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github.com/ome/omero-romio

Gradle project for the ROMIO library of OMERO
https://github.com/ome/omero-romio

Handle endianness correctly in Bio-Formats pixel buffers. (See #6124)

c863ffd0b23c2c1dbe89c7e367a0f6f66c9c7241 authored over 12 years ago by Chris Allan <[email protected]>
Replace https:// by http:// in trac URLs

2646ef5d63362ad7dc02e979e9ea4a992cd777a8 authored over 12 years ago by Sebastien Besson <[email protected]>
Replace omero by ome in trac URLs

ef3577251bf60c6f93ef7c844b9048e0fdf3b086 authored over 12 years ago by Sebastien Besson <[email protected]>
Merge remote-tracking branch 'origin/develop' into int_vs_long_srv

Conflicts:
components/insight/LIB/ome-io.jar
components/romio/ivy.xml
components/server/src/o...

3079d2420f3a692c0e505f272a491ac128fe08cd authored over 12 years ago by Chris Allan <[email protected]>
Merge pull request #156 from ximenesuk/8591_open_filehandles

Close bfReader. See #8591

23ba1530d4d82c6bd7609ca8332f02dab0a73cb5 authored over 12 years ago by Josh Moore <[email protected]>
Merge pull request #147 from joshmoore/homebrew-merge

Homebrew merge

b15594b47e788aef4f88cb75b677b303989e2013 authored over 12 years ago by Josh Moore <[email protected]>
Moving close to wrapper. See #8591

1e83dded04c1b556ab3f09ebb1fbfcba180bf135 authored over 12 years ago by Colin Blackburn <[email protected]>
Close bfReader. See #8591

6ad0b8237f9668651d01efbf047feb2b897546bf authored over 12 years ago by Colin Blackburn <[email protected]>
Migrate all Ivy references to use internal deps

Now using two orgs: "ome" and "omero". We may want
to unify everything on "ome".

This includes ...

aa3d708dca1e89def8ab7cca0f8a990ba160c173 authored almost 13 years ago by jmoore <[email protected]>
Merge remote-tracking branch 'origin/develop' into int_vs_long_srv

Conflicts:
etc/omero.properties
lib/repository/jai_imageio-362b9a2.jar
lib/repository/loci-co...

9ae79884654d241bc1eda19aa41be9721d32a936 authored almost 13 years ago by Chris Allan <[email protected]>
Ensure scifio is included in the romio component's dependencies.

63bb94a89bba8f0ea608bc67614bf24e402c2bbd authored almost 13 years ago by Chris Allan <[email protected]>
Merge pull request #37 from melissalinkert/7017-omexml-link

Do not link objects that have already been linked

f27ba048877205d51f5542ce9c2c865d7a38649e authored almost 13 years ago by Chris Allan <[email protected]>
Merge pull request #57 from joshmoore/sprint6-server-backlog

Sprint6 server backlog

20caf830e96e0113660ccb456ee3658666c800a5 authored almost 13 years ago by Josh Moore <[email protected]>
Fix minor logging issue in nio FS service

94e447d0adfa2e9c70c0d615ab8562123c7be5b1 authored almost 13 years ago by jmoore <[email protected]>
Further porting of PixelsService.

This port is the upcasting of sizeX * sizeY in the context of
calculating whether or not a pyram...

81e1de9f9d45d24357c48280c3cede8cea9ce7c0 authored almost 13 years ago by Chris Allan <[email protected]>
Do not assume that pyramid tiles are little-endian

Fixes #7134.

c1a9bddedccecea1521c23480cf40bcd05aa0c20 authored almost 13 years ago by Melissa Linkert <[email protected]>
Update Bio-Formats JARs to include results of running xsd-fu

50f780e35e2e6bf6fa616fd06dc1c0a6112f4d9d authored almost 13 years ago by Melissa Linkert <[email protected]>
Ported Bio-Formats based I/O classes.

224298d11a67f677d38e2ea88081dd5a8c773076 authored about 13 years ago by Chris Allan <[email protected]>
Ported PixelsService.

da3703e6c2174ba029c4a658c439d1a683027c00 authored about 13 years ago by Chris Allan <[email protected]>
Ported InMemoryPlanarPixelBuffer.

40cfb5af41da9ce6653e203ffc27ced8aaa2fbe0 authored about 13 years ago by Chris Allan <[email protected]>
Ported RomioPixelBuffer.

Included in the port is a new safeLongToInteger() static method which
will be universally respon...

a6273e151150b369367f5d3920e1e12d53a92b95 authored about 13 years ago by Chris Allan <[email protected]>
Row and column sizes really should still be Integer.

0d19ff3924f391c4b8480419926821485125489b authored about 13 years ago by Chris Allan <[email protected]>
PixelBuffer (the lowest level) Integer --> Long switch.

6628c0c380728f4e10a3a4cced60c1e1d2ac320c authored about 13 years ago by Chris Allan <[email protected]>
Ensure read-only status is verified. (Fixes #6419)

1ac128b3c4c88c979d595cf2acc181bb3a223578 authored over 13 years ago by Chris Allan <[email protected]>
Write pyramids as BigTIFF files.

This prevents pyramid generation from failing if the pyramid file size
ends up being greater tha...

f67e4a3ca810418421c39a9322030fc55f480ae2 authored over 13 years ago by Melissa Linkert <[email protected]>
Remove tile size and offset restrictions from BfPyramidPixelBuffer.

32b7b1dd1292061054650f74bb3c083d8afec920 authored over 13 years ago by Chris Allan <[email protected]>
Implemented getHypercubeSize in InMemoryPlanarPixelBuffer. See #6121

deef76567c83f7081b61a8fb8d25c54780f592e4 authored over 13 years ago by Colin Blackburn <[email protected]>
Slight reorganisation as getHypercubeSize is no longer a private helper and it does bounds checking. See #6121

f66299070a5b3e7fce091b9fc5765653816ac571 authored over 13 years ago by Colin Blackburn <[email protected]>
Changed getCubeSize to getHypercubeSize for consistency with other get size methods. See #6121

57ca89e5751fa6e01157e5c68ddc55079acea03a authored over 13 years ago by Colin Blackburn <[email protected]>
Implemented getHypercube in RawPixelsStore. See #6121

a9b962884bd61ef26a1434aa0efd4decff4a8029 authored over 13 years ago by Colin Blackburn <[email protected]>
Fix test compilation issues introduced in

[41d3da151e3733966fb9370fd7f8f9d3fc6702ab/ome.git].

7c222f129e859210b8921ae9786b48c69b2e2727 authored over 13 years ago by Chris Allan <[email protected]>
Handle endianness correctly in pyramid pixel buffers. (Fixes #6124)

f0767508f91f290c7847ca7d9f1887de1b6af449 authored over 13 years ago by Chris Allan <[email protected]>
Fix typo in tile exception message.

70fa7b81e96f7216a8d54b5e5f28da23b58e8002 authored over 13 years ago by Chris Allan <[email protected]>
`TileSizes` interface with `ConfiguredTileSizes` implementation (Fix #5952)

456d2ce3965e4317b8f600d4346cd5390660fcea authored over 13 years ago by jmoore <[email protected]>
`BackOff` interface with `SimpleBackOff` implementation (Fix #5190)

4b5d56b804a9507af9abe24adfcb0f15a62e7650 authored over 13 years ago by jmoore <[email protected]>
Merge branch 'legal/5820' into develop (Fix #5821)

Conflicts:
components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/public/public.html
...

52a33e792af552181537e1fbd6970c10cf77b44f authored over 13 years ago by jmoore <[email protected]>
Revert "Setting default tile sizes to 256x128 for testing. (See #5224)"

This reverts commit fdcfdf0e2787ea9f2f5bc07963bde28f43c912f1.

Conflicts:

components/romio/src...

f59cf28c5a3d2a69706a477d62acf616a9cb7f9a authored over 13 years ago by Chris Allan <[email protected]>
Bumping big image "limit" to 3192x3192.

4a67712ee2393e44ea23a13ca143f83ea88c7352 authored over 13 years ago by Chris Allan <[email protected]>
Add missing copyrights found by checkstyle

efc24721129fc391dd012c0e41e1d07104b3664a authored over 13 years ago by jmoore <[email protected]>
Removing `DeltaVision` classes and tests (unused; missing headers)

4f38adb41b21257e39d10f6be6b01a43c730e0fd authored over 13 years ago by jmoore <[email protected]>
Made log levels more sane for Bio-Formats implementations. (See #5839)

da0f991b0139c60fc4a92165ac5aacd2db25ba12 authored over 13 years ago by Chris Allan <[email protected]>
Fix pyramids where sizeX or sizeY < tile width or tile height. (Fixes #5837)

b3abba5e5bf0b50c69a3bc0e355aa299995159d9 authored over 13 years ago by Chris Allan <[email protected]>
Progress based logging. (Closes #5816)

15ca63db8be40359b326c8d61b6ce99a5fe48154 authored over 13 years ago by Chris Allan <[email protected]>
Revert "Ensure FS lite images requiredPixelsPyramid() returns true. (Closes #5613)"

This reverts commit 048f2b7351877f7767972b077d2cc8b391e155f6.

7f013e10e63c7fe0c070ad71783e0764263dac84 authored over 13 years ago by Chris Allan <[email protected]>
Setting default tile sizes to 256x128 for testing. (See #5224)

9e995e404bc487815dc81ef034979c233f75585b authored over 13 years ago by Chris Allan <[email protected]>
Don't allow whacky tile sizes. (See #5224)

25aceceee8d97ad86d823fe0a9004bce1c242e8f authored over 13 years ago by Chris Allan <[email protected]>
Fix `ByPramidPixelBuffer` ctor and closeWriter (Fix #5787)

150721245dbb038603588026e994bd467b39c893 authored over 13 years ago by jmoore <[email protected]>
Add functionality to specify the read-write context of getPixelBuffer().

4d16bfb338eac01f16682bd810e42ea2c13f78ac authored over 13 years ago by Chris Allan <[email protected]>
Additional delete tests added for pyramid files plus refactoring. See #5593

f584251645b0d1c7f90fd9b6baa1b0651b929082 authored over 13 years ago by Colin Blackburn <[email protected]>
Fixing NPE in `RomioPixelBuffer` (Fix #5671)

a76154ed35e8db88df94ed281c782ace074d0b24 authored over 13 years ago by jmoore <[email protected]>
Prevent deletion of lockFile (Fix #5655)

23f4f12758e0e4fd8080c695297cd011df3bb0b6 authored over 13 years ago by jmoore <[email protected]>
Ensure FS lite images requiredPixelsPyramid() returns true. (Closes #5613)

6667249d79f7d57a5da81486676f717e49eea3f7 authored over 13 years ago by Chris Allan <[email protected]>
Call super.close for `OmeroPixelsPyramidWriter` in finally block (Fix #5595)

b632263744ce19b33e2b496431a4795084a31126 authored over 13 years ago by jmoore <[email protected]>
Logging changes to ease debugging. (See #5577)

6fc060fbcbf57595146604b787615ce604d8a25f authored over 13 years ago by Chris Allan <[email protected]>
acquireLock in ctor for `BfPyramidPixelBuffer` (Fix #5433, See #5551)

0676001d8ea3f1ecd3c0d76bd3394551d591e518 authored over 13 years ago by jmoore <[email protected]>
Closing leaked file handles for proper Windows functioning (See #5433)

3f38ad9dd57cbf27bf2efe9b7db59097d8499a67 authored over 13 years ago by jmoore <[email protected]>
Fix erroneous logging in BfPyramidPixelBuffer.

079ac763edfd2721868ffafd1d248fdfc5f0ced7 authored over 13 years ago by Chris Allan <[email protected]>
Handle remaining pixels correctly.

74812134f508221192a366c4ae570b23d635acc9 authored over 13 years ago by Chris Allan <[email protected]>
Binding dimension calculations to 1.

aeeec67636059d29dca02311866f9429ff8293da authored over 13 years ago by Chris Allan <[email protected]>
Test compilation build fix.

b1821fe1c36ebda7d1f6d7c3eda1f53915c786df authored over 13 years ago by Chris Allan <[email protected]>
Merge branch 'feature/5238' into develop

* feature/5238: (Closes #5238)
Add series support to BfPixelBuffer.
Enforce pyramid creation...

605a2ced26454605e78b9e36aaca8259906bbb1b authored over 13 years ago by Chris Allan <[email protected]>
Updating to [330dd7fa929926ec071a808316392e952ea5b58e/bioformats.git] (Fix #5351)

Adds metakit dependency to romio/ivy.xml

1367f15f3d99074bc386c868dfbc9a9e5603e357 authored over 13 years ago by jmoore <[email protected]>
Add series support to BfPixelBuffer.

e94a4d16214fe8c3fa59d9c04b20004d45bf8b78 authored over 13 years ago by Chris Allan <[email protected]>
Enforce pyramid creation when using original data files.

951e79988298eadc082f7b9e4ea3de483ba63880 authored over 13 years ago by Chris Allan <[email protected]>
Unifying downstream naming. (Closes #5240)

33d448b90c3d987ef8908b95210eedc271874120 authored over 13 years ago by Chris Allan <[email protected]>
Checking writerFile for `BfPyramidPixelBuffer.isWrite` (See #5175, Fix #5249)

518dac60c348d9b9e96659268272387965d5e1f8 authored over 13 years ago by jmoore <[email protected]>
0-size pyramid after exception forces `ResourceError` (Fix #5189)

a7588b11223d22c2eba6a675311eae079d09fb03 authored over 13 years ago by jmoore <[email protected]>
Small logging fix.

8f00d2d4224148871d3e309e409a087542feb147 authored over 13 years ago by Chris Allan <[email protected]>
Proper arithmetic during writer initialization. (Fixes #5175)

a05e0f50ab340eaa403b77287c26cd0f02e68e73 authored over 13 years ago by Chris Allan <[email protected]>
Reducing 'Missing pyramid' log to INFO

d27c2d47324074ee81e84d02e2f4f1ba9a0e8232 authored over 13 years ago by jmoore <[email protected]>
Moving createSubpath to within createPyramidBuffer (Fix #5159)

1d8aa9a346db8fa105fec3767c71f3de4227cbaa authored over 13 years ago by jmoore <[email protected]>
Using an inline min/max calculator.

28d27af0efbaa10ead31aa27f2ea71030b493b84 authored over 13 years ago by Chris Allan <[email protected]>
Get Min/Max values from files. See #5098

eacdc0dc749d0a0b005c29b63d0b19f5b109ad5c authored over 13 years ago by Colin Blackburn <[email protected]>
Initial interface changes. See #5098

b312fdf8089e1b16454b6b8aacb881211b4a02ff authored over 13 years ago by Colin Blackburn <[email protected]>
Ensure pyramid pixel buffers are re-usable. (Fixes #5171)

ed988d9cc5c7fac2f41bd48959bfdc11efbc568e authored over 13 years ago by Chris Allan <[email protected]>
IOException(String message, Throwable cause) only available in Java 6.

ec06f0416db47959045726fab4f6c807e0179477 authored over 13 years ago by Chris Allan <[email protected]>
Ensure that rows per strip is populated correctly.

7c1e09d1262bb85e1626d2d34632a407d7f4b3d9 authored over 13 years ago by Chris Allan <[email protected]>
Skipping makePyramid if pyramid file exists

db0d072b69062f48ca99f4188e80f7ffacb72a25 authored over 13 years ago by jmoore <[email protected]>
Bye-bye closeQuietly().

1c47b31dcc7632e2dfd7f7a7c59962997d0992f8 authored over 13 years ago by Chris Allan <[email protected]>
Move to our own custom Bio-Formats reader and writer.

8dc9e27c793f816ebbe288f7fe373369f52b6716 authored over 13 years ago by Chris Allan <[email protected]>
Pyramid pixel buffer defaults and exceptions while in write mode (See #5083)

492c27279a6ff16421eacd45f0d50430924bda3a authored over 13 years ago by jmoore <[email protected]>
Fixing `PyramidPixelBufferUnitTest` after pixelBuffer.close()

6449a96df53bf138b76e69a0c211179d2df80ad7 authored over 13 years ago by jmoore <[email protected]>
Fixing FD leak from unclosed `TiffReader`

ff22c7f2cf5ccc0fdae5f87a81674d3dd59982db authored over 13 years ago by jmoore <[email protected]>
Writing pyramids as a temp file then moving (See #5083)

0f4a72b1d1c4ea407f13564f588a288f7cd7d6a0 authored over 13 years ago by jmoore <[email protected]>
Making `PixelBuffer` extend Closeable

d0e46b7c86f45769feb9db92fc671803d7455f30 authored over 13 years ago by jmoore <[email protected]>
Making `BfPyramidPixelBuffer` read or write with locking

7eaf0ecff4c9fcbdd238a675c0ff7c7fa1ebd990 authored over 13 years ago by jmoore <[email protected]>
Fixing `GetPixelBufferUnitTest` (See #5099)

7f07d61fd86414e1e14c02d6fddbac85459e2788 authored over 13 years ago by jmoore <[email protected]>
Fixing tile size retrieval.

f09fc5252a6911cac71b02f590d1a157c0f08e62 authored over 13 years ago by Chris Allan <[email protected]>
Remove unneeded variable.

3c6c524aa92bad34f041e829c47900d247229347 authored over 13 years ago by Chris Allan <[email protected]>
Make Bio-Formats reader stack OMERO compatible.

65c733fd1fa2b3b6b46a323a09eb0913231fe236 authored over 13 years ago by Chris Allan <[email protected]>
Use file path resolver in Pixel Data worker and makePyramid().

c6dd4271982b6a759991e315cc390118ee388a45 authored over 13 years ago by Chris Allan <[email protected]>
Switch to using file path resolver.

e2f70c86ab64ca1d47948b56d5c8f997fdf253f7 authored over 13 years ago by Chris Allan <[email protected]>
Adding xalan and serializer to romio dependencies (Fix #4669)

1872ed0ec2b3a0a6161396b714617e0a6ecf7d2e authored over 13 years ago by jmoore <[email protected]>
Initial version of metadata only import for big images. (Closes #3518)

36646c40fb6c0d5cd7e546e1f590760f2c8c6ff7 authored over 13 years ago by Chris Allan <[email protected]>
Changing `MissingPyramidException` superclass to `TryAgain` (Fix #4738)

ad3008cb58217db4ae0d9441b8a9964163f1d6aa authored over 13 years ago by jmoore <[email protected]>
Merge branch 'feature/4985-pixeldata-fun' into develop (Fix #4985)

27c9433e68a211cef60612990dd3c7c059b5c9c8 authored over 13 years ago by jmoore <[email protected]>
Reversing rollback in rbf6bfd8 plus extra tests. See #3518

0d9d2ee264d8e45743119c7aeb2e07f91edbb5bc authored over 13 years ago by Colin Blackburn <[email protected]>
Hard-coding tile size in `PixelsService.makePyramid`

0f6f52c75c2fe37b4ad19fb7a7e76fe7e148c45f authored over 13 years ago by jmoore <[email protected]>
Using buffer.calculateMessageDigest rather than Utils.pathToSha1 (Fix #4956)

a7929228b0894dd27a37dcd959b630ef894e8aa3 authored over 13 years ago by jmoore <[email protected]>
Use pyramid calculated tile width and height.

a0327d7c7de4a726e3e408aca5b25c9fc6e36f46 authored over 13 years ago by Chris Allan <[email protected]>