrnenenenenenennnnnne 11 35 splash screen E 25 Standard Interactivity o oocococcononeno 70 Standard Views
169. volume typically good for color data or append a component to the input volume e g making a one component greyscale volume into a two component column If the input volume already has four components then you cannot append another component onto it Instead it will replace the last component Crop This filter crops a volume to fit within the current settings of the cropping planes regardless of if they are currently visible This is useful for reducing a large volume to a smaller subvolume prior to applying a time consuming localized segmentation algorithm Gradient Magnitude IIR ITK This filter applies IIR filters to compute the equivalent of convolving the input image with the derivatives of a Gaussian kernel and then computing the magnitude of the resulting gradient Merge Volumes This filter computes a new volume by merging the components of two volumes together So if both of your volumes had one component per voxel then after 53 Table Of Contents merging the result would be a two component per voxel volume The two volumes must be of the same dimensions The resulting volume will be the same scalar type as the original volume If the combination of the two volume would result in more than four components then the second volume will replace some of the components of the original volume For example if a four component volume merged with a one component volume the last component of the four component volume would be replaced by
170. w session so you cannot use the mouse to point out a structure 66 Views And Lights Projection Type The Projection Type area on the Views amp Projection Type x Lights panel allows you to switch between amp Parallel Projection parallel and perspective projections and tO perspective Projection set the view angle for perspective ia projections This interface will appear similar P tve view angle RI E to the example on the right In a parallel projection also known as an orthographic projection viewing rays all travel parallel to each other perpendicular to the view plane This means that it will be difficult to tell whether objects are closer or farther away since an object will remain exactly the same size regardless of how far away from the observer it is In a perspective projection viewing rays all emanate from the viewing location also Known as the camera position or the eye point This is similar to what you see when observing the world around you Objects that move further away from the observer will appear to shrink in size The view angle controls how much of the world you can see in the window Larger view angles will work best in close areas Such as viewing data from the inside in virtual colonoscopy but will cause images that appear distorted a fish eyed appearance Smaller view angles will appear closer to a parallel projection Both projection types can be useful Parallel projection can be handy
171. when you want to place a scale marker in the volume window This marker is only valid when a parallel viewing type is utilized since the size of the scale marker will be the same regardless of how deep within the image it is drawn Since we are used to viewing our world in perspective sometimes a parallel viewing will appear wrong For example when viewing just the bounding box of an object it is not possible to tell the front faces from the back with an orthographic projection you can switch the box back and forth in your mind Since you expect the back faces of the box to appear smaller because they are further away the box may appear distorted because it is lacking the perspective effect Also it will not be possible to view objects from the inside with a parallel projection type Standard Views The Standard Views area on the Views amp standard Views x Lights panel allows you to reset the camera l to a view down one of the major axes The A Se Sess labels in this area will depend on whether you x Y z are in a General or Medical application area The interface will appear similar to one of the two shown on the right with the top example Standard Views X being the General application area and the Right Anterior Superior bottom example being the Medical Left Posterior Inferior application area Clicking on one of the six buttons with reset the camera to a view down the X Y or Z axis positive or negative di
172. y Process Dated UpdateG lu H vvFilterFeolniti d Developer ser Y FilterFoo Plugin Source Code Installation Dir bin emm I I I i l I I I i i l l l l l Plugins l I i l 78 Extending Filters With Plugins The initialization function The initialization function of the plugin must conform to the following API extern C void VV PLUGIN EXPORT vvlITKGradientMagnitudelnit vtkVVPluginInfo info where the symbol VV PLUGIN EXPORT and the structure vtkVVPluginInfo are both defined in the public header file vtkVVPluginInfo h This initialization function is invoked by VolView at start up time just after the shared library has been dynamically loaded The typical content of this function is shown below vvPluginVersionCheck setup information that never changes info gt ProcessData ProcessData info gt UpdateGUI UpdateGUI info gt SetProperty info VVP_NAME Gradient Magnitude IIR ITK into gt Set Property natos VYP GROUP Utility gt info gt SetProperty info VVP TERSE DOCUMENTATION Gradient Magnitude Gaussian IIR info gt SetProperty info VVP_FULL_DOCUMENTATION This filter applies IIR filters to compute the equivalent of convolving the input image with the derivatives of a Gaussian kernel and then computing the magnitude of the resulting gradient inFo gt S tkbr p ertyiink VVP S
173. y step using each one the individual filters 55 Table Of Contents Segmentation Region Growing This category of filters provides four different segmentation methods based on the region growing concept Each of these methods are described in more detail below Confidence Connected ITK This filter applies an region growing algorithm for segmentation The criterion for including new pixels in the region is defined by an intensity range around the mean value of the pixels existing in the region The extent of the intensity interval is computed as the product of the variance and a multiplier provided by the user The coordinates of the seed points are used as the initial position for start growing the region Connected Threshold ITK This filter applies an region growing algorithm for segmentation The criterion for including new pixels in the region is defined by an intensity range whose bound are povided by the user These bounds are described as the lower and upper thresholds The region is grown starting from a set of seed points that the user should provide in the form of 3D markers Isolated Connected ITK This filter applies a region growing algorithm for segmentation You must provide two seed points the filter will extract a region connected to the first seed point and not connected to the second one This is quite useful for separating adjacent structures The method will grow a region around the first seed point in such a way

Download Pdf Manuals

Related Search

Related Contents

Antérix 8 - ANTERISQUE  GRIF 2012 Fault Tree User Manual - GRIF  DVD/CD/USB/SD receiver Boss Audio BV9567BI with Bluetooth  1010/1210/1410 - Landtechnik Service Benn  Samsung SH026EAV1 manual do usuário  VARIMOT® ATEX, Reductor con variador mecánico antiexplosivo y  Phase 1 :  ワイヤレス窓センサー送信器  Spyder with PhotoCAL User Guide  Philips Coffee jug CRP716  

Copyright © All rights reserved. Failed to retrieve file