www.eu-eela.org e-science grid facility for europe and latin america marcelo risk y juan francisco...
TRANSCRIPT
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..
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
DAG Job 2/4DAG Job 2/4
Another WN gets txt and dat files from SE and is processed obtaining final file .csv
RR Results File
SE
LFC
ProcessingFiles
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
DAG Job 3/4DAG Job 3/4
Another WN gets csv file and is processed obtaining final res file
SE
LFC
ProcessingRR Results
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
DAG Job 4/4DAG Job 4/4
Delete files from SE and physical address stored in the LCG.
SE
LFC
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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; ]; ];
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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}};];]
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
24 hours HR series24 hours HR series
File inputfile.csv
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
Basic statistical analysis of RRBasic statistical analysis of RR
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
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.
www.eu-eela.eu Itacuruça (Brazil) , E2GRIS1, 2.11.2008 – 15.11.2008
CardioGrid Portal diagramCardioGrid Portal diagram
LFC WMS
WN´s
CESE
User
Smart Phone
Patient´s ECG