VolViewerUserManual - Revision history

JeromeAvondo at 10:25, 27 March 2012

2012-03-27T10:25:24Z

← Older revision		Revision as of 11:25, 27 March 2012
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	==Loading Data==		==Loading Data==

	To load data into the viewer, this can be achieved by one of ~~four~~ mechanisms:		To load data into the viewer, this can be achieved by one of three mechanisms:

	* Using the '''FILE''' dropdown menu.		* Using the '''FILE''' dropdown menu.
	* Using the '''Drag&Drop''' event.		* Using the '''Drag&Drop''' event.
	* ~~Setting a default file to load in~~ the '''~~settings.ini''' file~~		* Using the '''scripting interface'''
	* Parsing a directory name as a '''command line parameter'''

	===The File Dropdown Menu===		===The File Dropdown Menu===
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	The Drag&Drop accepts drops of either; a single image file in you stack, a .dat file or a .raw file.		The Drag&Drop accepts drops of either; a single image file in you stack, a .dat file or a .raw file.

	===~~The Settings.ini file~~===		===Scripting Interface===

	~~The viewer also supports loading of data via the settings~~.~~ini file~~. ~~The settings~~.~~ini file can be found in the root of the viewer folder~~. ~~The settings~~.~~ini file contains many parameters to control the default behaviour of the viewer, all parameters have comments explaining what they do.~~		See [http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI this] site for more information.

	With regards to data loading, you are able to setup a file the viewer will load automatically every time you launch it. This is particularly useful if you plan on using the viewer to display data during a talk/~~presentation.~~

	~~The entry you need to modify in the settings.ini file is:~~

	~~file_default_filename=""~~

	~~You can specify the default file to load inside the "" marks. This can be an absolute file path, ie: "C:\MyStuff\SomeDirName\Data\CylindersRGB.dat" or a relative file path ie: "Data\CylindersRGB.dat"~~

	~~===Command Line Parameter===~~

	~~It is also possible to parse a file as a command line parameter for the viewer to load. For example under windows you may want to create a .bat file and call the viewer as follows:~~

	~~VolViewer voldir="%CD%\Data\seedling\Slice000.png"~~

	~~This will load the image stack who's first file is Slice000.png. One useful tip~~ for ~~windows users is that the %CD% command gets the path of your current working directory~~.

	'''*Exercise 1:'''		'''*Exercise 1:'''

JeromeAvondo at 13:41, 5 March 2012

2012-03-05T13:41:56Z

← Older revision		Revision as of 14:41, 5 March 2012
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	Use the visual bookmarks to save two different views of you volume, and toggle between them by double clicking the thumbnails.		Use the visual bookmarks to save two different views of you volume, and toggle between them by double clicking the thumbnails.
	Use the movie icon to save the frames for a movie		Use the movie icon to save the frames for a movie

	~~=Command Line Arguments=~~

	~~This page contains details about running VolViewer from the command line.~~

	*[[VolViewerCommandLineArguments\|Command Line Arguments]]

JeromeAvondo at 15:59, 8 November 2011

2011-11-08T15:59:52Z

@@ Line 153: / Line 153: @@
 =Command Line Arguments=
-Below is a list of command line arguments supported by the VolViewer application:
+This page contains details about running VolViewer from the command line.
-==General==
+*[[VolViewerCommandLineArguments|Command Line Arguments]]

JeromeAvondo at 11:49, 8 June 2011

2011-06-08T11:49:03Z

← Older revision		Revision as of 12:49, 8 June 2011
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	render=1 //Creates a png of the volume in the root folder		render=1 //Creates a png of the volume in the root folder

			==Watchfile==

			watchfile=XXXXX //A path to a file to watch

			This allows the viewer to be setup to watch a specific ascii file. The file can then contain any of the command line arguments and the program will react to any modification done to this file while launched. This is a simple way to script or interact with the viewer from an external application.

	==OMERO==		==OMERO==

JeromeAvondo at 11:46, 8 June 2011

2011-06-08T11:46:28Z

← Older revision		Revision as of 12:46, 8 June 2011
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	==General==		==General==
			voldir=XXXXX //To specify a local directory containing an image stack
			msr=XXXXX //To specify a local MSR file (measurement geometry object) to load
			tfunc=XXXXX //To specilfy a local TFN file (transfer function) to load
			slc=XXXXX //To specify a local SLC file (clipping planes) to load
			auto_close=1 //Tell the application to automatically close once all command line arguments are executed
			auto_hide=1 //Tell the application to hide and run in a gui less mode

	~~To specify a local directory containing an image stack~~		==Movies==
	~~voldir~~

	~~To specify a local MSR file (measurement geometry object) to load~~		movie_rotate(sampling, savefolder, x, y, z, angle) //To create a rotation movie from an image
	~~msr~~

	~~To specilfy a local TFN file (transfer function) to load~~
	~~tfunc~~

	~~To specify a local SLC file (clipping planes) to load~~
	~~slc~~

	~~To create a rotation movie from an image~~
	movie_rotate(sampling, savefolder, x, y, z, angle)

	*sampling: is the angle step size		*sampling: is the angle step size
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	*angle: the angle to rotate about		*angle: the angle to rotate about

	~~Tell the application to automatically close once all command line arguments are executed~~		movie_rock(sampling, savefolder, angle) //To create a rock movie from an image
	~~auto_close~~

	~~Tell~~ the ~~application~~ to ~~hide and run in a gui less mode~~		*sampling: is the angle step size
	~~auto_hide~~		*savefolder: is the folder we wish to save frames to
			*angle: the angle to rock by (+angle to -angle)

			==Projections==

			set_view( x, y, z) //Set the default view of the volume as euler angles
			render=1 //Creates a png of the volume in the root folder

	==OMERO==		==OMERO==

	To specify the url of an omero server		omero_server=XXXXX //To specify the url of an omero server
	~~omero_server~~		omero_username=XXXXX //To specify a username to connect to the omero server
			omero_password=XXXXX //To specify the password for the given username to connect to the omero server
	To specify a username to connect to the omero server		omero_sessionid=XXXXX //To specify a session id to join on the omero server
	~~omero_username~~		omero_port=XXXXX //To specify the port of the omero server
			omero_imageid=XXXXX //To specify the image id on the omero server we wish to load in volviewer
	To specify the password for the given username to connect to the omero server
	~~omero_password~~

	To specify a session id to join on the omero server
	~~omero_sessionid~~

	To specify the port of the omero server
	~~omero_port~~

	To specify the image id on the omero server we wish to load in volviewer
	~~omero_imageid~~

JeromeAvondo at 11:27, 8 June 2011

2011-06-08T11:27:23Z

← Older revision		Revision as of 12:27, 8 June 2011
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	===The Settings.ini file===		===The Settings.ini file===

	The viewer also supports loading of data via the settings.ini file. The settings.ini file can be found in the root of the viewer folder.		The viewer also supports loading of data via the settings.ini file. The settings.ini file can be found in the root of the viewer folder. The settings.ini file contains many parameters to control the default behaviour of the viewer, all parameters have comments explaining what they do.

	~~This facility allows~~ you to setup a file the viewer will load automatically every time you launch it. This is particularly useful if you plan on using the viewer to display data during a talk~~. See section '''BLAH''' for more details about using the viewer with a~~ presentation.		With regards to data loading, you are able to setup a file the viewer will load automatically every time you launch it. This is particularly useful if you plan on using the viewer to display data during a talk/presentation.

	The entry you need to modify in the settings.ini file is:		The entry you need to modify in the settings.ini file is:
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	===Command Line Parameter===		===Command Line Parameter===

	It is ~~aslo~~ possible to parse a file as a command line parameter for the viewer to load. For example under windows you may want to create a .bat file and call the viewer as follows:		It is also possible to parse a file as a command line parameter for the viewer to load. For example under windows you may want to create a .bat file and call the viewer as follows:

	VolViewer voldir="%CD%\Data\seedling\Slice000.png"		VolViewer voldir="%CD%\Data\seedling\Slice000.png"

JeromeAvondo at 10:59, 8 June 2011

2011-06-08T10:59:12Z

← Older revision		Revision as of 11:59, 8 June 2011
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	[[Image:VolViewerSettings.png]]		[[Image:VolViewerSettings.png]]

	* '''visual bookmarks icon''': Allows you to save an orientation and ~~clip~~ state of your volume as a bookmark		* '''visual bookmarks icon''': Allows you to save an orientation, clip state and transfer function state of your volume as a bookmark
	* '''movie icon''': Allows you to save movie frames for your volume.		* '''movie icon''': Allows you to save movie frames for your volume.
	* '''lighting icon''': Allows you to apply lighting to your volume data.		* '''lighting icon''': Allows you to apply lighting to your volume data.

JeromeAvondo at 10:58, 8 June 2011

2011-06-08T10:58:00Z

← Older revision		Revision as of 11:58, 8 June 2011
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	This will load the image stack who's first file is Slice000.png. One useful tip for windows users is that the %CD% command gets the path of your current working directory.		This will load the image stack who's first file is Slice000.png. One useful tip for windows users is that the %CD% command gets the path of your current working directory.

			'''*Exercise 1:'''
			Try loading a volume by downloading the sample volume [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip here] and using the drag and drop method.

	=Saving Volume Data=		=Saving Volume Data=

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	(NB) Currently the centre of rotation is not affected by the translation, and the volume will still rotate about it's centre even after translation. The ability to change this behaviour will be introduced in a future release.		(NB) Currently the centre of rotation is not affected by the translation, and the volume will still rotate about it's centre even after translation. The ability to change this behaviour will be introduced in a future release.

			'''*Exercise 2:'''
			Try rotating and zooming the volume.

	=Toolbars=		=Toolbars=

JeromeAvondo at 10:53, 8 June 2011

2011-06-08T10:53:49Z

@@ Line 59: / Line 59: @@
 You can specify the default file to load inside the "" marks. This can be an absolute file path, ie: "C:\MyStuff\SomeDirName\Data\CylindersRGB.dat" or a relative file path ie: "Data\CylindersRGB.dat"
-==Toolbars==
+===Command Line Parameter===
-===Viewing===
+==Viewing==
 [[Image:VolViewerMenuTools.PNG]]
@@ Line 86: / Line 116: @@
   Use the on/off menu to toggle the axis
-===Tools===
+==Tools==
 [[Image:VolViewerTools.png]]
@@ Line 102: / Line 132: @@
   Open the filter widget to apply some Gaussian smoothing to your volume.
-===Settings===
+==Settings==
 [[Image:VolViewerSettings.png]]
@@ Line 114: / Line 144: @@
   Use the visual bookmarks to save two different views of you volume, and toggle between them by double clicking the thumbnails.
   Use the movie icon to save the frames for a movie
 =Command Line Arguments=

JeromeAvondo at 10:52, 8 June 2011

2011-06-08T10:52:38Z

← Older revision		Revision as of 11:52, 8 June 2011
Line 58:		Line 58:

	You can specify the default file to load inside the "" marks. This can be an absolute file path, ie: "C:\MyStuff\SomeDirName\Data\CylindersRGB.dat" or a relative file path ie: "Data\CylindersRGB.dat"		You can specify the default file to load inside the "" marks. This can be an absolute file path, ie: "C:\MyStuff\SomeDirName\Data\CylindersRGB.dat" or a relative file path ie: "Data\CylindersRGB.dat"

			==Toolbars==

			===Viewing===

			[[Image:VolViewerMenuTools.PNG]]

			This toolbar allows you to control various viewing options.

			* '''I''': Toggles the volume greyscale channel
			* '''R''': Toggles the volume red channel
			* '''G''': Toggles the volume green channel
			* '''B''': Toggles the volume blue channel
			* '''S''': Toggles the iso-surface (if computed)
			* '''mip''': Toggles the Maximum Intensity Projection mode
			* '''BG''': Allows you to specify the background colour
			* '''3D''': Allows you to enable stereo rendering (requires a 3D screen)
			* '''camera icon''': Takes a screen grab of the current view and prompts you with a save file dialogue.
			* '''qual''': Various viewing quality presets.
			* '''view''': Various view direction presets.
			* '''on/off''': Various viewing toggles.

			'''*Exercise 3:'''
			Enable/Disable the red channel
			Toggle the MIP rendering mode
			Use the view menu to view your data from the LEFT orientation.
			Use the on/off menu to toggle the axis

			===Tools===

			[[Image:VolViewerTools.png]]

			* '''graph icon''': Brings up the transfer function widget.
			* '''crop icon''': Brings up the crop widget.
			* '''clipping plane icon''': Brings up the clipping widget.
			* '''measure icon''': Brings up the measure widget.
			* '''surface icon''': Brings up the iso-surface widget.
			* '''filter icon''': Brings up the filter widget.

			'''*Exercise 4:'''
			Open the transfer function widget and adjust the opacity and threshold the volume.
			Open the clipping widget to clip the volume
			Open the filter widget to apply some Gaussian smoothing to your volume.

			===Settings===

			[[Image:VolViewerSettings.png]]

			* '''visual bookmarks icon''': Allows you to save an orientation and clip state of your volume as a bookmark
			* '''movie icon''': Allows you to save movie frames for your volume.
			* '''lighting icon''': Allows you to apply lighting to your volume data.
			* '''settings icon''': Allows you to control various performance and quality setting

			'''*Exercise 5:'''
			Use the visual bookmarks to save two different views of you volume, and toggle between them by double clicking the thumbnails.
			Use the movie icon to save the frames for a movie

	===Command Line Parameter===		===Command Line Parameter===