Center to rays

How to parallelize this step?

It’s possible to split the work for each camera instead of doing all the camera in a row, for this you can use the function Centers2RaysParallel which will give a number x file center_camx.mat, with x the number of camera.

Once you have those file for all the camera, you can use the function Ray_recombinaison.m which will gathered all the rays in one file rays.mat

Center2RaysParallel takes 6 arguments:

  • session : structure containing paths of MyPath folders,

  • ManipName : name of the experiment,

  • Calib : calib.mat file,

  • kcam : the number of the cam you want to treat,

  • FirstFrame : the first frame to treat

  • Ttype (optional) : type of the transformation to use. ‘T1’ for linear transformation (defaut). ‘T3’ for cubic transformation.

Rays_recombinaison.m takes 3 arguments:

  • session : structure containing paths of MyPath folders,

  • ManipName : name of the experiment,

  • camID : list of camera numbers. ex: [1,2,3] if you have 3 cameras numbered 1,2,3 respectively,

How to run a compiled version of Center2Rays?

It can be useful to run this step at the PSMN and for this you can compile the Matlab function and use the bash submission function. The matlab function to use is submission_Centers2Rays.m.

  1. If you don’t have the compiled files yet (an executable submission_Centers2Rays and a bash script run_submission_Centers2Rays), compile the script submission_Centers2Rays.m doing in a matlab terminal:

    mcc -m submission_Centers2Rays.m -a /applis/PSMN/generic/Matlab/R2017b/toolbox/images/images

  2. Modify the line 30 of the file run_submission_center_finding.sh to add the path of the executable file like this:

eval "/MyPath/submission_Centers2Rays" $args

  1. To run it in your machine:

    sh run_submission_center_finding.sh $MCRROOT "$kcam" "$CalibPath" "$ManipName" "$FirstFrame" "$Session_INPUT" "$Session_OUTPUT"

How to split this step into many jobs on the PSMN?

If you want to run the function at the PSMN and use parallelisation, once you have executed the previous paragraph, use the file submission_Centers2Rays.sh:

  1. Change the parameters at the begining of the script to use your own parameters

kcam=4          #The camera on which you want to trace the rays
CalibPath="/MyPath/calib.mat"   #The path of the calibration file
ManipName="MyExperiment"
FirstFrame=400
Session_INPUT="/MyWorkspace/"           #The path of the PROCESSED_DATA directory, where the "center_camX.mat" are
Session_OUTPUT="/MyWorkspace/"          #The path of the PROCESSED_DATA directory, where the "rays_camX.mat" will be saved

CompileFileDir="/MyWorkspace/4d-ptv/Center2Rays"        #The directory where the file "submission_Centers2Rays.sh" is
LOG_path="/Xnfs/convection/Stage_EB_2020/Processed_DATA/Ra1.51e10_peudense_6/Centers2Rays_LOG"  #Log directory
OUT_path="/Xnfs/convection/Stage_EB_2020/Processed_DATA/Ra1.51e10_peudense_6/Centers2Rays_OUT"  #Matlab output directory

  1. Run this function for each camera in a terminal doing:

sh submission_Centers2Rays.sh

  1. Once you have all your file rays_camX.mat, launch the function Rays_recombinaison.m in a Matlab terminal doing:

    Rays_recombinaison(session,'MyExperiment',[1 2 3 4])