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Acessing data from commandline (bartek palak)


 Listing pulse files


Info
titleitmdbs command

Usage: imasdbs [OPTIONS] [COMMAND]

This program lists existing databases.

Possible commands are:

        list <shot number>- list existing databases

       slices <shot number> <run number> - list existing databases, including number of timeslices and time range for time-dependent IDSes

        times <shot number> <run number> - list existing databases, including number of timeslices their time points for time-dependent IDSes

        tokamak - list existing tokamaks (with data versions)                                                                                

        dataversion - list existing dataversions (with tokamaks)                                                                             

If the optional arguments shot number and run number are given, only databases with these numbers will be shown.

If no command is given, the list command is performed.

To see databases stored in the public database, use 'public' as the user name.

Options:

  -h, --help            show this help message and exit

  -u USER, --user=USER  Show databases of specified user

  -t TOKAMAK, --tokamak=TOKAMAK                         

                        Show only databases for specified tokamaks

  -v VERSION, --version=VERSION                                   

                        Show only databases for specified data version

  --backend=BACKEND     Show databases written with given backend(s).  Comma-

                        separated list of backends (Currently supported:     

                        mdsplus, hdf5). By default all backends are shown.   

  -c, --compact         Compact/reduced output



shell> imasdbs -t test slices 9999 2
Tokamak: test
   Data version: 3
      UAL Backend: mdsplus
         Shot    10
             Run:     40
                 core_profiles:   25 slices (345.0 - 345.48)
                  core_sources:   25 slices (345.0 - 345.48)
                core_transport:   25 slices (345.0 - 345.48)
                   equilibrium:   25 slices (345.0 - 345.48)
               transport_solver_numerics:   25 slices (345.0 - 345.48)
                          wall:   25 slices (345.0 - 345.48)


shell> imasdbs  -u palakb
Tokamak: test
   Data version: 3
      UAL Backend: mdsplus
         Shot     1 Runs:     1
         Shot     2 Runs:     3   666   777   999
         Shot    10 Runs:    30    40    42    60    61    64    65    66    80    81    99   123   666   999  1234
         Shot    12 Runs:     1     2    99
         Shot    13 Runs:     1


 Dumping pulse files

To list the content (all data) of an IDS,  use idsdump  script

shell> idsdump
Usage: idsdump <USER> <TOKAMAK> <VERSION> <SHOT> <RUN> <IDS>


shell> idsdump $USER test 3 9999 2 equilibrium
class equilibrium
Attribute ids_properties
        class ids_properties
        Attribute comment:
        Attribute homogeneous_time: 1
        Attribute source:
        Attribute provider:
        Attribute creation_date:
[.......]
Attribute code
        class code
        Attribute name: 12 34 56 78 90
        Attribute commit: 12 34 56 78 90
        Attribute version: 12 34 56 78 90
        Attribute repository: 12 34 56 78 90
        Attribute parameters: 12 34 56 78 90
        Attribute output_flag
        [-819925519  678927020  358961885  263985221 -518535735 -656888240
          885898039 -949201251  187087431  189678740  306846126  536940120
         -842545485 -121858537 -867824798  103609281 -986039164 -761981263
         -444948662 -178414734   91809633  -65221224  575637439 -526052305]
Attribute time
[ 1.  2.  3.  4.  5.  6.  7.  8.  9. 10. 11. 12. 13. 14. 15. 16. 17. 18.
 19. 20. 21. 22. 23. 24.]

Dumping an IDS node

Getting a subset of an IDS enables reading only a node (and its descendants if the node is a structure), making the GET operation much faster. To retrieve only requested node one should call the script idsdumppath . 

idsdumppath
Usage: idsdumppath <USER> <TOKAMAK> <VERSION> <SHOT> <RUN> <IDS> <DATA_PATH>

Path syntax:

  • The path to requested node(s) is separated by slashes (“/path/to/node(s)”).  
  • Nodes representing arrays must contain indexes (“/path/to/array(idx)/field”) or “Fortran style” indices (“path/to/array(x:y)/field”) 
  • Limitation: In case of nested arrays, it is not allowed to specify set of indices for AoS ancestors. Only given values of AoS ancestors indices are handled: (e.g. “field/with/ancestorAoS(x:y)/field/AoS(n :m)” is not managed)

Data query examples: 

  • “flux_loop(1)/flux/data(1:5)” 
  • “bpol_probe(2:3)/field/data” 
  • “loop(:)/current” 
  • “time(4:-1)”
  • “profiles_1d(2)/grid/rho_tor_norm(2:4)” 



shell> idsdumppath  $USER test 3 9999 2 equilibrium "code"
Type: <class 'imas_3_24_0_ual_4_2_0.equilibrium.code__structure'>
----------------------------------------------
----------------------------------------------
class code
Attribute name: 12 34 56 78 90
Attribute commit: 12 34 56 78 90
Attribute version: 12 34 56 78 90
Attribute repository: 12 34 56 78 90
Attribute parameters: 12 34 56 78 90
Attribute output_flag
[-819925519  678927020  358961885  263985221 -518535735 -656888240
  885898039 -949201251  187087431  189678740  306846126  536940120
 -842545485 -121858537 -867824798  103609281 -986039164 -761981263
 -444948662 -178414734   91809633  -65221224  575637439 -526052305]


shell> idsdumppath $USER test 3 9999 2 equilibrium "code/output_flag(0)"
Type: <class 'numpy.int32'>
----------------------------------------------
----------------------------------------------
-819925519


Copying database files directly

In case you know user name, machine name, shot number and run number, you can import users' database files copying them directly from the users' public directories. Database files are located inside:

~$USERNAME/public/imasdb/$TOKAMAKNAME/$DATAVERSION/0/ids_SSSSRRRR.*


Take a look at the example below. We will copy data from user michalo, machine test, shot: 12 and run: 2


# change directory in your $HOME
cd $HOME/public/imasdb/test/3/0/
 
# copy data files (pay attention to *_dot_* at the end of command line!)
cp ~michalo/public/imasdb/test/3/0/ids_120002.* .
cp ~michalo/public/imasdb/test/3/0/ids_130003.* .


Adapting user code into IMAS - 22.09

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