Center finding

How to run a compiled version of the CenterFinding2D.m?

It is possible to compile CenterFinding2D.m function to run it outside a MATLAB instance directly in a terminal. This can be useful to run it on cluster, for instance at the PSMN. The matlab function to use for that is submission_center_finding.m.

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

    mcc -m submission_center_finding.m

    An executable file submission_center_finding and a bash file run_submission_center_finding.sh will appear in the same folder.

    1. Modifie the line 30 of the file “run_submission_center_finding” to add the path of the executable file like this:

    eval "/MyPath/Submission_center_finding" $args

  1. To run it in your machine:

    sh run_submission_center_finding.sh $MCRROOT "ManipName" "CamNum" "FirstFrame" "Nframes" "Th" "Size" "Session_INPUT" "Session_OUTPUT"

Warning

Even if some parameters are numbers (integers or floats), you need to tipe them as string by using the quote “.

How to split CentersFinding into many jobs on the PSMN?

If you want to run the function at the PSMN and use parallelisation, use the file submission_CenterFinding.sh:

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

ManipName="MyExperiment"
CamNum=3                                                                #The camera on which you want to find the center
FirstFrame=300                                                  #The first frame (useful if you don't start at one)
Nframes=36000                                                   #The final frame to treat
Th=6500                                                                 #Threshold to detect a part (it has to be tuned with the function ``CenterFinding.m`` and with test=true
Size=5                                                                  #The size of a part (in pixel)
Session_INPUT="/MyWorkspace/"           #The path of the DATA directory, where all the images are
Session_OUTPUT="/MyWorkspace/"          #The path of the PROCESSED_DATA directory, where the centercamk.mat will be saved

CompileFileDir="MyPath/4d-ptv/CenterFinding"                        #The directory where the file "runSubmision_center_finding.sh" is
LOG_path="/MyWorkspace/MyExperiment/CenterFinding_LOG"          #log directory (warning: the directory has to be created before launch the code)
OUT_path="/MyWorkspace/MyExperiment/CenterFinding_OUT"          #matlab output (warning: the directory has to be created before launch the code)

  1. Run this function in a terminal doing:

sh submission_CenterFinding.sh

This will launch a job at the PSMN, on the queue PIV, you can check if everything is ok by looking at the file center_camCamNum.log in the LOG directory.