Difference between revisions of "VolViewer Scripting in more detail"

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*[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#set_watchfile List of VolViewer commands]
 
*[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#set_watchfile List of VolViewer commands]
 
*[[VolViewer commands by function|Table of VolViewer commands by function]]
 
*[[VolViewer commands by function|Table of VolViewer commands by function]]
 +
*[[VolViewer msr file specification|VolViewer saves spatial data in msr files]]
  
=VolViewer scripting and accessing VolViewer from Matlab=
+
=<span style="color: Navy">VolViewer scripting and accessing VolViewer from Matlab</span>=
==VolViewer scripting==
+
==<span style="color: Navy">VolViewer scripting</span>==
 
A script is a limited form of program - a list of commands. In this case the commands (http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI see VolViewerScriptsAPI]) cover most of the operations that you would usually do interactively. On Windows, VolViewer is an exe file that can ''either'' be<br>
 
A script is a limited form of program - a list of commands. In this case the commands (http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI see VolViewerScriptsAPI]) cover most of the operations that you would usually do interactively. On Windows, VolViewer is an exe file that can ''either'' be<br>
 
'''interactive''', i.e. launched by clicking its icon or from the command prompt using the command<br>
 
'''interactive''', i.e. launched by clicking its icon or from the command prompt using the command<br>
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It is '''not practical to script''' VolViewer using these commands manually. It is better to''' use VolViewer as a tool''' that is controlled through a library of commands in, for example, Matlab. Or, when running VolViewer on the server side of a server/client session where the user is interacting with VolViewer through a client web page.
 
It is '''not practical to script''' VolViewer using these commands manually. It is better to''' use VolViewer as a tool''' that is controlled through a library of commands in, for example, Matlab. Or, when running VolViewer on the server side of a server/client session where the user is interacting with VolViewer through a client web page.
==Matlab to Volviewer==
+
==<span style="color: Navy">Matlab to Volviewer</span>==
 
The DArT_Toolbox contains a [[VolViewer access from Matlab| library of functions]] for using and controlling VolViewer from Matlab.
 
The DArT_Toolbox contains a [[VolViewer access from Matlab| library of functions]] for using and controlling VolViewer from Matlab.
 
===Accessing VolViewer from Matlab===
 
===Accessing VolViewer from Matlab===
 +
 +
{| border="0" cellpadding="5" cellspacing="3"
 +
|- valign="top"
 +
|width="300pt"|There is a VolViewer Matlab class library: launching and controlling Volviewer for the display of 3D volume images (the display window has zoom, rotate, etc.). On computers with an appropriate graphics card and stereo display VolViewer can be used to display volume images and graphics objects from msr files.
 +
|width="300pt"|[[Image:VolViewer_Monitor_Illustration.jpg|400px|right|VolViewer as a viewport for Matlab]]<br>VolViewer viewport without its usual menu-bars and under control of a Matlab program. It shows endogenous fluorescence signal from a young leaf that has been annotated with a series of points set on the mid point of trichomes and joined by lines. These points characterise the 3D shape of the leaf and are stored in an MSR text file.<br>To manipulate the view: left-click-drag '''rotate''', middle-click-drag '''translate''', right-click-drag '''zoom.''' <br><br>
 +
This image was created using steps 2, 3, and 4 below.
 +
|}
 
1) '''Install''' VolViewer
 
1) '''Install''' VolViewer
 
*For example, in 'C:\VolViewer_x64'. This is the '''PathToVolViewer'''.
 
*For example, in 'C:\VolViewer_x64'. This is the '''PathToVolViewer'''.
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           PathToWatchFile: D:\VolViewer_x64  
 
           PathToWatchFile: D:\VolViewer_x64  
 
           WatchFileNumber:    1.00000  
 
           WatchFileNumber:    1.00000  
        PathToImageStack:  
+
                      PathTo:  
 
           imageFilenames:  
 
           imageFilenames:  
 
               msrFilename:  
 
               msrFilename:  
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3) '''Display an image''' stack in VolViewer
 
3) '''Display an image''' stack in VolViewer
 
*The key step is to notify VolViewer where to find the images by putting a command into WatchFile1.txt. This is done automatically with the following
 
*The key step is to notify VolViewer where to find the images by putting a command into WatchFile1.txt. This is done automatically with the following
   VO=imshowVOL('VolViewerObject',VO, 'PathToImageStack','D:\Shape_T1_only\Image_data\11to14DFS\1554')
+
   VO=imshowVOL(VO, 'PathTo','D:\Shape_T1_only\Image_data\11to14DFS\1554')
 
In this case the image stack is in the directory 'D:\Shape_T1_only\Image_data\11to14DFS\1554'. Notice, that VOL has been updated
 
In this case the image stack is in the directory 'D:\Shape_T1_only\Image_data\11to14DFS\1554'. Notice, that VOL has been updated
 
  >> VOL
 
  >> VOL
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           PathToWatchFile: D:\VolViewer_x64  
 
           PathToWatchFile: D:\VolViewer_x64  
 
           WatchFileNumber:    1.00000  
 
           WatchFileNumber:    1.00000  
        PathToImageStack: D:\Shape_T1_only\Image_data\11to14DFS\1554  
+
          PathTo: D:\Shape_T1_only\Image_data\11to14DFS\1554  
 
           imageFilenames:  
 
           imageFilenames:  
 
               msrFilename:  
 
               msrFilename:  
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               objFilename:  
 
               objFilename:  
 
                 Commands:  
 
                 Commands:  
4) '''Display an MSR''' (results) file
+
4) '''Display an MSR''' (results: points/lines/planes) file
 
*Put the command into WatchFile1.txt using
 
*Put the command into WatchFile1.txt using
 +
  VO=imshowVOL(VO,'PathTo','D:\Shape_T1_only\Image_data\11to14DFS\1554','msrFilename','1554_T1_Shape.msr')
 +
To hide the image
 +
VO=commandsVOL(VO,'set_channels(0,0,0)');
 +
To see the image again
 +
VO=commandsVOL(VO,'set_channels(1,1,1)');
 +
To clear the MSR points/lines/planes
 +
VO=commandsVOL(VO,'set_clear_all_MSR()')

Latest revision as of 14:19, 11 April 2012

Back to VolViewer overview

See also

MSR file specification MSR file specification (MSR stands for Measure.) MSR files describe 3D objects and are used to pass data between the 3D BanghamLab toolboxes: VolViewer, GFtbox and AAMToolbox.
VolViewerScriptsAPI The VolViewerScriptsAPI enables external applications, such as the AAMToolbox, to exploit VolViewer.

VolViewer scripting and accessing VolViewer from Matlab

VolViewer scripting

A script is a limited form of program - a list of commands. In this case the commands (http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI see VolViewerScriptsAPI]) cover most of the operations that you would usually do interactively. On Windows, VolViewer is an exe file that can either be
interactive, i.e. launched by clicking its icon or from the command prompt using the command

VolViewer.exe

or scripted. In which case the operations (commands) are stored in a script file. In which case VolViewer is launched with

VolViewer set_watchfile('file.txt')

where file.txt contains the commands. For example, if VolViewer is to be a viewing tool for an external program, e.g. a Matlab program, then the file.txt could contain

open_image_stack(0, 'E:\VOLUME DATA\ScanID1934_Leaf1\')

where ScanID1934_Leaf1 is a directory containing a stack of images. VolViewer will automatically load and display these images as soon as it finds that the watchfile has been updated.

Other examples

It is not practical to script VolViewer using these commands manually. It is better to use VolViewer as a tool that is controlled through a library of commands in, for example, Matlab. Or, when running VolViewer on the server side of a server/client session where the user is interacting with VolViewer through a client web page.

Matlab to Volviewer

The DArT_Toolbox contains a library of functions for using and controlling VolViewer from Matlab.

Accessing VolViewer from Matlab

There is a VolViewer Matlab class library: launching and controlling Volviewer for the display of 3D volume images (the display window has zoom, rotate, etc.). On computers with an appropriate graphics card and stereo display VolViewer can be used to display volume images and graphics objects from msr files.
VolViewer as a viewport for Matlab

VolViewer viewport without its usual menu-bars and under control of a Matlab program. It shows endogenous fluorescence signal from a young leaf that has been annotated with a series of points set on the mid point of trichomes and joined by lines. These points characterise the 3D shape of the leaf and are stored in an MSR text file.
To manipulate the view: left-click-drag rotate, middle-click-drag translate, right-click-drag zoom.

This image was created using steps 2, 3, and 4 below.

1) Install VolViewer

  • For example, in 'C:\VolViewer_x64'. This is the PathToVolViewer.

2) Launch VolViewer from Matlab

  • Temporary data files on paths are saved in '...\DArT_Toolshed\ToolBag\VolViewerAPI\CLASSFILES'

This should mean that once VolViewer is installed on a computer - the system will remember where to find everything without having to respecify paths.

 VO=VolViewer(1,'D:\VolViewer_x64','D:\VolViewer_x64')

creates a VolViewer object - which, because there is no semicolon at the end, is displayed as:

         PathToVolViewer: D:\VolViewer_x64 
         PathToWatchFile: D:\VolViewer_x64 
         WatchFileNumber:    1.00000 
                     PathTo: 
          imageFilenames: 
             msrFilename: 
             tfnFilename: 
             slcFilename: 
             vvrFilename: 
             objFilename: 
                Commands: 

Notice that the paths have been filled in and that this is the first copy of VolViewer (WatchFileNumber is 1).
3) Display an image stack in VolViewer

  • The key step is to notify VolViewer where to find the images by putting a command into WatchFile1.txt. This is done automatically with the following
 VO=imshowVOL(VO, 'PathTo','D:\Shape_T1_only\Image_data\11to14DFS\1554')

In this case the image stack is in the directory 'D:\Shape_T1_only\Image_data\11to14DFS\1554'. Notice, that VOL has been updated

>> VOL
         PathToVolViewer: D:\VolViewer_x64 
         PathToWatchFile: D:\VolViewer_x64 
         WatchFileNumber:    1.00000 
         PathTo: D:\Shape_T1_only\Image_data\11to14DFS\1554 
          imageFilenames: 
             msrFilename: 
             tfnFilename: 
             slcFilename: 
             vvrFilename: 
             objFilename: 
                Commands: 

4) Display an MSR (results: points/lines/planes) file

  • Put the command into WatchFile1.txt using
 VO=imshowVOL(VO,'PathTo','D:\Shape_T1_only\Image_data\11to14DFS\1554','msrFilename','1554_T1_Shape.msr')

To hide the image

VO=commandsVOL(VO,'set_channels(0,0,0)');

To see the image again

VO=commandsVOL(VO,'set_channels(1,1,1)');

To clear the MSR points/lines/planes

VO=commandsVOL(VO,'set_clear_all_MSR()')