Annot3D Downloads and Installation |
To successfully install ANNOT3D, be sure to complete all of the instructions for "Downloads" and "Getting Started".
Downloads
Getting Started
Optional Features
Support
Downloads |
Download the software
WindowsUnix
- Get the Annot3D directory Annot3D_2.2.zip.
- Unzip the Annot3D directory onto your computer (recommended somewhere in C:/~/).
- Get the Annot3D directory Annot3D_2.3.tar.gz.
- Unzip and untar the Annot3D directory onto your computer
Checkout a copy from CVS
Note: If you are unfamiliar with CVS, please take a look at the intro to CVS before checking out a working copy.The way that you check out files from a cvs repository is different depending on whether you are working on a machine that is on the same filesystem as the cvs repository or not. If you are on the same filesystem, you are working locally. If not, you are working remotely. In the case of Annot3D, the cvs repository is stored on the SCI filesystem.
If you're working on Windows, you'll need to run the commands below in a cygwin terminal or log into a Unix machine and run them from a Unix terminal. If you choose to use cygwin, you'll need to make sure cvs and ssh are installed. To check to see if cvs and ssh are installed in cygwin, open a cygwin shell and type the following:
> cvs
If you get a "command not found" message, you need to install cvs. Do the same to see if you have ssh installed. If cvs and ssh aren't installed, download cvs and openssh for cygiwin from the cygwin home page.Here are the instructions for local and remote checkout of the Annot3D cvs repository:
Locally (from a machine on the SCI filesystem):Remotely (from machine not on SCI filesystem):
- Set environment variables:
> export CVSROOT=/usr/sci/projects/cvsrepository
> export CVS_RSH=ssh
-OR-
> setenv CVSROOT=/usr/sci/projects/cvsrepository
> setenv CVS_RSH=ssh
- Change to the directory where you would like to put your copy of the Annot3D files.
- Check out a copy of the Annot3d files by typing this command:
> cvs checkout Annot3D
You should now have a folder called 'Annot3D' with a bunch of subfolders. This contains all Annot3D files except the DATA directory, which can be downloaded separately and placed in the Annot3d directory.
- Set environment variables:
Make sure you have ssh set as the access mechanism of the remote host will chuck you out.
> export CVS_RSH=ssh
-OR-
> setenv CVS_RSH ssh
- Checkout Annot3D
The command for doing this remotely is:
cvs -d :ext:username@server.host:server-cvs-dir checkout module-name
e.g.,
cvs -d :ext:simpson@jello.sci.utah.edu:/usr/sci/projects/cvsrepository checkout Annot3D
If you have problems with CVS, send mail to simpson@cs.utah.edu.
Get the software
WindowsUnix
- Go to the VTK recent download page.
- Scroll down to Additional files and click on tcl832.exe .
- Save the file on your computer.
- Open the tcl832.exe file and complete the given installation instructions.
- Tcl is usually installed with linux. Check to see if tcl is installed on your system by running the command:
> rpm -qa tcl
- This should give you the version of tcl that is installed, i.e. tcl-8.3.3-74. If the version is lower than 8.3.x, or if tcl is not installed, you can install tcl either from your linux installation cd or you can download it from the TclTk home page.
Get the software
WindowsUnix
- On the VTK recent download page, scroll down to Wintel Pre-Compiled Binaries (Windows 9x/NT) and click on vtk42-LatestRelease.exe .
- Save the file on your computer.
- Open the vtk42-LatestRelease.exe file and complete the given installation instructions.
- On the VTK recent download page, download the following Vtk files:
- VTK-x.x-LatestRelease.tar.gz
- VTKData-x.x.tar.gz
- Go to the CMake download page.
- Download the following Cmake files:
- cmake-x.x.x.tar.gz
- Go to the directory where the Cmake tarballs are and run the following commands:
> gunzip cmake-x.x.x.tar.gz
> tar xvf cmake-x.x.x.tar
> cd cmake-x.x.x
> ./configure
> make
- Add the path the cmake-x.x.x/Source line to your .cshrc or .bash_profile and source the file. For example:
setenv PATH ~simpson/programs/cmake/cmake-1.6.7/Source:$PATH
> source .cshrc
-OR-
export PATH=$PATH:~simpson/programs/cmake/cmake-x-x-x/Source
> source .bash_profile
- Go to the directory where Vtk tarballs and dirs are and unzip and untar all tarballs. Once you've done this, make a directory called linux (or whatever you'd like to call it) on the same level as VTK-x.x.x. Then run the following commands:
> cd linux
> cmake -i ../VTK-x.x.x
> make
(Note: For the cmake command you can pretty much follow the defaults except where you're required to put something. If you have problems send mail to simpson@cs.utah.edu. )
Getting Started |
Set the Variables
WindowsVTK_DATA_ROOT = C:\Program Files\vtk42 and ANNOT_ROOT = C:\~\Annot3D
Note: If you are using a version of Windows other than WindowsXP, you will need to set the environment variables using forward slashes ( / ) instead of backslashes ( \ ) and "PROGRA~1" instead of "Program Files". Your variables will look something like this: VTK_DATA_ROOT = C:/PROGRA~1/vtk42 and ANNOT_ROOT = C:/~/Annot3DUnix
- Right click on My Computer and select Properties.
- Choose the Advanced tab at the top of the window.
- Click on the Environment Variables button at the bottom of the window.
- Under User variables, click on the New button.
- Enter Variable name: VTK_DATA_ROOT and Variable value: C:\Program Files\vtk42 (set this to be the same folder address where vtk installed on your computer).
- Click Ok, Ok, Ok to save your changes.
- Repeat for Variable name: ANNOT_ROOT and Variable value: C:\~\Annot3D (set this to be the same folder address where you unziped the annotation package eairlier).
- Add the path for vtk.exe (located in the bin directory under your install directory) to your PATH variable.
- Set ANNOT_ROOT to represent the path to the Annot3D directory that you downloaded in STEP 1.
Here are excerpts of sample .bash_profile and .cshrc files after this is done:.bash_profileNext source the .bash_profile or .cshrc file as follows:
# VTK settings
PATH=$PATH:~simpson/programs/vtk/linux/bin
ANNOT_ROOT=~simpson/annotation/current/Annot3D
export PATH
export ANNOT_ROOT
.cshrc
# VTK settings
setenv PATH ~simpson/programs/vtk/linux/bin:$PATH
setenv ANNOT_ROOT ~simpson/annotation/current/Annot3D
> source .bash_profile
-OR-
> source .cshrc
Using example.tcl files
WindowsUnix
- Right click on any .tcl file in one of the C:\~\Annot3D sub-directories (the Annot3D/demo files are good to start with).
- Select the Open With > then Choose Program... option.
- Click on the Browse... button.
- Select the vtk program C:\Program Files\vtk42\bin\vtk.exe and click the Open button.
- Check the Always use the selected program to open this kind of file box.
- Click Ok. Your example should be running fine.
The behavior of and any additional settings needed for each demo are described on the Annot3D documentation page.
- Change to the annotation/current/demo directory and run any of the .tcl demos (the Annot3D/demo files are good to start with) as follows:
> vtk [filename]
For example:
> vtk parserHeadDemo.tcl
The behavior of and any additional settings needed for each demo are described on the Annot3D documentation page.
Subscribe to the Annot3D mailing list
To SubscribeTo Send Mail
- Send an empty email to annot3d-on@sci.utah.edu
- Reply to the confirmatin request message that will be sent to you.
To Unsubscribe
- Once you have subscribed, you can send mail to the Annot3D list at annot3d@sci.utah.edu
- Send an empty (or non-emply, it doesn't matter) email to annot3d-off@sci.utah.edu
- Reply to the confirmatin request message that will be sent to you.
Optional Features |
Download the Example Data
Windows
- These files should be saved in C:/~/Annot3D/data/
- You will need to unzip the folders for each data set into this location
- When you are finished, the file structure should match that of the FILE STRUCTURE on the Annot3D documentation page.
Click on the link to download each data set:
Unix
- 276 MB bosBones.zip
- 749 KB headsq.zip
- 55 MB mummyRaw.zip
- 2.0 MB phantom.zip
- 139 MB surfaces.zip (you will need to combine files from the existing surfaces folder with these files)
- These files should be saved in C:/~/Annot3D/data/
- You will need to unzip the folders for each data set into this location
- When you are finished, the file structure should match that of the FILE STRUCTURE on the Annot3D documentation page.
Click on the link to download each data set:
- 276 MB bosBones.tar.gz
- 749 KB headsq.tar.gz
- 55 MB mummyRaw.tar.gz
- 2.0 MB phantom.tar.gz
- 139 MB   surfaces.tar.gz (you will need to combine files from the existing surfaces folder with these files)
Install the Tcl Web Server
Windows
You shouldn't need to do anything to install the web server. However, you'll need to install the tcllib in order to run the web server.Check to see if the tcllib is already installed:
- Run C:/Program Files/tcl/bin/tclsh8.3.exe
- at the prompt, type
package require tcllib
- If it says something like can't find package limit, you need to Install the tcllib .
Otherwise, the tcllib is already installed and you can Run the tcl web server.Install the tcllib:
- download this file to C:/Program Files/Tcl/ :
tcllib-1.3.zip- Unzip the file into the same directory.
- Run C:/Program Files/Tcl/tcllib-1.3/INSTALL.BAT .
- Now repeat the previous steps to Check to see if the tcllib is installed. It should be.
Run the tcl web server:
- Complete the rest of Annot3D installation before testing this.
- Once you have completed the Annot3D installation, test the web server by running
C:/~/Annot3D/src/webServerProcedures/libWebServer.tcl .
You should have a window pop up that says something like this:can't find package limit
Running with default file descriptor limit
No .htaccess support: can't find package crypt
httpd started on port 8015- Bring up a web browser (i.e. Internet Explorer or Netscape) and type the following URL to connect to the current machine:
http://127.0.0.1:8015/ .
You should see a page titled "Tcl-Httpd Home Page".- To use the Annot3D Viewer, type the following URL:
http://127.0.0.1:8015/renderer/ .
You should see a page titled "Annot3D Viewer".- To use the server from a different machine, type
>ipconfig
in a windows command prompt (Start-> Programs-> Accessories-> Command Prompt). Use the given "IP Address" for the server machine in the URL:
http://IPaddress:8015/ .
Unix
- Change to the directory Annot3D/webserver/tclhttpdx.x.x (where the x's represent version numbers).
- Configure Tclhttpd:
> ./configure
- Compile Tclhttpd:
> make
- Run the web server to make sure it works:
> tclsh bin/httpd.tcl -port 8015
At this point you should get the same results as described for the Windows Run the tcl webserver.
Support |