Conflicts:
components/server/src/ome/tools/hibernate/HibernateUtils.java

Replace tabs by spaces in ThumbnailService

As part of the general cleanup goal and to speed up build times, this PR
reviews all Javadoc war...

Without gitversion.xml imported, any component-level
build like ant -f components/tools/OmeroJav...

If not a build-time dependency, this should at least be a runtime dependency
since romio is call...

Without the interface changes from previous commits,
this test cannot possibly succeed (or even ...

This reverts commit 566c4042a2978f30b9b08c52dfa5a2d4e04e2863.

The NPE is a trivial fix. The passing of false to the
getPixelBuffer method should be looked int...

The addition of PixelsBuffer subclasses to the create
methods in PixelsService broke the mocked ...

The fact that OMEROWrapper was using setMetadataFilter(true)
but the PixelsService was not led t...

By importing version.xml, executing the subprojects
directly with an has all the version informa...

Fs cleanups

assist #11675: prevent some leaking direct buffers

11709 tile access (rebased onto develop)

Bio-Formats dependency on lwf-stubs JAR for lurawave

The change (basically to not lock on read) makes
this test pass where before it was failing (whe...

In order to be able to intercept (and block) certain
methods of BFPPB for concurrency testing me...

Each of the `get*Direct` methods now call
swapIfRequired. Non-direct methods should
not call the...

The other `get*Direct` methods all contain a call to
`reader.swapIfRequired()`. The same logic i...

This removes the last location with /tmp/memo hard-coded.
Along with a change to Bio-Formats, ca...

There is almost certainly more cleanup that can be done in terms of
where the reader stack is co...

This reverts commit d37c4c7806ccd81013eeaaf7940e05c4db2328f3.

This reverts commit 6f69e3843e790b0481cae71e032d789984cf8cbe.

Conflicts:

components/romio/src...

Two branches both tried to refactor the copy-n-paste
issues with reader creation. The combined s...

Add OriginalMetadataRequest command (See #10349)

To simplify cleanup, having all caches written into a single
directory was added to the `loci.fo...

Reduce the number of locations that OMEROWrapper is created,
passing directory when it is clearl...

Add Bio-Formats' turbojpeg artifact to the classpath

Convert logging to logback predominantly via slf4j

Fix #10602 and clean up IO code. (rebased)

The dummy implementation from the ROMIO pixel buffer and
the in-memory pixel buffer was also cop...

Will need to be rebased back to dev_4_4.

Big images fs 9701 (develop)

Calculate hash digests on a per plane basis (Fixes #10073)

Provide a list of ResolutionDescription objects which should
eventually represent the entire geo...

There are some edge cases, such as electron microscopy, where the stack
size is huge. Often 100...

Should fix ticket #10202.

The RGB channel count and pixel type/byte width can vary for every
series, so it is incorrect to...

Fixes #9711.

Pyramid reader: do not override initFile (rebased onto develop)

With the new subresolutions support, MinimalTiffReader's initFile
implementation performs all of...

Once a user has read access for an original file object,
the `RawFileBean` does not prevent writ...

Conflicts:
components/blitz/src/ome/formats/importer/ImportLibrary.java