BEAM in Batch-Mode - PowerPoint Presentation

Slide1

BEAM in Batch-Mode

CoastColourBEAM WorkshopLisbon, October 21, 2011Slide2

Use BEAM’s command-line tools

from a command-line shellfrom shell scriptsfrom Python, IDL, MATLAB, ... using dedicated systemUse the BEAM Java API to call BEAM functions

from your Java program

from your Phython program

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,

2

Options Slide3

Have a look into the ${BEAM-HOME}/bin directorygpt

–Used to execute various “BEAM operators” and chains of operators.pconvert – Used to convert product files into other data and images formats (will become a gpt opertaor)binning meris-smac – Envisat MERIS smile correction

meris

-cloud – Envisat MERIS cloud screeningflhmci – Envisat MERIS/AATSR FLH/MCI processorsaatsr-sst – ATSR/AATSR SST processor

mosaic – deprecated, use gpt

Reprojectmapproj – deprecated, use

gpt Mosaic

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,

3

BEAM Command-Line ToolsSlide4

Most important BEAM batch-mode toolOther command-line tools will become BEAM operators in the futureUsage

gpt <op>|<graph-file> [options] [<source-file-1> <source-file-2> ...]Which operators are available?gpt –hNote

that

list of operators may vary depending on the installed BEAM plug-ins

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,

4

BEAM

gptSlide5

Refer to gpt documentation in BEAM VISAT help

Operator index lists only standard operatorsSept. 27, 2011WaterRadiance, Progress Meeting 6,

5

BEAM gpt Operator IndexSlide6

Many of the BEAM gpt operators and command-line tools have a counterpart in the VISAT tools menu

You can save a parameter file from an operator’s GUI in VISAT and use it with BEAM gpt on the command-lineSept. 27, 2011

WaterRadiance, Progress Meeting 6,

6BEAM gpt

ParameterisationSlide7

input-path='~/

eodata/MER_RR__1P.N1'

gpt.sh

Reproject -Pcrs

=AUTO:42001 -f NetCDF

$input-path

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,

7

Calling BEAM

gpt

from Shell ScriptsSlide8

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,8Calling BEAM gpt from Python

import

subprocess

gpt

= '~/software/beam-4.9/bin/gpt.sh'

operator = '

Reproject

'

parameters = '-

Pcrs

=AUTO:42001 -f

NetCDF

'

input_path

= '~/

eodata

/MER_RR__1P.N1'

process =

subprocess.Popen

(

gpt

+ ' ' + operator \

+ ' ' + parameters + ' '+

input_path

,\

shell=True, \

bufsize

=1 ,\

stdout

=

subprocess.PIPE

, \

stderr

=

subprocess.STDOUT

)

trace = open('

gpt.stdout

', 'w')

for line in

process.stdout

:

trace.write

(line)

trace.flush

()

trace.close

()

process.stdout.close

()

code =

process.wait

()Slide9

Advantages: no intermediate files written, no I/O overhead

reusability of processing chainssimple and comprehensive operator configurationreusability of operator configurations Usage examplegpt iop-graph.xml

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,9

Processing chains: Using gpt GraphsSlide10

Single operator = single node:

Sept. 27, 2011WaterRadiance, Progress Meeting 6,10

BEAM

gpt Graph XML Example 1Slide11

Two operator chain: (1) IOP, (2) subset

Sept. 27, 2011WaterRadiance, Progress Meeting 6,11

BEAM

gpt Graph XML Example 2Slide12

Using gptgpt

–hIn BEAM VISAT Help Topics: Graph Processing Framework (GPF)Setting up a gpt processing chain:http://www.brockmann-consult.de/beam-wiki/display/BEAM/Creating+a+GPF+Graph

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,12

Getting Help – Command-lineSlide13

BEAM Java API Documentation:http://www.brockmann-consult.de/beam/doc/apidocs/index.html

BEAM home page / downloadsBEAM Java Programming:http://www.brockmann-consult.de/beam-wiki/display/BEAM/Development Sept. 27, 2011WaterRadiance, Progress Meeting 6,

13

Getting Help - JavaSlide14

Call the BEAM API from C-Python

with JPipe:http://jpype.sourceforge.net/Use the BEAM API with Jython:http://www.jython.org/

Sept. 27, 2011

WaterRadiance, Progress Meeting 6,14

Integrating BEAM code in Python