glow: eliminate problematic characters

For discussion, see:
https://groups.google.com/d/msg/fiji-devel/zManMs4CVug/FH-fmDNtFA0J
Updating mpicbg and TrakEM2 submodules.
Use the current sezpoz version in the Eclipse files

We recently upgraded sezpoz to a new version (1.9-imagej) so sezpoz-1.9
is no longer downloaded by Maven. Therefore, we need to adjust all the
.factorypath files.

This commit was performed by:

perl -pi -e 's/1.9\/sezpoz-1.9/1.9-imagej\/sezpoz-1.9-imagej/' \
	$(git grep -l sezpoz-1.9)

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a helper to perform renaming merges

A "renaming merge" is a merge of an originally independent project into a
subdirectory. In this particular case, it is the merge of the SPIM Viewer
into fiji.git's src-plugins/spim_viewer/ directory.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Trainable Weka Segmentation: add "deprecated" tag to old plugin.
Trainable Weka Segmentation: add "deprecated" tag to old plugin.
Merge branch 'master' into trainable-seg-gui

Conflicts:
	src-plugins/Trainable_Segmentation/src/main/java/trainableSegmentation/Trainable_Segmentation.java
added possibility to make all psf's the same size so that one can optimize the blocksize
Merge branch 'master' of git://fiji.sc/fiji
Fix Make Screencast

The ReadInto class moved in the meantime.

Reported in http://fiji.sc/bugzilla/show_bug.cgi?id=613 by Alex Sossick.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Remove unused import

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Do not override Edit>Options>Memory... any longer

Since imagej.git commit 021946ca6f(ImageJ Launcher: parse new-style
ImageJ.cfg), the launcher now prefers ImageJ.cfg over jvm.cfg. This
was done partially to allow ImageJ 1.x to use the ImageJ launcher
(rather than the previous, platform-specific launchers written in
Pascal and C++ or even using MacOSX' JavaWrapper.

So there is no longer a need to write out jvm.cfg in Fiji.

But since ImageJ 1.x refuses to write out a new ImageJ.cfg, we have to
write one ourselves if it does not yet exist.

Reported by Stoyan Pavlov.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Memory & Threads...: Fix ImageJ.cfg writing

ImageJ 1.x tries to be clever when parsing the ImageJ.cfg file to find
out whether the memory was specified in megabytes or gigabytes. If there
was no specifier, however, it defaults to kilobytes.

Work around this by making sure to write out the 'm' specifier.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
enabled the fusion that computes different output images to load images sequentially
fixed a bug for the multi-channel registration
added the option to set the initial viewID
Added the option to preAlign the views before global optimization
bUnwarpJ: update stack methods to use modern calls.
bUnwarpJ: make javadoc comment more clear.
bUnwarpJ: improve javadoc comments.