www.eu-eela.org e-science grid facility for europe and latin america marcelo risk y juan francisco...

www.eu-eela.org

E-science grid facility for Europe and Latin America

Marcelo Risk y Juan Francisco García Eijó

Laboratorio de Sistemas Complejos

Departamento de Computación

Facultad de Ciencias Exactas y Naturales

Universidad de Buenos Aires

Argentina

Itacuruça (Brazil), 2-15 November 2008

CardioGrid Portal: Final Report

www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008

Steps implementedSteps implemented

• R waves detection from ECG algorithm in C++, ported from C# code.

• RR interval algorithm in C++, ported from C# code.

• ECG raw data of 24 hours is 80 MB (dat file).

• SE to store a large ECG file.

• Implementation a type job DAG.

• Implemented a Secure Copy Transfer.

• Added the code to calculate RR intervals from ECG.

• Added statistical analysis of RR intervals..


Saving ECG in SE Saving ECG in SE

Dat file is stored using SE, and its physical address is stored in a catalogue

ECG raw data

LFC

SE


Saving ECG in SE Saving ECG in SE

We used a bash script to save the ECG in the SE.

We will use the Portal to save the ECG when will be available.

The main line in the bash script to copy the file in the SE and to register it in the LFC:

lcg-scr --vo e2gris1.vo.eu-eela.eu -l lfn:PathSE-d m09-e2gris1.eela.ufrj.br file://$PWD/FileName


DAG Job 1/4DAG Job 1/4

The WN gets dat file from SE and is processed to obtain file .txt

SE

LFC ECG Detection

ECG Raw Data Processing



Another WN gets txt and dat files from SE and is processed obtaining final file .csv

RR Results File

SE

LFC

ProcessingFiles



Another WN gets csv file and is processed obtaining final res file

SE

LFC

ProcessingRR Results



Delete files from SE and physical address stored in the LCG.

SE

LFC


JDL codeJDL code[ Type = "dag";nodes = [ convertDatTxt = [ description = [ JobType = "Normal"; Executable = "/bin/bash"; InputSandbox = {"convertBinTxt.sh","binToTxt.sh","binToTxt"}; Arguments = "convertBinTxt.sh lfn:/inputfile.dat"; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; ShallowRetryCount = 1; ]; ]; convertTxtCsv = [ description = [ JobType = "Normal"; Executable = "/bin/bash"; InputSandbox = {"convertTxtCsv.sh","txtToCsv"}; Arguments = "convertTxtCsv.sh lfn:/inputfile.dat lfn:/inputfile.txt"; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err","inputfile.csv"}; ShallowRetryCount = 1; ]; ];


JDL code (continued)JDL code (continued) readCsv = [ description = [ JobType = "Normal"; Executable = "/bin/bash"; InputSandbox = {"readFileCsv.sh","readFileCsv"}; Arguments = "readFileCsv.sh lfn:/inputfile.csv"; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err","outputfile.res"}; ShallowRetryCount = 1; ]; ]; deleteFilesSE = [ description = [ JobType = "Normal"; Executable = "/bin/bash"; InputSandbox = {"deleteFilesSE.sh"}; StdOutput = "std.out"; StdError = "std.err"; OutputSandbox = {"std.out","std.err"}; ShallowRetryCount = 1; ]; ]; dependencies = { {convertDatTxt,convertTxtCsv}, {convertTxtCsv,readCsv}, {readCsv,deleteFilesSE}};];]


24 hours HR series24 hours HR series

File inputfile.csv


Basic statistical analysis of RRBasic statistical analysis of RR


Next steps: CardioGrid PortalNext steps: CardioGrid Portal

• To develop the portal with Genius and integrate all the steps above described.

• To add more statistical analysis and frequency domain analysis of HR.


CardioGrid Portal diagramCardioGrid Portal diagram

LFC WMS

WN´s

CESE

User

Smart Phone

Patient´s ECG


Questions …

www.eu-eela.org e-science grid facility for europe and latin america marcelo risk y juan francisco...

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