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IRIS Explorer User`s Guide (in pdf with no images

1. 83 information To replace a node type in an array or set glyph select the glyph you want from the Data Types palette and drop it exactly on top of the node type slot This inserts the new glyph into the node type slot Note Be careful when you position the new glyph over the node type slot If the new glyph is dropped over the title bar it replaces the complete array glyph not just the node type You can replace the node type with a scalar array or set glyph For example each array in Figure 7 7 has a different node type If you drop an array or set glyph onto the node type icon you can construct a data hierarchy For example if you open the vector glyph in the 4 D Array glyph in Figure 7 7 you see the nested vector structure see Figure 7 9 which must in turn be defined The new data structure consists of a 4D array where a vector exists at each node For more information see Hierarchy in Arrays Figure 7 9 A Hierarchical Array Component Menu Button The Component Menu button see Figure 7 6 lets you list an isolated segment of an array as a separate item which can then be connected to other templates For example you can list all the x coordinate values of a 3D dataset or all the pressure values in a pressure temperature dataset For information on isolating the fragments see Selecting Array Components For more information on glyphs see Data Structures 7 4 2 Building a Script This example illustrat
2. start modulename at X Y quit explorer unmaxi modulename unmicro modulename unselect modulename unselected mods Table B 2 Skm Command Syntax manne eNO Some commands have an alternate syntax Any command that takes a double quoted string specifying a module name can also take a variable of type lt Explorer Module gt Such variables are returned by the start command when it executes successfully Similarly a shortcut way of specifying a connection is to use a variable of type lt Explorer Connection gt These variables are returned by the connect command Use of these special variables is explained in greater detail later B 1 4 IRIS Explorer related Command Descriptions This section discusses the most commonly used IRIS Explorer related Skm commands along with those whose operation is not obvious start The start command is used to start modules Here are a few examples start ReadImg start SharpenImg at 200 300 The start command returns a value of type lt ExplorerModule gt which contains the name of the started module therefore you can assign the return value in the following manner define mod start ReadImg The variable mod can now stand in for the string ReadImg whenever needed destroy Modules can be destroyed using the destroy command So to destroy the module ReadImg you can type destroy ReadImg or if the value returned by start was saved in a varia
3. 2 Now bring up the output template s pop up menu and select dims The blue connection wire appears in the Overview pane see Figure 7 29 Figure 7 29 Making the First Connection 3 Assign the data by bringing up the pop up menu on the file template and selecting matrix 4 From the output template pop up menu select data The lattice output template now has all the information it needs to convert the data file into IRIS Explorer To test the script select Parse from the File menu The DataScribe traverses the script and tests for errors such as undefined symbols and illegal links If any error messages appear in the Messages pane refer to Tracking Down Errors Save the script and then create the data file described in Figure 7 24 Enter the name of the data file into your new DataScribe module in the Map Editor You can try it out by connecting its output to Contour 96 Figure 7 30 A Script Using Patterns 7 11 Selecting Array Components Frequently a file will contain a dataset that is too big to be read completely into memory or perhaps only part of the data is relevant such as one slice of a 3D array or every other node in the dataset You can separate out the relevant parts of a dataset and turn them into independent data items that can be wired into other data items in a template These parts are called array components or fragments and you isolate them using the Array Component Dialog window To display t
4. Global Namespace There is a single global namespace in the script interpreter shared by the user typing at the IRIS Explorer user interface console and by all modules issuing scripting commands The global namespace can be exploited by certain applications but it also represents a hazard to the unwary For example suppose you have written a module MyMod that under certain conditions will issue a scripting command to start another module You have assigned the value returned by the start command to a variable called mod used for subsequent manipulations of the launched module A problem arises though if a user launches more than one instance of MyMod All instances of MyMod will assign the result of the start command to the global interpreter variable mod The result is that mod1 will contain a reference to the last started module and earlier references will be overwritten The solution to this problem is to name variables distinctively so that other modules avoid touching them A good way to get distinctive names is to prepend the module name to the variable Module names are unique within IRIS Explorer so the variable namespaces should not overlap In some cases this does not matter For instance in an IRIS Explorer application in which there is only one module that issues scripting commands the module can name variables without restriction There can even be more than one module issuing script commands in an application as long as
5. which takes two numbers and adds them together define add pair procedure argl arg2 argl arg2 add pair 2 2 4 B 3 1 Using a Skm Procedure Connecting image processing modules in IRIS Explorer is a common occurrence Image processing modules that operate on a single input typically have an input port named Img In and an output port named Img Out This procedure simplifies connecting such modules by supplying these port names automatically define image conn procedure modl mod2 connect modl Img Out mod2 Img In You can use this procedure as follows image conn SharpenImg DisplayImg B 3 2 Skm Output Skm output is handled by the print command It takes one or more arguments and generates output to the IRIS Explorer console the shell from which IRIS Explorer was launched define vl abc define v2 123 120 define ml start ReadImg print vl v2 abc123 print My module is m1 My module is lt IRIS Explorer Module Ref ReadImg gt B 3 3 Looping In Skm the procedure for loop is used to implement a style of iteration similar to that used by C The format of the for loop call is for loop start op stop step loop body proc Like the typical C for loop structure the Skm for loop takes a start count a comparison operator a stop count and an increment Instead of having a loop body as does the C construct for loop takes as its final a
6. 18 you can type further text into the window if for example you wish to annotate the output The menu appears when you click the right mouse button in the Log window To change the Log back to a read only window the default select the Un Editable Log option The other two options let you clear the window and save its contents Figure 2 18 Log Window Pop up Menu You can also send the log output to the UNIX shell from which you launched IRIS Explorer To have text messages sent to standard output start IRIS Explorer with this command explorer debug printAlert If you use this option you can still use the Log windows for reviewing text messages 2 8 Understanding IRIS Explorer Data Types In IRIS Explorer the data that modules accept and pass on is characterized by the data type The data type is the form that data takes in IRIS Explorer There are five IRIS Explorer data types lattice pyramid geometry parameter and pick All data is passed through the module input and output ports each of which accepts or outputs only one data type Modules may however have several ports with a different data type on each one 2 8 1 Defining the Data Types The IRIS Explorer data types are Lattice A series of arrays in one or more dimensions that hold dimension variables nodal data values and coordinate values For example data that defines a volume such as a 3D CT scan of a bone is in lattice format This is the most c
7. 43 Slice has two outputs a 2D slice lattice and a transform to LatToGeom The transform sets the orientation of the slice lattice with respect to the parent in Render It must be connected to LatloGeom which correctly positions the slice Figure 3 10 shows a map using Slice Figure 3 10 Slicing a Volume with Slice 3 4 3 Using ProbeLat The ProbeLat module works only with curvilinear lattices and its action is not restricted to plane surfaces seeFigure 3 11 Figure 3 11 The ProbeLat Module It takes slices from a curvilinear lattice in the form of a single planar slice a trihedral which is three mutually perpendicular planes see Figure 3 12 a paddlewheel which is three planes radiating from a center at 120 to one another see Figure 3 12 The module accepts a transform from TransformGen which sets the orientation of the slice The slice is output in the form of a pyramid You can select the form the probe takes Probe Type and the area of the slicing plane Clip Size from theProbeLat control panel Note For pyramids you can use SlicePyr and ClipPyr Figure 3 12 Probe Forms Figure 3 13 shows a paddlewheel probe generated by ProbeLat Figure 3 13 Slicing a Volume with ProbeLat 3 5 Generating a Histogram You can examine data distribution in a lattice by connecting any module that has a lattice output into the Histogram module and generating one or more histograms The histogram see Figure 3 14 show
8. WireFrame creates a frame that defines the boundaries of the storm data GenerateColormap modifies the colormap for the buoyancy data VolumeToGeom converts the volume data to geometry for Render Render displays the rain density isosurface and the water buoyancy volume Note For volume rendering techniques to display the volume as shown in this map you require alpha blending hardware Some workstations do not have this hardware but they can display the volume adequately if the Splat type on VolumeToGeom is set to Point see Experimenting with the Volume Map below 10 1 6 2 Experimenting with the Volume Map This map uses both surface rendering the isosurface and volume rendering the haze in one visualization to show the relationship between a number of variables which have been calculated in 3 D space during the modelling of the evolution of the storm IsosurfaceLat see Figure 1 13 calculates an isosurface from the density data and outputs it as geometry The threshold value is the density value for which an isosurface is created You can change the threshold value by turning the dial on the control panel and thereby change the shape of the isosurface This indicates how the rain density varies throughout the storm space Figure 1 13 JsosurfaceLatControl Panel VolumeToGeom volume trenders the buoyancy data as a hazy cloud surrounding the isosurface The entities that make up the cloud are called splats small planar sh
9. choose one of the three options Pt to Pt Right Angle or Diagonal Click on each one in turn to see its effect It is an art to keep the wires in a map distinct and disentangled However no damage results from their being crossed or threaded underneath a module The map merely becomes a little harder to read You can create more aesthetic maps by collapsing several modules into a group module In this case all the selected modules disappear and are replaced by one control panel of your own design For more details refer to Chapter 5 Creating Groups and Applications Example 2 3 Wiring Modules Together This example illustrates how to connect modules to make a functioning map see Figure 2 14 In the previous example you saved a set of four modules Figure 2 14 Example of Map Connections Launch the map by dragging and dropping it in the Map Editor Then wire the modules together and set widgets as follows 1 Connect the Lattice output port of ReadLat to the Input Lattice port of the Contour module 2 Type a filename into the file browser of the ReadLat module A good lattice data file is in usr explorer data lattice testVol lat 3 Open the full scale control panel for Contour by clicking on the square Maximize button for more information see Resizing the Control Panel 4 Set the minimum and maximum values for Contour by turning the dials to 1 0 and 2 0 Connect the Lattice output port of GenerateColormap t
10. port outputs pick data to a picking module The other two ports let you take snapshots of the object in the Render window and export them to other modules This is useful for making animations 3 7 2 Modes of Operation Render has four mutually exclusive viewing modes The viewing mode is a way of considering how the camera in the scene is moving The viewing modes are selected from the Edit menu on Render s menu bar Each one lets you view the scene in the Render window in a slightly different way You can examine fly by or walk by the object or you can change the viewing plane You can zoom in and out as if looking at the object through a telephoto or wide angle lens The object appears closer when you zoom in although it actually remains the same distance from the camera To zoom in or out hold down the left and middle mouse buttons and move the mouse towards or away from the screen 3 7 3 Selecting an Object Render has two picking modes viewing or picking selecting an object In the Pick Edit or view mode you can change the camera parameters that is the position direction and field of view of the camera in relation to the object In the User Pick Mode you use the mouse and buttons to select objects attach manipulators and query objects through picking To select an object click the left mouse button on it The object appears surrounded by a red box see Figure 3 18 Figure 3 18 A Selected Object 3 7 4 Moving an
11. save them click on Apply You can set up menu stubs for parameters that currently do not exist and add the items to the menu at a later date if you wish 4 3 2 Setting up Menu Items To create the menu options for each item on the menu bar click on the Menu push button under the menu name The Menu Editor is displayed see Figure 4 8 You can create entries for the current menu For example reader modules or groups that have reader functions will usually have New and Open entries in their File menus Figure 4 8 The Menu Editor From the option menu next to the item name you can set the action to be taken when the user selects this item from the menu bar of the completed module control panel The action items are None No action to be taken useful as a placeholder Set param Sets the value of a widget by passing a specific value to a parameter in the module or group File selector Brings up a Motif file selector It comes up in the current directory by default Script command Carries out a Skm scripting command System command Carries out a UNIX command and displays the result if any in the shell window where IRIS Explorer is running Quit Destroys the module or quits IRIS Explorer when IRIS Explorer is running in application mode If you choose File selector a button appears in the next pane allowing you to define the file selector parameter If you choose Set param the button appears again with a text slot for ent
12. usr people jim explorer The easiest thing to do is to install IRIS Explorer in the same location on all machines which by default is usr explorer Using the Switch Statement in a Shared cshre If you have a single cshrc file on several workstations each of which may have IRIS Explorer installed in a different location you can use the csh switch statement to set EXPLORERHOME correctly according to the current machine For example switch hostname case billiejoe setenv EXPLORERHOME usr local explorer breaksw case bob setenv EXPLORERHOME usr people jim explorer breaksw endsw Note The character surrounding hostname in the previous example is an accent grave not an apostrophe A 1 3 The explorerrc File Both the IRIS Explorer config and explorerrc files can contain commands that configure IRIS Explorer The syntax is line oriented a backslash at the end of a line indicates that the next line is a continuation Exclamation points at the beginning of a line designate comments but the sign will also work The line syntax is very similar to that of shell scripts namely command arguments modifiers The first word designates the command and subsequent fields designate arguments or modifiers to the command 107 Either single or double quotation marks may be used to surround arguments that contain embedded blank characters Most arguments to commands m
13. 3 Creating a Parameter Function In this example see below a relationship is created between parameters from two different modules The upstream module is sosurfaceLat It has a Threshold parameter shown as a dial which will be wired to the minimum and maximum level inputs of Contour the downstream module see Figure 4 11 The parameter function is applied only when a upstream parameter one corresponding to a variable in the P Func expression is changed Threshold in this example It is not applied if you change the subject parameter Contour s Min Level or Max Level parameters in this example The change must be in the upstream parameter Example 4 1 Creating Simple Functions This example shows how to link parameters from different modules and then define the relationships between them Launch the map named simple consisting of ReadLat connected to IsosurfaceLat connected to Render To make a parameter connection see Figure 4 11 1 Launch a Contour module Connect up Contour s Input Lattice input port to ReadLafs Output Lattice port 2 Connect up Contour s Contours Geometry port to Render s Input Geometry Opt port Create a parameter connection by wiring sosurfaceLat s Threshold output port to Contour s Min Level input port 4 Now turn the dial on the sosurfaceLat module You ll see both sosurfaceLat and Contour fire Figure 4 11 Connections for a Parameter Fu
14. 4 Inthe Parameter Function box type in the expression A B 2 0 This averages the two inputs that are fanned into Threshold 5 Click on the Apply button to establish the relationship 6 Set Contour s Min Level dial to 0 0 and the Max Level dial to 1 0 Set the number of contour levels to 4 or 5 From now on when you turn Contour s Min and Max Level dials the Map Editor sends these values to IRIS Explorer s parameter interpreter It evaluates the expression and feeds the result to JsosurfaceLat s Threshold parameter You can see the calculated value reflected in the position of IsosurfaceLat s Threshold slider There are now contour levels outside the isosurface You can change the transparency of the isosurface in Render so that you can see the contour values inside the surface as well For more information see Visualizing Data in Chapter 3 Using Modules 64 Chapter 5 Creating Groups and Applications This chapter describes how to extend map construction into more complex realms It explains how to streamline maps by combining the functions of several modules into one thus creating a group of functions It covers types of groups selecting modules for a group using the Group Editor editing input and output ports creating a group control panel creating an application 5 1 Overview In a remarkably short time maps tend to overflow the available space even with micro control panels To reduce the cl
15. 4 Summarizing the Process This is a summary of the steps you take to create a parameter function in the P Func Editor 1 Select the input parameter for which you want to establish a parameter function from the Input Parameter option menu It must have at least one connection to an upstream module as shown in the Connections and Variables boxes 2 Ifyou wish to change the default variable names A B C click on the variable name you wish to change in the Variables box see Figure 4 12 3 Type anew name for the variable and press lt Enter gt to have the new name accepted The default names are A B C and so on but you can type in any name you like to replace them Note The P Func Editor is case insensitive 4 Inthe Parameter Function box enter an expression that defines the relationship you want between the variables in the Variable box if any Saving the Parameter Functions Use the four buttons at the bottom of the Editor to save or reject modifications to the input parameter The buttons function as follows OK Accepts the changes you have made implements them and closes the Editor window Apply Accepts the changes you have made implements them and keeps the Editor window open Check Checks the validity of the function and sends a message to the Message pane Cancel Closes the Editor window without accepting or implementing any changes on the screen Example 4 2 Creating a Complex Function This exam
16. Add this line to the explorerrc file 106 host bob Do this for every host you want to run modules on When you execute IRIS Explorer again these host names will be listed on the Hosts menu in the Module Librarian window IRIS Explorer uses the rsh command to create a computation server on machines used for execution of remote modules Hence you must be able to access the remote hosts you use with the rsh command IRIS Explorer also provides an alternative to rsh which is cxrexec It is capable of prompting for a password See Remote Execution and Passwords for more information A 1 2 If IRIS Explorer Is Not Installed in usr explorer If IRIS Explorer is not installed in the directory usr explorer then you must either create a symbolic link from usr explorer to the actual installation directory If your system uses shared libraries as do UNIX systems you must install the symbolic link define an environment variable EXPLORERHOME to contain the name of the directory where it is installed See IRIS Explorer Environment Variables For example if IRIS Explorer on the machine billiejoe is located at usr local explorer then you must set EXPLORERHOME to be usr local explorer in the cshrc file see csh 1 Suppose that on the remote machine bob IRIS Explorer is located at usr people jim explorer Then the cshrc file in your home directory on host bob must contain this line setenv EXPLORERHOME
17. Contour IsosurfaceLat IsosurfacePyr LatToGeom PyrToGeom PickLat ReadGeom VolumeToGeom Increase the maximum arena size for larger data sets set arenasize 24mb A 1 4 Configuration Commands The commands that are accepted in an IRIS Explorer configuration file are described below Optional portions are enclosed in square brackets Ellipses denote that the previous argument may be repeated any number of times Commands reserved words are shown in bold Setting the Module Path The module path is a list of directories in which IRIS Explorer looks for modules and maps The default list contains only EXPLORERHOME modules but the Explorer config file shipped with IRIS Explorer extends it You can reset module paths from scratch or you can extend them using the append or prepend modifiers The modulepath command states where to look for modules modulepath prepend path modulepath append path 108 This command defines a list of directories to be used By default the existing module path is extended by the list for directories this is equivalent to using the append modifier The default path value is EXPLORERHOME modules Used alone the command clears the module path to the default path value If the prepend modifier is used the path is added at the head of the current directory list set You can use the set command to set the temporary directory and the size of the arena set tempdir IRIS Explore
18. CropPyr lsosurfacePyr PrintPyr PyrToGeom PyrToLat Transform WritePyr Geometry Render WriteGeom Pick Annotation Ball CropLat2D CropLat3D InterpLat Table 2 1 Input Data Accepted by Modules Table 2 2 lists some IRIS Explorer modules according to the data type Lattice Pyramid Geometry or Pick they can produce on an output port Qutput Port Data Modules Lattice AtomicSurf ChannelSelect ColorXform CropLat2D CropLat3D DisplaceLat Displaylmg GenerateColormap GenLat Gradient Histogram Interpolate LatFunction MagnitudeLat Mixer OrthoSlice PyrToLat ReadLat ReadPlot3D Render SampleCrop ScaleLatNode Shell Slice SubSample Transform 28 Pyramid Geometry Pick TransformGen WaveFormColormap CullPyr CropPyr LatToPyr ProbeLat ReadPyr ReadPDB Transform Triangulate2D Triangulate3D Annotation Ball BallStick BoundBox BoundBoxPyr Contour CropLat2D CropLat3D DrawText IsosurfaceLat lsosurfacePyr LatToGeom Legend MultiSlice PyrToGeom ReadGeom VectorGen VolumeToGeom WireFrame Render Table 2 2 Output Data Produced by Modules Note All modules that have input ports for parameters also have output ports for them Image Processing Modules The image processing modules listed in Table 2 3 manipulate lattices They accept only the lattice data type on their input ports and or produce it on their output ports Modules Absimg BlendAlphalmg CompassAnglelmg Complementlmg Expl
19. Explorer will open a dedicated window in which Skm interactions can take place see Figure 6 1 The Skm Editor Window can be opened and closed by toggling the Skm 78 Window option from the Map Editor s Layout menu Figure 6 1 The Skm Editor Window This main window is divided into four key areas described in the following subsections 6 5 1 The Skm Output Viewer All output from Skm is directed here including the commands you type and the Skm cursor One of the main advantages of using IRIS Explorer in this mode is that Skm output is separated from general IRIS Explorer standard output for instance from modules This makes it easier to keep track of what you have typed in Skm 6 5 2 The Skm Command History Window This window stores a list of commands previously entered in the Skm Command Input window You can use the arrow keys to scroll up and down the list you can also use the arrow keys with the same effect in the Skm Command Input window When using the Command History Window the currently selected item in the history list will be replicated in the Skm Command Input window To re run this command you can either double click on the return enter key here or alternatively a single return enter in the Skm Command Input window will execute the command 6 5 3 The Skm Cursor This tells you what state Skm is currently in the possibilities are Skm gt This means Skm is ready to accept input Type away Skm lt integer
20. Property Sheet contains 100 information about the array including its name bounds and any annotations It also contains a ruler for setting the format In this case you use the ruler in the Property Sheet to strip off the leading ASCII strings which are xcoord ycoord zcoord temp and pres Figure 7 40 Reading a Formatted ASCII File Figure 7 41shows the ruler for the 2D Array glyph in the FormattedFile template The arrangement of text in each line of the ASCII file is reflected in the ruler You set up each text field by dragging the Scalar icon from below the ruler and dropping it into the active area where it appears as a small box with handles Spaces between the boxes represent white space matching the white space in the file Once you have positioned the icon in the ruler you can Resize it by dragging on the handles at each end Move it around by clicking on the box and dragging it to the desired location Figure 7 41 Ruler for Reading an ASCII File Example 7 7Writing the Formatted File The DataScribe offers more options for creating an ASCII format for an output file These include setting the textual annotation the xcoord ycoord zcoord text in the previous example see Figure 7 6 Setting special delimiters such as tabs The next example demonstrates their use This example illustrates how to write the file similar to the one that the DataScribe module in the previous example is designed to read
21. Rename the lattice glyph from Lat to OutLat 3 Open the glyph to see the internal structure of this lattice data type You need to specify only one thing the number of data variables per node nDataVar1 So type 1 into the text slot to the right of nDataVar1 Wiring Input and Output Templates You associate items in the input template ArrayFile with their counterparts in the output template Lattice by wiring them together just as in the Map Editor You can use the ports on the templates themselves or on the overview templates The wires appear only on the overview templates see Figure 7 11 Figure 7 12 Overview Output Port To make the connections 1 Click the right mouse button on the output pad of the ArrayFile template or overview The port menu pops up see Figure 7 12 2 To set the size of the lattice select res from the port menu then click on the input pad of Lattice File and select dims1 A blue wire appears indicating that a connection has been made 3 To specify the data connect the Array2 output of the ArrayFile port to the data1 input of the Lattice File port in the same way 4 To save the script select Save As from the File menu and type a filename such as dsExample into the file browser The DataScribe saves the module in the default module directory with a default control panel 85 You have now built a complete DataScribe module which you can use in the Map Editor When you type the name of yo
22. The EofSimple script reads in an ASCII data file an example of which is in usr explorer data scribe EofSimple data This contains a 3 by N 2D array where N is unspecified explicitly in the file In the case of the example file provided N 10 The other two files can read the file usr explorer data scribe Eof data which contains a 1 19 Angstrom resolution density map of crystalline intestinal fatty acid binding protein Footnote Crystallographic data by James C Sacchettini Giovanna Scapin Peter Reiner Albert Einstein College of Medicine Here the file contains an 18 by 29 by N 3D array or N slices each of size 18 by 29 where N is to be determined by the reader Again in the specific case of the example file provided it turns out that N 27 You can run the EofSimple and EofSelectData modules in the Map Editor and wire them to PrintLat which will print out the results The EofSelectData module uses a parameter SelectData to extract a slice from the 3D dataset see Defining Parameters and Constants for more information on this To illustrate the action of EofAllData wire this map EofAllData to IsosurfaceLat to Render Set the Threshold dial on sosurfaceLat to 1 0 and look at the results 7 6 2 Reading in Lattices To read in an IRIS Explorer lattice that has been saved as an ASCII or binary file open an ASCII or binary template file and place an IRIS Explorer lattice glyph in it However you cannot add any other glyp
23. To display the ruler for an array select the array in the ASCII template and select Properties Properties on the Edit menu to display the Glyph Property Sheet The ruler for ASCII input arrays contains a scalar glyph icon You use this icon to delineate which fields of a line in an ASCII file contain data When the module fires it looks for a numerical value for this scalar in the given field of the line The data type of the number is given by the scalar type of the array For example if the array in the input template is double the values in the field are assumed to be double precision The ruler for output arrays has glyphs for scalars ASCII strings and tabs see Figure 7 39 Rulers for input arrays are simpler than those for output arrays Figure 7 39 The Output Template Ruler To place an icon in the ruler drag and drop it in position You can drag on the Scalar and String icon handles to extend them horizontally in the ruler The Tab icon takes up only one space The ruler can accept up to 132 characters but there are two restrictions on the way the space can be used Ifyou use the Scalar glyph to position floats or doubles in the ruler for output templates you must provide a minimum of nine spaces for each float or double value The DataScribe needs one space for the sign at least three for the number one for E and four for the magnitude sign plus three For example it formats 1 1 as 1 1E 100 For every extra dig
24. a widget you can Type values into the width and height slots in the Editor window This is useful if you have an exact dimension or 57 location for the widget in mind A typed in entry takes effect in the control panel when you press lt Enter gt To change the size of the widget interactively drag on any of the handlebox squares For really precise adjustments use the Grid menu to activate the grid You can size and position widgets exactly by snapping them to a grid The Grid menu contains a list of pixel resolutions that govern the location and size of widgets You can select any one of these options The default snaps to a grid size of 5 pixels When the snap to grid option is in effect all subsequent widget moves and resizes occur only in multiples of the grid size If you resize a widget in this mode it becomes a factor of the grid s width or height depending on the direction in which you resize it 4 2 3 Setting Widget Properties The Properties pane contains information specific to the widget including the scalar type for dials and sliders and label information for option menus and radio buttons A plain button has the port name as its label The primitive type is important for the proper operation of the module and should not be changed from its default value which is what the underlying module is expecting However you can change it under special circumstances To change the widget primitive type select
25. area is a blank rectangle on the control panel in which an image or visual object can be displayed see Figure 2 26 For example the modules DisplayIng and Render have drawing areas on their control panels Figure 2 26 A Drawing Area Widget You can control the size appearance and orientation of the subject in the drawing area by using the widgets on the control panel These vary from module to module depending on the module s function The window may take up varying amounts of space on the control panel When you enlarge the control panel the drawing area may be enlarged proportionally Click on the Maximize button of the full scale control panel to open up the control panel to full screen size Example 2 4 Experimenting with Widgets This example illustrates how you can affect an object in Render by using widgets to change parameter values Launch the map named widgets see Figure 2 27 by dragging and dropping it in the Map Editor It contains five modules ReadLat reads in a lattice data file Contour generates a contour surface of the volume IsosurfaceLat generates an isosurface of the volume WireFrame generates a box that defines the boundaries of the volume Render visualizes the objects in its window Note On workstations without two sided lighting the isosurface in Render may be dark Change the Flip Normal option on the IsosurfaceLat control panel from No to Yes to display the geometry properly 1 Open the full scal
26. as many modules as you require into the input port of Displaylmg Figure 3 15 An Image in the DisplayImg Module As each module upstream from Displaylmg fires an image appears in the DisplayImg window The image is placed at the bottom left hand corner of the window and each subsequent image is stacked on top of it To see the images underneath you can change the stacking position of the images with the lt PgUp gt and lt PgDn gt keys on the numerical keypad not the lt Page Up gt and lt Page Down gt keys to the left of the numbers Place the cursor over the image of interest To move the top image to another area of the window click on it with the left mouse button and drag it to a new position You can move all images around in the window by using this method To return an image to its original position place the cursor on the image and press the lt Home gt key on the numerical keypad If the window contains several images and the cursor is not on any one they all return to the lower left corner To increase or decrease the size of an image by using the zoom widget Click on the image you want to zoom The slider shows the current zoom factor for that image As you adjust the slider the zoom factor changes with the size of the image You can photograph the image in the window and send it on to another module to be processed by clicking on the Snap button You can arrange several images in the window and Snap will pro
27. as you wish You can also use the Maximize and Minimize buttons to open the maxi control panel to full screen size or to iconify it The maxi control panel shows the names ranges and current values for widgets It also has a menu bar with a Help menu but does not show the ports To close a maxi control panel click on the left button of the title bar and select Close from the Window menu or double click quickly on the left button of the title bar The full scale panel disappears but the Diminutif control panel remains in the network If you are working with a group of modules use the Select All option from the Map Editor Edit menu and then choose Make Micro or Make Mini from the Layout menu to swap between these forms You have to open each full scale panel individually Note If the maxi control panel disappears under other windows on the screen you can pop it up again by clicking on the Maximize button on the Diminutif or micro control panel Using the Pop up Menu The module pop up menu see Figure 2 9 appears when you click on the title of the module control panel with the right mouse button You can choose any one of these options Fire Now The module fires and sends processed data to the next module downstream Duplicate Makes a copy of the module which you can wire into the map Disable Temporarily deactivates the module A disabled module will not fire until you enable it again However you can still set its widge
28. browsers are specifically for locating files whereas you can use text type in widgets for any parameter type The scrolled list lets you make a selection from a list of items Depending on how the list is defined the user may be able to select only one or several objects at a time Widget similarities are shown in Figure 4 1 Widget Similar t Dials Sliders Text type in slots Radio buttons Option menus 56 Text type in slots File browsers Table 4 1 Similar Widgets You can change the type of widget associated with any parameter by clicking on the parameter name and selecting a new widget type Hiding Widgets The Initially Hidden button see Figure 4 2 lets you hide widgets under certain circumstances These are When you have allocated a parameter associated with a file browser or text type in slot to a menu in an application This process is explained in detail in Creating Menu Items When you are building a module in the Module Builder and you want a widget to be visible or hidden according to the context the module is in For example you may have placed a channel selector on the module control panel If the module is receiving data on one channel only you may wish to hide the channel selector If there is more data you may want the channel selector displayed For more information see cx nWdgtHide in the IRIS Explorer Module Reference Pages or the on line man pages Widget Decorations Use the Decorations menu to
29. can create a group control panel in two ways by default and by conscious design 5 4 1 The Default Control Panel Use the Group Editor to create a default layout To do this click on the OK button at the bottom of the Group Editor window after you have selected the ports and parameters you want This dismisses the Group Editor applies the changes and updates the Map Editor In the process it creates a default control panel for the group This is useful if the group does not have any parameters for which widgets are required or if you can use all the default settings and layouts for selected parameters 5 4 2 The Designer Control Panel Use the Control Panel Editor accessible from the Edit menu of the Group Editor to lay out the control panel of the new group and customize it see Chapter 4 Editing Control Panels and Functions Figure 5 6 shows the control panel for the new group in the Map Editor along with its maximized form It is easily recognizable as a group module because it is a different color If you select the input port access pad of the new group you see only those ports you selected in the Group Editor with the names you chose for them Figure 5 6 The Group Control Panel Example 5 2 Using a Drawing Area Figure 5 7 shows a group control panel with a drawing area It uses the collection of modules and maps from the previous examples but adds some of the DisplayImg module s widgets including its drawing a
30. command acts on all the objects in the scene not just on a selected object Figure 3 21 Wireframe Object in Render If you are viewing a complex scene with several objects it may take a long time to render each frame while moving it Wireframe rendering is much faster than rendering opaque objects so you may want the objects to be rendered in wireframe while they are moving and opaque when still 48 To draw the objects in wireframe as the camera moves use the move wireframe option When you release the mouse button the objects are again drawn in their original mode 3 7 8 Editing Object Properties Objects displayed in Render have a variety of attributes They include positional properties such as translation rotation and scale and surface properties such as color specularity and transparency You can change or edit all these attributes using the Render editors in User Pick mode You edit object attributes by picking the object and then selecting an editor from the Editors menu Each editor provides access to various attributes of the object see Table 3 3 Editors Material Editor Sets the material properties of ambient diffuse and specular color shininess and transparency Color Editor Brings up a graphical color editor that lets you set the diffuse color on an object Transform Sliders Sets the exact placement scale and orientation of the object in the window Table 3 3 Object Editors Using the Material Edito
31. conceptually treated as broken by IRIS Explorer when it is computing which modules lie upstream of one another Figure 3 31 Looping Control Arc The special control arc wiring helps to clarify otherwise ambiguous loops such as the one in Figure 3 32 which shows a symmetrical map with separate While loop controllers for each nested loop Either While module can control loop 3 You will be able to deduce which module controls loop 3 by reading the controller arcs You can change which 53 module controls loop 3 by selecting arcs and controller buttons carefully Figure 3 32 Ambiguous Looping Scheme Saving Loops If you save a map or part of a map that contains a loop IRIS Explorer saves the identity of the active controller and will restore the map with this configuration In general you would group most loops that perform a complex iteration However controller capability cannot be promoted from the controller module in the loop to the group module If you wire a group module into a loop the loop must include its own separate controller In this case the grouped loop constitutes a nested loop in the map 3 8 5 Halting a Loop Iteration An iterating loop may be terminated by the controller module or it may be interrupted by the Map Editor This is called breaking the loop which is different from disconnecting the loop where inter module connections are removed In the Map Editor you can also use the Break Loop option
32. data 7 6 Reading in Data You can read data files in ASCH binary and IRIS Explorer formats into a DataScribe template which is created using the New Template Dialog box see Figure 7 3 If you select the binary file option the DataScribe can check to see whether the file is a Fortran generated file with record markers It then converts the data accordingly 86 7 6 1 Checking EOF The DataScribe can read to the end of an ASCII or binary data file EOF and calculate its dimensions internally without your having to stipulate the file length provided that you have no more than one undefined dimension variable per template The dimension variable can appear only in array glyphs or sets not in lattices all dimensions must be defined in an IRIS Explorer lattice The undefined dimension variable must be ina top level array glyph For example you cannot have an undefined dimension variable in an array within a lattice or in a nested array inthe final item listed in the template That is an array glyph that contains an undefined dimension variable cannot be followed in the template by another glyph the slowest varying variable in the array It will be assigned a value that you can use in your output Example 7 1Modules that check EOF Three examples of DataScribe modules which feature EOF checking are in usr explorer scribe EofSimple usr explorer scribe EofSelectData and usr explorer scribe EofAllData
33. direction color and intensity of each light in the scene by using the Lights menu to toggle lights on and off and to edit their attributes You can also edit ambient light levels Note If you cannot see the Lights menu on the Render menu bar just enlarge the Render window to the right Changes to the lights affect all the objects in the scene unlike changes to the transform and material properties which apply only to the selected object Editing a Light To edit the properties of a light for example the headlight select Headlight from the Lights menu and click on Edit The Edit window appears see Figure 3 25 displaying the light you have selected 50 Figure 3 25 Light Editor You can change the intensity of the light emanating from the source by moving the widget on the Inten slider to increase or decrease the light intensity The change is reflected in the image of the light You can also adjust the angle at which the light shines on the object by clicking on the directional arrow and changing its position in the window The Edit menu provides access to the Color Picker window for changing the color of the light The Color Picker works in the same way as the Color Editor 3 7 11 Manipulating Objects The Manips menu options let you rotate and translate objects in a scene by attaching one of several manipulators to them You can use only one type of manipulator at a time but you can attach it to each of several objects at
34. gt gt This means you have already typed something into Skm put have not finished entering the Skm command A Skm command is complete when the number of left parenthesis match the number of right parenthesis The integer in the bracket represents the number of unclosed right parenthesis Skm This means Skm is busy Further input will not be accepted until the interpreter is ready 6 5 4 The Skm Command Input This is where you type Skm commands Like other text input areas you can cut and paste text out of and into the Skm Command Input Press return or enter to pass the command input to the interpreter Each command line will be stored in the Skm Command History window see above A single Skm command can be split over more than one command line 79 Chapter 7 Using the DataScribe This chapter explains the DataScribe environment and describes how you can use it to create data conversion modules You can use these modules in the Map Editor to read external array data into the IRIS Explorer and also to write data out to external files In the DataScribe you create scripts and control panels for the conversion modules The chapter covers the components of the DataScribe introducing foreign data into IRIS Explorer using data elements in a template working with binary files working with arrays and lattice structures creating conversion scripts from templates creating a module control panel for the DataScribe module tr
35. gt If you then use a connect command that explicitly refers to ReadImg you will be referencing the wrong module The solution is to avoid referring to modules by the name used in the start command Instead assign the result of the start command to a variable and use the variable for subsequent references to the module For example define modl start ReadImg connect modl Output SharpenImg Img In 6 3 2 Testing Variable Types Skm provides the commands module and connection to test the type of a variable They return the value for false or t for true For example skm gt module m1 t means that the variable m1 contains information about a module started some time in the past It does not however necessarily mean that the module still exists Similarly when connection returns a value of t rue it indicates that a particular connection once existed and information about that connection persists but the connection itself may possibly have been broken 77 Creating a Procedure You can create a procedure in Skm with the define and procedure commands This example demonstrates how to define a procedure that takes a single argument declared formally asa and adds 1 to it The value returned by the procedure if any is the last value of the procedure procedure a a 1 This procedure does not have a name yet procedures can be anonymous in Skm To give the procedure the name plus 1 type d
36. has three data variables the output lattice will be 3D Each side of the output lattice is divided evenly into the number of buckets defined for the input lattice The data buckets are formed by dividing the 3D lattice into smaller cubes each of which contains the data points in that section of the total volume Example 3 2 Generating Histograms This example illustrates how you can generate a histogram for each data channel of GenerateColormap using Histogram 1 Launch a GenerateColormap module and a Histogram module from the Module Librarian 2 Connect the GenerateColormap module s Colormap Lattice output port to Histogram s data input port When GenerateColormap passes data to Histogram you can create a histogram for the data coming in from a single channel or for the data coming in from all four of GenerateColormap s channels 3 Use the slider to change the selected channel and see what happens 3 6 Displaying Images At times you may find it useful to display an image as opposed to a geometric object on the screen perhaps to see what the original image data looks like before it is processed through a map or so that you can compare two images or create a composite image from two separate images 45 The DisplayImg module see Figure 3 15 accepts image data in the form of a 2D lattice either black and white or in color You can display several images in the DisplayImg window at any given time Simply wire
37. in usr explorer scribe You can view the script in DataScribe using the command dscribe usr explorer scribe dsExamplel 7 5 Designing Templates for Your Data A template describes a file structure in terms of generalized data types In the DataScribe you can use the same template to define different components of a data type at different times which means that You can use the same template for all files of the same structure not just the one for which it was written Your data transform may contain several input templates that are connected to a single output template For example when you convert a PLOT3D dataset which consists of two files into an IRIS Explorer lattice you set up a separate input template for each file but only one lattice output template Similarly you may have a single input template but several output templates For example a file may have five components each of which you want to visualize as a lattice You can define a separate output template for each of the components and select the one you want when you fire the map You need not convert or even specify all the data in a particular dataset You can select the parts that you want to visualize using the Component Dialog window see Component Menu Button and convert only those For example if you have a vast amount of data about a weather front you can extract the pressure and velocity data but ignore the temperature humidity and turbulence
38. in usable condition or they may need processing to get them into a form that the machines can accept So the materials controller is important The factory also needs machines a different one for each process that takes place on the floor Some machines may be standard models but for certain tasks the factory needs custom built machines The machine shop then is also very important The way in which IRIS Explorer operates is analogous to the workings of this factory Think of IRIS Explorer itself as the factory The Map Editor corresponds to the factory floor and the modules to the machines The raw materials are the data fed in at one end and passing through the system into the visualization unit the inspection area Here the finished product which is the visual object or image is inspected and if necessary tweaked A little more color here a slightly smoother isosurface there and the object is ready for its destiny to be interpreted Alongside the Map Editor is the Module Librarian where the modules are stored These correspond to functioning machines a variety of which are brought out of storage and reconnected each time a new design is implemented on the factory floor So specific modules are launched in the Map Editor and wired together into a map Raw materials are critical to the manufacturing process The IRIS Explorer factory uses data as the manufacturing unit It makes some of its own raw materials in the form of genera
39. input ascii template and an output IRIS Explorer template Figure 7 3 New Template Dialog Box If you select an input filetype of Binary you can specify the record structure of the file The default Maybe checks for a Fortran record structured file and converts the data accordingly If you know for sure whether the file is Fortran record structured or not you can select True or False 3 Click on the OK A template opens in the DataScribe and its wiring overview appears in the Overview pane see Figure 7 4 You can open as many input and output templates as you need The input template appears on the left of the DataScribe window and the output template on the right You can distinguish them by the arrow icon next to the template name The DataScribe View menu can be used to hide and redisplay the various panes in the main window Thus for example you can toggle the appearance of the Outputs pane if required If one pane is switched off the dividing line down the center of the DataScribe disappears and the displayed template appears on the left To select a template for editing click on the arrow icon A selected template is outlined in black see Figure 7 4 Figure 7 4 Input and Overview Templates To change the data type for a template once it has been defined or to make notes about a template select the template by clicking on its arrow glyph Then select Properties from the Edit menu and use the Glyph Property Sheet see
40. input connections only Output breaks output connections only you can drag a module to the Disconnect icon This operation breaks both input and output connections As for all the drop icons if the module has been selected the operation is applied to all selected modules When you use Disconnect IRIS Explorer will remember a module s connections so that they can be re wired later if desired using Reconnect If another disconnect operation is applied to it only the connections most recently broken will be remembered The Reconnect operation using either the Map Editor Edit menu or the Reconnect drop icon can be applied to a module after a Disconnect This operation will attempt to restore its connections to the state prior to the last Disconnect If an individual connection to another module cannot be re instated for example the other module has been destroyed then that connection will be skipped If a connection has already been re instated for example the user has already manually wired it up then again the connection will be skipped The operation will also work on a module that has been destroyed and re launched 2 5 5 Wire Routing You can change the direction or slant of the wires that connect the modules in a map using Wires on the Map Editor Layout menu Each option to Wires changes the alignment of the wires between modules as their titles indicate To change the slant of the connecting wires
41. into the last bucket ifAdd is specified The range of data counts is indicated by the height of each bucket 3 5 3 Selecting Channels The option menus let you choose whether you want to generate a histogram for only one data channel of the input lattice or for all channels Each channel shows the values for one variable in the input lattice To select a data channel move the Channel slider this slider is displayed only if more than one channel may be selected from the input lattice You can also type a number into the Current Value slot at the top of the slider To choose between displaying one channel or all channels click the relevant radio button If you select One Channel a single histogram showing the data distribution in the selected channel is displayed If you select All Channels you see as many separate but overlapping histograms as you have channels The active histogram is white It shows the currently selected channel which is the channel corresponding to the number on the slider You can change the active histogram by using the slider to select another channel while in the One Channel mode When you select One Channel or All Channels Histogram produces a 1D output lattice When you select Multi Dimensional you do not get a display and the output lattice has a different format The number of data variables in the input lattice defines the number of dimensions of the output lattice For example if the input lattice
42. is simply a map run in a special mode For details on creating a group refer to Module Groups For details on creating group control panels refer to Chapter 4 Editing Control Panels and Functions In most applications you will want a drawing area in order to visualize the results of the process that the application is performing on the incoming data Setting Parameters in an Application 70 When you are building an application special attention should be given to the values of parameters in the application map When a map is run as an application the parameters in the map will have whatever values they were set to when the map was saved This matters particularly for parameter widgets associated with input and output filenames For example suppose you are building an image processing application from a map that contains ReadImg While testing the map you typed the filename fish rgb into ReadImg and then saved the map When you run the map as an application ReadImg will be given the specific input filename fish rgb and therefore will attempt to read in fish rgb each time it starts up In an image processing application for general use this may not be the best behavior However for some parameters setting the values in the map to default initial values may be the correct thing to do When you save a map that will be used as an application be careful to set parameters to the start up values that the application user ex
43. its scrolling columns and Librarian shelf Each Module Librarian has the name of its host system on the title bar Use the Module Librarian and its menus to launch and save modules or maps in the Map Editor File menu reorganize modules into categories Categories menu store modules on the Librarian shelf Display menu add remote hosts if you are using a map distributed over several systems Hosts menu Figure 2 2 The Module Librarian 2 3 1 Launching a Module The act of bringing a module or map from the Module Librarian into the Map Editor and activating it is called launching To launch a module or map you can Place the cursor on a module or map in a Module Librarian column and drag it to the Map Editor while holding the left mouse button down Then drop it in place the drag and drop technique Place the cursor on the right side of the module or map in the Module Librarian and hold down the right mouse button The Launch menu appears see Figure 2 3 Select Launch Figure 2 3 Module Launch Menu Drag and drop a module from the shelf of the Module Librarian see Storing Modules on the Shelf 15 Use the Open option on the File menu A file browser appears from which you can select a module or map see File Browsers Maps in the Module Librarian are colored blue modules are beige Finding a Module in the Librarian Use the scroll bars in the Module Librarian columns to scroll up or down thro
44. j 3 outer loop i 2 inner loop j 1 inner loop j 2 inner loop j 3 outer loop i 3 inner loop j 1 inner loop j 2 inner loop j 3 outer loop i 4 inner loop j 1 inner loop j 2 inner loop j 3 B 3 4 Lexical Scoping of Variables Variables created with define are globally scoped regardless of the context in which define occurs Thus the following uses of define both introduce variables into the global environment define varl 1 J begin define var2 2 2 print varl var2 172 The begin block in the second example does not behave as does the creation of a local variable in C where the variable goes out of scope at the end of the block int var2 2 Arguments passed to a procedure in Skm are scoped locally to that procedure Thus in the following example define introduces neither a nor b into the global environment define test procedure ab define a 1 122 define b 2 It seems at first that the example above contradicts the earlier statement that define always introduces variables into the global environment However define here is not being used to create a variable the variables a and b are created at the entry to the procedure Rather define is being used to change the value of these variables You can also use the assigned operator set here The let Construct Skm provides a special construct called Jet which sets
45. see Figure 5 2 Figure 5 3 The Open Group 5 3 Editing a Group A group usually consists of several modules Each module can have several input and output ports and numerous widgets In the context of a group module not all these ports and widgets make sense or are usable The Group Editor see Figure 5 4 allows you to select the ports and widgets you want in the group create a group control panel using the Control Panel Editor described in Chapter 4 Figure 5 4 The Group Editor 5 3 1 The Group Control Panel The group control panel has ports widgets and a module pop up menu just like the module control panel It is however a different color The widgets on the control panel allow you to control the value of the module parameters directly You can reorder the module sequence in the Group Editor by grabbing the module title bar and dragging it to the desired location This changes the sequence in which ports are shown on the module control panel s input and output port lists If you are creating a group or application control panel you get a default widget setting The Control Panel Editor allocates to each parameter in the new control panel the same widget type and properties as the parameter had in its module control panel For example the SobelEdgeImg module has a slider for its Bias parameter If you create a group containing SobelEdgeImg and promote the Bias parameter to the group control panel the slider appe
46. select frames and dividers for your control panel Once you have selected a decoration it is listed in the Parameters pane see Figure 4 4 Figure 4 4 The Decorations Menu Editing a Scrolled List Four selection modes are available for the scrolled list widget see Figure 4 5 You can choose which mode suits the kind of parameter you have The options are Single Select Only one item at a time can be selected from the list but the module user need not select any Browse Select The user must select one item from the list Multiple Select Several adjacent items can be selected from the list at one time Extended Select Several items not necessarily adjacent can be selected from the list at one time Figure 4 5 Scrolled List Properties 4 2 2 Moving and Resizing Widgets Click on the widget to activate it in both the Preview window and the Editor window An active widget is enclosed by a handlebox of eight black squares see Figure 4 6 Figure 4 6 Widget Handlebox To change the location of the widget in the Preview window click on the widget and drag it to the desired location A solid box appears around the widget as you move it The Widget Attributes pane in the Editor contains the absolute location of the active widget The origin of the control panel is in the upper left corner As you move the widget the X and Y starting locations change You can type values directly into these text slots if you wish To resize
47. shell prompt type explorer map applicationname map When you run IRIS Explorer with this command the application is displayed along with the IRIS Explorer window The IRIS Explorer window gives you access to the Map Editor and the Module Librarian if you require it 72 Chapter 6 Scripting This chapter describes how to use the scripting language Skm to take full advantage of the command interface in IRIS Explorer It covers these topics running IRIS Explorer with a script examples of its use the structure and syntax of Skm commands the Skm Editor window 6 1 Overview IRIS Explorer provides two user interface mechanisms the graphical user interface GUI which is described in the previous chapters and a command interface The command interface allows you to run IRIS Explorer using text based commands You can issue these commands directly from the keyboard or you can write a script that IRIS Explorer runs using the IRIS Explorer scripting language called Skm pronounced scheme The scripting language is useful for three reasons You can set up a series of commands for testing new modules maps or applications You can run IRIS Explorer automatically by piping information into it which is handy for running batch jobs and test suites You can run IRIS Explorer remotely from another system such as a personal computer and you can write the results to a file To create a script you use the IRIS Explor
48. slope 3 2 2 Using Custom Colormaps GenerateColormapcreates a rainbow like colormap when you first launch it You can use a different colormap as your starting point if you wish To read in a custom colormap first launch a ReadLatmodule and connect it to the input port of GenerateColormap Then use the file browser in ReadLatto read in the colormap file The GenerateColormap module will approximate the input colormap as closely as it can You can use control points to edit the color curves that it creates IRIS Explorer has another module WaveFormColormap which uses ramp waves of variable frequency rather than direct manipulation to establish a relationship between data values and colors For more information refer to WaveFormColormap in the IRIS Explorer Reference Pages Creating a Custom Colormap A colormap is a lattice with a specific format it is a 1D 4 vector float uniform lattice with 2 to 256 components You can create such a lattice by saving a map produced by GenerateColormap or WaveFormColormap or by any other module or program that can produce a lattice in this format Saving a Colormap You can save a colormap to disk by connecting a WriteLat module to GenerateColormap s output port Then use the file browser to give the saved colormap a filename Example 3 1 Manipulating a Colormap This example illustrates how to generate a colormap for a lattice and alter the relationship between the data values and the colo
49. tell you whether you have entered a parameter function with incorrect syntax 4 5 2 Defining a Parameter Expression The P Func Editor provides a simple set of expressions for creating compound relationships among two or more input parameters in a module You can use all or any subset of the variables listed in the Variables box to construct your function For example if you have two connections with variables A and B you can type A 2 B orA B or A B 2 the average of two inputs Table 4 2 lists the expressions accepted by IRIS Explorer Type Expressions Arithmetic mod 60 Functions min A B max A B exp A log A log10 A pow A B abs A ceil A floor A rint A cos A sin A tan A acos A asin A atan A atan2 A B cosh A sinh A tanh A length returns the string length in characters Typecast long double string Relational I gt gt lt lt Boolean amp amp or AND or OR or NOT Ternary A B C if A then B else C Multiple if then clauses followed by a terminal else Table 4 2 Parameter Expressions The expressions are identical to the C language functions For more information refer to the C language manual pages for each function Typecasting Parameters IRIS Explorer accepts incoming parameters and turns them into floats by default If you want the parameter to have a different type you can use one of the typecast expressions see Tab
50. the begin operator It is analogous to curly braces in C and to begin end in Pascal like languages if eq expr 1l expr 2 begin do this do that do something else B 2 3 String Operators Skm provides the set of string operators listed below string Returns true if its argument is a string string length Returns length of string argument string ref Returns a character at indicated position string set Sets a character at indicated position string Compares two strings Returns true if equal substring Returns substring of given string between start and stop index string string is a predicate that tests an argument to see if it is a string It takes a single argument string returns t or depending on the type of its argument 118 string some string t string 23 string length string lengthreturns the length of a string argument string length some string 11 string ref string refreturns a specific character from a given string The first argument is the string the second is the index of the character to be extracted Indexing is origin zero that is the index of the first character in the string is zero The returned character is still a string and may be used in all string commands string ref hello 1 Won string set string set sets a character in a string The first argument is the target string the second argument is the index into th
51. the file path of a module s resource file mres file Print the name of the host a module is running on Print a list of a module s parameter value s Paste the contents of the editing buffer Cause the script execution to pause Switch off performance reporting for selected modules Switch on performance reporting for selected modules Print a list of a module s P Func value s Save selected modules to a named map file Select named modules List the selected modules Designate a maximized module control panel as the main window for an application If this window is quit while IRIS Explorer is in application mode the application itself quits Set a parameter value in a module Set min and max values for a range parameter Set a module s P Func value Expose a module s hidden widget see hide widget Start a map Start a module Exit IRIS Explorer Remove module s maximized control panel Unmicro ize the control panel of a module Unselect named modules List the modules not selected B 1 3 Command Syntax Table B 2 summarizes the command syntax Square brackets enclose optional arguments This information is available from within Skm by typing help You can also type help command prefix and you will get a list of all commands beginning with the given prefix Command all mods all groups connect modulename connection variable 114 break loop modulename portname modulen
52. the modules grouped according to function Table 2 1 through Table 2 3 in Chapter 2 list some of the the modules according to the kind of data they accept and deliver for example lattice or geometry data The IRIS Explorer Reference Pages list all modules alphabetically and sets out the specifications of each one Not all the modules listed are available on all systems The ZRIS Explorer Reference Pages indicates the modules available for general distribution A selection of modules is listed by function in Table 3 1 Footnote Note that the multimedia modules may not be available on all platforms as they were originally designed for Silicon Graphics systems Module Function Module Names Read data in or create it from ComposePyr GenerateColormap GenLat MopacView Read2Da scratch ReadAudio ReadAVS ReadAVSfld ReadAVSimage ReadAVSucd ReadAVSvol ReadGeom ReadHDF Readimages Readimg ReadLat ReadMovieBYU ReadNTF ReadPDB ReadPhoenics ReadPyr WaveFormColormap Process images AbsImg Addlmg Andimg BlendAlphalmg BlendlImg Blurlmg 37 CompassAnglelmg CompassDirlmg CompassImg Complementlmg Divimg Explmg ForwardFFTImg FourierConjgimg FourierCrossCorrlmg FourierDivimg FourierExpFlitImg FourierGaussFltImg FourierMagnitudelmg FourierMergelmg FourierMultlmg FourierPhaselmg FourierPwrlmg GaussBlurlmg GrayScalelmg HistEquallmg HistNormlmg HistScalelmg InverseFFTlmg LaplaceEdgelmg Logimg MaxFitlmg Maxlm
53. to extract data fragments from an array by using the Component Dialog window The sample script files are in usr explorer scribe called ReadXData mres through ReadXYZData mres The data files are located in usr explorer data scribe The example goes through the technique in detail for the first file You can open the other files and see how they build on the first one This is the first ASCII data file ReadXData data 80 0 8000 90 0 9000 100 0 1000 10 lt Dimension Variable 10 0 1000 0 lt Column 1 X Co ordinate values 20 0 2000 0 Column 2 Data values 30 0 3000 0 40 0 4000 0 50 0 5000 0 60 0 6000 0 70 0 7000 0 0 0 0 0 0 0 The following script called ReadXData mres extracts the X values from this and reads them into a 1D curvilinear lattice Open this file in the DataScribe and look at it see Figure 7 32 The input template is in ASCII format and has two glyphs one for the array dimensions and one for the data The res vector holds the dimension variable Its shape is 97 defined as 1 only one data variable and its value is Long It must be defined first because the 2D array for the dataset uses this value The dataSet 2D array glyph has its i value defined as 2 two columns in the data file and its j value defined as the first value of res the number of data entries which is the number of x values The output template is of IRIS Explorer type and contains a 1D curvilinear lattice called Da
54. types for parameter values Each must have a unique name You must use the Control Panel Editor to assign a widget to each parameter in a Parameters template so that they can be manipulated in the Map Editor 7 9 2 Making a Constants Template Occasionally you will want to have a collection of scalars whose values can be set and used by other templates You can achieve this by creating a Constants template Figure 7 28 shows the title bar of the Constants template It can be identified by the icon on the left a small circle containing a square Figure 7 28 Constants Template Title Bar To open a new Constants template select Constants from the Template menu A new Constants template appears in the DataScribe window 94 You can drop any number of scalars or sets of scalars into the Constants template You can use any of the scalar data types but no other data types from the DataScribe palette You can also enter values into the value slot of each data item These values can be in the form of symbolic expressions 7 10 Connecting Templates Once you have created input and output templates you need to associate the data items in the input templates with their counterparts in the output templates You do this by wiring the output ports of the input template to the input ports of the output template just as in the Map Editor There are two types of associations that you have to consider ordering variables within a script con
55. up a locally scoped environment The format of let is let varl init val var2 init val varN init val let body Any number of locally scoped variables can be created and initialized in the preamble of the let statement The variables thus created and initialized are visible only within the code present in let as seen in the following example let a 1 b 2 print inside let a a b b inside let as 1b 2 B 3 5 List Processing A list can be created using list last a be dy a b c d As indicated above when Skm prints out a list it surrounds the list with parentheses A Skm command that returns a list is all mods all mods SharpenImg ReadImg The first element of a list can be extracted using first A list with the first element removed is obtained through the use of the rest command Footnote firstis also known as car and rest is also known as cdr first a bc d rest a bc d a b c d The list a b c d is quoted so that it will not be evaluated by Skm before being passed to first and rest B 4 Module Interface to Scripting Modules in C or C may issue scripting commands through this API routine int cxScriptCommand char string This call sends a string containing the Skm code to the Map Editor for evaluation A valid example is 123 cxScriptCommand start ReadImg at 100 100 Embedded double quotes must be escaped
56. vector length to 2 select N and replace it by typing 2 in the text slot Now you have defined a file structure with two integers in it 5 To change the name of this vector select the text Array1 and type a new name for example res in its place The name res short for Resolution reminds us that this variable contains the dimensions of the 2D dataset 6 Drag a 2D Array glyph from the palette and drop it into the ArrayFile template see Figure 7 11 Open the glyph by clicking on the button Figure 7 11 A Simple DataScribe Script 7 Set the size of the array by clicking on the ending value for each dimension of the shape The size of the array is defined by the values stored in the res vector so you must Select N1 in the 2D Array shape and replace it with the first value of res res 1 Replace N2 with res 2 In the case of our dsExample1 data file res 1 equals 7 and res 2 equals 5 This completes the description of the sample file contents and you have finished constructing theArrayFile template The Output Template 1 Open a new template from the Data menu but this time make sure that the first radio button is set to Output instead of Input the second radio button is set to Explorer not ASCII You can leave the name of the template unchanged from the default which DataScribe selects for it 2 Select a 2D Unif two dimensional uniform lattice glyph from the palette and drop it into the output template
57. you can prevent any color change taking effect on the object until you are ready Use the two color squares to test new colors and store the previous one By clicking on the three arrowed pads beneath the squares you can switch back and forth between colors Figure 3 23 The Color Editor The new color is always on the left and the previous color on the right You can send the new color to the right square 49 or the old color to the left square The Color Pickers in the other editors work in the same way as the Color Editor although they affect the color of different items Using the Transform Sliders The Transform sliders see Figure 3 24 let you rotate translate and resize any object that is part of the scene in the Render window The changes affect only the selected object not all the objects in the scene The slider widgets are TRANSLATIONS changes the position of the object in the scene SCALES changes the relative size of the object in the direction of the three axes conveniently called x y and z The direction of the axes is defined by the SCALE ORIENTATION widget ROTATIONS changes the orientation of the object in the scene SCALE ORIENTATION changes the direction of the axes along which the object is scaled CENTER changes the center about which rotations take place When you click on a the title of a slider for example TRANSLATIONS the slider opens up and shows three text slots one each for the
58. All This brings an object that may be out of the viewing area into the center of the window 3 The module might not be reading in the data from disk Make sure that modules that need data from files such as ReadImg have been given access to those files 4 The module might be disabled Enable the module by bringing up the pop up menu from the control panel and selecting Enable You can also select all the modules by using the Edit menu in the Map Editor then choose Enable 5 The widgets might not be set to values which can produce data Check the settings turn the dial or move the slider if you have an active threshold parameter 2 11 3 No Change in Object with Change in Parameters If you have changed object parameters but the changes do not appear in the object try the following procedure 1 Enable the module by bringing up the pop up menu from the control panel and selecting Enable You can also select all the modules by using the Edit menu in the Map Editor and choose Enable from the Edit menu 2 Make sure all the required ports have data by connecting them to valid ports in other modules 3 Some modules such as GenerateColormap have Build Run toggle buttons If the module is in Build mode it will not fire and send data downstream Change the mode to Run 2 11 4 Viewing Lattice Data in the Render Module If the lattice is 1D or 2D such as an image 34 1 Connect the input port of aLatToGeom mod
59. IRIS Explorer User s Guide Release 3 Document Number NP2872 ISBN 1 85206 110 3 Copyright 1992 1993 Silicon Graphics Inc All Rights Reserved Copyright 1995 The Numerical Algorithms Group Ltd All Rights Reserved This document contains proprietary and confidential information of Silicon Graphics Inc and The Numerical Algorithms Group Ltd No part of this manual may be reproduced transcribed stored in a retrieval system translated into any language or computer language or transmitted in any form or by any means electronic mechanical photocopying recording or otherwise without the prior written permission of the copyright owner The copyright owners give no warranties and makes no representations about the contents of this manual and specifically disclaims any implied warranties or merchantability or fitness for any purpose The copyright owners reserve the right to revise this manual and to make changes from time to time in its contents without notifying any person of such revisions or changes Restricted Rights Legend Use duplication or disclosure of the technical data contained in this document by the Government of the United States of America is subject to restrictions as set forth in subdivision c 1 ii of the Rights in Technical Data and Computer Software clause at DFARS 52 227 7013 and or in similar or successor clauses in the FAR or in the DOD or NASA FAR Supplement Unpublished rights reserved under
60. NutraSweet Molecule The map takes configuration data for a NutraSweet molecule and creates a ball and stick representation of it and a dot surface that shows the region that is accessible by a probe atom The map contains seven modules FileList lets you select which of the available chemistry molecule data files you want to visualize ReadPDB reads in the molecular configuration data BallStick creates the ball and stick representation of the molecule AtomicSurf calculates a solvent accessible surface around the molecule It uses the USURF Footnote Written by Joseph J Moon and published under the auspices of the Quantum Chemistry Program Exchange QCPE Indiana University Program 566 program to define a solvent accessible surface around the molecule GenerateColormap produces a colormap which is used to color the atoms in the molecule and the dot surface LatToGeom converts the surface data in IRIS Explorer lattice format into geometry Render displays the ball and stick geometry of the molecule and the solvent accessible surface data as a dot surface 1 5 2 Experimenting with the Chemistry Map The molecular configuration data is read in by ReadPDB The input file is in the Brookhaven Protein DataBase PDB format a commonly used format for saving descriptions of proteins including atom positions and properties and bond locations BallStick see Figure 1 9 receives the data in pyramid form and gener
61. Object You can view an object in the Render window from a different position by manipulating it using the left or middle mouse button in Examiner viewing mode These actions change the camera position from which you are looking at the 47 object To roll the camera that is to rotate it on an axis perpendicular or normal to the screen hold the left mouse button down and drag the object either clockwise or counterclockwise The object spins in the direction in which you dragged it The object rotates faster according to the speed with which you push or drag it It continues to rotate once you release the mouse button To stop it click on the mouse button outside the object To move the camera view around the center point that is to move it in the plane of the screen hold the middle mouse button down and drag the object 3 7 5 Using the Pop up Menu The Render pop up menu see Figure 3 19 appears when you click on the background of the Render window If you zoom or truck in too far and lose sight of the object click on the window background with the right mouse button and select View All from the Functions submenu of the pop up menu Figure 3 19 Render Pop up Menu The View All option resets the camera position enabling you to see all the objects in the scene To center an object in the window choose View Selection from the Viewing menu this item is selectable only if more than one object is currently displayed in Rend
62. Pages 2 8 3 Looking at Module Data Types Certain modules can accept a pyramid or lattice data type and output a lattice or geometry data type after performing a data conversion These include PyrToLat LatToGeom and Contour Modules with several input ports may be able to accept two or more different data types one on each port For example Streakline has input ports for a lattice and a pick and an output port for geometry Render has input ports for geometry and parameter data and output ports for lattice geometry and pick data Mixed Data types Table 2 1 lists some of the IRIS Explorer modules according to the data type Lattice Pyramid Geometry or Pick they can accept on an input port Some modules that accept lattices are further defined by whether they can accept 1D 2D or 3D lattices or a combination For details refer to the input port specifications of each module in the IRIS Explorer Reference Pages Input Port Data Modules Lattice Ball BallStick BoundBox ChannelSelect ColorXform Contour CropLat2D CropLat3D DiffLat DisplaceLat GenerateColormap Gradient Graph Histogram InterpLat Interpolate IsosurfaceLat LatFunction LatToGeom LatToPyr Legend MagnitudeLat Mixer MultiSlice OrthoSlice PrintLat ProbeLat PyrToGeom SampleCrop ScaleLatNode Shell Slice SubSample Transform Triangulate2D Triangulate3D VectorGen VolumeToGeom WireFrame WriteLat Pyramid AtomicSurf BallStick BoundBoxPyr CullPyr
63. Simple Scripts This section gives examples of how to use the Skm scripting commands If you are entering commands interactively you type each command on a separate line after the Skm prompt skm gt If you are creating a script file simply type the commands each on a separate line The start command is used to start modules For example skm gt start ReadImg launches the ReadImg module in the Map Editor The name of the module is enclosed in double quotes The command skm gt start SharpenImg at 200 300 launches the SharpenImg module in the Map Editor at the specified location The coordinates specify the position of the top left hand corner in pixels Both the name of the module and the argument at are enclosed separately in double quotes Modules can be destroyed using the destroy command For example skm gt destroy ReadImg destroys the ReadImg module that was previously launched Maps are started by using the start map command For example skm gt start map cfd launches the cfd map The connect command specifies two ports to be connected The command lists the output module name the output port name the input module name and the input port name For example skm gt connect ReadImg Output SharpenImg Img In connects the Output port of ReadImg to the Img In port of SharpenImg Defining Command Variables You can use the define command to define a variable for use in other comm
64. Using the Glyph Property Sheet to make changes Using the Overview Pane Input and output templates are wired together in the same way that modules are wired together in the Map Editor The wiring overview in the Overview pane displays the actual wiring connections between input and output templates You can connect input and output template ports in the DataScribe window or use the ports on the overview templates in the Overview pane but you will see the wires only in the Overview pane see Figure 7 4 You can list all of a template s ports from its wiring overview by clicking on the port access pad with the right mouse button For more information on creating ports see Glyphs You can hide the Overview pane by toggling Overview on the View menu 7 4 The Data Type Palette The DataScribe Data Type palette see Figure 7 5 displays the data types available for data transforms in IRIS Explorer Data types are arranged in the palette in order of complexity and are identified by color coded icons called glyphs which are organized into scalars arrays lattices and sets The palette is displayed when the DataScribe starts up Selecting Palette on the View menu restores the window if it has been hidden or deleted To move a glyph from the palette to a template select it from the pallete using the cursor then press the left mouse button drag it onto the template and release the button You can also select the template then h
65. You can expand the mini control panel shown in Figure 1 1 of any module into the full scale control panel by clicking on the square Maximize button at the right top corner of the control panel When you do this the parameter widgets and their values are displayed for easier manipulation Figure 1 1 Module Control Panel 1 3 Image Processing This example illustrates how you can use IRIS Explorer modules to process an image The KoreaContour map takes an aerial image of a region of the Korean landscape renders it in 3D and overlays a contour map showing altitudes The resulting image is displayed on screen The map file is usr explorer maps KoreaContour map 1 3 1 Opening the Image Map To open the KoreaContour map displayed in Figure 1 2 type explorer map koreaContour map The seven modules are connected to one another by blue wires The two modules on the left read in the image files and the module on the far right displays the processed image In between these are four modules that manipulate the image data Figure 1 2 Processing an Image The seven modules in the map have the following functions Readimg lt 2 gt reads in the first image file 2D aerial image of a region of Korea ReadImg reads in the second image file altitude data for the same region DisplaceLatdisplaces each node of the aerial image in the vertical direction according to the local value of the altitude DisplaceLat lt 2 gt performs the same func
66. aScribe To exit from the DataScribe select Quit from the File menu The Data Type palette closes automatically along with the DataScribe 7 2 3 Scope of the DataScribe The DataScribe can only act on data arranged in ordered matrices or arrays including the IRIS Explorer lattice data type The modules that it creates can have parameter inputs see Making a Parameters Template whose values can be controlled from the module control panel However it does not handle the IRIS Explorer geometry pyramid or pick data types conditional expressions for selecting data or traversing data in files 7 3 Creating Scripts and Templates In each DataScribe session you create or modify a script A script consists of a number of templates along with rules that stipulate how data items are associated with templates A complete script has one or more input templates and one or more output templates with their wiring connections Each template describes the structure of a single file in terms of data types shown as glyphs The wiring connections show how each input data type will be converted into an output type When you add a control panel to a script you have a complete module You can save a completed script which consists of a scribe file and an mres file The scribe file contains the wiring specifications for the templates and the mres file contains widget specifications if any for the control panel To create a script you must firs
67. acking errors 7 1 Overview The DataScribe is a utility for converting users ASCII and binary data into and out of the IRIS Explorer lattice data type ASCII data must be in the form of scalars and or arrays A scalar is a single data item and an array is a structured matrix of points forming a lattice You can convert data into and out of IRIS Explorer lattice format by building a data conversion script in the DataScribe The script is a file consisting of input and output templates and their wiring The templates contain information in the form of glyphs about the data types that you want to convert Glyphs are icons that represent each data type and its components in visual form The wiring connections map an input data type to its output data type For example you may have arrays in an ASCII file that you want to bring into IRIS Explorer The glyphs in the input template represent the type of array you have such as 2D or 3D and those in the output template indicate how you want your array data to appear in IRIS Explorer For example you can select a small interesting section from a large and otherwise uninteresting array by connecting input and output glyphs so that only the data you want is converted into the IRIS Explorer lattice Once the script file has been set up you can create a control panel for it and save it as a module You then set up a map that includes your newly created module and type the name of the file that contains
68. ailable via man More information on this is provided in the on line ZRIS Explorer Reference Pages All of the on line documentation is available in hard copy form as the three volumes IRIS Explorer User s Guide IRIS Explorer Module Writer s Guide IRIS Explorer Reference Pages which contains all the information from the man pages for the modules and API routines Contact your IRIS Explorer supplier for more details Chapter 1 Getting Started This chapter introduces you to IRIS Explorer using five sample maps each from a different scientific field The examples cover image processing numerical mathematics molecular chemistry atmospheric physics computational fluid dynamics 1 1 Overview You can create maps for all occasions for example to generate a 3D image of vortices around hydro electric turbines or to visualize carbon dioxide concentration as a function of geographic location These activities involve a number of separate tasks such as reading the data into the map colormapping a gradient extracting a 2D slice of a 3D dataset and visualizing the result The modules in the map carry out tasks like these The five maps presented here use authentic data to illustrate the workings of IRIS Explorer Each map deals with a specific issue and the modules provide ways of altering or enhancing the data so as to make its significance clear and perhaps to elicit correlations that might otherwise have gone unnotice
69. ame portname connection list modulename copy modulename cut modulename destroy modulename disable modulename disconnect modulename dup modulename enable modulename exec hilite off modulename exec hilite on modulename fire modulename get param modulename get pfunc modulename help prefix help mod modulename hide widget modulename interrupt modulename log modulename loop ctlr variable loop ctlr capable variable loop ctlr off modulename loop ctlr on modulename main log off main log on maxi at modulename at X Y size W H maxi modulename micro modulename mini modulename module variable module to filename modulename module to host modulename param list modulename paste pause seconds perf report off modulename perf report on modulename pfunc list modulename save filename modulename select modulename selected mods set app main win modulename set param modulename portname value set param minmax modulename portname minval maxval set pfunc modulename portname value show widget modulename widgetname start map map name at X Y portname modulename portname portname portname widgetname Nn nnn nnn nnn nae eNO 115
70. aming a Port For example in the context of the group Bias needs some clarification so it can be renamed Sobel Bias You can rename ports and parameters at any stage of the grouping process by entering the new name in the Group Editor Click on Apply or OK to apply the changes and set up the new control panel 5 3 6 Grouping Optional Ports Some ports may not be required by an individual module but must be promoted once the module is part of a group because there are connections to other modules in the map outside the group at the time of creating the group Suppose you select ReadLat Contour and WireFrame to make a group The group has one outside connection a hookup from GenerateColormap to Contour The Colormap Lattice input port on Contour is not intrinsically a required port but in the context of the new group it becomes required because of its link to GenerateColormap Hence it is automatically promoted to a group level port This principle also holds true for output ports If a connection exists downstream of the group the port with that connection is automatically promoted and indicated as selected in the Group Editor 5 3 7 Grouping Modules in a Loop You cannot promote loop controller capability from the loop controller to a group module If you want to link a grouped loop into another loop you must include a separate loop controller module in the new loop 68 5 4 Creating a Group Control Panel You
71. an alternative from the Properties pane of the Control Panel Editor 4 2 4 Setting Widget Values and Limits To set the value of a widget you must first select it To select a widget for editing double click on it in the Preview window with the left mouse or click on it in the Parameters pane To select all the widgets in the control panel at once use Select All on the Edit menu of the Control Panel Editor To de select them click on the background of the control panel You can change the value of dial and slider widgets by typing a new value into the upper text slot or moving the widget pointer You can also set minimum and maximum values by typing them into the range text slots You must press lt Enter gt for settings to take effect You can also change the number of options in the Properties pane for radio buttons and option menus This might not have the desired effect however if you add labels beyond those expected in the module itself A good example of this is the Contour module It has three sets of radio buttons that control contouring in the I J or K directions Each radio button has two options On or Off If you add a third option such as Half On to one of these radio buttons the module will not process it Caution You can seriously confuse the Map Editor if you switch a module widget type to one that is incompatible with what the module expects To dismiss the Control Panel Editor click the OK button The Apply but
72. ands For example you can use this command skm gt define modl start ReadImg to start the module ReadImg and create a reference to the module in a variable called mod1 Then you can destroy ReadImg by giving the command skm gt destroy mod1 You can substitute the variable mod for ReadImg whenever you choose This is important when you launch more than one copy of the same module see Creating More Complex Scripts Similarly you can save information about a connect command in the variable c1 skm gt define cl connect ReadImg Output SharpenImg Img In 74 This particular connection can be referenced later as c1 For example you can break the connection using either of these commands skm gt disconnect ReadImg Output SharpenImg Img In or skm gt disconnect cl Variables containing module and connection information remain even after the IRIS Explorer objects to which they refer are gone so you can reconnect the modules just disconnected with the command skm gt connect cl Example 6 1 An Example Script Here is an example of a script that demonstrates the use of define in simplifing module connections These modules do not currently exist but you can use the script as a template and substitute your own module and port names in the appropriate places define ml start GenLat define m2 start testLattice define m3 start testLatticeFortran define m4 start testLatt
73. apes that simulate fuzzy blobs on screen You can control the splat configuration by changing the splat type and size on the module control panel Rendering splats can may take a long time You can set and adjust an error tolerance to get a balance between rendering time and splat quality To set the error tolerance use the dial on the control panel A low error value produces an accurate volume display but the display takes longer to generate ReadLat lt 3 gt reads the colormap settings for the volume rendering of the water buoyancy data into GenerateColormap The current setting for the colormap shows buoyant air containing little water in red and the saturated air in blue Once the data is in Render you can analyze it in detail Figure 1 14 displays the reflectivity from the storm Footnote R B Wilhelmson B F Jewett C Shaw L J Wicker M Arrott C B Bushell M Bajuk J Thingvold and J B Yost A Study of the Evolution of a Numerically Modeled Severe Storm International Journal of Supercomputer Applications Volume 4 No 2 Summer 1990 pp 20 36 The blue white surface encloses the area containing most of the large drops and hail Several light sources itiiminate the surface You can see the overhang observed by weather radar in many severe storms at mid level where the reflectivity surface comes out toward the viewer Figure 1 14 Storm Data in Render Above the storm there is a region of many colors volumetrica
74. ars on the group control panel by default You can change this default to whatever suits your needs at the group level 5 3 2 Promoting Ports Selecting a port for the group control panel is called promoting the port In deciding which ports and widgets to promote you need to determine how you want to reuse this group and how your users if any will be using the group To select a port click on the port button in the Group Editor Ports that are not promoted to the group level are not visible in the group control panel The ports still exist however and widget based parameter input ports retain the value they had when you first created the group You can adjust the values of hidden parameters by opening the group using Open on the Group menu 5 3 3 Required Input Ports Groups have two kinds of required input ports those that are required at the module level and hence at the group level also and those that are optional at the module level and have been promoted to the group Some module input ports must have data on them before the module will fire These ports are also required at the group level if there is no connection to them within the group otherwise the group will not fire In the Group Editor required ports are automatically promoted They appear in the Group Editor as selected and you cannot deselect them For example SharpenImg and SobelEdgelmg in Figure 5 4 both have required module input ports that also appea
75. as you go As with any exploration you could end up with a map that takes you into uncharted realms of discovery and shows you implications of your data that you would not have thought existed The inventors of today have a distinct advantage over their predecessors An ordinary factory floor is limited by the constraints of matter the IRIS Explorer factory floor is limited only by the power of your imagination How to Use This Guide The RIS Explorer User s Guide describes how to use IRIS Explorer which is a system for creating custom visualization programs and applications This guide is written for computational scientists and engineers in the fields of fluid dynamics chemistry meteorology cosmology physics and mathematics It addresses high level users who are experts in their fields but are not programmers and who will use the visual interface and tools in IRIS Explorer to create their models The guide assumes you have a basic understanding of the UNIX operating system and can create data files the X Window System and Motif and can use a mouse Contents of This Guide The RIS Explorer User s Guide has seven chapters and two appendices They cover the following topics Chapter 1 Getting Started provides five sample maps that visualize data from different scientific fields Chapter 2 Working with the Map Editor explains how to use the Map Editor and Module Librarian to create maps Chapter 3 Us
76. ata values For example you can pinpoint areas where the bone is badly damaged by coloring the image according to bone density values The Module Librarian displays available maps and modules You can launch single modules from the Module Librarian arrange them in the Map Editor and connect them to one another by their data input and output ports These ports allow the flow of data between modules the connections appearing as wire like blue lines Maps are usually arranged so that the data stream flows from left to right across the screen You can also launch complete maps The Map Editor and Module Librarian menus provide you with options for manipulating the modules in a map The modules themselves are accessible through their control panels These are rectangular panels displayed on screen which contain widgets the means of adjusting module parameters 2 2 The Map Editor The Map Editor see Figure 2 1 is the work area in which you assemble modules for the purpose of organizing them into an operational map A map is analogous to an application in that it comprises a series of algorithms performing mathematical operations on data Each module represents one discrete operation on the data 2 2 1 Opening the Map Editor To bring up the Map Editor type explorer at the shell prompt in the shell window The Module Librarian and the Map Editor appear 14 2 2 2 Quitting the Map Editor To exit from the Map Editor open the Admin menu an
77. ataScribe Category Elements Scalars Char Short signed and unsigned Integer signed and unsigned Long signed and unsigned Float Double Arrays Vector 2D Array 3D Array 4D Array Patterns Lattices Uniform lattice Unif Lat 1D 2D and 3D Perimeter lattice Perim Lat 1D 2D and 3D Curvilinear lattice Curvi Lat 1D 2D and 3D Generic input lattice 1D 2D and 3D Sets Any collection of scalars arrays and or sets Table 7 1 DataScribe Elements 7 7 1 Scalars Scalars are primitive data elements such as single integers floating point numbers single numbers bytes and characters They are used to represent single items in a template or to set the primitive type of an array Their bit length is dependent on the machine on which the script is run and corresponds to the C data type as below Table 7 1 lists the scalars and their representation Category Scalar 88 Signed integers Integer int type Long long int type Short short int type Unsigned integers Uint unsigned int type Ulong unsigned long int type Ushort unsigned short int type Floating point numbers Float float type Double double type Characters Char a single ASCII character 8 bits Table 7 2 Scalar Values 7 7 2 Scalar Glyphs Figure 7 14 A Scalar Glyph Scalars are unit data items Their glyphs have a text type in slot see Figure 7 14 where you can enter a name for each particular manifestation of the glyph For example you can name an integer gly
78. ategory or from the Librarian shelf You can restore a module you accidentally removed by selecting Update from the Display menu It restores the original setting so you also lose any unsaved changes you have made to the Librarian 2 10 5 Saving the Librarian Configuration Once you have arranged the IRIS Explorer modules and maps in categories and on the Librarian shelf to your satisfaction you can save the new organization for future operations 1 Select Save Librarian Config from the Module Librarian File menu 2 When the Save Configuration file browser appears save the configuration with a new filename 3 Use a text editor to incorporate the configuration changes in the new file into the explorerrc file in your home directory If you do not currently have one copy usr explorer Explorer config to this file The Category command in this file governs the layout of categories However the explorerrc file contains more information than IRIS Explorer provides when you save a new configuration so you should edit the file rather than overwrite it Add lines of the form category name module for each new category or category shelf module for each module on the Librarian shelf To set the module path that specifies the directories to search for modules and for further configuration commands see The explorerre Configuration File in Appendix A 2 11 Common Problems 33 When all the launched modules have been c
79. ates sphere and cylinder geometry The pyramid is an IRIS Explorer data type The radius of each sphere is calculated according to the van der Waals radius of the corresponding atom You can increase or decrease the radii of all spheres in BallStick proportionately by turning the dial on the module control panel Figure 1 9 BallStick Control Panel The molecule data also passes into AtomicSurf see Figure 1 10 It uses the van der Waals radius of each atom and adds a solvent probe radius to it The surface points in this solvation layer represent the positions in which a solvent probe would be in contact with the target molecule Figure 1 10 AtomicSurfControl Panel You can change the probe radius for which the solvent accessible surface is calculated by moving the slider on the control panel The smaller the value the finer the surface A value of 1 5 Angstroms approximates the radius of a water molecule a commonly used probe Probes that are too small or too large are not useful particularly as the probe size approaches that of the target molecule You can also change the surface dot density by turning the control panel dial The larger the value the larger the number of dots produced It is best to use lower densities for large molecules otherwise the visualization becomes very cluttered A density of about 10 dots Angstrom2 works well for molecules which have sizes comparable to that of NutraSweet GenerateColo
80. ay encode UNIX environment variables using the shell dollar sign notation For example S3EXPLORERHOME will expand to the value of the environment variable EXPLORERHOME as will EXPLORERHOME The C shell tilde notation for designating home directories is recognized as well However strings surrounded by single quotation marks apostrophes are not expanded in this manner If the file permissions are set to be executable the file will be executed and the output read as the configuration file If IRIS Explorer recognizes the CPP notation the file is run through the C preprocessor and all environment variables are defined to the C preprocessor as C preprocessor symbols This means you can use conditional statements for values such as hostname which makes the file more flexible Note If you use the CPP notation in your explorerrc file then you must use rather than at the beginning of a comment line This is an example of a typical explorerrc file Comments start with an exclamation point in column 1 l Define some remote hosts host willard host louis Also look for modules in my local directory modulepath append modules Set the directory where the arena and pipes go set tempdir usr tmp explorer Add some frequently used modules into the shelf category shelf Render DisplayImg IsosurfaceLat ReadImg ReadLat Contour Put the Geometric modules into their own category category Geometry BoundBox
81. ble named mod you can use destroy mod Note that assigning the value returned by start is more than a convenience it is required under some circumstances There you requested that the module ReadImg be launched It is possible though that a ReadImg module already exists If so then the module started as a result of this code will be named ReadImg lt 2 gt not ReadImg Subsequent connect commands that explicitly refer to the string ReadImg will reference the pre existing ReadImg module and will fail to have the desired effect The solution is to avoid referring to modules by the name used in the start command Instead assign the value returned by start to a variable and use the variable for subsequent references start map Maps are started using the start map command start map cfd 116 connect The connect command takes an output module and port and an input module and port connect ReadImage Output SharpenImg Img In As with start a value is returned by connect that may be saved in a variable define cl connect ReadImg Output SharpenImg Img In You can delete the connection with disconnect ReadImg Output SharpenImg Img In or disconnect cl Variables containing module and connection information persist even after the IRIS Explorer objects to which they refer are gone Thus you can reconnect the modules just disconnected with connect c1 Testing Variable Types Skm pro
82. both items appear on it They also appear on the port menus of the input template and its overview indented under the name of the glyph that contains them see Figure 7 35 Figure 7 35 New Menus for Input Template To isolate the x values in the output template you would 1 Open up the coord2 vector glyph Its data type is another vector nested inside the top level vector seeFigure 7 36 Open this vector The shape of the coord2 vector takes its value from the dims2 vector just above it The shape of the data type vector takes its value from the nCoordVar scalar see Figure 7 32 Figure 7 36 Output Lattice Coordinate Vector 2 Select New from the Component menu and fill out the text slots as shown in Figure 7 37 The fragment is called xCoord 98 Because this is a 1D lattice there is only ani variable which goes from to 1 that is the first value in the row 3 Click on the OK to apply your changes Figure 7 37 Output Coordinate Values xCoord The xCoord fragment has been defined as part of a vector within another vector and hence will not appear on the port menu Only top level array fragments can be connected to one another To promote the fragment to the level of the coord2 vector you must define another component at the top level that contains the lower level data fragment To promote the xCoord fragment to a port menu you would 1 Close the data type vector 2 Select New from the Component menu of the
83. by widgets in the control panel See Setting Module Parameters for a full description The control panel has three forms which are described in How Modules Work You can direct the activity in the module core through the ports and widgets on the module control panel 2 4 1 What Modules Do Modules accept data on their input ports and pass it along via their output ports after they have modified it When a module acts on data or executes it is said to fire A module may be turned off or disabled and it can be fired on a computer other than the one where you are running the Map Editor General Module Functions IRIS Explorer modules can be grouped according to their general function see Table 3 1 in Chapter 3 They can readin data files input modules such as ReadLat generate data from other data such as extracting a planar slice or computing a numerical result from a volumetric dataset feature extraction and analysis modules such as DisplaceLat process data to create a visual form geometric representation modules such as IsosurfaceLat display the geometric representations on screen the Render module write data to disk files output modules such as WriteLat Of these the Render module stands on its own It is the means whereby the data passing through the map is visualized and is likely to be an integral component of most maps Once the data has been visualized as an object in theRender window you can
84. complete maps make and break connections between modules edit a map including cutting pasting and duplicating selected modules manipulate module parameters save maps quit IRIS Explorer Table B 1 in Appendix B lists in alphabetical order the Skm commands you can use to perform functions in IRIS Explorer The structure of these commands plus any arguments they may take is listed in Table B 2 of Appendix B 6 2 1 Command Syntax In the Skm scripting language all commands precede arguments and operands and all expressions are enclosed in parentheses If you want to say do something the Skm expression is do something For example to add two numbers the addition operator precedes the arguments Numeric constants do not require quotes skm gt 1 2 3 White space separates operands and operators as well as commands and arguments You can use the space character a tab or a newline character Non numeric constants without spaces are preceded by a single quote for example all Character sequences that include spaces should be enclosed by double quotes 6 2 2 Interactive Help To obtain details on the syntax of a command from within Skm itself type help at the Skm prompt skm gt You can also type help command prefix and you will get a list of all commands beginning with the given prefix Example 6 2 Using Skm Commands You can use the commands in several different ways see Table 6 3 Comman
85. control panel attributes such as the widget layout or widget settings or add new parameters to the script then the new script will be inconsistent with the old module You will have to create and save a new module in order to run the new script It is better practice to create a new module control panel for each script Figure 7 13 shows a DataScribe module wired into a map in the Map Editor 7 15 Finding and Correcting Errors When you have constructed all the templates in a script you can use the DataScribe parser to test the script for inconsistencies and assignment errors To do this select Parse from the File menu 7 15 1 Tracking Down Errors The DataScribe produces messages for two types of discrepancies that it may find when a template is parsed These are Warning conditions Warnings indicate that something is amiss but the problem is not severe enough to invalidate the script You can still save the script and use it in a module although the results might not be what you desired Errors Errors encountered in the script render it invalid You need to correct each error before the module will work The Messages pane at the bottom of the DataScribe window displays a list of all the discrepancies encountered during parsing If you do not want to display the messages you can hide the window by selecting Messages from the View menu 7 15 2 Interpreting Parsing Messages Here is an abbreviated list of possible warnin
86. coord2 vector and fill out the text slots as shown in Figure 7 38 The fragment is called allX In the data type vector you defined one single item xCoord In this fragment you define the set of all xCoords The DataScribe will thus convert all instances of xCoord as defined in allX when this item is wired up The i variable goes from 1 to the last value in the dimensions vector dims 1 that is all the values in the column 3 The Selection element menu now contains two items the vector which is the data type and xCoord which defines a subset of that data type Select xCoord 4 Click on the OK to apply your changes 5 Click on the port menu and you will see allX displayed as an option see Figure 7 33 Figure 7 38 Output Coordinate Values allX To wire up the input and output templates make these connections res to dims2 dataSet xpos to coord2 allx dataSet data to data2 The above example demonstrated promoting lower level fragments to the top level so they appear on the port menu You could have omitted creating the xCoord and allX components and simply wired dataSet xpos to coord2 as nCoordVar2 is set to 1 therefore requiring only x co ordinates Example 7 5 Other Examples The file ReadXDataData mres has two data values for each x position In the script the input dataSet array has two data components for the data fx and gx instead of data in the previous example The output template has
87. ctor glyph in its node type slot When more than one layer exists in an array it becomes hierarchical an array of arrays For example a 2D image red green blue opacity can be represented as a 2D array with a nested vector of length 4 at each node Similarly a 3D velocity field is a 3D array with a vector at each node The vector is of length 3 for Vx Vy and Vz components A pressure tensor in a 3D field is a 3D array with a 2D array of size 3 by 3 containing the nine components Pxx Pxy P 89 XZ s Pzz Footnote J P R B Walton D J Tildesley and J S Rowlinson The pressure tensor at the planar surface of a liquid Mol Phys 1983 48 1357 at each node see Figure 7 16 Figure 7 16 A Complex 3D Array The glyph for the nested array is similar to a closed array glyph It has a node type icon a label and anOpen Close button If you click on the button the glyph opens to reveal the internal structure of the 2D array This array is offset from its parent to show containership The nested 2D array in the example of Figure 7 16 contains stress information at each node of the 3D array You can have as many levels as you need You can also use array indices to help streamline your efforts Using Array Indices in Expressions Arrays are stored using a column major layout the same convention as used in the Fortran programming language in which thei direction of an i j k array varies fastest However the DataScribe
88. d The maps are complete You need only launch or open the map in the Map Editor and then try varying the parameters as suggested in each example Chapter 2 explains how you set about creating your own maps Table 1 1 defines some of the terms you will encounter when you start IRIS Explorer Term Meaning Map Editor Work area for creating and modifying maps Module Librarian Lists maps and modules available for use Module Performs an algorithmic function on the data passing through it Control Panel Gives the user access to the module functions Widgets Dials sliders buttons and text slots for changing parameters Map A collection of modules that carry out a series of related operations on a dataset Image A 2D array that can be viewed using the Displayimg module Geometric Object A collection of points lines polygons or other shapes that can be displayed by the Rendermodule Table 1 1 Some Components of IRIS Explorer 1 2 Launching a Map You can open maps in two ways from the command line in the UNIX shell and from the Module Librarian in IRIS Explorer 1 2 1 Opening Your First Map If IRIS Explorer is not running you can use the command line in UNIX when you open a map for the first time Change to usr explorer maps and type the IRIS Explorer command at the prompt cd usr explorer maps explorer map mapname map The mapname map is the name of the map you want to open for example chemistry map The name of each map
89. d Action copy Contour Copies one module copy GenLat Contour Copies a symbol copy all mods Copies the list of all modules Table 6 3 Using Commands 6 3 Creating More Complex Scripts This section describes the Skm command syntax in more detail to help you create flexible scripts for performing activities in IRIS Explorer 76 6 3 1 Specifying Symbols Symbols are identifiers that are preceded by a single quote For example maxi modulename at X Y size W H You can then define var as a symbol define var size Setting Off Comments The semicolon is the comment character in Skm It comments out the remainder of the line on which it is located for example launch the Pick map and list the active modules Using the Define Command You assign values to a variable using the define command For example to define a variable called myVar and assign it the value simple you write define myVar simple To display the value of a variable type the name of the variable at the Skm prompt without using parentheses for example skm gt myVar simple The assignment of a module to a variable is important because the actual name of the module depends on whether or not there are other copies of the module running If for example you use the command start to launch a copy of ReadImg but there is already another active copy of ReadImg in the Map Editor your module will be named ReadImg lt 2
90. d description of the lattice data type refer to the IRIS Explorer Module Writer s Guide Figure 7 20 A 3D Generic Lattice 7 7 7 Sets The set glyph lets you collect any combination of data items you want into one composite item You can include integers floats vectors arrays and other sets in a set You can use a set to design a new data item containing elements of your choice consolidate a small collection of items that you use frequently To create a set open a set glyph in the template then drop glyphs for the data items you want into the open set Once your set is saved you can include it in a template instead of dealing with each item individually Saving a Set If you have a custom set that you plan to use often you can save it into a script and then read it into other scripts using Append from the File menu You can use the Edit menu options to cut and paste the set into various templates For example you can collect a group of scalars into a set and wire the set into an array in another template This is useful for setting the bounding box of a lattice A 2D uniform lattice requires an array that specifies the xmin xmax ymin ymax bounding box of the data You can wire a set consisting of four floats into the lattice to satisfy this constraint see Figure 7 21 Figure 7 21 A Set for a Bounding Box Using Nested Sets You can nest sets within other sets and within arrays To nest a set in an array drop the
91. d on a module port unless the port is marked as optional Opt For example GenerateColormap has an optional input port A module will not operate properly in a map unless all its required ports are connected to compatible ports on other modules and are receiving data A module with parameter based widgets always has an input and an output port for each parameter For example BlendImg has two data input ports and one parameter input port for Blend see Figure 2 10 It has one data output port and a corresponding parameter output port for Blend see Figure 2 11 Parameters are passed through the output ports and you can set and connect them so as to control widgets on other modules The synchronisation ports Fire and Firing Done are present on all modules and as their names suggest can be used to control a firing sequence See Using the Synchronization Ports A Firing Done output port can be connected to a Fire input port Loop controller modules have an additional output port Loop Ended See Constructing Loops 2 5 1 Making a Compatible Connection To select an input or output port click on the associated access pad using the right mouse button A list of the input or output ports and parameters associated with that module appears see Figure 2 10 and Figure 2 11 IRIS Explorer makes use of five data types Lattice Pyramid Geometry Parameter and Pick They are explained in Understanding IRIS Explorer Data Types You can connect o
92. d select Quit When you do this you automatically quit IRIS Explorer 2 2 3 Editing Maps and Modules You can select copy duplicate delete move single or multiple modules by using the Map Editor The modules may be free standing or already wired into a map Use the Map Editor pull down menus to duplicate cut copy paste destroy enable disable disconnect and reconnect modules Edit menu The operation is applied to all selected modules In Figure 2 1 only the Render module is highlighted as selected Some of the Edit menu options have keyboard shortcuts listed next to them group modules together and open or close groups Group menu control layout within the Map Editor such as of the connecting wires and the Log window Layout Menu Alternatively you can use the drop icons at the bottom of the Map Editor window for some module operations such as destroying disabling enabling and disconnecting reconnecting see Figure 2 1 Once a map is set up in the Map Editor you can run it so that the modules fire and send data to one another You can also incorporate several modules into a group or an application see Chapter 5 Creating Groups and Applications The object visualized in Figure 2 1 is a curved torus generated by GenLat Figure 2 1 The Map Editor 2 3 The Module Librarian The Module Librarian see Figure 2 2 is a file browser and selector that provides access to IRIS Explorer modules and maps through
93. directories in a completely different directory tree in two ways Simply type the directory or filename into the text slot This takes you directly to your destination Use the Current Directory option menu see Figure 2 23 Each directory entry in this hierarchy contains a cascading menu for all its contents Click on the Current Directory option menu choose the item you want from each menu and click on it to get to the next menu level 2 9 6 Option Menus and Scrolled Lists Option menus and scrolled lists let you select one or more items from a group of options Option menu buttons present a menu from which you can choose one option at a time The option may be a value a range of values or a property such as uniform or curvilinear see Figure 2 24 The option menu buttons are rectangular with a small raised bar on the right Figure 2 24 Option Menu Widgets Click anywhere on the button to display the menu and select the item you want A scrolled list widget lets you select one or more items from a list of options that may extend beyond the current list window You may be able to choose one option or several options at a time depending on how the properties of the particular list were defined when the module was created Click on an item to select it If the scrolled list allows you to select more than one item click on all the items you want to select Figure 2 25 Scrolled List Widget 2 9 7 Drawing Areas 31 A drawing
94. duce a single composite image that is the same size and shape as the original You can also remap the image Note The DisplayImg window should not be obscured by any other windows or the image will not be properly displayed Because the product of DisplayImg is also a lattice you can send the image to any module that accepts a 2D lattice through the lattice output port on Displaylmg Example 3 3 Comparing Two Images This example illustrates the use of DisplayImg to compare an image in its original form with the same image after it has been modified 1 Launch a ReadImg a BlurImg and a DisplayImg module in the Map Editor Connect the output port on ReadImg to the input port on Displaylmg Wire the output port on ReadImg to the input port on BlurImg by clicking on Connect in the cascade menu Wire the output port on BlurImg to the input port on Displaylmg Bote ee eS Open the file usr explorer data image flowers2 rgb in ReadImg When the module fires you should have two copies of the image in the DisplayImg window Use the mouse to position them in the full scale module window 6 Turn the dials on the Blurlmg module and compare the top image with the bottom one see Figure 3 16 Replace BlurImg with another image processing module and see what effect it has on the image Figure 3 16 Example Showing Two Images in DisplayImg 46 3 7 Visualizing Data Since IRIS Explorer visualizes numerical data after it has been p
95. dules 3 1 Overview Once you have data in IRIS Explorer you can perform many operations on it to make the visualizations more meaningful and easier to interpret For example you can emphasize areas of common density or intensity by redefining the color palette or examine more closely a specific subset of the data by cutting into or slicing the larger dataset You can also examine the relative density of data points within a dataset by drawing graphs or histograms to show their distribution When you have a geometric object or scene containing several objects displayed in the Render window you can move highlight and otherwise manipulate the objects in many ways to provide you with new insights into the nature of your data You can also animate an object and record its movements for later display Loop controller modules provide you with a means of constructing single and nested loops in your maps For example you may need a loop to capture successive frames in an animation sequence There are many operators for processing images embodied in the ImageVision Library modules listed in Table 3 1 under Process Images You can display and record these processed images in DisplayImg The modules supplied with IRIS Explorer vary widely in function and complexity providing you with the means to manipulate and process data in many different ways More information about specific modules is available in these places Table 3 1 lists some of
96. dules to visualize atmospheric data Intense storms can produce tornadoes high winds and hail and it is possible to simulate these storms by integrating a set of mathematical flow equations These equations can for example predict values for the wind speed and direction air temperature humidity pressure and water content every 5 to 10 seconds on a lattice of grid points 500 to 1000 meters apart The data in the example map is taken from a simulation of a single severe storm made by the storm group at the University of Illinois Footnote Dr Robert Wilhelmson NCSA Research Scientist and Professor of Meteorology in the Department of Atmospheric Sciences DAS at the University of Illinois at Champaign Urbana and Dr Lou Wicker post doc and Crystal Shaw research programmer both at NCSA and DAS The map shows an isosurface of rain density and a volume rendering of air buoyancy An isosurface is a surface which passes through all points in a 3 D dataset where the data has a particular value The data is in the form of a uniform lattice 1 6 1 Opening the Volume Map To open the volume map see Figure 1 12 type explorer map volume map Figure 1 12 Simulating an Evolving Storm The map contains eight modules ReadLat reads in the rain density data ReadLat lt 2 gt reads in the water buoyancy data ReadLat lt 3 gt reads in the colormap for the water buoyancy data IsosurfaceLat generates an isosurface of the rain density
97. e as a peak and the heat sink as a trough You can change the degree to which the peaks project from the surface by turning the dial on Displacelat This causes the data to be displaced out of the plane to a greater or lesser degree GenerateColormap colormaps the heat flux data according to temperature value You can change the colors associated with each temperature value by using the option menus on the control panel Refer to Creating Colormaps in Chapter 3 for more information LatToGeom uses the heat flux and colormap data which are both IRIS Explorer lattices to create geometry for display in Render see Figure 1 7 Render can only display geometry and all lattice data must be converted first Figure 1 7 Visualization of the Flux Peaks Once the data is displayed in Render you can change the background color of the window by selecting Edit Background Color from the Viewing menu When the Background Color Picker appears Click anywhere on the color wheel to select a color Drag the slider to increase the intensity of the selected color 1 5 Molecular Chemistry This example illustrates how you can use IRIS Explorer modules to construct a 3D model of a complex organic molecule and then calculate the optimal radius and likely path for a probe atom investigating the target molecule 1 5 1 Opening the Chemistry Map To open the chemistry map see Figure 1 8 type explorer map chemistry map Figure 1 8 Visualizing a
98. e target string the third argument is the character that replaces the indexed character in the target string The target string is changed as a side effect string set returns t if it succeeded and otherwise The index is origin 0 string set hello 0 J t 7 string is changed to Jello string The string function compares two strings for equality If equal t is returned string skm skm te string skm scheme substring The substring function returns a substring of a string using the supplied begin and end indices substring abcde 0 3 W abc W string append The string append function appends two strings string append abc def abcdef B 2 4 Loading Script Files 119 To read in a script file from within script code use the load command load myfile skm B 3 Procedures in Skm Creating a procedure in Skm is done with the define and procedure constructs The following defines a procedure that takes a single argument declared formally as a and adds one to it The value returned by the procedure if any is the last value of the procedure procedure a a 1 This procedure doesn t have a name yet procedures can be anonymous in Skm The following gives the procedure the name plus1 define plusl procedure a a 1 You would invoke this procedure with plusl 3 4 Here is the definition and use of a procedure called add pair
99. e Librarian When the file browser appears in the Selection type in slot enter the name of the map you saved previously You can add the map to the list in the Module Librarian by editing your personal configuration file This procedure is described in Appendix A Configuring Your IRIS Explorer Environment 21 To launch this map and connect the modules go to Wiring Modules Together 2 5 Wiring Module Ports Together Modules communicate by passing data from one to the next through their input and output ports see Figure 2 10 and Figure 2 11 Once you have modules in the Map Editor you can connect them together individually or severally disconnect them change your mind about connecting them and alter the appearance of the connecting wires Figure 2 10 Module Input Ports Figure 2 11 Module Output Ports Each module control panel has two port access pads one for input ports and parameters on the left of the control panel and one for output ports and parameters on the right A single module can have several input and or output ports Data port names are listed first on the port menu parameter port names are listed next followed by synchronisation port s The port name is followed by the IRIS Explorer data type that it can accept that is Lattice Pyramid Geometry Parameter and Pick Parameter ports are associated with widgets If the port is optional the type is followed by Opt A connection is require
100. e a large number of color entries in the window server such as GenerateColormap Running the X Server If you have more than one copy of a module in a map the second copy will have the number lt 2 gt after its name The third will have lt 3 gt and so on 2 3 2 Launching a Map Maps in the Module Librarian can be identified as blue You can launch a new map in the Map Editor by the drag and drop method from the Module Librarian see Launching a Module If the map you want is not listed in the Module Librarian you can select Open from the Module Librarian File menu Use the file browser to find the directory and then choose the map The top left module in a map is always launched at the launch point If you want to start IRIS Explorer and launch a particular map at the same time you can use the UNIX command line option map with a filename Type explorer map filename map The Map Editor opens and the map is launched and displayed automatically Note If you are not in the directory where the map resides either change to that directory before typing the command or use the full pathname of the map for example usr explorer maps cfd map 2 3 3 Saving Maps and Modules Use the Module Librarian File menu to save your maps You must save all IRIS Explorer maps with the filename 16 extension map otherwise IRIS Explorer will not be able to find the file when you try to open it again Click on the modul
101. e a new widget for each of the input parameters If you are editing a group you can only change previously defined widgets i e you can not add new widgets to input parameters which do not already have a controlling widget When you edit a control panel you can Select a widget for each parameter Arrange the widgets as you wish in the Preview window Set the initial value and the range of each widget Use the Menu Bar Editor to design the menus Set a widget attribute for each menu bar item 55 To save the menu and control panel configurations click the OK or Apply buttons at the bottom of each window 4 2 1 Choosing Parameter Widgets The widgets on the control panel allow you to control the value of the module parameters directly Parameter Types An IRIS Explorer parameter may be one of three types of scalar quantity each of which can be represented as a widget or a menu item on the module group or application control panel A parameter can be along integer 32 bit a double precision floating point 64 bit acharacter string For more information on parameters see Understanding IRIS Explorer Data Types in Chapter 2 Widget Types The widget types are listed on the Type option menu see Figure 4 2 and described in detail in Setting Module Parameters in Chapter 2 All widgets must have a valid type selected including those you place on a menu The widget attributes are listed in the rest of the Widge
102. e control panels for Contour IsosurfaceLat and Render by clicking on the Maximize button 2 Change the dial setting on IsosurfaceLat Notice what happens in the Render window 3 Change the slider position on Contour module Note the change in the Render window Figure 2 27 Experimenting with Widgets 2 10 Organizing the Module Librarian Modules and maps are organized into categories in the Module Librarian Figure 2 28 shows one category called Modules You can reorganize the contents of these categories displayed in scrollable columns as described below Figure 2 28 Module Category 2 10 1 Creating New Categories You can organize modules differently for each system on which you run IRIS Explorer For example you may create a category for each remote host or for all the complete maps on your system To create new categories in the Module Librarian select New from the Categories menu When the pop up menu appears enter the name you want for the new category This adds the name to the Categories menu Select the name from the menu and an empty column of that name appears in the Librarian To hide categories in the Librarian click on the category title with the right mouse button and select Hide when it appears To redisplay the category select the category name from the Categories menu To update a category select Update from the Display menu after you have added new modules or maps Note You cannot delete cate
103. e glyph in a template Figure 7 6 Glyph Forms The Shape Icon The arrow in the shape icon indicates the direction in which the axes are ordered see Figure 7 7 The fastest varying axis is at N1 that is the tail of the arrow and the slowest varying axis is at N2 2D or N3 3D that is the head of the arrow Data is stored in the direction the arrow is headed so it is stored first at the arrow s base You can change the name of the axis but not the direction in which the data varies You can set the starting and ending values of any vector and array shape icons to either constant or variable values To define the shape of an array you enter a starting value that is used for all dimensions of the shape and an ending value for each separate dimension Figure 7 7 The Shape and Node Type Icons The Node Type Icon The default node type in the array glyphs is the integer data type You can change the data type by dropping a different glyph onto the node type icon For example Figure 7 8 shows the 4D Array glyph from Figure 7 7 but with the array replaced by a Set glyph Figure 7 8 A New Array Structure Note Most of the glyphs within the lattice glyph are locked so that their node type cannot be changed to maintain equivalence with the definition of the lattice data type The exception is the lattice data glyph whose node type can be edited to produce a lattice of floats or of integers etc See Lattice Glyphs for more
104. e sure you use Save All from the Module Librarian File menu to save modules that are not highlighted 2 If you save certain modules only with Save Selected the title bars of those modules must be highlighted otherwise the map is saved without any modules in it 2 11 7 When You Try to Destroy a Module Nothing Happens When you select Destroy from the pop up menu IRIS Explorer sends the module a message to exit If the module is busy computing it may not get the message for a while If you want it to quit immediately select Destroy again from the module pop up menu This sends a kill message to the module s controller which then shuts down the module without waiting for a response from the module itself 2 11 8 You Cannot Launch a Module Librarian Remotely If you get messages from the Local Controller LC or Global Controller GC when you are trying to launch a Module Librarian for a remote system there is probably a command generating output from your cshrc file You will see the output from the command in the error message For example some people print a message of the day or a witty saying from the cshrc file This output interferes with the communication between the Local Controller which is needed by the remote Module Librarian and the Global Controller which starts up the Local Controller on the remote system The offending command and its output must be removed before you can run the Module Librarian on that
105. e title bar to select a module The title bar and access pads will be highlighted in white See Selecting a Module A file browser comes up and you are required to enter a filename for the map for example NewMap map From the File menu you can select Save All which saves everything in the Map Editor or Save Selected which saves only the highlighted modules into the map Modules can be saved only as part of a map but you can save incomplete maps and bring them up later for further work 2 3 4 Removing Maps and Modules You can remove some or all modules from the Map Editor at a time To remove the current map completely select Destroy All from the Map Editor Edit Menu To destroy only some of the modules in the map highlight the modules see Selecting a Module and select Destroy from the Map Editor Edit menu To remove a single module select Destroy from the module pop up menu see Using the Pop up Menu To bring up a new version of the module launch the module again from the Module Librarian The new version of the module will be numbered lt 2 gt or lt 3 gt if it is the third version to be launched Example 2 1 Launching a Map This example illustrates how to launch an existing map from the Module Librarian and carry out some simple operations 1 Inthe Module Librarian find the map called simple 2 Drag and drop the simple map into the top left corner of the Map Editor The map opens t
106. e user defined data types They work exactly as IRIS Explorer data types do handling data in a specific format The structure of the lattice data type is discussed in more detail in Chapter 7 Using the DataScribe All the data types are described fully in the JRIS Explorer Module Writer s Guide 27 2 8 2 Using the Data Types The IRIS Explorer data types represent groups of data A given instance of a data type on a port can be generic or highly specific For example a module may have an input port of Lattice type defined so that it will accept a wide variety of lattices of different sizes or so that it will accept only 2D scalar lattices of real numbers with uniform coordinate mapping For example the Contour module accepts a Lattice data type on its input port but the lattice must have two or three dimensions If you try to pass it data in the form of a 1D lattice you get an error message The module definitions give the data type specifications for the ports on existing modules When you build a module you can define each port as you like The more general the specification for a port the more modules you can connect to it but the harder the module is to write If you have any doubts about port compatibility when you connect modules into a map you can check the data types acceptable to each module by calling up the Help window from the module pop up menu reading the module definitions in the IRIS Explorer Reference
107. e widgets on the control panel The Parameter Function Editor lets you establish relationships between parameters in adjacent modules in a map The parameter value in the downstream module is then expressed as a function of the upstream parameter values This chapter describes how to use both these editors 4 2 Using the Control Panel Editor The Control Panel Editor see Figure 4 1 lets you modify a module control panel or create a new one by editing the parameter widgets and menu items You may change a widget s type position and resize them and change their limits and default values There are three places the Control Panel Editor can be used from To invoke the Control Panel Editor in the Map Editor you must be creating a group and the Group Editor must be open Select Control Panel from the Edit menu in the Group Editor To create a module control panel in the Module Builder click on the Control Panels push button in the Module Builder main window In the DataScribe select Control Panel from the View menu when you are creating a DataScribe module The Control Panel Editor consists of an Editor window and a Preview control panel window You stipulate the attributes of the panel in the Editor window and the result is displayed in the Preview window Figure 4 1 The Control Panel Editor When you create a module using mbuilder or a group via the Map Editor you can use the Control Panel Editor to change or creat
108. ection from its Firing Done port to a downstream module s Fire port can cause the downstream module to fire in exactly the same way that sending new data to the module would cause it to fire You can therefore use these synchronization ports to control a sequence of module firings rather than allowing the module firing mechanism to determine the ordering Normally this is controlled by the data flow therefore these ports are useful when there is no need for any data to be transferred between modules For example wiring modules as shown in Figure 2 15 will cause module firings to be sequential in the order D C B when A is fired Omitting the Firing Done to Fire port connections would cause the modules B C and D to attempt to fire simultaneously control successive firings of a module for example a module that sends out a sequence of data on one of its output ports The AnimateCamera module sends out a series of cameras usually to Render A new camera will be sent each time an upstream module that is connected to its Fire port fires Modules that are designed to fire repeatedly 25 are usually wired into a loop rather than a map with a linear dataflow See Constructing Loops for further discussion Figure 2 15 Controlling Module Firing with Fire Ports 2 6 3 Temporarily Disabling a Module There are a number of ways in which module s can be disabled you can use the Disable option from the Map Editor Edit menu to disable a s
109. efine plusl procedure a a 1 You can invoke this procedure as follows skm gt plusl 3 4 Using a Procedure This example shows how to carry out the action of connecting image processing modules in IRIS Explorer Image processing modules that operate on a single input typically have an input port called Img In and an output port named Img Out First you define a procedure that will connect specified ports in two different modules This procedure simplifies the connection of the modules by supplying the port names automatically define image conn procedure modl mod2 connect modl Img Out mod2 Img In Then you invoke the procedure and provide the names of the modules to be connected image conn SharpenImg DisplayImg 6 4 Output from Skm You can use the print command to print the output from a Skm command or script to the IRIS Explorer console either the shell from which IRIS Explorer was launched or the Skm Editor Window depending if IRIS Explorer was started with script or script print takes one or more arguments here are two examples of its use skm gt define vl abc skm gt define v2 123 skm gt define ml start ReadImg skm gt print vl v2 3 abcl2 and skm gt print My module is ml My module is lt IRIS Explorer Module Ref ReadImg gt 6 5 The Skm Editor Window If you started Explorer with the explorer script option
110. elected module or a number of selected modules temporarily The Enable option reactivates it or them again you can drag a module to the Disable icon located at the bottom of the Map Editor to disable it or if it has been selected disable it together with all other selected modules The Enable icon can be used to reactivate it or them again You can also use the Disable Enable toggle option on the control panel s pop up menu to affect a single module Disabling a module is useful if You want to modify several module parameters without having the module fire every time you make a change Your map contains a module that takes several minutes to finish firing Each time you made a connection to the module or altered a parameter you would have to wait several minutes while it fired before you could continue You can avoid the wait by disabling the module while you complete your operations then enable it again when you are ready to fire the complete map If you disable a module that is connected in sequence with other modules it will not send new data to the modules that follow it If those modules rely entirely on the disabled module for data they also cease to fire The flow of data will be blocked along this branch at least until you reenable the disabled module 2 7 Logging Module Output When modules fire in the Map Editor they often generate informative text messages For example PrintLat PrintPyr and PrintPick a
111. emplates Place a pattern an integer a pattern another integer a final pattern and a 2D array in the first input template Set the names of these glyphs as follows the termination string of the first pattern call it Header to size the name of the first integer to xres the name of the second pattern to Ypattern and its termination string to size the second integer to yres Give the last pattern PresHeader a termination string of Here Name the 2D array matrix and set its shape to xres by yres Create an output template of type IRIS Explorer and place a 2D uniform lattice in it nn FY e ee0enr Set the nDataVar entry to 1 You need to fill in two fields in this output template the dims vector and the data itself In the input template thexres and yres contain the dimension information but you cannot wire scalars directly to a vector However you can build a Constants template that organizes the two scalar values into a set which can be wired to the dims vector To build the Constants template 1 Create a new Constants template and place a set glyph in it 2 Name this set matrixSize and place two integers into the set 3 Name the first integer ires and set its value to xres 4 Name the second integer to be jres with a value of yres You can wire this set into the dims vector of the output lattice To wire up the templates 1 Bring up the port pop up menu from the Constants template and select matrixSize
112. en the mres file in the Map Editor The map comes in as a regular module and uses the IL Controller module as its alternate executable The main reasons for using the IL Controller module to execute a map are the increase in processing speed the reduction in memory use This is because the IL execution module is a pull model and requires much less information to compute a large image than IRIS Explorer which uses a push execution model 54 Chapter 4 Editing Control Panels and Functions This chapter describes how to use two of the IRIS Explorer editors They are the Control Panel Editor which you can use to create and modify module control panels the Parameter Function Editor which you can use to create relationships between parameters in linked modules These two editors allow users to modify modules and increase their power without using the Module Builder 4 1 Overview IRIS Explorer provides the user with the capacity to edit work in progress at many different stages in the creative process In the Map Editor the user edits the sequence of modules in a map In the Module Builder the user edits the module resources IRIS Explorer also provides editors for modifying aspects of the modules themselves The Control Panel Editor enables you to create new control panels for modules groups and applications and modify the appearance of existing control panels You can define new menus on the menu bar and add or rearrang
113. er s window You need to select an object in the Pick Edit mode first To restore the original camera angle after you have moved the object around select Home from the Functions submenu of the pop up menu You can also select the Draw Style for example wireframe switch Headlight and Decoration on and off and set some Preferences for display The single buffer double buffer and interactive buffer options on the Draw Style submenu of the pop up menu refer to the type of buffering you are using 3 7 6 Using Graphical Shortcuts The Render module provides several graphical shortcuts for manipulating objects in the Examiner Navigator and edit modes To use the shortcuts select Decoration from the pop up menu A frame containing several widgets appears around the Render window see Figure 3 20 The widgets include thumbwheels that control the camera rotation or tilt and trucking motion They also work in Pick Edit mode a slider that controls the zoom action eight buttons that correspond to View Pick Edit Help Home Set Home View All Seek and Camera Type Figure 3 20 The Render Decorations 3 7 7 Wireframe Rendering When you have an opaque object in the Render window it may be easier to examine or move around in wireframe form You can draw the object as a wireframe structure see Figure 3 21 by selecting Draw Style from the Render pop up menu in either viewing mode then clicking on wireframe Note This
114. er scripting commands The commands are described in Command Syntax 6 1 1 Running IRIS Explorer by Script To run a script when IRIS Explorer starts up at the shell prompt type explorer script scriptfilename A map file and a script file can be specified on the command line For example explorer map mymap script scriptfile skm To set up IRIS Explorer for interactive scripting at the shell prompt type either explorer script or o explorer script Both of these puts you into the Skm interpreter which displays this start up message and prompt IRIS Explorer Version 3 0 skm gt If you use the explorer script option this prompt appears in the shell window you invoked explorer from If you use the explorer script option then this message and subsequent scheme output appears in a dedicated scheme window see later 73 At this prompt you can type Skm commands as you go and have them executed in IRIS Explorer immediately 1 You can pipe commands to IRIS Explorer using explorer script with a UNIX pipe For example cat myFile skm explorer script If you do use a pipe although Skm output will appear as normal subsequent commands cannot be entered from the keyboard as IRIS Explorer will still be receiving its input from the pipe A pipe sends the output of one command into a second command For more information refer to the UNIX documentation 6 1 2 Creating
115. ering the name of the parameter If you choose Script command or System command a text slot appears for entering the name of the command 4 4 Menus in Group Control Panels When you create a group or application control panel you may wish to promote a menu item from an individual module to the group control panel Unlike other widgets which are promoted to the group panel along with their associated parameters the actual menu entry is not promoted Only the parameter passes to the group level You must 59 therefore create a new menu for the group control panel and redefine the parameter as a menu item at the group level 4 5 Using the Parameter Function Editor When a number of connections fan into the same parameter input port you may wish to express the value on that port as a function of some or all of the fan in connections For example you may wish to take the average value of all the connections into the port The Parameter Function P Func Editor see Figure 4 9 lets you set up relationships between the fan in values on an input parameter port so that the value of the parameter is expressed as a function of one or more parameter values from the upstream modules To do this you define each parameter in the P Func Editor and then create a mathematical expression that defines their relationship Any change in the value of the upstream parameter or parameters is then reflected in the value of the input parameter Fi
116. es are removed Settings for promoted ports and alias names are also retained There may be additional required ports that are promoted from the new modules within the group Note that it is possible for a port that was required for the original group to no longer be so For example by adding a module into the group that has a connection to an originally required port removes the need for that port to be promoted to the group This port will still be marked as promoted in the Group Editor but can now be deselected You can ungroup a closed or open group by selecting UnGroup from the Group menu You are left with the original collection of separate modules If the group is closed and only the group control panel is showing it opens before it is ungrouped 5 6 Defining an Application When you have created a group with its own control panel you can run it as an application An application is a module or map that runs in a special IRIS Explorer mode outside the Map Editor You can engage the application mode only when you start IRIS Explorer from the command line You cannot change an ordinary IRIS Explorer session into an application mode session Application mode operates on ordinary IRIS Explorer maps which consist of one or more modules or groups Usually a map contains several modules collected into one or more groups 5 6 1 Creating an Application There is no special procedure for creating an application since an application
117. es how to set up a script that will read a 2D array of ASCII into an IRIS Explorer lattice You require a data file an input template and an output template The Data File The data file contains two integers 7 5 that define the size of the subsequent 2D array 7 by 5 followed by the actual data i A S 90 85 73 57 40 25 14 8177 66 94 36 23 gt 13 60 S7 4953827 LT lt 9 36 34 29 23 16 10 6 P17 LA IL 38 5 3 Create this file in your usr tmp directory and save it as dsExample1 data You now have a 7 by 5 matrix of data ina file To get the data into an IRIS Explorer lattice you need to create a module to read data in this format The Input Template 1 Start the DataScribe and select Template from the Template menu When the New Template Dialog box appears type in a new name such as ArrayFile and select OK A new template pane appears on the input side of the DataScribe window with the wiring overview in the Overview pane 2 Select avector glyph from the Arrays list on the Data Types palette and place it in the ArrayFile template This glyph will be used to read in the dimensions of the 2D array as specified in the first line of the input file Figure 7 10 An Open Vector Glyph 3 Open the vector glyph by clicking on the Open Close button at its right edge The glyph has these active areas a name Array1 84 a primitive type integer a starting value 1 an ending value N 4 To set the
118. esetting the Color Bands You change the slope and hence the value of a color band in order to adjust the color spectrum in the colormap In this fashion you can emphasize certain subsets of your data and block out others This is easiest to do with the full scale GenerateColormap control panel see Figure 3 1 The control panel has three windows The palette window shows the spectrum of colors currently associated with the data range The colormap has 256 entries which are spaced uniformly through the range The editing window shows the relationship between the color bands You can use the RGB Red Green Blue or HSV Hue Saturation Value color systems to create a colormap The scale window shows the range of data values for the map You can change the minimum and maximum values for the domain by typing new values into the text slots on the dials Selecting an Output Mode Use the Output option menu to select a mode in which to work The Build option disables the module temporarily while you edit the color bands This is useful if you want to experiment without the module constantly firing and sending data to the modules downstream The Run option re enables the module All changes are reflected in the color palette as you make them and are simultaneously sent to the next module downstream Setting the Domain Limits Each map processes data with values over a specified range You can set the limits of the range affected by Ge
119. ess via rsh to that machine by typing the following command usr bsd rsh labserver pwd If it responds with the name of your remote home directory all is well If it responds with Permission denied you need to enable rsh You can enable access to that machine by creating a file named rhost in your remote home directory See the rsh 1 manual page for details The command modifier on the host line allows the redefinition of the command to use to try to get a module communications server running on a remote machine By default the rsh command is used This may not be appropriate for all installations because rsh does not allow for password prompting and the associated protections IRIS Explorer provides an alternate command similar to rsh that can prompt for a password This command cxrexec uses the rexec library call and prompts for a password in a small pop up window For example if access to a host named securehost requires a password the following line in explorerrc will result in the password prompt being issued 110 host securehost command cxrexec The command cxrexec has the same command line options as rsh Either command can be modified in explorerrc to add options However when additional rsh or cxrexec options are listed the entire command must be enclosed in quotation marks host superhost command rsh HOST 1 guest host superhost command cxrexec HOST l guest These examples demonstrate another feat
120. f IsosurfaceLat Turn the dial on the sosurfaceLat module control panel to change the threshold value of the isosurface and hence change the shape of the object displayed in Render Experiment with the menus on the Render window menu bar and the decoration icons around the border For more information on using Render see Chapter 3 Using Modules 2 4 Modules Modules are the individual units in a map They are the mathematical engines powered by data that make maps work Although their functions vary they all share a basic structure see Figure 2 5 Each module has a visible form its control panel by means of which you can direct the internal and invisible engine or core The internal portion of the module consists of module wrappers which mediate between the core and the control panel the module core itself which consists of a mathematical algorithm Each module has a different algorithm hence it carries out a different function in IRIS Explorer See the IRIS Explorer Module Writer s Guide for more information on the module core Figure 2 5 General Structure of a Module The visible portion or control panel which appears in the Map Editor is a rectangular window that contains input and output ports which allow the module to accept and pass on compatible data types See Understanding IRIS Explorer Data Types for an explanation of data types parameters scalar data values which can be set and altered
121. files one global to the host machine and one private to the user The global configuration file is in usr explorer Explorer config and the private copy is in the user s home directory in the file called explorerrc A 1 1 Remote Execution of Modules The general idea of IRIS Explorer is that you initially run it on your own workstation but then you can use it to run some modules on remote workstations Software Requirements Each machine that you use to execute modules remotely must have most of IRIS Explorer installed on it In general the version installed remotely must match the version installed on the local machine This sense of remote execution is different from that offered by the X Window System which lets you remotely log into a workstation on which IRIS Explorer is installed reset the DISPLAY environment variable to reference your own screen and then run IRIS Explorer In this case all of IRIS Explorer will initially be running on the remote machine but the user interface will appear on the local machine Defining Hosts for Remote Modules To execute IRIS Explorer modules remotely you must first add any host names used to your explorerrc file in this format host hostname For example suppose your local machine called billiejoe is networked to another machine named bob If you can remotely login into bob and IRIS Explorer is installed on it then you can very simply set up the two machines for remote execution
122. for creating powerful visualization maps each of which comprises a series of small software tools called modules A map is a collection of modules that carries out a series of related operations on a dataset and produces a visual representation of the result IRIS Explorer has three main components the Map Editor which is a work area for creating and modifying maps the DataScribe which is a data conversion utility for moving data between IRIS Explorer and other data formats the Module Builder which lets you create your own custom modules described in the IRIS Explorer Module Writer s Guide The IRIS Explorer System To understand how these components interact in the system think of a factory The purpose of a factory is to take raw materials and fashion them into an end product according to a specific design The raw materials are fed into an assembly line at one end go through a number of alterations and manipulations as they pass through the machines on the factory floor and then come out at the other end in the form of a finished product The product is inspected for the qualities stipulated in the design If they are not present or not satisfactory the machines on the floor can be adjusted until the quality of the product meets requirements The factory floor is not the only important area in a factory To make products the machines need raw materials that are suitable for the task at hand The materials may be delivered
123. g MedianFltImg MinFltImg Minlmg Multlmg Neglmg Orlmg Powerlmg PseudoColorlmg RankFltImg RobertsEdgelmg RotZoomimg SGlPalettelmg Sharpenlmg SobelEdgelmg SqRootlmg Squarelmg SubtractImg ThreshImg Xorlmg Generate data from other AtomicSurf ChannelSelect ClipPyr CropPyr DiffLat DisplaceLat Gradient data Gradient3D Interpolate LatFunction LatToPyr MagnitudeLat MinMax Mixer MultiChannelSelect MultiSlice OrthoSlice OutLine ProbeLat PyrToLat Ruler SampleCrop SamplePyr ShrinkPyr ScaleLatNode Shell Slice SubSample TriangulateDelauney Triangulate3D Develop geometric Annotation Ball BallStick BoundBox BoundBoxPyr Contour GnuPlot representations Graph3D IlsosurfaceLat IsosurfacePyr LatToGeom Legend MoleculeBuilder MultiSlice NAGAdvectSimple QueryLat PyrToGeom SliceLat SlicePyr Streakline VectorGen Vectors VolumeToGeom WireFrame Create images Displaylmg Histogram Graph RealityRender Render RenderRemote TransformGen Multimedia audio and video AnimateCamera Audioln AudioOut ReadAudio VideoControl VideoDevice VideoLabInWin VideoStarterln VideoStarterInWin VideoStarterOut WriteAnimation WriteAudio Control looping sequences AnimateCamera For Repeat Render Trigger While Miscellaneous CompressPyr DiffLat ExpandPyr NAGContour NAGGraph SwitchGeom Timer Trigger Write data to disk PrintLat PrintPick PrintPyr WriteGeom Writelmg WriteLat WritePyr Table 3 1 Modu
124. g conditions and errors with suggested solutions Uninitialized variables 1 WARNING Constants NumPixels gt Output data object does not have a value Please make a wire into this object or enter a value expression Failure to wire to an output that needs data 0 WARNING Lattice nCoordVar gt Output data object does not have a value Please make a wire into this object or enter a value expression An unset scalar in a Constants template 0 WARNING Constants Glyph gt Constant data object does not have a value Please enter a value expression for this constant 104 An undefined variable used in a component expression 0 ERROR foo has not been defined Bad end index 1 foo for fragment SingleComponent Failure to assign a termination string to a pattern 0 ERROR DataFile Pattern_1 gt No regular expression in pattern Setting a scalar to a non scalar value array or lattice 3 ERROR Non scalar Plot3DLattice used in expression Lattice Long_3 gt Bad value expression Syntax error in an expression 0 ERROR illegal statement Constants NumPixels gt Bad value expression Bad initial value for a scalar 1 ERROR Non scalar res used in expression Constants NumPixels gt Bad value expression Setting the value in a file based input template 0 WARNING DataFile Alpha gt A data object in a input template may not have a value expression The value expression will be ignored Cannot
125. g the Heat flux Map To open the heat flux map see Figure 1 6 type xplorer map heat flux map Figure 1 6 Map for a Heat Flux The map contains six modules which have these functions ZatFunction reads in a program script that sets up a heat source and a heat sink and generates the time varying temperature distribution around them DisplaceLat displaces the 2D lattice temperature data to create a 3D visualization of the way in which the temperature changes over time GenerateColormap colormaps the temperature lattice by value LatToGeom converts the displaced lattice data into a surface geometry Legend produces a scale showing the temperature gradient Render displays the surface and the legend Note A lattice is an IRIS Explorer data type which is used to store an ordered array of data For more information see Understanding IRIS Explorer Data Types in Chapter 2 1 4 2 Experimenting with the Heat flux Map LatFunction reads in a short program written in the Shape language which is described in detail inChapter 10 Module Prototyping with Shape in the RIS Explorer Module Writer s Guide It is a C like language that has capabilities for operating on whole lattices with a single statement The program is saved in a file calledheat flux in usr explorer maps and can be run as often you choose The data passes from LatFunction to Displacelat which displaces the 2D data into a 3D array to show the heat sourc
126. getting the results you want or think you should be getting To do this create an ASCII output template that will write the data it receives to an ASCII file This is the diagnostic template You can then wire up the troublesome input template to the diagnostic output template and create a diagnostic script Create a control panel for it fire the module in a map and read the results from the ASCII file The ASCII file shows the values of entities such as array coordinates and you can examine them for errors For example you might find that you have the coordinates x 0 y 0 wherex and y should be 8 Hence you have an empty area in the output lattice Once you have found the error you can change the input template to eliminate the error 103 7 14 Using a DataScribe Module with the Map Editor Once you have created a module from a script you can use it in the Map Editor to transform data You can launch the module from the Module Librarian just as you would any other module The default module control panel has two text slots one for the data filename and one for the script filename If you have created widgets for controlling module parameters those will appear as well If you have already built a DataScribe module and merely want to update its script you can save the new script as a script and then type its name into or select it from the module s file browser You should be careful when doing this however If you change any
127. gories only hide them 32 When you choose Update from the Display menu new categories that have not been saved already are deleted To save new Librarian categories see Saving the Librarian Configuration 2 10 2 Moving Modules Around You can move maps or modules from an existing category to a new one by dragging and dropping them in place Items in a category can be ordered by user preference which is not necessarily alphabetical You may want to put frequently launched modules at the top of the list and leave the others lower down Plan the order of your modules before you move them New modules are added at the end of the list and once they are in place they cannot be moved again within the category 2 10 3 Storing Modules on the Shelf The Librarian shelf see Figure 2 2 is a storage area for modules It is like a bookshelf where you place books to which you often refer For example you might stack modules that you use a lot such as Render DisplayImg or modules of your own creation on the shelf Shelved modules are still available from the Module Librarian as well To place a module on the shelf use the drag and drop technique Once a module is on the shelf you can launch it immediately or leave it there to be launched later You can launch it repeatedly from the shelf 2 10 4 Removing Modules from the Librarian Use the Delete option from the Module Launch menu see Figure 2 3 to remove a module or map from a c
128. gure 4 9 The Parameter Function Editor 4 5 1 Running the Parameter Function Editor You run the P Func Editor from the module containing the parameter you want to control Before you can write a parameter function for an input parameter you must have one or more connections from modules upstream wired to its port Figure 4 10 Module Pop up Menu To display the P Func Editor window 1 Select a module that has at least one input parameter connected to an upstream module 2 Click on the title bar of the module control panel and select P Func Editor from the pop up menu seeFigure 4 10 The title bar of the P Func Editor see Figure 4 9 displays the name of the module for which you are creating the parameter function The window also has these components The Input Parameter option menu displays all the input parameters to the module If the module has more than one parameter you can select a different one to work with from the option menu The Connections box lists all the connections to this input parameter from other modules in the network The Variables box shows a short unique alias for each incoming connection The alias simplifies the task of entering the parameter function into the P Func Editor The Parameter Function box shows the expression defining the relationship between the upstream parameters and the selected parameter The Message box displays a message after you click on Check or Apply It will
129. has been selected replace it together with all other selected modules You can also use the Replace option on the control panel s pop up menu to affect a single module Example 2 2 Creating an Incomplete Map This example illustrates the first steps in creating a map 1 Launch these modules from the Module Librarian by dragging and dropping each one in turn into the Map Editor aReadLatmodule to read data in a lattice format aContour module to create a contour plot of the lattice data aGenerateColormap module to colormap the contours according to value a Render module to visualize the contoured data You now have the basic components of a map in the Map Editor 2 Save these modules as a map by selecting Save All from the Module Librarian File menu This will pop up a file browser 3 When the file browser appears in the Selection type in slot enter the name of the file in which to save the map You can change directory by editting the Filter type in slot Note A map name must have map as a suffix for IRIS Explorer to recognize and treat it as a map for example incomplete map When you have typed in a name click on the OK button 4 Now destroy the modules in the Map Editor by selecting the Destroy All option from the Map Editor s Edit menu This will allow the saved map to be loaded onto a clean slate 5 To load the saved map select the Open option from the File menu in the Modul
130. he Array Component Dialog window click the right mouse button on the component menu button of any array glyph Initially the component menu contains only one entry lt New gt When you click on lt New gt the Component Dialog window appears see Figure 7 31 You use this window to select the subset of the original array in which you are interested Use the Name slot to call the component anything you like for example xValues for the x values of a 2D array You use the matrix of text type in slots to specify the region of the array that you have selected The From and To slots contain the starting and ending values for the data subset Figure 7 31 Array Component Dialog Window The Stride slot indicates the step size For example if the stride is 1 each consecutive value in the specified sequence is taken If the stride is 2 every second value is taken There are as many rows of slots as there are dimensions in the array two in Figure 7 31 arranged in order with the slowest varying variable first The default specifies all areas of the array but you can change the information in any of the slots see the following examples You cannot change the variable order however Note If the data component is nested within the structure of the item you must promote the fragment to the top level of the glyph This technique is illustrated in the examples below Example 7 4 Using the Component Dialog Window This example illustrates how
131. he arguments skm gt 1 2 3 To launch a module skm gt start ReadImg White space separates operands and operators White space is generally just the space character but may also be the tab or newline character Non numeric constants should be surrounded by double quotes Numeric constants do not require quotes Footnote Non numeric constants without embedded spaces may actually be preceded by a single quote Only strings containing embedded spaces need be surrounded by double quotes Assignment is performed with the define command To define a variable called var and assign it the value 3 write skm gt define var 3 To change its value write skm gt define var 4 To display the value of a variable type the name of the variable at the prompt without parentheses skm gt var 4 B 1 1 The Skm Data Types The basic Skm data types include numbers symbols strings lists procedures There is no distinction between real and integer numbers in Skm all numbers have floating point precision Symbols are identifiers that are preceded by a single quote For example var is a symbol below define var foo 112 Strings are character sequences surrounded by double quotes String operators are discussed in a later section Lists are sequences of identifiers surrounded by parentheses Procedures are discussed in a subsequent section Any variable in Skm can be used to contain any data type Thus
132. he capabilities of the module core via two main channels the input and output ports which allow you to pass data into and out of a module and between modules in a map see Wiring Module Ports Together They appear on the micro and Diminutif M forms of the control panel the widgets including buttons dials and sliders which allow you to set module parameters see Setting Module Parameters They appear on the Diminutif and full scale forms of the control panel The control panel also has atitle bar which contains the module name and access pads for the input and output ports seeFigure 2 6 Sizing buttons for enlarging or closing down the control panel 3 pop up menu which provides access to the module help files parameter function editor and other control options see Figure 2 9 Figure 2 6 Micro Control Panel Title Bar Selecting a Module Before you can move or save a module or use any of the Edit Menu operations on it you must select it To select a single module click on the module title bar with the left mouse button The title bar and both access pads are highlighted You can move the module around the Map Editor by holding down the left mouse button and dragging the mouse To select more than one module at a time you can lasso them by clicking in the background of the work area holding down the left mouse button and sweeping out a rectangle that encloses the desired modules When you release
133. hs The word in the termination slot on each glyph size size and Here indicate the point at which each pattern ends Figure 7 25 An Input Template Using Patterns 7 8 1 Using the Glyph Property Sheet Once you have created a template and defined the characteristics of each glyph in it you may want to change a property such as the name or data type of the template or of a glyph in it You can also annotate a complex script by adding comments on the templates glyphs and glyph components in the script These notes can save you time in the future To edit or annotate a template or glyph highlight it by clicking on its icon then select Properties from the Edit menu The Glyph Property Sheet is displayed The fields on the Sheet differ for each glph type Figure 7 26 shows the Glyph Property Sheet for a glyph VolumeData in a template ArrayFile 93 Figure 7 26 The Glyph Property Sheet Glyphs have limited space for names limits and values A property sheet shows more detailed information about them as well as providing a field for notes and comments such as the data format the data source any anomalous behavior to watch out for or why this data is important formatting information for ASCH files For more details about using the ruler in the Property Sheet see Converting Formatted ASCII Files Every time you make a change on the Glyph Property Sheet click on Apply to update the glyph or template Changes to the Pro
134. hs either lattices or other data types to an ASCII or binary template that already contains an IRIS Explorer lattice glyph DataScribe will issue a warning message if you try To convert two or more lattices in ASCII or binary format you must place each lattice in a separate template file You can place any number of lattices in an IRIS Explorer template for conversion to or from the IRIS Explorer lattice format but IRIS Explorer templates accept no other glyph type Each lattice glyph that is placed inside an IRIS Explorer template appears as a port in the module The port will be on the input or output side depending on which side of the script the template appears The name of the lattice is used as the name of the port To see an example of a module that manipulates lattices look at the Swap module in usr explorer scribe which accepts a 2D image lattice that consists of a sequence of RGB bytes swaps the contents of the red and blue channels and outputs the modified lattice 87 7 6 3 Reading in Binary Files The usr explorer scribe directory contains two example modules that handle binary files LatBinary reads in an ASCII file containing a 2D array in and outputs a 2D uniform lattice as well as the data converted to binary form The data is in usr explorer data LatBinary data ReadBinary reads in a 2D array from a binary file and outputs the data as a 2D uniform lattice You can use the data file generated by LatBinary as a sam
135. icePrint define m5 start ReadtstLattice define m6 start WritetstLattice set param m6 Filename foo foo define cl connect ml Output m2 Input define c2 connect m2 new m6 SuperLattice define c3 connect m2 new m4 SuperLattice define c4 connect ml Output m3 Input define c5 connect m3 new m6 SuperLattice define c6 connect m3 new m4 SuperLattice define c7 connect m5 SuperLattice m4 SuperLattice define c8 connect m6 Filename m5 Filename disconnect c8 fire ml fire m5 Saving a Script To use the script save it with the skm suffix for example Testlat skm then start IRIS Explorer with the command explorer script Testlat skm 6 1 3 Advanced Uses Skm is a comprehensive language that provides the capability for creating much more sophisticated scripts than are described in this chapter For more information on the Skm language syntax read Appendix B The Skm Language 6 2 Using the Skm Commands You can use the Skm commands to manipulate modules and maps in the Map Editor Some of the commands let you emulate options available from the Map Editor and module pop up menus Using a Skm script you can 75 launch a module and start maps and applications fire a module enable and disable selected modules or complete maps switch execution highlighting on and off destroy selected modules or
136. iddle mouse button 2 9 3 Dials Dials are circular widgets that allow the continuous adjustment of a parameter value between set limits see Figure 2 21 Like sliders each dial has a title and slots showing minimum maximum and current values You can type new values into any slot remember to press lt Enter gt and you can also change the current value by turning the dial pointer Dials generally have float values Figure 2 21 Dial Widgets The dials have a vernier action in that you can use the pointer for coarse settings Place the cursor on the pointer and push it clockwise or counterclockwise while holding the left mouse button down The values change linearly from minimum to maximum through a single revolution of the pointer To make a fine adjustment to the parameter value place the cursor on the dial center and push it clockwise or counterclockwise The values increment or decrement in minute steps and the inner dial revolves 50 times for one revolution of the pointer This is useful for fine tuning adjustments to a parameter that spans a large range of values or one that increments its value in minute steps 2 9 4 Text Type in Slots Text type in slots see Figure 2 22 accept alphanumeric characters Figure 2 22 Text Type in Slots 30 To type in data values or filenames click once or twice in the slot until the upright text cursor appears If necessary the slot scrolls to the left to give you enough room for yo
137. ighlighting disappears indicating that the connection has been made see Figure 2 13 The number following the data type on the port menu indicates how many connections the port has Figure 2 13 Making Multiple Connections To connect an input port to the output ports on several different modules follow the same procedure 2 5 4 Disconnecting and Reconnecting Modules You may wish to disconnect a module or a number of modules completely from the map or you may wish to simply break a single connection between two modules To break a single connection between two modules follow these steps 1 Choose either of the modules in the linkage and click on the access pad of the wired up port The cascaded port menu shows the name of the other module port connected to it see Figure 2 13 2 Select the connected port by clicking on its name not on the lt Conneci gt bar The connection between the modules is broken and the blue wire disappears This method is useful if you wish to break only one connection If you wish to break all a module s connections then it is easier to disconnect the module rather than breaking each connection in turn There are two ways to disconnect a module you can use the Disconnect sub menu from the Map Editor Edit menu to break the connections of a selected 23 module or a number of selected modules There are three options to the Disconnect sub menu All breaks all connections Input breaks
138. in accordance with C syntax for string constants The input string must contain a valid and complete Skm expression You may not start an expression in one call and finish it in a subsequent call as for instance in this example cxScriptCommand start ReadImg cxScriptCommand at 100 100 However multiple independent or nested expressions can be sent in a single call char string define a 1 define b 2 exScriptCommand string Multiple calls can be made as long as each one contains independent expressions cxScriptCommand define a 1 cxScriptCommand define b 2 Calling cxScriptCommand results in a message transmission and several context switches Where it is possible to bundle expressions in a single string performance will be improved Some validity checking is done before the script is sent to IRIS Explorer If cxScriptCommand returns a 1 then the validity test failed and no script code was sent Currently the validity test will fail if the string contains no parentheses or an uneven set of left and right parentheses Normal interpreter output for commands issued by modules is suppressed Only those error messages generated as a result of module script commands appear on IRIS Explorer s stderr Thus input that is valid when the user types it at the gt prompt is not valid when generated by a module in particular querying the value of a variable if the query is not in paren
139. in see Example 7 6 Figure 7 42 shows the script with its input and output templates Scripts may become very complicated as you strive to find ways of dealing with complex data Figure 7 42 Writing a Formatted ASCII File Figure 7 43 shows the ruler for the output array with its three icons The Scalar icon defines a portion of the output line to be filled in with a numerical value contained in the array Note that this produces E formatted float and double numbers so a length of at least 9 must be specified The String icon delimits a character field The Tab icon indicates where tabs should go into the output line String icons can be resized and positioned just as Scalars can To set the value of the string you can type directly into the icon once it is resized The scrollbar at the bottom of the ruler allows you to traverse the length of the line up to 132 fields Only a small portion of the output line is shown in the default Property Sheet at any given time However you can resize the entire window to reveal the entire line Figure 7 43 An Output Array Ruler Example 7 8 Building a Curvilinear Lattice Reader The module for this example dsCurvEx mres resides in the directory usr explorer scribe on your system The data is located in usr explorer data scribe dsCurvEx data The example shows a file of data points with x y and zoordinates and a value for each data point organized as a 3D array of data The data file lo
140. inate system Aerodynamic simulations commonly use it Each node in the grid has nCoordVar values that specify the coordinates For example the coordinates for a 3D curvilinear lattice can be a set of 3D arrays one for each coordinate direction The length of the coordinate array is determined by the number of coordinates per node The curvilinear lattice glyph has a vector for both data and coordinate values The data type in the vector determines the data type of the data and coordinate values respectively in the lattice Coordinate values for curvilinear lattices are stored interlaced at the node level in the Fortran convention the reverse of the uniform and perimeter formats Figure 7 19 A 3D Curvilinear Lattices The fourth type the generic lattice see Figure 7 20 is a convenient boilerplate lattice for use in input templates only It determines the primitive data type the number of data variables and the number of coordinate values from the actual lattice data The node types are always scalars you cannot use any other data type The generic lattice provides a level of abstraction one step above the closely defined uniform perimeter and curvilinear lattices The advantage of using a generic lattice is that you can be less specific about the data and coordinates and IRIS Explorer does more of the work The disadvantage of using it is that you get only a long vector of data with lengths for coordinate information For a more detaile
141. ing Modules gives detailed instructions for using some of the more useful or complex IRIS Explorer modules including loop controllers Chapter 4 Editing Control Panels and Functions describes the Control Panel and the Parameter Function P Func Editors used to create module control panels and parameter functions Chapter 5 Creating Groups and Applications describes how you can encapsulate a collection of modules into a single group and create an application from it Chapter 6 Scripting explains how to write scripts in the IRIS Explorer Skm language Chapter 7 Using the DataScribe explains how to convert external data into and out of IRIS Explorer data types through a DataScribe interpreter module Appendix A Configuring Your IRIS Explorer Environment describes how each of the IRIS Explorer menu options works AppendixB The Skm Language provides information on basic system configuration Some of the examples are complete and some are fragmentary Maps for all the examples are included with the IRIS Explorer software The companion volume to this guide is the IRIS Explorer Module Writer s Guide which provides information on how to build your own modules with the Module Builder In addition documentation for all IRIS Explorer modules is provided on line as man and help pages for each module Similarly the specification for each of the IRIS Explorer Application Programming Interface API routines is av
142. ing in one direction may differ from that in the other direction s A 2D image is a classic example of this lattice type Coordinate values in a uniform lattice are stored as floats in the C convention using row major format Figure 7 17shows how a uniform lattice is represented in the DataScribe The minimum and maximum values in each direction contained in the 2D Array called bBox1 define the coordinate mapping The data type in the nested data vector which is a float in Figure 7 11 is important because it determines the data type of the data values in the lattice Figure 7 17 A 3D Uniform Lattice The second type the perimeter lattice is an unevenly spaced cartesian grid Finite difference simulations frequently produce data in this form A perimeter lattice is similar to a uniform lattice in layout it differs only in the arrangement of its coordinates see Figure 7 18 You must define a vector of coordinate values for each coordinate direction If the lattice is 2D with three nodes in the X direction and five nodes in the Y direction the lattice will have eight coordinates The number of coordinates is the sum of the lattice dimensions array in this case dims 1 dims 2 dims 3 Coordinate values in a perimeter lattice are stored as floats in the C convention using row major format Figure 7 18 A 3D Perimeter Lattice 91 The third type the curvilinear lattice is a non regularly spaced grid or body mapped coord
143. integers in an input template and you want to connect them to a vector in an output template you can create a set that contains the integers in the input template You can then wire the set in the input template to the vector in the output template If you connect incompatible data items the DataScribe displays a warning message and the script may fail if you try to run it as a module Some wiring combinations may produce misleading results and the DataScribe may display a warning when the script is parsed In particular you should be careful when The data source is larger than the destination For example if you connect a five node set to a vector that is expecting three values the first three nodes of the set will be transmitted and the fourth and fifth ignored The source data is truncated to conform to the destination size The data destination is larger than the source For example if you wire a five node vector to a 5x5 node 2D array only five values will be filled in the 2D array 95 and the rest will be set to zero The destination is only partially filled with the source data Example 7 3 A Wiring Exercise This example expands on the previous one Example 7 2 to create a script that reads in the file with patterns see Figure 7 30 A copy of this script saved as a module called dsPatEx mres resides in usr explorer scribe The data file is located in usr explorer data scribe To build the input and output t
144. invoke myrsh x bob lt shell command to start the LC gt If the word HOST appears in the alternate command the hostname is substituted in its place when executing the command Therefore you can use the command host bob command rsh HOST 1 joe to start a remote LC under the account joe on bob A 2 IRIS Explorer Environment Variables You can set this environment variable EXPLORERHOME By default the IRIS Explorer system is installed into the directory usr explorer If you choose to move the directory elsewhere for example because you need the disk space then you will need to define a UNIX environment variable named EXPLORERHOME Normally this is not necessary A more reliable way to keep IRIS Explorer elsewhere is to place a symbolic link from usr explorer to the correct location There are also several environment variables that pertain to the building and installation of new modules They are described in Chapter 2 Understanding the Module Builder in the IRIS Explorer Module Writer s Guide A 3 Remote Execution and Passwords In this release IRIS Explorer uses the rsh command to start local communications servers LC on remote machines This takes place only the first time you create a librarian or launch a module on a remote machine In order for IRIS Explorer to be able to start LCs rsh to those machines must work For example if you want to launch modules on a host named labserver verify that you have acc
145. it in the number add one more space If you have formatting problems check your spacing The DataScribe does not support hexadecimal or octal numbering for example 0x186 hex or 0768 oct It also does not support commas or D format for example 1 0d 05 in Fortran Example 7 6 Reading the Formatted File This example describes how to use the ruler in the Glyph Properties Sheet to set the format of an ASCII file in the DataScribe Here is an example of a formatted ASCII file Sample Formatted Data Resolution is 8 10 12 Data Follows xcoord 0 000 ycoord 0 000 zcoord 0 000 temp 0 375 pres 0 375 xcoord 0 143 ycoord 0 000 zcoord 0 000 temp 0 432 pres 0 432 xcoord 0 286 ycoord 0 000 zcoord 0 000 temp 0 403 pres 0 403 xcoord 0 429 ycoord 0 000 zcoord 0 000 temp 0 295 pres 0 295 The script shown in Figure 7 40 reads the five arrays in this file three coordinate arrays and two data arrays To read this file into IRIS Explorer you must extract the resolution vector define the rest of the header with a pattern glyph and read the five arrays separating the character filler from the data You use a 2D array in the input template for reading in the data with five components defined for the x y and z coordinates and the two data values You need to set the formatting shown in the input template in the 2D array Property Sheet Bring up the Property Sheet by selecting Properties from the Edit menu The Glyph
146. iterate if you change one of its widgets In addition any module outside the loop or upstream of the loop controller can start the loop If you have a Repeat loop where the controller is at the end of the loop this includes modules in the loop as well upstream of the loop itself In a While loop upstream modules are all outside the loop If a frame results from a parameter change in a module inside a loop the While controller will not restart the loop whereas the Repeat controller will because the frame came from upstream This is important when for example Streakline is in a loop with Render If a parameter changes in Streakline Render can keep the loop going Controller modules such as While and Repeat pass their data through like a transistor turning off the flow by sending a sync frame when their Condition port parameter becomes zero Other controller modules like Render do not really control iteration but need to be control modules in order to support their normal wiring paradigms such as picking in the Render QueryLat map see Figure 3 27 Render needs to be a Repeat controller so that any module in the loop can start the loop 3 8 4 Wiring a Loop When you wire a loop in a map you must include a loop controller module in the loop If you try to close a loop without a loop controller you will get a message saying the connection has failed because there is no controller present You can have nested loops mul
147. le 4 2 For example if you have parameters A and B coming in as doubles and you require them in integer form you can cast them to type long as follows long A long B Using Strings You can feed string parameter values to the P Func Editor Strings are groups of alphanumeric characters The only operator you can use on strings is The expression string A string B indicates concatenation of the two terms You can also create an expression of the form string long 3 3 8 9 in which case IRIS Explorer returns the a string of the value of 12 You can add like terms only For example the expression A string B will produce an error If a string is not a number it goes to zero If it is a number it returns a value For example double 7 3 returns a double Combining Functions You can create more complex expressions using several functions Here are two examples min sin A 3 14159 180 0 cos B 3 14159 180 0 and If sin A lt 0 then this If sin A gt 0 then that lse the other 61 Linking Independent Parameters The upstream connections supplying the values for the P Func variables need not be related i e they can come from unrelated modules or the same module it does not matter If they come form different modules then there is no relationship between A and B the parameter function relates A and B to the input parameter independently of each other 4 5
148. les Listed by Function 3 2 Creating Colormaps When you are looking at large amounts of data it helps to be able to distinguish significant features easily and a convenient way to differentiate a range of values is by using color The GenerateColormap module control panel see Figure 3 1 lets you select a color space manipulate the color bands and send the results to Render where the visualized data object is colored according to its data values Figure 3 1 The GenerateColormap Module GenerateColormap has two input ports both of which accept the lattice data type and several input parameters that are connected to widgets on the module control panel The first input port accepts a colormap which means you can read a colormap data file that contains preset parameters into the map The volume map in Chapter 1 provides an example The second input port accepts data in the form of a lattice which means you can feed a lattice into the colormap to set the minimum and maximum limits of the domain Both these ports are optional The output port produces a colormap in the form of a 1D lattice You can connect GenerateColormap to any module that has a Colormap input port These include BallStick Contour LatToGeom PyrToGeom and VolumeToGeom Note You can have several GenerateColormap modules in a map if your X server contains enough entries in its colormap table See Running the X Server in Appendix A for more information 38 3 2 1 R
149. lete options default to Move after every insertion or deletion of a point To add a new control point to a color band select Insert from the Edit Mode option menu and click on the color band at 39 the place where you want the new point The point is centered between the existing points on that segment of the color band Move it by dragging on it The closer together the points are the more precise the changes that you can make to the shape of the curve However you cannot move a point past the one to its left or right To remove an existing control point from a color band select Delete from the Edit Mode option menu and click on that control point Note You can delete any point except the endpoints Using Slope Control Points Each control point except the end points has two empty squares associated with it which control the slope of the curve at a given point They are the derivatives of the curve at that point When you select a control point by clicking on it the slope control points appear on either side see Figure 3 3 They disappear when you select another point Figure 3 3 Slope Control Points To alter the slope of the curve in the vicinity of a point click and drag on the slope control points If you want to sharpen the curve toward the lower boundary of the window and the position of the slope control point blocks you simply add another point to the line near the first point and use its derivatives to alter the
150. ll output text strings describing their data Other modules may also produce messages in the course of a map cycle all of which are logged by IRIS Explorer You may be interested in seeing all generated messages or only those put out by a particular module 2 7 1 Logging Map Data The Map Editor Log window captures all the messages generated by modules in the Map Editor It is a read only scrolling text window that typically appears below the Map Editor see Figure 2 16 Messages in the window scroll upward with new lines inserted until the size limit of the Log is reached After that lines are deleted The Log lists the output from each module as it occurs with the name of the generating module as a prefix to each line Figure 2 16 The Map Log Window You can hide or display the Map Editor Log by toggling the Log Window option on the Map Editor Layout menu 2 7 2 Logging Module Data To see text messages for an individual module without having to reviewing the entire Map Editor Log you can open and examine a Module Log see Figure 2 17 Each Module Log displays messages generated by that module alone Open the Module Log by selecting Show Log from the module pop up menu see Figure 2 9 Figure 2 17 Module Log Window 26 2 7 3 Reviewing Log Messages You can cut and paste the information displayed in the Log windows into other windows By selecting the Editable Log option from the Log window pop up menu see Figure 2
151. lly rendered from the buoyancy a quantity used in the equations for vertical velocity It represents the instantaneous effects of temperature moisture and water mixed with ice on the velocity acceleration and is large at and above the top of the storm A wavy appearance is evident indicating the presence of strong gravity waves Yellow green indicates relatively high buoyancy blue indicates relatively low buoyancy The effect is roughly similar to throwing a rock into a pond but here it is the storm growing into the upper atmosphere You can change the opacity values on the colormap to affect the look of the volume rendering see Chapter 3 Creating Colormaps You can lower the opacity of a range of colors to make them more transparent and let you see other aspects more clearly You can increase the opacity of a color to emphasize a feature 1 7 Computational Fluid Dynamics This example illustrates how you can use IRIS Explorer modules to study the dynamics of air flow over the nose of an aeroplane The cfd map shows variations in air density surrounding the surface of the aeroplane The map generates an air flow field around the plane extracts 2D slices of the volume and colormaps them by density 11 value thus providing a means of examining different areas of the field The CFD group at Silicon Graphics created the plane from a model aeroplane by a digitized 3D scanning process and the air flow data was generated fro
152. m NASA s fluid dynamics program ARC3D Footnote US Public Domain Software For more information see Pulliam T and Steger J Implicit Finite Difference Simulations of Three Dimensional Compressible Flow AIAA Journal Vol 18 No 2 Feb 1980 pp 159 167 1 7 1 Opening the Cfd Map To open the cfd map see Figure 1 17 type explorer map cfd map The map contains nine modules ReadLat reads in the air density data file TsosurfaceLat generates an isosurface from the air density data OrthoSlice extracts the density near the plane s surface ProbeLat creates non orthogonal slices of the air density data TransformGen sets the orientation for the ProbeLat slice PyrToGeom converts the slice data from ProbeLat to geometry GenerateColormap creates a colormap for the density data LatToGeom converts the slice data from OrthoSlice to geometry Render displays the isosurface and the slices 1 7 2 Experimenting with the Cfd Map OrthoSlice see Figure 1 15 operates on the air density data to produce a curvilinear grid depicting the density field around the plane The slice number is 1 the minimum and this index increases in a direction normal to the plane s surface For J the grid actually lies along the surface of the plane Figure 1 15 OrthoSlice Control Panel You can change the slice number while holding the axis constant and see the grid move out from the plane surface As you vary the slice numbers y
153. matching port from the port menu Once you click on the second port the highlight disappears and a blue wire is shown running between the ports signifying that a connection has been made To cancel an incomplete connection when only one port has been selected click on the background of the Map Editor You exit the wiring mode automatically once a connection has been made Figure 2 12 Making Connections between Modules 2 5 3 Connecting Several Modules You can wire more than one input port to a given output port and vice versa provided that the data types on the ports are compatible This is called fanning connections out and in Figure 2 13 shows a ReadLat module with two connections on its output port one to the input port of Contour and one to the input port of Isosurface To make these connections 1 Select the output port of the module you want to connect ReadLat in Figure 2 13 2 Select the input port of the second module sosurface in this case A connection is made between the first and second modules ReadLat and Isosurface Select the input port of the third module Contour in this case 4 Then select the output port of the first module ReadLat again This port now has one other connection to it The cascaded port menu shows the names of the output module and port already connected below a lt Connect gt bar Click on the lt Connecf gt bar to add the new output port to the list in this case DiffLat The h
154. me The 12 bit TrueColor visual displays 4096 colors at one time with 4 bits for red green and blue Choosing the best visual depends on your workstations hardware and the other applications you run Your workstation must have at least as many bit planes as the depth of the visual that you choose You generally want to run the 24 bit TrueColor visual if you can otherwise try the 12 bit TrueColor or PseudoColor visuals High quality applications should run properly with any of these visuals but other applications may not Some applications such as those that do color table animation may not run with a TrueColor visual Some applications may make assumptions about the depth of a PseudoColor visual for example that the color index will fit into 8 bits You can start with the highest quality visual supported by your workstation try your other applications and then adjust the visual to fit your system s capabilities Note See your local documentation on how to reconfigure the X server 111 Appendix B The Skm Language This appendix describes the syntax and use of the Skm language to create scripts for the IRIS Explorer command interface B 1 Skm Syntax The Skm scripting language uses prefix notation All expressions are enclosed in parentheses and all commands precede arguments and operands If you want to say do something the Skm expression is skm gt do something To add two numbers the addition operator precedes t
155. mg FourierCrossCorrlmg FourierGaussFitlmg FourierMultImg GaussBlurlmg HistNormlImg LaplaceEdgelmg Maxlmg Minimg Orlmg Readimg SGI Palettelmg SqRootlmg Threshlmg Zoomlmg Addlmg Blendlmg CompassDirlmg Displaylmg ForwardFFTImg FourierDivimg FourierMagnitudelmg FourierPhaselmg GrayScalelmg HistScalelmg Loglmg MedianFltlmg MultImg Powerlmg RobertsEdgelmg Sharpenimg Squarelmg Writelmg Andlimg Blurlmg CompassImg Divlmg FourierConjgimg FourierExpFltlmg FourierMergelmg FourierPwrlmg HistEquallmg InverseFFTImg MaxFltlmg MinFltImg Neglmg RankFlitlmg RotZoomlmg SobelEdgelmg SubtractImg Xorlmg Table 2 3 Image Processing Modules 2 9 Setting Module Parameters Module parameters allow you to set and change scalar values for each module For example a parameter called Min Range that accepts integers may let you set the minimum value for a range of temperature values for the module Parameters are controlled through widgets on the module control panel Widgets are mechanisms for regulating a module s parameter values The parameter names are given on the module s input port menu and on the full scale control panel A single control panel may contain a number of widgets each controlling a different parameter Widgets include buttons sliders dials text slots scrolled lists radio buttons option menus and file browsers as well as drawing areas 29 2 9 1 Buttons Buttons are rectangular or diamond
156. mod in list validates its arguments by checking both the target module name and the list of modules to make sure they are not NULL The procedure assigns the first element of the list to the temporary variable m using a let statement and compares it with the target module name If equal the procedure returns t true If not equal the procedure continues the search by recursively calling itself with the target string and the module list is reduced by having the first element removed Here is an improved version of mod exists that performs some error checking on its arguments define mod exists procedure modname if null modname then print mod exists null arg else if not string modname then print mod exists supplied with non string arg else mod in list modname all mods As defined mod exists works only when given a module name as a string B 4 3 Known Bugs Launching a module on a remote machine with the on argument to the start command will not work the first time if no Module Librarian has been created for that machine and if no prior module has been launched on that machine in the current IRIS Explorer session When such a module fails to launch it will as a side effect cause a Module Librarian to be created for that remote machine After a few seconds have passed and the Librarian is present subsequent attempts to launch modules on that machine should succeed Parentheses
157. n be generated by one of several functions The default is sines which fills the data space with the product of sine functions evaluated over a certain number of cycles in each dimension The other functions are Random data Ramps modulo function Simulated gravity wells DataVec Length indicates the number of components at each node of the lattice 3 3 2 Displaying a Lattice To display lattice data in IRIS Explorer you can cut a slice using any of the three slicers see Slicing Volumetric Data create an isosurface with IsosurfaceLat see Figure 4 15 in Chapter 4 create contour lines using Contour see Figure 4 15 create vectors using VectorGen Since Render accepts only Geometry data you must wire modules that produce lattice or pyramid data to LatToGeom VolumeToGeom or PyrToGeom which in turn can be connected to Render You can also send a lattice directly to DisplayImg Figure 3 4 shows a lattice passed directly to LatToGeom 3 4 Slicing Volumetric Data A useful way to examine data is to make a 2D cut through a 3D volume that is to slice the volume and look at the data in that slice There are several ways to do this depending on the type of data you start with and the results you want to produce Table 3 2 shows which slicers you can use for each combination of lattice types Input Output Unif Perimet Curvili Uniform OrthoSlice Slice 42 Perimeter OrthoSlice Curvilinear O
158. nction To create a parameter function 1 Connect IsosurfaceLat s Threshold output to Contour s Max Level input port 2 Bring up the P Func Editor for Contour see Figure 4 12 Select the Min Level parameter from the Input Parameter list 3 A connection for sosurfaceLat Threshold appears in the Connections box This connection is defined asA in the Variables box 4 Select the Parameter Function box by clicking in it then type Be S Click Apply at the bottom of the Editor window to implement your modification 5 Similarly select the Max Level parameter from the option menu and type A 1 8 Click Apply again Figure 4 12 Parameter Functions for a Module Close the P Func Editor and save the modified map under a new name 62 Now when you move the dial on sosurfaceLat Contour fires as well Set the number of levels in Contour to 2 or 3 and see what happens The image should resemble that in Figure 4 13 The values of the contour lines therefore are always 30 to 80 higher than the isosurface threshold Figure 4 13 Simple Example with a Parameter Function If you click on the Check button the P func Editor tests the function you have entered to make sure that it is valid and prints a message in the Message pane The Editor window stays open For example the second expression in the Parameter Function pane in Figure 4 14 has been entered incorrectly Figure 4 14 Messages in the P Func Editor 4 5
159. necting dissimilar data items between templates 7 10 1 Ordering Variables in a Script Symbols are defined sequentially within a script and one variable can reference another only if the referenced variable is declared first The DataScribe traverses files including data files from top to bottom and left to right Hence if you want to use a variable to set the limits of an array or as a selection index for a sub array in a template you must define the variable before you use it You can define the variable ina Parameters or Constants template in which case this template must precede the file template in which the variable is used for example see Figure 7 30 earlier in the file template itself or example see Figure 7 45 You can use any variable in any template if it has been previously defined 7 10 2 Connecting Data Items Between Templates There are some basic rules for wiring together data items between input and output templates You can legally wire ascalar to a scalar aset toa set setto an array an array to an array of same or differing dimension This works if there are the same number of values in each data item Since a set has no shape however an ordering mismatch can occur even if the count is correct If you wire a scalar value into a non scalar data item such as an array then you will associate the scalar value with the first item of the array If you have some scalars for example
160. nerateColormap by turning the Min Domain and Max Domain dials Each dial has two text slots that you can use to define the range for minimum values and maximum values To change a domain value min max or current click on the text slot to highlight it and type in the new value then press lt Enter gt The new value appears in the text slot and in the scale window Selecting a Color Band You can edit only one color band at a time To select a color band 1 From the Color Space option menu select RGB or HSV depending on which system you want to use 2 From the Color Band option menu select the color band you want to adjust Inthe RGB color space your options are Red Green Blue and Opacity Inthe HSV color space your options are Hue Saturation Value and Opacity All four bands appear in the editing window In the HSV color space the bands might be superimposed on one another therefore more difficult to see The active band is named on the option menu button and stands out in the editing window because the control points shown as square boxes along the band are enlarged Adding and Removing Control Points You edit color bands by adding control points at intervals along their length and then dragging the points around in the editing window The points appear as filled boxes see Figure 3 2 Figure 3 2 Adding Control Points to a Color Band Use the Edit Mode option menu to add and remove control points The Insert and De
161. new script from scratch you save it as a script The DataScribe automatically appends the extension scribe to the filename you give it If your script has no parameters the DataScribe provides a default control panel and creates another file the module resource file when you save it The module resource file moduleName mres describes the module attributes including its control panel the executable name and all the ports The script file moduleName scribe includes all the templates and their connections Saving Modules with Control Panels You need only create a control panel if you have parameters defined in a Parameters template in your script Otherwise the DataScribe provides a default control panel If you save a script containing a Parameters template and have not yet created a control panel the DataScribe prompts you to do so Select Control Panel from the View menu The Control Panel Editor appears allowing you to assign widgets to each of the glyphs in the Parameters template position each widget and set their current values and ranges For information on using the Control Panel Editor see Chapter 4 Editing Control Panels and Functions Checking for Errors Before you save your script you can check it for errors To do so select Parse from the File menu For more information see Finding and Correcting Errors Creating a Diagnostic Template You can use a diagnostic template to check your script if you are not
162. ng the mouse to move the object in TransformGen s window GenerateColormap colormaps the grid produced by OrthoSlice according to its air density values It is a scalar field with one value at every point The domain in GenerateColormap is set to a density minimum of about 0 7 and maximum of 1 1 This colormap is also used to color the probe surface according to air density values PyrToGeom and LatToGeom convert pyramid and lattice data respectively to geometry which can be displayed by Render Once the data is displayed in Render see Figure 1 18 you can enhance the visualized data by using the Render menus For example click on the background of the Render window to bring up the Render pop up menu Select the Draw Style option and then select wireframe from the cascading menu To return all the surfaces to their original state bring up the menu again and select the as is option Figure 1 18 The Rendered Flow Field The grid isosurface and probe surface are separate objects which can be separately treated in Render For example you could make the probe surface transparent which would reveal the features behind it 13 Chapter 2 Working with the Map Editor This chapter explains step by step how to use IRIS Explorer tools to create and run maps It describes how you launch modules from the Module Librarian wire modules into a computational network or map use the map to visualize numerical data select modules with c
163. nly input and output ports that accept the same data type For example you can connect an output port called Colormap Lattice to the input port called Input Lattice but not to one called Input Pyr Only an output port of type Pyramid is compatible with the latter When you click on an output port to select it all the compatible input ports on other modules in the Map Editor are highlighted in green Likewise when you select an input port all compatible output access pads light up in a different shade of green Incompatible ports are grayed out so they cannot be selected Since a lattice can assume many forms the Map Editor does type checking for types of lattices and lets you connect only those modules that accept and produce the same type of lattice For more information on lattices see Chapter 3 Using the Lattice Data Type in the JRIS Explorer Module Writer s Guide 2 5 2 Wiring Modules Together Wiring modules together is a simple process You can wire input to output port or output to input port Figure 2 12 22 shows a connection from the output port of Contour to an input port of Render To make the connections follow these steps 1 Click on the access pad of the first module and select a port from the cascading menu The access pads on other modules in the Map Editor that have compatible ports are highlighted and you are in wiring mode 2 Click on one of the highlighted pads and select a
164. nnection between two modules dup Duplicate selected modules and groups enable Enable selected modules and groups exec hilite off Turn off execution highlighting exec hilite on Turn on execution highlighting fire Fire selected modules or groups get param Get the value of a module s parameter get pfunc Get the value of a module s P Func help Provide information about command syntax help mod Show module s help page hide widget Hide a module s widget interrupt Interrupt a running module log Show module s log window loop ctlr Test for the active loop controller module loop ctlr capable Test for a loop controller capable module 113 loop ctlr off loop ctlr on main log off main log on maxi at maxi micro mini module module to filename module to host param list paste pause perf report off perf report on pfunc list save select selected mods set app main win set param set param minmax set pfunc show widget start map start quit explorer unmaxi unmicro unselect unselected mods Table B 1 Skm Commands Turn loop controller module off Turn loop controller module on Toggle the Log window off Toggle the Log window on Create a maximized module control panel Maximize the control panels of selected module Micro ize the control panel of a module Minimize the control panel of a module Test a variable for module start information Print
165. o show the control panel of each module in the Map Editor Figure 2 4 shows the map you should see on your screen It visualizes the data in the file usr explorer data attice testVol lat Note On workstations without two sided lighting the isosurface in Render may be dark Change the Flip Normal option on the JsosurfaceLat control panel from No to Yes to display the geometry properly Figure 2 4 A Simple Map Example The simple map is a three module map consisting of ReadLat which reads in a file containing data for a lattice lattices are discussed in Defining the Data Types IsosurfaceLat which creates an isosurface a surface of uniform value in the test volume Render which visualizes the selected isosurface of the lattice All the module control panels are displayed with their wiring connections to one another visible There is also a full scale control panel for Render s volume visualization For more information on control panels see Resizing the Control Panel When you first launch a map all the module title bars and access pads are highlighted in white to show they are selected You can move the entire map by dragging on one title bar Before you can move individual modules you must deselect them Do this by clicking on the background of the Map Editor A module is reselected if you click on the title bar You can 17 Click on the square Maximize button to bring up the full scale control panel o
166. o the Colormap Lattice Opt port of Contour Notice that Contour has two connections on its input pad but they go to two separate input ports 6 Connect the Contours Geometry output port of the Contour module to the Input Geometry input port of the Render module An object appears in the Render window representing contour curves of equal value through the data in the lattice file 7 Move the slider on Contour to create more sets of contour lines 24 8 Break the connection to Render Notice that the contour lines disappear Connect it up again and they reappear 9 Disconnect GenerateColormap from Contour and see what happens If you want to keep the finished map remember to save it again 2 6 Firing Modules When a module is activated it fires and the user function operates on the data it has received from its input ports As the module fires its title bar turns yellow and stays yellow until the module has completed execution The color change is called execution highlighting This highlighting can be turned off by toggling the Exec Hilite option on the Layout menu This might take a fraction of a second or several minutes depending on the complexity of the user function and the amount of data it is processing Firing can occur at several different stages of the map building process A module fires when it is launched in the Map Editor provided it has all the data it needs on its input ports m
167. odules upstream of it in the map fire sending data to it a module upstream of it in the map fires that has a connection to its Fire port one of its parameter values is changed you choose Fire Now from the module pop up menu you connect it to an upstream module which has already fired and produced data on its output port you connect its Fire port to an upstream module which has already fired it is triggered by an external event for example data arrives on a port from an external file or process 2 6 1 Forcing a Firing You can force a module to fire by Selecting Fire Now from the module pop up menu This is useful for modules that have no parameters for example many of the image processing modules or if you do not want to change a parameter value Changing the value of a module parameter You change the value of a parameter by moving the widget that controls the parameter of interest You can turn a dial move a slider up or down or switch a button off or on see Setting Module Parameters Each time you alter a parameter or change a connection in a map in effect feeding in more or altered data values the affected modules automatically fire again This can cause a cascade of firings downstream of the module For an in depth explanation of the mechanism behind module firing see Appendix B of the IRIS Explorer Module Writer s Guide 2 6 2 Using the Synchronization Ports When a module fires successfully a conn
168. oks like this Output from XYZ Simulation Date 11 Sept 1991 Resolution 5 10 15 x coord y coord z coord function 0 10000E 01 0 00000E 00 0 00000E 00 0 50000E 00 101 0 18000E 01 0 00000E 00 0 00000E 00 0 50000E 00 0 26000E 01 0 00000E 00 0 00000E 00 0 50000E 00 0 34000E 01 0 00000E 00 0 00000E 00 0 50000E 00 0 42000E 01 0 00000E 00 0 00000E 00 0 50000E 00 0 50000E 01 0 00000E 00 0 00000E 00 0 50000E 00 0 80902E 00 0 58779E 00 0 00000E 00 0 50000E 00 0 14562E 01 0 10580E 01 0 00000E 00 0 50000E 00 0 21034E 01 0 15282E 01 0 00000E 00 0 50000E 00 0 27507E 01 0 19985E 01 0 00000E 00 0 50000E 00 Resolution gives the dimensions of this dataset of points The dataset is set up as a 3D array of 5 x 10 x 15 points The script for this file contains patterns to skip over the header a vector to get the data resolution a pattern to skip the text line beginning x coord a3D array of vectors for the coordinates and data The coordinates and data are interlaced so you need to unravel them by putting each set of coordinates in the 3D array into a separate output array This means collecting x y and z coordinates into three separate arrays using component selection To do this you create a component at the vector level that contains the first node xCoord and create another component at the 3D array level that contains everything at that level but only xCoord at the lower level This will
169. old down lt Alt gt and 82 click on the glyph You can reorder glyphs in the template by dragging them around and dropping them into the new position Figure 7 5 DataScribe Data Type Palette 7 4 1 Glyphs Glyphs are visual representations of data items that when collected together in various combinations define the contents of each input and output template Each data category is distinguished by the color and design of its glyph see Figure 7 5 Glyphs in the Data Type palette are closed When you drop a closed glyph into the template window it opens into the terse form see Figure 7 6 Note Each time you place a glyph in a template ports are created for each part of the data item that can be wired to another template see Connecting Templates Each glyph in a script should have a unique name DataScribe assigns a default unique name of the form Array 1 Array2 etc to each glyph as it is added to a template You can change this by selecting the name of the glyph using the left mouse button then typing the new name Scalar glyphs have two open forms depending on the template in which the scalar appears Array lattice and set glyphs have two open forms terse and verbose The terse form opens into the verbose glyph which shows the group structure of the glyph in the form of more glyphs see Figure 7 6 Click on the Open Close button at the right end of the slider to toggle between the terse and verbose form of th
170. ommonly used data type Pyramid A hierarchy of lattices with information on how the lattices are connected The pyramid data type is used to manipulate finite element data and molecular data For example data describing a complex organic molecule and a finite element mesh of a car body are both in pyramid format Geometry A collection of geometric primitives including polygons lines and points used to build a visual representation of a dataset For example a contour surface from a CT scan is a collection of polygons The vertices of each polygon can have associated color and surface normals Data is displayed in the Render module in geometry format Parameter A parameter holds a scalar value an integer real number or string The value of a parameter input to a module is controlled by a widget on the module control panel You can also perform arithmetic functions on them using the Parameter Function Editor see Chapter 4 Parameters are used to set values for slicing planes error tolerances quantities and filenames Pick A specialized data type that lets you select an area of an object in the display window of a render or image display module and collect data about the selected area This information can be fed to another module such as a query module It is possible to define new data types in IRIS Explorer and you may find that the input and output port menus of some modules list data types in addition to those described here Those ar
171. ompatible data types change the values of module parameters set parameter relationships in the Parameter Function Editor incorporate modules on remote systems into a map fix some common problems 2 1 Overview In the Map Editor you create an IRIS Explorer map A map is a collection of modules of different kinds connected in sequence which process numerical data to accomplish a task A module is a processing unit in a map Each module accepts data acts on it and sends the result to the next module downstream The Map Editor is the environment in which maps are created and executed or fired Maps can be used to perform a variety of tasks for example generating a visual image from a specific dataset A patient may arrive at a medical clinic with an injured leg The doctor generates a 3D CT scan which shows a compound fracture of the femur The CT scan data can be fed into an IRIS Explorer map and visualized as a 3D or volume image of the bone The doctor may extract a 2D slice from the CT scan data along a plane close to the break in the bone Then if necessary another slice can be taken from a slightly different angle for further elucidation In this way the doctor acquires a unique understanding of the fracture which can help when deciding on an appropriate treatment Data is read into IRIS Explorer by the first modules in a map sequence and the succeeding modules determine what form the results will take and for what range of d
172. onnected and your map is operational the modules fire and an object becomes visible in the Render or DisplayImg window in theory perhaps In practice this does not always happen Here are a few common problems and ways to fix them Note Ifa module port is required then it must be receiving valid data from an upstream module in order to work properly All ports are required unless marked as Opt ional 2 11 1 You Need a Larger Memory Arena than Your System Can Give You A message to this effect may appear when IRIS Explorer starts up It means that you do not have enough disk space to run IRIS Explorer properly You can 1 Clean off your disk to make more disk space for the shared memory arena 2 Create a temporary directory tempdir on another disk on your machine if you have one for details see The explorerre Configuration File in Appendix A 3 Reduce the size of your arena which is the amount of disk space necessary to hold all the IRIS Explorer files before you run IRIS Explorer see the reference in step 2 2 11 2 No Object Is Displayed in the Render Window If nothing appears in your Render window try the following procedure 1 Make sure all the required input ports on each module are connected to upstream modules that can send them valid data 2 Render might be looking in the wrong direction Click the right mouse button in the Render window which brings up a pop up menu and select Functions then View
173. ontrol panel from there In application mode the default behavior is the same that is double clicking dismisses maximized control panels This is fine for secondary windows that may have been exposed under the control of the application itself However if you dismiss an application main window in this manner you cause the application to cease operating This is because there is no visible Map Editor and thus no way for a user to recover the maximized control panel It is a good idea to add Quit to the menu bar on the main group control panel in your application map otherwise the only way to quit an application is through the Motif window menu You can also use the script command set app main win my module 71 to change the default behavior of the main window so that double clicking on the control panel for my module quits the application The user will be asked to confirm the quit operation 5 6 5 Application Busy Indicators In application mode the Map Editor is not visible and so the user does not observe the usual signals that a map is executing such as yellow highlighting and the Busy cursor Instead IRIS Explorer displays a Busy cursor over all control panels when any module in an application is executing Note If you turn execution highlighting off you disable the display of the Busy indicator Debugging an Application To run an application so you can check its development and do debugging tasks at the
174. ontrol panel that contains selected widgets from the constituent modules and only the widgets on this control panel work None of the individual modules or the internal wiring is visible A group can contain several modules and it can also contain other groups You can therefore create a nested hierarchy of modules under a single control panel 5 2 2 Selecting Modules You must select each module before you can include it in a group To select several modules easily at one time use the lasso technique click the left mouse in the Map Editor background and sweep it around the modules otherwise hold down the lt Shift gt key select individual modules one by one The selected modules are saved in the group with the exact relative placement they had when you selected them It is a good idea to arrange modules in as compact a structure as possible before you group them This eases the task of sorting them out if you ungroup them again Once you have grouped modules by selecting Group from the Group menu the modules behave as a single entity and have a single control panel If you select another module then reselect one module in an open group all the modules in the group are selected Likewise when you drag any module in the group they all move together 5 2 3 Creating a Group To create a new group or work with an existing group follow these steps 1 Select the modules you want to group together and click on Group from the Grou
175. ou get information about air densities at the plane surface and in its vicinity High air densities occur at the nose when there is a massive deceleration of fluid As the air flows away from the leading edge and accelerates over the wing the density drops You can also vary the axis If you select the K axis the slice is taken down the longitudinal axis of the wing and produces a cross section of the wing ProbeLat and IsosurfaceLat complement each other IsosurfaceLat generates an isosurface from the air density data This tells you how all the air of a given density is distributed around the plane You can change the threshold the value at which the isosurface is calculated by turning the dial on the control panel ProbeLat see Figure 1 16 probes the curvilinear flow field along an arbitrary axis The slice shows all density values in that region colormapped by value Figure 1 16 ProbeLat Control Panel You can control the area of the slice by turning the Clip Size dial on the control panel You can also change the form the probe takes by selecting a type from the Probe Type option menu InFigure 1 17 the selected probe type is a paddle Figure 1 17 Different Levels of Air Density 12 The axis along which the plane is cut is controlled by TransformGen You can slice in any direction you choose by using the widgets on the TransformGen control panel to set a different axis You can alter the orientation of the probe by usi
176. ou set up a template to bring external data into an IRIS Explorer lattice these are the groupings into which your data should be fitted Component nDim the number of computational dimensions dims a vector indicating the number of nodes in each dimension nDataVar the number of data variables per node primType the scalar type of the variables byte long short float or double coordType the type of physical mapping uniform no explicit coordinates except bounding box coordinates perimeter enough coordinates to specify a non uniformly spaced rectangular dataset curvilinear coordinates stored interleaved at each node nCoordVar the number of coordinate variables per node curvilinear lattices only Table 7 3 Lattice Components Lattice Types There are three IRIS Explorer lattice types defined according to the way in which the lattice is physically mapped The DataScribe however also offers a fourth generic DataScribe lattice which is an input lattice only You cannot use it in an output template Each lattice you include in a script appears as a port in the final DataScribe module If the lattice is in an input template it will appear as an input port and if it is in an output template it will form an output port The first IRIS Explorer type the uniform lattice is a grid with constant spacing The distance between each node is identical within a coordinate direction For a 2D or 3D uniform lattice the spac
177. p menu A single control panel appears for the new group which is closed 2 Use the Group Editor select Edit from the Group menu to promote the ports and parameters you want visible in the group control panel The Group Editor is described fully in Editing a Group 3 Use the Control Panel Editor to provide widgets for parameters in the group control panel The name of the new group module defaults to Group You can rename it anything you like in the Group Editor Group control panels are colored differently from individual modules Example 5 1 Creating a Group in a Map This example illustrates how to select three modules in a map and group them Figure 5 1 shows the original map with all the modules ungrouped It is a typical map it reads two images from disk using two ReadImg modules and filters both images One image is sharpened and the other is edge enhanced with a Sobel filter The resulting images are blended together and sent to Displaylmg The center three modules SobelEdgelmg SharpenImg and BlendImg can be collapsed into a single group to simplify the map Figure 5 1 An Image Processing Map 1 Select the modules and then select Group from the Group menu The default group control panel is shown in Figure 5 2 Figure 5 2 The Closed Group 1 To open the group select the group and then select Open from the Group menu The original modules appear 66 with a red border indicating that they are part of a group
178. parameters from the original set of modules that are not connected to the group control panel cannot be changed without opening the group 5 2 Module Groups A group is a collection of modules that serve a common purpose sharing a single control panel and having some of the parameters of the constituent modules raised to the group level From the viewpoint of the operating system the constituent modules are still separate processes from the user s point of view however they behave as a single entity You create groups of modules that are frequently used in combination or that together form a unit of computation For example you might want to create a map that processes an image using four different parameters each of which resides in a different module When you wire all the modules into the map you get the parameters you want as well as several others you don t need In this case you can simplify the map by creating a group for the four image processing modules This reduces the apparent number of modules and thus wires on screen as well as reducing the number of control panels and widgets 5 2 1 Types of Groups 65 Groups have two forms open and closed An open group retains much of the character of the constituent modules All the modules and their wiring connections are visible and their controls are operational The constituent modules are outlined in red A closed group takes on a new character It has a single c
179. pects 5 6 2 Saving the Application You must make sure that any map saved for later use as an application has at least one open control panel that is maximized to its full size otherwise nothing will be visible when you run the application In application mode the mini control panels are not visible and there is no way to maximize a module control panel You can save a map with more than one control panel maximized if you wish To save the map select Save Selected from the File menu on the Module Librarian Save each map with a name and the suffix map 5 6 3 Running an Application You can run an application using the command app To open and use a standard application at the shell prompt type explorer app applicationname map When you run an application only the application control panel is displayed on the screen The IRIS Explorer window the Map Editor window and the Librarian are not displayed 5 6 4 Quitting an Application Applications generally have a main window which is a control panel that must be visible for the application to work properly The Motif window Quit command is issued to a window when the user double clicks in the upper left hand comer of the Motif window frame When IRIS Explorer is running normally not in application mode the double click merely dismisses maximized control panels The user can still access the corresponding mini control panel in the Map Editor and can re maximize the c
180. perty Sheet update the glyph automatically when you click on Apply but changes to the glyph do not update the Property Sheet unless you close it and open it again Note The DataScribe does not limit the amount of information you can enter in a text slot on the Property Sheet Use the arrow keys to scroll up and down the lines of text and the down arrow when entering a new line 7 9 Defining Parameters and Constants The DataScribe provides two special input templates for setting up parameters and constants All other templates are bound either to a file one template per file or to a lattice one template per data type but they can also use the Parameters and Constants templates 7 9 1 Making a Parameters Template Parameters are those scalars that you want to manipulate when your DataScribe module fires in the Map Editor For example you may want to selecta particular dataset in a file cuta2D slice from a 3D dataset change the name of a file Figure 7 27 shows the title bar of the Parameters template It can be identified by the icon on the left a small circle containing an arrow pointing upward Figure 7 27 Parameters Template Title Bar To create a Parameters template select Parameter from the Template menu A new Parameters template appears in the DataScribe window You can drop any number of long long integer or double double precision scalar glyphs into this template IRIS Explorer does not accept any other data
181. ph Scalar_Integer The glyph structure is the same for all scalars not used in Constants templates In a Constants template the Scalar glyph has a third field scalar value You must set this value when you use a scalar in a Constants template You cannot set it in other types of template Note Glyph names should not contain spaces 7 7 3 Arrays Arrays are homogeneous collections of scalars other arrays or sets All values in a single array are of the same scalar type for example all integer or all floating point They range from 1D arrays vectors to 4D arrays The starting indices and dimensionality of the array can be symbolic expressions The array data types include Vector a 1D homogeneous array 2D Array 3D Array 4D Array Pattern a text based pattern see Using a Pattern Glyph for more information on its use 7 7 4 Array Glyphs Array glyphs have complex structures with at least one sublevel see Figure 7 15 in the node type A node type may be a scalar array or set but not a lattice You can edit all the elements of a verbose array glyph Figure 7 15 An Array Glyph Hierarchy in Arrays You may want to create nested data structures in your arrays or extract portions of very large datasets You can drop any of the scalar or array data types into the node type slot This means that a 2D array can be set tointeger by dropping an Integer glyph onto the node type slot or it can be set to vector by placing a Ve
182. ple illustrates how to create a more complex parameter function by establishing a relationship between three parameters The parameters are Contour s Min Level and Max Level and IsosurfaceLat s Threshold First create a map by launching a GenLat module a Contour module an IsosurfaceLat module and a Render module and wiring them together as shown in Figure 4 15 To create an object in Render like the one in Figure 4 15 open GenLat s full scale control panel and set these widgets as follows Coord Type curv torus Coord Representation curvilinear Function sines DataType float 63 You want the threshold value of the isosurface to lie directly in the midrange of the contour levels generated by the Contour module To do this you connect two output ports from Contour to an input port on sosurfaceLat and set up a relationship between the two output parameters and the input parameter Figure 4 15 A Parameter Function Using Two Variables To make these connections 1 Connect Contour s Min Level output parameter into sosurfaceLat s Threshold input parameter 2 Connect Contour s Max Level output parameter into sosurfaceLat s Threshold input parameter 3 Bring up the P Func Editor from IsosurfaceLat The parameter of interest on IsosurfaceLat Threshold is highlighted in the Input Parameters pane The Connections area has two listings Contour Min Level and Contour Max Level aliased as A and B
183. ple input data file 7 7 Data Structures The DataScribe processes arrays including complex 1D 2D 3D or 4D arrays which may also be nested or hierarchical For example the DataScribe can handle a matrix a 2D array of 3D arrays Each node of the matrix will contain a volumetric set of data To set up a template therefore it is necessary to understand how arrays work An array is a regular structured matrix of points In a 1D array or vector each node in the array has two neighbors except the end points which each have only one In two dimensions each internal node has four neighbors see Figure 3 5 in the RIS Explorer Module Writer s Guide An internal node in an nD array has 2 neighbors This structure is the computational space of the array To locate a particular node in the array use array indices see Using Array Indices in Expressions The DataScribe Data Types palette see Figure 7 5 lists the data items you can use to define elements of your data files in the DataScribe templates The items are organized according to their complexity into scalars arrays lattices and sets and visually represented as color coded icons or glyphs Scalars are always single data items Arrays lattices and sets are made up of a number of different data elements packed into a single structure Each data type and its visual glyph are fully described in the next few sections Table 7 1 lists the data elements in each category in the D
184. r The Material Editor see Figure 3 22 lets you change the color and texture of an object in a scene You can set Ambient intensity the level of ambient color Diffuse intensity the level of diffuse color Specular intensity the level of specular color Emissive intensity the amount of light the object emits Shininess the amount of surface shininess on the object Transparency the degree of transparency or opacity Figure 3 22 The Material Editor Use the sliders to set the brightness or intensity of each color To change the material color itself click on one of the radio buttons on the Editor The Color Picker appears and you can edit the ambient diffuse usually the same as ambient specular and emissive colors in turn By clicking on the square buttons to the right of the radio buttons you can select to edit one or more of these colors simultaneously In this case a tick mark appears to indicate which colors have been selected for editing Naturally in this situation they will all have the same color assigned to them For details on how the Color Picker works refer to Using the Color Editor below Using the Color Editor You can change the color properties of the object material using the Color Editor see Figure 3 23 Use the Sliders menu to select RGB HSV or both Choose colors from the color wheel Use the Edit menu to stipulate whether or not the change is immediately reflected in the object By selecting Manual
185. r as 67 required group input ports Neither module will fire unless it has a connection to its Img In Lattice port it has data on its Img In Lattice port These ports will be promoted to the group level and appear on the input port menu of the group control panel The group control panel will not fire unless both ports have data on them 5 3 4 Renaming Ports Port names are shown on the input and output port lists in the group control panel and on the parameter widgets so it is important that each port have a unique name However group modules often contain two modules whose ports have identical names For example there are two Img In ports in Figure 5 4 Sometimes you may want to rename a port even if the name does not conflict with another port in the group The focus of the group and the intent of an individual module are different and a new name may make more sense in the context of the group The Group Editor provides an alias text slot for each port so you can set up a unique name for it To change the name of a port type a new name in the text type in slot Figure 5 5 shows the Group Editor after both the Img In ports have been renamed 5 3 5 Selecting Parameters To complete the new group control panel select these parameters in the Group Editor Sharpness from SharpenImg Bias from SobelEdgelmg Blend from BlendImg You can change the parameter names if you wish Figure 5 5 Ren
186. r spectrum 1 Launch these modules from the Module Librarian GenLat LatToGeom Render and GenerateColormap 2 Wire them up as follows 40 GenLat to LatToGeom Output Lattice to Input GenLat to GenerateColormap Output Lattice to Data In GenerateColormap to LatToGeom Colormap Lattice to Colormap LatToGeom to Render Output Geometry to Input 3 Change the GenLat settings to create a 2D Curv Full Cyl curvilinear lattice with only 1 data variable You should have a map that resembles the one in Figure 3 4 To make it more similar increase the size of the lattice in GenLat GenerateColormap starts in HSV mode Figure 3 4 A Map using GenerateColormap Click on the Output option menu and select Run Then do the following and look at the results 1 Add two points to the red color curve Hue three points to the blue Saturation and two to the green Value 2 Move the points around as far as they will go See what happens to the objects in Render 3 Switch from HSV to RGB Observe how the position of the color curves has changed even though the color spectrum is still virtually the same 4 Edit a color band in Build mode then in Run mode 3 3 Generating a Lattice The GenLat module see Figure 3 5 enables you to generate synthetic lattice data for test maps You can create a large variety of lattices of different sizes shapes contents and representations in order to drive other module
187. r uses a number of temporary files during its execution While almost all of these are small the shared memory arena file can get quite large set tempdir path The set tempdir command states where to place any temporary files that may be needed during the course of execution such as named pipes and shared memory arena files if applicable Typically such files are placed in a uniquely named subdirectory of the directory The default value for the base directory is usr tmp Because shared memory arenas can become large it is often advantageous to place the tempdir somewhere other than below usr set arenasize On some workstations modules use shared memory for data communications The shared memory is mapped into a file that resides on disk as determined by the set tempdir command above set arenasize string For a shared memory system make the maximum size of the shared memory arena the designated size The string should be a number optionally followed by mb or kb for megabytes and kilobytes respectively This option may also be set from the command line The default size is 16Mb category Defines a new Module Librarian category with the name name and containing the list of modules given category name append filter arg module The append modifier appends a list of modules to a specified category The list of modules can contain module names such as GenLat or directory names In the latter case the di
188. rays into the output lattice but you probably want to look at only one at a time To do this you create a Parameters template that contains an integer to choose the component of the data vector You then assign a slider to that integer in the Control Panel Editor The completed control panel contains a widget for the component as well as text slots for the script coordinate and data files Two example input files for ReadPlot3D can be found in the directory usr explorer data plot3d here wingx bin is the coordinate XYZ file and wingq bin is the data Q file Finally the script file for the module see Figure 7 45 can be found at usr explorer scribe ReadPlot3D scribe 102 Figure 7 45 The PLOT3D Script 7 12 2 More Complex Expressions Complex expressions such as array bounds indices of selected fragments and constant values can be set to symbolic expressions in the DataScribe using a C like language You can use the same language syntax and operators as are used in the Parameter Function P Func Editor to evaluate these expressions For more information see Using the Parameter Function Editor in Chapter 4 7 13 Saving Scripts and Modules A data transform script consists of at least one input template at least one output template and the wiring that connects them Use the File menu to save your work and clear the work area To save a script or module select Save or Save As from the File menu If you create a
189. rea promoted by selecting Window Parameter in the Group Editor Notice the difference in size between this map and the one in Figure 5 7 A considerable savings has been obtained by combining four of the original six modules into a single group Figure 5 7 The New Group Control Panel 5 5 Opening a Group To display the full scale control panel click on the Maximize button just as you would an ordinary module To open a group again select Open from the Group menu The original modules reappear with each module outlined in red While a group is opened you can interact with any of the widgets of the constituent modules to change their parameter settings If you have a nested hierarchy of groups you may open all groups in the hierarchy However you can use Edit Group only on a top level group you cannot edit a group within a group Therefore you should have finalised selecting promoted ports before including it within another group Click on the background to deselect the open group To select one or more modules in the group hold down the lt Shift gt key and click on each module to toggle selection on and off To select one module in the group deselecting all other modules currently selected hold down the lt Alt gt key and click on the module To close the group and display the group control panel again select Close from the Group menu 69 5 5 1 Modifying Connections You can create and destroy connections wi
190. rectory is added to the module path and all modules and maps in the directory are added to the category For example category myModules explorer modules adds all modules in directory explorer modules to the category myModules You can use the filter modifier with an arg to filter the list of modules against the argument pattern The arg accepts shell wildcards such as and For example category Readers filter Read Modules puts all the Read modules in directory Modules in a category called Readers There is a designated category in the Module Librarian called shelf Modules in the shelf category are displayed in a small panel at the bottom of the Librarian s window host Modules are organized by categories and by hosts in the Module Librarian When you add a host modules can be executed on that machine host name command string 109 The modifier command may be used to define an alternate way of starting a local communications server LC on remote hosts The single argument after command which must be enclosed in quotation marks if it contains blanks specifies the alternate command The UNIX command IRIS Explorer uses to start the LC on a remote host is the given command rsh by default followed by the hostname followed by a shell command that will be invoked remotely to start the LC For example suppose this appears in your explorerrc file host bob command myrsh x IRIS Explorer will
191. remote system 35 Note The best place for such output is the Jogin file Other programs besides IRIS Explorer get confused and do not work properly when there is output from the cshrc file 2 11 9 You Get a Shared Library Error When You Launch Remote Module Error messages that mention a shared library indicate that some part of IRIS Explorer is not properly installed on the remote system For more information see Remote Execution of Modules 2 11 10 You Cannot Connect Two Modules or a Module Produces Unexpected Data You can check this in two ways 1 The module may be connected to an incompatible port and is therefore receiving the wrong data type Bring up the input and output port pads and check the port connections 2 Verify that the module is producing the desired data type by connecting it to PrintLat or PrintPyr and printing the output IRIS Explorer produces an ASCII file showing the structure and contents of the data which you can look at to track down any errors 36 Chapter 3 Using Modules This chapter describes in detail some of the modules you are likely to use often as well as a few of the more complex modules It explains how to create a colormap generate various types of lattices slice volumetric data create a histogram from your data display and manipulate images use Render to visualize your data create loops in maps create a single executable process from a group of ImageVision Library IL mo
192. rgument a loop body construct explained below or a procedure of one input argument The input argument to this loop body procedure is the loop count To create a loop that prints all numbers between zero and nine inclusive you write for loop 0 lt 10 1 Loop body i print i OMNIA BRWNRFR O The loop body construct is used as the final argument to for loop The loop body construct takes no arguments or a single input argument In the latter case the argument is a variable that is scoped locally to the loop body and that serves as the loop counter If the loop counter is not needed loop body is used as follows for loop 0 lt 3 1 do something 3 times Loop body do something Since the built in print procedure can be called with a single input argument the procedure can be used directly as the last argument to for loop without having to use the loop body construct Here is an alternate implementation of the print example above for loop 0 lt 10 1 print The next example presents a doubly nested loop The outer loop variable is i and the inner loop variable is j for loop 0 lt 5 1 Loop body i outer loop i i for loop 1 lt 41 121 for loop 1 lt 41 Loop body j print inner loop j j outer loop i 0 inner loop j 1 inner loop j 2 inner loop j 3 outer loop i 1 inner loop j 1 inner loop j 2 inner loop
193. rmap creates a default colormap for the molecule based on atomic number The domain is set at a minimum of 0 and a maximum of 16 to accommodate the atoms which are hydrogen carbon oxygen and nitrogen It also colormaps the dots in the solvent accessible surface according to the parent atom of each dot This provides you with information about which atoms a given probe will touch as it traverse the surface of the molecule You can change the default color settings by using the option menus on the control panel Refer to Creating Colormaps in Chapter 3 for more information You can use the capacities of Render to look at the NutraSweet molecule in great detail see Figure 1 11 You can rotate the molecule by holding down the left mouse button and dragging the molecule around with the cursor translate the molecule by holding down the middle mouse buttons and dragging the molecule around using the cursor zoom in and out on the molecule by holding down both the left and middle mouse buttons at the same time and moving the cursor up and down on the screen use the Lights menu to control the various light sources and highlight less distinct areas of the dot surface Figure 1 11 The Molecule in Render For more information on using Render read Visualizing Data in Chapter 3 You can use FileList to select another chemistry molecule to examine 1 6 Atmospheric Physics This example illustrates how you can use IRIS Explorer mo
194. rocessed in various ways the Render module see Figure 3 17 is naturally a very important part of the process It is Render that displays the geometric object which it renders from 3D geometry sent to it by compatible modules in its window provides a wide selection of visual enhancement techniques for studying the object further Figure 3 17 The Render Module The Render module can accept multiple inputs and it manages each one separately Its viewing and editing functions are available only in the full scale control panel When the full scale window is open the Diminutif window is blanked Render has several viewing modes and an edit mode in which an object can be selected and its attributes altered The functions and attributes of the Render module are described fully in the IRIS Explorer Reference Pages 3 7 1 Ports on Render Before you can display an object in the Render window you must wire Render into a map that generates the object Render has six input ports four of them accept geometry inputs and two accept lattices The most frequently used input port is the Input Geometry port which accepts the geometry necessary to create an object or scene from any module with a geometry output port The Annotation Geometry port accepts text labels for parts of the geometry in the Render window Its use is illustrated in the pick map in the Module Librarian Render has three output ports The Pick Pick
195. rthoSlice OrthoSlice OrthoSlice Pyramid ProbeLat Table 3 2 Slicing Options You can also use the DataScribe to create a single module which combines all these functions See Chapter 7 for more information 3 4 1 Using OrthoSlice The simplest way to slice data is to use OrthoSlice see Figure 3 6 This module extracts a 2D lattice from a 3D uniform perimeter or curvilinear lattice along one of the orthogonal axial planes It produces the same type of lattice as it receives except that the lattice is 2D For example if you feed in a 3D curvilinear lattice OrthoSlice produces a 2D curvilinear lattice Footnote For more information on lattices see Chapter 3 Using the Lattice Data Type in the IRIS Explorer Module Writer s Guide OrthoSlice cuts along the i j and k axes in computational space For a uniform or perimeter lattice these correspond to the x y and z physical axes Curvilinear lattices have a more complicated relationship between computational and physical space Figure 3 6 The OrthoSlice Module To select an axis for cutting a slice click on the Z Slice J Slice or K Slice radio button see Figure 3 6 The slice number corresponds to the node number The slice is taken along the axial plane at that particular node You can select a number up to one less than the number of nodes Figure 3 7 shows a map that uses OrthoSlice to display part of a lattice You can use any lattice data For example you can replace GenLa
196. rts data in the form of variables stored at the nodes and coordinates which specify the node positions in physical space It also has a dimension variable nDim and a vector dims defining the number of nodes in each dimension nDim and dims are the same for both the data and coordinate arrays of the lattice The data in a particular lattice is always of the same scalar type for example if one node is in floating point format all the nodes are Each node may have several variables For example a color image typically has four variables per node red green blue and degree of opacity A scalar lattice has only one variable per node All lattice data is stored in the Fortran convention using a column major layout in which the direction of the array 90 varies fastest When you are preparing a data file make sure that your external data is arranged so that it will be read in the correct order Coordinate values are always stored as floats Their order depends on the lattice type see Lattice Types For curvilinear lattices you can specify the number of coordinate values per node This describes the physical space of the lattice as opposed to the computational space which is the topology of the matrix containing the nodes and is determined by nDim and dims See Figure 3 13 in the IRIS Explorer Module Writer s Guide for various examples of curvilinear lattices Table 7 1 lists the components of an IRIS Explorer lattice When y
197. s govern the visual shape of the lattice For example the torus shape produces a lattice 41 whose coordinates are polar in the first two dimensions and linear in the others To set the visual shape of a lattice click on the Coord Type option menu and select an option To set the coordinate representation for a lattice click on the Coord Representation option menu and select an option You can generate a curvilinear lattice with coordinates that are uniform in computational space This option is useful for testing modules which require such lattices on their input ports Certain combinations of coordinate representation and coordinate style do not make sense though because only curvilinear representation can be used to store the position information for the torus and related coordinates Data Values The data values in lattices can be any of the primitive data types see Data Structures in Chapter7 These include byte short long float and double To set a data type click on the Data Type option menu and select an option Data values are scaled either in a fixed range of zero to 255 or their maximum possible range for the integer types char short or long However a range of 1 0 to 1 0 is used for float and double To set the data range click on the Coord Range option menu and select an option Note Using the maximum possible range for the long primitive type can generate very large numbers The values of the data ca
198. s how many times a data value occurs in the input lattice Figure 3 14 The Histogram Module The Histogram module has one lattice input port and one lattice output port The input port accepts any type of input lattice and the output port produces a count of the input data values in the form of a lattice 3 5 1 Displaying Histograms The Histogram control panel has a display window that shows the histogram itself and scale windows that show the domain horizontal or x axis and range vertical or y axis of the data values The domain changes automatically according to the channel selected You can override the default limits by entering new values in the Min Domain and Max Domain text slots on the control panel 44 3 5 2 Sorting the Data The Histogram module divides the range of data values in the lattice into a number of equal subranges calledbuckets It counts the number of nodes in the lattice whose values lie in each of the buckets and produces a histogram of the counts To set the number of subdivisions in the data domain you can move the Num of Buckets slider or type in a new value and press lt Enter gt If you define a domain with a narrower spread of values than the actual dataset in a channel then the out of range values are omitted from the histogram if Outliers is set to Omit all the data points below the minimum value on the scale are put into the first bucket and all the data points above the maximum are put
199. s that accept lattices For example you can easily verify that a given module performs properly on any type of input lattice Simply connect GenLat to the module and then start generating different types and styles of lattices GenLat has no input ports and only one output port for the generated lattice You can connect it to any module that accepts the type of lattice you want to generate Figure 3 5 The GenLat Module 3 3 1 Setting Lattice Parameters GenLat creates a single lattice each time it fires You can control the shape and contents of this lattice by manipulating the widgets on the control panel Controlling Lattice Size Two of the most important parameters of a lattice are its size and dimensionality If you increase these values GenLat creates larger lattices a process which takes commensurately more time GenLat always creates lattices with the same number of elements on each side for example 8x8x8 3D or 25x25 2D Note If you need test lattices that do not have the same number of elements on each side you may achieve this by combining GenLat with a module such as SampleCrop To alter these values move the Dimensions and Size sliders at the bottom of the control panel You can also type new values into the slider value areas to get an exact value Lattice Coordinates All lattices created by GenLat have coordinates which can be represented as uniform perimeter or curvilinear The data values of the coordinate
200. set glyph into the data slot in the array and then create the set by dropping glyphs into the set For example Figure 7 22 shows an open set glyph that contains a 3D Array glyph which in turn has a set glyph in the data type slot Note You must promote any component selections from a set up to array level in order to wire them into another template See Selecting Array Components for more details 92 Figure 7 22 Nested Sets The ASCII formatting feature described in Converting Formatted ASCII Files lets you retain or recreate the layout and spacing of ASCII data files in DataScribe input and output templates The layout is set with the ruler in the Template Property Sheet However you cannot format data in a set that is nested within an array If you want to use formatting in a set the set must be a top level set and may not contain any other sets itself 7 8 Using a Pattern Glyph Figure 7 23 A Pattern Glyph Pattern glyphs see Figure 7 23 are a special kind of array glyph that can be used only in input templates You can use them to traverse character strings in files and search for patterns in them The verbose pattern glyph looks similar to a vector but has three additional features a comparison or termination string which the DataScribe uses to determine the length of the pattern a wildcard toggle button When the button is on you can do simple searches using the two UNIX wildcard characters substitute with an
201. shaped widgets that let you select a value or switch a specific parameter on or off They come in two styles see Figure 2 19 The one shot or single button can be on or off It is usually oblong and contains a label on the button itself Diamond shaped radio buttons offer a set of choices only one of which is valid at a given time They have a colored center when on and are convex when off Use the left mouse button to click the buttons on and off Figure 2 19 Button Widgets 2 9 2 Sliders Sliders see Figure 2 20 are either horizontial or vertical bars that let you increase or decrease the value of a parameter in discrete steps Sliders generally have integer values Each slider has atitle giving the name of the parameter a thumb that moves from one end of the bar to the other allowing the sliders value to be changed text slots showing the minimum maximum and current values of the parameter Figure 2 20 Slider Widgets You can change any one of these values by clicking on the text slot to highlight it typing in a new value and pressing lt Enter gt To change a parameter value place the mouse cursor on the thumb and hold the left mouse button down while you push or pull the slider along its bar The current value changes as the thumb moves When you release the mouse button the new value is sent to the module To move the bar to the cursor position place the cursor in the slider slot and click on the m
202. shown in this chapter is given in the introduction to the map IRIS Explorer starts up and the map appears in the Map Editor All the modules are selected highlighted in white and you can move the entire map by dragging on the title bar of a single module Click on the background of the Map Editor to deselect the modules in the map before you experiment with individual modules The highlighting disappears 1 2 2 Opening Subsequent Maps Once IRIS Explorer is running you can use the Module Librarian to open a map Follow these steps 1 To clear the Map Editor of modules click on the Edit menu and select Destroy All 2 Go to the Module Librarian next to the Map Editor and use the vertical scroll bars to locate the maps which are shown in blue 3 Select the map you want by placing the cursor on the map name and clicking the right mouse button then selecting Launch from the pop up menu You can also hold down the left mouse button drag the map over to the Map Editor and release the button When you release the mouse button the map appears module by module on the screen The menu bar displays a number in angle brackets for example lt 5 gt which tells you initially how many modules are in the map the number decreases as modules appear on screen indicating how many modules remain to be launched Quitting IRIS Explorer To quit IRIS Explorer select Quit from the Admin menu in the Map Editor 1 2 3 Opening Modules
203. sing For or a multiple data set reader and convergence of a simulation using While For example Figure 3 27 illustrates a loop from Render to QueryLat and back to Render Figure 3 27 A Loop in a Map The user picks on an object in Render which fires and sends the pick coordinates to QueryLat QueryLat turns the coordinates into text and sends it to Render When the data arrives back at Render the loop is terminated To start the loop again the user has to make another pick The common goal in all loops is to feed data from one phase of an IRIS Explorer computation back around to the next phase of the computation As in most programming languages loops in IRIS Explorer are a basic and necessary semantic element It is also true that looped maps are more complex than linear or unlooped maps This section describes how you can conveniently and correctly employ looped maps in your IRIS Explorer data visualizations 51 3 8 1 Defining a Loop You can create two kinds of loops While loops and Repeat loops like the similarly named loops in C In While loops a specific condition evaluates to t rue and then an iteration takes place This sequence is repeated until the condition evaluates to false In Repeat loops an iteration takes place and a condition is then evaluated Similarly the sequence is reiterated until a stopping condition is reached 3 8 2 Loop Controllers Each loop must contain a loop controller module which controls and
204. soup The IRIS Explorer factory has a way to cope with this The manager scopes out a group of machines that for some reason are logically related probably because they carry out closely related tasks and selects certain of their functions to wire into a new control panel The machines themselves are relegated still intact to the basement and the connecting wires come through the factory floor to the administrative or group control panel In one easy move the factory floor has gained a large open space the assembly line has increased in efficiency and the individual machines in the group are unscathed simply out of sight until fetched up from the basement again If you plan carefully you could end up with one sleek control panel on the visualization unit and a completely clean and quiet floor The analogy should be clear You can encapsulate a collection of modules in a group and gain all the benefits of a streamlined work area without sacrificing the integrity of the individual modules IRIS Explorer is a powerful and versatile system The analogy of the factory necessarily simplifies its structure but the examples in Chapter 1 give you a sense of what can be accomplished To use IRIS Explorer effectively you should know what data you have but you need no blueprint for what kind of visualization you want to produce The great strength of IRIS Explorer is that you can innovate without retooling and the design of your map reveals itself
205. strip off all the x coordinates and deliver them into a 3D array the process is similar for they and z coordinates as well as the functional values If you want to sample the dataset in each direction prior to reading it in you can add a Parameters template to sample the volume in each direction independently Figure 7 44 shows the completed script Try it out in the Map Editor by connecting WireFrame to its output port Figure 7 44 A Curvilinear 3D Lattice Reader Example 7 9 Creating a PLOT3D Reader PLOT3D is a commonly used application in the field of computational fluid dynamics It has several specific file formats this example summarizes the process for building a module that can read the most commonly used variant of PLOT3D The data to be extracted is a 3D curvilinear lattice It resides in two input files one that contains the coordinate information and another contains the nodal values the real data The structure of both files is quite straightforward The coordinate file contains a short dimensioning vector followed by three arrays containing the coordinate data Thex y and z coordinates are grouped separately The data file contains the same dimensioning vector followed by four scalars that describe some of the flow regime After these scalars is the data array It is a 5 vector of 3D arrays This array can be viewed as either a 3 1D array or a 4D array This example takes the 4D approach You can put all five of the 3D ar
206. t Attributes pane The properties of the selected widget are shown in the widget properties pane on the right To display the widget properties double click on the widget in the preview control panel To select a widget from the Control Panel Editor 1 Click on the name of the parameter in the Parameters pane 2 Select a widget from the Widget Type option menu in the Widget Attributes pane see Figure 4 2 The widget appears in the Preview window Figure 4 2 Selecting a Widget Type In Figure 4 2 for example the parameter scale is highlighted in the Parameters pane The widget type selected for it on the Type menu is a Horz Slider horizontal slider The widget is highlighted in the preview window Its properties are listed to the right under Slider Properties Figure 4 3 shows a selection of widgets as well as the control panel decorations Decorations are vertical and horizontal lines frames and labels available from the Decorations menu see Figure 4 4 You can size them and move them around in the same way as you manipulate widgets Figure 4 3 A Selection of Widgets In general dials are used for double precision parameters and sliders are used for long integer parameters Text type ins can be substituted for dials and sliders with less functionality Radio buttons and option menus can be interchanged You can use text type in slots where file browsers are used although with more limited scope File
207. t create the templates Figure 7 1 shows how three input templates and two output templates can be combined to form a script as part of an IRIS Explorer module Figure 7 1 Templates and Scripts 7 3 1 Setting Up Templates You must set up a separate template for each data file you plan to read data from or write data to but you can have several input and output templates in a script Special templates exist for describing user defined constants and parameters associated with widgets see Defining Parameters and Constants Note Template glyph script and component names in the DataScribe should not contain blanks Opening a New Template You create input and output templates in the same way They are distinguished by the arrow icon in the top left hand corner of the template see Figure 7 2 Figure 7 2 Template Icons 81 To create a new template 1 Open the Template menu and select Template The New Template dialog box appears see Figure 7 3 You use it to set the general properties of the template such as its name whether it is an input or output template and the format of the data to be converted ASCII binary or IRIS Explorer 2 Type a name for the template and click on the radio toggle buttons to select the other attributes A small icon see Figure 7 2 to the left of the maximize button top right corner of the template indicates the file format you selected See Figure 7 4 for an example which includes an
208. t with ReadLat and read in an external lattice data file if you wish A good choice is usr explorer data lattice testVol lat You can also color the output with a colormap by wiring GenerateColormap to OrthoSlice The modules in Figure 3 7 are GenLat OrthoSlice LatToGeom and Render The slice is taken along the i axis of a half cylinder Figure 3 7 Slicing a Volume with OrthoSlice 3 4 2 Using Slice The Slice module see Figure 3 8 extracts a 2D uniform slice out of a 3D uniform lattice Figure 3 8 The Slice Module The slice axis need not be orthogonal to the axes of the lattice The Slice module has an input port that accepts transformation coordinates from TransformGen These coordinates define the plane of the slice You can Use the widgets on TransformGen to angle the slice in any direction you choose Use the Offset dial on the Slice control panel to position the slice plane perpendicular to its axis in the volume The plane is offset from the center of the volume Use the Resolution slider on the control panel to set the scale for the slice lattice It determines the number of nodes The size of the slice lattice can be larger than the original lattice depending on the slice plane At certain angles the slice may extend beyond the bounds of the original lattice see Figure 3 9 but the lattice is clipped to keep the number of samples outside the bounds to a minimum Figure 3 9 Slice Extended Beyond Lattice Bounds
209. taLattice The data variable nDataVar and the coordinate variable 1CoordVar are both defined as 1 Figure 7 32 Selecting the X Value of a 2D Array To select the x values only you need to create separate data components for the x and data input values in the 2D array dataSet glyph and a component for the x output values in the coord2 Vector in the curvilinear lattice The data values are connected straight into the data vector To isolate the x values in the input template you would 1 Select New from the Component menu and fill out the text slots as shown in Figure 7 33 The fragment is called xPos The i variable goes from 1 to 1 that is only the first value in the row is taken The j variable goes from 1 to the last value res in the column of x values 2 Click on the OK to apply your changes Figure 7 33 Component Dialog Window for X Values To isolate the data values in the input template you would 1 Select New from the Component menu and fill out the text slots as shown in Figure 7 34 The fragment is called data The i variable goes from 2 to 2 that is only the second value in the row is taken The j variable goes from 1 to the last value res 1 in the column of data values 2 Click on the OK to apply your changes Figure 7 34 Component Dialog Window for Data Values The dataSet 2D array has no nested data items and the x and data components were created at the top level When you click on the component menu
210. ted lattices But many designs will require materials from elsewhere external data that needs to be picked over and cleaned up sorted through and carefully sieved before the machines will accept it The DataScribe performs this task It accepts external data and lets the user build a module that converts the data into IRIS Explorer lattices which other IRIS Explorer modules can process With data coming in and modules firing the IRIS Explorer factory produces many interesting and informative geometric objects However the day may come when no modules are available in the Module Librarian to fulfill a part of the map design This calls for a trip to the machine shop the Module Builder Here you can build a module that will do exactly what you want it to do when it is wired into the map It looks just like the other modules with the same type of control panel and controls and it can be stored and used again Thus the scope of the factory has been enlarged However large factory floors have a disadvantage They can be noisy and messy with lots of wires snaking here and looping there and they tend to be crowded on the principle that an empty space is immoral Some machines may be running at less than their full capacity if a couple of their features are not needed for a particular design Likewise with the IRIS Explorer Map Editor When you create large maps you might be tempted to think less of visualization systems and more of a bowl of noodle
211. terminates loop iteration In While loops the loop controller checks the condition at the start of the loop and in Repeat loops at the end of the loop The While or Repeat sense of the loop is determined by the While or Repeat capability of the module controlling the loop Loop controllers have either While or Repeat capability but not both Loop controllers are identified in the Map Editor by a small square icon the controller icon in the left hand corner of the title bar in the mini control panel see Figure 3 28 Figure 3 28 Loop Controller Modules The controller icon is Off when a loop controller module is wired into a map but is not part of a loop or when it is in a loop controlled by another module When you wire a loop controller module into a loop the icon turns green For example in Figure 3 28 AnimateCamera is the loop controller even though both modules have controller capability see How Loops Work You can identify a loop controller module only after it has been launched in the Map Editor until then it is indistinguishable from other modules in the Module Librarian You can also look at the mres file in the Module Builder the Build Options window indicates whether the module is a While or Repeat loop controller or neither For example Figure 3 29 shows the controller status for AnimateCamera which is a Repeat loop controller module Figure 3 29 Build Options for Loop Controller You confer loop controller stat
212. the Copyright Laws of the United States Contractor manufacturer is Silicon Graphics Inc 2011 N Shoreline Blvd Mountain View CA 94039 7311 Silicon Graphics and IRIS are registered trademarks and IRIS Explorer IRIX DataScribe and Diminutif are trademarks of Silicon Graphics Inc Motif is a trademark of Open Software Foundation NutraSweet is a registered trademark of The NutraSweet Company NFS is a trademark of Sun Microsystems Inc UNIX is a registered trademark of UNIX System Laboratories X Window System is a trademark of Massachusetts Institute of Technology SIOD is copyrighted 1988 1992 by Paradigm Associates Incorporated Cambridge Massachusetts NAG is a registered trademark of The Numerical Algorithms Group Limited The Numerical Algorithms Group Inc The Numerical Algorithms Group Deutschland GmbH Introduction At the turn of the century someone defined an inventor as a person who makes an ingenious arrangement of wheels levers and springs and believes it civilization Footnote The Enlarged Devils s Dictionary by Ambrose Bierce Penguin Books 1967 Now nearly a hundred years later it could be said that an inventor is a person who concocts an ingenious arrangement of computer code and believes it intuitive Since everyone s intuition has its off days the IRIS Explorer User s Guide provides a few tips for using IRIS Explorer a decidedly ingenious arrangement IRIS Explorer is a system
213. the data you want to convert into the module s text slot When the map fires your conversion module transforms the data according to the specifications in the conversion script You can use this new module as often as you like The DataScribe has three main functions to convert data from an external source in ASCII or binary format such as an application or disk file into IRIS Explorer lattices to convert to and from different data types within IRIS Explorer itself For example converting a single channel dataset nDataVar 1 for an image to a three channel dataset nDat aVar 3 to convert data from one file format to another For example from ASCII to binary or vice versa 7 2 The DataScribe The DataScribe window is the work area in which you assemble templates to create a data conversion script The templates may contain data glyphs parameters or constants the overview pane of the DataScribe window shows the wiring scheme that defines the rules for data conversion in each script You can use the Control Panel Editor to edit the control panel of a completed module script if the module has 80 parameters If not the DataScribe generates a default control panel For more details see Chapter 4 Editing Control Panels and Functions 7 2 1 Opening the DataScribe To bring up the DataScribe type dscribe at the prompt in the shell window The DataScribe window and the Data Type palette appear 7 2 2 Quitting the Dat
214. the module writer has coordinated them with respect to interpreter variable naming To be perfectly safe an application map must be run as an application and not as a simple map When run as an application the application controls which modules are started When run as a map the application is not in total control since the user has access to the Module Librarian and the Map Editor and can thus always launch unrelated maps and modules that may themselves issue script commands B 4 2 A Complex Example This is an example of advanced Skm programming Given the built in function mods to list we will construct a procedure that determines if a particular module exists The procedure is named mod exists and is specified as follows define mod exists procedure mod mod in list mod all mods mod exists is fairly simple It passes its single argument mod and the output of all mods to a helper procedure mod in list which is defined below As mod in list is the last statement in the procedure its return value will be returned by mod exists Here is the definition of mod in list define mod in list procedure mod m list if null mod if null m list let m first m list if null m if string mod m t 125 mod in list mod rest m list mod in list takes two arguments a module name string and a list of module name strings First
215. the mouse button all modules that are completely enclosed by the lasso will be selected Alternately you can hold down the lt Shift gt key and click on each module in turn To select all the modules currently in the Map Editor open the Edit menu and click on Select AIL Use the lt Shift gt key with the sweep gesture to add more modules to an already selected group To deselect all selected modules move the cursor off the title bar and click any mouse button To deselect one module hold down the lt Shift gt key and click on the module Resizing the Control Panel The sizing buttons let you switch between the different forms of the module control panel When you first launch a module it appears in the Diminutif form see Figure 2 7 which shows the title bar port access pads and general widget layout Figure 2 7 Diminutif Control Panel 19 Click on the Minimize button to fold the panel into the micro form see Figure 2 6 This saves space in the Map Editor You can toggle back and forth between the Diminutif and micro control panels Click on the Maximize button to open the full scale or maxi control panel see Figure 2 8 the Diminutif panel remains in the map You can also open the maxi control panel from the micro control panel Figure 2 8 Full scale Control Panel The full scale panel shows details of the widgets and the parameter values You can move it outside the Map Editor window and enlarge it as much
216. the same time You can use these manipulators to reposition the object in the scene The movement is not as precise as that achieved by using the sliders in the Transform Editor but it is a more direct manipulation To remove a manipulator from an object click on None or select another manipulator from the Manips menu Example 3 4 Using the Trackball The Trackball manipulator see Figure 3 26 consists of opaque stripes surrounding the object These stripes are aligned with the local axes of the object To rotate the trackball place the cursor on the stripes and drag the mouse in the desired direction with the left mouse button held down When you release the mouse the ball continues to spin until you click the left mouse button To rotate the trackball in the direction of a single axis place the mouse on one of the stripes then drag it in the direction of the stripe Figure 3 26 The Trackball Manipulator If you start the trackball spinning and then move the mouse outside the sphere the ball continues to spin within the plane of the screen You can use the Transform Editor to monitor the object s degree of rotation as reflected in the rotation slider values 3 8 Constructing Loops You may sometimes need to go beyond the linear dataflow model of existing IRIS Explorer maps to build maps containing dataflow loops They are needed for example for data interrogation through picking in Render iteration through data sets u
217. theses Given this definition define var 100 100 the following is valid when typed by a user but is not accepted from a module since the printing of evaluated expressions is suppressed for module input var 100 CxScriptCommand performs asynchronously with respect to module execution and IRIS Explorer does not acknowledge Skm code execution Footnote cxScriptCommand returns 1 if the Skm code was not sent to IRIS Explorer at all Consequently a module cannot know for sure whether the script code had the desired effect For debugging purposes however certain types of errors are noted on IRIS Explorer s console output st derr As with input typed in directly by the user script commands perform synchronously with respect to one another when required Thus in the following sequence ReadImg and DisplayImg will exist when the connect command is issued assuming no failure during launch char stringl define ml start ReadImg char string2 define m2 start DisplayImg char string3 connect ml Output m2 Img In char string LONG_LEN strcpy string stringl 124 strcpy string stringi Streat string Stringz streat string string3 exScriptCommand string Remember to not refer to modules by the name used in the start command since the actual module launched may have an instance number appended to its name Instead use the name returned by the start command
218. thin the opened group those between modules belonging to the group Use the port menus to create and destroy a connection as usual When creating a connection you will see that compatible ports are highlighted only on modules within the group If you use the Disconnect and Reconnect options on these modules only those connections between modules within the group are broken with Disconnect and recreated with Reconnect Using Disconnect and Reconnect on a closed group breaks and recreates the connections from the promoted ports of the group but not the connections internal to the group You cannot create a connection from inside the group to outside You should promote the inside port to the group using Edit Group on the closed group and then connect selecting from the port menu of the closed group You will see when disconnecting to ports of modules within a group that the name of the module is preceeded by the name of the group to further identify the connection 5 5 2 Redefining a Group The modules within a group can be reselected retaining the attributes of the edited group using the Regroup option on the Group menu Select modules from the open group leaving as unselected those to be omitted from the redefined group and selecting modules not currently within a group to be added to the group Then select Regroup The control panel of the original group is retained except that widgets corresponding to parameters from omitted modul
219. thout specific written prior permission PARADIGM DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS IN NO EVENT SHALL PARADIGM BE LIABLE FOR ANY SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER IN AN ACTION OF CONTRACT NEGLIGENCE OR OTHER TORTIOUS ACTION ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE 127
220. tion as DisplaceLat but with greater vertical distortion LatToGeom creates polygons of the displaced data from DisplaceLat Contourcreates contours colormapped according to height using the displaced data from DisplaceLat lt 2 gt Render displays the output from LatToGeom and Contour as the surface with overlaid contours 1 3 2 Experimenting with the Image Map Both the aerial image and the altitude data go through DisplaceLat see Figure 1 3 which displaces the image data so that topographical features become 3D You can regulate the scale of the 3D rendering by turning the Scale dial on the module control panel The result is a 3D version of the original 2D image showing topographical features of the Korean countryside Figure 1 3 DisplaceLat Control Panel The output of DisplaceLat lt 2 gt passes into Contour see Figure 1 4 which creates a series of lines at varying heights above sea level just as in a topographic map The scale factor for DisplaceLat lt 2 gt should be greater than that for DisplaceLat to make the contour lines visible Figure 1 4 Contour Control Panel To set the relationship between scale factors the Scale parameter output port on DisplaceLatis wired to the Scale parameter input port on DisplaceLatk2 gt You can alter the number of contour levels by moving the slider widget on the module control panel You can also change the altitude range for which contours are shown by resetting the minimum and ma
221. tiple loops with a single controller multiple controller capable modules in a single loop with only one of them selected as the active controller and hopefully anything else that makes programming sense You cannot have intertwined loops where two control modules are each in the other s loop or where a single module is controlled by more than one controller Each loop controller module has an additional synchronisation port Loop Ended When the module is the active controller you can wire this port to the Fire port of another module outside of the loop to cause that module to fire when the loop completes when the loop controller has detected the end of loop condition and stops the loop This can be useful to control nested loops as demonstrated in the example map usr explorer maps Animatelso map Figure 3 30 shows the wiring of the nested loops within this map AnimateCamera is the loop controller for the inner loop and sends cameras to Render For controls the outer loop The Loop Ended port of AnimateCamera is wired to the Fire port of For to start the next iteration of this outer loop Figure 3 30 Loop Wiring in Animatelso Map Control Arcs The special coloring of loop control arcs see Figure 3 31 can help you understand loops Each loop has a single control arc which is adjacent to the loop controller that governs it The control arc is upstream of a While controller and downstream of a Repeat controller A control arc is
222. ton saves the layout information without closing the Editor window The Cancel button dismisses the Editor without implementing your changes 4 3 Creating Menu Items You can link a parameter with a menu item on the module menu bar instead of giving it a widget on the control panel For example instead of having two file browser widgets on the control panel for opening and saving files you can set up a File menu with the menu items Open and Close each linked to a file selector The Preview control panel has a default menu bar with an empty Help menu already in place see Figure 4 3 58 Note For each parameter linked to the menu bar you need to specify a widget attribute in the Control Panel Editor as well Use the Initially Hidden button to keep them from appearing on the module control panel 4 3 1 Setting up the Menu Bar To display the Menu Bar Editor select Menu Bar from the Edit menu on the Control Panel Editor The Menu Bar Editor appears see Figure 4 7 You can create up to eight different menus with up to sixteen items on each menu depending on the parameters you want to associate with a menu item Note It will help the users of your modules if you follow the conventions for menu placement that is File menu on the far left then Edit menu then your other menus Figure 4 7 The Menu Bar Editor Set up your menus by typing the name of each menu in the text slots in the Menu Bar Editor for example File To
223. ts P Func Editor Opens the Parameter Function Editor which lets you establish relationships among module parameters It is described in Using the Parameter Function Editor Show Log Brings up the module Log window which displays all the module output resulting from the current map operation see Logging Module Output Help Explains the purpose of the module and lists its ports and parameters Credits Brings up information about the module s author Replace Replaces the module with a newly launched module with the same connections and parameter settings Interrupt Interrupts a running user function without destroying the module You may get unpredictable results from a map if you halt a module when the map is still firing Destroy Completely removes the module from the map and the Map Editor Figure 2 9 Module Pop up Menu Using Drag and Drop Operations The Drop Icons at the bottom of the Map Editor window can also be used to perform operations on a single module or many selected modules by dragging a module onto the icon Press the middle mouse button over the module control title bar This will show the drag cursor a representation of a module Keeping the middle mouse button pressed drag the cursor to the required icon and release to perform the operation If the module dragged has been previously marked for selection then the operation is applied to all the selected 20 modules otherwise the operation is onl
224. two 1D curvilinear lattices fx is connected to the data vector in the first one and gx to the data vector in the second one res is connected to the dims vector and xPos to the coord vector in both lattices The files ReadXYData mres and ReadXYZData mres have two and three sets of coordinate values respectively for each set of data values You can extract an xPos and a Ypos component in the input dataSet array and create an xCoord and yCoord fragment which are in turn promoted to allX and allY in the coordinate vector in the output template In the second script you can also extract the zCoord fragment The file ReadX YZ3DData mres shows how to extract the x y and z coordinate values separately as well as the data This script has only one set of data values A nested vector appears in the input 3D array so the coordinate components must be promoted in the input template as well as in the output template this time 7 12 Converting Formatted ASCII Files Languages such as Fortran support a large number of formatting options and parsing the output from a program can take time and effort The DataScribe provides a ruler for formatting ASCII data that makes reading and writing 99 formatted files easier 7 12 1 Using the Property Sheet Ruler You can use rulers only in templates for ASCII data files top level arrays and sets an array may not contain another array a vector for example and a set may not contain any other sets
225. ugh the lists of available modules and maps To scroll easily through the module categories Put the cursor on the list and type the first letter or two of the module name For example if you want to launch the Render module place the cursor on the list and type re The list scrolls down to the first module name starting with Re The Librarian is not case sensitive so you could also type RE Place the cursor in the scrolling channel above or below the scroll bar and click on the mouse The left mouse button moves you up or down one page at a time The middle mouse button moves you up or down to the cursor position Placing the Module In the Map Editor If you use the file browser to launch a module from a directory the module comes up in the current launch position which is the active point in the Map Editor You can change the launch position by clicking the left mouse button on another spot in the Map Editor background before you launch the module The next module is launched at that site To launch a module or a map from a remote system select the remote host Librarian from the Hosts menu by clicking on the host name and then selecting the maps or module you want You must first install the host in your host list using the New Host option on the Hosts menu You can launch as many copies of a module as you like although some modules might require special window server resources Footnote To launch many copies of modules that requir
226. ule to the Output Lattice port of the module that is reading in or generating lattice data 2 Connect the LatToGeom module s Output Geometry port to Render If the lattice is 3D such as a volumetric dataset 1 Select a module that will provide the visual representation you want for example JsosurfaceLat Contour Slice OrthoSlice WireFrame or VolumeToGeom 2 All these modules except Slice and OrthoSlice produce geometry They can be connected to Render by wiring their Output Geometry ports to Render The two slicers produce lattices which must be passed through a LatToGeom module first See Slicing Volumetric Data in Chapter 3 for more information about using slicers 2 11 5 The Module Librarian Does Not Display a Saved Map If you want a map to be displayed in the Module Librarian after you use Update the map must be in a directory that the module Librarian recognizes To ensure this 1 Check that the directory in which you saved the map is in the module path You can check this and or add subdirectories to the module path by editing the explorerrc file See Appendix A for details The default directory is usr explorer maps 2 Check that you used the correct pathname when you saved the map It might be in another directory that is not in the module path 2 11 6 A Saved Map is Empty When Reopened You need to save the map again To prevent this from happening a second time 1 Mak
227. ur ASCII data file into the datafile slot the DataScribe module fires and converts the data into a 2D IRIS Explorer lattice see Figure 7 13 Running IRIS Explorer 1 Start up IRIS Explorer by typing explorer at the prompt 2 Launch the DataScribe module dsExample1 from the Module Librarian The Script File slot displays the name of the script dsExample1 scribe 3 Inthe empty ArrayFile text slot on the control panel type the filename usr tmp dsExample1 data which you created at the start of this exercise 4 Launch the NAGContour module from the Module Librarian Connect the OutLat output from dsExample to the InLat port of the NAGContour module You should see a set of contour lines in NAGContour s display window see Figure 7 13 You can modify the number of contour lines by adjusting the Contours slider on the NAGContour module control panel By default the module selects the heights for the contour lines automatically based on the range of the data and the number of lines requested Try changing the heights by setting the Mode parameter toNumber of Contours or Contour Interval and setting the levels using the dial widgets Figure 7 13 The DataScribe Module in the Map Editor You might like to use your map to look at another example file which is in the dsExample1 format You can find the file in usr explorer data scribe dsExample1 data Finally you may like to look at the shipped version of the dsExampleI module which is
228. ur text Text type in slots appear in some input modules as part of a file browser widget see below 2 9 5 File Browsers The file browser widget appears in modules that read or write files from or to the file system To use the file browser you must have the full scale control panel of the module open see Figure 2 23 Figure 2 23 A File Browser The file browser has two windows The top one Contents displays the contents of the current directory including files and subdirectories The bottom one Selection shows the current selection file or subdirectory You can list the files in any subdirectory on your system Rather than having to type a filename into a text slot on the module you can simply select the file from the file browser You can move up a directory hierarchy by selecting the _ entry the first one in the list To select a file or directory from the Contents list double click on the name If your selection is a directory the file browser displays its contents in the Contents window and its path and name in the Selection window If it is a file it sends the filename to the module The filename appears in the Diminutif control panel text slot and the module fires To open a file you can also click once on the filename to select it and then click on the OK button The filename appears in the text type in slot of the Diminutif control panel and the module fires You can use the file browser to traverse
229. ure of the alternate command option wherever the word HOST appears the name of the remote host will replace it If the word HOST does not appear in the command it is appended to the end Hence the following two lines are functionally equivalent host superhost command rsh HOST host superhost command rsh Other UNIX programs may be used instead of rsh and rexec depending on local conventions A 4 Running the X Server The type of visual you run on your X server determines the number of colors available for modification and this affects how many GenerateColormap modules you can run at one time A 4 1 Selecting a Visual The X server supports several classes of color visuals Each visual class uses a different method to display color The GenerateColormap module is designed to function properly with the PseudoColor and TrueColor visual classes The PseudoColor visual uses the hardware colormap to display a small number of colors from a much larger palette of possible colors The TrueColor visual class writes colors directly to the graphics frame buffer The visual classes have a depth that specifies the number of bit planes it uses for display A PseudoColor visual with a depth of 8 displays 256 colors at one time one with a depth of 12 displays 4096 colors The TrueColor visual supports depths of 24 and 12 bits The 24 bit TrueColor visual can display 8 bits for red green and blue or over 16 million possible colors at one ti
230. us on a module in the Build Options window of the Module Builder see Figure 3 29 Selection of While Repeat or None which is the default prompts the MCW to provide the correct interface for the module The distinguishing characteristic of a loop controller module is its ability to break its loop IRIS Explorer has While and Repeat modules whose sole function is to control While and Repeat loops but other modules can also function as loop controllers Table 3 4 lists the IRIS Explorer loop controllers While Loops For AnimateCamera Trigger Render While Repeat Table 3 4 Loop Controller Modules 3 8 3 How Loops Work There can be only one active loop controller in a loop If the loop contains more than one module with loop controller capability IRIS Explorer selects the active loop controller based on information from the loop connections You can change the active controller by clicking on the loop icon A message appears asking for confirmation Note Even though IRIS Explorer allows you to change controllers the change may not make sense from a programmatic point of view It is up to you to make sure that the looped map makes computational sense and 52 that it will terminate A loop fires until the loop controller detects an end of loop condition and stops the loop To fire a loop or to start up a loop that has been terminated you can fire the loop controller module The controller module can always cause its loop to
231. use arrays sets or lattices in expressions 1 ERROR Non scalar SingleComponent used in expression Lattice nCoord Var gt Bad value expression Wiring mismatch 0 WARNING gt Source of wire is a scalar but its destination is a non scalar 0 WARNING gt Source of wire is an array but its destination is not an array 0 WARNING gt Source of wire is a lattice but its destination is not a lattice Excessive wiring 0 WARNING Lattice nDataVar gt Data object has both an input wire and a value expression The value expression will be ignored Note The DataScribe module does not produce diagnostic error messages beyond those typically found in an IRIS Explorer module 105 Appendix A Configuring Your IRIS Explorer Environment This appendix explains how to configure various aspects of your system in order to use the IRIS Explorer more effectively It includes modifying your explorerrc file setting environment variable s configuration commands remote execution and passwords running the X server creating a larger kernel A 1 The explorerrc Configuration File IRIS Explorer reads configuration information from files on start up This information tells IRIS Explorer among other things where to look for modules how to configure the Module Librarian where and how to run remote modules what size the memory arena should be This information can come from two separate
232. use the graphic capabilities of Render itself to enhance certain aspects of the object and to view it from various angles The other modules operate on the data in various ways to produce a geometric object that makes it easier to understand interpret and extrapolate from the original data Render and some of the more commonly used modules are described fully in Chapter 3 Specific Module Functions 18 To decide which modules you want in a map you need to have more information about what each one does what data it accepts and what it produces for other modules to use as well as what parameters it can have You can find information in these places All the available IRIS Explorer modules are listed in the Module Librarian You can move them from one category to another in the Librarian For details see Organizing the Module Librarian To see the modules listed by function refer to Table 3 1 in Chapter 3 To see the modules listed by the data types they accept as input and produce as output refer to Table 2 1 through Table 2 3 To find out in detail what the module does see the module definitions in IRIS Explorer Reference Pages or use the module Help option see Getting Help 2 4 2 How Modules Work When you launch a module from the Module Librarian the module control panel see Figure 2 6 through Figure 2 8 appears in the Map Editor Module control panels are rectangular windows that give you access to t
233. uses the notation of the C programming language for array indexing So the ith element of an array is Array i but for a 2D array the th element is Array 4 i Similarly the node located at ijk is Array k j i The ij k axes correspond to the x y z physical axes You can use zero or one based addressing in the arrays if you wish one based is the default Since i varies fastest for a 2D uniform lattice the Xmax element of the bounding box is bBox 1 2 and the Ymin is bBox 2 1 These are laid out in memory as follows bBox 1 1 Xmin bBox 1 2 Xmax bBox 2 1 Ymin bBox 2 2 Ymax This is important when you use a set to define a collection of scalars that you later connect to an array 7 7 5 Lattices IRIS Explorer lattices exist in three forms 1D 2D or 3D with uniform perimeter or curvilinear coordinates The lattice data type is described in detail in Chapter3 Using the Lattice Data Type in the RIS Explorer Module Writer s Guide 7 7 6 Lattice Glyphs Lattice glyphs are pre defined sets that contain array and scalar glyphs Each type of lattice glyph has the correct data elements for that particular IRIS Explorer lattice For examples see Lattice Types You can replace only the node type icon in the data array If you try to replace another node type icon the DataScribe informs you that the glyph is locked and cannot be altered Lattice Components A lattice has two main pa
234. utter and simplify the map you can cluster related modules together under a single control panel called agroup A group is an encapsulated collection of modules with its own module control panel When you have an elaborate map containing several opened control panels it is possible to misplace some of them they become hidden behind one another or behind other windows on the screen To minimize the visual complexity of a map you can group several related modules under one control panel creating a more manageable network of modules Even with a smaller number of modules you will probably have more accessible controls than you really need for a specific map Frequently the creator of a map is not the end user but is producing the map or application for a group of co workers or customers Such a map is created for a specific purpose and many of the module parameters available to the map developer will not be needed by the end user The developer can group modules in the Group Editor to reveal only those parameters relevant to the application at hand This restricts the functionality of the map but also streamlines its user interface You can use the Group Editor to promote specific widgets and their ports from individual modules to the group control panel When you have placed the widgets on the group control panel you can edit them using the Control Panel Editor which runs from inside the Group Editor Once you have established the group those
235. vides the predicates module and connection to test the type of a variable module cl connection cl t A predicate returns either false or t true The following module m1 t means that the variable m contains information about a module started some time in the past The t rue return value does not necessarily mean the module still exists B 2 Skm Language Features The sections that follow describe the programming language features of Skm B 2 1 Comparison Operators Skm provides two basic comparison operators eg and eqv The first eg determines if two symbols evaluate the same The latter eqv is more general It determines the equality of both symbols and numbers eq Below are examples using eq to test the equality of symbols eq test test 1 eq test hat But you can t use eq for numbers 117 eqv Here eqv is shown for numbers and symbols eqv 3 3 t eqv 3 4 eqv test test t Numbers can also be compared with the following operators gt You can use these operators only to compare numbers B 2 2 Conditional Operators A conditional test can be performed using the if operator which takes the form if test expr then expr els Xpr For example if eq expr 1l expr 2 do something do something else If more than one statement belongs in either the then or the else portion of the ifconstruct use
236. which appears only on the module pop up menu of active loop controllers see Figure 3 33 It forcibly terminates a looping cycle Figure 3 33 Module Menu on Active Loop Controller If your looping map seems to be hogging resources with execution highlighting on try switching it off before you initiate a loop 3 9 The IL Controller Module This module is used to create a single executable process from a group of ImageVision Library IL modules The module takes map file information about the constituent modules and their ports and connections and creates an IL operator for each IL module in the map It then chains these operators to execute the modules in effect creating a single executable process from all the alternate module executables The IL Controller module sits between the Image Vision Library and IRIS Explorer It is similar to the dataScribe module that uses a scribe file except that the IL Controller module uses a map file There must be both amodulename map file and an mres file for the module to function To use the IL Controller module this is the procedure you follow 1 Create a map from several IL modules 2 Group the modules in the Group Editor and save the map as a group 3 Save the grouped map file by using the Save Selected item on the Librarian File menu You will be prompted to confirm that the map is saved as an imaging process If you click on OK then an mres file is created with the map filename 4 Op
237. within double quoted strings may confuse the Skm parser Note When setting the value of a parameter using set param you may need to know something about the type of widget associated with the parameter B 4 4 References Skm is similar to the Scheme programming language A good Scheme language text may be of some value to those seeking advanced understanding of Skm A thorough well written text is Scheme and the Art of Programming by Springer and Friedman A quick and amusing introduction is The Little Lisper by Friedman and Felleisen Additional information may be found on the network for pointers see http www nag co uk 0 visual IE iecbb Info html B 4 5 Copyright Notice Skm is based on the SIOD interpreter by George Carrette Note that features of SIOD not explicitly documented herein are not supported The following copyright notice accompanies SIOD as distributed on altdorf ai mit edu COPYRIGHT 1988 1992 BY PARADIGM ASSOCIATES INCORPORATED CAMBRIDGE MASSACHUSETTS ALL RIGHTS RESERVED 126 Permission to use copy modify distribute and sell this software and its documentation for any purpose and without fee is hereby granted provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation and that the name of Paradigm Associates Inc not be used in advertising or publicity pertaining to distribution of the software wi
238. x y and z coordinates Enter the new value and see how the position of the object changes Figure 3 24 The Transform Sliders Next to the slider name in the open slider is a Style button It offers three different layout styles for the widgets in the slider To see the different widget layouts click on Style 3 7 9 Displaying Transparent Objects If you want to make an object transparent use the Transp slider in the Material Editor see Using the Material Editor To display the transparent object you can select Screen Door Transparancy or any of the other sorted transparency widgets on the Viewing menu Note Some workstations do not support sorted transparency They can only display transparent objects in Screen Door format As its name implies Screen Door Transparency renders objects as meshes that you can see through Sorted transparency also called blended transparency gives a more accurate rendering of the transparent object but the scene is drawn more slowly than in Screen Door format 3 7 10 Changing the Lighting The Render module has a headlight that is situated in the camera position which is defined as being just over your left shoulder The headlight moves with the camera You can also create point spot and directional lights which remain with the objects in the scene Thus if the camera moves left the lights appear to move to the right You can have as many as you like on at any given time You can change the
239. ximum levels The result is shown in Render see Figure 1 5 You can open the Render window by clicking on the Maximize button and rotate the object in the window To move the object place the cursor on the object hold down the left mouse button and drag the object around It continues to rotate when you release the mouse button To stop the object click on the background of the Render window Figure 1 5 The Contour Map in Render For more information on using the Render menus to manipulate objects see Visualizing Data in Chapter 3 1 4 Numerical Mathematics This example illustrates how to use IRIS Explorer modules to read in a short program script describing a mathematical function and visualize the data in the Render window The mathematical function describes diffusive heat flow It is a finite difference Footnote For more information on finite difference techniques see Mitchell A R and Griffiths D F The Finite Difference Method in Partial Differential Equations John Wiley and Sons 1980 stencil for solving problems in parabolic differential heat conduction The form of the equation in this example is dimensionless it serves as a normalized thermal model A map using a The form of the equation in this example is dimensionless it serves as a normalized thermal model A map using a specific form of such an equation with actual data can be used for example to test the conductivity of steel 1 4 1 Openin
240. y applied to the dragged module Destroy Replace Help Show Log and Disable Enable icons provide the same functionality as above options in the module pop up menu but can be applied to many modules Disconnect and Reconnect icons provide an alternative to using the options on the edit menu Getting Help Each module has a Help window associated with it which explains the purpose of the module and lists its input ports output ports and parameters To open this window click on the title bar of the control panel with the right mouse button and select Help from the pop up menu see Figure 2 9 To close the Help window click on the left button of the title bar and select Close from the Window menu or double click quickly on the left button The modules are listed alphabetically and described in detail in the RIS Explorer Reference Pages and by gt their individual Help files and man pages Replacing Modules Replace provides a convenient one step method of disconnecting destroying re invoking and reconnecting a module This is particularly useful when developing a module The module can be replaced with the new version of the executable in one easy step The new module is re invoked with all the old s existing connections P Func and Widget values There are two ways you can instigate a replace you can drag a module to the Replace icon located at the bottom of the Map Editor to replace it or if it
241. y string and substitute with any single character You can also use UNIX search expressions such as grep or egrep to search for a specific string To activate this capability open the Glyph Property Sheet for the pattern glyph and click on the Reg Exprs button see Using the Glyph Property Sheet Clicking on Exact or Wildcards on the Property Sheet is an alternative to toggling the wildcard button the choice is shown on this button when Apply is selected aCase Sensitive toggle button to activate case sensitivity When it is on the DataScribe matches the upper lowercase pattern in the termination string When the button is off it ignores case for example Explorer matches explorer Example 7 2 Creating a Template with Pattern Glyphs This example illustrates how to use the pattern glyph in an input template A file is usually composed of a header followed by several arrays The header consists of a number of character strings that provide sizing information and other clues to the file s contents Figure 7 24 shows an example of such a file Figure 7 25 shows an input template that describes this file structure using pattern glyphs To read the file into IRIS Explorer see Example 7 3 Figure 7 24 File Structure for Pattern Template The sections shown in Figure 7 24 up to the 2D floating point array correspond to the glyphs in the FirstFile template shown in Figure 7 25 The text is converted by means of pattern glyp
242. you can store both a number and a string into the same variable skm gt define var 23 23 skm gt define var hello there hello there The Comment Character The semicolon is the comment character in Skm It comments out the remainder of the line on which it is located As seen above the define operator returns a value that is printed after the Skm statement is evaluated In the discussion that follows the printing of a return value when present is sometimes omitted for the sake of simplifying the presentation B 1 2 IRIS Explorer Operators This section introduces the Skm commands used to perform functions in IRIS Explorer Those commands that accept one or more module names as arguments can handle zero or more module names listed in sequence or a Scheme list of module names The semantics of the commands when given no arguments depends on the particular command but in general it means to apply the command to all selected modules Table B 1 lists the available commands Command Purpose all mods List all modules all groups List all groups break loop Break a loop by halting a named module connect Establish a connection between two modules connection Test a variable for connection information connection list List all modules connections copy Copy selected modules and groups cut Cut selected modules and groups destroy Destroy selected modules and groups disable Disable selected modules and groups disconnect Remove a co

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