fft: Clean up style
fft2: FFT methods now all specify and ackn. the number of threads to use.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Example 1b: update type use/comments

Clarified the ImgOpener behavior and provided a bit more information on
how Img types relate to data, and ImgOpener/ImgOptions use.

Also clarified that the images should look the same despite being
different Img types.
Use Jama release from Maven Central repository

The previous Jama artifact is not currently present on Central,
but it looks like Jama is there with groupId gov.jist.math.
So let's use the latest version of that!
imglib2-tests: use consistent mpicbg version

We have a properties for mpicbg groupId and version to ensure that all
components use the same ones. Let's use them in imglib2-tests, too.
Clean up dependency organization

Dependencies are organized into three major categories:
1) Project dependencies
2) External dependencies
3) Test scope dependencies

(A fourth category is "Runtime scope dependencies" but nothing in
ImgLib2 needs that scope.)

Furthermore, dependencies that are not available (or planned to be
available soon) from Central are flagged with FIXME, so that do not
forget to resolve them somehow.

These dependencies can be seen with:

    grep -A 5 -B 1 FIXME $(git ls-files '*pom.xml')

And further grepping for artifactId reveals the following artifact
dependencies which we will need to somehow address:

    loci-common, mines-jtk, mpicbg, udunits

Fortunately, none of these is a dependency for the most critical core
ImgLib2 components.
SubpixelLocalization: do not update position if Matrix is singular.

Jama, on which we rely for the quadratic offseting, throws a
RuntImeException if the hessian Matrix is singular. This happens in some
cases.
Because the SubpixelLocalization generates threads to process its
tasks, these exception cannot be caught.
This commit adds a check to ensure we do the offset upate ONLY id the
matrix is not singular.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
SubpixelLocalization: a better fix,

following the advices of Tobias.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Bump to pom-scijava 1.111

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Merge pull request #46 from imglib/fft2-no-multithreading

fft2 package has some methods that are silently multithreaded. Enforce nThreads specification
fixed contructor in dilate gray
fft2.FFT: restore expecting scaling behavior when calling to FFTMethods

Noticed by Stephan Preibisch:
The recent changes I introduced to the class, aimed at making it
prossible to control the number of threads used for computation,
introduced some mistakes related to the expected scaling of the results.

When using FFTMethods calls in the FFT class, the scaling must be as
following:
- calls to complexToComplex(): if forward=true then scaling=false
  if forward=false then scaling=true.
- complexToReal(): scaling is always true.
- realToComplex(): scaling is always false.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
added corresponding methods that do not require to specify the number of threads
For some reason this fails to compile on jenkins, reverting it

Revert "added corresponding methods that do not require to specify the number of threads"

This reverts commit 23c1fc20ace5e1f091f0117c1458c86d4259742b.
Revert reversion

The Jenkins failure was due to the ImageJ Nexus service being down.

I brought it back online, and all should be well now.

Revert "For some reason this fails to compile on jenkins, reverting it"

This reverts commit ce27291ce50eb888c2606916daebcfed56e329ad.
fixed missing license header in projector package
License in Volatile2DRandomAccessibleProjector fix
fixed licenses of DoubleConverters
added missing licenses
Merge pull request #47 from imglib/license-issue

Thanks @dietzc for rectifying.