Extend either shiva.ActionCommand or shiva.ToggleCommand.
Call
shiva.Main.addCommand ("comandName", command)
to add the command to SHIVA command pool. The current naming convention for the command name is
plugin/action. For instance: "Painter/saveVolume".
If the command is a ToggleCommand, modify shiva/resources/command.xml to indicate
command group s.t. only one ToggleCommand is selected at any given time.
To add the command to the menu, modify shiva/resources/menu.xml
To add the command to the toolbar, modify shiva/resources/toolbar.xml
Icons used in toolbar.xml in general are located in shiva/resourcies/icon/.
A CIVM image is consisted of a header file and bunch of files each representing
a slice. AKAIK the header file resembles brucker image file format.
Header format:
The general format is like a property file where
[attribute] = [value]
is the general format.
There are plenty of redundancies in the header. Sometimes one or more attributes
can be missing. So it is good to check all the redundant attributes in case one
of them is missing.
For the image data type, it should be short, signed or not. But SHIVA does not care.
Old Civm file naming convention:
Header file: [abc].headfile
Data files: [abc]roimx.001, [abc]roimx.002, etc
Newer file naming convention uses the same header and header type, just
the data file names are changed to consider the possibility of over 1000 slices.
Header file: [abc].header
Data files: [abc]roimx.0001.raw, [abc]roimx.0002.raw, etc
Possible property list:
X_DIM_STR_LIST = { "S_xres_img", "imatrix_X", "RH_image_size", "dim_X", "PARTAG_CUBESIZEX", "xray_FOV_width", "RH_xres", "S_xres", "rhuser6" };
Y_DIM_STR_LIST = { "S_yres_img", "imatrix_Y", "RH_image_size", "dim_Y", "PARTAG_CUBESIZEY", "xray_FOV_height", "RH_yres", "S_yres", "rhuser7" };
Z_DIM_STR_LIST = { "S_zres_img", "slquant", "PARTAG_CUBESIZEZ", "xray_no_images", "RH_zres", "S_zres", "rhuser8" };
X_FOV_STR_LIST = { "RH_xfov", "dfov" };
Y_FOV_STR_LIST = { "RH_yfov", "dfov_rect" };
Z_FOV_STR_LIST = { "RH_zfov", "slthick" };
The following file formats are currently supported by SHIVA.
Image volume files
Analyze(tm) (*.img, *.hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf
Nifti header files are supported.
SHIVA can also read GZIP compressed image files (*.img.gz).
Big volume is supported for uncompressed image files with byte, short, and rgb formats only.
Currently, SHIVA supports the following file types:
binary (1-bit, converted to byte format internally)
byte (8-bit)
short (16-bit, signed/unsigned)
rgb (24-bit)
float (32-bit, converted to short format internally)
Nifti (*.nii): http://nifti.nimh.nih.gov/nifti-1/
SHIVA can only handle Nifti volumes with transformation matrix with scaling and shifting. Other transformations are treated as an identify matrix.
SHIVA can also read GZIP compressed image files (*.nii.gz).
GUI_RC is an XML file which describes what the SHIVA frame should look like. It is written in CookSwing. shiva.ShivaGUI class extends JFrame to
have an setter for skinlf for loading SkinLF related themepack.
The default SHIVA GUI frame looks like:
Preview your changes to the wiki web page by clicking the rectangular button labelled "Preview Changes"
Once you are satisfied with the web page, save the changes by clicking the "Save Changes" button.
Add a Wiki page
A Wiki web page is considered to describe a specific topic. To add a new topic:
Edit an existing Wiki page and add a WikiWord defining the name of your new Wiki topic.
Preview and Save your changes to the existing web page. Your new Wiki Topic will have a small question mark inserted after the word. This means the new topic has not yet been created.
Click the new topic.
Enter a SHIVA Wiki user name and password if prompted to do so.
You will be viewing a Wiki Edit web page. Enter the contents of your new topic.
Preview the changes and revise until you are satisfied (see above for details).
* Save the changes to your newly created Wiki Web page.
Adding Images to a Wiki page
*See "Attaching a file to a Wiki page", below.
Attaching a file to a Wiki page.
You may at time want to associate an external file with a SHIVA Wiki topic.
Examples of this might be to add the detailed agenda of a meeting, or a spreadsheet table containing experimental results,and so forth.
To do so,
Ensure the file is on your local computer.
Click the button labelled "Attach a file". You will be asked to locate the file you want to upload, and to supply a comment that describes the file.
Click the "Upload File" button at the bottom of the upload page.
Your file will be sent to the SHIVA Wiki web site and a table of file attachments to this web page will appear at the bottom of the web page if it not already there.
If you select the "Link" checkbox before uploading the file and it is an image format recognized by our Wiki software (Twiki) the picture will appear in the web page. You may then Edit the page (see above) if you want to modify the text before the picture, or it's location on the web page.
Deleting an attached file
Locate the attached file in table of files (usually at the bottom of the wiki web page).
Click "Manage"
Click "Move Attachment" (at the bottom of the management web page).
Choose "Trash" from the drop-down Web menu of projects.
Type "TrashAttachment" into the Topic text entry area.
Label index files (*.lbl, *.txt) are ascii files used by Duff and SHIVA.
Each line contains information of the label id, color (optional),
tag name, and the long description. The fields are separated by a tab character.
Without Color:
idtagdescription
With Color:
id0xrrggbbtagdescription
The color field sometimes may not be in a full six digit hex number, but
the writer should attempt to produce all six digits.
The two styles correspond to two different entry functions defined above. The order
of loading the plugins may be important since some plugins depend on other plugins to
work.
For example:
package foo;
import shiva.interfaces.ShivaPlugin;
public class DemoPlugin implements ShivaPlugin
{
public final static String PLUGIN_DESCRIPTION = "A Plugin Demo";
public static void start ()
{
System.out.println ("==== Hello World! ====");
}
}
Then in shiva/resources/start.xml, add the following line
<load plugin="foo.DemoPlugin"/>
At this point, the plugin can be loaded by SHIVA.
For specific types of plugins, check the following links:
Note that not all ReaderWriters have to implement both reader and writer.
Creating a ReaderWriter for VolumeBuffer.class
Besides the requirement above, file reader is welcome to provide a mechanism pre-viewing the properties
of an image volume input file. To do so, the reader class needs to implement shiva.io.VolumeInfoReader.
For specific mechanism of how shiva.io.VolumeInfoReader works, see shiva.plugins.volumepreview.VolumePreview.
In general, VolumeBuffer.class readers should internally have a class that implements shiva.interfaces.VolumeReader.
This is not required, but a recommandation. It simplifies the actual reader/writer class implementation.
Show Progress
In general, most image volumes are fairly big and take a while to load. It is desirable to show the progress bar while loading. Shiva provides two ways displaying progress.
The input stream based progress is useful for reading large files through stream. The following example
shows how typically it is used. When the inputstream is closed, the progress bar also hides.
InputStream is = new FileInputStream (imgName);
InputStreamProgress progress = new InputStreamProgress (is);
progress.getProgress ().setTitle (file.getPath ());
is = progress;
try
{
// some code
}
finally
{
is.close ();
}
STARTUP_RC points to an XML list of plugins to be loaded. It should be noted that how SHIVA looks is mainly specified using plugins. It is written in CookXml.
shiva.PluginManager is responsible loading this file. It provides a tag library for CookXml. The tag library can be dynamically changed at run time by plugins, so additional tags may be supported.
By default, PluginManager supports the following tags:
<plugins> is the XML document root.
<load plugin="pluginClassName"> for loading a plugin class that does not the additional configuration parameter.
For example:
<load plugin="trogdor.about.About"/>
<load plugin="pluginClassName" config="parameter"> for loading a plugin class that requires the additional configuration parameter. Usually this parameter specifies an configuration resource file location. For example:
shiva.plugins.VersionLoader introduces this tag so that plugins enclosed are loaded only if the release
name of the jar package matches the title specified. title attribute must be specified. default
attribute is used to specify the release configuration to use if the jar package release is not specified.
For example:
shiva.workspace.WorkSpaceLoader introduces this tag to the PluginManager for workspace configuration. In general, it is
geared toward classes that inherit shiva.workspace.XmlWorkSpace, but other workspaces can also be configured as the default workspace. src attribute specifies the resource file used for the workspaces that inherits XmlWorkSpace to configure its menu and toolbar, etc. default attribute is used to set the default workspace.
For example:
In shiva.Main class, there are two global class variables START_RC and GUI_RC which can be changed to point to different resource file locations before shiva.Main's main funciton is called. Thus, to have a completely different set of configurations w/o touching the SHIVA core, you can do the something like below:
/*
*
* $Id: StartConfigure.txt,v 1.1 2006/01/06 23:15:41 HengYuan Exp www $
*
*/
package trogdor;
/**
* @author Heng Yuan
* @version $Revision: 1.1 $
*/
public class Main
{
public static String STARTUP_RC = "trogdor/resources/start.xml";
public static String GUI_RC = "trogdor/resources/shivagui.xml";
public static void main (String[] args) throws Exception
{
shiva.Main.STARTUP_RC = STARTUP_RC;
shiva.Main.GUI_RC = GUI_RC;
shiva.Main.main (args);
}
}
The Subversion repository location is svn+ssh://cvs.loni.ucla.edu/cvs/map . The following is the directory structure under trunk/ , which contains all the source codes, libraries, and build scripts.
This directory contains some sample image volumes and BrainGraph files.
/doc/
Some text documentations.
/lib/
Shared binary libraries.
/resources/
Resources for each build.
/resources/braingrapheditor/
resources for BrainGraph Editor build.
/resources/kali/
resources for BrainGraph Editor build.
/resources/mbat/
resources for MBAT build.
/resources/shiva/
resources for SHIVA build.
/src/
Source code directory, which include not only Java source codes, but also various other resources, including build scripts. Its direct child directories are sources for different builds, core_src/ or plugin_src/.
/src/braingrapheditor_src/
This directory contains the sources for the BrainGraph Editor workspace and its standalone build sources.
/src/core_src/
This directory contains the core frame work. It is used by all other builds.
/src/kali_src/
This directory contains the sources only needed by Kali build. Kali is aimed to be a compact of SHIVA with only limited features.
/src/mbat_src/
This directory contains the sources only needed by MBAT build.
/src/plugins_src/
This directory contains various plugins that are not needed by all the builds.
/src/plugins_src/braingraph_src
This directory contains sources for BrainGraph internal structure, file IO filters, and GUI viewing components.
/src/plugins_src/ccdb_src/
This directory contains clients for connecting to CCCDB services.
/src/plugins_src/imagereg_src/
This directory contains archaic image registration (point and curve) workspaces.
/src/plugins_src/ntclient_src/
This directory contains Heng's client implementation to NeuroTerrain server.
/src/plugins_src/registration_src/
This directory contains Erh-Fang Lee's image registration workspaces.
/src/shiva_src/
This directory contains the sources needed to build SHIVA builds. Currently it also contains plugins needed by MBAT and Kali builds. Eventually many of these plugins would be moved to /src/plugin_src/.
This following description is obtained from LONI ShapeTools edu.ucla.loni.ccb.shapeio.tm.parser.TmAsciiShapeParser.
The conventional suffix for a LONI Triangle Model files is `.tm'.
Syntax:
nVertices nFaces
{vertex coordinates, one per line, as X Y Z tuples}
{triangle face indices, three per line}
Note: The index of the third point of a triangle face
may have a "-" prefixed. This sign may indicate orientation.
It is ignored when the file is read.
Note: vertex indices start at 1, not 0. These are adjusted
by subtracting 1 before the face definitions are stored.
Example:
Statistics for SHIVA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 2139 0 0 399 ...
File Formats The following file formats are currently supported by SHIVA. Image volume files Analyze(tm) ( .img, .hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf ...
Subversion Repository Structure The Subversion repository location is svn+ssh://cvs.loni.ucla.edu/cvs/map . The following is the directory structure under trunk/ ...
Server Protocols ArcIMS ArcXML Programmer's Reference Guide for ArcIMS 9.1 Neuroterrain Atlas Server Network Protocols Web Services Description Language (Axis Client ...
UCF Format Universal Contour Files (UCF) is a format devised at LONI. It is an ascii based file in the following format: Header 384 256 200.000000 200.000000
LONI Triangle Model Format This following description is obtained from LONI ShapeTools edu.ucla.loni.ccb.shapeio.tm.parser.TmAsciiShapeParser. The conventional suffix ...
Label Index File Format Label index files ( .lbl, .txt) are ascii files used by Duff and SHIVA. Each line contains information of the label id, color (optional), ...
SHIVA Web Preferences The following settings are web preferences of the SHIVA web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
CIVM Format A CIVM image is consisted of a header file and bunch of files each representing a slice. AKAIK the header file resembles brucker image file format. Header ...
GUI RC is an XML file which describes what the SHIVA frame should look like. It is written in CookSwing. shiva.ShivaGUI class extends JFrame to have an setter for ...
STARTUP RC points to an XML list of plugins to be loaded. It should be noted that how SHIVA looks is mainly specified using plugins. It is written in CookXml. shiva ...
In shiva.Main class, there are two global class variables START RC and GUI RC which can be changed to point to different resource file locations before shiva.Main ...
SHIVA can be configured to have completely different look and feels. 1. Configure startup resource file location. 1. Configure ToggleComamnds 1. Configure menu 1 ...
Steps to create a plugin 1. Implement shiva.interfaces.ShivaPlugin . 1. Have public final static String PLUGIN DESCRIPTION "Some Description"; in the class. 1. Define ...
Steps adding a new file reader/writer 1. Implement shiva.io.ReaderWriter . 1. Create a shiva.io.DocFilter . The easiest way is using the following template. / file ...
Steps to add menu/toolbar actions 1. Extend either shiva.ActionCommand or shiva.ToggleCommand . 1. Call shiva.Main.addCommand ("comandName", command) to add the command ...
How To Use the SHIVA Wiki We encourage you to change the contents of a SHIVA Wiki web page and to add your own web page topics that is what a Wiki is all about ...
This is a subscription service to be automatically notified by e-mail when topics change in this SHIVA web. This is a convenient service, so you do not have to come ...
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...
TWiki's SHIVA web SCRIPTURL /view SCRIPTSUFFIX /SHIVA The SHIVA web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE{" TWIKIWEB ...
Steps to add menu/toolbar actions 1. Extend either shiva.ActionCommand or shiva.ToggleCommand . 1. Call shiva.Main.addCommand ("comandName", command) to add the command ...
CIVM Format A CIVM image is consisted of a header file and bunch of files each representing a slice. AKAIK the header file resembles brucker image file format. Header ...
File Formats The following file formats are currently supported by SHIVA. Image volume files Analyze(tm) ( .img, .hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf ...
GUI RC is an XML file which describes what the SHIVA frame should look like. It is written in CookSwing. shiva.ShivaGUI class extends JFrame to have an setter for ...
How To Use the SHIVA Wiki We encourage you to change the contents of a SHIVA Wiki web page and to add your own web page topics that is what a Wiki is all about ...
Label Index File Format Label index files ( .lbl, .txt) are ascii files used by Duff and SHIVA. Each line contains information of the label id, color (optional), ...
Steps to create a plugin 1. Implement shiva.interfaces.ShivaPlugin . 1. Have public final static String PLUGIN DESCRIPTION "Some Description"; in the class. 1. Define ...
Steps adding a new file reader/writer 1. Implement shiva.io.ReaderWriter . 1. Create a shiva.io.DocFilter . The easiest way is using the following template. / file ...
STARTUP RC points to an XML list of plugins to be loaded. It should be noted that how SHIVA looks is mainly specified using plugins. It is written in CookXml. shiva ...
Server Protocols ArcIMS ArcXML Programmer's Reference Guide for ArcIMS 9.1 Neuroterrain Atlas Server Network Protocols Web Services Description Language (Axis Client ...
SHIVA can be configured to have completely different look and feels. 1. Configure startup resource file location. 1. Configure ToggleComamnds 1. Configure menu 1. ...
In shiva.Main class, there are two global class variables START RC and GUI RC which can be changed to point to different resource file locations before shiva.Main ...
Subversion Repository Structure The Subversion repository location is svn+ssh://cvs.loni.ucla.edu/cvs/map . The following is the directory structure under trunk/ ...
LONI Triangle Model Format This following description is obtained from LONI ShapeTools edu.ucla.loni.ccb.shapeio.tm.parser.TmAsciiShapeParser. The conventional suffix ...
UCF Format Universal Contour Files (UCF) is a format devised at LONI. It is an ascii based file in the following format: Header 384 256 200.000000 200.000000 200 ...
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...
This is a subscription service to be automatically notified by e-mail when topics change in this SHIVA web. This is a convenient service, so you do not have to come ...
SHIVA Web Preferences The following settings are web preferences of the SHIVA web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
TWiki's SHIVA web SCRIPTURL /view SCRIPTSUFFIX /SHIVA The SHIVA web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE{" TWIKIWEB ...
Statistics for SHIVA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 2139 0 0 399 ...
This is a subscription service to be automatically notified by e-mail when topics change in this SHIVA web. This is a convenient service, so you do not have to come back and check all the time if something has changed. To subscribe, please add a bullet with your TWiki.WikiName in alphabetical order to this list:
Main.CraigSchwartz
Format: TWiki handles entries in bullet list (<space><space><space>*) format containing the TWiki.WikiName of a user; a WikiName with e-mail address; or a TWikiGroup. Examples:
Main.FredBloggs
Main.FredBloggs - secondary@home.com
Main.EngineeringGroup
The first entry is the default form, the notification gets sent to the e-mail address specified in the user's home page. The second entry lists an alternative e-mail address. The third entry specifies a group, the notification gets sent to each member of the group.
Related topics: TWiki.WebChangesAlert, Main.TWikiUsers, TWiki.TWikiRegistration
The following settings are web preferences of the SHIVA web. These preferences overwrite the site-level preferences in TWiki.TWikiPreferences, and can be overwritten by user preferences (your personal topic, eg: Main.TWikiGuest in the Main web).
Preferences:
Set SKIN = dragon
TWiki.PatternSkin settings:
Set TWIKILAYOUTURL = /twiki/pub/TWiki/PatternSkin/layout.css
Set TWIKISTYLEURL = /twiki/pub/TWiki/PatternSkin/style.css
Set TWIKICOLORSURL = /twiki/pub/TWiki/PatternSkin/colors.css
CCB / Loni Customisations
Image, URL and alternate tooltip text of TWiki logo: (can be overwritten by web preferences)
Web specific background color: (Pick a lighter one of the TWiki.StandardColors)
Set WEBBGCOLOR = #D0D0D0
List this web in the TWiki.SiteMap:
If yes, set SITEMAPLIST to on, do not set NOSEARCHALL, and add the "what" and "use to..." description for the site map. Make sure to list only links that include the name of the web, e.g. SHIVA.Topic links.
Set SITEMAPLIST = on
Set SITEMAPWHAT = SHIVA project documentation
Set SITEMAPUSETO = document the SHIVA project
Exclude web from a web="all" search: (Set to on for hidden webs)
Set NOSEARCHALL =
Prevent automatic linking of WikiWords and acronyms (if set to on); link WikiWords (if empty); can be overwritten by web preferences:
Set NOAUTOLINK = on
Note: Use the [[...][...]] syntax to link topics in case you disabled WikiWord linking. The <noautolink> ... </noautolink> syntax can be used to prevents links within a block of text.
Default template for new topics and form(s) for this web:
WebTopicEditTemplate: Default template for new topics in this web. (Site-level is used if topic does not exist)
A preference is defined as: 6 spaces * Set NAME = value Example:
Set WEBBGCOLOR = #FFFFC0
Preferences are used as TWiki.TWikiVariables by enclosing the name in percent signs. Example:
When you write variable %WEBBGCOLOR% , it gets expanded to #D0D0D0 .
The sequential order of the preference settings is significant. Define preferences that use other preferences first, i.e. set WEBCOPYRIGHT before WIKIWEBMASTER since %WEBCOPYRIGHT% uses the %WIKIWEBMASTER% variable.
You can introduce new preferences variables and use them in your topics and templates. There is no need to change the TWiki engine (Perl scripts).
Related Topics:
TWiki.TWikiPreferences has site-level preferences.
Main.TWikiUsers has a list of user topics. User topics can have optional user preferences.
TWiki.TWikiVariables has a list of common %VARIABLES%.
TWiki.TWikiAccessControl explains how to restrict access by users or groups.
TWiki's SHIVA web
http://www.loni.ucla.edu/twiki/bin/view/SHIVA
The SHIVA web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World.en-usCopyright 2009 Laboratory of Neuro Imaging, UCLA.TWiki Administrator [webmaster@loni.ucla.edu]TWiki Administrator [webmaster@loni.ucla.edu]TWikiTWiki.SHIVASHIVA home.SHIVA
http://www.loni.ucla.edu/twiki/bin/view/SHIVA
WebStatistics
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/WebStatistics?t=2009-11-16T12:33Z
Statistics for SHIVA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 2139 0 0 399 ... (last changed by guest)2009-11-16T12:33Zguest1.1230updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebStatisticshttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebStatisticsFileFormats
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/FileFormats?t=2007-04-12T20:05Z
File Formats The following file formats are currently supported by SHIVA. Image volume files Analyze(tm) ( .img, .hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf ... (last changed by HengYuan)2007-04-12T20:05Zheng1.8updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/FileFormatshttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/FileFormatsSubversionRepositoryStructure
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/SubversionRepositoryStructure?t=2007-04-11T23:06Z
Subversion Repository Structure The Subversion repository location is svn+ssh://cvs.loni.ucla.edu/cvs/map . The following is the directory structure under trunk/ ... (last changed by HengYuan)2007-04-11T23:06Zheng1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/SubversionRepositoryStructurehttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/SubversionRepositoryStructureDOC
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/DOC?t=2007-04-05T18:20Z
Shiva Developer Documentation $ Repository Structure : svn+ssh://cvs.loni.ucla.edu/cvs/map $ Plugin Documentation : For developers who wish to write plugins for SHIVA ... (last changed by HengYuan)2007-04-05T18:20Zheng1.6updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/DOChttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/DOCWebHome
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/WebHome?t=2007-03-13T18:16Z
SHIVA $ Manual : http://www.loni.ucla.edu/download/SHIVA/SHIVA MAP.pdf $ Download : Release version $ Developer Documentation : SHIVA documentation for developers ... (last changed by HengYuan)2007-03-13T18:16Zheng1.20updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebHomehttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebHomeServerProtocols
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/ServerProtocols?t=2006-11-11T05:09Z
Server Protocols ArcIMS ArcXML Programmer's Reference Guide for ArcIMS 9.1 Neuroterrain Atlas Server Network Protocols Web Services Description Language (Axis Client ... (last changed by HengYuan)2006-11-11T05:09Zheng1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/ServerProtocolshttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/ServerProtocolsUCFFormat
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/UCFFormat?t=2006-07-07T22:53Z
UCF Format Universal Contour Files (UCF) is a format devised at LONI. It is an ascii based file in the following format: Header 384 256 200.000000 200.000000 200 ... (last changed by HengYuan)2006-07-07T22:53Zheng1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/UCFFormathttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/UCFFormatTMFormat
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/TMFormat?t=2006-07-07T19:27Z
LONI Triangle Model Format This following description is obtained from LONI ShapeTools edu.ucla.loni.ccb.shapeio.tm.parser.TmAsciiShapeParser. The conventional suffix ... (last changed by CraigSchwartz)2006-07-07T19:27Zcraig1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/TMFormathttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/TMFormatLabelIndexFileFormat
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/LabelIndexFileFormat?t=2006-07-06T23:19Z
Label Index File Format Label index files ( .lbl, .txt) are ascii files used by Duff and SHIVA. Each line contains information of the label id, color (optional), ... (last changed by HengYuan)2006-07-06T23:19Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/LabelIndexFileFormathttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/LabelIndexFileFormatWebPreferences
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/WebPreferences?t=2006-06-21T06:43Z
SHIVA Web Preferences The following settings are web preferences of the SHIVA web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ... (last changed by HengYuan)2006-06-21T06:43Zheng1.22updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebPreferenceshttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/WebPreferencesCIVMFormat
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/CIVMFormat?t=2006-06-21T06:36Z
CIVM Format A CIVM image is consisted of a header file and bunch of files each representing a slice. AKAIK the header file resembles brucker image file format. Header ... (last changed by HengYuan)2006-06-21T06:36Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/CIVMFormathttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/CIVMFormatGUI_RC
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/GUI_RC?t=2006-01-06T23:25Z
GUI RC is an XML file which describes what the SHIVA frame should look like. It is written in CookSwing. shiva.ShivaGUI class extends JFrame to have an setter for ... (last changed by HengYuan)2006-01-06T23:25Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/GUI_RChttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/GUI_RCSTART_RC
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/START_RC?t=2006-01-06T23:24Z
STARTUP RC points to an XML list of plugins to be loaded. It should be noted that how SHIVA looks is mainly specified using plugins. It is written in CookXml. shiva ... (last changed by HengYuan)2006-01-06T23:24Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/START_RChttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/START_RCStartConfigure
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/StartConfigure?t=2006-01-06T23:15Z
In shiva.Main class, there are two global class variables START RC and GUI RC which can be changed to point to different resource file locations before shiva.Main ... (last changed by HengYuan)2006-01-06T23:15Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/StartConfigurehttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/StartConfigureShivaConfiguration
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/ShivaConfiguration?t=2006-01-06T23:05Z
SHIVA can be configured to have completely different look and feels. 1. Configure startup resource file location. 1. Configure ToggleComamnds 1. Configure menu 1. ... (last changed by HengYuan)2006-01-06T23:05Zheng1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/ShivaConfigurationhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/ShivaConfigurationPlugin
http://www.loni.ucla.edu/twiki/bin/view/SHIVA/Plugin?t=2006-01-06T22:55Z
Steps to create a plugin 1. Implement shiva.interfaces.ShivaPlugin . 1. Have public final static String PLUGIN DESCRIPTION "Some Description"; in the class. 1. Define ... (last changed by HengYuan)2006-01-06T22:55Zheng1.3updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/Pluginhttp://www.loni.ucla.edu/twiki/bin/rdiff/SHIVA/Plugin
