Posted By: Bennett Landman - Sep 6, 2013
Tool/Resource: JIST: Java Image Science Toolkit
Good evening,

We have released JIST 3.0 which is compatible with MIPAV 7.0+. I just posted final JIST 2.0 build which are compatible with MIPAV 5.4.X. These are SIGNIFICANT upgrades and the .layout formats are not fully backward compatible. Please read through the changes and consider upgrading.


JIST 3.0 Changelog
Major Changes
• Removed all duplicate/conflicting jar files in JIST / JIST Plugins that conflict with new MIPAV7
o E.g., j3dcore, j3d-core, j3dutils, camino, etc.
• Default preferences have changed
o Filetype -> nii
o Compression -> gzip
o Layout type LayoutXML
o Hypervisor off
• LayoutXML format should be compatible with all layouts and, as far as we know, there is no reason not to use the LayoutXML format for all layouts.
o All .layout specific code will be removed from a future release.
• Several of the “Source” types have changed, specifically, for Volumes, Surfaces, and Files there are three types of sources
o Volume/Surface/File Set
 A set of files/volumes/surfaces specified manually, via text file, or through directory search that are passed individually (one at a time).
o Volume/Surface/File Collection
 A collection of files/volumes/surfaces specified manually, via text file, or through directory search that are passed en masse (as a single collection).
o Volume/Surface/File Collection Set
 A set of file/volume/surface collections that are passed individually and specified via a comma separated text file (a set of collections are passed).
• Added “post-it note” module for adding notes to your layout. This module does not affect the process manager in any way.
• Added ability to change color of modules (right-click on module). This can be useful for large layouts to differentiate between different sections.
Minor Changes/Bug Fixes
• Fixed bug causing GlobalPreferences to ask library to re-build twice.
• Made AlgorithmInformation and all sub-classes implement serializable to avoid no-args constructor errors.
• Removed nearly all “System.out/err” and replaced with JistLogger system.
• All file/volume/surface selections should use the previously used directory.
• Fixed bug related to saving empty layouts.
• Empty layouts no longer ask you to save before exiting.
• Fixed bug submission system for automatically posting bugs to nitrc tracker site (please use!).
• Fixed tons of unnecessary checks that were causing layout to require saving unnecessarily.
• Fixed updater dying when process manager closed (should make process manager much more stable).
• Fixed JGraph bug causing parameters not to update when edges/modules changed/removed/deleted.
• Dramatically simplified code to display input/output parameters (JIST-II stuff).
• Fixed bug causing previous layout list to be read inappropriately.
• All sources/destinations are now presented in a sorted order.
• Updated JISTLayoutAdapter to use better names for input/output parameters
• JISTPluginSelector is now compatible with MIPAV 7.
• Selecting “View in process manager” changes the layout in the process manager if necessary.
• Created a new port color for parameters that are invalid (i.e., empty) but are not mandatory
o Note, this only really matters for files/volumes/surfaces.
• Open/save layout uses previous directory – a directory that is separate from previous file/surface/volume directory).
Known Bugs / Future Changes
• JISTLayoutAdapter needs a little bit of work to make it more useful for simplifying large layouts.
• JISTPluginSelector needs better visualization for several of the input/output parameters.
• The JIST Command line interfaces needs work to simplify the usage process.
• External sources should keep the mandatory settings of their ancestors.
• Avoidance routing (how JGraph selects the path) could be better (less overlapping edges).
• Several known graphics bugs
o In particular, bugs that never actually touch the JIST code but occur when interacting with the layout/process manager.
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