Editing Scanco User Instructions (section)

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>. 
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory.  A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]: 
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]: 
!> Reading AimVersion020 
Start Slice [0]: 
End Slice [179]: 5
Number of images thereof (count) [6]: 
Scale Factor (Integer) [1]: 
global_pos (1=true, 0=false) [0]: 
Max value to norm to 255 [32767]: 
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1  WISDOM_L_R05_0000.TIF;1                 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1                 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1                 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$ 
</pre>


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]] 

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename             []: 
Print-Filename       [SYS$SCRATCH:TEMP_3D.PS]: 
Ambient   (0.0..1.0) [0.200]: 
Shadows        (0/1) [1]: 
Size       (1..1024) [1024]: 
Elevation  (-90..90) [30]: 
Rotation (-180..180) [35]: 
Copies        (0..9) [1]: 

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

You can also add/remove patient name, etc, in <code>options -> object/display properties</code>. Make sure you render your image before you save your preset!

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

 Generates a 3D image from a segmented file.  

 The outputs include:
  - two 3D renderings (TIF)

 Use full pathnames for the segmented AIM.

 P1 - Segmented AIM

 Usage:
 @COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to  use a custom preset file.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B' 

<b>Note:</b> To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.) 

<b>Notes/Hints:</b>
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]

===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
  -input_solid               trab
  -input_transp              all
  -output                    out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

<b>Step by Step Example:</b> Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished 

<b>Step by Step Example:</b> Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished


[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]