VolViewer Scripting in more detail - Revision history

AndrewBangham at 13:19, 11 April 2012

2012-04-11T13:19:00Z

← Older revision		Revision as of 14:19, 11 April 2012
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	\|- valign="top"		\|- 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"\|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.'''		\|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

AndrewBangham at 09:37, 3 March 2012

2012-03-03T09:37:27Z

← Older revision		Revision as of 10:37, 3 March 2012
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	\|- valign="top"		\|- 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"\|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.'''		\|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.'''
	\|}		\|}
	1) '''Install''' VolViewer		1) '''Install''' VolViewer

AndrewBangham at 09:22, 2 March 2012

2012-03-02T09:22:39Z

← Older revision		Revision as of 10:22, 2 March 2012
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	\|- valign="top"		\|- 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"\|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.		\|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.'''
	\|}		\|}
	1) '''Install''' VolViewer		1) '''Install''' VolViewer
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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, 'PathTo','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

AndrewBangham at 21:30, 1 March 2012

2012-03-01T21:30:16Z

← Older revision		Revision as of 22:30, 1 March 2012
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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]]

	=<span style="color: Navy">VolViewer scripting and accessing VolViewer from Matlab</span>=		=<span style="color: Navy">VolViewer scripting and accessing VolViewer from Matlab</span>=

AndrewBangham at 21:29, 1 March 2012

2012-03-01T21:29:01Z

← Older revision		Revision as of 22:29, 1 March 2012
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	{\| border="0" cellpadding="5" cellspacing="3"		{\| border="0" cellpadding="5" cellspacing="3"
	\|- valign="top"		\|- valign="top"
	\|width="300pt"\|There is a VolViewer Matlab class library: launching Volviewer~~, displaying~~ 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 ~~points-lines-planes~~.		\|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.		\|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.
	\|}		\|}

AndrewBangham at 21:26, 1 March 2012

2012-03-01T21:26:42Z

← Older revision		Revision as of 22:26, 1 March 2012
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	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 Volviewer, displaying 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 points-lines-planes.
			\|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.
			\|}
	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'''.

AndrewBangham at 19:49, 1 March 2012

2012-03-01T19:49:12Z

← Older revision		Revision as of 20:49, 1 March 2012
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	*[[VolViewer commands by function\|Table of VolViewer commands by function]]		*[[VolViewer commands by function\|Table of VolViewer commands by function]]

	=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===

AndrewBangham at 19:38, 1 March 2012

2012-03-01T19:38:36Z

← Older revision		Revision as of 20:38, 1 March 2012
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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('VolViewerObject',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()')

AndrewBangham at 17:23, 1 March 2012

2012-03-01T17:23:02Z

← Older revision		Revision as of 18:23, 1 March 2012
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	[http://rico-coen.jic.ac.uk/LabGuide/index.php?title=MSR3_File_Specification 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.<br>		[http://rico-coen.jic.ac.uk/LabGuide/index.php?title=MSR3_File_Specification 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.<br>
	[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI VolViewerScriptsAPI] The VolViewerScriptsAPI enables external applications, such as the AAMToolbox, to exploit VolViewer.		[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI VolViewerScriptsAPI] The VolViewerScriptsAPI enables external applications, such as the AAMToolbox, to exploit VolViewer.
	*[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#set_watchfile ~~'''Launching~~ VolViewer~~''' so that it '''follows~~ commands~~''' in a watchfile~~ ]		*[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#set_watchfile List of VolViewer commands]
	*~~Contents~~ of ~~watchfile~~		*[[VolViewer commands by function\|Table of VolViewer commands by function]]
	**[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#open_image_stack Opening an''' image stack''' ]
	**[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI#open_msr Opening an '''MSR (results) file''' ]~~<br><br>~~

	=VolViewer scripting and accessing VolViewer from Matlab=		=VolViewer scripting and accessing VolViewer from Matlab=

AndrewBangham at 17:55, 29 February 2012

2012-02-29T17:55:11Z

← Older revision		Revision as of 18:55, 29 February 2012
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	*For example, in 'C:\VolViewer_x64'. This is the '''PathToVolViewer'''.		*For example, in 'C:\VolViewer_x64'. This is the '''PathToVolViewer'''.
	2) '''Launch VolViewer''' from Matlab		2) '''Launch VolViewer''' from Matlab
	*~~Assuming temporary~~ data files on paths are ~~to be~~ saved in ~~PathToVolViewer~~		*Temporary data files on paths are saved in '...\DArT_Toolshed\ToolBag\VolViewerAPI\CLASSFILES'<br>
			This should mean that once VolViewer is installed on a computer - the system will remember where to find everything without having to respecify paths.<br>
	VO=VolViewer(1,'D:\VolViewer_x64','D:\VolViewer_x64')		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:		creates a VolViewer object - which, because there is no semicolon at the end, is displayed as: