KEYWORD Profiles ImageColor WaveColor BkgColor Zoom Interp Resolution Scalebar ScalebarColor ScalebarDir ScalebarThick ScalebarPos GrDisRange ColorList ImageWindowSize Border ShowTools MultDisplay Step AutoRepeat ShowImg BufferImg Complex ScalingMethod HelpButtonsActive HelpBrowsingMethod HelpBrowserName ContactBrowserCommand LaunchBrowserCommand HelpBrowserUsesHTML DESCRIPTION Preferences This dialog allows you to view and edit the settings which control the behavior of the help system and the initial appearance and behavior of image windows. Once an image window is started, its controls and the "Display Attributes" application can be used to customize it. You can have different versions of the image window settings and switch between them using the selection widget near the top of the dialog. Each version is referred of the settings is referred to as a profile. For more information on profiles and their management see the help under "Profiles". To view and edit a subset of the settings, use the "Preferences" menu (the second menu at the top of the dialog). After selecting a category, a dialog will appear in which you can examine and change the values. Changes are not saved and will not affect new image windows until the Save button is pressed; you can remove any changes made since the last save by selecting "Restore" from the "File" menu. Profiles Each profile is a complete set of the parameters available for controlling an image window and the help system. The profiles currently defined are listed in the selection box near the top of the dialog, and the one currently in use is highlighted and also shown below the dialog. The following paragraphs describe how to use the "Preferences dialog" to switch, create, and delete profiles. To switch profiles, simply choose one of the other choices in the selection box. If you made any changes to the current profile, you will be asked if you want to do the switch and discard the changes. A switch takes effect immediately and affects all windows launched after the switch (except for the parameters in the "Startup" category; changes there only take effect if you exit and restart Priism). Select "New..." from the "File" menu to create a new profile. You will be prompted for the name of the profile (this can not be the same as the name of an existing profile), whether to use the current profile as the starting values for the new one (otherwise the unmodified system defaults are used), and, if changes have been made to the current profile, whether or not to save those changes before switching to the new one. Profiles are saved as text files with the in the .iveprefs subdirectory of your home directory. The files with the .ivepref extension contain the image window preferences, and the files with the .helppref extension contain the help system preferences. Selct "Delete" from the "File" menu to delete the current profile and associated disk file. The new current profile will be the system defaults. PseudoOffset When displaying pseudocolor images, Priism has the option to offset its color table at the expense of addition computation in order to avoid colormap flashing when you switch from Priism to another application. On SGIs when no offset is applied, colormap flashing always happens when running SGI GL applications (jot, showcase, snapshot) and Priism simultaneously; using an offset greater than 256 (1000 has been used in the past) will avoid this except on Indys with 8 bit graphics. The offset has no effect when using the default colormap or when emulating pseudocolor. NumberOfImageColors This is the maximum number of colors that Priism will use when displaying images in pseudocolor (i.e. if the image is displayed with a grey colormap then this is the number of greys used). You may want to limit this number if you simultaneously use Priism and other applications that require many colors and allocate them from the default colormap. You may specify that the maximum number of colors used is the default number (read from CONFIG/Monitor.def in the Priism directories), the maximum number possible, or the value that you enter. UseDefaultColormap If your hardware only supports a small number of installed colormaps (you can determine this number by looking at the output of xdpyinfo) and you want to use the additional colormaps for applications other than Priism, turn on the toggle labeled "Use default colormap". This causes Priism to attempt to allocate its colors from the default colormap. You will also likely want to reduce the number of pseudocolors that Priism attempts to allocate. If the hardware only supports one installed colormap, Priism always attempts to use the default colormap. EmulatePseudo By turning on the toggle labeled "Emulate pseudocolor", displaying images in pseudocolor will be done using an RGB visual rather than a colormapped one. This eliminates potential color table conflicts with other applications but will likely slow down image display. EnableStereoInWindow When the toggle labeled "Stereo in window" is on, Priism will use visuals capable of displaying stereo images in a window if the hardware provides them. If the toggle is off, Priism will prefer visuals that are not capable of stereo images in a window. Because stereo-capable visuals may have more overhead or fewer available colors, you may want to turn this toggle off if you do not display images in stereo. PreferDoubleBuffer When the toggle labeled "Prefer double buffer" is on, Priism will preferentially use double-buffered visuals. For most uses that is desirable because it allows for smoother updates of displayed images. When the toggle is off, Priism will prefer single-buffered visuals. That may be useful for testing or benchmarking, to reduce the resources Priism uses, or to work around problems with double-buffered visuals and the system's graphics drivers. ImageColor Specifies whether images are composed of one wavelength in false color (psuedocolor mode) or of one to three wavelengths where each wavelength is represented by a different color component (RGB mode). WaveColor These menus specify the colors used for each wavelength when the image window is in RGB mode. In RGB mode, the image displayed contains the data from one to three wavelengths each represented by different color components. BkgColor Specifies the color for regions not covered by the image. Zoom Scales the size of the displayed images. Interp For zoom factors greater than one, specifies whether to bilinearly interpolate the image. Resolution When multiple resolutions are available, selects the resolution used by default when the zoom factor is one. One is the highest resolution; each higher value lowers the resolution in x and y by a factor of two. Scalebar Selects whether to display a line to demonstrate the physical scale of the image; the "Label" option adds a label for the length of the line. ScalebarColor Selects the color of the scale bar line and label. The color options are set by the current set of graphics' colors. ScalebarDir Selects whether the scale bar line should be oriented vertically or horizontally. ScalebarThick Specifies the width of the scale bar line in pixels. ScalebarLength Specifies the length of the scale bar in physical units (typically microns for optical microscopy data and angstroms for electron microscopy). ScalebarPos Specifies the location (of the center of the left edge for horizontal scale bars and of the middle of the bottom edge for vertical scale bars) of the scale bar relative to lower lefthand corner of the image window. ShowGraph Specifies whether or not graphics are overlayed on the image. This does not affect the section number display. GrDisRange When an image window displays a section of data, the graphics from nearby z slices and time points can be included in the display. Let f1, f2, f3, and f4 be the four values shown in the "Display range" field. Then the section with z index, z0, and time point index, t0, will include the graphics from sections whose z index is between z0 minus f1 and z0 plus f2 and whose time point index is between t0 minus f3 and t0 plus f4. ColorList Specifies the set of graphics' colors used. These sets can be created or modified using "Change Colors". ImageWindowSize Specifies the size of image portion of the monitor window. This differs from "Display Attributes" where the size of the entire monitor window is set. Border Specifies the border drawn around the monitor window. ShowTools Specifies whether or not to show the controls displayed along the left side of the monitor window. MultDisplay The image windows can display multiple sections at once in a grid arrangement. "# of columns" and "# of rows" control the default size of the grid. "Order" specifies the ordering of sections within the grid. With the "Bottom to top" option (also referred to as the "data format"), the current section is displayed in the lower lefthand corner and the grid is filled from left to right and from bottom to top. With the "Top to bottom" option (also referred to as the "text format", the current section is displayed in the upper lefthand corner and the grid is filled from left to right and from top to bottom. In either case as the grid is filled, the next section is determined on the basis of the step parameters. Step These options control the default behavior for determining the next section when scrolling through sections or displaying multiple sections at once. The increment specifies the number of sections to jump. You can also specify the dimension along which scrolling is done. The "Section" option for dimension specifies that the data be scrolled through in the order in which it is stored in the data file. "Wave synching" specifies what happens when a user scrolls through sections in one (or more) waves and then switches to view a wave that wasn't in view. The "Same Z Sec" option specifies that when waves are switched, the z and time indices for the section do not change. With the "Independent" option, the next section to view in a wave is not changed by scrolling through the other waves: when waves are switched the last section viewed in the new wave is the one that is displayed. With the "Coupled" option, scrolling in a wave or waves causes the next section to view in all other waves to be changed by the same amount; it differs from the "Same Z Sec" option in that it does not force the next section to be the same (only changes are coupled). AutoRepeat When interacting with the image window, pressing and holding a key or pressing and holding a mouse button can repeat an action until the key or mouse button is released. Two parameters affect the repetition: the autorepeat delay is the time the key or mouse must be held before the action is repeated for the first time and the autorepeat interval is the time that elapses between each subsequent repetition after the first. ShowImg Specifies whether or not images are shown in monitor windows (this may be useful if you want to see the overlayed graphics more clearly). BufferImg Controls whether or not the scaled data used to draw images is buffered. When on, monitor windows can typically respond faster when redisplaying an image at the expense of increased memory usage. Complex Specifies how to convert complex data to a single value per pixel so it can be displayed as an image. The options include using the magnitude, phase, real component, or imaginary component as the displayed quantity. ScalingMethod Specifies which algorithm to use when scaling data for an image. The "Fast" method is about twice as fast as the "Accurate" one, but with floating point or complex data, the "Fast" method is subject to increasingly severe rounding problems (missing intensity levels in the image) as the scaling becomes more nonlinear. For linear scales and non-complex integer data, there is no difference between the two methods. HelpButtonsActive Most graphical user interfaces in Priism use a type of button as labels. If the "Help buttons active" toggle is on, pressing one of those buttons causes the related help topic to be displayed; otherwise pressing one of those buttons has no effect. HelpBrowsingMethod The "Method" menu controls the mechanism used to display help information. The available options (which are controlled by the help_browser.def configuration file in Priism's CONFIG directory) are: Internal .hlp Viewer Uses a primitive browser to display help files in the .hlp format. This works on all systems but some of the .hlp files are out of date and the .hlp format does not allow for links or embedded images. X Windows Netscape Compatible For Linux or IRIX systems, uses a web browser which is compatible with the remote control features of Netscape for X Windows to display HTML help content. Web browsers which are compatible with this mechanism are Firefox, Opera, Mozilla, and Netscape; you can adjust which browser is invoked by entering the executable name for the browser in the Browser field. The default is an executable provided by Priism, ive_netscape_wrapper, which will use either Firefox, Mozilla, or Netscape depending on what is installed on your system. AppleScript OpenURL For Macintoshes, uses a web browser which supports the OpenURL command to display HTML help content. Many web browsers (including Internet Explorer 5.2 and Mozilla 1.3) understand and correctly handle the OpenURL command. Known exceptions are Safari (does not understand OpenURL) and Netscape 7 (displays a blank page for file URLs). You can adjust which browser is invoked by entering the executable name for the browser in the Browser field. Konqueror (KDE 3) Uses the KDE 3 version of Konqueror to display HTML help content. This method assumes that the KDE communication server (dcopserver) is running. Safari For Macintoshes, invokes Apple's Safari to display HTML help content. At a minimum, requires the second beta version or newer. Custom To display the help in a web browser not handled by one of the above methods, use the Custom method which will allow you to set any of the configurable parameters for invoking the browser. HelpBrowserName The contents of the Browser field are substituted for the first occurrence of %b in the commands to contact an existing browser or to launch a new one. For some methods, the contents of the Browser field are fixed; other methods allow you to change the name of the browser. ContactBrowserCommand If the Contact field is not empty, the help system replaces the first occurrence of %b in the field with the browser name and the first occurrence of %s with the name of the content to display (if you want a %b or %s that will not be expanded, use %%b or %%s). The help system then uses the result as a command to display the help content. If the command fails (by returning a nonzero exit status), then the help system will attempt to use the command, if any, given in the Launch field. As an example, if you wanted to use a text- mode browser like lynx, you could use xterm -e '%b' '%s' as the contact command, nothing for the launch command, and enter the executable name for the browser in the browser field. For other examples of contact and launch commands, look at the help_browser.def file within the CONFIG directory of the Priism distribution. LaunchBrowserCommand If the Launch field is not empty and the Contact field is empty or the attempt to display the help content with the contact command failed, the help system replaces the first occurrence of %b in the field with the browser name and the first occurrence of %s with the name of the content to display (if you want a %b or %s that will not be expanded, use %%b or %%s). The help system then uses the result as a command to display the help content. The description of the Contact field describes where to find examples of contact and launch commands. HelpBrowserUsesHTML If this toggle is on, the browser displays HTML content and the help system will pass the browser a URL in the form file:///file_name#topic_name otherwise, the browser displays content in the .hlp format and the help system will indicate the content to display by passing file_name#topic_name In both cases, the topic name and leading pound sign may or may not be present.