Adjusting galaxy parameters using galfit

Created: 2012-07-26 12:56:18 Last updated: 2012-09-07 12:57:59

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This workflow creates galfit configuration files using data from a votable, it runs galfit, its results is added to the votable, it creates new config files for galfit using the previous results, it runs galfit a second time considering galaxies that have and do not have bars in order to adjust the objective parameters and it finally includes the results into the votable. It requires the specification of the columns that contain file names (these files should be accesibles from taverna). If the configuration files contain references to other files, they must be accesible from taverna. Configuration files are created (one for every row in the votable) using a template whose keys are replaced by data from a votable. Keys must appear also in the vocabulary file and match column names in the votable. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (1)

Inputs (11)

Name	Description
FileVotablePath
galfitVocabulary
galfitTemplateForAdjustCenter
ColumnNameWithGalfitConfigFile
GalfitTemplateWithoutBar
GalfitTemplateWithBar
ColumnNameWith2ndConfigFile
Bar_partition_criteria
NoBarPartitionCriteria
ColumnNameForSecondGalfitIterationResult
ColumnNameFor1stGalfitIteResult

Processors (7)

Name	Type	Description
CreateGalfitTemplates	workflow
Read_File	beanshell	Script import java.io.BufferedInputStream; import java.io.File; import java.io.FileInputStream; import java.io.IOException; String readFileAsString(String filePath) throws java.io.IOException{ byte[] buffer = new byte[(int) new File(filePath).length()]; BufferedInputStream f = null; try { f = new BufferedInputStream(new FileInputStream(filePath)); f.read(buffer); } finally { if (f != null) try { f.close(); } catch (IOException ignored) { } } return new String(buffer); } string = readFileAsString(filePath);
FillVotableWithGalfitResults	workflow
CreateGalfitTemplates_2nd_Iteration	workflow
Run_2nd_Galfit_iteration	workflow
Run_1st_galfit_iteration	workflow
FillVotableWith2ndGalfitResults	workflow

Beanshells (8)

Name	Description	Inputs	Outputs
Read_File		filePath	string
Create_galfit_script		votable columnNameWithNewConfigFile columnNameWithConfigFile	script
Create_galfit_script		votable columnNameWithNewConfigFile columnNameWithConfigFile	script
CreateVotableFromGalfitConfigFiles		columnNameWithConfigFile FileVotablePath	resultVotable
Read_File		filePath	string
Read_File		filePath	string
transform_BuDS_or_BDBS_GalfitFile	it reads galfit configuration file if its components are: disk, bulb, bar and sky or disk, bulb and sky.	galfitFileContent	resultTable
MakeDoubleTypes		in	out

Outputs (5)

Name	Description
Galfit2ndIterationResult
Galfit1stIterationResults
votableWithGalfitResults
ResultGalfitFiles1stIteration
ResultGalfitFiles2ndIteration

Datalinks (31)

Source	Sink
Read_File:string	CreateGalfitTemplates:votable
galfitVocabulary	CreateGalfitTemplates:vocabulary
galfitTemplateForAdjustCenter	CreateGalfitTemplates:template
ColumnNameWithGalfitConfigFile	CreateGalfitTemplates:columnNameWithConfigFilePath
FileVotablePath	Read_File:filePath
FileVotablePath	FillVotableWithGalfitResults:FileVotablePath
ColumnNameFor1stGalfitIteResult	FillVotableWithGalfitResults:ColumnNameWithConfigFile
Run_1st_galfit_iteration:Tool_STDOUT	FillVotableWithGalfitResults:Precedence
galfitVocabulary	CreateGalfitTemplates_2nd_Iteration:vocabulary
FillVotableWithGalfitResults:VotableWithnewColumns	CreateGalfitTemplates_2nd_Iteration:votable
GalfitTemplateWithoutBar	CreateGalfitTemplates_2nd_Iteration:template1
GalfitTemplateWithBar	CreateGalfitTemplates_2nd_Iteration:template2
ColumnNameWith2ndConfigFile	CreateGalfitTemplates_2nd_Iteration:columnNameWithConfigFile
Bar_partition_criteria	CreateGalfitTemplates_2nd_Iteration:partitioningFilter2
NoBarPartitionCriteria	CreateGalfitTemplates_2nd_Iteration:PartitioningFilter1
ColumnNameWith2ndConfigFile	Run_2nd_Galfit_iteration:ColumnNameWithConfigFile
ColumnNameForSecondGalfitIterationResult	Run_2nd_Galfit_iteration:ColumnNameWithNewConfigFile
FillVotableWithGalfitResults:VotableWithnewColumns	Run_2nd_Galfit_iteration:votable
CreateGalfitTemplates_2nd_Iteration:results	Run_2nd_Galfit_iteration:Precedence
CreateGalfitTemplates:Template_filler_report	Run_1st_galfit_iteration:Precedence
ColumnNameWithGalfitConfigFile	Run_1st_galfit_iteration:ColumnNameWithConfigFile
ColumnNameFor1stGalfitIteResult	Run_1st_galfit_iteration:ColumnNameWithNewConfigFile
Read_File:string	Run_1st_galfit_iteration:votable
ColumnNameForSecondGalfitIterationResult	FillVotableWith2ndGalfitResults:ColumnNameWithConfigFile
FillVotableWithGalfitResults:VotableWithnewColumns	FillVotableWith2ndGalfitResults:votable
Run_2nd_Galfit_iteration:Tool_STDOUT	FillVotableWith2ndGalfitResults:Precedence
Run_2nd_Galfit_iteration:Tool_STDOUT	Galfit2ndIterationResult
Run_1st_galfit_iteration:Tool_STDOUT	Galfit1stIterationResults
FillVotableWith2ndGalfitResults:VotableWithnewColumns	votableWithGalfitResults
Run_1st_galfit_iteration:ResultGalfitFiles	ResultGalfitFiles1stIteration
Run_2nd_Galfit_iteration:ResultGalfitFiles	ResultGalfitFiles2ndIteration