Notes on MC generation of umSetup data

Generate config files for Gate script generation

Location

~/software/build/gate\_tools/cpp

File

makePhantomConfig

Setup

~/software/build/gate\_tools/config\_files/phantom{,2}\_{pc,grid}.cfg

Generate Gate scripts

Location

~/software/build/Gate/umSetup/scripts

Scripts:

For projects (uniform, edge) use:

generateProject.sh

For phantom use

generatePhantom.sh

Config

Phantom uses generated config files (see above). Nevertheless, they are all in

~/software/build/Gate/umSetup/config

Usually they come in standard and Grid labelled variety. They mostly differ in location of the generated scripts and path to data files (none for grid!).

Generate xrsl file from templates

Location

/data0/studen/jobs/umSetup/scripts

File

For projects use:

multiplyJobs.sh [tmplt] [N] [output file] [Nstart]

For phantom use:

phantomJobs.sh [tmplt] [N] [output file]

In both casses number of repetitions is specified. In first case, the same project is repeated N times, in the second case rods up to N are concatenated to the job list. For simulation continuation or failed submissions, Nstart is provided to provide means to generate jobs from Nstart to N-1 rather than 0 to N-1. In this case, only N-Nstart jobs are placed in the output file. Parameters from N onwards are optional, output file defaults to fullJob.xrsl and Nstart defaults to 0.

Config

Templates are stored in 

/data0/studen/data/jobs/umSetup/tmplt

There is one for each type of run (uniform,edge,phantom; the same for setup2).

Submit

Location

/data0/studen/jobs/umSetup/scripts

File

sub.sh *.xrsl [joblist.xml]

Remember to do arcproxy before submission. Adjust joblist; although optional, running multiple jobs will be easier if jobs are delegated to contextual files. Use aglomerated xrsl file generated in the previous step

Config

None

Query status

Use arc:

arcstat -i joblist.xml

Get the results

Location

/data0/studen/jobs/umSetup/scripts

File

updateJobs.sh matches.config

Config

In

/data0/studen/jobs/umSetup/setup/matches.config

is a defult list of matches between joblist files and done files. Done files contain jobid descriptors of jobs succesfully completed. When issuing updateJobs.sh all jobs are querried, and finished jobs are transferred and erased from the joblist file and added to the done file.

Update dirlist

Location

Scripts are still grid based:

/data0/studen/jobs/umSetup/scripts

Resulting output is outside of grid area, together with pc generated data:

/data0/studen/data/Gate/dirlist/umSetup{,2}

File

copyDirList.sh file.matches

The scripts will check all xml files containing done keyword in the file name. The file.matches associate a particular done.xml file and a dirlist in the data area. The scripts extracts directory name from the jobid and adds it to the dirlist file that gets copied to the Gate area.

Config

In

/data0/studen/jobs/umSetup/setup

a file matchesDirlist.config has a corelation of grid side done.xml filename convention and Gate side file name convention.

Converting raw Gate (ROOT) files to umSetup format

Location

~/software/build/gate\_tools/scripts

File

processList.sh dirlist setup

Generates a filelist of the same base as dirlist (exepct with suffix dirlist replaced with filelist) where files of umSetup format as generated (coincidence type wise). processList.sh uses gate2um executable which searches for coincidences, does the gate to um module id matching, performs a randomization of the collected bgo positions and stores the files in the appropriate formats. The required parameters for conversion are drawn from the setup file, for setup0 by default and to be supplied directly for setup2.

Config

Uses by default:

/data0/studen/data/imageRec/layout/setup0/gateSetup.in

and should use

/data0/studen/data/imageRec/layout/setup2/gateSetup.in

for setup2 simulation.

Usage in reconstruction routines

Location

~/software/build/observer_tools/coinc/root_scripts

After new data is generated, sinograms etc. need to be remade.

File

scripts_drawPositions.C
scripts_gateSensitivity.C
scripts_importData.C

File drawPositions contains routine draw, which, for a supplied filelist (with _sp in the name) draws source positions of generated events:

root [] draw(h2,"/data0/studen/data/Gate/dirlist/umSetup/umSetup_phantom_grid_sp.filelist")

File gateSensitivity collects MC data generated by a uniform source and performs scaling along the p sinogram axis. Needs a configuration file (gateSensitivity.in).

File importData stores sinogram of the (newly) simulated MC data. Requires a configuration file (setupGate10.in).

Configuration

File:

/data0/studen/data/imageRec/layout/setup{0,2}/gateSensitivity.in

is used in sensitivity generation. In there, specify which filelist are used in sensitivity generation and where sensitivity will be stored.

File:

/data0/studen/data/imageRec/layout/setup{0,2}/setupGate10.in

is an equivalent of the data file setup10.in in the same directory. Rather than pointing to real data, it points to sinograms created from MC generated data. One can adjust filters, etc.

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