Graphana - user manual
Contents
1. Name Syntax Description Application Ide 1 2 carta Executes the operation with the key Ide with the given arguments Returns the result of the exe cution Addition z y Returns the sum of x and y or the concatenation if x or y is a String Subtraction z yY Returns the difference of x and y Multiplication x y Returns the product of x and y Division fame ae Returns the quotient of x and y If x and y are integers then integer division is done And x amp amp y Returns true if and only if x and y are both true If x is false then y is not evaluated Or xz lily Returns true if and only if x or y is true If x is true then y is not evaluated Unary Minus x Returns the negative value of x Not Ig Returns true if and only if x is false Equal to y Returns true if and only if x is equal to y Not equal to x y Returns true if and only if x is not equal to y Less than r lt Y Returns true if and only if x is smaller than y Greater than x gt y Returns true if and only if x is greater than y Less than lt y Returns true if and only if x is smaller than or or equal equal to y Greater than x gt y Returns true if and only if x is greater than or or equal equal to y Assignment Ide X Assigns X to the variable Ide Creates the vari able if it does not exist Returns X Postfix Ide Increases the value of the existing variable Ide increment by 1 Returns the value of Ide before it wa2. 2 1 Operations In simple cases statements only contain operation calls to modify the current graph or to run algorithms Operations are called using the following syntax operationkey argument_1 argument_2 argument_n If an operation does not need any arguments then no brackets need to be written but it is recommended The most important operations are listed in graphana_ops pdf The signature keyword parameters return type and the description of a particular operation can also be printed at runtime with the HELP keyword HELP operationkey If only HELP is typed in then a runtime help is printed The vertex cover size algorithm is one example operation It has the following signature vertexCoverSize useGreedy Boolean Integer That means the algorithm is called via vertexCoverSize and needs one argument of type Boolean to decide which heuristic to use Furthermore the signature indicates that the re turn value is of type Integer Calling the algorithm looks like this vertexCover true In the example true is passed as argument and therefore a greedy algorithm is used If an operation returns a result then the result can be shown for example as a console output which is the default or can be written into a text file The latter will be described later Some types of results can also be visualized Some operations have optional parameters Within the operation signature these are denoted with a
3. file PRINTLN Vertices vertexCount edges edgeCount PRINTLN Average degree averageDegree max degree maxDegree 11 3 Using graphana as framework The functionality of Graphana can also be accessed within a java application This section demonstrates the easiest way to do this To use the framework in an eclipse project the graphana jar must be added as external jar This can be done by clicking Project Properties gt Java build path Libraries Add external jars and choosing graphana jar The easiest way to initialize the framework and to execute operations is to create a GraphanaAccess instance This class initializes Graphana and automatically registers all the default operations and libraries GraphanaAccess graphanaAccess new GraphanaAccess After the framework is initialized operations can be called by using the executeX methods where X stands for the type which is expected to be returned So for example if an operation which returns an integer is executed then executeInt must be called The methods expect a string in graphana syntax as input argument The following example initializes the framework creates a random graph and prints the average degree GraphanaAccess graphanaAccess new GraphanaAccess graphanaAccess execute createErdosRenyiGraph 10 0 5 float averageDegree graphanaAccess executeFloat averageDegree System out prin
4. and therefore weights are ignored when reading the file After the graph was loaded some data and graphparameters are printed The PRINTLN key word prints the given String In the example some graph operations and algorithms are called Firstly graphSize is called This graph operation does not need any arguments so the brackets are empty In this case the brackets may be omitted like it was done in the very first example The operation maxFlow needs two arguments In the example two vertices are given as arguments Vertex constants are written with vertexIdentifier A vertex with the respective identifier must exist in the current graph As already mentioned above PRINT and PRINTLN are no operations but keywords which do not need any brackets The result of the whole Expression will be printed The next sample script demonstrates how to write some graphparameters into a formatted text file Write graphparameters into a file setOutputFile Graphparameters txt true WRITE Vertex count vertexCount WRITE Edge count edgeCount n WRITELN Average Degree avrgDegree PRINT Diameter diameter closeFile PRINTLN Wrote into Graphparameters txt Save degree distribution as a CSV file distribution degreeDistribution writeWholeFile degrees txt distribution At first the output file is set The file writing will be done into the chosen file from then on The second
5. 2 3 Advanced usage What follows in this subsection is necessary to write more complex script files The first example deals with conditions 10 if averageDegree lt 5 amp amp maxDegree lt 10 setCVDHeuristics SUCCESSIVE MAXDEGREE else setCVDHeuristics CONNECTEDCOMPONENT ALL PRINTLN cvdSize The example takes the average degree and the maximum degree of the current graph to decide which cvd heuristic see graphana_ops pdf might be the most applicable for the graph The next example deals with for loops for i 1 i lt 120 i createRandomGraph i 0 5 writeWholeFile graphs random graph i dim graphAsDimacs Note the semicolon at the very end of the sample In Graphana also statement blocks are closed with semicola In the loop 120 graphs are created with a simple random graph generator and saved as partic ular dimacs files Another loop is the for each loop The loop iterates over a Set or a Vector The following example iterates over a constant set foreach x in 3 7 10 11 PRINTLN x 2 The for each loop is useful when working with multiple input files in most cases graph files The following example uses the getFiles command which returns a set of files that are con tained in the given directory non recursive and have one of the given file extensions dim in this case foreach file in getFiles graphs dim loadGraph file PRINTLN
6. After loading the vertex and edge count of the loaded graph are printed by typing and executing vertexCount and edgeCount In the end the program is closed Other operations including algorithms are called the same way as in this simple example By pressing up and down it can be navigated through previously executed inputs When typing an operation tab can be pressed to complete the operation identifier For example if loadgr is typed then pressing tab yields loadGraph note that typing load and pressing tab won t work because several operations start with load When pressing tab while the caret is positioned between empty brackets a dialog is opened to assist setting up the argu ments of the call So in the loadGraph example a dialog will appear to choose the file argument via open dialog 1 2 Main menu The main menu consists of the following items e File Creating and loading graphs e Tasks Default program tasks Tasks are sequences of operations e All operations Contains all Graphana operations By clicking the respective operation a call assistant of the operation appears including a description of the operation By setting up the arguments and pressing Execute the operation is executed Alternately Insert can be pressed to only insert the operation call as text into the text input field It can then be executed by pressing enter e Syntax Contains all keywords of the script language the la
7. and a default value behind the parameter type operationkey parameter_1 default 1 parameter_2 default_2 If no argument is given for these then the respective default value will be used There are three different types of operations e Graph operations During the whole runtime of the program there is exactly one current graph to operate on more graphs can be managed in the background but that is not important for the beginning Graph operations are working on this current graph For example loading a graph or adding vertices are graph operations e Algorithms Algorithms are special graph operations which compute graphparameters in most cases A sample for a simple algorithm is the average vertex degree of a graph e Commands These are used to configure the program or to get some system informa tion Commands do not operate on graphs For example there are commands for time measurements Graphana internally uses various graph libraries to create graphs and operate on them Every graph is built up in exactly one graph library At runtime the user can chose which library to use The chosen library influences the performance and the set of available algorithms Some algorithms do not depend on the internal graph library others are specialised on particular ones If it is necessary Graphana automatically converts from one graph library to the one which is needed Some libraries do not allow every graph configuration F
8. the end result of the input and is printed even without a PRINT keyword Statements also can be read from a script file This is done with the script command script scripts operations txt Scripts are written with the same syntax as console inputs but they are not parsed line wise So a statement with no semicolon followed by another statement in the next line is a syntax error in most cases Line comments begin with Block comments are surrounded with and and can be nested Comments are completely ignored when executing the script For example a script looks like the following one Create and load graph createGraph false false true JGraphT loadGraph graphs sample dim Print some properties PRINTLN Graph size graphSize PRINTLN Vertex cover vertexCoverSize false PRINTLN Max flow between pita and fan maxFlow pita fan At first the graph is created using the createGraph command This command initializes an empty graph with the given configuration In the example the first three arguments determine that the graph is undirected unweighted and always simple The fourth argument determines the graph library which is to be used internally In this case the JGraphT library is set As a reminder for the arguments to pass HELP createGraph can be typed in After the graph is created and initialized it is constructed by loading a DIMACS file The graph is unweighted
9. the type can be entered as text input in the running program 17
10. Graphana user manual The main functionality of Graphana is the analysis of graphs concerning structural properties These are measured using graphparameters The main input of Graphana are graphs and user inputs The main output are analysis results In addition Graphana is able to e generate graphs by random graph generators by script by GUI e visualize graphs and algorithms e load external java classes to import algorithms and graph libraries e do time measurements on algorithms Contents 1 Program flow 1 1 TesttinputandOulpilis ssc ia a ee Si le a ee A eh ah ee eh ee LO Man ment pa unr ba he A ee ea ee Se ee ee Oe he ee AE LS Status IAL sora he cae ede te gn oi De A wee a ete NE nro OY sales a Mad wale dig bA Graph le set window ras onik acs anmu ae a he a a ee E EA ro RIVA SIS Aa k Ss AE e SE eae Ge ge Ee sorte AA ea an He T w6 Histograms s eink 4 do GG Opi oh Pie a d he OM A Me pt Di que 2 Script language Dil Opera onS ences os are eho tes a ee DR un wee ete oe OS Ge oe e 2 2 Syntax examples ssp eaor iow Soh Seo ge O KR Meath May tek eae Sl BE 0 og 8 2 30 Advanced USADOS he we HON weed Sie wed Bande towed cade pat eee se was 3 Using graphana as framework Appendix A Syntax Appendix B Types 10 12 15 17 1 Program flow Graphana can be started with the following command java jar graphana jar Since Graphana sometimes needs much memory on large graphs it is recommend
11. argument of the setOutputFile determines whether almost every console output including warnings and errors is also to be written into the output file The WRITE keyword works in a similar way as the PRINT keyword but writes into the file which was set previously instead of the console output In the example three strings are explicitely written into the file Afterwards there is a PRINT keyword The given string will be printed in the console output as always but since the second argument of the setOutputFile at the beginning is set to true the string will also be written into the output file When the file writing is complete the file must be closed using closeOutputFile Now the file is complete and can be read in the file system After the call there is no output file set and therefore it is not allowed to call WRITE until a new output file is set The last part of the example demonstrates how to create a whole text file at once At first a Histogram is created representing the degree distribution of the current graph The operation writeWholeFile needs two arguments The first one is the target file and the second one any object The text representation of the given object will be written into the target file The file will be closed automatically In the example a Histogram is passed The string representation of a histogram is a CSV string So the resulting file is a CSV file and can be used in respective external programs for example
12. ed to run it with a large heap as well as with a large stack when planning to load large graphs For example java jar graphana jar Xms1024m Xssi6m This runs graphana with 1GB heap space and 8MB stack memory If the memory is not sufficient Graphana may return an error when running respective algorithms on too large graphs When Graphana is started a window appears containing the following elements Main menu File Tasks Alloperations Syntax Help Executing init txt E Init execution finished oa ie ee Text input field Text input execution oadGraph sample dim Execute Status bar 1 1 Text input and output The text input field gives access to all functionalities of Graphana Text can be typed in which will then be evaluated by Graphana The text output will then print the given input and if the evaluation yielded a result it will be printed as well The typed input can be executed by pressing enter or by pressing the Execute button The following sequence of inputs form a simple use case gt loadGraph sample dim gt vertexCount 6700 gt edgeCount 21274 gt QUIT In the examples of this manual the user inputs are denoted with a gt at the beginning of a line All other lines are text output Firstly a graph is loaded from the given DIMACS file In Graphana the loadGraph statement is a so called operation This will be described in detail later
13. er is set to 5 therefore it s type is Integer In the second line a mathematical term is calculated and printed The symbol stands for modulo The next input increases number and prints out the new value If the symbol would have been placed after the number then it still would be increased but the non increased value would have been printed The last input has no PRINTLN but still the result is printed The reason is that the result of the input if it has one is always printed In this case the result of number 5 is 11 Even an assignment has a result the assigned value To prevent printing the result the input must end with a like it was done in the previous inputs Leaving out the semicolon is a comfortable way for quickly printing results as seen in the very first example The semicolon is also necessary to execute more than one statement within one line In the following example the statement contains several sub statements separated by semicolons gt PRINTLN number before number number 2 PRINT number after number number before 6 number after 12 gt quit In this example four statements are executed iteratively e Print the value of the number with no changes e Multiply the number with 2 e Print number after but not number e Execute number which means in this case just take the value of number The last statement is not closed with a semicolon so the value of number is
14. h file set window but the set can be edited freely This has no influence on the main graph file set e directed weighted With these checkboxes the respective property can be set for the graphs to load The settings only apply to graph formats which do not specify this properties For example the DIMACS format does not specify if the graph is directed as opposed to the Dot format So when loading a graph file of the Dot format the directed checkbox has no effect e alwaysSimple If this checkbox is checked then loops are always ignored when loading graphs e algorithmSelection The algorithms to compute on every chosen graph After pressing Edit the checkboxes can be used to determine which algorithms to run Every selected algorithm will be run on every chosen graph file For a description of the algorithms see graphana ops pdf e output The file to write the result into The analysis result is a CSV table in which the columns are the selected algorithms and the rows are the chosen graph files The values are the algorithm results e separator The value separator for the CSV output 1 6 Histograms Some graph algorithms deliver not a single number but a 2D mapping These mappings can be saved as CSV file or can be visualized directly within the program One possibility is the use of the Show histogram task of the Tasks menu After choosing the algorithm to execute and pressing Execute the histogram viewer is displayed and sh
15. in ErrIde catch Errlde and CatchStmnt is executed Returns true if CatchStmnt and only if there was no error in the execution of TryStmnt Further information e The Graphana language is not case sensitive but the identifiers of vertices are e Whitespaces can be inserted arbitrarily e It is not possible to declare variables with the same identifier as a prefix keyword of the syntax an operation or a type e Identifiers must not start with a digit 16 Appendix B Some types As already demonstrated in the previous subsection some operations are called with one or more arguments of various types A list of the most important types for a quick overview is given below Type Description Examples in Graphana syntax Integer Integral number 67 45 PositiveInteger Natural number 32 0 Float Floating point number 5 6 3 0 Boolean Truth value true false String Character string Long Text Name File A file or a filename as string directory new _ file txt ExistingFile An existing file directory file txt Graph A whole graph getCurrentGraph Histogram Histogram or CSV string distanceDistribution newHistogram Color RGB Color color 255 128 0 Vertex A vertex of the graph v1 Edge An edge of the graph v1 v2 To lookup operations terms and all types the graphana ops pdf can be used Alterna tively HELP followed by the operation the term or
16. les can be added to the list by pressing Add files Multiple files can be chosen by holding Ctrl or Shift respectivley After confirming the chosen files appear within the list By double clicking one of the graphs in the list the graph is loaded into the program This is a quick alternative of using the loadGraph operation Graph files can be marked and then removed with the Remove button or by pressing the delete key In the list multiple files can be marked at once by holding Ctrl or Shift However only one graph can be loaded at a time The whole list can be saved by clicking Save and choosing a file and loaded by clicking Open and choosing the respective file In addition the current graph file list is always saved when closing Graphana The list is then loaded with the next start of Graphana 1 5 Analysis One important functionality of Graphana is the analysis of multiple graph files The analysis task can be found in the main menu under Tasks Analysis Arguments graphFiles sample dim testgraph1 dim testgraph2 din directed 1 weighted always Simple algorithmSelection Vertex count true Edge count true Vertex output output txt separator e graphFiles The files to analyze By pressing Edit a popup menu appears containing the same interface as contained in the previously described graph file set window By default the set is equal to the main grap
17. nd edges try 13 graphanaAccess execute createGraph true true fails because of forgotten second integer argument graphanaAccess execute addVertexRow 10 vertex not executed graphanaAccess execute addEdge vertexl vertex2 graphanaAccess execute addEdge vertex4 vertex7 keatch GraphanaRuntimeException exception System err println Error O exception getInputKey exception getExecutionError getStringRepresentation J or simply System err printin exception getMessage Visualize the graph try graphanaAccess get UserInterface showGraph GRD true catch ArrangeException exception fails because of invalid layout key System out println Graph_ visualization failed _ exception getStringRepresentation i Print a sum try fails because of wrong return type System out println graphanaAccess executeInt 1 0 4 3 2 keatch GraphanaRuntimeException exception System err println exception get Message Furthermore it is possible to simply start the console user interface by calling graphanaAccess get UserInterface mainLoop The method is blocking until the user quits 14 Appendix A Syntax The following table describes the whole syntax of the Graphana script language Syntax which is written in bold square brackets is optional
18. nguage is described in the next section By clicking the repective keyword it can be inserted into the text input field e Help Documentation and informations about the program In general everything which can be done with the main menu also can be done with the text input field except for the Help item The main menu can be seen as a collection of default text inputs to make it easier to work with the program especially without knowing all operations and the syntax For example the same use case as shown in the previous subsection can be achieved with the main menu without knowing the commands by doing the following e File Load graph clicking open choosing sample dim and confirming e All Operations gt Graph operations General graph properties vertex Count Execute then pressing enter The same with edgeCount e File Exit 1 3 Status bar The status bar informs the user about the current state of the program When the program is idle then nothing is displayed During computations a label shows the current activity and a progress bar depicts the percental progress of it In addition a stop button appears when starting a computation This can be used to interrupt the current computation 1 4 Graph file set window The graph file set can be opened by clicking File gt Graph file set File Edit Add files Remove The graph file set offers quick user access to often used graph files Graph fi
19. or example in JGraphT it is not possible to create graphs which are directed and not simple Initially the JUNG2 library is set It allows every configuration 2 2 Syntax examples Statements may not only contain operation calls However these are sufficient for the basic usage of Graphana In this subchapter the underlying Graphana syntax is explained with the use of examples The first syntax example deals with handling variables gt greetingVar Hello gt PRINT greetingVar World n Hello World Firstly a variable is created and assigned by writing the identifier greetingVar followed by a and the value Hello which is a constant string Therefore the variable greetingVar is a string from now on Every variable is global and usually lives until quitting the program String constants can be surrounded either by quotation marks or by tick marks or The values and also the types of variables can be changed at any time by assigning the variable to a new value Afterwards console output is done by writing the keyword PRINT attention PRINT is not an operation but a keyword of the syntax which does not need brackets to pass the argument The printed sample string is concatenated with the symbol The n yields a linebreak The next example deals with handling numbers gt number 5 gt PRINTLN number 3 5 16 3 41 gt PRINTLN number 6 gt number 5 11 The variable numb
20. ows the result of the chosen algorithm For example if degrees was chosen then the X axis is the degree and the Y axis the number of vertices with that degree The histogram viewer contains a menu bar in the upper edge CSV to file LI Logarithmic scale _ Lines CSV to clipboard 7 Begin at index 0 The left buttons can be used to export the histogram as a CSV string It can be exported as a file or it can be put it into the clipboard for example to insert it directly into a spreadsheet program like OpenOffice The checkboxes on the right hand side influence the visual output of the histogram If logarithmic scale is activated then the Y Axis is a log scale axis This is useful whenever the values are varying widely Especially the log scale yields a linear output for exponential mappings as depicted in the following example Normal scale Log scale 16464 16464 100000 100000 15640 15640 14817 14817 E ne ro ro 12348 12348 11524 11524 10701 10701 9878 9878 1000 1000 9055 9055 8232 7409 7409 6585 6585 100 100 5762 5762 4939 4939 4116 4116 3293 329 10 10 2470 470 1646 1646 823 823 o 0 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 1 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 If Begin at index 0 is not checked then the X axis starts at the first index where the value is non zero Otherwise the X axis always starts at index zero Begin at first non zero index Begin a
21. raph jGraphTgraph System out println graphanaAccess executeInt vertexCover true a The sample firstly creates a small JGraphT graph using the methods of JGraphT Afterwards the framework is initialized and the just created graph is given in to compute the vertex cover size of the graph If no graph is given in like in the first two examples then an empty JUNG2 graph is set Note that only one GraphanaAccess instance should be created per application since the constructor invokes a complete initialization of the framework Furthermore if graphs are not passed as GraphLibrary they are converted within setCurrentGraph so this method should only be called if the graph changed All previous samples did not do error handling Therefore if errors would occur the stack trace would be printed and the program would be closed The GraphanaAccess methods throw GraphanaRuntimeExceptions These can be catched to extract detailed error informations and to print appropriate error messages The following sample tries to create a graph and to visualize it whereas some exceptions are thrown public static void main String args Initialize GraphanaAccess graphanaAccess new GraphanaAccess Output a string try fails because of incomplete statement graphanaAccess execute PRINT_ Hello kcatch GraphanaRuntimeException exception System err println exception get Message Create some vertices a
22. s in creased Prefix Ide Increases the value of the existing variable Ide increment by 1 Returns the value of Ide after it was in creased Postfix Ide Decreases the value of the existing variable Ide decrement by 1 Returns the value of Ide before it was de creased Prefix Ide Decreases the value of the existing variable Ide decrement by 1 Returns the value of Ide after it was de creased Statements X X3 ES qa Executes X to Xn Returns result of Xn 15 Name Syntax Description If then else if Cond Executes ThenStmnt if Cond is true Executes ThenStmnt ElseStmnt if it is given and Cond is false else ElseStmnt 1 Returns e Result of ThenStmnt if Cond is true e Undefined if Cond is false and no else is given e Result of ElseStmnt if Cond is false and an else is given While loop while Cond Executes Stmnt as long as Cond Boolean is full Stmnt filled For loop for Init Cond lter Firstly executes Init and then repeatedly Stmnt Stmnt and Iter as long as Cond Boolean is fullfilled Vector L1 2 2 Ln Returns a vector with the given entries Vector access Ideli Returns the i th entry of the existing vector Ide The first entry is at i 0 The last entry is size Ide 1 Set 1 2 Ses Ln Returns a set containing the given values Try catch try Executes TryStmnt If an error occurs execu TryStmnt tion is aborted the error is stored
23. t zero index 26 26 25 25 24 24 22 22 21 21 20 20 19 19 17 17 16 16 15 15 14 14 12 12 1 11 10 10 9 kg 6 5 5 z f 1 222 227 232 237 242 247 252 257 262 267 272 277 282 287 292 12 32 52 72 92 112 132 152 172 192 212 232 252 272 239 The histogram view can display multiple histograms at once For example after the degrees of one graph are displayed another graph can be loaded without closing the histogram view When running the histogram task again without enabling the clearPrevious checkbox the degree distribution will be displayed within the same view This enables a visual comparison Sometimes it is better to select the Lines checkbox when displaying multiple histograms Multiple histograms The same with lines mode 7 G 2 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 2 11 24 55 86 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 7273 74 75 76 77 78 79 80 81 82 83 84 Ep 0807 05 00 69 Gt G2 CF 64 ES ES 7 CS CD TO TI PESO o a a x w v N 1 1 o o o o Baas OCS aS iL Bee See 54 55 56 57 58 59 60 61 G2 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 To use separate views instead different titles must be given when running the histogram task 2 Script language The user inputs and other inputs that will be described later as the ones of the simple session example contain so called statements This section describes syntax and semantics of these statements
24. tln averageDegree The next example loads a graph instead of creating one and prints the number of connected components graphanaAccess execute loadgraph graphs sample dim int ccCount graphanaAccess executeInt getConnectedComponentCount System out println ccCount If there is already a graph instance within the application it is also possible to apply graph op erations on this graph by using the method GraphanaAccess setCurrentGraph The method can either be called with a JUNG2 graph a JGraphT graph or an instance of GraphLibrary the latter is described in graphana_extension pdf All graph operation calls which follow after the setCurrentGraph call will use the given graph The following example demonstrates the usage of the framework with an externally created graph instance public static void main String args Construct sample JGraphT graph SimpleWeightedGraph lt String Object gt jGraphTgraph new SimpleWeightedGraph lt String Object gt JGraphTWeightedStatusEdge class 12 jGraphTgraph addVertex VI jGraphTgraph addVertex V4 jGraphTgraph addVertex V8 jGraphTgraph addVertex TT jGraphTgraph addVertex X jGraphTgraph setEdgeWeight jGraphTgraph addEdge V1 V4 7 jGraphTgraph addEdge V8 V4 jGraphTgraph addEdge TT X Use framework GraphanaAccess graphanaAccess new GraphanaAccess graphanaAccess setG
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