Kepler Exercise Deana Pennington University of New Mexico January 9, 2007

Graphing data Vegetation biomass test data 1.With EML 2.Without EML

Sevilleta LTER Biomass Plots Biomass = f(species, cover%, height, season)

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

Get data file Copy from tundra://training_lab/downloadsCopy from tundra://training_lab/downloadsveg_data_test.csvvegdataDP.xmlvegdata2DP.xml Copy toCopy to c:\kepler\workflows\eco c:\kepler\workflows\eco

View the end result Open vegdataDP in keplerOpen vegdataDP in kepler –File->Open->vegdataDP.xml RunRun

With metadata (easier) Open a new graph editor in KeplerOpen a new graph editor in Kepler File->New->Graph Editor Switch to the Data tabSwitch to the Data tab Remove KU Digir and Geon from SourcesRemove KU Digir and Geon from Sources Search for “test”Search for “test” Add “Vegetation Test Data” to canvasAdd “Vegetation Test Data” to canvas Drag and drop

Explore the dataset Look at the metadataLook at the metadata Right-click on icon- > Get Metadata Tool tips on portsTool tips on ports

Director Add a directorAdd a director Click on the Components tab Double-click on Components Double-click on Directors Drag and drop the SDF Director onto the canvas Configure directorConfigure director Double-click or right-click- >configure Change iterations to 9 (the number of rows to be read in the file) Click Commit to save

Display the file Search for “display”Search for “display” Find the Display actor (last icon)Find the Display actor (last icon) Drag and drop the Display actor onto the canvasDrag and drop the Display actor onto the canvas

Hooking up ports Find the “cover” portFind the “cover” port Use tool tips Note double type Click-hold the cover port and drag to the input port on the Display actorClick-hold the cover port and drag to the input port on the Display actor Run the workflowRun the workflow Click the teal triangle or Delete the Display actorDelete the Display actor

Add graph Search for “plotter”Search for “plotter” Add XY Plotter actor to canvasAdd XY Plotter actor to canvas Hook up cover and height output ports to graph input portsHook up cover and height output ports to graph input ports RuRu

Run the workflow Note lousy plot formatNote lousy plot format Close the displayClose the display Change the plot formatChange the plot format Click on plot format icon

Reformat the plot Change Title to something meaningful (I used Vegetation Volume)Change Title to something meaningful (I used Vegetation 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\workflows\eco \veg_data_xxx.xml, where xxx is your initials

Without EML The harder way, without EML- described metadataThe harder way, without EML- described metadata

Cheat-look ahead Open vegdata2DP.xml from Kepler->File->Open File-> [locate file] Opens the file Separates file into columns Extract cover and height columns Converts to decimal number Converts array to elements Constructs graph Note: all this would not be necessary if EML used

Start a new workflow Open the workflow editorOpen the workflow editor File->New->Graph Editor Select a directorSelect a directorComponentsDirectors Drag and drop SDF Director Configure directorConfigure director Right click on director Change number of iterations from 0 to 1 CommitCommit

Read 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 veg_data_test.csv fileConfigure Expression 1 to hold the path and file name for the veg_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 contentsRun the workflow – it should show you the file contents

Plot the columns Get the R Expression actor from General Purpose Right-click Configure Ports Add an input port named df1

Plot the file (cont’d) Hook up the dataframe output port from Read Table to the new input portHook up the dataframe output port from Read Table to the new input port Configure the actor – change the R script to specify the cover and height columns (as shown below) and to plotConfigure the actor – change the R script to specify the cover and height columns (as shown below) and to plot

Plot the file (cont’d) Get Image JGet Image J Hook the graphics file output port of R Expression to the input port for Image JHook the graphics file output port of R Expression to the input port for Image J Run workflowRun workflow