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Release Notes 3.1.1

Introduction

Release Date: June 2004

This document describes changes and improvements in version 3.1.1 of the Visualization and 3D Reconstruction system amira. This version is a service release.

Supported Platforms

- Windows 98/ME/NT4/2000/XP (recommended Windows 2000/XP)
- Linux (RedHat 8.0 with glibc-2.3.2.so or higher)
- Linux Itanium 64 bit (RedHat AW 2.1)
- Linux AMD 64 (SuSE 9.0 or compatible)
- HP-UX 11.0, 32/64 bit code
- SGI Irix 6.5.x, 32/64 bit code
- SUN Solaris 8 or 9 (SunOS 5.8 or 5.9), 32/64 bit code

Details about Software and Hardware configuration are listed in the section "System Requirements" of the User's Guide included in this distribution.

In order to add custom extensions to amira also a C++ compiler is required. Details about the supported compilers and compiler versions can be found in the section "System Requirements" of the Programmer's Guide included in the amira developer version.

- Windows: Visual Studio 6 and Visual Studio .NET 2003
- Linux: gcc 3.2.x
- Linux Itanium 64: gcc 2.96
- Linux AMD 64: gcc 3.3.1
- HP-UX 11.0: aCC 3.35 with new C++ standard lib
- SGI Irix 6.5.x: CC MIPSpro 7.3.1
- SUN Solaris 8: CC Workshop 6 Update 2

Changes Since amira 3.1.1

Changes in amira Standard Edition:

* New: Support for the Linux x86_64 architecture (AMD 64).

* New: End user license agreement (EULA) is displayed when amira is started the first time.

* New: Arithmetic now supports also data defined on surfaces (HxSurfaceScalarField and HxSurfaceVectorField).

* Release 3.1.1 of amira is a service release and mainly combines all patches for version 3.1 in a new self-contained distribution. The following gives a list of all patches together with a short description of the problems they fix.

Patch31-02-amiraMol:
- possible crash when saving networks on Linux and Windows
- crash in when saving networks if no data is connected to module HxCompMolInterface
- warnings when loading old scripts containing HxSecStructure modules

Patch31-03-fortranlibs:
- It provides required Fortran run-time libraries for SunOS, which might not be installed on all Solaris systems.

Patch31-04-amiraVR:
- A bug fix in the tracker calibration routine (calibration was incorrect unless the lower left corner of the first screen in the config file was at the origin).
- For the values option of the amiraVR module a font was used which was not available on a standard Suse Linux installation.
- Configurations could not be reliably saved in cluster mode.
- Set a blank cursor in the viewer window of cluster slaves.
- Send changes in the main window's light menu to cluster slaves.
- Send changes in the viewer background dialog to cluster slaves.
- Do not replace symbolic links when creating an absolute file path in the file browser. This makes it much easier to share data on all nodes of a cluster configuration.
- Ensure that the current point is always drawn in red or orange in calibration mode.
- Fixed a bug causing the stereo to disappear sometimes.
- Support for custom lights in the config file (3D configs only). Before, the menus were always illuminated by a single directional light pointing in negative z-direction. This was not appropriate for example for putting the menus on a side wall in a CAVE. No custom lights can be defined in the config file using the same coordinate system as for the screens. Only if no custom lights are defined the standard directional light is created.

Patch31-05-surfaceview:
- SurfaceView module can now display surfaces with more than 256 materials.

Patch31-06-rollup:
- Modules Scale and Annotation are now rendered correctly in tiled snapshots.
- Registration now also works on images with only one slice (2D images).
- Gradient and Merge no longer cause a crash when applied to a single slice.
- DXF output of amira can now be read by AutoCad2000 and higher.
- EPS output is improved (document structure comments).
- Leica binary import (.lei) now also works in drag&drop mode.
- Some issues concerning Voltex with Nvidia FX based video adapters have been fixed (clipping planes, rendering into multiple viewers)
- Bug fix in Tcl interface of HxLattice3 (getValue/setValue).
- HxCluster recomputes cached bounding box values after applying a transformation.
- SurfaceCut and GridCut provide a new button Create surface which can be used to convert the cross section into a surface object.
- ImageFilters: ports are now correctly saved in network scripts and results are recomputed automatically.
- Transformations of MultichannelField objects are stored correctly in network scripts.
- A problem with Save Network of TimeSeriesControl that occured when whitespaces are within a path has been fixed.
- Viewer masks of downstream objects are now stored correctly in network scripts, if upstream mask is off but downstream mask is on.
- The StandardView module now has no more side effects on Voltex, which caused problems when both modules were used simultaneously.
- The documentation of Voltex, Digital Image Filters and DemoMaker has been updated.

Patch31-07-cluster:
- Fixed synchronization bug in fly mode (different views were computed on the slaves due to unsynchronized timers).
- File format selection dialog now works in cluster mode.

Patch31-08-VolPro500:
- It adds support for the old TeraRecon VolumePro 500 volume rendering board to Amira 3.1. The standard VolPro module in Amira 3.1 is based on the latest TeraRecon drivers, which do not support the VolumePro 500 board anymore. As a workaround this patch contains the Amira 3.0 VolPro-500 module recompiled for Amira 3.1.

Patch31-09-VolPro1000:
- Standard Amira clipping planes are now correctly applied to the VolPro output.

Patch31-10-segy:
- It updates the Amira SEG-Y reader so that it also supports data files with swapped byte order (little endian). It also improves the heuristics for determining the dimension of the data array. SEG-Y files can be read via script without showing the reader dialog using the following command:
load -segy <filename> -nogui [-dims <nx> <ny> <nz>] [-littleendian]

Patch31-11-dicom:
- Multiple images listed in a DICOMDIR file sometimes could not be read.
- Images from the Philips MOSAIC small animal PET system could not be read.
- When scaling data values according to slope and intercept values stored in the DICOM header it is checked if a data overflow would occur. If this is the case the user is asked if the scaling should be ignored, if the data values should be clamped, or if the scaling should be adjusted.

Patch31-12-amiraVR:
- It fixes amiraVR for HP-UX platforms. On such platforms amira could not successfully onnect to a tracking system via trackd.

Patch31-13-nogui:
- Amira will terminate correctly if started with the -no_gui command line option, even if errors or exceptions occurred during the processing of command scripts.

Patch31-14-cluster:
- On older Linux systems, where a more recent version of the loader ld- linux.so.2 has to be copied into the directory lib/arch-Linux-Optimize in order get Amira running, slave instances of AmiraVR cluster could not be started successfully.

Patch31-15-MagicWand:
- In the image segmentation editor limit lines defined by the MagicWand tool were not restored when reopening the image segmentation editor.
- For convenience, it is now possible to select all seeds in a slice one after the other by pressing key N.

Patch31-16-align:
- When a label field was connected as a mask in the slice aligner, wrong images were displayed and no alignment could be achieved.
- When reading a list of images using Stacked Slices as Large Disk Data the pixel sizes were interpreted as integer numbers. Depending on the values specified in the file, the bounding box of the image stack was wrong or even degenerated (zero extent).