Known Problems and Limitations in IVE/Priism

Overview

The known problems have been categorized by application; those which apply to many applications can be found in the general category.

Topics

General Problems

Almost all applications internally use single precision floating-point values to store image data; that is not enough precision to adequately handle images stored as 32-bit integers.
Priism does not clean up properly if you log out or the X server dies while Priism is running. There is a chance (for versions prior to Priism 4.1.6 it is a certainty) that the remains of the Priism session will interfere the next time Priism is started. Use of ivekill (see the answers to questions 7 and 9 in the IVE 4 FAQ) is the recommended solution.
The layout of directories and files in the Priism distribution is not compatible with those for an application in /opt according to the Filesystem Hierarchy Standard.
Some documentation, not directly related to deconvolution, references the deconvolution documentation which is not included with the publicly distributed version.
(IRIX only) The HTML-based help system response is slow with Netscape.
(OS X 10.3 and earlier) If the shared memory file is on a HFS+ file system (which is the normal case), the first Priism application that is closed takes an unusually long time to exit (the time is apparently spent in the close() system call on the shared memory file).
(OS X only) The same user can not run multiple Priism sessions each of which has a different shared memory file.
(OS X with Apple's X11 beta quartz-wm) If an application has iconified dialogs, iconifying the application's main dialog causes the previously iconified dialogs to appear on the screen without window manager decorations.

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Image Windows

The effect of different offsets for different waves (i.e. as set with the Align program) is not taken into account when drawing graphics on top of the images (except for object library graphics which are used by Clouds).
When a scratch window is not full, it is possible to step past the end of the sections that have been used so far.
In RGB mode, if an application sets the currently displayed wave to one that is not drawn, the slider along side the image still functions to change the current section but the mouse buttons do not.
Applications are not notified when the monitor window changes size. So if they have graphics which are drawn in window coordinates (rather than the coordinates for the image data), they will be not be able to update their graphics are not able to update their graphics appropriately (this affects picking regions in EMTAR).
The File->Save function always uses the native byte ordering but every other Priism application saves images with big-endian byte ordering. This is of no concern if the files are used by other Priism applications, but may make a difference for other applications that read MRC format files.
The positioning of images within the window changes when the resolution is changed.
Have observed incorrectly redrawn image windows after resizing the window on XFree86 4.1 systems and the Window Maker window manager. Changing sections (or anything else that causes a redraw) causes the correct display to be drawn.
It is not uncommon for window managers to ignore requests to change the window border and title bar decorations; under window managers that do so, the IWAlDisWinBdr function call has no effect.
(OS X with Apple's X11 or XFree86 4.3) When an application adds a graphic (for instance Pick Points or Edit Polygon) the graphic does not appear until something forces a full redraw. With Apple's X11, you can turn off the "prefer double buffer" startup option in the preferences to avoid the problem. XFree86 4.3 only provides double-buffered visuals and there is no known solution to the problem.
(OS X on Intel-based IMac and ATI graphics card) Dragging or resizing the region of interest for EM reconstruction causes the image to disappear. In some other instances, the image disappears when an application adds a graphic to an image window. Forcing a redraw causes the image to reappear. Turning off the "prefer double buffer" startup option in the preferences appears to solve the problem. We do not know if this problem affects other Mac hardware configurations.
(OS X with Apple's X11) Image window contents are not refreshed when the computer returns from sleep.
(IRIX only) When Priism is used simultaneously with an application that uses a 12-bit color-indexed visual, colormap flashing occurs. Examples of such applications include showcase, snapshot, and jot from SGI and Chimera from UCSF's Computer Graphics Laboratory. If the other application only uses a limited range of entries in the 12-bit colors table, then use the startup preferences in Priism to specify an offset for Priism's color table so that it does not conflict with the other application. If the other application uses the full 12-bit color table (this is true for Chimera), the "emulate pseudocolor" option can be turned on to avoid colormap flashing (at the cost of longer times to draw pseudocolor images).
(IRIX only) Copying an image from an image window into showcase with the image gizmo frequently just grabs a black image or an image of a different section (the Priism window is double-buffered and showcase may be reading from the wrong buffer). Forcing a redraw of the image window, which is possible by selecting the Redraw option in the image window's Image menu, can cause Showcase to grab the correct image. For an alternative to the image gizmo, SGI's mediarecorder is recommended; it reliably captures images from image windows.

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Processing Applications

The convolution, Filter 2D, and Filter 3D applications do not work with complex data.
CCDCor and Convolution are missing documentation in the old-style format.
CTFPlot is missing documentation.
(Linux, OS X) CTFPlot only writes a PostScript result rather than opening a previewer with the graph.
The bead alignment and EMTAR user interfaces occasionally die because of X window errors when parameter subdialogs are displayed or hidden.
The bead alignment applications only handle data sets with 500 sections or less.
The elliptically-weighted backprojection step in EM reconstruction only handles tilt series with widths up to 16384.
For simplex, the extended header on the output is likely not correct if the input wavelengths are drawn from multiple files.

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Modeling Applications

In 3D Model, connecting a branch point in one object to a branch point in another causes parts of the objects to be lost.
In 3D Model, an attempt to connect an object to itself causes an infinite loop.
In 3D Model, dots added with the "just dots" option are not visible unless lighting is on and the background is not black.
The option in 3D Model to turn off the special mark for the current point does not affect what is displayed in image windows.
Pick Points watches for presses of the tab key in the image window to change the current picking mode, but Motif uses the tab key to transfer focus from one dialog control to another.
In Region Growing or Find Points, if region growing results for the mask or masked input are only generated for a subset of the input z, time, or wavelength values, then the extended header of the generated data is not appropriately shuffled.
Output of multiple wavelengths is unreliable with strait's cookie option: the data for the all wavelengths except the last can be lost.
Tracer only works with image windows.
With a synthetic test case (an image with two greylevels), Tracer and 3D Model's automodel did not perform well because an early termination condition in the search is sensitive to round-off error.

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Other Applications

(Linux, OS X) 2D Plot and MonToPS only support the option to print to a file; print preview and sending the result directly to a printer are not enabled.
Flip may thrash badly if the input is an image window and even more so if the output is another image window.
Line Profile's x, y, or diagonal profiles are not handled correctly when the source image window displays multiple sections and the step direction is not z.
The rendering of graphics drawn on images is different in MonToPS than it is in the image window: graphics in window coordinates are not clipped at the window edges and graphics from 3D Model are not shown.
The Priism menu bar does not need resize handles.
Projection algorithm in Rotfast breaks down as the tilt approaches +90 or -90 degrees (for instance get completely black image at +90).
A dialbox affects all image windows currently used by Volume Viewer for interactive display; no method is provided to restrict the dials to affect the image window with focus.
There is a half-pixel (in data coordinates) offset in x and y between VolumeViewer results and the overlay models from 3D Model.
The software renderer in VolumeViewer effectively cuts off a one pixel (in data coordinates) from the top, right, and upper edges of the input volume.
Volume Viewer does not handle complex-valued data.
Volume Viewer is missing documentation in the old-style format.

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IM Library

The mechanism for detecting when byte-swapping is necessary limits the x or y dimensions of a data set to be less then 65536. The library can not detect if byte-swapping is necessary if the x and y dimensions of a data set are both zero.
When an application uses IM calls without any calls to IWAlScl or IWAlSecScl and writes a result to an image window, the results often do not appear "right" because each section is scaled separately. The default scaling done in this case should be drawn the minimum and maximum values from the header.

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IW Library

The following functions are possibly useful to clients but are poorly documented: IWAlQuePri, IWCopyPartialData, IWGetAppXDisplay, IWGrGetGrPtr, IWRetArenaPtr, IWRtCurDataGraphics, IWRtCurWinGraphics, IWSetAppXDisplay, IWSetComplexNormalValue, and IWTransformPartialDataType.
The following functions set or retrieve state information that has no effect on image window behavior: IWAlOffsetGroup, IWRtOffsetGroup, and IWRtScrnGeom.
The following functions have no effect: IWLowerWin, IWRaiseWin, and IWRtLastDLWin.
The following functions have out-of-date internal implementations: IWAllocTrueColor, IWRtFontAscent, IWRegDisChg, IWRegEvt, IWUnregDisChg, and IWUnregEvt.
IWCopyPartialData and IWTransformPartialDataType do not work with data in the IW_COMPLEX_SHORT format.
It is not uncommon for window managers to ignore requests to change the window border and title bar decorations; the values returned by IWAlDisWinBdr and IWRtWinDisWinBdr do not indicate whether or not the window manager honored the request.

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WM Library

The following functions are possibly useful to clients but lack documentation: WMInitChainCmd, WMStopChainCmd, WMProcessEvent, WMSync, WMNotExecutable, WMProcClientMessage, WMCancelClientMessage, WMUpdateFuncList, WMRetAppContext, WMGetShellWidget, WMProcExtEvent, WMCancelExtEvent, and (in the Fortran interface only) WMGetEnv. Also, the functions for working with the saved parameters and scaling preferences are not documented.
(Linux, OS X) The version of the WM library compiled with the LessTif library ignores requests to put menus or dialogs into the overlay planes even if they are available.

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IP Library

Assumes at least one input file is specified.
Allows the user to append to data sets with multiple resolutions, but does not fill in the lower resolution versions of the appended data.
The tests for whether or not it is safe to have an input and output have the same name are overly restrictive.
Some callback constants mentioned in the header file are not used anywhere (REG_DIS_CHG, UN_REG_DIS_CHG, ENV_CMD, VIEW_FILE).

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modified $Date: 2008/05/03 01:48:32 $

IVE Development Team (ive@msg.ucsf.edu)

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