Tutorial on ParaView - Revision history

Enodwell: Deleting, Replaced with Using ParaView page

2010-09-15T17:04:08Z

Deleting, Replaced with Using ParaView page

← Older revision		Revision as of 17:04, 15 September 2010
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	~~==Purpose==~~

	~~This is a tutorial that will demonstrate how to use ParaView to examine AIM file.~~

	~~This tutorial was done on OS-X, but should be essentially similar for Windows or Linux, with some minor differences.~~

	~~==Prerequisites==~~

	You'll need ParaView built with the bonelab extensions. You should be able to find in on the server mike . On OS-X, click on this link: afp://mike.kin.ucalgary.ca/Data0/Software/ParaView_with_extensions/ . On Windows, enter \\mike\Data0\Software\ParaView_with_extensions in an Explorer address bar. In either case, you'll need to be on the university network.

	~~You can find the data file used in this tutorial, SAWBONE51_BC_CSTR.AIM on the server mike at /Data0/Tutorials/ParaView_and_vtkski .~~

	~~==Background Material==~~

	*There is a book on ParaView floating around the lab that will be useful if you want to learn more.

	~~==Model Overview==~~

	~~The file SAWBONE51_BC_CSTR.AIM contains a scan of bone with a screw in it. The data has been processed so that the screw has material type 127, and the bone 126.~~

	~~==Examining the AIM file with ParaView==~~

	Open ParaView. Click File->Open, and browse to SAWBONE51_BC_CSTR.AIM . Click OK. Our custom version of ParaView with bonelab extensions is able to open AIMs, but it may inquire about the file type, as shown in the following dialog. Just select "AIM File" and proceed.

	~~[[Image:Open_data_with.png]]~~

	~~Click the Apply button in the Object Inspector. You should see the following, which is so far only the outline of the bounds of the data.~~

	~~[[Image:Paraview_open_aim.png]]~~

	In order to convert this data, which is a 3D matrix with position information (called an "Image" in VTK and ParaView) to something that can be rendered, a number of different filters can be used. We are going to use the Threshold filter. You can find this at the menu item Filters->Common->Threshold . There is also a button for it on the toolbar. Click it. Now in the Object Inspector, set the Lower Threshold to 1. (If you keep the default value of 0, you just end up rendering a box with the size of the bounds of the data.) Now hit Apply.

	~~[[Image:ParaView_Threshold_AIM.png]]~~

	We still don't see much! Why not? Well, this is such a large data set, that ParaView has decided to render just the outline for now, to save time. To see the object, go to the Display tab of the Object Inspector, scroll down to the Style box, and change the Representation to Surface. Voila!

	~~[[Image:ParaView_Change_Representation.png]]~~

	You can click and drag on the image to rotate it. You can also right-click and hold down shift and control, with different effects. We are now going to show only the screw, which can be identified as material 127. Make sure the Threshold filter is selected, then select the Properties tab in the Object Inspector, and set both Lower and Upper Threshold to 127, as shown. Also in the Display tab, I have scrolled to the Color box, and clicked on "Set Solid Color" to make the screw blue.

	~~[[Image:ParaView_Blue_Screw.png]]~~

	Now we are going to show the bone as well. Make sure that SAWBONES51_BC_CSTR.AIM is selected in the Pipeline browser, then click on the Threshold button to create a second Threshold filter. Change its Lower and Upper Thresholds to 126, then click Apply.

	~~[[Image:ParaView_screw_and_bone.png]]~~

Enodwell at 19:56, 21 June 2010

2010-06-21T19:56:33Z

← Older revision		Revision as of 19:56, 21 June 2010
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	==Prerequisites==		==Prerequisites==

	You'll need ParaView built with the bonelab extensions. You should be able to find in on the server mike . On OS-X, click on this link: [[afp://mike.kin.ucalgary.ca/Data0/Software/ParaView_with_extensions/]] . On Windows, enter \\mike\Data0\Software\ParaView_with_extensions in an Explorer address bar. In either case, you'll need to be on the university network.		You'll need ParaView built with the bonelab extensions. You should be able to find in on the server mike . On OS-X, click on this link: afp://mike.kin.ucalgary.ca/Data0/Software/ParaView_with_extensions/ . On Windows, enter \\mike\Data0\Software\ParaView_with_extensions in an Explorer address bar. In either case, you'll need to be on the university network.

	You can find the data file used in this tutorial, SAWBONE51_BC_CSTR.AIM on the server mike at /Data0/Tutorials/ParaView_and_vtkski .		You can find the data file used in this tutorial, SAWBONE51_BC_CSTR.AIM on the server mike at /Data0/Tutorials/ParaView_and_vtkski .

Enodwell at 19:46, 21 June 2010

2010-06-21T19:46:55Z

← Older revision		Revision as of 19:46, 21 June 2010
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	[[Image:Paraview_open_aim.png]]		[[Image:Paraview_open_aim.png]]

	In order to convert this data, which is 3D ~~image data~~ to something that can be rendered, a number of different filters can be used. We are going to use the Threshold filter. You can find this at the menu item Filters->Common->Threshold . There is also a button for it on the toolbar. Click it. Now in the Object Inspector, set the Lower Threshold to 1. (If you keep the default value of 0, you just end up rendering a box with the size of the bounds of the data.) Now hit Apply.		In order to convert this data, which is a 3D matrix with position information (called an "Image" in VTK and ParaView) to something that can be rendered, a number of different filters can be used. We are going to use the Threshold filter. You can find this at the menu item Filters->Common->Threshold . There is also a button for it on the toolbar. Click it. Now in the Object Inspector, set the Lower Threshold to 1. (If you keep the default value of 0, you just end up rendering a box with the size of the bounds of the data.) Now hit Apply.

	[[Image:ParaView_Threshold_AIM.png]]		[[Image:ParaView_Threshold_AIM.png]]

Enodwell at 19:09, 21 June 2010

2010-06-21T19:09:43Z

← Older revision		Revision as of 19:09, 21 June 2010
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	==Purpose==		==Purpose==

	This is a tutorial that will demonstrate how to use ParaView to examine AIM ~~files, and how to use vtkski and python scripting to construct finite element models with complicated coundary conditions~~.		This is a tutorial that will demonstrate how to use ParaView to examine AIM file.

	This tutorial was done on OS-X, but should be essentially similar for Windows or Linux, with some minor differences.		This tutorial was done on OS-X, but should be essentially similar for Windows or Linux, with some minor differences.
Line 9:		Line 9:
	You'll need ParaView built with the bonelab extensions. You should be able to find in on the server mike . On OS-X, click on this link: [[afp://mike.kin.ucalgary.ca/Data0/Software/ParaView_with_extensions/]] . On Windows, enter \\mike\Data0\Software\ParaView_with_extensions in an Explorer address bar. In either case, you'll need to be on the university network.		You'll need ParaView built with the bonelab extensions. You should be able to find in on the server mike . On OS-X, click on this link: [[afp://mike.kin.ucalgary.ca/Data0/Software/ParaView_with_extensions/]] . On Windows, enter \\mike\Data0\Software\ParaView_with_extensions in an Explorer address bar. In either case, you'll need to be on the university network.

	~~You'll also need python. Windows users can get it from [[http://www.python.org/]] ; everyone else has it already.~~		You can find the data file used in this tutorial, SAWBONE51_BC_CSTR.AIM on the server mike at /Data0/Tutorials/ParaView_and_vtkski .

	~~You will need a compiled version of the vtkski library. To compile it yourself, refer to [[Bone lab libraries#Build_Instructions]] .~~

	You can find the data file used in this tutorial, SAWBONE51_BC_CSTR.AIM~~, as well as the python script that we will construct,~~ on the server mike at /Data0/Tutorials/ParaView_and_vtkski .

	==Background Material==		==Background Material==

	* If you're not familiar with Python, you might want to go through the tutorial [[http://docs.python.org/tutorial/]] .		*There is a book on ParaView floating around the lab that will be useful if you want to learn more.
	* There ~~are~~ a ~~couple of books~~ on ~~VTK~~ floating ~~about~~ the lab~~, "The Visualization Toolkit" and "VTK User's Guide".~~
	* The API documentation for VTK is at [[http://www.vtk.org/doc/release/5.6/html/index.html]] . This is where you go to ~~find out exactly what classes are available in VTK and exactly how to use them.~~
	* The API documentation for vtkski is at [[http://mike.kin.ucalgary.ca/vtkski/index.html]] .

	==Model Overview==		==Model Overview==

	~~We want to construct a finite element model of an~~ AIM ~~file that~~ contains a scan of a bone with a screw in it. ~~Physical tests were done in which~~ the ~~bone was constrained with a ring~~ and the ~~screw was pulled out. We want to model this with a finite element model~~.		The file SAWBONE51_BC_CSTR.AIM contains a scan of bone with a screw in it. The data has been processed so that the screw has material type 127, and the bone 126.

	==Examining the AIM file with ParaView==		==Examining the AIM file with ParaView==

Enodwell: Tutorial on ParaView and vtkski moved to Tutorial on ParaView: vtkski part being moved to another tutorial.

2010-06-21T19:03:59Z

Tutorial on ParaView and vtkski moved to Tutorial on ParaView: vtkski part being moved to another tutorial.

← Older revision	Revision as of 19:03, 21 June 2010
(No difference)

Enodwell at 19:03, 21 June 2010

2010-06-21T19:03:30Z

← Older revision		Revision as of 19:03, 21 June 2010
Line 47:		Line 47:

	[[Image:ParaView_Blue_Screw.png]]		[[Image:ParaView_Blue_Screw.png]]

			Now we are going to show the bone as well. Make sure that SAWBONES51_BC_CSTR.AIM is selected in the Pipeline browser, then click on the Threshold button to create a second Threshold filter. Change its Lower and Upper Thresholds to 126, then click Apply.

			[[Image:ParaView_screw_and_bone.png]]

Enodwell at 18:59, 21 June 2010

2010-06-21T18:59:00Z

← Older revision		Revision as of 18:59, 21 June 2010
Line 43:		Line 43:

	[[Image:ParaView_Change_Representation.png]]		[[Image:ParaView_Change_Representation.png]]

			You can click and drag on the image to rotate it. You can also right-click and hold down shift and control, with different effects. We are now going to show only the screw, which can be identified as material 127. Make sure the Threshold filter is selected, then select the Properties tab in the Object Inspector, and set both Lower and Upper Threshold to 127, as shown. Also in the Display tab, I have scrolled to the Color box, and clicked on "Set Solid Color" to make the screw blue.

			[[Image:ParaView_Blue_Screw.png]]

Enodwell at 18:52, 21 June 2010

2010-06-21T18:52:52Z

← Older revision		Revision as of 18:52, 21 June 2010
Line 32:		Line 32:
	[[Image:Open_data_with.png]]		[[Image:Open_data_with.png]]

	Click the Apply button in the Object Inspector. You should see the following, which is so far ~~not much~~.		Click the Apply button in the Object Inspector. You should see the following, which is so far only the outline of the bounds of the data.

	[[Image:Paraview_open_aim.png]]		[[Image:Paraview_open_aim.png]]

			In order to convert this data, which is 3D image data to something that can be rendered, a number of different filters can be used. We are going to use the Threshold filter. You can find this at the menu item Filters->Common->Threshold . There is also a button for it on the toolbar. Click it. Now in the Object Inspector, set the Lower Threshold to 1. (If you keep the default value of 0, you just end up rendering a box with the size of the bounds of the data.) Now hit Apply.

			[[Image:ParaView_Threshold_AIM.png]]

			We still don't see much! Why not? Well, this is such a large data set, that ParaView has decided to render just the outline for now, to save time. To see the object, go to the Display tab of the Object Inspector, scroll down to the Style box, and change the Representation to Surface. Voila!

			[[Image:ParaView_Change_Representation.png]]

Enodwell at 18:43, 21 June 2010

2010-06-21T18:43:19Z

← Older revision		Revision as of 18:43, 21 June 2010
Line 28:		Line 28:
	==Examining the AIM file with ParaView==		==Examining the AIM file with ParaView==

	Open ParaView. Click File->Open, and browse to SAWBONE51_BC_CSTR.AIM . Click ~~Open~~. Our custom version of		Open ParaView. Click File->Open, and browse to SAWBONE51_BC_CSTR.AIM . Click OK. Our custom version of ParaView with bonelab extensions is able to open AIMs, but it may inquire about the file type, as shown in the following dialog. Just select "AIM File" and proceed.

	[[Image:Open_data_with.png]]		[[Image:Open_data_with.png]]

			Click the Apply button in the Object Inspector. You should see the following, which is so far not much.

			[[Image:Paraview_open_aim.png]]

Enodwell at 18:38, 21 June 2010

2010-06-21T18:38:41Z

← Older revision		Revision as of 18:38, 21 June 2010
Line 30:		Line 30:
	Open ParaView. Click File->Open, and browse to SAWBONE51_BC_CSTR.AIM . Click Open. Our custom version of		Open ParaView. Click File->Open, and browse to SAWBONE51_BC_CSTR.AIM . Click Open. Our custom version of

	[[Image:Open_data_with.~~tiff~~]]		[[Image:Open_data_with.png]]