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The Bio7 User Guide

1. Tmesteps 0 samofsoem Illustration 11 Before the resize Illustration 12 After the resize 1000 1000 When moving the sliders for the field size several views and arrays will be updated according to the new values The following panel with their underlying arrays will be 27 No Plant selected Coordinates X 0 Y 0 E Change global Illustration Individual Properties Anthesis start Anthesis end Shoot height Shoot width Shoot surface Root depth Root width Rootsurface Dispersal month Establishment p w 0 Distance of dispersal 0 13 28 updated when a resize event takes place The Quadgrid panel the Hexgrid panel the soil panels and the visualization of these in 3d the 3d panel After resizing the new indexes are instantly available for plants and numeric values e g programmatically When the checkbox Resize after adjust is activated the resizing takes place after the button Resize has been pushed This is recommended when the field size is gt 400 because the resizing then is done in one call Info The speed of a resize event is also dependant on the amount of grid panels which are currently visible in the Bio7 window 6 2 4 2 Plant Individual If the item Plant Individual is activated a panel will be opened which embeds
2. File location Extension Action Navigator bsh Interpreting BeanShell Navigator java Compiling Java Compiler Navigator ecor Interpreting R Navigator txt Executes an ImageJ Macro Navigator pdf Opens a pdf file Navigator bat Executes a batch file Windows Navigator sh Executes a shell file Linux Navigator argument Assignment to BatchModel argument String External exe Execution with argument when available External XXX Execution of the registered program 7 4 8 Important to know The dropped file components in the flow can be opened and edited with a double click on that component If a flow is executed a modal dialog will appear each time a file is executed Please select the General gt Always run in background option in the preferences dialog to avoid this A static variable is available to trigger the cancellation This can be used for example in swt shells See the Bio7 API for more methods Class Bio7Flow Table 20 Code snippet Bio7Flow setCancel true 75 8 The Preferences The preferences dialog in Bio7 is divided in the preferences for the platform Generals Help Install Update and the Bio7 Preferences Each of the preferences are organized hierarchically in a tree viewer structure for a better overview Table 21 From Eclipse 3 2 The Preferences dialog is the dialog used to set user preferences The Preferences dialog pages c
3. You can use the Export wizard to export resources from the Workbench to an archive file in the file system 1 In one of the navigation views select the resources that you want to export 2 From the main menu bar select File gt Export The Export wizard opens 3 Select General gt Archive File and click Next 4 By default the resources that you selected will be exported along with their children Optionally use the checkboxes in the left and right panes to select the set of resources to export and use push buttons such as Select Types to filter the types of files that you want to export 5 Specify the path and name of the archive file into which you want to export the selected resources 6 Click Finish 126 14 7 Execute evaluate and plot a R script To execute evaluate and plot a RScript the following procedure can be applied 1 Create a new RScript with the Wizard of Bio7 File gt New gt Bio7 gt RScript 2 Insert the code from Table 42 in the script 3 Then interpret the RScript 4 Open the expression dialog R gt Evaluate Expression and evaluate the following expression a summary d gt prints a summary of the interpoint distances to the console 5 Now create a simple boxplot of the interpoint distances Add the following line at the end of the script in Table 42 a boxplot d 6 Then mark this line by selection with the plotmarker in the context menu 7 Interpret the
4. 2 setRdepthmin 13 int rdepthmax Root depth gt maximum root depth 1 getRdepthmax 2 setRdepthmax 14 int rwidthmin gt minimum root width 1 getRwidthmin 2 setRwidthmin 15 int rwidthmax Root width gt maximum root width 1 getRwidthmax 2 setRwidthmax 16 int rsurface Root surface gt surface of the root a getRsurface 2 setRsu rface 17 boolean vegetative gt ability to disperse vegetatively 1 isVegetative 2 setVegetative 18 boolean sexuell gt generally true can be also apomictic 1 isSexuell 2 setSexuell 19 int dispersalmax Distance of dispersal gt maximum dispersal distance of seeds 1 getDispersalmax 2 setDispersalmax 20 int dispersalmin gt minimum dispersal distance of the seeds 1 getDispersalmin 2 setDispersalmin 21 int spreadafter Dispersal month gt age of first reproduction of plant 1 getSpreadafter 2 setSpreadafter 22 int established Establishment p w gt How many seedlings will survive and can establish 1 getEstablished 2 setEstablished 23 boolean near gt disperses the plant in the near surroundings 1 isNear 2 setNear 24 boolean far gt does the plant species disperse over long distances 1 isFar 2 setFa r 25 boolean seedbank gt importance of seedbank for plant species and its survival 1 isSeedbank 2 setSeed bank 106 The followi
5. Bsh Console An outline is not available E Properties Illustration 35 Opened Java editor Compilation Compilation of the active Java file will be easily executed when clicking on the Compile Java toolbar item which is visible when a java file has been opened The compiled class is programmatically available by a static variable method in the class Compiled Compiled getEcoclass ecomain gt will call the ecomain method which has been compiled by the embedded compiler A lot of imports are transferred to the compiler by default to access all Bio7 methods and the API Extra imports can be made like in regular Java files see Snippets Note The default imports for the java compiler can be changed in the file plugins com eco bio7_1 0 0 bin imports compiler properties Windows It is also possible to create a setup method If you embed a method with name setup public void 59 setup after the compilation you will be able to call this method with an embedded script to set states or call another setup method Scripts gt General Scripts gt Setup You can also change the script for calling custom methods etc from the compiled class 7 3 2 BeanShell The BeanShell editor as well as the Java editor supports the Java syntax Code templates identically to that in the Java editor are available too some script code templates can differ In General BeanShell is capable to interpret or
6. not recursive e A loop can be connected point to a decision 5 Decisions a A decision gets an input from a component and has to have two outgoing connections One connection has to be set to false and the other has to be set to true b A decision can be connected to another decision else if C A decision cannot be connected point directly to a loop d It is allowed in Bio7 to place a decision right after the start Pl Illustration 48 Example of decisions inside a flow 72 e The condition of a decision component can be set directly in the properties view or in the component itself The static variable decision has to be set to true or false type String to follow a connection with the appropriate value gt BatchModel setDecision true gt Illustration 49 A flow with an info 6 Info An info component can be placed outside the connected flow for an information It is also allowed to draw connections to a file component as a pointer you can mark this connection with a changed line style Console Bsh Console Properties gt Property Value Boolean true LineStyle Solid Illustration 50 A decision with an expression and a connection with a boolean value 73 7 4 6 How to Cancel a flow A loop can be cancelled with the Cancel button in the progress dialog the dialog is only displayed for long operations or by selecti
7. Bio7 User Guide Version 1 1 Department of Experimental and Systems Ecology M Austenfeld 1 Introduction S 1 2 Why Bio7 5 3 2 1 Ecological Background 3 The components of Bio7 S 4 3 1 Image Analysis 3 2 Statistical Analysis 3 3 Visualisation 3 4 Database 3 5 Plants 3 6 Nutrients 3 7 Sensitivity Analysis 4 Getting Started sii 5 The Platform Architecture S 14 5 1 The Toolbar 5 2 The Menu 6 The Perspectives of Bio7 S 18 6 1 The Resource Perspective 6 1 1 The Navigator 6 1 2 The Editor Area 6 1 3 The Consoles of Bio7 6 1 4 The Snippets view 6 2 The 2d Perspective 6 2 1 The Quadgrid 6 2 2 The Hexgrid 6 2 2 1 Storage of patterns and IBM properties 6 2 3 The Linechart and the Piechart 6 2 4 The Control 6 2 4 1 Time and Space 6 2 4 2 Plant Individual 6 2 4 3 Disturbance 6 2 4 4 Abiotic Factors 6 2 5 Plants States 6 2 6 Spreadsheet 6 3 Image Perspective 6 3 1 ImageJ Canvas 6 3 2 Points panel 6 3 2 1 Using the Points panel for spatial continuous simulations 6 3 3 Thumbnails 6 4 The Soil Perspective 6 4 1 The Soil 6 4 2 Nitrate 6 4 3 Phosphate 6 4 4 Carbon 6 4 5 Water 6 4 6 Root Density 6 4 7 Additionally 6 5 The Database Perspective 6 6 The 3d Perspective 6 7 Custom Perspectives 6 7 1 Custom Views 6 7 2 Custom Menus 6 7 3 Custom Startup 7 The Editors of Bio7 52 7 1 General Features 7 1 1 Code Templates 7 1 2 Preferences of the Editors 7 2 The R Editor 7 2 1 Evalu
8. Bio7 offers several visualization panels for spatial models The application can visualize discrete hexagons and quads in 2 dimensional and 3 dimensional space For spatial analysis and modelling Bio7 offers a 2 dimensional drawing panel This panel can be used to discretize values via the Image Analysis support and set values which then can be send to the statistical tool to make all kind of spatial analysis All panels can be accessed and modelled within an editor The 2 dimensional panels are highly interactive to support the settings of values for nutrients and plants File Edit Preferences Scripts R OpenOffice Bsh Window Help AO We A Rebs 6 fey Resource 2 Image EH Soil Database 2d 1 3D i 3 E s ee i k ee t OO 0e ee se ese eses se a a 03 Ha Re A aa oseeses Wren Da PH sete ve R v Timesteps 8 47mofsoam i 3 4 Database All plants for simulation or analysis can be stored in an object orientated database The database form contains general attributes which are useful in simulation and also descriptive for the plant species For a simulation the database plants can be activated by the spreadsheet form After activation the plant object and all of the plant attributes from the database are accessible Also deleting or updating of values of a plant in the database is easily done by activating it in
9. centerofmass To transfer this values it is necessary to select all particle measurements to be transferred before the analysis is started Analyse gt Set Measurments Set Measurements IV Area iV Mean Gray Value Standard Deviation Modal Gray Value IV Min amp Max Gray Value V Centroid V Perimeter Fit Ellipse Feret s Diameter Median Kurtosis Area Fraction Slice Number Limitto Threshold J Display Label Invert Y Coordinates Redirect To None v Decimal Places 0 9 g Illustration 84 Set measurements dialog 1 In the dialog all required measurements have to be selected before a Particle Analysis is started The Centroid option always needs to be selected and is by default 2 Then the particles can be analysed 118 3 Now instead of the first points transfer method the second method must be selected in the detached Image Methods view When executing this action all measured particle values will be transferred directly to R without detour over the Points panel Bsh Console ETTE les Ex bi ef peo E Bio Console 1 area area_fraction centerofmassx 4 centerofmassy centroidx centroidy 7 circularity ellipse_angle ellipse_major 10 ellipse_minor ferrets_diameter integrated_density 13 invert y kurtosis labels 16 limit max mean 19 median min mode 22 perimeter rect_height rect_width 25 rectx sk
10. highest 6 4 5 Water A Panel for water availability is also available for displaying water content in a discrete grid Values from white to blue will display values from 0 1000 44 6 4 6 Root Density A further panel visualizes the root density in a grid This Panel can be used to model belowground activities of plants Low values are yellow high values are marked black 6 4 7 Additionally The panels can also be used to visualize other important driving factors in an ecosystem For example the Root Density Panel can be used to visualize mycorhizzal activities or the nitrate panel can be used to display the amount of nitrogen fixation of bacteria etc All soil panels serve to visualize simplified and generalized information of complex processes in the belowground sphere of ecological systems 6 5 The Database Perspective The Database perspective offers two views In the Formular view a form is available for creating Plants in an object oriented database dbo4 These stored plants are used as templates for the Quadgrid Hexgrid Plant array The database will be updated with a new plant when the Send action has been invoked Update and deletion of plants is similarly simple If plants in the database are to be updated or Bio7 wleles File Edit Preferences Scripts R OpenOffice Bsh Window Help Wl O o k ARIUS BY Resource 3 Image Soil E Database EEE 2a E Species Synonym Enable Coryn
11. x Perspectives 7 Open a new perspective In the same window O In a new window Open a new view within the perspective O As fast view Open the associated perspective when creating a new project Odlways open O Never open Prompt Available perspectives EEE 2d default E 2 Database A Image D Resource Resource 38 soil Note Reset takes effect the next time the perspective is opened F gt Cancel Illustration 60 Perspective options of Bio7 85 8 2 6 File Associations Table 27 From the Eclipse Workbench User Guide http help eclipse org On the General gt Editors gt File Associations preference page you can add or remove file types recognized by the Workbench You can also associate editors with file types in the file types list File types list Add Adds a new file or file type extension to the predefined list In the resulting New File Type dialog type the name of a file or a file extension If you are adding a file extension you must type either a dot or a before the file type e g xml or xml as opposed to simply xml e Remove Removes the selected file type from the list Associated editors list e Add Adds a new editor to the list of editors associated with the file type selected above In the resulting Editor Selection dialog you can choose an editor to launch either inside the Workbench internal or outside the Workbench external click
12. Browse to locate an editor yourself if the editor you want is not displayed in the list e Remove Removes the association between an editor and the file type selected above e Note Any editor that is bound by content type may not be removed from this list Currently there is no mechanism available to remove these editors e Default Sets the selected editor as the default editor for the file type selected above The editor moves to the top of the Associated Editors list to indicate that it is the default editor for that file type For more information about the preferences of the platform please read the Workbench User Guide Eclipse platform 86 9 Help 3w Help Welcome d Help Contents Dynamic Help rpc er hig Add Update 01 About Bio Illustration 61 Help in the help dialog For a first help simply activate a Dynamic Help selecting a view and activating the F1 key After activation a context help will be shown in the help view can be changed to an infopop in the preferences if activated By selecting the submenu Help Contents the regular help will be opened The Welcome action opens a welcome page for the Bio7 application The About Bio7 dialog opens an information about the current release of Bio7 10 Installing new features with the update manager Table 28 From the Eclipse Workbench User Guide http help eclipse org To locate and install a new feature into a pro
13. Window Oy Emoe ian aul d Image Methods Alpha Image Resize Points Panel I E Thumbnails 5 Fieldsize Y 300 mam s gt 10 gt 15 gt Small feldsize x Point Size Alpha MEK Particles Point selections Timesteps 0 isMof 23M Illustration 91 Transferred image with a random function 130 8 Now the images which are opened in tabs in the ImageJ view can be converted to a stack with the command Image gt Stacks gt Convert Images to Stack v Image Process Analyze Plugins Wind B Type dT Bio Bio Bio Adjust Sa Rotate gt Colour gt Stacks gt Add Slice Zoom gt Delete Slice Lookup Tables Next Slice gt Show info Previous Slice lt Properties Set Slice Crop Convert Images to Stack Duplicate Convert Stack to Images Rename Make Montage Scale Reslice Z Project 3D Project Plot 2 axis Profile Start Animation Stop Animation Animation Options T Illustration 92 Convert images to a stack 9 After the Stack has been created it is possible to add text or fill shapes inside a frame of the Stack a To do that we select the first frame of the stack to create a custom info Illustration 94 The text tool applied Illustration 93 Using the tools of to the presentation ImageJ to create a presentation 131 10 Use the the Polygon select
14. 2 3 4 5678 9 1 Play Pause gt Starts or stops a simulation run This action will start the calculation thread of the application The calculation thread will call the ecomain method in the embedded Ecoclass When using the embedded compiler a new object of that class will be created The visible part in a new created Java file is the classbody which will be compiled to use in the calculation thread See the different snippets for examples 2 Reset gt Resets the discrete grid in the application This action will reset all states in the Quadgrid Hexgrid arrays to the value O and to soil object Plant array The submenu item resets the plant array to a null reference 3 Counter Reset gt Resets the counter to null This action will reset the time to the value 0 and will also update the Linechart 4 Random gt Distributes selected plants from the database in the discrete field There are two random functions available in the menu of this item to randomize the field If you press directly on the button only activated plants from the database and the soil state will be dispersed objects and numeric values for use in a IBM model If you select the submenu item all states will be dispersed in the numeric array except the objects in the Plant array see section 6 2 1 The Quadgrid If you want to disperse random cells for example for the Game of Life the last option is sufficient 15 5 OpenOffice gt Will open a connection to Ope
15. 47 Dynamic R in Bio7 This Snippet is an easy example how to get variables from R after a calculation and embed it in an simulation run try catch are necessary import org rosuda JRclient RSrvException 140 public void ecomain double result null try Rserve getConnection eval A lt c runif 100 100 Get the results from R result double RServe getConnection eval summary A getContent catch RSrvException e System out printIn e getRequestErrorDescription t for int i 0 i lt result length i System out printin result i 141 14 16 Import external libraries to BeanShell To import external libraries to BeanShell simply right click in the Navigator on a jar Java library file The action will only be visible in the context menu of the Navigator if a jar file is selected New Open Open With gt gt Copy 3 Delete Move Rename gy Import L Export Refresh Add jars to bsh classpath Properties Illustration 103 Add jar to BeanShell Multiple selections are possible and will be added to the namespace of the BeanShell interpreter See the BeanShell manual for more information 142 14 17 Compile and run Java files In the context menu of the navigator another option is available to compile and run an opened java file This menu point is enabled when a java file was select
16. B D 2002 Modern Applied Statistics with S Springer Verlag NY Michael J Crawley 2007 The R Book Wiley amp Sons Ltd Kaluzny S P Vega S C Cardoso T P et al 1998 S Spatial Stats User s Manual for Windows and UNIX 1 Auflage Berlin Springer Image Analysis Burger Wilhelm Burge Mark 2007 Digital Image Processing in Java Springer Verlag London 148 17 Addendum View Id 3Dgrid com eco bio7 3d Piechart com eco bio7 piechart Linechart com eco bio7 linechart Quadgrid com eco bio7 quadgrid Spreadsheet com eco bio7 spreadsheet Form com eco bio7 form State com eco bio7 states Hexgrid com eco bio7 hexgrid Custom Chart com eco bio7 custom_chart Points com eco bio7 points Image Methods com eco bio7 image_methods Nitrate com eco bio7 nitrate Bsh Console com eco bio7 bsh Control com eco bio7 control Soil Parameter com eco bio7 soil_parameter Phosphate com eco bio7 phosphate Water com eco bio7 water Carbon com eco bio7 carbon Roots com eco bio7 roots Custom Controlls com eco bio7 custom_controls Custom 3d com eco bio7 custom_3d Navigator org eclipse ui views ResourceNavigator Progress org eclipse ui views ProgressView Bookmark org eclipse ui views BookmarkView Tasks org eclipse ui views TaskList Problems org eclipse ui views ProblemView Console org eclipse ui console ConsoleView Properties
17. Export Scripts The script is added automatically to the menu and will be executed when selected 137 O content context_help 2 database E html O icons ijplugins Ordner export_scripts Neuen Ordner erstellen Illustration 100 Script location File Edit Preferences Scripts R OpenOffice Bsh Window H Py New e Load Pattern ke Save Pattern Process Analyze Export_Pattern Import Scripts b Ctrl S All Ctrl Shift 5 2ave AS s Import e Export Exit Convert Line Delimiters To Open File Illustration 101 Embedded script in the menu The same procedure is applicable to the other script menus Macros for ImageJ have to be dropped to the ImageJ Scripts location with the same procedure 138 14 13 Compile Java files to BeanShell To add a compiled Java file to the BeanShell namespace you have to simply right click on a java file in the Navigator Only if a java file is selected the menu will be extended with the action Add Java to bsh classpath el New gt aoa GetBeans eld OPen Snippet_comp Fa Copy OpenGL Snippets OpenOffice Snipp Delete Move 1e not available Import L Export Refresh Compile and Run Add java to bsh classpath Illustration 102 Extended the context menu in the Navig
18. Furthermore an advantage of this platform is the plugin structure which can be extended with all kind of third party plugins to support theoretical hypothesis on ecosystems functioning and the understanding of complex systems The following picture illustrates the different components of Bio7 2 Why Bio7 2 1 Ecological Background One research area of the chair of experimental and systems biology Bio7 are dry acidic grasslands on inland sand dunes Only specialists like Corynephorus canescens Polytrichum piliferum etc can settle on this nutrient poor water limited sandy soils Additionally high temperatures on the surface of the soil and erosion make it very hard for other species to settle there In comparison to other ecosystems this habitat is less complex in its species structure and nutrient dynamics which facilitates monitoring of vegetation dynamics to identify the driving forces or key factors of the system With the survey of this ecosystem several questions and hypothesis should be answered and verified Because many specialized plants and animals occur in this habitat the main question is how we can protect and preserve this valuable ecosystem at all Also the key Factors are from high interest and can maybe serve to identify similar processes in more complex systems like the tropical rainforest From various experiments in these systems we have knowledge about seed dispersion competition and nutrients availability or dependenci
19. Not only a call to a R method is possible by means of compiled code but also calls from the BeanShell interpreter can be realized to transfer values to a BeanShell workspace Table 29 Code Snippet Transfer values from R to Beanshell Rserve getConnection eval A lt c 3 5 3 6 Rserve getConnection eval B lt c 3 6 4 5 Rserve getConnection eval C lt A B double result double Rserve getConnection eval summary A getContent RServe print C for int i 0 i lt result length i System out print result i 91 Because the bidirectional transfer of data in between for example R and BeanShell or Java is possible the following interaction methods can be done 1 Custom GUI s can be created in BeanShell and the values can be evaluated in R After evaluation the results can be sent back to the BeanShell namespace or to a method in Java 2 Build frontends for R methods with created GUI s in BeanShell 3 Interaction between R and the API of ImageJ to do profound Image Analysis and statistical evaluation with BeanShell or by compiled code 4 Extend the script menus of Bio7 with R methods called by BeanShell 5 Creation of a complete flow from easy data transfer OpenOffice over evaluation RScript up to data visualization Also possible in one file with BeanShell 6 The Flow editor can be used to arrange a flow of interacting files which guides the
20. This editor can be opened with a right click in the Snippets view Copied text from any text based editor of Bio7 can be pasted directly as a snippet after a category has been created inside the view Also more complex templates with variables and a detailed description can be created This is extremely useful if you want to create custom formulas or statistics A created template will be transferred to an active editor with a double click of the mouse device Optional the different categories can also be folded and customized for a better overview 22 6 2 The 2d perspective Bio7 amx File Edit Preferences Scripts R OpenOffice Bsh Window Help W od k Ahi g pad 3d Resource 3 Image FH Soil B Database i 2a HH state 23 Ta a Spreadsheet 2 ora re Species Synonym Enable Select Plant1 lant FSOTC 2 nt e Piechart lt a a States 0 Oo g Control A Time and Space Plant Individual Disturbance Planti 836 soil W Pianti M Plant2 co PcG Peo R Abiotic Factors tw Linechart ea States 0 25 0 50 075 1 00 Iteration soil W Planti Plant2 Timesteps 8 samofsosm iy Illustration 6 The 2d perspective of Bio7 The 2d perspective offers several views for displaying and adjusting simulations of spatial disc
21. activated the Area of Analysis will be adjusted to the size of the Quadgrid 19 Area of Analysis 6 The next slider has the function to zoom out of the panel for an overview When zooming has been activated the points still stay selectable or dragable because the coordinates are automatically translated The scrollbar will be adjusted to the size of the Area of Analysis 36 7 The size of the Area of Analysis can be adjusted with the two spinners Fieldsize X Fieldsize Y which can be set from 1 10 6 units When the size of the area will be changed automatically the scrollbar will be fitted to the new size of the green rectangle 8 The size Particle Size and the alpha value Alpha of the points or particles can be changed with the spinners below the size spinners 9 With the Pic gt button it is possible to transfer images that have been loaded with ImageJ directly to the Points panel to use as a matrix to select point patterns etc The size of the Area of Analysis will be changed according to the size of the image 10 The below Pic lt button sends an rgb image back to the ImageJ canvas It is important to know that the transferred image to ImageJ depends on the Area of Analysis and the zoom factor of the Points panel If the Points panel is not zoomed and the Area of Analysis is 1000 1000 this will result in a 1000 1000 image in ImageJ If the Points panel was s
22. browser Thumbnails offers the possibility to open directories and the included images as thumbs which than can be opened directly in ImageJ 32 Bio7 BAX Fie Edit Preferences Scripts R OpenOffice Bsh Window Help HW O H k ALRI hHS Ey Resource E Image iii Soil DBDatabase ii 2d d ImageJ Canvas File Edit Image 7 Process Analyze Plugins Window 7 Thumbnails 2 amp 2 s gt 10 gt 15 gt Small Medium Large 10 x Timesteps 0 3am ofsoam i Illustration 17 The image perspective 6 3 1 ImageJ Canvas For a complete description of the program ImageJ follow the link http rsb info nih gov ij The differences between the regular version of ImageJ and the integrated version in Bio7 are described here 1 The ImageJ Canvas is embedded in Bio7 2 The Toolbar of ImageJ Illustration 18 is integrated in a view when called form the menu Window gt ImageJ Toolbar as a detached view aoao NA OZ 77a Magnifying glass or use and keys Illustration 18 ImageJ tools as a detached view Simply drag and drop images on the view to open them 33 3 The menu of the integrated application has been reprogrammed as a view menu which is similar to the original ImageJ menu 4 All images are opened in tabs and can be edited separately 5 Since Bio7 1 1 external plug
23. discrete Field El 2 Bio _Examples public void ecomain Ecological Modelling randomwalk static void randomwalk int tmpi 0 int tmpu 0 int zuf 1 0 1 for int i 0 i lt getHeight i for int u 0 u lt getWidth u int zi int Math random 3 int zu int Math random 3 BE Outline 5 O E Bsh console El console amp Properties Ex BE cf ey is An outline is not available Bio Console g Timesteps 8 Writable Sma ert 42M of 508M m Illustration 2 Opened Flow editor 20 opened file Compilation for Java Interpreting for BeanShell or R and execution of a Flow See Section 7 The Editors of Bio7 for more information 6 1 3 The Consoles of Bio7 The consoles of Bio7 are important for the output of information gained from the embedded Java compiler or from the different script languages The Bsh Console Beanshell can interactively communicate with the Bio7 application or simply interpret different instructions in Java or the optional scripting language The Console is responsible for the 1 Output messages for the interpreter 2 Output messages of the embedded Java compiler compiler warnings infos etc 3 Output of the R interpreter Rserve warnings etc and evaluated expressions in R For example a call like System out printIn Hello World will be printed in the Console if executed in the BeanShe
24. ecomain for int i 0 i lt Field getHeight i for int u 0 u lt Field getWidth u E For iterate over array A ffor int index 0 index lt Field getHeight index ight modulo die r bio gt modulo 2d A loop over 2 D bio array E bio gt random loop with random function for iterate over array with temporary variabl For iterate over collection E foreach iterate over an array or Iterable while iterate with enumeration Illustration 29 An example of Code Completion 53 Table 15 From the Eclipse Workbench User Guide http help eclipse org Templates are a structured description of coding patterns that reoccur in source code The Bio7 editors support the use of templates to fill in commonly used source patterns Templates are inserted using content assist Ctrl Space For example a common coding pattern is to iterate over the elements of an array using a for loop that indexes into the array By using a template for this pattern you can avoid typing in the complete code for the loop Invoking content assist after typing the word for will present you with a list of possible templates for a for loop You can choose the appropriate template by name iterate over array Selecting this template will insert the code into the editor and position your cursor so that you can edit the details Templates for the language
25. examples which should facilitate the development of ecological models The examples are so called Snippets short programming examples which are numbered and divided into two projects One project Bio7_Examples contains snippets for the different components of Bio7 which demonstrates how to use them and the flexibility of the platform in general The other project Ecological Modelling contains snippets as examples for ecological modelling This Snippets also show that you can use the different embedded application and modules to understand and analyse complex systems or bundle them in ecological modelling for more complex purposes The examples are available as projects Please import the file File gt Import gt Existing Projects into Workspace into the workbench see Section 14 6 1 for details about import 96 14 How to s In this section several tutorials describe the abilities of the Bio7 platform 14 1 First steps 14 1 1 Game of Life 1 2 3 4 5 Open the Game of Life in the Project Ecological Modelling gt Cellular Automata Game_of_Life java or Easier_Game_of_Life java with a double click of the mouse Compile the source directly with the compile action which is active when the file has been opened Create an additional state Now select the random function which disperses active states in the cell select the first random function which disperses all states Soil dead alive 1 Press the start action o
26. graphic program like Gimp to facilitate the automatic recognition of these in ImageJ 119 Image Analysis z N Pi SAAE a IT Wy 1 ira a ae tat ul aa ee Q Aa aN R A ie P manii J ere hs ae E oy a E i E hts a Rie a Ta T Sip e She 3 om Si AS n hos R s gyt aN J lee Shs EES 7 Ces g d AK 4 xa oh at 3 IE tgs oN ARE e E a a at a K A R n Steg Piet ATEA SIA Illustration 86 Different species added to the Points panel for vegetation analysis A good start for similar topics are the tutorials on the Imagej website which may be applicable to complex vegetation issues Additionally R offers strong packages for spatial analysis Visit the RSpatial project website at http sal uiuc edu csiss Rgeo for more information 14 5 Transfer a spatial point pattern to a grid In Bio7 it is possible to map a spatial pattern from an image to the discrete Quadgrid and indirectly to the Hexgrid To do this follow exact the procedure of the previously described method to transfer points from an analysed image to the Points panel The difference is that the Quadgrid has to be activated in the Points panel This can be archieved with the method set or unset discrete grid field in the Points panel If the grid is activated it will be shown as an additional layer in the Points panel The alpha for the grid can also be adjusted to make all activated components visible in the panel image or
27. inside the array plant of type Plant and the optional temporary array planttemp gt not necessary in this example 8 In the last step if the value for the state soil 0 has been selected 9 A soil object will be created at the specified index To create the method we compile everything to the calculation thread and then start the calculations with the Start Pause action 14 3 1 How to get and set Plant values in the Quadgrid Hexgrid E g if a Quadgrid was filled with Plants the first step to change a value would be to use the individual plant panel in the Control view Every plant which has been selected is an individual object and none of the modifications to this does reflect on the other objects in the grid If the action Change global is selected all values of the selected individual will modify the values of all objects that belong to the same species identified by the species name in the grid This can also be done programmatically by selecting an individual through its index in the Plant array Then the attributes of this selected plant can be adjusted The following list is a description of all available database attributes from a Plant object with methods to access it get set Underlined individual attributes with their Control view synonym in brackets are adjustable in the Control gt Individual Plants view For some individual attributes the maximum values will be adjusted for instance sheightmax Shoot height
28. loaded and used for simulation purposes in Bio7 2 The Save Workspace action saves the current workspace which has been established with the Rserver 3 Evaluate Expression opens a dialog where R expression can be evaluated The evaluated expression will be displayed in the Console of the Bio7 platform 90 4 Evaluate Selection evaluates the selected line in the R editor and then jumps to the next line Since Bio7 works with one connection to R sometimes it is necessary to delete all variables from the current workspace The action Remove all objects removes all objects from the current workspace Because sometimes capabilities of Bio7 in respect to R do not fullfill the needs for a direct evaluation for example plotting error analysis it is possible to start a complete standard RGui Windows with the current workspace a temporary workspace will be created and then opened with the RGui This will be invoked with the Start RGui with Workspace action The path to the temporary file can be adjusted in the Preferences of Rserve Another feature is a direct interaction with OpenOffice if installed where values easily can be transferred to the current workspace of R see OpenOffice features Additionally a nice feature in Bio7 is the direct interaction with the Rserve interpreter Not only for evaluation but also to obtain values from R to Java or BeanShell is valuable for the creation of ecological models
29. option allows you to determine whether the window context help will be opened in a dynamic help view or in an in a dynamic context help infopop help view In Bio7 press F1 to activate the context help This option allows you to determine whether the dialog Open dialog context help will be opened in a dynamic help section of help in dialog tray context help view or in an infopop Help view document open This option allows you to determine whether the documents selected in the help view will be opened in place or in the Open in place mode editor area Determines whether potential hits should be shown while Show all Search searching Showing potential hits will increase search potential hits performance at the cost of potential loss of accuracy faster 8 2 5 Perspectives On the General gt Perspectives preference page you can manage the various perspectives defined in the Workbench Table 25 From the Eclipse Workbench User Guide http help eclipse org Option Description Default Open a new Use this option to set what happens when you open a new P P pp y P In the same erspective erspective Do you want the perspective opened within aR PE y pirak P window leave the current Workbench window or opened in a new this option as it is window in Bio7 Open a new Use this option to specify what happens when a new view is view opened It is either opened to its defau
30. org eclipse ui views PropertySheet Outline org eclipse ui views ContentOutline To use programmatically Work openView Id Example Work openView com eco bio7 quadgrid 149 Perspective Id 2d com eco bio7 perspective_2d 3d com eco bio7 perspective_3d Database com eco bio7 perspective_database Image com eco bio7 perspective_image Soil com eco bio7 perspective_soil Resource org eclipse ui resourcePerspective To use programmatically Work openPerspective Id Example Work openPerspective com eco bio7 perspective_2d A saved custom perspective is available by it s name For example Saved as Custom gt Work openPerspective Custom Bio7 API A small API is integrated in Bio7 The API is available within the help of Bio7 150 18 Definition of expressions Area of Analysis A name for the area in the Points panel which is marked by a green rectangle for spatial point patterns Programmatically Using programming to accomplish a task Namespace BeanShell A namespace in which methods variables and imports class names live Workspace R A saveable environment in which methods variables and objects exists Workspace Bio7 The location where the projects and files are stored Calculation thread A time dependant execution of a compiled method ecomain in Bio7 started e g with the Play Pause button Discretize In Bio7 the process
31. points 1 Activate and scale the Quadgrid in the Points panel Scaling can be done with the scroll wheel for the Quadgrid in the Points panel a The scaling can be used to calibrate the size of the grid to which particles should be mapped grid resolution 120 2 Open the blobs example in the ImageJ view File gt OpenSamples gt blobs gif 3 Adjust the threshold of the image the way that all blobs are selected and marked with red Image gt Adjust gt Threshold 4 Send the image to the Points panel to adjust the Area of Analysis You can remove the image afterwards iii State 2 O 5 Select an activated state in the Plants view p Plant2 ici a 6 Now execute a particle analysis Analyze gt Analyze Particles 7 Transfer the particle values to the Points panel Illustration 87 The Plants 8 Which grid cell will be marked as adjusted state depends on view to select a state the centroid values from the particles measurement rounded values Illustration 88 Transfer of Points to the Quadgrid 121 14 6 Import and Export Projects and Files 14 6 1 Import existing projects Table 37 From the Eclipse Workbench User Guide http help eclipse org 1 From the main menu bar select File gt Import The Import wizard opens Bio7 File Edit Preferences Scripts R OpenOffice Bst P New td go Load Pattern Database H Save Pattern m Import S
32. sequence of activation determines the numeric value of the state inside the Quadgrid and the Points panel starts with O By default one state is enabled in the Plant view This is the state soil 0 which is useful for simulation of plants this application initially was intended to deal with If plants are enabled for simulation in Bio7 additional buttons will be labelled with the name of the plants and set into the panel in the sequence they have been enabled If you want an image to appear instead of the name on a button an appropriate image with the name of the species in the database e g Hieracium_pilosella bmp can be dropped to the pics folder of Bio7 plugins com eco bio7_1 0 0 bin pics If a Button gets pressed a colour dialog pops up for changing the colour of the enabled state in the simulation automatically colours for the states in the Quadgrid and in the charts will be updated The default states can be changed programmatically and it is also possible to set states independent of the database See section 14 11 The colour changes made in this view will effect the Quadgrid Hexgrid Points panel Linechart Piechart and the 3d panel 31 6 2 6 Spreadsheet In the top right of the perspective the Spreadsheet offers a visualization of stored plants in a object oriented database The species name and the synonym are displayed by default Also two columns with check boxes are displayed By enabling a check box in the column
33. values as a dataframe With the action Data with head to R numeric values type double with a head can be transferred directly to R With the menu Data to BeanShell values will be transferred to the workspace of BeanShell will be stored in a static double array gt OpenOffice sheetdata With the action Send Bio7 counts counted values of the activated states in a simulation for all time steps are transferred to an opened spreadsheet which then can be stored to all kinds of data files There is also a small API available for the transfer of data get and set inserting new sheets getting values from sheets and the marking of the data in a spreadsheet see Snippets and API Table 30 Example to set values programmatically OpenOffice openSpread Open a new spreadsheet String name Customsheet OpenOffice newSheet name Insert a new sheet String head A B C D double values new double head length 40 Defined 4 columns for int i 0 i lt values length i for int u 0 u lt values 0 length u 93 values i u Math random 150 OpenOffice sheetInsertValues values head OpenOffice activateSheet name 12 3 ImageJ features of Bio7 Also ImageJ offers a vast amount of methods in a clean accessible API With the methods of ImageJ it is possible to make statistical image analysis shape analysis pattern analysis particle count etc All kind
34. will be transferred as an RGB Image 3 Adjust the magnification of the Points panel which determines the size in ImageJ 4 Transfer the first image to ImageJ by triggering the transfer button 129 Bio7 File Edit Preferences Scripts R OpenOffice Bsh Window Help H O ouk ALRIS Fy Resource Image EE Sol Database Fii 2d ImageJ Toolbar amp Eolo aeae racie Flood Fill Tool Fie gt Edt Image 7 Process Analyze gt Plugins Image Methods Alpha Image Alpha Quadorid i n mT i x Resize Points Panel E Thumbnails Fieldsize x Fieldsize Y 5 gt 10 gt 15 gt Small zoo 300 Point Size a 255 d Points d Pic lt d Pixel Alpha MAR 13Mof 16m We Flood Fill Tool Timesteps 0 Illustration 90 Transferred Area of Analysis 5 Now select the random function in the toolbar of Bio7 which disperses all default states in the Quadgrid 6 Select the Points panel to trigger a repaint event for the Points panel and then transfer the changed image 7 Repeat the steps several times 10 times Bio7 File Edit Preferences Scripts O nN k ARIS Fey Resource 2 Image Soll S Database 83 2d oO Weed R OpenOffice Bsh Window Help 4 PEY Eorna aea Point selections KATZEA e p Points amp alm 3 gt Edit Image Process gt Analyze Plugins
35. 14 3 The first gridded IBM Model S 101 14 3 1 How to get and set Plant values in the Quadgrid Hexgrid 14 3 2 Annotation 14 3 3 Copying instead of creating new objects 14 4 Point Pattern Analysis S 111 14 4 1 Additionally 14 4 2 Getting all attributes of a Particle Analysis 14 4 3 Conclusion 14 5 Transfer a spatial point pattern to a grid S 120 14 6 Import and Export Projects and files S 122 14 6 1 Import existing projects 14 6 2 Import resources from the file system 14 6 3 Import resources from an Archive file 14 6 4 Export resources to the file system 14 6 5 Export resources to an Archive file 14 7 Execute evaluate and plot a R script S 127 14 8 Create a custom GUI for a Rscript S 129 14 9 Create a Flash file presentation from a simulation S 129 14 9 1 Note 14 10 Open perspectives and views programmatically S 134 14 11 Add states without the database S 134 14 12 Add self defined menus to Bio7 with scripts S 136 14 13 Compile Java files to BeanShell S 139 14 14 Call compiled methods in BeanShell in the calculation thread of Bio7 S 140 14 15 Use R calculations interactively in a Java method S 140 14 16 Import external libraries to BeanShell S 142 14 17 Compile and run Java files S 143 15 Notes S 144 15 1 Notes about R 15 2 Notes about BeanShell 15 3 Notes about the Java Compiler 15 4 Notes about ImageJ 16 Literature and Links S 147 16 1 Useful Libra
36. 53M of 508M 3 2 Statistical Analysis As a fundamental part of complexity analysis we have connected our application with the well known statistical program R to get well proofed statistical methods for our simulation Simple scripts can be written to send data from a simulation to the statistical package and evaluate different scenarios An integrated RScript Editor allows the writing of required scripts and can send them to R It is also possible to get values from R Bio7 offers also a panel to make spatial analysis The values can be sent directly to R to make a point pattern analysis etc p o8 E DE at ri a T2 a a b rori E F 4 a j E opa i F a jm ain a a a y m Prag F r ERLIE etree oe Py f al ra _ a Bio7 WBE File Edit Preferences Scripts R OpenOffice Bsh Window Help WO we ARIUS Fry D Resource Image Sol BDatabase HE 2d 5 Navigator 2 0 RScript please enter yo ode here This Snippet calculates the oint distances from existent x y values Bio7_Examples S E Ecological Modeling Uses the library spatstat library spatstat d lt nndist x y dmean lt mean a dmax lt mean a dmin lt mean d EE Outline 2 OE Bsh Console El console 1 amp properties fe BE rf D raan An outline is not available Bio Console ithe Timesteps 0 Writable Sma ert 45M of SoM j 3 3 Visualization
37. 55 255 JButton jb new JButton JSlider j new JSlider j setBounds new java auwt Rectangle 6 12 200 23 j setMax imum 2000 v tw Custom Chart 5 o Bsh Console amp Console Properties Custom 3D 2 m Bubble Chart X Bubble Plot Demo o amp o 1 75 2 00 2 25 250 2 75 3 00 3 25 3 50 3 75 4 00 X E Plants Timesteps 0 13M of 19M amp Illustration 27 Custom views in Bio7 Table 12 How to transfer the animator Animator animator new Animator canvas animator start Custom3D setPanel glpanel name animator Each animator can also be stopped by calling the stop function inside the BeanShell console 50 6 7 2 Custom Menus Another nice feature of Bio7 is the simple way to extend the Script menus in Bio7 with BeanShell scripts and ImageJ macros Bio7 recognizes files dropped to special folders For the path open the Preferences of Bio7 automatically and extends the menus with the filename of the dropped files Menus which can be extended are Table 13 Custom menus Location Name Category Script type File Menu Import Scripts File import BeanShell File Menu Export Scripts File export BeanShell Scripts General Scripts General BeanShell Scripts Statistic Scripts Statistic BeanShell Scripts ImageJ Macros Image Analysis Macros Scripts Chart Scripts Charts BeanShell The menus can be extended i
38. API can be used to get values from an OpenOffice spreadsheet and send the R results back to the office application In the Bio7_Examples gt R_BeanShell_Snippets gt Snippet8_GuiForR bsh a spreadsheet will be opened and the user will be asked to insert values After selection by the user a summary function is invoked and the results will be sent back to the spreadsheet as a new table 14 9 Create a Flash file presentation from a simulation To create a presentation from a simulation in Bio7 and to display the results e g in a website Bio7 embeds a tool which can convert avi files to swf files avi2swf from swftools The possibility to transfer images from the Points panel to ImageJ allows to capture all kind of activities in the Points panel and to transfer them to ImageJ In ImageJ the tabbed images then can be converted to a stack In an ImageJ stack all converted images are available as frames which can be edited It is possible to create context information or shapes in a stack by means of the different methods in ImageJ After the frames have been edited the stack can be stored as an avi file The avi file can be converted to a swf file with the embedded converter in Bio7 1 Open the Image perspective of Bio7 and then open the toolbar of Image Window gt ImageJ Toolbar and Bio7 Toolbar in the ImageJ view 2 In the Bio7 Toolbar activate the Quadgrid layer By default this should fit into the Area of Analysis which
39. Enable Plant species from the database will be enabled for simulation The following changes occur after activation 1 Automatically a random function disperses the activated species from the database template in the grid 2 The Linechart and the Piechart will be updated with the activated plants The Piechart will display the numbers of the different plants in the Quadgrid matrix 3 In the top left panel Plants dynamically buttons occur to a show the activated plants b change the colour of the plants after activation See Section 6 5 for the database options of the spreadsheet 6 3 Image Perspective At startup the image perspective shows three different views for several tasks in the area of image analysis point pattern analysis and simulation of 2 dimensional spatially continuous models In the ImageJ Canvas view a complete version of the well known image analysis tool ImageJ has been integrated in the Bio7 application for profound image analysis and measurements of ecological parameters Because ImageJ offers also complete API Application Programming Interface the development of customized image methods are possible Directly connected to this view a scalable Points panel for adjustments and visualization of point pattern has been integrated This panel is also programmatically available by means of a small API which facilitates the construction of 2d continuous also IBM Models simulation models An easy to use thumbnail
40. Juni eclipse plugins com eco bio _1 0 0 database database yap Restore Defaults Apply Illustration 54 Preferences Database of Bio7 Preferences BeanShell Edit Preferences Database Bio Preferences Java Editor C Start with shell Preferences R Editor Preferences RServe Preferences State install path at startup Preferences HX type filter text Preferences RServe er H Hg Path to temporary RData file no empty space allowed Install Update Preferences Bio Path to temporary RData file C Restore Defaults Apply OK Cancel Illustration 55 Preferences Rserve 8 1 5 Preferences Rserve The preferences for the Rserve application Preferences Bio7 gt Preferences Rserve offers three options The first option is an adjustable path to a temporary R file which will be stored and opened when the RGui application is called in the R menu It is important that the path to the temporary file has no empty space due to some Rserve restrictions of the path By default the location is set to C Windows The second option installs a registry path for the embedded R only windows at startup If selected the third option starts the Rserve application with an opened shell 79 8 2 Default Platform Preferences A detailed description of the preferences of the platform can be found on http help eclipse org Only some important preferences for the Bio7
41. Reset can be used to return to the default value 81 Color settings can be changed by clicking color to the right of the tree area when a color is selected Reset can be used to return to the default value 6 Preferences ow type fiter text Colors and Fonts ae 7 rine Colors and Fonts any character any string _ mal Fonts type filter text Label Decorations J a Bask sua BB Active hyperlink text color if Keys Aa Banner Font Perspectives Aa Dialog Font l Startup and Shutdown E Error text color Welcome Aa Header Font Workspace E Hyperlink text color Help Aa Text Font Install Update a a ssd en rolden Preferences Bio7 Description Basic colors and fonts used throughout workbench dialogs and editors Preview No preview available eons Ca Illustration 57 Preferences for the Text in Bio7 8 2 3 Text Editors Preference Page The following preferences can be changed on the General gt Editors gt Text Editors page fw Preferences OE type filter text Text Editors E7 General ry Undo history size 200 Appearance Content Types Displayed tab width 4 k paei EET insert spaces for tabs Text Editors V Highlight current line Accessibility C Show print margin Annotations Hyperlinking Linked Mode Show line numbers Quick Diff Show range indicator keys Spelling Cl Show whitespace characters Perspectiv
42. Shell 1 Create a BeanShell Script in the previously created project File gt New gt BeanShell Script 2 It is not necessary to have a ecomain method in BeanShell 3 Insert the same code in the file but at the end call Table 33 or delete the ecomain method Table 34 Table 33 with ecomain method public void ecomain With the ecomain method for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x Field setState x y int Math random Bio7State getStateSize t ecomain Table 34 without ecomain method for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x Field setState x y int Math random Bio7State getStateSize Interpret the code with the Interpret action of BeanShell Bsh Window Help i Illustration 70 Interpret in action of BeanShell 100 14 2 3 Explanation The method is the same as the method for the Java Compiler Different is that the source is interpreted directly and executed in the Quadgrid similar to one timestep in the compiled code if started in the calculation thread If the ecomain method was placed in the code the method should be called for interpretation at the end of the source in Table 33 If no ecomain method is present the expressions will simply be interpreted Table 34 14 2 4 Conclusion The Interpreter can be used to protot
43. To add other new features at the same time before restarting click No and repeat If this was a new feature and can be dynamically installed into the current configuration you will also be presented with a Apply Now button This will not restart the platform but configures the feature and the plug ins into the current configuration 88 11 Additional views in Bio7 By default some more views are available in Bio7 The Bookmarks view is a view which shows marked bookmarks in all language editors of Bio7 for easily find points in code which have to be edited Bsh Console Console Tasks Problems Bll Bookmarks X 1 items Description Resource Path Location 4 Bookmark randomoyvals bsh Bio _Examples Image line 14 Illustration 62 The Bookmarks view Bsh Console Console Tasks Problems Bookmarks zE 2 YY C 2 items v Description Resource Path Location 4 voronoiplot RScripts line 4 This is atask randomoval Bio _Examples Image line 19 Illustration 63 The Tasks view The Tasks view in the R Editor serves as a marker for plots in the source code For all other editors it can be used to leave some information about tasks that have to be done or as information in the Bio7 language editors They can be marked with different priorities The Problems view has no function in Bio7 at the moment but it can be a useful resource for later developments The Ch
44. a Oo FL ROCESS d Image Methods Fie Edit Image Process Analyze Plugins Window 7 Alpha Image ed New i Sra J Open 1 i Open Next s Open Recent x Import Alpha Quadgrid Close All Tabs i i Save g Saveas a a Open Samples gt particles gif pea Revert blobs gif Page Setup mri stack zip Resize Points Panel Print leaf jpg as Convert Avi gt Swf See v sil i Fieldsize X Fieldsize Y gt 1000 1000 e 4 Thumbnails 23 muns Particle Size Alpha m 25 st um aroe 100 e d Points Q Particles the Version 1 35s 260 commands 16 macros Timesteps 0 21M of 508M oO d Illustration 73 Open an example 1 Open the Bio7 toolbar Image Methods 2 Convert the image to 8 bit image Image gt Type gt 8 bit for particles gif example not necessary 111 Bio7 Jeg File Edit Preferences Scripts R OpenOffice Bsh Window Help il O o k AaQiebeaia 6 E Resource E Image Image EH Soil 3 Database gss 2d yes a SiE Points 2 N cL d Image Methods 5 File Edit Image Process Analyze Plugins Window Alpha Image Is particles aif x Type nh D ti ss J z Adjust 16 bit heeveenearucvreesporneet Rotate 32 bit a a z Colour 8 bit Color x Stacks RGB Color Aipha Quadgrid SS Zoom RGBStak fo a f aaan Lookup Tables gt HSB Sta
45. according to the sliders in the Individual Plants view 103 104 String species gt the name of the species 1 getSpecies 2 setSpecies String synonym gt the synonym of the species 1 getSynonym 2 setSynonym String lifeform gt the lifeform of the species hemikryptophyt kryptophyt 1 getLifeform 2 setLifeform String lifespan gt the life span how long does the species exist can be casted for a numeric value or used as categoric annual the slider in the Control panel expect s a numeric value 1 getLifespan 2 setLifespan String anthesisstart Anthesis start gt the start of the anthesis 1 getAnthesisstart 2 setAnthesissta rt String anthesesisend Anthesis end gt the end of the anthesis 1 getAnthesisend 2 setAnthesisend int sheightmin gt minimum shoot height to use as an intervall with the height 1 getSheigthmin 2 setSheightmin int sheightmax Shoot height gt maximum height of the shoot 1 getSheightmax 2 setSheightmax 105 Q int swidthmin gt minimum width or diameter of the shoot 1 getSwidthmin 2 setSwidthmin 10 int swidthmax Shoot width gt maximum width or diameter of the shoot 1 getSwidthmax 2 setSwidthmax 11 int ssurface Shoot surface gt value for the shoot surface 1 getSsurface 2 setSsu rface 12 int rdepthmin gt r root minimum root depth 1 getRdepthmin
46. an be searched using the filter function To filter by matching the page title simply type the name of the page you are seeking and the available pages will be presented below The filter also searches on keywords such as appearance and Java The history controls allow you to navigate through previously viewed pages To step back or forward several pages at a time click the drop down arrow and a list of the most recently viewed preference pages will appear The Preferences dialog can be found from the main workbench Window menu under Window gt Preferences Preference pages contributed by plug ins will be found in this dialog 8 1 The Bio7 Preferences f Eoi Preferences oE type filter text Preferences Bio7 er 4 General Help Install Update Path to R D ExportBio Junijeclipse plugins Bundled_R_1 0 0 R Preferences Boz Path to OpenOffice C P OpenOffice org 2 24 i Preferences BeanShell Edit Path to OpenOffice Programme OpenOffice org 2 2 program FOWSE Preferences Database Bio Preferences Java Editor Script location ip Preferences R Edtor Path to Startup Scripts D E tBio Juni ecli i bio _1 0 0 start ipt Preferences RServe ath to Startup Scripts ExportBio Juni eclipse plugins com eco bio _1 0 0 startup_scripts FOWSE Preferences State Path to Import Scripts D ExportBio Juni eclipse plugins com eco bio7_1 0 0 importscripts Path to Export Scripts D E
47. an if statement According to a self defined condition a static variable Bio7Flow setDecision true can be set to true or false The direction of the flow then depends on the linked connection which can be set to true or false in the properties dialog by selecting the connecting lines 5 Info A single line label for description which can be changed directly in the shape 6 Connection To determine the sequence of the flow Connections are available to connect components If selected in the Palette directed connections can be drawn from component to component 7 Selections can be made with the Marquee tool and the Select tool multiple selections are possible The execution of a flow will be triggered with the item FlowAction in the top right of the toolbar 65 7 4 2 Options for the Layout There are several tools available for adjusting the components and the layout of the flow In the toolbar of Bio7 several items will be enabled when components are selected alone or ina group w Sega te Ti of ot ee MM 100 vA A ia Illustration 40 Added items to the toolbar of Bio7 By default the zoom action and the flow action are enabled With the Zoom In Out actions it is possible to zoom in or to zoom out in the flow by using the combo box or the lens items If an opened flow was changed the toolbar items for undo and redo could be used to undo or redo changes in the flow Furt
48. ap Turn this option on to display an indicator showing Status information about current Java heap usage sl You can select one of the following methods for opening resources e Double click Single clicking on a resource will select it and double clicking on it will open it in an editor e Single click Select on hover Hovering the mouse cursor over the resource will select it and clicking on it Double Open mode once will open it in an editor click e Single click Open when using arrow keys Selecting a resource with the arrow keys will open it in an editor Note Depending on which view has focus selecting and opening a resource may have different behavior 8 2 2 Colors and Fonts Many of the fonts and colors as used by eclipse components can be set using the General gt Appearance gt Colors and Fonts preference page A tree is used to navigate among and show a short preview of the various colors and fonts The current face but not size of any font is previewed in its label Colors are previewed in the icon associated with its label Additionally some categories Workbench in particular provide a more detailed preview of their contributions This preview is shown below the description area if available Font settings can be changed either by selecting the font from the list and clicking Use System Font to choose the Operating System font setting or by clicking Change to open up a font selection dialog
49. art parameters The Piechart visualizes the count of the activated states inside the Quadgrid Hexgrid every second Changes can easily be viewed by setting states with the mouse inside the Quadgrid The Linechart displays the amount of states in dependence of the simulation steps When a simulation is started different coloured lines will visualize the amount of states over the time The colours of the charts will be automatically adjusted when changing colours for a state in the Plants view Piechart amp FV Linechart 33 States States soil 310 1200 1000 da sk aa re S soo Se Plant 1 120 amp 600 EA T 400 _ _ aI Plant1 1 070 n o 460 475 500 525 550 575 600 Iteration B soil MW Plants Plant2 W soil B Planti Plant2 Illustration 9 The Piechart and the Linechart of Bio7 26 6 2 4 The Control ml gt gt Time and Space oO Time amp Space Time steps 0 Month July Year 0 Speed Fieldsize Y gt 50 2 Fieldsize X gt 50 C Resize after adjust In the ExpandBar of the Control view several panels are by the Time amp Space Individual items Abiotic selecting ExpandBar Plant accessible Disturbance Factors 6 2 4 1 Time and Space The topmost item is called Time amp Space When this item is enrolled a panel appears showing information about
50. at the end External packages can also be used for custom expression Some library s offer a huge amount of well proofed functions Some of these library s are embedded in Bio7 Colt JScience Apache commons math by default When a new formula has been expressed in the textfields f t the changes occur when equations have been compiled This can be done by selecting the Compile button To plot the compiled functions as a preview the function Preview plots the different equations over the time according to the adjusted Repeat after value To use the formulas and embed it in a simulation see the following Code Snippet which calls the compiled ecomain method to recalculate the equation with the dynamic variable t or 30 Time getCounter Table 5 Code snippet public void ecomain AbioticFactors f Compiled getAbioticFactors if f null Call the main method f ecomain Get the values double light f light double nitrate f nitrate double phosphate f phosphate double water f water double temp f temp double carbon f carbon System out printin light nitrate phosphate water temp carbon else System out printin Formulas are not compiled 6 2 5 Plants States The Plants view is responsible to display all activated states in a simulation or a spatial analysis in Bio7 and the setup of the colours of the different activated states Furthermore the
51. ation 7 2 2 Plotting 7 3 The Java and BeanShell Editor 7 3 1 Java 7 3 2 BeanShell 7 3 3 Differences 7 3 4 The context menu of the Java BeanShell editor 7 4 The Flow editor 7 4 1 The Palette of the Flow editor 7 4 2 Options for the Layout 7 4 3 The Context menu 7 4 4 The Properties for the Components 7 4 5 What to consider when creating a flow 7 4 6 How to cancel a flow 7 4 7 Executed Files 7 4 7 1 Dropped from the Navigator 7 4 7 2 Dropped from outside the Navigator 7 4 8 Important to know 8 The Preferences S 76 8 1 The Bio7 Preferences 8 1 1 Application Paths 8 1 2 Script Paths 8 1 3 Bio7 Editor Preferences 8 1 4 Preferences Database 8 1 5 Preferences Rserve 8 2 Default Platform Preferences 8 2 1 General 8 2 2 Colours and Fonts 8 2 3 Text Editors Preference Page 8 2 4 Help Preferences 8 2 5 Perspectives 8 2 6 File Associations 9 Help S 87 10 Installing new features with the update manager S 87 11 Additional views in Bio7 S 89 12 External tools S 90 12 1 R features of Bio7 12 2 OpenOffice features of Bio7 12 3 ImageJ features of Bio7 13 What else S 96 13 1 Plugins for Bio7 13 2 Programming examples for Bio7 14 How to s S 97 14 1 First steps S 97 14 1 1 Game of Life 14 1 2 Random Walk 14 1 3 Gears 3d 14 1 4 A Matrix Model in R 14 2 The first selfmade grid based simulation S 99 14 2 1 Explanation 14 2 2 Again in BeanShell 14 2 3 Explanation 14 2 4 Conclusion
52. ator When the action is invoked the file will be compiled from the embedded compiler The compiled class is then available with the name of the selected file To call for example the ecomain method of the compiled file Ca culate java you have to type Cal culate ecomain Additional methods in the file are called in the same way for example Ca culate print for the print method in the file Furthermore it is possible to select more than one file in the Navigator which will be compiled and added to the namespace of BeanShell They can also be called directly from the BeanShell console The compiled methods are much faster than the default interpreted methods in BeanShell Normally the embedded compiler is only used to compile one file to the main calculation thread With BeanShell it is possible to store the compiled class by means of a reference to a static variable the current compiled class Bio7 offers The compiler compiles a class of the type Ecoclass to the Ecoclass variable Compiled ecoclass You then can set a reference to that instance in BeanShell with Ecoclass eco Compiled getEcoclass Now you can call eco ecomain If you compile another file with a different ecomain method you will be able to set another reference to the compiled class like Ecoclass eco2 Compiled getEcoclass 139 which gives you a reference to the currently compiled file Now two different references and ecomain methods are availab
53. be opened gif jpeg png bmp tiff with preview pnm pcm without preview txt e g macros results roi single ROI zip Stacks ROI Manager files The images can be opened in the ImageJ view by selecting the images in the left panel press to open If you set the mouse over a thumbnail some information about the image will be displayed 41 Annotation If some images in the correct file format do not open in the ImageJ view it will be necessary to rename the extension of the images to the previously mentioned endings Some image extensions JPG instead jpeg opened by the thumbnail browser cannot be recognized by ImageJ the thumbnail browser uses swt to draw the thumbs 6 4 The Soil Perspective The Soil perspective supports the visualization of several abiotic factors in a discrete grid which are 1 Nitrate 2 Phosphate 3 Carbon 4 Water 5 Root Density The different soil panels can be magnified like the Quadgrid panel Furthermore values can be set using the mouse according to adjustment in a specialized option panel drag values like in the Quadgrid panel The field size of the different soil panels is equivalent to the field size of the Quadgrid If the Quadgrid is resized the soil panels will be resized too All values in the underlying grid array can be accessed and altered through a small API programmatically It is also possible to make the grids dynamic in the calcula
54. caled with a 1000 1000 Area of Analysis the resulted transferred picture to ImageJ would be a scaled image lt 1000 1000 which shows the same area 11 The two Points button are responsible for transferring Particle Analysis data from ImageJ to the Points panel or directly to R a The first button selects a method which will transfer particle measurements to points in the Points panel If activated in ImageJ as by default the rounded centroid coordinates values gt 1 5 result in 2 values lt 1 5 result in 1 are used to set points in the Points panel see Section 14 4 These values then or the values which have been set by hand will be transferred to R if active when the R button is pressed A message dialog confirms the transfer With this procedure the following values will be transferred to R alpha gt the alpha value of the points diameter_panel gt the diameter of the points in the panel fieldx fieldy gt the size of the Area of Analysis species gt the species which have been set x y gt the coordinates of the points b To support a kind of pattern or shape recognition the other Points button will execute a method which directly transfers particle measurements from ImageJ to R If a particle analysis with selected measured attributes Set measurements see Illustration 21 was made with ImageJ the selected attributes would be transferred 37 to R for further statistical analys
55. ck Show info a i O eee pee Crop Fg i Duplicate Resize Points Panel panen y Rename F i l mi Jt Feldsize x Fieldsize Y gt t r 1000 l 1000 ie F Thumbnails ea a m a aaa iaa Particle Size i Alpha 5 258 S dium Large v 10 x prms inka Timesteps 0 36m of soem ij Illustration 74 Convert image 3 Adjust the threshold of the image in the way that all particles are marked with red Image gt Adjust gt Threshold james ves Process Analyze Plugins Window v Threshold i he F F Zo as are 4 Illustration 75 Hepes the threshold 112 4 Now open the Particle Analysis dialog Analyze gt Analyse Particles v Image 7 Process Y Analyze Plugins Winde Gels r T 0 gt i Measure Analyze Particles Summarize Distribution Label Clear Results Set Measurements Set Scale FE Calibrate 4 Histogram nis Plot Profile ag Surface Plat uN FIERA ve a Illustration 76 Analyse particles menu 5 Select the appropriate options in the dialog a Select the particle size and the circularity interval of the particles which should be selected for measurements b The Show combobox item will let you select options to display an image with the measured particles C Display results will actively show you the current measurements in a spreadsheet Only keep activated when y
56. cripts gt Export Scripts gt Import LE Export Exit Convert Line Delimiters To gt Open File 2 Select General gt Existing Project into Workspace and click Next 3 Choose either Select root directory or Select archive file and click the associated Browse to locate the directory or file containing the projects 4 Under Projects select the project or projects which you would like to import 5 Click Finish to start the import 122 14 6 2 Import resources from the file system Table 38 From the Eclipse Workbench User Guide http help eclipse org You can use the Import Wizard to import resources from the local file system into an existing project 1 From the main menu bar select File gt Import The Import wizard opens 2 Select General gt File System and click Next 3 Click the Browse button on the next page of the wizard to select the directories from which you would like to add the resources 4 In the import selection panes use the following methods to select exactly the resources you want to add e Expand the hierarchies in the left pane and select or clear the checkboxes that represent the folders in the selected directory Then in the right pane select or clear checkboxes for individual files 5 Click Filter Types to filter the current selection for files of a specific type 6 Click Select All to select all resources in the directory then go through and deselect
57. d values will be dispersed from 0 1000 units randomly across the whole field 2 If the Homogeneous button is pressed all values inside the field will be set to zero 3 Additionally if the Gradient button is pressed values in the field from 0 1000 units will be dispersed in a gradient from left to right The values are displayed with 256 colours by default 6 4 2 Nitrate The Nitrate Panel visualizes a discrete field for nitrate values Values can be set from 0 1000 units with the Soil Parameter panel The lowest values are coloured yellow The highest 43 File Edit Preferences Scripts R OpenOffice Bsh Window Help ip O We ALRIS FEY Resource 2 Image HE soi B Database 88 2d 3 Roots z iE if Nitrate 3 lt a Phosphate 2 ass Water RAL pal 3Dgrid 3 Nitrate carbon Water Phosphate Root Density pll Timesteps 0 imois D Illustration 24 The different soil panels and the visualisation in 3d values are in red The 1000 possible units will be displayed with 256 colours 6 4 3 Phosphate The Phosphate Panel visualizes phosphate values from the lowest values green to the highest values black in a discrete grid 6 4 4 Carbon Like the above described panels the Carbon panel visualizes another important nutrient in ecological systems The values will be displayed in the colours white lowest and black
58. d directly within the different editors in Bio7 by compiling or interpreting them All standard functions of ImageJ 34 are integrated Macros are fully supported and can also be added dynamically to the main menu of Bio7 for efficient image analysis In the menu of the ImageJ view some additional menu points gt Windows have been added for 1 Opening the toolbar of ImageJ ImageJ Toolbar as a detached view 2 Opening a control panel for the Points panel with functions for the exchange and adjustment of images between ImageJ and the Points panel 6 3 2 Points panel In the Points panel points can be set or deleted with the mouse by left or right click in the selected coordinates Additionally points can be dragged to any locations inside the boundary of the adjusted size inside the Area of Analysis of the Points panel marked by a green rectangle The coordinates pixel location are displayed in the status bar of the Bio7 application The panel itself can be resized to a virtual size of 10 6 10 6 units pixel inside a scrolling panel e g you can set points in a virtual area of 10 6 10 6 cm as unit which means that you can adjust points in an area of 10km with cm precision Also zooming is supported when a big area is required If the panel is zoomed or scaled down the points automatically will get translated resized and stay selectable It is also possible to add the quads from the Quadgrid panel to the Points pane
59. dinary Java code but also has complete scripting capabilities to facilitate the development process of programming Scripting code as well as Java code can be executed with the item which appears when a BeanShell file bsh has been opened For more scripting examples visit the website of BeanShell http www beanshell org Bio7 oles File Edit Preferences Scripts R OpenOffice Bsh Window Help H O AQ GHWS FET Q gt Resource Image Soll S Database 2d interpoint ecor 6 Easier_Game_of_Life java Snippet_poinpanel_2 bsh amp This example shows how to get the points from the Points panel Ecological Modelling import java aut Point Point point PointPanel getPoints for int i 0 i lt point length i int x point i getX int y point i getY System out println X x 4 4 y BE Outline E Bsh Console El Console 53 E Properties Ex BE rf ee An outline is not available Bio Console Illustration 36 The BeanShell editor The reasons that BeanShell and a seperate Java compiler have been added to Bio7 are the following 1 Need for speed in complex applications gt The embedded Java compiler compiles the Java code to bytecode while BeanShell interprets the code which is much slower and 60 2 3 sometimes not sufficient for resource intensive calculations thoug
60. duct ordinarily requires web access 1 Open the Install Wizard by clicking Help gt Add Update This opens the wizard 2 Select the second button Search for new features to install and click Next 3 Create a bookmark for an update site where Eclipse features and plug ins are published In the sites to search list select Add Update Site to add a remote site or Add Local Site if the site is available on a local drive including a CD or Add Archived Site when the site is available locally but is packaged as a jar or zip file 4 In the add site dialog give the site a name such as Company A and enter the URL such as http companyA example com eclipseupdates 5 After adding the site expand it to the categories of feature versions available at that update site This will contact the web site to discover what features are available 6 Select the categories you want to search and click Next 7 Wait for the search to finish and selecting the features to be added You can view the description or more detailed properties for any feature by selecting the feature and 87 pressing the Properties button 8 Once you re decided which features to install click Next 9 Carefully review the license agreements for the features If the terms of all these licenses are acceptable check I accept the terms in the license agreements Do not proceed to download the features if the license terms are not acceptable 10 1If a feat
61. e Plants 2 J Do you want to delete plants in the plantpanel Illustration 78 Add or delete existing points 12 The points are drawn in the Points panel with the colour of the default state You can change the state colour in the Plants view File Edit Preferences Scripts R OpenOffice Bsh Window Help ipl O aw k Leesa i tt Fy Resource 2 Image Soll S Database 2d File Edit Image 7 Process Analyze Plugins Window E ZE o d Image Methods Alpha Image a Thumbnails x h Ag a Resize Points Panel 3 ae t Ee 5 gt j10 gt 15 gt Small Medium Large 0 v S 1000 Timesteps 0 eamofsoam i Illustration 79 Transferred values as points in the Points panel 13 To transfer the data to the R workspace start the Rserver and transfer the measured points to the R workspace by pressing the R transfer button 14 Open the R expression dialog of Bio7 and list the transferred values R gt Evaluate Expression type s for a list Ist Evaluate expression Illustration 80 Expression dialog 115 Bsh Console onsole X Properties Ex BE rf my Bio Console 1 alpha diameter panel fieldx fielday 5 Species PP yy FF ryger Illustration 81 The to R transferred values 15 Optional you may start the RGui Windows with the
62. e current flow to the before defined file Save as in the Bio7 main menu available 2 The Save Image method will save an image in the formats gif jpeg ico to a file The current size of the flow will determine the pic size the rulers display the size of the flow in pixel So be cautious not to store large images with a resized flow 3 The following methods Manhatten Router and Shortest Path are responsible for the layout of the connections a The Shortest Path method applies the shortest path algorithm to find paths around obstacles in the flow b The Manhatten Router algorithm will use rectangular lines for connections in the flow 4 The Debug Mode option enables a visualization of the current flow by bleaching the active shape to mark files that are currently interpreted or compiled etc 7 4 4 The Properties for the Components If a shape or a connection is activated the properties of the component or the connection can be adjusted in the properties view This view can be activated in the Windows gt Show View dialog Bsh Console Console Properties amp G Ea Property Value File Loop Info Ecological Modelling Cellular Automata selse bsh Filetype bsh Height 52 Initloop Loop count 0 Width 64 x 405 T 509 Illustration 44 The properties view of the Flow editor The properties dialog will only be necessary if you want create a decision inside a flow All other component attr
63. e opened or closed The menu Help offers help for the application and the possibility to make updates and installations of new components for Bio7 17 6 The Perspectives of Bio7 In the Perspective Bar five different perspectives can be activated via the Perspective Buttons All the views or editors in the perspective can be closed opened detached or moved The perspectives in Bio7 can be extended by several other views which can be opened in the Windows gt Views menu or with the action in the status bar at the bottom left of the Program Additionally self defined perspectives can be created or deleted See Section 6 7 Table 1 From the Eclipse Workbench User Guide http help eclipse org Perspectives provide combinations of views and editors that are suited to performing a particular set of tasks For example you would normally open the Debug perspective to debug a Java program To open a new perspective 1 Click the Open Perspective button on the shortcut bar on the left side of the Workbench window This provides the same function as the Window gt Open Perspective menu on the menu bar 2 To see a complete list of perspectives select Other from the drop down menu 3 Select the perspective that you want to open When the perspective opens the title bar of the window it is in changes to display the name of the perspective In addition an icon is added to the shortcut bar allowing you to quickly switch back
64. eat Sheets view can be used to load created Cheat Sheets from Eclipse Thumbnails Saye es Load Thumbs opened 20 From 75 Illustration 64 The Progress view 89 The Progress view shows information about running jobs in the application Each time a job has started this progress view can be opened in the progress dialog in the status bar Load Thumbs 58 jC Illustration 65 The progress dialog in the status bar 12 External tools 12 1 R features of Bio7 Bio7 embeds R as a Statistical application to do profound statistical analysis of ecological models To interact with the Bio7 application and all of its components the Rserve connection has to be started In a start process the Bio7 app tries to connect to the Server displayed in the progress dialog If the connection trials exceed 10 trials 1 second the operation will be aborted After the connection has been established several methods for the interaction with R are available By using the R editor see section 7 2 RScripts can easily be interpreted Additionally some specialized methods are available in the R menu of Bio7 s R OpenOffice Bsh Window Help A amp Start Rserve Ctrl R Load Workspace Save Workspace Evaluate Expression Alt x Evaluate Selection Alt R Remove all objects Start RGui with Workspace T Illustration 66 R menu of Bio7 1 With the Load Workspace action R Workspaces can be
65. ed with a right click of the mouse By executing this action the selected file will be compiled and referenced in BeanShell Then the ecomain method will automatically be invoked like the main method in a regular java file New Calculate GetBeans OPen Snippet_ce Open With gt b OpenGL Snipp 2 copy b OpenOffice 5 r XM Delete ne es Move s not available Rename gg Import ey Export Refresh C Compile and Run Add java to bsh classpath Properties Illustration 104 Compile and Run in Bio7 143 15 Notes 15 1 Notes about R Preferences RServe Path to temporary RData file no empty sp lt Path to temporary RData file C C Install path at startup Start with shell Illustration 105 Shell option You can start the Rserve applications with two options If you enable the option Start with shell in the preferences dialog Preferences gt Preferences Bio7 gt Preferences Rserve you can start the Rserve application with an opened shell In this shell errors are displayed and you can also use the scan function which by default is not possible with the regular connection mode It is recommended to start and work with two options to see the differences and the advantages of both The Rserve application is not stable on Windows Evaluation of a wrong expression will lead to an interruption of the communication to the server The server then has to be re
66. een layers Mouse Drag up down Rotation of layers Key Arrow left right Move layers left right Key Arrow up down Move layers up down 47 6 7 Custom Perspectives It is also possible to define custom perspectives with Bio7 All views from the application can be used to define a specialized perspective for certain tasks Table 9 From the Eclipse 3 2 Platform If you have modified a perspective by adding deleting or moving docking views you can save your changes for future use 1 Switch to the perspective that you want to save 2 Click Window gt Save Perspective As 3 Type a new name for the perspective into the Name field 4 Click OK The name of the new perspective is added to the Window gt Open Perspective menu The Custom perspective can be deleted in the Preferences dialog Preferences gt General gt Perspectives There you can simply remove the perspective 6 7 1 Custom Views Besides the possibility to extend Bio7 with custom perspectives also three custom views are available Custom3d Custom Controls Custom Charts for embedding self defined GUI s in Bio7 Self defined JPanels Swing swt canvas and Draw2d Panels can be easily embedded in the CustomControlls view Furthermore for embedding OpenGL a GLCanvas can be sent to the Custom3d view in Bio7 Finally it is possible to integrate JFreecharts into the Custom Charts view 48 Table 10 Custom views API View Component H
67. ephorus_c grey hair grass v i Polytrichum pif awned hair cap eS Form Plant Scientific name Synonym Life Form Life span January wv Anthesis start January m Anthesis end Height min Height max Width min Width max Surface Depth min Depth max Width min Width max Surface vegetative sexuell re Timesteps 0 13M of 14M Illustration 25 The Database perspective 45 deleted they have to be selected in the Spreadsheet view After the selection of the right plant in the Select column the current attributes of the plants appear in the form of the Formular view For deletion also for updating and sending it is required to disable all active plants in the spreadsheet column Enable for a simulation If plants have been stored in the database they can be enabled for simulation in the Spreadsheet view By selecting them in the appropriate row with the checkbox in the column Enable plant objects will be crea
68. es V Enable drag and drop of text Startup and Shutdown M Warn before editing a derived file D WEEN Z Smart caret positioning at line start and end Help E Show affordance in hover on how to make it sticky Install Update Preferences Bio Appearance color options Line number Foreground Color Current line highlight Print margin Find scope Selection Foreground color Selection background color Background color Foreground color Hyperlink More colors can be configured on the rs and Fonts preference page Restore Defaults Apply Illustration 58 Appearance options 82 Table 23 Appearance From the Eclipse Workbench User Guide http help eclipse org mode is enabled or disabled Option Description Default Displayed tab width This option allows you to set the displayed tab width for 4 the text editor Undo history size This option allows you to undo the history size for the 25 text editor Highlight current line This option controls whether or the current line is On highlighted or not Show print margin This option controls whether the print margin is visible Off or not Show line numbers This option controls whether or not line numbers are Off shown on the left side of the text editor Show range indicators This option controls whether or not range indicators are On shown in the text editor Support hyperlink style This
69. es y x the state the diameter and the alpha value Tip The parameters diameter and alpha value for example can be used to display fitness or age in a simulation Table 7 2d continuous model Individual individual new Individual 1000 public void ecomain PointPanel delete for int i 0 i lt individual length i int x int Math random 1000 int y int Math random 1000 int species int Math random Bio7State getStateSize float alpha float Math random 255 int diameter int Math random 50 individual i new Individual x y species diameter alpha PointPanel setIndividual individual 40 Illustration 23 The thumbnail browser 6 3 3 Thumbnails With the thumbnail browser it is possible to open a directory of images as thumbnails Different options are available for the display of thumbs 1 With the x gt buttons you can select how many thumbs should be created in a row 2 The Small Medium Large labelled buttons will create preview images with a size of 100 100 150 150 or 200 200 pixel 3 The button with the folder image opens the directory which should be displayed 4 The combobox will adjust the level of magnification The thumbs will be resized by means of the lens blue rectangle in the right panel for the overview Images or file extensions in the following formats will
70. es from different species which are typical for this habitat We use the capabilities of this application to express the features of this system in syntactical rules for simulation 3 The Components of Bio7 3 1 Image Analysis Image Analysis is a fundamental method to observe patterns and processes behind them Bio7 addresses this with direct integration of the well proofed analysis tool ImageJ With this interface it is possible to detect pattern and integrate real pattern in a spatial simulation It is also easy to combine the image analysis with the statistical tool R to make well known point pattern analysis voronoi diagrams kriging etc This is realized by a special second drawing panel which offers the possibility to set points on top an optional image These placed coordinates can be sent directly to R Another feature of Bio7 uses the strength of ImageJ to detect patterns by combining spatially explicit simulation models with the detected pattern from image analysis The measured patterns can be automatically transferred and assigned to a discrete pattern File Edit Preferences Scripts R OpenOffice Bsh Window Help O WN ae 4ReHs Fy Resource 6 image ji Soil Database FEE 2d vas x mageJ Can File Edit Image Process Analyze Plugins Window 7 E Thumbnails amp gt lo gt 15 gt Small Medium farce C i
71. ewness 28 slice std_dev Illustration 85 All attributes from an ImageJ measurement transferred to R Note After each transfer the Analysis has to be repeated 14 4 3 Conclusion This description is a simple example for the analysis and the mapping of particles to the Points panel of the Bio7 application and R If you see this example in the context of plant communities the particles in this examples could also be examples for plants which were measured in the field or selected from digital photographs When selecting plants from digital photographs Bio7 is capable to automatically transfer these values to the Points panel or directly to R If the vegetation is not easily to separate into different species more advanced methods of Image Analysis can be used with the API of ImageJ or by using pattern recognition methods in R Furthermore it is possible with this application to examine spatial setups of different plant communities using the advanced spatial statistic methods in R In the plants dialog different species can be selected and then be added to the Points panel after the analysis You can also write custom scripts for the imports of x y values to the Points panel see the Points panel Snippets Tip for digital images If a vegetation is to homogeneous to be identified automatically from an image it could be a good approach to prepare the image before the analyses is taking place mark the different species in a
72. ews the associated editor opens in the Workbench If there is no associated editor for a resource the Workbench attempts to launch an external editor outside the Workbench On Windows the Workbench will first attempt to launch the editor in place as an OLE document This type of editor is referred to as an embedded editor For example if you have a doc file in the Workbench and Microsoft Word is registered as the editor for doc files in your operating system then opening the file will launch Word as an OLE document within the Workbench editor area The Workbench menu bar and toolbar will be updated with options for Microsoft Word Any number of editors can be open at once but only one can be active at a time The main menu bar and toolbar for the Workbench window contain operations that are applicable to the active editor Tabs in the editor area indicate the names of resources that are currently open for editing An asterisk indicates that an editor has unsaved changes By default editors are stacked in the editor area but you can choose to tile them in order to view source files simultaneously 7 1 1 Code Templates Alternatively to the simple Snippets view see 6 1 4 all language editors offer Code Completion by pressing Ctrl Space or by right clicking the Context menu gt Code Completion Easier_Game_of_Life java 6 For the game of life soil dead barrier alive public void
73. f Bio7 to see the applied rules in the Quadgrid Hexgrid 14 1 2 Random Walk 1 2 3 4 Open the Random Walk java file Ecological Modelling gt Continous Compile it and then switch to the Points panel Press Start Stop to see a random walk in a continuous space where the precision can be adjusted according to the virtual size of the Points panel etc In the Points panel points will be set according to their coordinates 14 1 3 Gears 3d Modelling in 3d is also possible The gears example is an OpenGL script which shows the popular Gears example in a Custom 3D view 1 2 97 Open the gears example Snippet_OpenGL_1_Gears bsh Bio7_Examples gt OpenGL Snippets Interpret the script with the interpret action 14 1 4 A Matrix Model in R 1 Open a connection to Rserve and then the file Les ieMatrix ecor EcologicalModelling gt MatrixModel 2 Execute the Script with the RScript action 4 Now open the R expression dialog and type in n1 to print an output of the abundance after one timestep t 1 n VPE Upc LAPLEDDLUN ULALUY AUU cucu CuLcE nit You L lt mat Birtt probe L 2 1 lt 0 7 L 3 2 lt 0 9 L 4 3 lt 0 5 AES print the results in one Abundance n0 lt c 9 5 4 2 ibundance after one timestep t 1 ni lt L n0 Bsh Console Gl Console 3 E Properties Bio Console 1 1 34 0 2 6 3 3 4 5 4 2 0 Illustration 68 Matrix model w
74. f cause possible to mix database states with the states that have been defined programmatically In case the state soil is not needed for simulation it is legal to remove it to avoid unnecessary states in a custom simulation 135 14 12 Add self defined menus to Bio7 with scripts In this example we will add an export script to the Bio7 menu Bio7 File Edit Preferences Scripts R OpenOffice Bsh Wi Pa New WwW es Load Pattern Database HI Save Pattern Import Scripts gt Process 7 Export Scripts gt Empty ety Import e Export Exit Convert Line Delimiters To gt Open File Illustration 98 No export script available We will create a script BeanShell for the export of the numeric values from the grid array Therefore we define a script Export_Pattern bsh in Table 45 which creates an export dialog and saves the grid pattern to a file with a self defined ending pattern Table 45 Source of Export_Pattern bsh JFrame frame new JFrame Pattern frame setDefaultCloseOperation JFrame DISPOSE_ON_CLOSE frame setAlwaysOnTop true JFileChooser file new JFileChooser if file showSaveDialog frame JFileChooser CANCEL_OPTION File pict file getSelectedFile BufferedWriter out new BufferedWriter new OutputStreamWriter new FileOutputStream pict for int i 0 i lt Field getHeight i for int u 0 u lt Field getWidth u out write Integer toStri
75. ficial lines of the Flow editor as a help for alignment Table 18 From the GEF website http www eclipse org gef Rulers and Guides GEF viewers can now display accessible rulers along their top and left edges Guides can be created on the ruler by clicking on an empty spot on the ruler Parts in the graphical editor can be dragged and attached to the guides They can also be attached when resizing Alternatively snapping can be disabled by holding down the Alt key while dragging Feedback is shown in the form of a red line when a part is being attached to a guide Grid GEF now provides a grid Parts can be snapped to a grid during creation moving or resizing Alternatively snapping can be disabled by holding down the Alt key while dragging Grid snapping and visibility are two distinct properties and it is possible to enable one without the other Like the rulers the grid can be turned off if so desired Snap to Geometry The feature allows you to quickly align parts being dragged to other parts in the diagram Edges of parts being resized can be snapped as well Constrained Move and Resize Holding down the Shift key while moving a part will restrict that part s movement to one of the primary eight directions N S E W and the intermediaries Doing the same while resizing will cause a proportionate resize the height to width ratio will be maintained Centered Resize 67 Holdin
76. g down the Ctrl key while resizing will cause a resize to happen in the opposite direction of the drag as well such that the center of the part being resized will not change after the resize is done Fly out Palette For clients that require the palette to be always visible and to provide further customizability to the end user the fly out palette is also being introduced The palette flies out over the top of the editor when the user hovers over it or clicks on it and auto hides when not in use The user can also pin it open if so desired It can be resized docked on either size of the editor and is completely accessible The fly out is only visible when the palette view is not It automatically comes up when the palette view is closed or when the user switches to a perspective in which the view is not open and disappears when the palette view is opened The palette state selection drawer expansion etc is maintained when switching from the view to the fly out and vice versa Panning With the PanningSelectionTool it is possible to pan by moving the mouse while holding down spacebar and mouse button 1 left mouse button 68 7 4 3 The Context menu Manhatten Router Shortest Path Save Save Image Debug Mode Illustration 43 The context menu of the Flow editor The context menu offers some of the mentioned methods and several new methods The new methods are 69 1 The Save method will save th
77. getHeight ImageProcessor ip imp getProcessor for int i 0 i lt 1000 i int w int ran nextDouble width 2 1 int h int ran nextDouble width 2 1 int x int ran nextDouble width w 2 int y int ran nextDouble height h 2 ip setColor new Color int ran nextDouble 255 int ran nextDouble 255 int ran nextDouble 255 Roi roi new OvalRoi x y w h null ip setMask roi getMask ip setRoi roi getBoundingRect ip fill ip getMask if i 10 0 imp updateAndDraw Random_Ovals ov new Random_Ovals ov run null A lot of documents are linked to the ImageJ website http rsb info nih gov ij and also API documents or well written books are available for ImageJ see literature etc Note Bio7 integrates the version number 1 39 of ImageJ 95 13 What else 13 1 Plugins for Bio7 Because Bio7 is a RCP application it is possible to create perspectives with views as an Eclipse plugin to extend the abilities of Bio7 For instance it is easy to create a plugin which embeds other views and perspectives This is a higher level of customization as the easy to use customization methods which were previously mentioned for Bio7 see Section 6 7 A useful resource for all kind of tutorials articles and links is the eclipse website at http www eclipse org 13 2 Programming examples for Bio7 The application Bio7 is distributed with a rich set of programming
78. h compiled code will be executed also very efficiently by BeanShell Scripting capabilities gt With BeanShell it is possible to create highly dynamic applications with customized scripts Script templates like the Snippets can easily be recycled for custom modification Scripts can be used to extend the Bio7 script menus Direct interaction gt With the BeanShell console you can interact directly with methods and integrated API s of Bio7 Code which was written for the Java compiler can easily be switched to BeanShell Supports full Java syntax A complete manual with the features of BeanShell and the use of the scripting capabilities is available at the mentioned website of BeanShell In Bio7 the console of BeanShell is also embedded for direct interaction with the interpreter of BeanShell and the Bio7 environment Table 16 BeanShell Uses source BeanShell website BeanShell Uses Interactive Java try out object features APIs and GUI widgets hands on Scripting extension for applications Allow your applications to be extended via scripts in an intuitive and simple way Macro Languages Generate scripts as macros and execute them live in your VM easily Education Teach Java in a hands on live environment Expression evaluator for scientific financial apps and rules engines evaluate complex expressions with conditions and loops Remote debugging Embed a live remotely accessible shell command li
79. he Bio7 application at runtime see Section 14 12 The import and export scripts will update the file menu The other scripts and macros General Statistic Image Chart will update the scripts menu in Bio7 The locations of the scripts can be browsed easily with the browse action and files can be transferred simply by copy and paste from the Navigator The files will be detected automatically and displayed in the appropriate menu for execution 8 1 3 Bio7 Editor Preferences The Preferences of the different language editors in Bio7 R BeanShell Java offering methods to adjust the default language and colours of the editors as well as to create or change templates for them Preferences Bio7 gt Preferences BeanShell Editor or Java Editor R Editor for changing the default colours Preferences Bio7 gt Preferences BeanShell Editor gt Template Editor BeanShell or Template Editor Java Template Editor R for modification or creation of the templates Note It should be mentioned that some aspects of the language editors can be changed in the default text preferences of the platform e g font attributes 77 Preferences DoE type filter text Preferences BeanShell Editor mT F w Bio BeanShell Editor Help Install Update Colour Keywords Preferences Bio Preferences BeanShell Edit SEE Uae mm Preferences Database Bio Colour String Preferences Java Editor mm Preferences R Edito
80. hermore components can be Flowaction deleted with the delete item and so removed from the flow or by Zoom In Ctrl f i pressing the key Delete If more than one component is S Zoom Out Ctrl selected the alignment actions Align Width etc and the v Rulers Grid Match Width Height actions will be available to align shapes to v Snap to Geometry the first selected shape or adjust the width or the height of selected shapes to the properties of the first selected component Additionally the added menu Flowaction in the menubar of Bio7 Illustration 41 The offers three further options for the alignment and layout of the Flowaction menu added to components When the option Rulers is selected and marked Bio7 rulers in the flow will be made visible for the exact layout of the flow components By dragging horizontal and vertical lines from the ruler like it is known from text editors components can easily be aligned to the visible ruler lines The alignment will be supported by artificial lines red lines which occur when alignment criteria are met The option Grid will enable a grid in the flow When enabled the components can be arranged in discrete coordinate steps according to the default grid size in the flow Furthermore artificial lines will occur green lines with the enabled option Snap to Geometry when a translated component matches the alignment of another component in the flow 66 Illustration 42 Arti
81. http www beanshell org R http www r project org Rserve http www rforge net Rserve ImageJ http rsb info nih gov ij Java Compiler http www janino net Database dbo4 http developer db40 com Spatial Analysis R Spatial Projects http sal uiuc edu csiss Rgeo Spatstat http www spatstat org Forums and mailing lists for information http www nabble com search for the different applications BeanShell R ImageJ Janino 147 16 3 Useful Literature Ecological Modelling J RGENSON S E 2001 Fundamentals of Ecological Modelling Elsevier Amsterdam HAEFNER J 2005 Modeling Biological Systems Principles and Applications Chapman amp Hall NY GOTELLI N 2001 A primer of Ecology Sinauer Associates Inc Massachusetts GERHARDT M SCHUSTER H 1995 Das digitale Universum Vieweg Braunschweig DIECKMAN U LAW R METZ J 2000 The Geometry of Ecological Interactions Cambridge P Grimm V S F Railsback 2005 Individual based Modeling and Ecology Princeton Univ Press D Brown P Rothery 1993 Models in Biology Mathematics Statistics and Computing John Wiley amp Sons Gotelli N J 2001 A Primer of Ecology 3rd edition Sinauer Associates Inc Sunderland MA Peitgen Jurgens Saupe 2004 Chaos and Fractals New frontiers of science Springer Verlag NY Gergel Turner 2003 Learning landscape ecology Springer Verlag NY Statistics Venables W N Ripley
82. ibutes are adjustable by clicking the mouse The File Loop Info Condition property displays the following attributes in dependence of the selected component 1 The filepath of a dropped component relative path in the workspace This path will be used for execution 2 The amount of loops which should be made when the loop component has been selected 3 An info text if the info component has been selected 4 When a decision component has been selected this property will be interpreted as a scripting expression in BeanShell Console Bsh Console Properties 2 Property Value File LoopjInfo Decision if sum 3 amp amp Field xyold y x 1 BatchModel decision true Filetype Hrinht 5 Illustration 45 An expression if a loop component has been selected 5 The Filetype property shows the extension of the selected file which has been dropped into the flow has no effect on the other components 70 6 The properties Height Width X Y display the size of the component and the location inside the flow panel which can also be adjusted in the properties view 7 There are two properties for the connections a The property LineStyle can be set to dashed or solid by default the style is solid b The Boolean property is important when a decision is to be created in the flow The property can be set to true or false Property Value Boolean v LineStyle Solid Illustration 46 The properties of a con
83. idth x rand int Math random 2 Field setState x y rand We also fill the temp array Field setTempState x y rand The arrays can be accessed by means of a small API to facilitate the development of such models In the panel it is possible to zoom in or zoom out with the scroll wheel of the mouse The state of cells can be adjusted by clicking and dragging on them The value to which a cell will be changed is dependant on the previously changed button in the Plants view see Section 6 2 5 By default this value is the value of the soil By right click on the Quadgrid panel a context menu appears with the possibility to select plant individuals in the Quadgrid panel Keys Alt S When a plant has been selected the individual properties will be displayed in the Control view under the tab Plant Individual and will be displayed in the status bar too In the Control view the individual attributes of the plant can be adjusted etc see Section 6 2 4 2 24 Table 3 Quadgrid Hexgrid Device Event Function Mouse Dragged Set numeric values or plants last selected Plant or State Mouse Scrolled Zoom in out Panel Menu gt Select Plant gt Mouse Pressed Select a Plant Mouse Pressed Set numeric values or plants 6 2 2 The Hexgrid Hexgr x yt ists spd Ge Illustration 8 Hexgrid in Bio7 It has sometimes advantages to create hexagonal design
84. ients To analyse the effect of nutrient patterns in time and space the application offers possibilities to model the nutrient dynamics of different ecosystems The dynamics of nutrients in a year can be set in a form The model allows to set different nutrient layers parallel to the plant layer The rules for the nutrient dynamics can be set in the editor The layered view allows to analyse the dynamics with the plant layer above This is helpful if you want to look at direct effects of nutrient dynamics File Edt Preferences Scripts R OpenOffice Bsh Window Help ol O we ARebs FY Jaf aa Resource Image if Soll Database 28 2d Z m J Nitrate Carbon Water Phosphate Root Density iil Timesteps 8 H 3iMof 508m File Edit Preferences Scripts R OpenOffice Bsh Window Help MO on k 4A aQebs FS puilsd Resource 5 Image 5 Database HE 2d HE Nitrate fi Phosphate iif vat Timesteps 8 2 ssmofsoam fy 3 7 Sensitivity Analysis Ecosystems are highly dynamic in their aboveground and belowground processes To test hypotheses on system functioning it is often required to run simulations under different conditions nutrients competition etc and compare the results with the real system The Flow editor in Bio7 is capable to handle the required flexibility to analyse a huge space of different situations and possibilities All programmed methods and statis
85. indow because of its size a blue rectangle will be displayed in the Outline for a flow selection The selection is the part of the flow which will be displayed in the main Flow editor window 64 Palette gt i Select E Marquee Connection L gt Flowchart Loop AH Stop HP Start A Decision gt Files Info Illustration 39 The Palette 7 4 1 The Palette of the Flow editor For the creation of a running flowchart it is necessary to create a start and a stop element in the flowchart By activating an element in the Palette these elements can be placed anywhere in the flowchart with the mouse at the appropriate coordinates pressing mouse button will drop the component Additionally when an element has been placed in the flow it can be dragged to any coordinates in the flow panel All other elements in the Palette can be placed by this procedure too The following elements are available and their values can be adjusted in the properties dialog Furthermore some properties can be changed directly in the shape mouseclick on the element The following elements are available 1 Start The Start of the flow gt necessary for execution 2 Stop The end of the flow gt necessary for execution 3 Loop A loop will repeat a sequence in the flowchart The number of iterations can be adjusted with an integer value directly in the shape 4 Decisions A decision in the flow will execute
86. ins are supported It depends on the plugins if they work correctly with the embedded ImageJ uses Swing 6 Macros can extend the main menu of Bio7 and can be created like in the regular version 7 Two OpenSource plugins for ImageJ have been added to the view menu of Bio7 a The first is a plugin for multiple image analysis where multiple images can be opened and edited by macros at once http ciar rcm upr edu projects image J b The second plugin FracLac 2 5 http rsb info nih gov ij plugins frac lac html is a specialized plugin for the analysis of fractals in digital images For more information about these plugins visit the different websites for manuals which are available 8 For Windows a small application has been added for convenience which embeds an Avi to Swf Converter http www swftools org It enables the conversion of created avis by means of a stack to swf files which then can be used to visualize presentations from Bio7 see Section 14 9 9 The ImageJ API is accessible by means of the embedded compiler or with BeanShell scripts 10 Bio7 offers some specialized methods for transferring particle values to the Points panel or to R all particle measurements can be transferred from ImageJ gt see Section 14 4 2 As mentioned before functions of ImageJ can be directly called from the Java compiler or from BeanShell A lot of available examples from the ImageJ website can be execute
87. ion from the toolbar of ImageJ to create a message box selection Select the colour dialog and then select an appropriate colour Fill the selection with the Fill method in the context menu 11 Select the colour dialog opened as a tab in Bio7 to adjust the colour again and then select the Text tool to create a text in the message box open context menu and fill text or type Ctri d 12 Now customize the presentation with some animation options framerate Image gt Stacks gt Animation Options to a reasonable framerate amp Animation Options Speed 0 1 100 fps 7 Loop Back and Forth V Start Animation Illustration 95 Speed 13 Export the Stack as an avi file File gt Save as gt Avi to a location on the local filesystem 14 Then open the dialog for the avi to swf conversion tool and select the file to convert to a swf file File gt Convert Avi gt Swf 132 Shell x Avi to Swf Converter J Quality J Scale C Enable best quality Start Conversion Illustration 96 dialog of the Avi to Swf converter The converted file can now be embedded in a website as a presentation of simulation results etc 14 9 1 Note This is just one example of the many possibilities to create a presentation from a simulation You can also embed pictures cut elements out of an image and paste them into the frame of a stack add stack frames or delete them
88. is Here the exact not rounded gt doubles values will be transferred to R Illustration 22 Set the alpha value of the image inside the Points panel Remove an image inside the Points panel Load an image in the Points panel Set the alpha value of an activated Quadgrid field Fieldsize x 1000 Point Size a Delete all points in the Points panel Set or inactivate the Quadgrid in the Points panel Zoom or scale down the Points panel Adjust the size of the Area of Analysis Adjust the size of the points Adjust the alpha value Send an image to the of the points Points panel Set points from a particle Transfer an image analysis ImageJ in the from the Points panel Points panel to ImageJ Transfer thresholded pixel from ImageJ to the Quadgrid field Transfer Points panel Transfer particle points to R values from ImageJ directly to R Illustration 20 Points panel methods 38 mx V Mean Gray Value Modal Gray Value V Min amp Max Gray Value IV Centroid vV Center of Mass Perimeter Fit Ellipse Feret s Diameter Median Kurtosis Set Measurements Standard Deviation Bounding Rectangle Circularity Integrated Density Skewness 12 With the Pixel button thresholded pixel from the ImageJ view will be mapped to the active state of the Quadgrid If the Quadgrid size is gt 1 pixel than the thresholded pixel
89. ith R 98 14 2 The first self made grid based simulation 1 Create a new project under File gt New gt General gt Project and choose a name for it 2 Create a new Java file in this project File gt New gt Bio7 gt JavaFile and name it random java 3 In the ecomain method of this file insert the code from the table below 4 Now compile the Java code with the compile action of the embedded Compiler 5 Start the simulation with the Start Pause action Table 32 Source random method public void ecomain Your code goes here for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x Field setState x y int Math random Bio7State getStateSize Ho 8 Database ae 2d Illustration 69 The compile action top right 14 2 1 Explanation In every timestep t 1 the ecomain method will be automatically invoked by the calculation thread of the Bio7 application This method automatically disperses all states the function Bio7State getStateSize will return a number of all activated states which are activated by change in the Quadgrid Furthermore in each time step the amount of every state will be calculated and stored in a vector Tip The counted data of each cell over the time can easily be transferred to OpenOffice with the OpenOffice menu Open a connection gt Open a spreadsheet gt Send Bio7 Population Data 99 14 2 2 Again in Bean
90. itors if opened offer more or less customized menus and toolbars and also offer custom context menus for the work with the different languages By activating a language editor typical text tools are activated in the edit menu of the main menubar of the Bio7 application e Before creating a file a Project has to be created where the files can be placed File gt New gt General gt Project e A file can be created by using a wizard which can be activated in the File menu File gt New gt Other gt Java File or in the context menu of the Navigator e g New gt Other gt Java File e The file itself will be opened in the editor area which can be hidden or shown in a perspective by selecting the action Window gt Show Hide Editor In the Flow editor Java R or BeanShell files can be dragged directly to the flow ie New leg Select a wizard lt gt Wizards type filter text ae CS Folder D Project Untitled Text File amp Bio BeanShell Script Flow Java File R Script Cancel Illustration 28 The Select a wizard dialog of Bio7 52 Table 14 From the Eclipse Workbench User Guide http help eclipse org Most perspectives in the Workbench are comprised of an editor area and one or more views You can associate different editors with different types of files For example when you open a file for editing by double clicking it in one of the navigation vi
91. l and to select this quads by setting a point inside its area see Section 14 5 Table 6 Points panel actions Device Event Function Mouse Left click Double click Set point Mouse Right click Delete point Mouse Left click Drag Move point Mouse Right click Double click Move ImageJ viewport with resized image in Points panel To archive this a special toolbar is available in the Window menu Window gt Bio7 Toolbar of the ImageJ view If selected a view gets detached which offers several possibilities to use the Points panel in interaction with ImageJ The following methods Illustration 20 are available 35 1 With the Alpha Pic slider the alpha value of a loaded image in the Points panel can be adjusted 2 The two Buttons below open an image in the Points panel or remove it When an image is loaded From ImageJ or from Bio7 the size of the Area of Analysis will be adjusted automatically to the image size and the new size will be displayed in the spinners Fieldsize The Area of Analysis is displayed by the green rectangle in the Points panel 3 The following slider can adjust the alpha value of the Quadgrid field which can be added or removed with the below left button 4 With the right button all points that have been activated in the Points panel will be deleted 5 With the left button the Quadgrid can be activated for an overlay in the Points panel When the Quadgrid is
92. le in the BeanShell namespace which both can be invoked with BeanShell You can also automize this e g in a flow for a simulation setup 14 14 Call compiled methods in BeanShell in the calculation thread of Bio7 In Bio7 it is possible to invoke the interpreter with compiled code in the main calculation thread of the application the calculation thread which calls the ecomain method in Bio7 at each timestep In the following example Table 46 two methods from two different files Calculate Calculate_plus will be executed in the calculation thread which has been compiled to BeanShell Table 46 Call the interpreter of BeanShell public void ecomain Interpreter doInterpret Calculate ecomain null Interpreter doInterpret Calculate_plus ecomain null With this option it is possible to execute more than one compiled class available as an object in the main execution thread if a model is more complex and the code is dispersed to more single files 14 15 Use R calculations interactively in a Java method Another nice feature in Bio7 is the possibility to use calculation results or R methods directly in the main calculation thread of Bio7 This can be realized by invoking the R interpreter directly from the Compiler and receive the results from R calculations The following source in Table 47 calls the Rserve interpreter directly and prints the received output to the console in each timestep Table
93. les gif x s E at Image Methods 2 Alpha Image f gt 15 gt Smal Medium Large 1 100 a Alpha Quadgrid La fo Resize Points Panel Fieldsize X Fieldsize 2000 1000 2 O Eraser Tool Timesteps 0 Particle Size Alpha oO 5 m 255 a Illustration 82 Transferred points from selection in ImageJ The points of the selection will be transferred to R as an array selectionx selectiony which supports the analysis of irregular regions methods for this kind of analysis are available in the default installed package spatstat Bsh Console E Properties Ex BE ef Bio Console 1 alpha diameter panel fieldx fieldy 5 selectionx selectiony species nym 9 tyger Illustration 83 Transferred values with the selection values 117 Tip The whole procedure of particle analysis can be automated in ImageJ with self defined macros which can be recorded and executed for repetition Then this recorded macro can be dropped to the Bio7 folder for the ImageJ macros which extends the Scripts gt ImageJ Macros menu 14 4 2 Getting all attributes of a Particle Analysis In Bio7 it is also possible to get more attributes from a particle analysis By selecting all options in the Set Measurements dialog before the Particle Analysis many more attributes can be transferred to R Furthermore coordinates will be transferred without being rounded
94. ll Console or Java Otherwise a call like print Hello World will be written to the BeanShell console if executed in the same BeanShell console Evaluations of R expression will be sent to the Console ale onsole X console Properties EJ Bsh Console Glo x E Properties Ex b rf e m Bio Console Illustration 4 The Platform console 21 The default platform console Illustration 4 will display results from different editors and also display errors which occur when compiling or interpreting a file There are also several actions in this console available to clear displayed text or copy the text from the console to the clipboard available in the context menu 6 1 4 The Snippets view In the Snippets view code templates can be created and stored for the different editors in Bio7 By default every text based editor of Bio7 Java BeanShell R has an integrated template editor see section 7 So Customize Palette 4 P x B z fs Anova J New Delete Move Down Import Name 3 H R Anova A Anova Description Java s ie Hide Variables Name Description Default Y Template Pattern o SSN CONnSoIe GI Consore Properes Ssnippes a _ SS a m ESR Anova fs Java Illustration 5 Create code snippets To create snippets inside this specialized view category s have to be created inside a template editor
95. lready described field size objects and states will be stored 9 Print gt Prints the content of an opened editor If an editor in Bio7 has been opened this method will print the content Annotation When a file has been opened additional entries occur according to the opened editor see Section 7 5 2 The Menu The menubar of the Bio7 application offers several menus for the work with the different components of the application The File menu offers methods for import and export of projects and files which can be extended by BeanShell scripts 16 The Edit menu offers several methods for the work with the different editors in Bio7 The Preferences menu opens the preferences of the Bio7 application The Scripts menu with several submenus is extendable for self defined scripts BeanShell and ImageJ Macros in different categories see Section 14 12 The R menu offers methods for the interaction with R and to transfer data to the embedded R application The OpenOffice menu offers actions for acquiring and setting values from and to OpenOffice Three further methods can transfer data to R or BeanShell which facilitates data acquisition through the options of OpenOffice application The menu BeanShell offers two methods to clear the namespace of the embedded interpreter and to reassign the default Bio7 imports In the Window menu perspectives and views can be opened Additionally the editor area can b
96. lt position within the Within the current perspective or it is opened as a fast view and docked to the side of the current perspective perspective 84 Option Description Default options New project all Use this option to specify the perspective behaviour when a new project is created You can set it to switch the current perspective to be the one associated with the project type and open the perspective in the same Workbench window as the current one switch the perspective and open it ina new Workbench window or not to switch perspectives at Open perspective in the same window Table 26 Available Persp From the Eclipse Workbench User Guide http help eclipse org Option Description Default Make Sets the selected perspective as the default perspective Resource Default Reset Resets the definition of the selected perspective to the default n a configuration This option is only applicable to built in perspectives that have been overwritten using Window gt Save Perspective As Delete Deletes the selected perspective This option is only applicable to user n a defined perspectives built in perspectives can not be deleted 6 Preferences type Filter text General Appearance Content Types Editors Keys Perspectives Welcome Workspace Help Install Update Preferences Bio Startup and Shutdown
97. n different categories for the execution of custom methods in Bio7 The categories all be a help in organizing custom methods in Bio7 In addition it is possible to execute R scripts by means of a BeanShell Script and the Rserve connection See Section 14 12 for a detailed description how to add a menu 6 7 3 Custom Startup BeanShell scripts can be used to customize the platform directly behind the start of the Bio7 application These scripts will be executed with the BeanShell interpreter The scripts have to be placed in a specialized folder Preferences Bio7 gt Custom Startup for custom activities like e BeanShell imports at startup e Loading a Custom Perspective or a view e Execute a startup setup in the different panels e Invoke an action from the Bio7 platform e Import libraries e Start Server application at startup See Section 14 12 for placing a script for the Bio7 application 51 7 The Editors of Bio7 7 1 General Features There are several editors integrated in Bio7 which support the syntax of different programming languages and a specialized Flow Editor to drop files from the other editors for execution The language editors support the syntax of the languages Java BeanShell uses also a Java editor and R For an instant help select an active Editor Java R BeanShell Flow editor and press F1 A text editor is also offered by default integrated in the platform an editor for arbitrary files as well All ed
98. n the console Note If the key F3 inside the text field of the expression dialog is pressed a command list will open with some common expressions for R If you press F2 a history dialog will be displayed 56 7 2 2 Plotting Another feature and one advantage of R are the plotting functions which are not available directly with the server connection in Bio7 you can create plots in pdf jpeg or png files with the Server and open them There are two actions available to imitate this plotting function in the context menu of the Bio7 editor where you can set or unset plot markers for plotting operations If a regular R command for a plot is marked inside a script This can be done by line selection By default the blue marked line is the selection and the script is executed a temporary file pdf will be created and automatically opened by the default pdf application multiple line selection is possible The plot selections are created as tasks in the Bio7 platform the taskview of the Bio7 platform can be opened as a management tool for the marked plots in different ecor files It is important to know that the marked plot instructions are evaluated after the script has been evaluated So it is an advantage to write the plotting instruction at the end of the script If more than one plot is marked in one script the resulting pdf file contains all the plotting instructions in one file In addition there is a method available in
99. nOffice If you select this action Bio7 tries to connect to OpenOffice with the OpenOffice API Application Programming Interface A progress bar in the bottom right will show the progress The path to OpenOffice will be fetched from the Preferences and can be adjusted there Windows If OpenOffice is installed it will be automatically fetched from the Registry 6 R gt Will open a connection to R by means of a Server Rserve This action will connect Bio7 to the Rserve application which builds a connection to the statistical tool R A progress bar in the bottom right will show the progress 7 Open gt Opens a simulation pattern with the Individual Based Models properties IBM file If you open a pattern file for Bio7 all stored states and some adjustments will be loaded to the Quadgrid Hexgrid If objects have been stored all objects will be assigned to the array for use in a IBM model in the Quadgrid Hexgrid The stored field size the states and the sequence of activation and therefore their numeric values will be recreated too States which are active at the moment of loading but were not active as the pattern was stored will be inactivated in the spreadsheet The condition for a successful recreation of a pattern is that the required state exists in the database only for IBM models not necessary when states out of the database context were stored 8 Save gt Saves simulation pattern with the IBM properties IBM file As a
100. ne in your application with just a few lines of code Use BeanShell declaratively to replace properties files and replace startup config files with real scripts that perform complex initialization and setup with the full Java syntax at their disposal Bio7 uses one connection like in R or namespace in BeanShell That means that a defined variable or class is active as long as it is not removed from the namespace By call the function clear all variables methods and imports will be cleared from the namespace of the connection this command is available in the BeanShell menu The interpreter itself can also be accessed programmatically by calling Interpreter doInterpret a 4 61 It is also possible to combine a compiled class with an Interpreter call Before you can call the methods the Java files have to be compiled to BeanShell by a right click on the Java files in the Navigator Multiple selections are possible See Section 14 13 for more details Table 17 Code snippet public void ecomain Interpreter doInterpret zufall ecomain null Interpreter doInterpret zufall2 ecomain null Note The default imports for the BeanShell interpreter can be changed in the file plugins com eco bio7_1 0 0 bin imports beanshell properties Windows 7 3 3 Differences In principle the embedded compiler and BeanShell are compatible to each other in their language fea
101. nection Note The properties File and Filetype are important for the execution of a file inside the Flow editor The file type information is used to select the appropriate interpreter or compiler 7 4 5 What to consider when creating a flow It should be mentioned that some rules are important for the creation of a regular flow in the Flow editor 1 A start and a stop have to be placed in the flow and they have to be connected with the components for a regular Bio7 flow 2 A flow follows the outgoing direction directed graph marked with an outgoing arrowhead 3 Files a A dropped file in the Flow editor rectangular shape can only be connected with another file or by means of a loop which connects two files Two ancestors shapes are allowed and necessary if a loop is connected to a file component b A file component has to have one outgoing connection C Files in the Flow editor will be executed sequently by means of the information in the file property and the filetype property the appropriate interpreter or program will be selected automatically 71 4 Loops a A loop can have one incoming and one outgoing connection b A loop cannot be the first component after the start in a Bio7 flow C It is possible to execute a loop with one file component Illustration 47 A connected loop which executes a file 5 times d Loops can be created nested The loops are executed iteratively
102. ng 7 attributes are chosen Ellenberg numbers which can be useful in a simulation but can also be used for other purposes 26 int light 1 getLight 2 setLight 27 int temperature 1 getTemperature 2 setTemperature 28 int kontinental 1 getKontinental 2 setKontinental 29 int moist 1 getMoist 2 setMoist 30 int reaction 1 getReaction 2 setReaction 31 intn 1 setN 2 getN 32 int salt 1 getsalt 2 setSalt 107 The following attributes do not appear in the database but are attributes of all Plant objects 33 int age Age not available in the database 1 getAge 2 setAge 34 int x not available in the database 1 getX 2 setX 35 int y not available in the database 1 getY 2 setY To set or receive a value simply call in this example for the attribute age 1 get int age Field getPlant x y getAge 2 set Field getPlant x y setAge 10 In the following simple example attributes from randomly dispersed plants are printed to the console Table 36 Simple example for a printed output of IBM properties public int zuff public void ecomain Call method to set activated Plants randomly random Access and print some properties e g species and age if Field getPlant 10 10 null Plant pl Field getPlant 10 10 System out printIn pl getSpecies System out printin pl getAge public void random f
103. ng Field getState u i out newLine Linebreak out close 136 1 After storing this file in the Navigator we simply copy it to the clipboard open the preferences in Bio7 and select the Preferences Bio7 dialog O Preferences Ka E type filter text General Help Install Update Preferences Bio Preferences Bio7 Path to R Path to OpenOffice Script location Path to Startup Scripts Path to Import Scripts Path to Export Scripts Path to General Scripts Path to Statistic Scripts Path to Image Scripts Path to Chart Scripts Illustration 99 Preferences of Bio7 D eclipse SDK 3 3R C4 win32 eclipse Bundled_RiR Browse C Programme OpenOffice org 2 2 program Browse D eclipse SDK 3 3RC4 win32 eclipse com eco bio startup_scripts Browse D eclipse SDK 3 3RC4 win32 eclipse com eco bio importscripts Browse D eclipse SDK 3 3RC4 win32 eclipse com eco bio export_scripts Browse D eclipse SDK 3 3RC4 win32 eclipse com eco bio scripts Browse D eclipse SDK 3 3RC4 win32 eclipse com eco bio statistic_scripts Browse D eclipse SDK 3 3R C4 win32 eclipse com eco bio image_scripts Browse Jn D eclipse SDK 3 3RC4 win32 eclipse com eco bio chart_scripts Browse Restore Defaults Apply 2 Then we browse to the export_scripts location and simply paste our file to that location 3 Now we open File gt
104. ng and unboxing by the embedded compiler which compiles the file from the editor directly to the calculation thread of Bio7 The Java wizard creates a file which contains a main method ecomain which is necessary for the compilation of the file If a Java file was compiled and the calculation thread was started by pressing the start pause button in every time step this main method would be invoked To go into more detail the embedded compiler compiles a class which visible part is the class body that can be defined by the user 58 Ecoclass X Not visible import com eco example public int a 0 public void ecomain not visible Bio7 Woes File Edit Preferences Scripts R OpenOffice Bsh Window Help lO Wwe SZQeHS E Lf Resource 1 Image SE Soil Database Had 5 Navigator 2 S0 interpoint ecor 6 Easier_Game_of_Life java al Flea public int frames 0 public void ecomain 3 Bio _Examples amp Ecological Modelling for int i 0 i lt getHeight i for int u 0 u lt getWidth u function for getting the sum of the moore neighbourhood or extended moore r int n 1 int sum torusMooreSum n u i special function to sum the neighbourhood if sum 2 amp amp getState u i 1 setTempState u i 1 else if sum 3 amp amp getState u i 0 ixynew i u 1 setTempState u i 1 lt gt BE Outline 2 O
105. ng the key combination CTRL X short and long operations In some cases where the application Rserve is involved it can become necessary to stop and restart the application this can be done with the Rserve connection action in the toolbar of Bio7 If possible it is highly recommend to test all files before they are used in the Flow editor 41000 1100 1200 130 serrereeseeseredtenreterrerss arereateesesseserserseseettsteretres eer prsereareeterseorenreeseereseeredtesetsertereer ses paseestreaeesereerersersareererenses sendeesenerereereesersereetartert arereeredstrneretreseesees H Si mi OO a B E B00 Illustration 51 A complete defined flow in the Flow editor 7 4 7 Executed Files 7 4 7 1 Dropped from the Navigator The Flow editor recognizes several different file types Files created with the Bio7 editors will be executed in the flow with the appropriate interpreter or the embedded compiler bsh java ecor Additionally the Flow editor will also execute exe files Files with the extension argument can be created and dropped before the exe file in the flow sequence This will execute the dropped program with an argument xxx argument 74 7 4 7 2 Dropped from outside the Navigator Files dropped from outside the navigator will be opened or executed with the registered program of the operating system Table 19 Action according to location and extension
106. o special variables for simulation purposes The first variable is the t variable This variable can be used to Nutrients Wiles f t amp Abiotic Factors time Nitrate Phosphate Water Temperature Carbon Light c1 c2 c3 c4 05 ingtration 15 Abiotic factors plotted over the time simulate a time series function over the year For example if you have rain precipitation data from different years and want to use an average function for your simulation Then you simply have to add the t variable in your formula which represent a modulo function to repeat the values when a special self defined value has been reached This self defined value can be adjusted in the Repeat after textfield By default this value is adjusted to 12 for a year So by default after 12 time steps calculation begins with 0 the t variable will bet set to 0 again F t Carbon F t Custom1 F t Custom2 F t Custom3 F t Custom4 F t CustomS Repeat after Illustration 16 Abiotic factors and the formula will be reset for the year to start again Optional a second variable is available This is the counter variable t when a progressing variable is needed So in that case the simulation steps can be used as an argument in the self defined formula The formulas must be expressed in Java which offers a lot of mathematical expressions by default it s not necessary to set a char
107. of methods are available Furthermore in the combination with R and Bio7 the strong image methods can help detecting patterns and offer a more flexible support for the analyses of spatial patterns in time and space on different scales Additionally with the powerful libraries from Java everything can be combined for a thorough analysis of ecological models Table 31 Example from the ImageJ Website as a BeanShell Script import ij import ij process import ij gui import java awt import java util Random import ij plugin public class Random_Ovals implements PlugIn public void run String arg IJ run New name Random Ovals type 32 bit RGB width 400 height 400 if IJ altkKeyDown drawOvalsFaster else drawOvals void drawOvals ImagePlus imp WindowManager getCurrentImage Random ran new Random int width imp getWidth int height imp getHeight for int i 0 i lt 1000 i 94 int w int ran nextDouble width 2 1 int h int ran nextDouble width 2 1 int x int ran nextDouble width w 2 int y int ran nextDouble height h 2 IJ setForegroundColor int ran nextDouble 255 int ran nextDouble 255 int ran nextDouble 255 IJ makeOval x y w h IJ run Fill void drawOvalsFaster ImagePlus imp WindowManager getCurrentImage Random ran new Random int width imp getWidth int height imp
108. of transferring continuous data to discrete data IDE Integrated Development Environment a type of software that assists in developing software Snippets In Bio7 a small piece of programming source code to demonstrate some of the Bio7 features 151
109. ons These are beside the regular actions of the platform 1 Add Block Comment gt Surrounds the selected code with a block comment Remove Block Comment gt Removes a selected block comment A precise selection is necessary 3 Format Java gt Formats regular java code To work with BeanShell please create java code inside the BeanShell editor 4 Format selected Java gt Formats only the selected code This is sometimes necessary if the formatter can not format the entire code 5 R Source Conversion gt Converts Rscript code Rscript expressions can be executed inside java and BeanShell This converter helps to convert R expressions for use e g in an Rscript Please select the R expression and then execute this action 63 7 4 The Flow editor The Flow editor of the Bio7 application is capable to handle and execute different files by their extension and display and arrange them in a flowchart like structure e It can be used to create complex sensitivity analysis for created models e It can serve as a guide for complex analysis of all tools offered by Bio7 e Or it simply can be used to visualize complex workflows The main strength of this tool is that you can assemble all methods and information created by files for modelling statistical analysis or image analysis in a profound analysis The Flow editor of Bio7 helps to organize and visualize the creation and analysis of ecological models A flowchar
110. option controls whether or not hyperlink style n navigation navigation is supported Hyperlink style navigation This option sets the hyperlink style navigation key Gt r key modifier modifier Disable overwrite typing This option controls whether the overwrite typing mode ae Appearance color options This option controls various appearance colors 8 2 4 Help preferences On the Help preferences page you can indicate how to display help information Preferences ex type filter text Help General Appearance Content Types Editors Keys Perspectives Startup and Shutdown Welcome Workspace Help Install Update 2 Preferences Bio Use external browser Open Modes Open window context help Oin a dynamic help view Open dialog context help Oina dialog tray Specify how help information is displayed ar Oin an infopop Oin an infopop Restore Defaults Apply Illustration 59 Help preferences 83 Table 24 From the Eclipse Workbench User Guide http help eclipse org Option Description Default If embedded web browser is supported on your system help window uses an embedded help browser to display help Use external contents whenever possible and this option is available Off browsers Select it to force help to use external browsers Use Web Browser preference page to select browser to use Open window This
111. or int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x State getStateSize gt how many states a present gt 0 soil 108 zuff int Math random Bio7State getStateSize if zuff gt 0 Zero is the value of the Soil Field setState x y zuff Field setTempState x y zuff Set individual in the array Planttemplate p Bio7State getPlanttemplate zuff Get a plant template by chance Create a new individual from the given template properties Plant plant new Plant y x p Field setPlant x y plant Field setTempPlant x y plant else if zuff lt 1 Field setState x y 0 Field setTempState x y 0 Field setPlant x y Field getSoil x y Field setTempPlant x y Field getSoil x y 14 3 2 Annotation Use the tempstate planttemp arrays getTempArray x y getTempPlant x y for storing intermediate patterns for the grid This will be necessary if all cells shall be calculated in one timestep under the same conditions Once the calculations for the whole field are done the temporary values can be copied to the state plant arrays as a setup for the next calculation step 109 Illustration 72 One time step in a discrete simulation 14 3 3 Copying instead of creating new objects Creating and deleting instances in an object oriented approach is a cost and time intensive procedure For a bet
112. or draw different shapes to create a full featured presentation Also you can take R Charts and animate them for presentation plot a voronoi several times with different parameters and then combine them to an animation The avi2swf converter is also able out of the context of Bio7 to convert arbitrary avi files 133 14 10 Open perspectives and views programatically For presentation issues or for guiding users through self defined methods for instance in a flow perspectives editors and views can be accessed programmatically Table 43 Example which opens a view Work openView com eco bio7 quadgrid See the Bio7 Snippets for more examples 14 11 Add states without the database In Bio7 it is possible to define states programmatically without using the database for instance if you want to make a simulation with animals etc States can be defined set or removed programmatically When a state has been defined by name the Plant view will automatically produce a button with the name for that state or will display an image if available Furthermore the charts will be updated automatically and a counter will be added to each defined state The states can be saved or loaded as usual with the Load Save pattern method Bio7 will automatically update all views and activate plants which have been stored to that file and inactivate plants which have been not All states get a numeric value according to the sequence of c
113. or is working by default Windows For the convenience of the user the following applications are embedded For statistical computing Installation of R and packages spatstat tripack odesolve with the connecting application Rserve A Java Runtime Environment gt 1 5 0 Linux Because of the different Linux distributions an installation of R is required On the R website http www r project org several R versions for different distributions are available Also the installation of the Rserve library is required This can be easily done inside R by typing install packages Rserve dependencies TRUE in the console After the installation of R the path to the R application has to be adjusted inside Bio7 Preferences gt Preferences Bio7 Please install also the following libraries spatstat tripack for the Bio7 examples The Bio7 application was tested on Ubuntu and Suse linux 11 Installation Windows and Linux The installation of Bio7 is similar to the installation of the Eclipse environment Simply decompress the downloaded zip file in a preferred location on your file system After decompressing with a standard zip tool like WinZip Win Rar the typical file structure of an Eclipse based application will be created To start the application simply double click or click linux on the Bio7 exe Windows or Bio7 linux file Note Windows It is also possible to install Bio7 on an Usb Stick with the desc
114. ou want to see the measured values in a table gt slower Analyze Particles 0 00 1 00 Size pixel 2 Circularity 113 Show Nothing IV Display Results IV Clear Results Summarize Illustration Exclude on Edges Include Holes Record Starts 77 measurement options Particle 114 6 Confirm the dialog to analyse the particles 7 Go to the Image methods dialog Window gt Bio7 Toolbar and transfer the image to the Points panel which will calibrate the Pont Pie gt panel s Area of Analysis 2000 1000 for the particles gif example 8 Before you proceed you have the possibility to select a plant in the Plants view activated plants from the spreadsheet or a state which was defined before programmatically to map the points to a special state or plant species from the database For this example the points will simply be mapped to the default soil state 9 The alpha value of the points and the size of the points can also be adjusted before the points will be transferred 10 Now press the top Points button to create points in the Points panel according to the coordinates of the measurements coordinates with values gt 1 5 will be mapped to 2 0 int values 11 Select Yes in this dialog if you want delete all points that are present in the panel Select No if you want to add points to existing points in the Points panel Delet
115. ough and deselect the ones that you do not want to add 7 Click Deselect All to deselect all resources in the directory then go through and choose individual resources to add 8 Specify the Workbench project or folder that will be the import destination 9 When you have finished specifying your import options click Finish 124 14 6 4 Export resources to the file system Table 40 From the Eclipse Workbench User Guide http help eclipse org 1 In one of the navigation views select the resources that you want to export 2 From the main menu bar select File gt Export The Export wizard opens 3 Select General gt File System and click Next 4 By default the resources that you selected will be exported along with all their children Optionally use the checkboxes in the left and right panes to select the set of resources to export and use push buttons such as Select Types to filter the types of files that you want to export 5 Click the Browse button on the next page of the wizard to select the directory you would like to export the resources to 6 Specify the directory in the file system that will be the export destination 7 Click Finish Tip You can also export folders and files by dragging them from the Navigator view to the file system or by copy and paste 125 14 6 5 Export resources to an Archive file Table 41 From the Eclipse Workbench User Guide http help eclipse org
116. ow to call CustomControlls JPanel CustomView setPanel JPanel name Swing CustomControlls Canvas Swt Composite parent CustomView getComposite name see Table 11 for details CustomControlls GLCanvas Custom3D setPanel canvas name animator OpenGL see Table 12 for details Draw2d LightweightSystem Iws CustomView getDraw2d name similar to Table 11 see Snippets Custom Charts JFreechart ChartView setChart chartPanel name 0 9 20 Table 11 How to wrap swt org eclipse swt widgets Composite parent CustomView getComposite name Display dis CustomView getDisplay dis syncExec new Runnable public void run The Code goes here DD To OpenGL It is likely that an Animator instance starts in an OpenGL script For this case it is required to pass an animator variable to the Bio7 function If the view or the panel is closed the animator will be stopped too with the command animator stop which would not happen if no animator reference was passed to Bio7 49 Bio7 File Edit Preferences Scripts R OpenOffice Bsh Window Help Hw O AQeHs EI D gt Resource 2 Image 33 soil C3 Database HEE 2d gt gt u Snippet_OpenGL_1_Gea Snippet_CustomPanel x4 1 ts Navigator Outline custompanel X example to show bad ynment First start the JPanel jp new JPanel jp setBackground new Color 255 2
117. platform are described here Notes and additions regarding Bio7 are marked red 8 2 1 General Preferences le type Filter text General Pr An Always run in background Help Install Update Keep next previous editor view and perspectives dialog open Preferences Bio M Show heap status Open mode Double click O Single click Note This preference may not take effect on all views Restore Defaults Apply Illustration 56 General preferences General settings for the Workbench The term Workbench refers to the desktop development environment Each Workbench window contains one or more perspectives Perspectives contain views and editors and control what appears in certain menus and tool bars More than one Workbench window can exist on the desktop at any given time The following preferences can be changed on the General preference page 80 Table 22 From the Eclipse Workbench User Guide http help eclipse org Option Description Default Turn this option on to perform long running operations in the Always run in background without blocking you from doing other work Off background P Please turn on for Bio7 Z If this option is turned on then the editor and view cycle eep dialogs will remain open when their activation key is let go next previous OFF Normally the dialog closes as soon as the key combination is part dialog open release Show He
118. r Colour Single Comment Preferences RServe Preferences State Colour Default a ra gt Restore Defaults Apply Illustration 53 Colour preferences of the BeanShell editor 8 1 4 Preferences Database In the preferences of the database Preferences Bio7 gt Preferences Database the default location of the database is displayed in a textfield With the textfield for the Default Datatable Size the size of the table which displays the plants e g in the Database perspective can be changed according to the size of the self defined database The changes occur after the Bio7 application has been restarted Normally it is not necessary to do so because it is sometimes not plausible to do simulations gt 100 plants But if you want to build up a database for different simulations the backend for this application is a full featured object oriented database dbo4 If you want to backup the database simply browse to the database file database yap and copy it elsewhere for storage Also databases can be exchanged for different analysis 78 Preferences Bio Preferences BeanShell Edit Preferences Database Bio Preferences Java Editor Preferences R Editor Preferences RServe Preferences State Default Datatable Size 5 1000000 100 iw Preferences cle type filter text Preferences Database Bio Cr General Preferences Bio Database Help Install Update Default Plant Database D ExportBio7
119. r has no method for an interruption of a running interpretation It is a good approach to test all scripts before they are e g embedded in a flow The default imports for the interpreter are available in a text file and can be changed in the file plugins com eco bio7_1 0 0 bin imports beanshell properties Windows Please consider to make a backup before you change the file For more information about BeanShell visit http www beanshell org 15 3 Notes about the Java Compiler Sometimes in a running simulation an exception can occur A typical error message of the compiler is java lang NullPointerException Generally this means that an error occurred at the line number 71 of the compiled java source If that is the case please recompile everything to restart a simulation For more information about the compiler visit http www janino net The default imports for the compiler are available in a text file and can be changed in the file plugins com eco bio7_1 0 0 bin imports compiler properties Windows Please consider to make a backup before you change the file 15 4 Notes about ImageJ It is recommend to visit the website from ImageJ There are a lot of programming examples and tutorials which help to create image based calculations and analysis The ImageJ version used in this application is based on the version 1 39 The integration of ImageJ followed the approach to change the original as less a
120. r so that the default editor can recognize the file If a R file has been opened the toolbar of the Bio7 application displays two new items which have some special functions if a connection to the Rserver and R has been established The Interpret RScript button executes the interpretation of the active RScript file you can also choose a splitted view with two files in the editor area By selecting this action the whole file will be interpreted Created variables will be accessible by means of the second item or in the main menu of Bio7 R gt Evaluate Expression 55 7 2 1 Evaluation The Evaluate Expression action simulates a kind of console like in R When this action is selected a dialog with a textfield inside pops up where R expressions can be evaluated All evaluated expressions are shown in the console of the Bio7 application Because Bio7 uses a server Rserve as a fast connection to R there are some differences between a regular R BAX Illustration 32 Expression dialog version and the R version of Bio7 Bio7 tries to mimic some of the functions which are normally not available with the Rserve application The functionality of a shell in R is imitated in Bio7 with the action Evaluate Expressions which mimics a kind of R console in Bio7 EJ Bsh Console Elo amp E Properties Ex BE rf e 1 alpha diameter panel fieldx fieldy 5 species Pyr reer Illustration 33 Output i
121. reate new projects from an archive file or directory F jj Select a directory to search for existing Eclipse projects a Select an import source O Select root directory type filter text 7 Yp Select archive file C Dokumente und Einstellungen localadmin Desktop Browse G Archive File Project faeedsdet st Aa AORO rojects LS Existing Projects into Workspace E L File System V Bio7_Examples Select All E Preferences V Ecological Modelling Deselect All Refresh Select the archive file Examples zip and the two projects Bio7 Examples and Ecological Modelling Press Finish to import them into Bio7 they will be imported to the workspace location For the first steps it is recommended to read through the section 14 How to s of this document to start with the examples of Bio7 13 5 The Platform Architecture Perspective Bar oro laren O76 14 After the Bio7 application has been launched the typical Workbench window is displayed A Bio7 window offers one or more perspectives A perspective contains editors and views such as the Navigator In the first Workbench window that is opened the Resource perspective is displayed as default In Eclipse terms A window contains a page which contains an arrangement of views and editors whose layout is defined by a perspective 5 1 The Toolbar The toolbar offers several actions H 0 AQebtsS 1
122. reation starts with 0 In the following Snippet 50 states will be added to Bio7 without deleting the soil state but can also be removed for instance when creating a cellular automata like the Game of Life Table 44 for int i 2 i lt 50 i Bio7State createState Integer toString i 134 Bio7 SAX File Edit Preferences Scripts R OpenOffice Bsh Window Help M O o k AeQes FEY Resource Image Soil Database E 2d 2d ii state 52 UE m B Spreadsheet G u Species Synonym Enable Select Tei ez 2 Plant1 plant Plant2 plant lt 2z ox f States Dooa Doo o2 e2 02 02 o e5 o 02 o e2 02 02 on oe oon oe A T Q Control s al Time and Space Plant Individual Eso M1 E2 E3 H4 M5 Be m7 Bs wo Disturbance Mio M11 M12 M13 W14 Mis Mie M17 Mis M19 20 M21 M22 M23 W24 W25 Abiotic Factors m20 M27 W28 B20 W30 M31 W32 B33 M34 M35 M36 O37 Mss W39 40 M4 Bao B43 B44 B45 Ma 47 B48 Ba of Timesteps 0 35Mofsosm jj Illustration 97 Fifty states defined programmatically Note The states which will be created with this procedure are just numeric values and no individual Plant properties are available like for the states from the database The states can be dispersed in the Quadgrid with the mouse drag or click It is o
123. rete models and spatial discrete individual based models of plants 6 2 1 The Quadgrid The Quadgrid panel like the by default hidden Hexgrid panel visualizes a simulation field for discrete simulation models By default only soil as state with value O is dispersed in the Quadgrid respectively Hexgrid field The panel itself is a visualization of states stored in an two dimensional grid array In the grid array called xystate numeric states of type integer are stored for simulation purposes Furthermore in a second two dimensional grid array plant of type Plant plant individuals can be stored as an object The two array approach has been chosen because of the advantage to easily choose between the creation of classical cellular automata or grid based models and grid based individual models By default there are also two further temporary arrays available xytempstate tempplant with the appropriate type for an intermediate store of states when calculating patterns for the next timestep t 1 as it is usual in grid based modelling 23 Illustration 7 The arrays with the different types are accessible with the same index Table 2 Code snippet A simple example to show how to produce and set random cells without setting any individual plant information from the database States soil 0 plant 1 int rand public void ecomain for int y 0 y lt Field getHeight y for int x 0 x lt Field getW
124. ribed procedure Moreover OpenOffice can also be installed portable with Bio7 Download the portable version http portableapps com apps office openoffice portable and adjust the OpenOffice path to the OpenOfficePortable App openoffice program subfolder in the Preferences After the first start Please select the option Preferences gt General gt Always run in background to disable the progress monitor dialog of Bio7 This avoids a blocking dialog in many operations of Bio7 important for the integrated Flow editor 6 Preferences ole type filter text General General Help Install Update Keep nextjprevious editor view and perspectives dialog open Preferences Bio v Show heap status v Always run in background Open mode Double click O Single click Note This preference may not take effect on all views Restore Defaults Apply Troubleshooting for Windows and important to know The Rserve application on Windows is sensible to wrong input If a failure in an R expression occurs the Server has to be restarted again 12 Examples On the Bio7 SourceForge website you can download examples for the Bio7 application To install the Bio7 examples please import the examples from the Examples zip file File gt Import gt Existing Projects into Workspace O import leg Gimport oy Select x Import Projects r C
125. ries 16 2 Documentation and programming links 16 3 Useful Literature 17 Addendum S 149 18 Definition of expressions S 151 1 Introduction The application Bio7 is an integrated development environment for ecological modelling with a main focus on individual based modelling and spatially explicit models The application itself is based on a RCP Eclipse Environment Rich Client Platform which offers a huge flexibility in configuration and extensibility because of its plug in structure and the possibility of customization In this platform powerful known tools were integrated for the purpose of simulations and analysis of ecological systems A lot of complexity of a modelling process is hidden behind a user friendly flexible Graphical User Interface which should assist the development and analysis of simulation models for different ecosystems Therefore Bio7 offers and embeds also powerful and well proofed third party tools which are capable to do Image Analysis ImageJ Statistical Analysis R an easy to learn scripting language BeanShell to ease the development of simulation models and an embedded Compiler for the need of speed in complex calculations Additionally editors Java R BeanShell and different panels for visualization are integrated for an easier development Communication in between the different components is possible by means of scripts and compiled code and can be collected in a flowchart for Sensitivity Analysis etc
126. s These projects and their files can than be exported or imported as zip files for data exchange The Navigator of Bio7 allows you to create Java files BeanShell files RScript files Flow files textfiles and arbitrary files in their own editor environment with a help of an installed wizard Some specialized integrated functions allow the compilation of Java files to BeanShell after java files have been selected multiple files allowed gt see Section 14 13 and the integration of Java libraries in BeanShell by right click on a jar file Double click on the file in the Navigator will open the file in the editor area According to the selected file the appropriate editor for the file will be opened See Section 7 The Editors of Bio7 for more information 6 1 2 The Editor Area The editor area is the area where all files are opened and edited The context menu varies depending on which file is opened The R BeanShell and Java editors when opened offer typical text functionalities like Copy Paste Undo Redo Cut Find Replace Print etc in the context menu and in the edit menu menu bar of Bio7 When a file has been opened editor specific buttons will be added to the toolbar which execute an editor action according to the Bio7 Weoley File Edit Preferences Scripts R OpenOffice Bsh Window Help MO Ne LReos G Fey Dafad Resource 2 Image Soll BjDatabase 83 2d Navigator 5 import static com eco bio
127. s can be created and stored in the preferences dialog when opening Preferences gt Preferences Bio7 gt Preferences BeanShell Editor gt Template Editor BeanShell Oo Preferences o type filter text Templates g General Help Install Update Context Description bio gt for Ant Script 4 loop over 2 D bio a bio gt mo Ant Script 4 loop over 2 D bio a bio gt ra Ant Script loop with random Func cast Ant Script dynamic cast catch Ant Script catch block do Ant Script do while statement else Ant Script else block elseif Ant Script else if block For Ant Script iterate over array For Ant Script iterate over array with For Ant Script iterate over collection For 2d Ant Script 4 loop for 2 d array Foreach Ant Script iterate over an array Create edit or remove templates Preferences Bio Preferences BeanShell Edit Preferences Database Bio Preferences Java Editor Template Editor Java Preferences R Editor Preferences RServe Preferences State Remove bad 3 3 3 KS ES ES ES 3 K3 KS ESS Preview For int index 0 index lt Field getHeight index For fint index2 0 index2 lt Field getwidthQ index2 4line_selection 4 c gt Restore Defaults Apply Illustration 30 Creation of templates Annotation The templates can also be used to create custom formulas to facilitate the de
128. s in experimental setups which will reproduce a binned pattern more naturally instead of the Quadgrid A central cell in a Hexgrid is surrounded by six neighbours All have the same euclidean distance from the centre of the central cell Bio7 offers a hexagonal grid which is by default hidden but can easily be activated with Window gt Show View gt Other gt Bio7 Panels gt Hexgrid 6 2 2 1 Storage of patterns and IBM properties To store the pattern of the cell grid and the IBM properties of each cell the Save pattern action stores all properties from every plant in the grid Also the grid size and the selected species in the spreadsheet will be stored when selecting this action sequence will be preserved The file will be stored as a database file yap which can be opened again with the Load pattern action When this action is selected the state of all stored cell with there IBM properties are restored and the stored plant species will automatically be selected in the 25 spreadsheet view for simulation Furthermore the field size will be adjusted according to the stored value 6 2 3 The Linechart and the Piechart The Linechart and the Piechart views serve as a monitor to watch population size and count the different states in a simulation run Regardless how fast a simulation runs the charts get updated every second By right click on the charts several options are available For example to store an image of the chart or to adjust some ch
129. s possible to get the highest compatibility between the original version and the version of Bio7 ImageJ macros for a startup can be placed in the macros folder StartupMacros txt plugins com eco bio7 image_1 39 4 macros ImageJ plugins can be placed in the 145 plugins folder plugins com eco bio7 image_1 39 4 plugins It is important to know that some of the free available plugins http rsb info nih gov ij plugins may not work correctly for the embedded ImageJ because of the different GUI Swing instead AWT approach New ImageJ plugins can be accessed in the plugins menu of the ImageJ view Simple plugins extend the plugins submenu of the ImageJ menu Plugins gt Plugins Plugins located in a jar are accessible and executable with the help of the Control panel Plugins gt Utilities gt Control Panel Additionally Since Bio7 1 1 it is possible to compile ImageJ plugins directly with Bio7 using the embedded IBM Compiler To start the compiled plugins the source has to be compiled to the plugins folder or the Bio7 application has to be restarted After a restart of Bio7 the compiled plugins are accessible in the plugins submenu 146 16 Literature and Links 16 1 Useful Libraries JScience http jscience org Colt http dsd Ibl gov hoschek colt Apache commons math http jakarta apache org commons math 16 2 Documentation and programming links Programming BeanShell
130. script again Automatically a pdf will be opened from a temporary file with the registered pdf viewer The temp file is named temp_plot last selected line number pdf Table 42 Interpoint distances libra ry spatstat x lt c 20 45 23 100 50 45 25 y lt c 45 22 30 34 56 2 56 d lt nndist x y 127 10dmean lt mean d 1lidmax lt mean d 12dmin lt mean d 1 3boxplo 44 14 Undo Typing Ctrl Z Revert File Save Show In Alt Shift W Shift Delete Paste Ctrl ae Preferences fh Conso Content Assist Ctri Space 7 Console Content Tip Ctrl Shift Space Delete Plotmarker Add Comment Illustration 89 A plot with Bio7 Annotation A wrong input in Windows will cause the Rserve application to close and a loss of the current workspace will occur save the workspace to avoid a loss of valuable data Simply restart the Rserve application when no server connection is available any more 128 14 8 Create a custom GUI for a Rscript With the Bio7 application it is possible to create a Graphical User Interface GUI for statistical methods in R With this GUI the user can be guided through a complex sequence of necessary steps These steps can be arranged in a flow or by using the resources of BeanShell to communicate with R and OpenOffice Therefore BeanShell can be used to create a custom GUI for R methods For a better input and output the OpenOffice
131. several sliders for adjusting of individual parameters for the selected Quadgrid cells Hexgrid Additionally information will be displayed about the position of a cell in the grid and the plant species if available which has been selected This information will also be shown in the status bar of the Bio7 application When a cell has been selected with an existing plant object in the underlying plant object array no null reference the individual properties will be displayed by means of the sliders All sliders will be updated with the values received from the object By changing the values of the sliders the values of the object at the selected index y x will be updated automatically So every individual plant object in the grid array can be updated separately from the others It is also possible to update all other plants which represent the same species in the grid with the action Change global This is analogue to nature where we have individuals of one species which often differ in some characteristics It is a generalization when these properties are responsible for every individual of the same kind by pressing the button If a cell is selected which has no plant object in the array plant planttemp of type Plant the message No plant selected occurs For example when only a cellular automata is needed with custom states there is no need to use the plant array with the templates for the database In that case only the array of
132. started If the server is restarted in Bio7 an embedded application Windows will kill all running Rserve instances to guarantee that only one Rserve instance is active else communication errors could occur Bio7 offers also the possibility to set the registry path for the embedded R By default this tool is disabled That the Bio7 installation does not harm any settings of the user You can enable this option in the preferences dialog Preferences gt Preferences Bio7 gt Preferences Rserve gt Install path at startup After the path was recreated after a restart of the Bio7 application you can disable this option again An installation of R also offers the option to create or delete a registry path in Windows Please read the R FAQ for this options u Preferences RServe or Path to temporary RData file no empty space allowed Path to temporary RData file C _ Install path at startup C Start with shell Illustration 106 Set the registry path Browse For more information about the Rserve application and the Windows version and also for examples which can be used in Bio7 visit http www rforge net Rserve 144 15 2 Notes about BeanShell Sometimes it is necessary to clear the namespace of BeanShell to correctly interpret a script because Bio7 works with one connection to the interpreter Bsh gt Clear In the console with the command clear The BeanShell interprete
133. t by definition is a schematic representation of a sequence of operations In the flowchart of Bio7 files can simply be dragged from the navigator of Bio7 and dropped into the Flow editor of the application According to their file extension these files are executed in the sequence of the flow which has been created A created Flow editor file has the extension ecoflow Some other files will be handled by default from the Flow editor when they are dragged from outside the workspace Executable files exe will be executed too and it is also possible to execute these files with an argument by creating a file with the extension argument Files from outside that have different extensions will be executed according to their registration in the system environment e g if you have an pdf file and the registrated program for that filetype is the Acrobat Reader the file will be opened by default with this program If the editor is opened a lot of items will be added to the Bio7 toolbar and a new menu will appear in the menubar of the application Additionally a specialized context menu will be available for calling different methods inside the Flow editor A new palette bar will also be displayed for inserting flowchart elements in a new created file Furthermore an Outline on the left will show an Illustration 38 Outline of the Flow overview of the flow if the flow cannot easily be editor displayed in the main w
134. ted according to the selected Plant template from the database and dispersed in the Plant array plant tempplant as well as in the numeric array xystate xytempstate of the Quadgrid Hexgrid The object properties of the dispersed plants can easily be altered and accessed programmatically Additionally in a specialized view these properties can individually be changed without any effort of programming see Section 6 2 4 2 46 6 6 The 3d Perspective GBo Or File Edit Preferences Scripts R OpenOffice Bsh Window Help UO Nae ZL Rebs E pu ad eS Resource 2 Image 2 Soil 3 Database 85 2d Dgrid X Nitrate carbon water Phosphate Root Density Timesteps 0 i moim i Illustration 26 Layered grids in 3d In this perspective the Quadgrid panel and one optional soil panel are visualized With the Buttons in the toolbar the different soils can be activated in this view Dragging the mouse in the view to the left or to the right shifts the layers between front and back Dragging the mouse up or down will change the rotation axis of the displayed grids With the scroll wheel of the mouse the distance of the layers can be altered Finally by pressing the arrow keys of the keyboard you can move the layers up and down left or right for calibration Table 8 Functions Device Event Function Mouse Drag left right Bring layers to front back Mouse Scroll Distances betw
135. ter performance and memory use in a fixed grid it is a better approach to copy Plant objects in the Plant array instead of creating and deleting Plants each time In a simulation you can simply copy not referencing all attributes from one grid place to another e g when a plant disperses to a new grid place Then values can be adjusted according to the needs for example set the age to the value O etc Attributes can also be copied to a soil place because the soil state is also a plant object import static com eco bio7 discrete Field A static reference to the Field Ae ISON E Get the plant which will disperse to x and to y in the grid Plant p getPlant x y Get the temporary plant also soil is a plant object at the new place Plant temp getTempPlant to_x to_y Copy the species name and values which are important for the simulation to the temporary plant array We do not reference the old object temp setSpecies p getSpecies Set the new age of the dispersed individual temp setAge 0 etc if needed 110 14 4 Point Pattern Analysis Open an example particles gif from ImageJ in the ImageJ view menubar File gt Open Samples then follow the steps described below OBio7 oog File Edit Preferences Scripts R OpenOffice Bsh Window Help WO ouk ALRIS EO ies PS Resource E Image EH Soil 3 Database in 2d mua 5
136. the time steps a simulation has proceeded Additionally for plant interactions every time step is calculated as a month and 12 time steps are summarized as a year which will be shown too Furthermore several sliders for the adjustment of the parameters calculation speed time resolution and field size capacity are available Additionally a checkbox and a button are displayed which enable the resize event after an adjustment The first slider Speed is responsible for the calculation speed of the calculation thread It can be set to values from 10 1000 units The visible sliders below Fieldsize can be moved to values from 1 to 1000 They are responsible to adjust the field size of the different grids in Bio7 Illustration 10 The Controll Quadgrid Hexgrid Nitrate So the maximum field size Panel Time amp Space which can be adjusted in Bio7 is a field size of aux s i fe ffice Bsh Window Hel Zx MOAT CRrCIINDEISE H O o k Aas Hs O T Mfd Ey Resource 2 image Ei sol Daaba Gi 2a m afad amp Resource 2 image iii se Database 55 2d ii state 2 gt D spreadsheet 1 E heet 5 ial Ele pa i Enable Select il ier fl Oooo Ho0000000 O00200 S
137. the context menu of the R editor which places a comment at the selected lines All other functions which are available in the context menu of the editor and the edit menu inside the main menu bar of Bio7 are well known functions like undo redo cut copy paste delete select all print and find replace open a search dialog for the document 57 7 3 The Java and the BeanShell Editor 7 3 1 Java The Java editor of Bio7 is a regular Java editor which supports Code templates and the colouring of the syntax of Java Text functionalities Copy Paste etc are the same as in the RScript editor For the compilation of the Java file the Janino compiler is used embedded in Bio7 http www janino net A new Java file can be created with the Java wizard in the Bio7 File menu New gt Bio7 gt JavaFile The instructions of the wizard will guide you through the procedure of file creation O new ax Select a wizard lt gt Wizards type filter text B General amp Bio amp BeanShell Script Illustration 34 Creating a Java file When a Java file has been created with the wizard one item will be added to the Bio7 toolbar for an easy compilation of the Java file The syntax of the Java file must be the syntax of the Java lt 1 5 0 1 4 2 specification All new Java gt 1 5 0 features like annotations or generics etc are not supported exceptions are static imports and autoboxi
138. the ones that you do not want to add 7 Click Deselect All to deselect all resources in the directory then go through and choose individual resources to add 8 Specify the Workbench project or folder that will be the import destination 9 When you have finished specifying your import options click Finish Tip You can also import folders and files by dragging them from the file system and dropping them into one of the navigation views or by copying and pasting 123 14 6 3 Import resources from an Archive file Table 39 From the Eclipse Workbench User Guide http help eclipse org You can use the Import wizard to extract files from_an archive file into the Workbench 1 From the main menu bar select File gt Import The Import wizard opens 2 Select General gt Archive File and click Next 3 Click the Browse button on the next page of the wizard to select the archive files that contain the files you want to extract and import into the Workbench 4 In the import selection panes use the following methods to select exactly the resources you want to add e Expand the hierarchies in the left pane and select or clear the checkboxes that represent the folders in the selected directory Then in the right pane select or clear checkboxes for individual files 5 Click Filter Types to filter the current selection for files of a specific type 6 Click Select All to select all resources in the directory then go thr
139. the spreadsheet File Edit Preferences Scripts R OpenOffice Bsh Window Help ib O Wd amp AZeaeHs BY Resource J Image HEE Soll E Database JH 2d Spreadsheet X 0 B Form amp Species Synonym Form Plant Scientific name Synonym C Lo Life form January Anthesis start January x Anthesis end Life span Height min __ Width min Width max Height max Surface Depth min Depth max Width min Width max Surface C vegetative O sexuell Opp0oppp0pp0pp0pp0p0p00p00p0p0p0p00TmTH opgppgoppgoppgoprprppgrppppppgprpgporaTnnrnn Timesteps 8 zemof soem i 3 5 Plants Bio7 is an integrated development environment with a strong support for individual based models After activation in the database every cell in the visualization represents an individual plant Each plant individual can then be adjusted by certain parameters File Edit Preferences Scripts R OpenOffice Bsh Window Help WO WW al alae FEY Resource J Image Soil C3 Database 355 2d Synonym Enable Select K Dogg pooo0o2ga conri FO Time and Space Plant Individual Disturbance Abiotic Factors 0 25 0 50 0 75 Iteration soil W Plant Plant2 3 6 Nutr
140. the type int state tempstate for the states is needed 6 2 4 3 Disturbance Often ecosystems are marked by random disturbances by means of biotic or abiotic factors Disturbance Disturbance 0 i yY Illustration 14 Panel a a Disturbance Table 4 Code snippet The item Disturbance contains a slider for the adjustment of an embedded disturbance function in Bio7 This function can be used in a custom simulation by calling Environment randomDisturbance y x When this function is called cells which are affected by the function A cell has a change to be affected with a probability of the slider value 0 1000 will receive the numeric value 0 state tempstate which is by default the value of the soil Additionally the object array for the plants will receive a null reference An example for this special function is the following piece of code Table 4 public void ecomain for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x Environment randomDisturbance x y 0 Plant s are deleted by chance according to the disturbance value 29 6 2 4 4 Abiotic Factors Behind the last item in the Expandbar a panel is hidden which offers several textfields for custom formulas of abiotic factors Self defined formulas can be compiled and directly be used in a custom simulation These formulas can be made dynamic by adding tw
141. tical analysis which are required can be dragged into the Flow editor Because of the possibility of creating loops and decisions in between a flow of files hundreds or thousands situations with different parameters can be analysed with statistical well proofed methods R and summarized Obie oog File Edit Preferences Scripts R OpenOffice Bsh Window Help Flowaction H O k L4RQebs O Be da oF oft E N 0 A A e rG Palette N Select E Marquee Connection gt Flowchart Loop Stop H Start y Decision Extra Info f Timesteps 0 esMofSoam D 10 4 Getting started System requirements It is recommended that your computer should have at least 512 mb ram and a ighz processor The installation requires about 150 mb free space on the hard disk A 3d Graphics Card which is OpenGL enabled only necessary for 3D view and for 3D programming To use the OpenOffice feature of Bio7 an installation of OpenOffice gt 2 0 is required The path to OpenOffice will be automatically fetched by Bio7 from the registry or is adjusted Linux to the default path See section 8 The Bio7 Preferences For the Flow editor Older Windows versions require the gdi library which has to be downloaded from Microsoft and installed e g copied in the Windows System32 folder Candidates are Windows NT Windows 2000 Windows 98 Windows ME This is not necessary if the Flow edit
142. ties can be adjusted in the Control view public int zuff public void ecomain for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x State getStateSize gt how many states a present gt 0 soil 3 zuff int Math random Bio7State getStateSize 4 if zuff gt 0 Zero is the value of the Soil 5 Field setState x y zuff Field setTempState x y zuff Set individual in the array 6 Planttemplate p Bio7State getPlanttemplate zuff Get a Plant template by chance Create a new individual from the given template Plant plant new Plant y x p Field setPlant x y plant Field setTempPlant x y plant 8 else if zuff lt 1 Field setState x y 0 Field setTempState x y 0 9 Field setPlant x y Field getSoil x y Field setTempPlant x y Field getSoil x y 102 1 Variable which stores the random values 2 We create a nested loop over all cells in the grid 3 By change a state will be selected with a random generator the index is the number of the sequence of activation If Plantl and Plant2 is enabled in the spreadsheet 0 soil 1 Planti 2 Plant2 4 If by chance a value for a plant has been selected gt 0 5 We set the state the numeric value at the specified index in the array 6 A reference to the plant template with the selected number will be created 7 A new object Plant will be created at the index
143. tion thread of Bio7 A simple example how to transfer data dynamically to the soilpanels public void ecomain for int y 0 y lt Field getHeight y for int x 0 x lt Field getWidth x Fill array from the different panels with random values Nitrate setNitrate x y int Math random 999 Carbon setCarbon x y int Math random 999 Phosphate setPhosphate x y int Math random 999 Water setWater x y int Math random 999 RootDensity setRootDensity x y int Math random 999 42 Only for painting required Nitrate doPaint Carbon doPaint Phosphate doPaint Water doPaint RootDensity doPaint The different panels are also visualized in the 3d view of the program so that the influence of certain abiotic factors on the plant composition etc is directly visible 6 4 1 The Soil In the top right of the Soil perspective a detached dialog can be activated to adjust parameters for the soil panels Values 0 1000 units can be adjusted for the different panels with a slider After adjusting they can be set directly with the mouse in the activated panels The values are displayed in units which then can be assigned or mapped to any scale of concentration etc The three available buttons in the panel offer methods to bring in random homogeneous or gradient values in the soil fields 1 If the Rand button is presse
144. to that perspective from other perspectives in the same window 18 6 1 Resource perspective After Bio7 has been started the perspective in front is the Resource perspective The parts of the Resource perspective are The Navigator to import export open and manage files The Editor area where files are opened The Consoles for Bio7 and BeanShell An Outline active when the Flow editor has been opened oe ee ee The Properties view which shows and enables attributes of selected elements Also important for the adjustment of the Flow editor properties 6 The Snippets view in which general snippets for the different text based editors of Bio7 can be created Bio7 aax File Edit Preferences Scripts R OpenOffice Bsh Window Help HO ouk L4Res E R Resource s Image HH Soil 3 Database in 2d 5 Outline 22 m Bsh Console El Console 2 Properties 5 Snippets Ex BE rf a 5 An outline is not available Bio Console fi Timesteps 0 34M of 508M Illustration 1 The Resource perspective of Bio7 19 6 1 1 The Navigator In the Navigator view files can be managed and stored The context menu offers several possibilities to import and export files for BeanShell R Java and the Flow editor All the files are managed by projects which can have folders and subfolders etc for managing a large amount of different file
145. transferred values temporary workspace file and type the command for list s in the R Console The transferred values for this method are e The alpha value for the points can be used as an additional attribute in modelling displaying the magnitude of certain parameters competitive strength etc e diameter_panel will give you a list of all point diameters in the panel e imagex imagey are the attributes for the Area of Analysis e species is a numeric value 0 1 2 which indicates the species or state from Bio7 e x y are the coordinates of the state One index in the list alpha 1 x 1 y 1 belongs to one point of the analysis For a further analysis you now can proceed with a custom analysis see R_snippets for point pattern voronoi etc Note R plots differ from the Points panel paintings in the origin of the y coordinate The 0 0 coordinate can be found in the top left of the Points panel whereas the 0 0 coordinates in a plot of R can be found in the bottom left 116 14 4 1 Additionally If you select an ROI Region of interest in ImageJ only this region will be analysed So it is possible to create an irregular region for analysis OBio7 oog Fie Fdit Drafaranrar Serinte D NnanNffica Reh Windom Holm d ImageJ Toolbar amp Hooven aoe e alaa lt 0 m Eraser Tool s55 Points 22 File Edit Image Process Analyze 7 Plugins Window 7 partic
146. tures because BeanShell is also capable to interpret Java source code The combination of both forms a strong tool as described previously Some differences have to mentioned 1 The BeanShell script will not be executed in the calculation thread 2 Both compiled classes and BeanShell methods can be used independently from each other 3 In a BeanShell script it is not necessary to have an ecomain method but will be created by default Afterwards this method or other methods can be accessed directly from BeanShell 4 BeanShell can access the compiled class of the compiler access to methods variables etc 5 The compiled class in Java can select the interpreter of BeanShell to execute methods etc so you can use BeanShell methods also in the calculation thread 62 6 Both the compiler and BeanShell can interact with Rserve the interpreter of Rserve for calling statistical methods and transferring results in both directions For more information about the differences please consult the BeanShell manual Show In Alt Shift wW gt Paste Ctrl Preferences Content Assist Ctrl Space Add Block Comment Remove Block Comment Format Java Format Selected Source R Source Conversion Illustration 37 The context menu 7 3 4 The context menu of the Java BeanShell editor The context menu of the BeanShell editor and the Java editor offers some methods for editing the source and for source conversi
147. ure selected for install include optional features a page will show up allowing you to select whether you want them installed or not Optional features typically carry functionality that is not essential for proper functioning of the main feature 11 The Install Location page controls where the new feature s files are to be installed on the local computer Select the directory into which the product is installed and hit Next If the product is installed in a directory to which you do not have write access you should contact your system administrator and get them to install this feature so that it will be generally available The other option is to click Add and point to a directory to which you do have write access 12 Feature versions can be digitally signed by the company that provides them This allows you to verify more easily that the features and plug ins that are about to be downloaded and installed are coming from a trusted supplier Warning Because of the possibility of harmful or even malicious plug ins you should only download features from parties that you trust Click Install to allow the downloading and installing to proceed Once the new feature and plug ins have been downloaded successfully and their files installed into the product on the local computer a new configuration that incorporates these features and plug ins will be formulated Click Yes when asked to exit and restart the workbench for the changes to take effect
148. user through a complex process of statistical analysis See the Code Snippets for more examples 12 2 OpenOffice features of Bio7 If the free Office Software OpenOffice is installed some methods for data acquisition and a small API for interaction with the OpenOffice spreadsheet are available in Bio7 To use the OpenOffice features it is necessary to establish a connection between OpenOffice and Bio7 Scripts R OpenOffice Bsh Window Open Spreadsheet R A pen Sp Data toR Data with head to R Data to Beanshell Image AH g Ts Send Bio counts I Illustration 67 OpenOffice menu of Bio7 92 This will be done automatically when selecting the action OpenOffice connection in the toolbar of Bio7 If a connection is established several methods for the interaction with OpenOffice will be available in the OpenOffice menu 1 To receive or transfer values from or to the spreadsheet of OpenOffice it is necessary to open a spreadsheet This can easily be done with the action Open Spreadsheet After a spreadsheet has been opened also possible by means of a small API the spread can be filled with values by hand or with values from a file in the opened spreadsheet menu of OpenOffice Insert gt Sheet from file With the action Data to R OpenOffice spreadsheet values can be transferred to the active R workspace by means of the Rserve connection the columns will be stored as lists and the selected
149. velopment of ecological models By default it is possible to share this self defined code templates with 54 others by using the integrated import export functions of the different template editors available for each language in Bio7 7 1 2 Preferences of the Editors In the preferences dialog of Bio7 there are a lot of functions available to customize the different language editors For example the fonts for all editors can be customized under General gt Appearence gt Colours and Fonts If the colours of the keywords etc should be changed it could be done under Preferences Bio7 gt Preferences BeanShell Editor for the BeanShell editor 7 2 The R Editor The R Editor of Bio7 supports the syntax of the R language If an R file is created with the default wizard the extension of the created RScript file is ecor instead of R to distinguish between other editors which use R as extension If you have an R file outside the workbench this file can simply be dropped to a Project of Bio7 The only change which has to Bio7 Lely File Edit Preferences Scripts R OpenOffice Bsh Window Help WO we ALRI FO E Resource 2 Image Sif Sol Database HE 2d Show In At ShftAW gt Paste Cre Preferences Content Assist Ctrl Space Set Plotmarker Delete Platmarker Timesteps 0 Writable Sma ert moim D Illustration 31 Opened R editor be made is to rename the file extension to eco
150. will fall into one quad coordinate of the scaled Quadgrid looks structure If the pixel size of the Quadgrid is 1 all like a coarsening of the thresholded pixels will fall into one Quadgrid quad of the available Quadgrid area Area Fraction Limit to Threshold Invert Y Coordinates Redirect To None v Decimal Places 0 9 8 Illustration 21 attributes Slice Number I Display Label Particle Properties area centerofmassy circularity ellipse_minor ImageWidth kurtosis max w mm i n w rect_height rect y m std_dev Illustration 22 Particle area fraction centroidx ellipse_angle ferrets_diameter integrated_density labels mean nmo de w rect_width skewness centerofmassx centroidy ellipse _major ImageHeight invert y limit median perimeter rectx slice values from ImageJ tranferred to R 39 Ex Bi e E riran 6 3 2 1 Using the Points panel for spatial continuous simulations The Points panel can also be used to create spatially continuous models The following snippet demonstrates the use of the Points panel for simulations in the calculation thread of the Bio7 application Therefore an one dimensional point array type Individual has to be created and transferred to the Points panel setIndividual The Individual objects must be parametrized with the coordinat
151. xportBio Juni eclipse plugins com eco bio _1 0 0 export_scripts Path to General Scripts D ExportBio Juni eclipse plugins com eco bio7_1 0 0 scripts Path to Statistic Scripts D ExportBio Juni eclipse plugins com eco bio _1 0 0 statistic_scripts Path to Image Scripts D ExportBio7 Juni eclipse plugins com eco bio _1 0 0 image_scripts Path to Chart Scripts D ExportBio Juni eclipse plugins com eco bio _1 0 0 chart_scripts al gt Restore Defaults Apply Illustration 52 The Preferences of Bio7 paths 76 8 1 1 Application Paths If the topmost item in the Bio7 Preferences dialog is selected several text fields are displayed which store different paths for the Bio7 application Preferences Bio7 The two topmost paths Path to R Path to OpenOffice are paths for the R application embedded and Open Office if installed which will be automatically fetched from the registry Windows when Bio7 starts They can also be adjusted manually to any location in the file system where R or OpenOffice are installed Browse button It should be mentioned that the path to R can be changed to any R installation The communication between Bio7 and R will be successful if the Rserve application is installed correctly in that location 8 1 2 Script Paths The following paths in the Preferences Bio7 are script path locations where scripts and macros ImageJ macros can be dropped which update the menu except Startup Scripts of t
152. ype different methods or to debug some piece of code e g it can directly interact with the Quadgrid For example if you type and execute return an expression like Field setState 0 0 1 the cell at the coordinates 0 0 top left in the BeanShell Console of Bio7 will directly be marked in the Quadgrid with the colour of the state 1 14 3 The first gridded IBM Model 1 Create a database of plants with the help of the form in the Form view 2 Now select the plants for simulation by activating them in the Spreadsheet view The plants will be dispersed in the Quadgrid C Wok File Edit Preferences Scripts R OpenOffice Bsh Window Help mw O wek ARves 26 E Resource Image f Soll Database i 2d HE state 5 polana x Planti Plant2 popoonaa pooponogo Control 2 u Time and Space Plant Individual Disturbance Abiotic Factors Timesteps 0 16M of 508M Illustration 71 Species 1 3 as states in the Quadgrid 3 Now create a Java file with a random function which disperses Objects in the Quadgrid 101 Table 35 Source First IBM Model This Snippet shows how to create discrete individual based models In this this example activated plant objects are set by chance The default properties are the properties from the database After the creation of plants individual proper

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