Figure 2-1 The Map Editor
This chapter explains, step by step, how to use IRIS Explorer tools to create and run maps. It describes how you:
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 data 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 maximized and Diminutif(tm) control panels. These are rectangular panels, displayed on-screen, which contain widgets, the means of adjusting module parameters.
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.
To bring up the Map Editor, type
explorerat the shell prompt in the shell window.
The Module Librarian, the Map Editor, and the Log Window appear.
To exit from the Map Editor, open the Admin menu and select Quit. When you do this, you also quit IRIS Explorer after confirmation at the prompt.
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:
Some of the Edit menu options have keyboard shortcuts listed next to them.
With this menu you can also display or remove from view features such as the Main Log and Skm Window.
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.
The Module Librarian (see Figure 2-2) is a file browser and selector that provides access to IRIS Explorer modules and maps through 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:
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:
Maps in the Module Librarian are colored blue, modules are beige.
Use the scroll bars in the Module Librarian columns to scroll up or down through the lists of available modules and maps. To scroll easily through the module categories:
If you use the file browser to launch a module or map 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). If you have more than one copy of a module in a map, the second copy will have the number <2> after its name. The third will have <3>, and so on.
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 command line option -map with a filename.
Type:
explorer -map filename.map
The Map Editor opens and the map is launched and displayed automatically.
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, $EXPLORERHOME/maps/cfd.map, where $EXPLORERHOME is the root directory where IRIS Explorer is installed on your machine.
Use the Module Librarian File menu to save your maps. You must save all IRIS Explorer maps with the filename extension .map; otherwise, IRIS Explorer will not be able to find the file when you try to open it again.
Click on the module 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:
Modules can be saved only as part of a map, but you can save incomplete maps and bring them up later for further work.
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 <2> (or <3>, if it is the third version to be launched).
This example illustrates how to launch an existing map from the Module Librarian and carry out some simple operations.
Figure 2-4 shows the map you should see on your screen. It visualizes the data in the file $EXPLORERHOME/data/lattice/testVol.lat.
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.
The simple map is a three-module map, consisting of:
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:
For more information on using Render, see Chapter 3 - Using 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:
See the IRIS Explorer Module Writer's Guide for more information on Creating a User Function for the module core.
The visible portion, or control panel, which appears in the Map Editor, is a rectangular window that contains:
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.
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.
IRIS Explorer modules can be grouped according to their general function (see Table 3-1 in Chapter 3 ). They can:
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 the Render window, you can 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.
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:
When you launch a module from the Module Librarian, the module control panel (see Figure 2-6, Figure 2-7 and Figure 2-8) appears in the Map Editor. Module control panels are rectangular windows that give you access to the capabilities of the module core via two main channels:
The control panel also has:
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 the mouse button, all modules that are completely enclosed by the lasso will be selected. Alternately, you can hold down the <Shift> 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 All.
Use the <Shift> 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 <Shift> key and click on the module.
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.
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 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 for the whole group simultaneously. You have to open each full-scale panel individually.
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.
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:
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 modules, otherwise the operation is only applied to the dragged module.
Destroy, Replace, Help, Show Log and Disable/Enable icons providethe same functionality as above options in the module pop-up menu, but can beapplied to many modules. Disconnect and Reconnect icons provide an alternative to using the options on the edit menu.
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 IRIS Explorer Reference Pages and in their individual Help files and man pages.
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:
This example illustrates the first steps in creating a map.
You now have the basic components of a map in the Map Editor.
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.
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.
To launch this map and connect the modules, go to Wiring Modules 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.
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 required 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.
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 only 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, it is highlighted in green and all the compatible input ports on other modules in the Map Editor are highlighted in a lighter shade of green. Likewise, when you select an input port, all compatible output access pads light up in a lighter shade of green. Incompatible ports are not highlighted and 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 Using the Lattice Data Type in the IRIS Explorer Module Writer's Guide.
Wiring modules together is a simple process. You can wire input to output port or output to input port. Figure 2-12 shows a connection from the output port of ReadPhoenics to an input port of ChannelSelect.
To make the connections, follow these steps:
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.
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 SampleCrop module with two connections on its output port, one to the input port of WireFrame and one to the input port of NAGAxis. To make these connections:
To connect an input port to the output ports on several different modules, follow the same procedure.
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:
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:
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.
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, choose one of the three options, Pt to Pt, Right Angle, or Diagonal. Click on each one in turn to see its effect. The option that is currently in force is greyed out and cannot be selected.
You can also change the way in which the wires are colored. By default, all wires are colored blue, apart from the control arc in a loop, which is colored magenta. An option to color each wire according to the data type that is being passed along it is available through the resources used by IRIS Explorer. Copy the relevant lines in the section called New Wire Options for Version 4 from the file $EXPLORERHOME/lib/X11/app_defaults/Explorer into your .Xresources file to use as a template, and change them as required. Then type
xrdb .Xresourcesbefore starting up IRIS Explorer.
A further option - Explorer*showAllConnections - allows you to display multiple connections between modules (by default, only one wire is drawn, irrespective of the number of connections). You can set this option in your .Xresources file in the way described above.
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.
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.
Launch the map by dragging and dropping it in the Map Editor. Then wire the modules together and set widgets as follows:
Notice that Contour has two connections on its input pad, but they go to two separate input ports.
If you want to keep the finished map, remember to save it again.
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:
You can force a module to fire by:
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.
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.
When a module fires successfully a connection 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
There are a number of ways in which module(s) can be disabled:
Disabling a module is useful if:
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 re-enable the disabled module.
When modules fire in the Map Editor, they often generate informative text messages. For example, PrintLat, PrintPyr, and PrintPick all 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.
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.
You can hide or display the Map Editor Log by toggling the Log Window option on the Map Editor Layout menu.
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).
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 2-18) 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 into a file.
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.
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.
The IRIS Explorer data types are:
This is the most commonly used data type.
Parameters are used to set values for slicing planes, error tolerances,
quantities, and filenames.
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 are user-defined data types. They work exactly as IRIS Explorer data types do, handling data in a specific format.
All the data types are described fully in the IRIS Explorer Module Writer's Guide.
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:
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.
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 theIRIS 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, CropPyr, IsosurfacePyr, PrintPyr, PyrToGeom, PyrToLat, Transform, WritePyr |
| Geometry | Render, WriteGeom |
| Pick | Annotation, Ball, CropLat2D, CropLat3D, InterpLat |
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.
| Output Port Data | Modules |
|---|---|
| Lattice | AtomicSurf, ChannelSelect, ColorXform, CropLat2D, CropLat3D, DisplaceLat, DisplayImg, GenerateColormap, GenLat, Gradient, Histogram, Interpolate, LatFunction, MagnitudeLat, Mixer, OrthoSlice, PyrToLat, ReadLat, ReadPlot3D, Render, SampleCrop, ScaleLatNode, Shell, Slice, SubSample, Transform, TransformGen, WaveFormColormap |
| Pyramid | CullPyr, CropPyr, LatToPyr, ProbeLat, ReadPyr, ReadPDB, Transform, Triangulate2D, Triangulate3D |
| Geometry | Annotation, Ball, BallStick, BoundBox, BoundBoxPyr, Contour, CropLat2D, CropLat3D, DrawText, IsosurfaceLat, IsosurfacePyr, LatToGeom, Legend, MultiSlice, PyrToGeom, ReadGeom, VectorGen, VolumeToGeom, WireFrame |
| Pick | Render |
All modules that have input ports for parameters also have output ports for them.
Table 2-3 lists some of the image processing modules provided. Image processing modules manipulate lattices and only accept and produce objects of the lattice datatype.
| AbsImg | AddImg | AndImg | BlendAlphaImg |
| BlendImg | BlurImg | CompassAngleImg | CompassDirImg |
| CompassImg | ComplementImg | DisplayImg | DivImg |
| ExpImg | ForwardFFTImg | FourierConjgImg | FourierCrossCorrImg |
| FourierDivImg | FourierExpFltImg | FourierGaussFltImg | FourierMagnitudeImg |
| FourierMergeImg | FourierMultImg | FourierPhaseImg | FourierPwrImg |
| GaussBlurImg | GrayScaleImg | HistEqualImg | HistNormImg |
| HistScaleImg | InverseFFTImg | LaplaceEdgeImg | LogImg |
| MaxFltImg | MaxImg | MedianFltImg | MinFltImg |
| MinImg | MultImg | NegImg | OrImg |
| PowerImg | PseudocolorImg | RankFltImg | ReadImg |
| RobertsEdgeImg | RotZoomImg | SGIPaletteImg | SharpenImg |
| SobelEdgeImg | SqRootImg | SquareImg | SubtractImg |
| ThreshImg | WriteImg | XorImg | ZoomImg |
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.
Buttons are rectangular or diamond-shaped widgets that let you select a value or switch a specific parameter on or off. They come in three styles (see Figure 2-19):
Use the left mouse button to click the buttons on and off.
Sliders (see Figure 2-20) are either horizontal 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:
You can change any one of these values by clicking on the text slot to highlight it, typing in a new value, and pressing <Enter>.
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 middle mouse button.
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 <Enter>), and you can also change the current value by turning the dial pointer. Dials generally have float values.
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.
Text type-in slots (see Figure 2-22) accept alphanumeric characters.
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 your text.
Text type-in slots appear in some input modules as part of a file browser widget (see below).
The file browser widget appears in modules that read or write files from or to the file system. See Figure 2-23 To use the file browser, you must have the full-scale control panel of the module open.
The file browser has a number of areas:
The first entry of the list (../) may be used to move up one level in the hierarchy to the directory which contains the current directory.
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.
You can use the file browser in two ways:
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.
A scrolled list widget (see Figure 2-25) 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.
A drawing area is a blank rectangle on the maximized and Diminutif control panel only in which an image or visual object can be displayed (see Figure 2-26). For example, the modules DisplayImg and Render have drawing areas on their maximized and Diminutif control panels.
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.
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:
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.
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.
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 Category when it appears. To redisplay the category, select the category name from the Categories menu. You cannot delete categories, only hide them. To update a category, select Update from the Display menu after you have added new modules or maps.
When you choose Update from the Display menu, new categories that have not been saved already are deleted. To save new Librarian categories, so they remain visible the next time you start up IRIS Explorer, see Saving the Librarian Configuration.
You can copy 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.
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.
Use the Delete option from the Module Launch menu (see Figure 2-3) to remove a module or map from a category 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.
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.
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 .explorerrc Configuration File in Appendix A.
When all the launched modules have been connected 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.
If a 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).
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:
If nothing appears in your Render window, try the following procedure:
This brings an object that may be out of the viewing area into the center of the window.
If you have changed object parameters, but the changes do not appear in the object, try the following procedure:
If the lattice is 1D or 2D, such as an image:
If the lattice is 3D, such as a volumetric dataset:
See Slicing Volumetric Data in Chapter 3 for more information about using slicers.
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:
The default directory is $EXPLORERHOME/maps.
You need to save the map again. To prevent this from happening a second time:
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.
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 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 remote system.
The best place for such output is the .login file. Other programs besides IRIS Explorer get confused and do not work properly when there is output from the .cshrc file.
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.
You can check this in two ways: