User Macro Document - DistanceMapSegmentation

<table cellspacing="0" cellpadding="0"> <tr height="150"> <td align="left"><img src="../../../../img/logo.gif" alt="IAC logo"></img></td> <td width="100%" rowspan="2" align="left" valign="center"> <table cellspacing="0" cellpadding="0"> <tr> <td> <table class="navigate_doc" width="100%" border="0" align="center"> <tr bgcolor="c6c6e0" align="center"> <th nowrap width="1%" height="32">P0212</th> <th nowrap width="98%">DistanceMapSegmentation</th> <th nowrap width="1%">26th March 2004</th> </tr> <tr> <td align="left" colspan="3"> <p><b>Authors:</b> Dr Krzysztof Nowinski, Warsaw University; Anja Bindrich, MVC; Tobias Schiebeck, MVC <b>Version:</b> 1.0 <b>Path:</b> iac_proj/distmap/</p> <a href="../../mappers.shtml" target="_top"><img src="../../../../img/mapper.gif" width="58" height="30" border="0" alt="Mappers"></a> <a href="distmap.shtml" target="_top"> <img src="../../../../img/doc_umac.gif" border="0" width="30" height="30" alt="User Macro Document - DistanceMapSegmentation"></a> <a href="distmap_dlg.shtml" target="_top"> <img src="../../../../img/doc_umac.gif" border="0" width="30" height="30" alt="User Macro Document - DistanceMapSegmentationDialog"></a> <a href="../../source/mappers/distmap/distmap.tar.gz"> <img src="../../../../img/targz.gif" border="0" width="52" height="30" alt="Archive - distmap.tar.gz"></a> <a href="../../source/mappers/distmap/distmap.tar.Z"> <img src="../../../../img/tarz.gif" border="0" width="52" height="30" alt="Archive - distmap.tar.Z"></a> <a href="../../source/mappers/distmap/distmap.zip"> <img src="../../../../img/zip.gif" border="0" width="52" height="30" alt="Archive - distmap.zip"></a> <a href="image_distseg.shtml" target="_top"> <img src="../../../../img/image.gif" border="0" width="42" height="30" alt="Example Application using the DistanceMapSegmentation module"></a> <a href="image_distseg_dlg.shtml" target="_top"> <img src="../../../../img/image.gif" border="0" width="42" height="30" alt="DistanceMapSegmentationDialog Window"></a> </td> </tr> </table> <br> </td> </tr> <tr> <td>  <h1>DistanceMapSegmentation</h1> <h3>Synopsis</h3> <p>The DistanceMapSegmentation performs a 3D segmentation based on the difference in the value of neighboured pixels. The segmentation itself is done by region growing. This module works only with byte data.  <p align="center"><img border="0" src="source/mappers/distmap/distseg.png" width="90%" height="90%" alt="Screen Shot of the Example application using the DistanceMapSegmentation module"></p> </p> <p> <h4>Input Ports</h4> <table class="parameters" summary="Input Ports used by DistanceMapSegmentation"> <tr> <td width="100"><b>Name</b></td> <td width="75"><b>Type</b></td> <td width="425"><b>Description</b></td> </tr> <tr> <td colspan="4"><hr></td> </tr> <tr> <td width="100"><i>in</i></td> <td width="75">Mesh_Unif + Node_Data</td> <td width="425">Input data from which the segmentation will be performed</td> </tr> <tr> <td colspan="4"><hr></td> </tr> </table> <h4>Parameters</h4> <table class="parameters" summary="Parameters used by DistanceMapSegmentation" width="668"> <tr> <td width="150"><b>Name</b></td> <td width="53"><b>Type</b></td> <td width="322"><b>Description</b></td> <td width="125"><b>UI Control</b></td> </tr> <tr> <td colspan="4" width="662"><hr></td> </tr> <tr> <td width="150"> <i>axes</i><br> <i>plane</i></td> <td width="53">int</td> <td width="322">values defining slice number and viewing direction of 2 D input</td> <td width="125">UIradioBoxLabel<br> UIslider</td> </tr> <tr> <td width="150"> <i><br> init_mask<br> init_points<br> reset</i></td> <td width="53">int</td> <td width="322">triggers functions to initialize the mask<br> removes all values from current mask<br> removes all points from current mask<br> deletes all masks and points</td> <td width="125">UIbutton</td> </tr> <tr> <td width="150"> <i>fill_mode</i></td> <td width="53">int</td> <td width="322">decides which operation should be performed with the masks (replace, add, intersect, subtract) </td> <td width="125">UIradioBoxLabel</td> </tr> <tr> <td width="150"> <i>mask_num</i></td> <td width="53">int</td> <td width="322">current mask number (between 1 and 100)</td> <td width="125">UIslider</td> </tr> <tr> <td width="150"> <i>tolerance</i></td> <td width="53">int</td> <td width="322">value declares the accepted difference in the voxel-value from the picked value to be part of this mask</td> <td width="125">UIslider</td> </tr> <tr> <td width="150"><i>fill_val</i></td> <td width="53">int</td> <td width="322">value of the region of interest, usually picked by mouse</td> <td width="125">UIfield</td> </tr> <tr> <td width="150"><i>cutoff</i></td> <td width="53">int</td> <td width="322">provides threshold for segmentation; values below this threshold are set to 0</td> <td width="125">UIslider</td> </tr> <tr> <td width="150"><i>smooth</i></td> <td width="53">int</td> <td width="322">threshold used for mask operations</td> <td width="125">UIslider</td> </tr> <tr> <td width="150"><i>smooth_out</i></td> <td width="53">int</td> <td width="322">decides about the kind of smoothing (no smoothing, smooth diam 3, smooth diam5)</td> <td width="125">UIradioBoxLabel</td> </tr> <tr> <td width="150"><i>do</i></td> <td width="53">int</td> <td width="322">starts the calculating of the 3D segmentation</td> <td width="125">UIfield</td> </tr> <tr> <td colspan="4" width="662"><hr></td> </tr> </table> <h4>Output Ports</h4> <table class="parameters" summary="Output Ports used by DistanceMapSegmentation" width="624"> <tr> <td width="100"><b>Name</b></td> <td width="95"><b>Type</b></td> <td width="415"><b>Description</b></td> </tr> <tr> <td colspan="4" width="618"><hr></td> </tr> <tr> <td width="100"><i>data_obj</i></td> <td width="95">DefaultObject</td> <td width="415">2D output of current slice with isoline of segmentation</td> </tr> <tr> <td width="100"><i>out_field</i></td> <td width="95">Mesh_Unif + Node_Data</td> <td width="415"> 3D output of the segmentation, includes a 'shadow' of not segmented objects</td> </tr> <tr> <td width="100"><i>fill_obj</i></td> <td width="95">DefaultObject</td> <td width="415">2D output of the distance map of the segmentation of the current slice</td> </tr> <tr> <td width="100"><i>res_obj</i></td> <td width="95">DefaultObject</td> <td width="415">resulting 2D output of segmentation of this slice, includes a 'shadow' of not segmented objects</td> </tr> <tr> <td width="100"><i>mask_obj</i></td> <td width="95">DefaultObject</td> <td width="415">2D output of the segmentation mask of the current slice, different masks are displayed in different colours</td> </tr> <tr> <td colspan="4" width="618"><hr></td> </tr> </table> </p> <h3>Description</h3> <p>The DistanceMapSegmentation macro provides a way to segment a 3 D byte volumes using a distance map. The user selects a area of interest by picking a point out of it with the left mouse button while the Ctrl-key is pressed. A border gets drown around an area with similar values. With the <i>tolerance</i> and <i>cutoff</i> sliders this area can be adjusted. The <i>do</i> button starts the calculation of the 3D segmentation of this area. The fill window shows the distance map derived from this area. The mask window shows the mask, if there are several masks they get drawn in different colours. The result window shows the current slice with the distance values used in the 3D scene window.</p> <p>Around the picked points a region growing is performed to select areas with approximately the same values. This segmentation is used to create distance map. Values below a threshold (cutoff) get ignored.</p> <p>There is the possibility to have up to 100 mask of the same volume. This masks are not independent of each other. Point in one mask cannot be also points in another mask. Therefore mask operations are provided. You can add new segments to an existing mask, or replace the values with the new ones; you can also intersect or subtract two masks. To reset the current mask the user can press <i>reset mask</i>, to initialize all point <i>init points</i>, or to reset everything <i>reset</i>.</p> <h3>Inputs</h3> <p><b><i>in</i></b></p> <p>Input of 3D volume data, usually provided by a <i>Read Field</i> module. This is the data which should be segmented using this module. This input is required.</p> <h3>Parameters</h3> <p> <b><i>axes </i></b><br> <i><b>plane</b></i></p> <p> This values define the current slice. The axis provides the viewing direction on the volume data, the plane the depth of the selected slice in the volume.</p> <p><b><i>init_mask<br> init_point<br> reset</i></b></p> <p> This are parameters which trigger functions to reset the current mask, or to reset all picket point points, or to reset everything, so all masks and all points get deleted.</p> <p><b> <i>fill_mode</i></b></p> <p>There is the choice between four mask operations. You can replace an existing mask, you can add new values to it, or intersect two masks or make the difference between  them. It is impossible that two masks have points at the same place. The default fill mode is replace the old mask with the new one.</p> <p><b> <i>mask_num</i></b></p> <p>You could have up to 100 different masks for the same volume. This parameter specifies the current.</p> <p><b> <i>tolerance</i></b></p> <p>The <i>tolerance</i> provides a value to specify the allowed difference between neighboured voxels to belong to the same area of interest.  This is one of two possibilities to select the correct area of the volume, the other parameter is <i>cutoff</i>.</p> <p><b><i>fill_val</i></b></p> <p>The value of the voxel which was picked as part of the area of interest. Pixels around this voxel with a value within the choosen tolerance get selected as part of the area of interest.</p> <p><b><i>cutoff</i></b></p> <p>The second value to influence the mask. It provides a threshold. After the distance map was created all voxels which have not the same value as the picked one are represented by their difference in value. If the difference is bigger than this threshold they get excluded from the mask.</p> <p><b><i>smooth</i></b></p> <p>This is the threshold for the mask opperations. Only values above this threshold get considered.</p> <p><b><i>smooth_out</i></b></p> <p>The user has the choice between <i>no smoothing</i>, <i>smooth diam 3</i>, or <i>smooth diam 5.</i> The difference between the two smoothing methods is the radius which gets considered (one voxel on each side or two).  This is useful if you want to prevent the creation of pointy areas. </p> <p><b><i>do</i></b></p> <p>If this value gets set, it triggers the calculation of the 3D segmentation.</p> <h3> <b>Outputs</b></h3> <p><b><i>data_obj</i></b></p> <p>DefaultObject containing the current slice in the specified direction in which the segmentation is represented by an isoline.</p> <p><b><i>out_field</i></b></p> <p>This is the segmented output field. The current selected mask is used to calculate this output. It includes also a 'shadow' of the other not currently segmented objects in the data.</p> <p><b><i>fill_obj</i></b></p> <p>This is a 2 D representation of the current slice as shown in the <i> data_obj</i> output. The values come from a distance map calculated from the selection in that slice.</p> <p><b><i>res_obj</i></b></p> <p>This is a 2 D representation of the current slice as shown in the <i> data_obj</i> output. The values come from a global distance map from the current selected mask (same values as in the <i>out_field</i>). It includes also a 'shadow' of all not currently segmented objects in that volume.</p> <p><b><i>mask_obj</i></b></p> <p>This is a 2 D representation of the current slice as shown in the <i> data_obj</i> output. It represents the masks in this slice. Each mask is shown in a different colour.</p> <h3>Utility Macros</h3> <p>The functional macro <i>DistanceMapSegmentationFunc</i> uses the low-level modules  <i>dist_fill</i>, <i>create_outf</i>, <i>reset_all</i>, <i>init_mask</i>, <i>init_point</i> and the macros <i>distance_map_slice</i> which uses in one instance the module <i>add_points</i>, and <i>mask_field</i> which uses <i>create_outm</i>. The user macro <i>DistanceMapSegmentation</i> uses this functional macro and the user interface macro <i>DistanceMapSegmentationUI</i>. The <i>distmapParams</i> parameter block is used to connect these components together.</p> <h3>Example</h3> <p>The DistanceMapSegmentationEg example application loads a file and displays all outputs in separate windows.</p> <h3>Files</h3> <p><i>"../iac_proj/distmap/dstmppar.v"</i>  contains the V definition of the parameter blocks. <i>pt_params </i>defines the point parameter needed; <i>pt_init_params</i> defines the reset of the picked points; <i> fill_params</i> includes all needed parameter to fill a mask; <i>out_params</i> includes all needed parameter to do the segmentation; <i>points</i> include all picked points; <i>distmapParams</i> include all other parameter blocks.</p> <p><i>"../iac_proj/distmap/dstmpmod.v"</i> contains the V definition modules. <i>add_points </i>handels the picking of new points from the input slice; <i>create_outf</i> creates the 3 D output; <i>create_outm</i> creates the mask output; <i>dis_fill</i> creates the distance map; <i>init_points</i> resets all  picked points of current slice; <i>init_mask</i> resets the mask of current slice; reset_all resets the points and masks of all slices;</p> <p><i>"../iac_proj/distmap/dstmpmac.v"</i> contains the V definition of the macros. <i>DistanceMapSegmentationUI</i> describes the user interface of this module; <i>distance_map_slice</i> creates the data input slice according to the selected axis and plane; <i>DistanceMapSegmentationFunc</i> is the functional macro in this library; <i>DistanceMapSegmentation</i> and <i> DistanceMapSegmentationDialog</i> are the user macros.</p> <p><i>"../iac_proj/distmap/dstmpapp.v"</i> contains the V definition of the example applications. <i>DistanceMapSegmentationEg </i>is a multi-window application that uses the <i>DistanceMapSegmentation</i>  user macro, separate output windows; <i>DistanceMapSegmentationDialogEg</i> uses the <i> DistanceMapSegmentationDialog</i> as user macro, all windows are displayed in one viewer.</p> <h3>Authors</h3> <p> <pre> Dr Krzysztof Nowinski Warsaw University </pre> </p> <h3> Modifications</h3> <p> <pre> Anja Bindrich, Manchester Visualization Centre Tobias Schiebeck International AVS Centre</pre> </p> <h3> Contact</h3> <p> <pre> International AVS Centre Manchester Visualization Centre Manchester Computing University of Manchester Oxford Road Manchester United Kingdom M13 9PL </pre> </p> <h3>See Also<h3> <ul> <li>DistanceMapSegmentationDialog</li> </ul>  </td> </tr> </table> </td> </tr> <tr height="100%"> <td class="sideLink" width="25%" align="left" valign="top" nowrap="nowrap"> <p><a href="../../../../general/index.shtml" target="_top">General Information</a></p> <p><a href="../../../../repository/index.shtml" target="_top">Repositories</a></p> <p class="sideLinkLevel2"><a href="../../../new/index.shtml" target="_top">  New Releases</a></p> <p class="sideLinkLevel2"><a href="../../../download/index.shtml" target="_top">  Download</a></p> <p class="sideLinkLevel2"><a href="../../../submit/index.shtml" target="_top">  Submit</a></p> <p class="sideLinkLevel2"><a href="../../../pfiles/index.shtml" target="_top">  Project Files</a></p> <p class="sideLinkLevel2"><a href="../../../avs5/index.shtml" target="_top">  AVS5</a></p> <p class="sideLinkLevel2"><a href="../../../express/index.shtml" target="_top">  AVS/Express</a></p> <p class="sideLinkLevel3"><a href="../../atoz.shtml" target="_top">    A to Z</a></p> <p class="sideLinkLevel3"><a href="../../number.shtml" target="_top">    Project #</a></p> <p></p> <p class="sideLinkLevel3"><a href="../../data_io.shtml" target="_top">    Data IO</a></p> <p class="sideLinkLevel3"><a href="../../filters.shtml" target="_top">    Filters</a></p> <p class="sideLinkLevel3"><a href="../../mappers.shtml" target="_top">    Mappers</a></p> <p class="sideLinkLevel3"><a href="../../misc.shtml" target="_top">    Miscellaneous</a></p> <p class="sideLinkLevel3"><a href="../../special.shtml" target="_top">    Special Projects</a></p> <p class="sideLinkLevel2"><a href="../../../pog/index.shtml" target="_top">  Project Guidelines</a></p> <p><a href="../../../../usergroup/index.shtml" target="_top">User Group</a></p> <p><a href="../../../../training/index.shtml" target="_top">Training Materials</a></p> </td> </tr> </table> <table width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="c6c6e0"> <tr> <td><img src="../../../../img/foot1.gif" alt="IAC" width="155" height="25"></td> <td width="100%"> Last Updated:  26th March 2004 </td> </tr> </table>