/*******************************************************************************
*         McStas instrument definition URL=http://www.mcstas.org
*
* Instrument: Tomography
*
* %Identification
* Written by: Peter Willendrup, based on work by Reynald ARNERIN
* Date: June 20th, 2008
* Origin: Risoe
* %INSTRUMENT_SITE: Templates
*
* Instrument to study tomographic imaging by means of the feature of OFF shape samples.
*
* %Description
* Instrument to study tomographic imaging by means of the feature of OFF shape samples.
* The sample (geometry, an OFF file, default socket.off) is rotated by omega around the
* vertical axis, and the transmitted beam is recorded on a 2D detector (monitor).
*
* A tomography is a scan of omega over a full rotation, e.g.
*   mcrun Tomography.instr omega=0,355 -N72 -n1e7 -d TomoScan
* (to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts
*  are needed)
*
* Use the provided tomo_recon.py (numpy + matplotlib) in this folder to reconstruct a 3D
* volume of the object from the scan directory: python tomo_recon.py TomoScan [--save]
*
* %Example: omega=0 Detector: monitor_I=9.37708e-10
* %Scan: mcrun Tomography.instr omega=0,355 -N72 -n1e6 Detector: monitor_I={
*   9.42128e-10,9.25881e-10,9.14476e-10,9.04288e-10,8.94769e-10,8.8652e-10,8.84254e-10,8.86881e-10,
*   8.87397e-10,8.86793e-10,8.80893e-10,8.80094e-10,8.82899e-10,8.84653e-10,8.8854e-10,8.9252e-10,
*   9.01629e-10,9.10865e-10,9.22842e-10,9.09788e-10,8.99241e-10,8.92795e-10,8.87909e-10,8.83615e-10,
*   8.80372e-10,8.81549e-10,8.8362e-10,8.86581e-10,8.88443e-10,8.89103e-10,8.85436e-10,8.86795e-10,
*   8.92286e-10,9.02972e-10,9.15912e-10,9.25596e-10,9.39192e-10,9.28645e-10,9.15208e-10,9.03769e-10,
*   8.93097e-10,8.87378e-10,8.87768e-10,8.88077e-10,8.88221e-10,8.88865e-10,8.84663e-10,8.81642e-10,
*   8.83464e-10,8.85594e-10,8.8875e-10,8.90938e-10,8.98263e-10,9.09941e-10,9.22377e-10,9.11957e-10,
*   8.98938e-10,8.90529e-10,8.85399e-10,8.83245e-10,8.80727e-10,8.78931e-10,8.82134e-10,8.84583e-10,
*   8.84924e-10,8.87263e-10,8.88867e-10,8.87931e-10,8.92295e-10,9.00247e-10,9.15281e-10,9.26476e-10 }
*
* %Parameters
* geometry: [string]  Name of the OFF file describing the sample shape
* omega: [deg]        Sample rotation around y
* sigma_abs: [barn]   Sample absorption xs
* frac_scatt: [1]     Fraction of neutrons to scatter in the sample
* div_v: [deg]        Source vertical divergence (angular height)
* div_h: [deg]        Source horisontal divergence (angular width)
* source_w: [m]       Source width
* source_h: [m]       Source height
* det_w: [m]          Detector width
* det_h: [m]          Detector height
* opts: [string]      Monitor_nD options string
*
* %Link
* http://shape.cs.princeton.edu/benchmark/documentation/off_format.html
*
* %End
*******************************************************************************/
DEFINE INSTRUMENT Tomography(string geometry="socket.off", omega=0, sigma_abs=100, frac_scatt=0, div_v=1e-4, div_h=1e-4, source_w=0.4, source_h=0.2, det_w=0.25, det_h=0.15, string opts="x bins=128 y bins=64")
DEPENDENCY " -DUSE_OFF "

TRACE

COMPONENT Origin = Progress_bar()
AT (0,0,0) ABSOLUTE

COMPONENT source = Source_div(xwidth = source_w, yheight = source_h, focus_aw=div_h, focus_ah=div_v, E0=14, dE=.5)
AT (0, 0, 0) RELATIVE Origin 

COMPONENT samplearm = Arm()
AT (0,0,1+0) RELATIVE Origin
ROTATED (0,omega,0) RELATIVE Origin

COMPONENT sample=Incoherent(p_interact = frac_scatt, geometry = geometry, yheight=0.1, sigma_abs=sigma_abs, focus_xw=det_w, focus_yh=det_h, target_index=1)
AT (0,0,0) RELATIVE samplearm 

COMPONENT monitor = Monitor_nD(xwidth=det_w,yheight=det_h,options=opts)
AT (0, 0, 2) RELATIVE source

END