Kepler ExerciseKepler Exercise

Deana PenningtonDeana Pennington

University of New MexicoUniversity of New Mexico

January 9, 2007January 9, 2007

Graphing dataGraphing data

Vegetation biomass test dataVegetation biomass test data

1.1. With EMLWith EML

2.2. Without EMLWithout EML

Sevilleta LTER Biomass PlotsSevilleta LTER Biomass Plots

Biomass = f(species, cover%, height, season)Biomass = f(species, cover%, height, season)

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Web Center

120

12

24

3660

72

84

96

108

144

132

13

145

37 25

61

49

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109 121

13397

85 100 M10 M

North Plot

East Plot

South Plot

West Plot

Quad 2Quad 3

Quad 1Quad 4

Figure 2. Quadrat Layout

Center Stake

Quadrant Stakes

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E

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This ExerciseThis Exercise

• Using a subset of the data for 1 species Using a subset of the data for 1 species in 1 quadrat, extract vegetation coverin 1 quadrat, extract vegetation cover% and height, and create graphs of % and height, and create graphs of those values through timethose values through time

Get data fileGet data file

• Copy from Copy from tundra://training_lab/downloadstundra://training_lab/downloadsveg_data_test.csvveg_data_test.csv

vegdataDP.xml vegdataDP.xml

vegdata2DP.xmlvegdata2DP.xml

• Copy toCopy to c:\kepler\workflows\ecoc:\kepler\workflows\eco

View the end resultView the end result

• Open vegdataDP in keplerOpen vegdataDP in kepler– File->Open->vegdataDP.xmlFile->Open->vegdataDP.xml

• RunRun

With metadata (easier)With metadata (easier)• Open a new graph Open a new graph

editor in Keplereditor in KeplerFile->New->Graph File->New->Graph

EditorEditor• Switch to the Data Switch to the Data

tabtab• Remove KU Digir and Remove KU Digir and

Geon from SourcesGeon from Sources• Search for “test”Search for “test”• Add “Vegetation Test Add “Vegetation Test

Data” to canvasData” to canvasDrag and dropDrag and drop

Explore the datasetExplore the dataset

• Look at the Look at the metadatametadataRight-click on icon-Right-click on icon-

> Get Metadata> Get Metadata

• Tool tips on portsTool tips on ports

DirectorDirector• Add a directorAdd a director

Click on the Components tabClick on the Components tabDouble-click on ComponentsDouble-click on ComponentsDouble-click on DirectorsDouble-click on DirectorsDrag and drop the SDF Director Drag and drop the SDF Director

onto the canvasonto the canvas• Configure directorConfigure director

Double-click or right-click-Double-click or right-click->configure>configure

Change iterations to 9 (the Change iterations to 9 (the number of rows to be read in number of rows to be read in the file)the file)

Click Commit to saveClick Commit to save

Display the fileDisplay the file

• Search for Search for “display”“display”

• Find the Display Find the Display actor (last icon)actor (last icon)

• Drag and drop Drag and drop the Display the Display actor onto the actor onto the canvas canvas

Hooking up portsHooking up ports• Find the “cover” portFind the “cover” port

Use tool tipsUse tool tipsNote double typeNote double type

• Click-hold the cover Click-hold the cover port and drag to the port and drag to the input port on the input port on the Display actorDisplay actor

• Run the workflowRun the workflowClick the teal triangle orClick the teal triangle or

• Delete the Display actorDelete the Display actor

Add graphAdd graph

• Search for Search for “plotter”“plotter”

• Add XY Plotter Add XY Plotter actor to canvasactor to canvas

• Hook up cover Hook up cover and height output and height output ports to graph ports to graph input portsinput ports

• Ru Ru

Run the workflowRun the workflow• Note lousy plot Note lousy plot

formatformat• Close the Close the

displaydisplay• Change the Change the

plot formatplot formatClick on plot Click on plot

format iconformat icon

Reformat the plotReformat the plot

• Change Title to Change Title to something meaningful something meaningful (I used Vegetation (I used Vegetation Volume)Volume)

• Add axis labelsAdd axis labels• Select dotsSelect dots• Unselect ConnectUnselect Connect• ApplyApply• Close Run WindowClose Run Window• Run from run buttonRun from run button• Save your workSave your work

File->Save-> c:\kepler\File->Save-> c:\kepler\workflows\eco\workflows\eco\veg_data_xxx.xml, where veg_data_xxx.xml, where xxx is your initialsxxx is your initials

Without EMLWithout EML

• The harder way, without EML-The harder way, without EML-described metadatadescribed metadata

Cheat-look aheadCheat-look ahead

Open vegdata2DP.xml from Kepler->File->Open File-> Open vegdata2DP.xml from Kepler->File->Open File-> [locate file][locate file]

Opens the fileSeparates file into columnsExtract cover and height columnsConverts to decimal numberConverts array to elementsConstructs graphNote: all this would not be necessary if EML used

Start a new workflowStart a new workflow• Open the workflow Open the workflow

editoreditorFile->New->Graph File->New->Graph

EditorEditor• Select a directorSelect a director

ComponentsComponentsDirectorsDirectorsDrag and drop Drag and drop

SDF DirectorSDF Director• Configure directorConfigure director

Right click on Right click on directordirector

Change number of Change number of iterations from iterations from 0 to 10 to 1

• CommitCommit

Read the fileRead the file• Browse Components=> Data Input => Local input; drag and drop Read TableBrowse Components=> Data Input => Local input; drag and drop Read Table• From General Purpose, get two copies of the Expression actorFrom General Purpose, get two copies of the Expression actor• Configure Expression 1 to hold the path and file name for the Configure Expression 1 to hold the path and file name for the

veg_data_test.csv fileveg_data_test.csv file• Configure Expression 2 to specify the delimiter “,”Configure Expression 2 to specify the delimiter “,”• Link the output port of Exression 1 to the file name port of Read TableLink the output port of Exression 1 to the file name port of Read Table• Link the output port of Expression 2 to the delimiter port of Read TableLink the output port of Expression 2 to the delimiter port of Read Table• Add the Display actor and hook it up to the string output portAdd the Display actor and hook it up to the string output port• Open Read Table and remove the “pairs” statement at the endOpen Read Table and remove the “pairs” statement at the end• Change the R working directory to your directoryChange the R working directory to your directory• Uncheck the graphical display check boxUncheck the graphical display check box• Run the workflow – it should show you the file contents Run the workflow – it should show you the file contents

Plot the columnsPlot the columns

Get the R Expression actor from Get the R Expression actor from General PurposeGeneral Purpose

Right-click Configure PortsRight-click Configure Ports

Add an input port named df1Add an input port named df1

Plot the file (cont’d)Plot the file (cont’d)• Hook up the dataframe output port from Read Hook up the dataframe output port from Read

Table to the new input portTable to the new input port• Configure the actor – change the R script to Configure the actor – change the R script to

specify the cover and height columns (as specify the cover and height columns (as shown below) and to plotshown below) and to plot

Plot the file (cont’d)Plot the file (cont’d)• Get Image JGet Image J• Hook the graphics file Hook the graphics file

output port of R Expression output port of R Expression to the input port for Image Jto the input port for Image J

• Run workflowRun workflow