Overview
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 preferences 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
Managing Profiles.
To view and edit a subset of the settings, select a category from 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 take effect until the
Save is selected from the File menu. You can remove any
changes made since the last save by selecting Restore from the
File menu.
Topics
Overview |
Managing profiles |
Settings (by category)
Related Priism Topics
Priism |
Image windows |
Display Attributes
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 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 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.
Select Delete from the File menu to delete the
current profile and associated disk file. The new current profile will be the
system defaults.
Topics
Overview |
Managing profiles |
Settings (by category) |
- Startup
-
- Pseudocolor offset
- 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.
- # of image colors
- 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.
When pseudocolor is emulated, the maximum number of pseudo colors is
always used.
- Use default colormap
- 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.
- Emulate pseudocolor
- 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.
- Stereo in window
- When the toggle labeled "Stereo in window" is on, Priism will
prefer 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.
- Prefer double buffer
- 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.
- Image color
-
- Display mode
- 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).
- Wave 0, Wave 1, Wave 2, Wave 3, Wave 4
- 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.
- Background
- Specifies the color for regions not covered by the image.
- Zoom / resolution
-
- Zoom factor
- Scales the size of the displayed images.
- Interpolate zoomed images
- For zoom factors greater than one, specifies whether to bilinearly
interpolate the image.
- Resolution level
- 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.
- Scale bar
-
- Display mode
- 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.
- Color
- Selects the color of the scale bar line and label. The color
options are set by the current set of graphics' colors.
- Direction
- Selects whether the scale bar line should be oriented vertically
or horizontally.
- Thickness
- Specifies the width of the scale bar line in pixels.
- Length
- Specifies the length of the scale bar in physical units
(typically microns for optical microscopy data and angstroms
for electron microscopy).
- Position
- 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.
- Window graphics
-
- Show graphics
- Specifies whether or not graphics are overlayed on the image.
This does not affect the section number display.
- Display range
- 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.
- Color list
- Specifies the set of graphics' colors used. These sets can
be created or modified using
Change Colors.
- Window geometry
-
- Size
- 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.
- Decorations
- Specifies the border drawn around the monitor window.
- Show tools
- Specifies whether or not to show the controls displayed along the
left side of the monitor window.
- Multiple image display / step
-
- # columns
- Specifies the number of columns of images to be displayed at
once in each monitor window.
- # rows
- Specifies the number of rows of images to be displayed at
once in each monitor window.
- Order
- When multiple images are displayed in a monitor, specifies the
order in which the grid of images is filled. 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.
- Increment
- Specifies the number of sections to jump when scrolling though
sections in the monitor window or when displaying multiple sections
at once.
- Dimension
- Specifies the dimension along which the user can move when
scrolling through sections or along which the user can view the
data set when displaying multiple sections at once. The
Section option specifies that the data be scrolled through
in the order in which it is stored in the data file; the other
options specify to use the z, time, or wave dimension of the data
for scrolling.
- 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).
- Keyboard and mouse settings
-
- 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.
- Miscellaneous settings
-
- Show image
- Specifies whether or not images are shown in monitor windows
(this may be useful if you want to see the overlayed graphics
more clearly).
- Buffer image
- 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 data as
- 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.
- Scaling method
- 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.
- Help browser
-
- Help buttons active
- 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.
- Method
- 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.
- Browser
- 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.
- Contact
- 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.
- Launch
- 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.
- Use HTML
- 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.
Topics
Overview |
Managing Profiles |
Settings (by category)