Support runs of Vaa3d pbd difference bytes that cross input stream block boundaries.
Stitching_Grid: add default BF settings

When running BF.openImagePlus, always ensure the dimension input order
will match the underlying dataset's order, and the output order will be
XYCZT to match the ImageJ constraints.

Also, ensures crop will be false.
Stitching_Grid: add "TilesToRois" checkbox

When this option is selected, all tiles in the stitched image will be
added as Rois to the RoiManager. Each will be labeled with its
appropriate Z,C,T and imageIndex coordinates in the underlying dataset,
as well as the file name on disk that the tile was read from.
Merge branch 'stitching-display-tiles'

Adds a checkbox to grid stitching allowing all tiles to be added as Rois to the
RoiManager.

Each Roi is labeled with the identifying series, z, c, t coordinates as well as
slice position in the image.

Also, each label contains the file name associated with that tile.
Stitching: Created RoiPicker tool

This tool is automatically loaded when stitching & "Add tiles as ROIs"
is enabled.

The RoiPicker can be used to select, via clicking on an image directly,
one or more Rois containing the given position in an image. Repeated
clicking cycles through the matching Rois.
Merge branch 'roi_picker'

Created a RoiPicker tool, which allows for manually selecting Rois by clicking
on an image.

Enabled when stitching and "Add tiles as ROIs" is selected.
Set the context class loader before running Jython scripts

This corresponds to the commit 2a1d5292(Refresh_JRuby_Scripts: set the
context class loader correctly) which fixed the same issue for JRuby
scripts.

Noticed by Jean-Yves Tinevez in bug 657.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Stitching_Grid: fix ROIs when computing overlap

Updated the generateRois method of Stitching_Grid to properly generate
ROI coordinates for datasets stitched using the "compute overlap"
functionality.

Previously, the stage coordinates from metadata were used exclusively,
which could result in improper ROI coverage of an image stitched with
overlap computed.

Now, the actual translation values from the 0,0 position are used
instead, which works in determining tile positions whether or not
compute overlap was used.
Stitching_Grid: save ROIs when writing fused image

Previously, when fusing and writing to disk, ROIs were simply discarded.

The RoiManager has a command to write Rois to disk, however. So the
generateRois method and invocation were refactored to writing the final
ROIs to disk (in a "tile_rois.zip" in the output directory).

These saved ROIs can be applied after opening the saved dataset, by
opening the RoiManager and running "More >> Open...".
Merge branch 'compute_overlap_roi_fix'

Fixes a bug when generating ROIs for datasets fused with "Compute Overlap"
enabled.
Merge branch 'stitching_save_rois'

Enables writing ROIs to disk when the fused dataset is also saved to disk.
Stitching_Grid: add downsample option

The Stitching_Grid plugin now provides the option to downsample tiles
before stitching.

Effectively, this runs the "Image > Scale..." plugin on all tile images
before any stitching/fusion/etc... operations take place.

This functionality can be used to significantly reduce the size of a
dataset, e.g. when the resultant stitched image will not fit in memory.
Merge branch 'stitching_downsample'

Adds a "Downsample tile" option to the Stitching_Grid plugin, allowing for
downsampling of tiles before they are fused (significantly reducing the overall
dataset size, reducing memory and time requirements).
Stitching_Grid UI: remove erroneous warning

The "Add Tiles as ROIs" option mistakenly said it was restricted to
"Fuse and Display" output only.

This is no longer accurate. If the output is written to disk, the ROIs
are as well.
Report our custom-patched javac version

As reported by Curtis Rueden in bug 656,

	java -jar jars/javac-*.jar -version

did not report a valid version. The reason is the
version.properties-template file which we did not parse into a proper
version.properties file. We cannot do that anyway because we extracted
javac from OpenJDK6 b24 as per Ubuntu's sources (and applying custom
patches to address ImgLib2's overzealous use of overly-complicated
generics constructs), and therefore the JDK_VERSION would not even be
available.

So let's do the next best thing and hard-code the appropriate version
strings.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump javac to a release version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of github.com:fiji/fiji
Build.sh: switch javac to a release version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Do not use underscore in javac's version number

It confused MiniMaven...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
open-in-gitweb: try to use the current branch's remote

We used to hardcode the remote called 'origin' which might not even
exist at all.

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