Trainable Weka Segmentation: fix rank of threshold application.

This way one can apply those methods to a single threshold.
Use imglib2.version property for imglib2 deps

Previously, the imglib2.version property may have seemed gratuitous,
since ImageJ2 and ImgLib2 were being versioned together. But we realized
the folly of this approach, and the version numbers will soon be
diverging to give us more flexibility. So imglib2 dependencies must use
the correct property now.
Fix whitespace
Update Bio-Formats dependencies to 4.4.8

This change upgrades the parent pom-scijava to the latest version, which
now has bio-formats.groupId and bio-formats.version properties distinct
from those of SCIFIO. These Fiji plugins need to depend on Bio-Formats
4.4.8 (because the updater currently ships BF 4.4.8), so we use the
bio-formats.* properties instead of the scifio.* ones.
Use fiji.version property for inter-plugin deps

Previously, many Fiji plugins referenced each other using the
imagej.version property, which was not guaranteed to match the version
of the Fiji multimodule project itself (and in fact no longer does, with
the pom-scijava bump to 1.48, since imagej.version now points to the
2.0.0-beta-7 release instead).
Trainable Weka Segmentation: added method to compute the precision and recall based on the pixel classification after warping (only for splits and mergers).
Tell Maven that pom-scijava is outside the reactor

Otherwise, by default it will look in .. for the parent POM. And while
it typically will not find it there, it is better to be safe and ensure
it does not even try to look.
Upgrade TrakEM2 to the newest pom-scijava version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
updated deconvolution to the "final" state
Use shorter URL in download-launchers

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'dep-versions'

This upgrades to a new pom-scijava version.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Follow ImageJ2's SNAPSHOT versions for now

The development between Fiji and ImageJ2 is still very closely
related. For example, in the next weeks there will be a lot of work
reconciling ij-legacy with fiji-compat. For that reason, let's follow
ImageJ2's SNAPSHOT versions at least until ImageJ2's beta8.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Remove the TrakEM2 module for now

Until we have a state which we know Jenkins can build without problems,
it does not make sense to keep it in 'master'.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update the ImageJ2 submodule

With the recent update of pom-scijava, we also need to update ImageJ2's
source code.

All of these problems will go away when we finally have release
couplings, but until that time, the problems will persist,
unfortunately.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Aaargh... update TrakEM2 to a temporary fork

TrakEM2 references Fiji components with ${imagej.version} but that
no longer works. So we have to move the .gitmodules pointer to our
fork until the pull request gets accepted.

In the same run, we also have to update mpicbg because TrakEM2 no
longer compiles with the old version.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fixed a bug in the weighting scheme, normalizing only if sumweights > 1,
otherwise artifacts at the edges are significantly enhanced in some cases
Merge branch 'master' of github.com:fiji/fiji
3D Objects Counter: be less impolite

Given how usage varies among different parts of ImageJ and the Plugins, this
message is really rude and annyoing. Just be informative instead.
Merge branch '3d-objects-counter' of https://github.com/imcf/fiji

This makes the 3D Objects Counter less rude.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Move resource back where it belongs

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