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Batch Processing in COVISE

Batch Processing in COVISE

The Batch Processing function has been provided together with COVISE version 5.3.1., and this Appendix provides a short introduction to (actual a presentation of) this topic.

What does Batch Processing mean?

Historically: A term from the early age of computing: A stack of input-decks (the program) was brought to an operator to be processed.
Today: A set of commands which covers the whole functionality of a software to be processed without a Graphical User Interface (GUI)

Applications

User:

Creation of individual converters.
Preparation of huge data-sets for interactive analysis (VR) or presentations. Typical tasks: Cutting (CropUSG), Sampling (Sample), Assembling (BlockCollect)...
Specific animations.

Developer:

Testing
New applications
Rapid prototyping

Implementation

New user interface: the command-line

Language used: PYTHON

Advantages of Python:

Open source (www.python.org) and widespread in scientific computing
Comprehensive syntax
Rich on features (object orientation, huge package-library)
extensible

Mapping of COVISE to PYTHON

**Figure:** Mapping of COVISE to PYTHON

Figure 7.1: Mapping of COVISE to PYTHON

Rule: Each module on the map-editor corresponds to an object in Python; the map itself translates to an object called net

How to begin?

Run Python-interface by typing: covise - script [filename]

[gromit|SNAP] ~ > covise -- script

***************************************************************
* COVISE 5.4_a1 starting up, please be patient....            *
* Flexlm license of type STD_UI checked out...                *
*                                                             *
* Starting local request broker...                            *
* Starting user interface....                                 *
*  ******* COVISE PYTHON INTERFACE ********                   *
* ...done initialization                                      *
***************************************************************
  COVISE PYTHON INTERFACE ready

covise>

Note: Using the Python Interpreter provided by your Vendor

On some Linux distributions incompatibilities between existing libraries and the python interpreter included in covise may occur. In those cases using the python interpreter provided by your linux distributor can resolve the problem. Known are incompatibilities at SuSE 9 and Mandrake 9.0 systems.

In order to circumvent those problems do:

Find out if python is already installed on your system:
```
 rpm -qa | grep python
```
should show you that the package is installed. If not, install python according to the rules of your distribution. The packages are currently included in all known linux distributions.
Find the path to your python binary by typing `which python`
Set the environment variable COVISE_LOCAL_PYTHON to the result of the previous command (/usr/bin/python in many cases).

After entering covise -script you should receive the following output:

	***************************************************************
	* COVISE 5.3.2 starting up, please be patient....             *
	* Flexlm license of type STD_UI checked out...                *
	*                                                             *
	* Starting local request broker...                            *
	* Starting user interface....                                 *
	* using local python interpreter  /usr/bin/python
	*  ******* COVISE PYTHON INTERFACE ********                   *
	* ...done initialization                                      *
	***************************************************************
		  COVISE PYTHON INTERFACE ready

	covise>

On some systems you might obtain a warning like:

RuntimeWarning: Python C API version mismatch for module _covise: This Python 
has API version 1012, module _covise has version 1011

In most cases you can ignore this warning but nevertheless it is recommended to check the proper functionality by converting an example COVISE map with the tool map_converter:

map\_converter -P -o converted.py $COVISEDIR/net/tutorial/channel.net

and run the resulting python-script in COVISE-python by typing the command

covise --script convertedNet.py

In case problems occur due to version incompatibilities of covise and the version of python provided by your linux-distributor please contact support@visenso.de.

Python syntax

Not COVISE related:

covise> a=3                        
covise> b=14

----- Assignment

covise> print a+b		
17

----- Output

covise> i=0
covise> for i in range(0,3):      
...     print i
...
0
1
2

----- Loop

covise> s="hello World"		
covise> print s
Hello World

----- String

Comprehensive tutorial:
http://www.python.org/doc/2.2p1/tut/tut.html

COVISE-related:

covise> myNet=net()

----- Create a net object - implicit after opening the map-editor

covise> rin=RWCovise()

----- Create a RWCovise object

covise> myNet.add( rin )

----- Add module to the net - drag RWCovise module to the visual programming area (VPA)

covise> rin.showParams()		
  set_grid_path( x )

----- Utility function

covise> rin.showPorts()
mesh_in
mesh

covise> rin.set_grid_path("share/covise/example-data/COVISE/airbag.covise")

----- Set parameter

covise> render=Renderer()

----- Create Renderer module

covise> myNet.add( render )

----- Add Renderer to net - drag Renderer to the VPA

covise> myNet.connect(rin, "mesh", render, "RenderData")

----- Create connection between modules

covise> runMap()

----- Guess what- (-;

Mapping rules: COVISE - Python

The Visual Programming Area is represented by the object net()
Each COVISE-module is represented by a Python object of the same name: Renderer ->Renderer()
Each parameter of a COVISE-module is mapped by a member-function with the prefix set_

Example:

covise> re=ReadEnsightNT()
covise> re.showParams()
  set_case_file( x )
  set_data for sdata1( x )
  set_data for sdata2( x )
  set_data for vdata1( x )
  set_data for vdata2( x )
  set_choose_parts( x )
  set_repair connectivity( x )

Note:
Due to technical reasons you MUST set a parameter after you have added the module to the network!

Details of the Python net() object:

myNet.add( module )

----- Add module to net

[ mynet.remove( module ) ]

----- Remove module from net

myNet.save( filename )

----- Save module into a COVISE net file

myNet.connect( module1, portName1, module2, prtName2 )

----- Connect two modules

myNet.finishedBarrier()

----- Wait until all modules have finished their work !!

Details of the Python module objects:

Parameter methods
Utility methods

module.showParams()

module.showPorts()

Note:
Due to technical reasons you MUST set a parameter after you have added the module to the network!

One step forward - one step back

COVISE-net file to Python:

    map_converter -P -o myFile.py myFile.net

Example airbag.net:

#
#   converted with COVISE (C) map_converter
#   from /home/ralfm_te/covise_snap/net/examples/Airbag.net
#
# create global net
#
theNet = net()
#
# MODULE: RWCovise
#
RWCovise_1 = RWCovise()
theNet.add( RWCovise_1 )
#
# set parameter values
#
RWCovise_1.set_grid_path( "share/covise/example-data/COVISE/airbag.covise" )
#
# MODULE: Renderer
#
Renderer_1 = Renderer()
theNet.add( Renderer_1 )
#
# CONNECTIONS
#
theNet.connect( RWCovise_1, "mesh", Renderer_1, "RenderData" )
#
# uncomment the following line if you want your script to be executed after loading
#
#runMap()
#
# uncomment the following line if you want exit the COVISE-Python interface
#
#sys.exit()

COVISE-net file to Python: use the save( fileName ) method of the net() object

Authors: Martin Aumüller, Ruth Lang, Daniela Rainer, Jürgen Schulze-Döbold, Andreas Werner, Peter Wolf, Uwe Wössner

COVISE Version 2021.12

COVISE Online Documentation

Batch Processing in COVISE