Merge pull request #15 from larrylindsey/fiji-archipelago-security

Fiji Archipelago
Fix version of TrakEM2_Archipelago's parent POM

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fixed another underscore-imagej-scripting-bug
Merge branch 'master' of github.com:fiji/fiji
Segmentation Editor: Prevent modification of interpolation result.

Probably the only simple way to make this even more secure (the result
can still be modified during the final copying phase) would be to
create a copy of the ROI array.  This would mean a substantial memory
overhead though.

Previously if a slice with an empty ROI was selected during
interpolation, it would stay empty even if it should have received
some ROI.
Segmentation Editor: Fixing bug #509. Old label stacks are recognized as valid again.

Removed check for "CoordType" in AmiraParameters.java since it does not seem to be used anywhere anymore.
fixed a bug that causes crash if all views have 100% inlier ratio
Segmentation Editor: Sets initial slice correctly.
Script Editor: mention that we're starting up

... because it takes a while, the first time.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of github.com:fiji/fiji
Fix usage of analyze-dependencies

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix analyze-dependencies' -debug option

It needs to be done differently now, because the updater moved.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Port find-jar-for-class to Beanshell

Because of the startup time of Jython.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
find-jar-for-class: show all .jar files

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'segm_editor_fixes' of https://github.com/quazgar/fiji

This branch contains these small fixes to the segmentation editor:

- Prevent modification of interpolation result. Previously, if a slice
  with an empty ROI was selected during interpolation, it would stay
  empty even if it should have received some ROI.

- Fixed bug 509. Old label stacks are recognized as valid again.

- Sets the initial slice correctly.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
added dependency on ImgLib2 (thanks Johannnes)
Added ImgLib1 to ImgLib2 wrappers for common data types
added wrappers from ImgLib2 to ImgLib1
renamed methods to reflect that they convert arrays only
added classes that allow wrapping of cell container