Editing Scanco Administration (section)

=== Rotated Reconstruction (about z-axis)===
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to measure the angle for the rotated reconstruction. 
#*To start the program type <code>$ uct_evaluation </code> in a DEC terminal, or use the graph button. 
#*Load your sample and select the angle measurement button.  
#*Drag the ends and the intersection of the green lines to measure the desired rotation angle. 
#:[[File:Angle meas.preview.jpg|600px]]
#Rotate and reconstruct
#*Use <code>$ @com:reco_all </code> to reconstruct all slices.
#*Use <code>$ @com:uct_reconstruction_angle </code> to reconstruct selected slices from an RSQ. 
#Use the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] to check the sample after the rotated reconstruction:
#:[[File:Rotated_reconstruction.preview.jpg|600px]]


*'''General Usage''':
<pre>
$ @com:reco_all.com P1 P2 P3

      P1: Angle in degrees
      P2: Sample number
      P3: Measurement number

$ @com:uct_reconstruction_angle.com P1 P2 P3 P4 P5

      P1: RSQ Filename
      P2: Slice number (A – all, start:finish)
      P3: Log file of batch job
      P4: Delete log file (true/false)
      P5: Angle in degrees
</pre>
*The angle of rotation uses the right-hand rule:  a counterclockwise rotation is positive and a clockwise rotation is negative.
*The angle of rotation uses a single decimal place.  
*By default the reconstruction jobs will be placed in the sceva3_slow queue.
*Both functions are executed from the measurement directory.


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====Reconstruct all slices====
The following examples are for a 19.1 degree counterclockwise rotation of sample 6876, measurement 15417, C0005086.RSQ.
<pre>
$ @com:reco_all.com 19.1 6876 15417
</pre>
*Delete the ISQ file from the measurement directory.

====Reconstruct a selection of slices====
*A valid ISQ must exist.
*There is an offset of 1 slice when designating slice selection.

To reconstruct slices 36 to 41:
<pre>
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 sys$scratch:reco610.log true 19.1
$ @com:uct_reconstruction_angle.com DK0:MICROCT.DATA.00006876.00015417]C0005086.RSQ 35:40 "" "" 19.1
</pre>
*"" is used as a null input for optional parameters.

Instead of submitting in the terminal and running interactively, submit it to the queue as follows
<pre>
$ submit/noprint/que=sys$slow com:uct_reconstruction_angle.com/log=sys$scratch:TEST.LOG/para=(DK0:[XTREMECT2.DATA.00002816.00014743]D0012841.RSQ,A,sys$scratch:TEST.log,"",156.1)
</pre>

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