Older Changes In IVE/Priism

Overview

Changes are broken down by the version in which they were incorporated. Older releases are:

IVE 4.1.9 (internal; June 3, 2004)
IVE 4.1.8 (March 15, 2004)
IVE 4.1.7 (November 17, 2003)
IVE 4.1.6 (internal; October 10, 2003)
IVE 4.1.2.1 (August 21, 2003)
IVE 4.1.5 (internal; May 2003)
IVE 4.1.4 (internal; March 17, 2003)
IVE 4.1.3 (internal; December 10, 2002)
IVE 4.1.2 (December 5, 2002)
IVE 4.1.1 (internal; September 18, 2002)
IVE 4.1.0 (internal; September 12, 2002)
IVE 4.0.11 (internal; August 12, 2002)
IVE 4.0.10 (internal; July 24, 2002)
IVE 4.0.9 (internal; July 17, 2002)
IVE 4.0.8 (June 21, 2002)
IVE 4.0.7 (May 20, 2002)
IVE 4.0.6 (internal; March 14, 2002)
IVE 4.0.5 (March 5, 2002)

IVE 4.1.9

Features added in 4.1.9 are:

Reworked coordinate calculations in the EM tomographic reconstruction applications, ewbp and tapir, to improve speed.
Added capability to scale to 8-bit in mrc2tiff.
The initial output size for VolumeViewer is now the size for which the entire input can be rotated without clipping.
Modified WMChangeText so it works with the buttons generated by WMAddGetFile.

Problems fixed in 4.1.9 are:

Switching back and forth between virtual desktops in KDE 3.2 no longer causes all image windows to become iconified.
Corrected the handling of per-section scaling and statistics fields when a scratch window fills up.
Removed memory leaks when an image window with overlayed graphics was deleted or overwritten.
Image windows incorrectly pruned the list of clients when a client went away without warning.
Corrected the fallback scaling calculation in image windows to cover the case where the input data is 32-bit signed integers.
Modified the 3D cursor to avoid missing button release events on Mac OS X.
PostScript output can now be printed directly by the Mac OS X Print Center.
2d_plot no longer crashes if unable to load the plot file.
Modified 3DModel so it would not crash when changing colors in certain circumstances.
Changed the printing of the scale fields in CopyRegion to protect against buffer overflows.
Corrected the deconvolution front-end to expand shell variables when testing whether an entry in CTF.def is a pupil function or CTF.
Changed ewbp so the input y line increment is factored into the pixel spacing included in the reconstruction's header.
Changed tapir so if -proj_pros=1 is not supplied on the command line, tapir still fills the padded areas with the value that indicates that no data is available in those areas.
Corrected bead alignment for tomographic data so that the initial guess calculation works if the z coordinates are fixed.
ImgToMat did not allocate the correct size for a buffer when generating a command-line script.
Restructured the Movie application dialog so that it would fit on small screens even if there are many open image windows. Removed busy wait in the Movie application.
Corrected enabling/disabling of single/multiple page controls in mrc2tiff when a new file is loaded.
When not rendering with a VolumePro 1000 board, Volume Viewer would crash in rgb/opacity mode if the n selected wavelengths were not the first n available wavelengths.
Made a number of corrections to the erase options in Volume Viewer: the invert3d erase option now works as documented, rescaling of the input now correctly updates the erased data window in the invert2d and invert3d cases, update of controls in the erase dialog no longer has unexpected side effects in the main dialog.
Disable the "Do it" button in Volume Viewer until a file is loaded; in previous versions pressing the "Do it" button when no file had been selected caused a crash.
Modified WMAddGLwMDrawWidget() to not die on an X error when asked to create a drawing area in an already realized dialog.
The restore button added by WMAddSaveButton() would not function correctly in applications with one or more on/off status indicators. Removed a memory leak when saving the state of an application with a function button list.
Modified WMRegMouseButton() to work with buttons 4 and 5 and WMUnRegMouseButton() to work with button 1.
WMSetSubExitFunc(0) was not strictly the same as WMSetExitFunction() as intended with the changes in version 4.1.4.
In previous versions, the WM library did not correctly handle reducing the size of a scrolled list by two or more items.
WM.inc had swapped the definitions for WM_RIGHT_ARROW and WM_LEFT_ARROW.

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IVE 4.1.8

Features added in 4.1.8 are:

Added a command-line interface for ImgToMat.
Added a C language interface to the iomenu routines.
(UCSF version only) Modified the deconvolution application to include depth-dependent deconvolution and the ability to use pupil functions or non-radially symmetric CTFs as the description of the imaging conditions. The handling of apodization (now more like standard tapering) and the smoothing filter (if the analytic expression would be significantly truncated in the frequency domain, compute in the spatial domain and transform) has changed. Added some command-line applications (phretavr, pffit, pf2psf, and pfimage) to manipulate pupil functions.

Problems fixed in 4.1.8 are:

Fixed the interactive bead alignment application so that turning on the "Image" toggle button when the data had not been loaded into a window and then turning of the "Image" toggle button does not cause the application to crash.
Corrected mrc2tiff and mrc2txt so that they generate correct output when asked to convert less than the full x/y range of the input.
Corrected problems in Line Profile that could cause it to report the incorrect width for the closest peak or to garble the displayed peak width values when there was no peak. Modified Line Profile to keep the z and time values in the XYZT field in sync with the displayed section in the current window.
Corrected a problem that caused region selection (or the box that Examine Data draws around the displayed region) to break drawing in image windows on some Macs with Apple's X11.
Protected against an image window crash if asked to scale a very limited floating-point range.
Removed artifacts (due to the behavior of atan2(0,0)) in the display, profiles, and histograms of the phase of complex data.
Modified the IM library so the sequence of calls, IMPosn(), IMWrSec(), IMAlSiz(), and IMWrHdr(), works to extend an image file and update the header.
Corrected a problem that could cause the front-ends to command-line applications to not be able to overwrite a preexisting command file via NFS.
Modified the front-ends to command-line applications write out the command-line option for the time range if the time step is different than one. Also modified the front-ends to command-line applications so that the time step is reset when the user selects a new file.
Added documentation for the iomenu interface.

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IVE 4.1.7

Features added in 4.1.7 are:

Added DataViews->Rotation->Reverse, an application to reverse one or more of the x, y, and z axes.
Changed EditHeader's interface to include controls to change the mapping of rows, columns, and sections to x, y, z and to provide better feedback when changing the titles (because of the new controls and other changes, now use EditHeader.save in the user's home directory rather then menu.save for EditHeader's Save and Restore buttons).

Problems fixed in 4.1.7 are:

Extended the field for the image scaling in Display Attributes to accommodate a wider variety of scaling values.
Fixed EditHeader so pressing Close File when no file is open does not cause the application to crash. Removed the number of wavelengths control which duplicated (and was not kept in sync with) the corresponding value in the ZWT field. Now use multiple columns to display the extended header entries if there are a large number of entries per section.
Fixed Examine so it does not crash when the width is reduced till no columns of data are visible.
Fixed Image Arithmetic to write out correct batch scripts when the "use region from first input" toggle is on.
Line Profile did not remove image window graphics when closed from a window manager.
Changed Bead Finder to improve speed and more gracefully handle situations when the number of candidate features would exceed an internal limit.
Generate a less cryptic error message if unable to write the script from CCDCor and similar user interfaces.
Corrected instances where command-line applications wrote binary characters to log files.
Fixed problems with the cursor in image windows (the cursor in grab and stereo mode did not appear with Mac OS X systems and XFree86 run in rootless mode; on Linux with XFree86 4.3 the crosshair cursor did not appear and, if the grab mode was used, the grab cursor would not go away).
IMTrFmt is now functional (caused problems with little-endian data loaded into a window with ViewFile).
For IMRtFmt, an image window now indicates that its format is little-endian on little-endian systems and big-endian on big-endian systems. Previously, image windows always said their format was big-endian.
Corrected or clarified the descriptions for the mx, my, mz, dx, dy, dz, alpha, beta, and gamma fields in the MRC header.

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Applied Precision requested that the deconvolution application not be included in the publicly available version. IVE 4.1.2.1 is IVE 4.1.2 without the deconvolution application, sample CTFs, and the supporting applications to help calculate CTFs.

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IVE 4.1.6

Features removed in 4.1.6 are:

Applied Precision requested that the deconvolution application not be included in the publicly available versions; therefore, the publicly available IVE 4.1.6 does not include the deconvolution application, sample CTFs, or helper applications specific to calculating CTFs.

Features added in 4.1.6 are:

CopyRegion will copy lower resolutions if the result would be the same as if the same resolutions were recalculated.
Added an application to manipulate alignment parameter files for EM reconstruction: can scale the shifts for resampling of the data or adjust the projections included. Added an application to manipulate bead list files to account for changes in pixel spacing, image origin, or projection indices.
Modified the bead alignment programs to accept alignment parameters in the .bprmMn format as well as the .bprm format.
Added x86 Linux versions of the converters to and from Matlab's .mat format.
Added versions of libimcompat.a that are compatible with g77 and Intel's Fortran compiler; added a version of libiomenu.a that is compatible with Intel's Fortran compiler.

Problems fixed in 4.1.6 are:

Added a mechanism to reduce the likelihood that Priism attaches to a shared memory file from a dead session.
Added protection against buffer overflows in the user interface fields for floating-point and integer value entries.
On OS X, the "Restore" button in some graphical interfaces (front- end to decon or EM reconstruction, for instance) no longer causes labels to disappear.
Changed the Linux plugin to save images as Quicktime movies so that it did not crash when writing uncompressed files or when it failed to open the output file.
The deconvolution with the force 2D option now allows disabling of the prefilter by setting the prefilter limits to 0, 0.
Changed Distance to allow it to work with complex-valued data sets.
Changed EditHeader to avoid crashes when a user modifies a field and the file is not open.
Changed Examine Data so it would not crash if the height of the window is reduced to the point that no rows of data are visible.
Corrected the handling of limited range of projections in the final stage of bead alignment.
Changed ewbp to record the correct mean value in the output header.
In the case where the header's "sampling interval" values were different than one, Line Profile used incorrect values for the pixel spacing in the calculation of the peak width in header units. Fixed.
Changed Region Min/Max/Mean to correctly coerce z index upper bounds that are too large.
Scale no longer crashes for scaling [3.4 x 10^38, -3.4 x 10^38, 0, 0].
Corrected setup script for sh shells so IVE_SHMDIR is not changed if already set.
Modified ivekill to make the cleanup of semaphores on OS X optional.
Image windows did not correctly calculate fallback scaling for complex short pixel formats.
Changed the method for determining whether or not to swap bytes in image data. No longer use the ID field in the header for that purpose.
Turning off display of graphics (via Options->Attributes in the image window or IWAlGrDis) now affects all 3D Model graphics as well.
Changed IWGrAddMultStr, IWGrAddMultStr2D, IWGrAddLns, IWGrAddLns2D, IWGrAddMultLns, IWGrAddMultLns2D, IWGrAddPoly, IWGrAddPoly2D, IWGrAddPts, and IWGrAddPts2D to assign the graphics ID based on the correct z index. Changed IWGrAddMultStr and IWGrAddMultStr2D to correctly copy the label coordinates.
Included declarations of IWStart, IWStop, and IWRetShmDirectory in the public headers. Fixed spelling of IWAlDisDelay in the public headers. For IW library call prototypes, added const qualifiers to array arguments which are not modified in the function call.

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IVE 4.1.5

Features added in 4.1.5 are:

Added more control over the behavior of the help system including defaults to work with common HTML browsers for Linux and Mac OS X; moved control over the help system from the Priism->Help menu to the preferences dialog.
Reworked the interactive bead list editor for bead alignment. Editing of matched lists now allows generation of matched lists from scratch and reduces the amount of clicking necessary to reposition a point.
Added an input parameter to bead_finder and bead_chaser so the user can have them perform the segmentation on a lower resolution (helpful for low SNR data or to speed up operation).
Added translations to turn scroll wheel events into scrolling actions for text fields, scrolled lists, and scroll bars.
For Image Capture on Linux systems, added the ability to generate QuickTime movies via Quicktime 4 Linux.
In 3D Model, separated the operations of animating the model display and saving a movie; saving a movie now supports formats other than TIFF via the image capture plugin mechanism.
Added option to EMRECON to display massnorm fit results.

Problems fixed in 4.1.5 are:

Increased the default working unit size to 16 megabytes.
Changed massnorm so it can run without an input alignment parameter file.
Changed decon and ffilter to avoid "nwork too small" errors when processing in 2D.
The decon user interface did not correctly terminate CTF file names read from CTF.def.
Changed ffilter so that it would not crash at exit if the ctf file is "none". Changed the ffilter user interface to not force an existence check on the optional ctf input and to correctly pass the z padding and 2D processing options to the command-line application.
Changed bead_matcher and bead_chaser so they would not die when run with an sbl file on OS X.
Fixed image windows so that overwriting an image window not currently displaying the highest resolution does not result in garbled images.
Changed image windows so that image windows start up properly when a pseudocolor visual is not available and the user has set a custom set of graphic colors.
Changed image windows to correctly handle split screen stereo and interpolated zoom.
Changed image windows so that stepping in z or time with the cursor keys keeps the multiple waves in synchrony when images are displayed in matrix mode with the step direction in waves.
For stereo display of tilt series, changed image windows to correctly choose the images for the right and left eye regardless of the sign of the angle increment.
Changed Volume Viewer to avoid misalignment of models in monoscopic displays, to not apply a different scaling to the left and right images for stereo displays, and to not attempt to use a 2 x 1 display mode if the output window is using hardware stereo.
For user interfaces like those for decon and EMRECON, changed so that entering an existing file for the primary input and then entering an empty file name for the primary input does not cause the application to exit on OS X.
Changed handling of user interface control to start a job so that it is possible to close the user interface before the job completes.
For bead alignment, loosened tolerances to make picking easier in zoomed down images.
Modified the image window Clear Graphics option to correctly redraw the display if graphics not clipped by the image boundaries are present.
Changed the interactive last step of bead alignment so that adding a position updates the image window and error display immediately. Sped up resizes of the error display by avoiding redrawing labels unless necessary.
Fixed a change from 4.1.4 that causes file dialogs to appear in the top left corner when used with some window managers or when used with LessTif.
Modified ivekill to extract the process group ID from running Priism or image window processes rather than relying on stored value on disk. Made the kill more reliable on OS X.
Modified the IW library so that IWAlSecScl, IWRtSecScl, IWAlSecMMM, IWRtSecMMM, IWAlZWTMMM, IWRtZWTMMM, IWAlSecThreshold, and IWRtSecThreshold operate on parameters that apply to all resolutions.

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IVE 4.1.4

Features added in 4.1.4 are:

The tiffmovie application from previous versions has been renamed "Image Capture". It has the capability to use plugins to generate output in different formats. For Mac OS X, a plugin is available to generate QuickTime movies. For IRIX, the process of generating QuickTime movies automatically removes the intermediate TIFF files generated.
Image windows and 3DModel can take advantage of quadbuffered stereo in a window on Linux if it is available.
If an image window displays multiple resolution data, the current resolution shown is adjusted automatically when the user adjusts the zoom factor.
Merged in changes to Volume Viewer from the version which used a Volume Pro 1000 board to do the rendering; now load the components specific to the Volume Pro 1000 as a plugin.
Added support for dial boxes when used in conjunction with Xi Graphics X server.
Added preference to prefer double- or single-buffered visuals for image windows.

Problems fixed in 4.1.4 are:

With Apple's X11, image windows took a long time to start.
With Apple's X11, 3DModel would crash at startup.
With Apple's X11 (version 0.1 only), BlendColors would crash when the color wheel dialog or color parameter dialog was opened. ChangeColors would crash at startup.
With Apple's X11, image windows did not properly clear the contents of the window when started.
The ProcFunc framework did not allocate sufficiently large buffers for applications processing a complex-valued input and generating complex-valued output.
Many of the command-line only applications did not gracefully handle cases where an input or output file could not be opened.
Removed an undocumented limit of 256 polygons per section from FindPoints and Volume Builder
Fixed problems in rotfast that caused it to generate blank images for tilts between 90 and 270 degrees and to set the image coordinate systems in the header differently than Volume Viewer does.
3DModel would crash if asked to generate TIFF files but was unable to open one of them.
BlendColors would crash on Mac OS X if asked to open a color parameter file and was unable to open the file.
Scale assumed that the source data set remained fixed in size which is not true for the interactive output of Volume Viewer.
The bead_finder and bead_chaser applications for EM data no longer assume that images are 1024 x 1024 or smaller. Corrected problems in bead_chaser that caused it to access uninitialized data and replaced a slow sorting algorithm in bead_chaser with a faster one.
In FFilter2D, FFilter3D, FPwrSpec2D, FPwrSpec3D, FTransform2D, and FTransform3D padding with a linear ramp in the frequency domain made use of an uninitialized variable.
The dialog for selecting the region to reconstruct for EM data relied on the starting section number in the file header; instead, do a search for the matching tilt angle.
The pixel spacing of the output from EWBP and TAPIR is forced to be isotropic which it must be since those two applications assume the input has square pixels.
The section number display overlayed on images can now be controlled via the menus as well as by keystrokes.
With the Preferences dialog and Merge/Reorder, the selected item from a scrolled list now stays in sync with the highlighted item.
With LessTif, option menus used a different font for the currently selected item than for the entries in the menu.
Empty scrolled lists no longer generate a Motif/LessTif warning about mismatching XmNitemCount and XmNitems.

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IVE 4.1.3

Problems fixed in 4.1.3 are:

massnorm could crash in the histogram computation if the input had a few negative intensity values.
The massnorm documentation did not define what -toffset=90 does.
There was a buffer overrun in the scan for command-line options controlling padding (affected FFilter2D, FFilter3D, FPwrSpec2D, FPwrSpec3D, FTransform2D, and FTransform3D).
Because of an uninitialized variable, FPwrSpec2D and FPwrSpec3D could generate incorrect results when the output y size is less than or equal to two and the user selected the option to center the zero frequency.

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IVE 4.1.2

Features added in 4.1.2 are:

Command-line interfaces to FixBadPixel, FTransform2D, FTransform3D, FFilter2D, FFilter3D, FPwrSpec2D, FPwrSpec3D, HisEqual, LCE, Normalize, Rotate3D, RunProj, Threshold, and T-RunProj were added. Retired rot3d_i and rot3d since Rotate3D now supplies a compatible command-line interface.
By default, the script and log files used by the front-ends to CCDCor, deconvolution, EM alignment, EM reconstruction, and FindPoints (among others) are placed in the same directory as the input image file and not in the users home directory.
Added documentation for the CTF format expected by the deconvolution application and an outline of a procedure to measure a CTF. Added radialft_asym and superimpose_psf, two command-line applications to assist with generation of CTF files.
Now use g++ as the C++ compiler for the basic Priism libraries on x86 and Alpha Linux systems and use linker scripts on those systems to hide internal symbols in the shared libraries. Applications on Linux compiled with the new shared libraries will not run with versions of Priism prior to 4.1.2. Applications with C++ code that were built with the Portland Group compiler on x86 Linux systems or the Compaq C++ compiler on Alpha Linux systems will likely require relinking to operate with the version 4.1.2.
For x86 Linux systems, now allow up to 64-bit file offsets in image files.
The environment variables to hook Priism to a queueing system now include QDEFAULT to specify the default destination.
Interpolated zoom for Mac OS X is more heavily optimized.
In FindPoints, added an option to fit the peak profile to a Gaussian profile in order to refine the position estimate.
Added LCE3D, a simple-minded extension to 3D of the 2D local contrast enhancement application.
The converters to and from Matlab's .mat format are now available for Mac OS X. The IRIX version still uses Matlab converters which require Matlab 5; IRIX converters for Matlab 6.5 are available as a patch. The installation script now asks questions about where Matlab is installed so it is not necessary to manually set library paths before running ImgToMat and MatToImg.
Added mrc2txt which writes the data values from a Priism image file as columns of plain text.
In addition to selecting pixels with intensities that are above or equal to a threshold, changed Threshold to have the option to select pixels with intensities below or equal to a threshold or pixels with intensities that match an arbitrary criteria.
Incorporated the watershed segmentation application, Watershed.

Problems fixed in 4.1.2 are:

Modified applications so that they will accept file names up to 256 characters long. Some instances (the name that can be associated with the data in a Priism window, the name of the Priism shared memory file, and the length of the base part of the file name stored in the scale preferences) still have lower limits.
The 4.1.0 version of the IP (ProcFunc) framework did not allocate enough memory if the input and output share a buffer and the output is complex (one symptom: CopyRegion would dump core when asked to convert a file to complex).
The IP (ProcFunc) framework handler for -no_overwrite intercepted all command-line options beginning with n.
Made Priism somewhat more tolerant of cases where the value of the IVE_WORKING_UNIT environment variable is smaller than the size of a loaded section. Can now load such data when Priism is initially started, but if shared memory has already been broken into chunks which are the size of IVE_WORKING_UNIT, the data can not be loaded.
Because of bugs in the data collection software, some image files have labels which include binary characters. Modified the IM library so that binary characters in labels are printed out as a backslash plus the character value in octal since printing the binary characters unmodified can put XFree86 X terminals in a strange state.
Clarified that the maximum length passed to WMAddCharField and WMAddGetFile includes space for a terminating null. This is what most applications had assumed.
The HTML help system did not load pages correctly if netscape was a link to mozilla (observed with Mozilla 1.0.0).
When using the LessTif library, the interactive final stage of the EM bead alignment would crash just before displaying its interface.
The front-end to the deconvolution application had hardwired defaults for the default CTF for a given lens number. The default CTF for a lens number is now configurable on a installation-wide basis by CONFIG/CTF.def or on a per-user basis by a CTF.def in the user's .iveprefs directory.
EditHeader would crash if the user selected a file that did not exist and then selected a file that did exist.
If the input had one or more leading sections completely filled with zeros, the first section with non-zero values written by FFilter2D would be autoscaled by the image window.
FFilter3D and FTransform3D did not attempt to propagate the extended header.
The FindPoints curve fit method would crash when run in batch mode.
In FindPoints, fixed many instances where calculations would cause floating-point exceptions on Alpha processors.
mrc2tiff has a memory leak and did not disable the template field at startup.
Modified Merge/Reorder so that simply asking it to copy a file with a different interleaving does not scramble the sections.
If Normalize wrote to a window, the first section in each wavelength was scaled differently than the rest of the wavelength.
Rotate3D would crash when processing complex short data.
The rolloff calculation in Rotate3D had instances of uninitialized variables.
The perimeter average in Rotate3D excluded the y=0 and y=ny-1 rows for sections that were not the top or bottom sections.

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IVE 4.1.1

Problems fixed in 4.1.1 are:

Models did not appear correctly in the second and later sections of VolumeViewer movie output if the z pixel spacing was different than the x and y pixel spacing. The origin on interactive stereo windows corresponded to a rotation angle halfway between the two views rather than the rotation of the first view.
Polynomial fits to complex input in the Fourier tools applications were incorrect.

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IVE 4.1.0

Features added in 4.1.0 are:

The base for many Priism applications was extended to support command-line interfaces, text-only interaction, and additional capabilities for appending to existing data or overwriting an input. Applications which have been modified to take advantage of the command-line interface are: CopyRegion, Edge Enhancement, Filter2D, Filter3D, Find Border, Flip, Image Arithmetic, ReduceRes, and Resample2D.
For the IRIX version, now use the FFTW libraries rather than SGI's Complib.
EMRECON's elliptically-weighted backprojection for tomographic reconstructions is somewhat faster for typical cases.
Volume Viewer now suppresses the background value when scaling interactive results. This is done to avoid sudden scale changes when the rendered volume moves from completely within the dataset to partially outside.

Problems fixed in 4.1.0 are:

Because of a logic error, synchronization between applications and image windows failed after a "force unlock" message was printed; the failure of synchronization would generally lead to image window crashes later.
Swapping data in and out of image windows used calculations that would would mishandle file offsets greater than 2 GiB on systems that support such offsets.
Copy Region would generate IMILsec_loc was -1 messages when run with the RGB toggle on.
Copy Region when converting data to byte format could use a range different than 0 to 255 depending on the system graphics hardware and software; the range is now 0 to 255 in all cases.
Edge Enhancement would incorrectly set the data range values and scaling parameters when processing data with two z sections.
EMRECON's elliptically-weighted backprojection would crash and not give a helpful message if unable to open the input or output data set.
EMRECON's elliptically-weighted backprojection would fail if the width of the tilt series was greater than 1024. The new limit is 16384.
The mechanism for suggesting file names in the EMRECON applications replaced everything after the first '.' in the name; changed so those applications replace everything after the last '.' when suggesting file names.
Find Points would crash during Region Growing in some cases; the widths reported in the column data output from Find Points may have been too large in some cases.
Volume Viewer did not account for prior rotations when setting the tilt angles for its output. Movie output did not have correct origin and pixel spacing values for zoom factors different than one.
Convolution, NewConvolution, and T-RunProj reported the incorrect mean value for the first wavelength.
Applications which set the file pointer via IMPosn, IMPosnZWT, or implicitly with IMAlZWT and then modified the extended header size or data size would then have a file pointer at an inconsistent location.

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IVE 4.0.11

Problems fixed in 4.0.11 are:

Image windows would crash or display incorrect results when asked to display multiple wavelengths with different offsets in RGB mode and at a zoom less than one.
The Reset button in Volume Viewer set the center inappropriately if a preloaded region was used whose origin was not (0, 0, 0).
The input scaling dialog in Volume Viewer recalculated the histogram when it was not necessary to do so.

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IVE 4.0.10

Features added in 4.0.10 are:

For mice with scroll wheels, if the scroll wheel is mapped to buttons 4 and 5 (which appears to be common practice) the image windows will respond to the scroll wheel by moving up and down through the image stack.
Added user preferences to control autorepeat for the image windows.
VolumeViewer's RGB/Opacity projection method only worked when the input had four wavelengths. Modified to work with any number of wavelengths. With one wavelength, that wavelength is used for both intensity and opacity (and thus is identical to the Progressive method). With two to four wavelengths selected, the last selected wavelength is used as the opacity channel and the others provide intensity information. With five or more wavelengths selected, only the first four wavelengths are used and the fourth selected wavelength is used as the opacity channel.
Added a button in VolumeViewer's dialog and a hot key to reset the orientation.
Extended VolumeViewer's options for handling of out-of-range values when scaling the input data.

Problems fixed in 4.0.10 are:

Handling of autorepeat in image windows has been improved. It was too fast (reported for 2GHz P4 systems) or jerky (on Mac OS X systems).
With a click-to-type focus policy and KDE 2.0's default window manager, region selection was canceled after releasing the mouse button and not when the mouse left the image window.
TIFF output from 3DModel and TiffMovie was saved with a non-default orientation which caused some TIFF readers (Mac OS X's Preview and and Priism's Tiff2mrc for instance) to generate images with the incorrect orientation.
3DModel did not allow the root part of TIFF output file names to be long enough.
ccdcor would exit if the input data set did not have an extended header.
EditHeader would crash if the specified file was a directory.
MeasureFPS's continuous sampling mode displayed incorrect results if no samples were recorded.
The Priism menu bar would not appear on some Linux configurations (Debian woody, for instance) because a buffer overflow caused an application crash.
If a set of Priism preferences was stored in a file whose name contained whitespace and those preferences were selected as the current profile, the default preferences would be used instead.
Changed the default compression mode to none in TiffMovie since whether or not LZW compression is supported since unpatched versions of libtiff later than 3.5.2 generate uncompressed results when asked for LZW compression.
VolumeViewer could crash when asked to load a file after viewing another file.
VolumeViewer had problems switching between to and from the RGB/Opacity projection method.
VolumeViewer assumed that the data viewed had at most 512 sections.
VolumeViewer would crash on Linux systems after the user selected the option to scale the input data.
VolumeViewer ignored the third (exponent) and fourth (handling of out of range values) when scaling input data.
VolumeViewer mechanism for determining if a dial box is present was not compatible with XFree86.
VolumeViewer would not display a refined image after dial input had ceased.
The IM library call IMAlWav would not update the wavelength toggle labels in the Monitor correctly.

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IVE 4.0.9

Problems fixed in 4.0.9 are:

Contrary to the documentation, a call to IMUnit would crash if the stream was not open.
Consecutive writes to a scratch window without an intervening IMPosn call would stop appending data to the window.
The istart parameter to IMRtExt and IMAlExt was not interpreted like it was in IVE 3.3 and earlier versions of Priism.
IM library documentation did not correctly represent the ordering of the x, y, and z origin fields in the header.

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IVE 4.0.8

Features added in 4.0.8 are:

Packaged the deconvolution application and additional FFT-based applications (those in Priism's Fourier Tools menu) for x86 Linux and Mac OS X.

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IVE 4.0.7

Features added in 4.0.7 are:

Ported most modeling applications (the exception is Clouds), TiffMovie, 2D Plot, and the image window printing utility from Priism 3.3.
Added mrc2tiff to convert directly to TIFF.
Scale remembers the histogram bounds for each wavelength as long as it remains active.
Rearranged user interface for the preferences editor.
Changed the default fonts for confirmation, error, information, and file selection dialogs to be similar to those used for other widgets.
Made a version for IRIX available since feature set is now much closer to IVE 3.3.

Problems fixed in 4.0.7 are:

Image windows did not properly display signed 32-bit integer (long) data.
For IW_COMPLEX_SHORT data, image windows did not allow choice to view the magnitude, phase, real component, or imaginary component.
Redisplay of the image window using the fast graphics calls could cause the graphics on the image to be shown with incorrect colors.
ive_conf.h reset _XOPEN_SOURCE and other feature-set macros.
The lookup mechanisms for IWAlcNamedSHM and IWFindNamedSHM were not synchronized.
The temporary files used to hold data swapped out of the shared memory file had names that would conflict with those of another user.
WMGetFile modified one of the obsolete arguments that the documentation suggested would not be accessed.
Multiple file selection dialogs created via WMGetFile would interfere with each other if active at the same time.
The old-style help viewer had a memory leak.
The window for the old-style help viewer would appear when Priism was started on Linux or Mac OS X.
Many applications would place themselves at locations that were off the screen for monitors that run at less than 1280 x 1024 resolution. Added WM calls so applications could get the display resolution and make more sensible placement decisions.
Applications based on the IP framework did not allow the user to force the output to be complex short, 16-bit unsigned integer, or 32-bit signed integer.
applycal would improperly complain about opening the bad pixel list on Alpha Linux systems.
The bead list display and editing utility for tomographic data did not handle unsigned 16-bit and signed 32-bit image data.
Blend Colors did not take into account how the Mode menu was set.
Edit Header did not recognize the codes for the unsigned 16-bit integer and signed 32-bit integer pixel formats. EditHeader would crash if an unrecognized pixel format was encountered.
Merge/Reorder did not handle unsigned 16-bit and signed 32-bit image data.
The preferences editor would leave the save option disabled when a new profile was created.
Rotate 3D would write the output file header incorrectly if writing multiple wavelengths or time points to a file.

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IVE 4.0.6

Features added in 4.0.6 are:

Added calls to the IW library to set and retrieve a recommended threshold (either on a per-section or per-wavelength level) for an image window. Modified Scale to include an option which modifies the recommended threshold level.

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IVE 4.0.5

Problems fixed in 4.0.5 are:

For image windows created by View File, applications which read small chunks of the data could receive data that had not been appropriately byte swapped. Most likely noticeable for profiles created by Line Profile along the z or time dimension.
The region selection mechanism and similar interactions with image windows did not work with click-to-type focus policies. Corrected two problems in libSelectRegion.a which affected Region Min/Max/Mean and Volume Viewer: translating an existing region did not work and initialization for non-square datasets was incorrect.
Priism 4.0.4 required libGLU.so.1 on Linux. Since libGL and libGLU will typically be installed as part of the same package but the Linux Standard Base specification mandates libGL.so.1 and not libGLU.so.1, it is more convenient if Priism does not require libGLU.so.1.

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