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| ==Print out report sheets==
| | REDIRECT [[MicroCT Evaluation and Analysis#Print outs and Reports]] |
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| The postscript report sheets can be generated and printed on the command line. For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
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| <pre>
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| $ UPAT_LIST
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| </pre>
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| Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
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| :* UU:UPAT_EVAL_FUP05_SCUSA.PS
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| :* UU:UPAT_EVAL_BASELINE_SCUSA.PS
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| For other options, see the upat_list help:
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| <pre>
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| $ UPAT_LIST -h
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| </pre>
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| One particular option that may be useful, is to turn off slice matching:
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| <pre>
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| $ UPAT_LIST -nomatch
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| </pre>
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| For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
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| <pre>
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| $ RUN UM:UCT_RAY_BATCH.EXE
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| </pre>
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| If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive). Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC. You must transfer the postscript file in ASCII mode. The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS. A program such as Adobe Photoshop can convert the postscript file to a different format.
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| See also our custom scripts:
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| <pre>
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| $ @COM:PRINT_2D.COM
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| $ @COM:PRINT_3D.COM
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| </pre>
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| ==Combining two volumes to create transparent image==
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| First create your two start "seg.aim" images
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| Start by running either the normal eval, or $ voi to get one _seg.aim file of one region
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| Rename it to a better name in the session manager, e.g. c0001234_all.aim
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| 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.
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| Load them in the 3D viewer ('all files') to check that they look like expected.
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| Now we will go into IPL and concatenate those two volumes.
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| <pre>
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| $ ipl
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| /read all xx_all.aim
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| /read trab xx_seg.aim
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| /transparent
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| -input_solid trab
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| -input_transp all
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| -output out
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| </pre>
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| Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
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| is the smaller (inner) of the two.
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| <pre>
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| /write out xxx_transp.aim
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| /quit
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| </pre>
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| 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.
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| See IPL FAQ or 3D program FAQ if you need help with these parts.
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| <b>Step by Step Example:</b> Showing your chosen trab VOI within whole bone
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| :* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
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| :* WAIT UNTIL THE JOB IS FINISHED!
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| :* Rename xxxx_seg.aim to xxxx_all.aim
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| :* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
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| :* WAIT UNTIL THE JOB IS FINISHED!
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| :* go into ipl and combine the two, see code above
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| :* Voila, finished
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| <b>Step by Step Example:</b> Showing high-dense volume surronded by lower density volume
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| :* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
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| :* WAIT UNTIL THE JOB IS FINISHED!
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| :* Rename xxxx_seg.aim to xxxx_high.aim
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| :* If wished: read out 3d result database with $ uct_list
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| :* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
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| :* WAIT UNTIL THE JOB IS FINISHED!
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| :* go into ipl and combine the two, see code above
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| :* Voila, finished
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| ==Make an animation==
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| 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.
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| This is a 'step by step' guide to create an animation using TIFF files:
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| :* Open your sample in the 3D program.
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| :* Now, open 'options','Animation'
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| :* 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'
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| :* 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'
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| <b>Note:</b> To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
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| :* Click the START button again, wait till the build-up of the 3D image is finished.
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| :* DO NOT HIT 'START CALCULATION' YET!
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| :* First, you also need to set-up the 'Auto-Print' mode:
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| :* 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.
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| :* Click on the 'Auto-Print' box. Then 'ok'
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| :* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
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| :* 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.)
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| <b>Notes/Hints:</b>
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| :* 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'
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| :* 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).
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| :* 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)
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| :* 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.
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| :* 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.
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| ==Convert AIM to TIF series==
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| Use the utility SEQ_TO_IMAGE located in the UT directory. A symbol has been set up to run this called TIF.
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| <pre>
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| $ mcr ut:seq_to_image
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| Program: seq_to_image V1.1b
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| Input-File []: WISDOM_L_R05.AIM
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| File Format [TIF]:
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| Default TIF Names: WISDOM_L_R05_xxxx.TIF
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| Output-File [WISDOM_L_R05]:
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| !> Reading AimVersion020
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| Start Slice [0]:
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| End Slice [179]: 5
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| Number of images thereof (count) [6]:
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| Scale Factor (Integer) [1]:
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| global_pos (1=true, 0=false) [0]:
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| Max value to norm to 255 [32767]:
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| Slice: 0
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| Slice: 1
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| Slice: 2
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| Slice: 3
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| Slice: 4
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| Slice: 5
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| $ dir wisdom*
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| Directory DISK1:[MICROCT.SCRATCH]
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| WISDOM_L_R05.AIM;1 WISDOM_L_R05_0000.TIF;1 WISDOM_L_R05_0001.TIF;1
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| WISDOM_L_R05_0002.TIF;1 WISDOM_L_R05_0003.TIF;1
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| WISDOM_L_R05_0004.TIF;1 WISDOM_L_R05_0005.TIF;1
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| Total of 7 files.
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| $
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| </pre>
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