github.com/ome/bio-formats-examples commits | Ecosyste.ms: OpenCollective

Uncap Sphinx in Travis

a807f05ed7d49f39a557f93379952e3934524e48 authored over 7 years ago by Sebastien Besson <[email protected]>

Merge pull request #11 from dgault/Bio-Formats-5.5.1

Bump Bio-Formats version to 5.5.1

5ca558fc27c8d878bcbf015714df44670eca13c3 authored over 7 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.5.1

057f209f720c64aa17788657028a5e3256ae2311 authored over 7 years ago by David Gault <[email protected]>

OrthogonalReader: change logging levels to DEBUG

b0bb44dc61e4782fc66a49c7ec4971f6eb45f750 authored over 7 years ago by Melissa Linkert <[email protected]>

OrthogonalReader: add license header

17ea12206531d0a38c5655f2409ce2bae61134a4 authored over 7 years ago by Melissa Linkert <[email protected]>

Merge pull request #10 from dgault/Bio-Formats-5.5.0

Bump Bio-Formats version to 5.5.0

08e463859444b6a26b25dabf97af5985e4e2ae0b authored over 7 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.5.0

e7509faebf6e86dc8d6c14f9c0010c77d88906e7 authored over 7 years ago by David Gault <[email protected]>

Add OrthogonalReader to example test suite

9d9ef5e4544882c06a35c7caaad523b93b00ea91 authored over 7 years ago by Melissa Linkert <[email protected]>

OrthogonalReader: remove dependency on argparse4j

10d6aa0bed72e794f437a515b80a995e107fe6a2 authored over 7 years ago by Melissa Linkert <[email protected]>

Update package and class name

bd231d9d057eddb379f2c0beceb6ffeafd98ddd4 authored over 7 years ago by Melissa Linkert <[email protected]>

Original version of OrthogonalReader example from @emilroz

53f0ebb4ae844345243be4f28f4909f707547d4c authored over 7 years ago by Melissa Linkert <[email protected]>

Merge pull request #9 from dgault/Bio-Formats-5.4.1

Bump Bio-Formats version to 5.4.1

b1d98099d5976a9477910b03e8f154e12a98c522 authored over 7 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.4.1

3d986157ba5cd12f1d735d418a7cf2d5999dca1a authored over 7 years ago by David Gault <[email protected]>

Add to ExampleSuite

2c5b4f7063258ab80f7ecddb234d1b925608591c authored over 7 years ago by David Gault <[email protected]>

Add ReadWriteInMemory to Examples

1a709f6788f72ed749c3e5dd7913670d688d66f3 authored over 7 years ago by David Gault <[email protected]>

Merge pull request #8 from dgault/Bio-Formats-5.4.0

Bump Bio-Formats version to 5.4.0

be4eccc6721c071fc10763fd0d6e33639ee478e8 authored almost 8 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.4.0

1a9ce79bf0e80841f982981e2cebc61bd9edbfc1 authored almost 8 years ago by David Gault <[email protected]>

Update copyright headers

Repository: openmicroscopy/bioformats
Already up-to-date.

Generated by BIOFORMATS-DEV-latest-co...

363c27fb8c5abc2b4eea5890f4ae8c756d45d3eb authored almost 8 years ago by Snoopy Crime Cop <[email protected]>

Merge pull request #7 from dgault/Bio-Formats-5.3.4

Bump Bio-Formats version to 5.3.4

72e31bbbf70edff6e06caa257112021f7f474f49 authored almost 8 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.3.4

7f911340a016207cd8df4f86836720a3db051ac9 authored almost 8 years ago by David Gault <[email protected]>

Merge pull request #6 from dgault/Bio-Formats-5.3.3

Bump Bio-Formats version to 5.3.3

45fff8bb678b53391e242f75e3849d220e54230e authored almost 8 years ago by Sébastien Besson <[email protected]>

Bump Bio-Formats version to 5.3.3

a255716f1832f5bdbc83d78879131079813799fe authored almost 8 years ago by David Gault <[email protected]>

Delete example output files if they already exist

940ebe576e08fe60116a4c1c20878cb5c58cfd3e authored almost 8 years ago by David Gault <[email protected]>

Remove warning for unchecked or unsafe operations

181104d193e14763a3c7b67d7deabc1377520f54 authored almost 8 years ago by David Gault <[email protected]>

Split single method into initialise and readeWriteTiles

1f163e34f7d85b8e021e83217a7eedac021c1708 authored almost 8 years ago by David Gault <[email protected]>

Use OME-Tiff instead of OME Tiff

e64be9f5f69879fa04130bc52cc84c86704d9889 authored almost 8 years ago by David Gault <[email protected]>

Bug fix - correct writer name

fc0e1ce87d899d930c56995b19fb89b1fd41ae0f authored almost 8 years ago by David Gault <[email protected]>

Improve Javadoc to document exceptions

b85a237401a8fe7286bfa91bf4ec7a2bbab6c1a5 authored almost 8 years ago by David Gault <[email protected]>

Use finally to always cleanup resources while still throwing exception

072f8a521041418a58d0ec83ccd449e2d1df85a5 authored almost 8 years ago by David Gault <[email protected]>

OverlappedTiledWriter - Improve Javadoc

bcb609294fcf7e948d75bc9e4b818d3f236d5e67 authored almost 8 years ago by David Gault <[email protected]>

Add new non square tile examples

fa43588454f41ff51b0862ec137f455260361677 authored almost 8 years ago by David Gault <[email protected]>

Add new fake file to prevent NPE

289831026dd8ae54e29173c27b69cb6fb7f204b1 authored almost 8 years ago by David Gault <[email protected]>

Remove redundant boolean

0254de0b20066928c51f067389eb9ff9416a093e authored almost 8 years ago by David Gault <[email protected]>

Update copyright to 2017

e0a825ba976e6c021299db4f0604ce71ed9d4973 authored almost 8 years ago by David Gault <[email protected]>

Remove unused effective size calculations

e27887def87e8e1ad34806083f6ebe8702c2607e authored almost 8 years ago by David Gault <[email protected]>

Fix start tag for example code

bdfcdc456b1d3c774b9ecf18460c411cd1f87148 authored almost 8 years ago by David Gault <[email protected]>

New Overlapped Tiled Writer example

500f78579035362e05706cc4919549e8a3e43c9c authored almost 8 years ago by David Gault <[email protected]>

Add overlapped tiled writer sample to example suite

Makes use of sizeX and sizeY attributes with fake file also

c75acb561ffae589245b995b5b8747376627eb8c authored almost 8 years ago by David Gault <[email protected]>

Throw exceptions rater than catching them

89582ab5933b1972777d16b4e3f30da63cc8e9f2 authored almost 8 years ago by David Gault <[email protected]>

Re add exceptions for cleanup to ensure closure.

Also removes unused boolean for catching exceptions in initialistaion

e1b8392937d6b91c6a3545fc99c2a5611f2e46fd authored almost 8 years ago by David Gault <[email protected]>

Fix TiledReaderWriter initialisation

89ce26c35f1cb1e4398fe277a1ff548982c7627d authored almost 8 years ago by David Gault <[email protected]>

Throw exceptions rather than catching them

316b6ce5bee5e58febc04df3b17d944309df5e1f authored almost 8 years ago by David Gault <[email protected]>

Merge pull request #4 from sbesson/java_library

Java library examples

778205d88a75b45eb82d3d041289adace7ca186c authored almost 8 years ago by Sébastien Besson <[email protected]>

Add newline

d51a0bbcc5f348873f87190926ca721426592b5b authored almost 8 years ago by Sebastien Besson <[email protected]>

Bump Bio-Formats to version 5.3.2

143e4b32624a149d3599d085bc1267b73c399c75 authored almost 8 years ago by Sebastien Besson <[email protected]>

Also exclude build and target directories

8ab43040db09d7dad0d3d85b13592bdd138c643f authored almost 8 years ago by Sebastien Besson <[email protected]>

Add default goal

f6edfde7baabe1b365ffcfed271df8938893bf9f authored almost 8 years ago by Sebastien Besson <[email protected]>

Update README to document new usage of the repo

72bc86e008f5b98f7e92b24fe36b446599fc6e62 authored almost 8 years ago by Sebastien Besson <[email protected]>

Also add Unidata repository to POM

534a3bb3fea5cf2142179cd3610091e9c4652b44 authored almost 8 years ago by Sebastien Besson <[email protected]>

Add Unidata repository

e16a7f0fee10521fe8fdb67525870380094b3e8d authored almost 8 years ago by Sebastien Besson <[email protected]>

Also removegradlew in Maven matrix job

fdaa06c03242bea26f8122b9470aa09ea3f32f8c authored almost 8 years ago by Sebastien Besson <[email protected]>

Add .gitignore

719bae66d9442da53796c450b55d382ad848f905 authored almost 8 years ago by Sebastien Besson <[email protected]>

Add gradle wrappers

b6b1d42aa6a9cae1bd38b0bc0050ca341a87abd1 authored almost 8 years ago by Sebastien Besson <[email protected]>

Copy over Gradle and Maven examples along with minimal Travis script

7e31217d7663ee0a0c0388dad31b2ea7665acea8 authored almost 8 years ago by Sebastien Besson <[email protected]>

For detailed example use scenario with overlapped tiling

73bf442f3200f7736dd379ed517aec5f3da5b370 authored about 8 years ago by David Gault <[email protected]>

Import FormatTools

07d2a7c536ae33cd2c27cd93a77325b3290070e2 authored about 8 years ago by David Gault <[email protected]>

Use literal include markup for example code

4169f409aa0b3ac5d2a6aa58daec5b40a20ce8c5 authored about 8 years ago by David Gault <[email protected]>

Reuse buffer for read/write

118ddf1f717ed8d952863a59f7d0d24ba91388aa authored about 8 years ago by David Gault <[email protected]>

Consistent use of tileSizeX and tileSizeY

a40cebcd502ad5fb9da2bae47a31e3cb4de65924 authored about 8 years ago by David Gault <[email protected]>

Wrap long lines and use 2 try catch blocks for cleanup

6a01095ac6005d4878024ecf294cb35d3ad29379 authored about 8 years ago by David Gault <[email protected]>

EOL at end of ExampleSuite

33aef5167cf0ca17a08e7edb4be777b12aba564c authored about 8 years ago by David Gault <[email protected]>

Add tiling examples to ExampleSuite

b2ddad72ad106915d62464fe955ca565ac78f313 authored about 8 years ago by David Gault <[email protected]>

Add tiling sample files

96f4af87c5e91461bd1f3ffa3c1a804d1c334e93 authored about 8 years ago by David Gault <[email protected]>

Remove metakit component and use jar from maven central

46b1a80033ad7eabe1b167fa342fd2b21726f020 authored about 8 years ago by Roger Leigh <[email protected]>

Merge pull request #2654 from sbesson/test-build_cleanup

Test build cleanup

70033cf634405860c5be6883a2dcc191a959ff89 authored about 8 years ago by Josh Moore <[email protected]>

Remove non-existing folders from classpath-template

cb8ae114bb357010f57b8050e9f5c7be2d301594 authored about 8 years ago by Sebastien Besson <[email protected]>

Simplify .gitignore

All lines should be contained in the build folders (test-output, target...)

7560845d0c0de18b1cddc2fb96b8b3607be04af0 authored about 8 years ago by Sebastien Besson <[email protected]>

travis: Don't require fetching of git tags

aea7b408b701bcf90d37b29035da59b510986f70 authored about 8 years ago by Roger Leigh <[email protected]>

Remove mdbtools from build files

363bf6cda48ca980c15b1aa899f0c90d2eea1865 authored about 8 years ago by David Gault <[email protected]>

Remove findbugs from Travis and simplify the yml configuration file

The findbugs:findbugs Maven phase was added to the Travis test script as a way
to flag errors. H...

55891319ea8b303f77d0e4b87f2769e194702127 authored about 8 years ago by Sebastien Besson <[email protected]>

Merge pull request #2609 from sbesson/docs_pdf

Ant: remove the pdf generation from the top-level documentation target

3bc585156bd6ef281cb36486e681b0285765cb71 authored about 8 years ago by Sébastien Besson <[email protected]>

Add Sphinx build test to the Ant matrix components of Travis

19fa6c07fb7eda4f3f401c8b9769d6b8b6a8c71f authored about 8 years ago by Sebastien Besson <[email protected]>

Remove references

9617b78b5e6da10baa234bd2cf01bc87f8c5a521 authored about 8 years ago by Sebastien Besson <[email protected]>

Add execute() calling the main method of example classes by reflection

fccff46586e1783df7073e7e444e79b3c5f746b1 authored over 8 years ago by Sebastien Besson <[email protected]>

Add ExampleSuite class executing all examples of usage of Bio-Formats

Use class.getResource() to access resources relative to the main class

0412d875ae5c38fc70ddd4534a5aa8b9c32b750f authored over 8 years ago by Sebastien Besson <[email protected]>

Migrate other Sphinx Java examples under developers/examples

12d605cfff426de149f59939918350669303c57a authored over 8 years ago by Sebastien Besson <[email protected]>

Remove ExampleSuite in favor of direct specification

36c0ba72de30ca3f8e0581acf6d212b34ec56312 authored over 8 years ago by Sebastien Besson <[email protected]>

Set root level OFF

5e848cab60dd494fe18e9a5fd905a6fa1b72c00d authored over 8 years ago by Sebastien Besson <[email protected]>

Add top-level class for running all examples

a3a865c5a7b2de7808311130cc2159e1fafc5e9d authored over 8 years ago by Sebastien Besson <[email protected]>

Add simple top-level POM compiling/executing the examples

1ee73972d56a4af38e9c7a0dd07646cda0e95312 authored over 8 years ago by Sebastien Besson <[email protected]>

Migrate physical size example under examples

4d68eeebba803833223fdad979e0a9cdd227e0cb authored over 8 years ago by Sebastien Besson <[email protected]>

Fix MATLAB root logger level overriding in bftest.m

9603edcfa4bf40f9f363170362b7204cb0201ecd authored over 8 years ago by Sebastien Besson <[email protected]>

Merge pull request #2419 from rleigh-dundee/model-enum-units-metadata

Model enum units metadata

c8f3ee4e81fa3c054a4dd368a334171f3df3c045 authored over 8 years ago by Sébastien Besson <[email protected]>

specification: Add metadata for unit names and enums

In addition to the symbol in current use, add:
- name (including plural form)
- alternate name (...

6be4e2a4da5b8a82c3560d85fe81f857016111a8 authored over 8 years ago by Roger Leigh <[email protected]>

Remove JACE C++ bindings from the Bio-Formats source code repository

The bindings have been decoupled to a separate source code repository

7c77d4f013d7ee59db6bd3cfbaf7dac1811f00fb authored over 8 years ago by Sebastien Besson <[email protected]>

Add logging calls to bftest

147fbadc719dd9e0be6b609f509400fea788174a authored almost 9 years ago by Sebastien Besson <[email protected]>

developers/examples/bftest.m: simplify by using Matlab and Octave core functions.

3f5585b4c3c2d3a06ba772dabc1909c64b67cddc authored almost 9 years ago by Carnë Draug <[email protected]>

update README.md to current status

f17210534efe699cef2df71a22f80b9ad5eaa6bc authored about 9 years ago by simleo <[email protected]>

Only test openjdk7

Since Oracle JDK 7 should be tested via the OME CI infrastructure, testing it
on the Travis matr...

69f8f32dc1b03954ef784d1eae93a500b7fa9b36 authored about 9 years ago by Sebastien Besson <[email protected]>

Merge remote-tracking branch 'origin/develop' into java7

ddbb4f9776694f96440e971741e7bf313518c8a3 authored about 9 years ago by Roger Leigh <[email protected]>

Re-add boost for cppwrap

f2ef13c0130002872a077499ab77b00f1e1e64b1 authored over 9 years ago by jmoore <[email protected]>

Only run maven_findbugs on JDK7+

a7a16e283822a4c18714ce3bc1b25d8cf7992ba0 authored over 9 years ago by jmoore <[email protected]>

Switch back to excluding oraclejdk8 for cppwrap

eb9d4e427bfcdf8e8a759bfcac7a973d2f185c12 authored over 9 years ago by jmoore <[email protected]>

Fix sphinx target

13d620ba2b3e9dad1ff131d710dafde6b1a3e6fc authored over 9 years ago by jmoore <[email protected]>

Simplify travis builds

As proposed, this drops the C++ builds and the
Latex/Sphinx builds in order to move us to the
co...

0156017936b46c8de71449312506f6cd5f228cb5 authored over 9 years ago by jmoore <[email protected]>

Activate findbugs is travis

gh-1965 was merged into the daily build and had priority HIGH
findbugs warnings. If findbugs had...

57ec5b161bb2d67259145b148839f6e81db5ab93 authored over 9 years ago by jmoore <[email protected]>

Merge pull request #1753 from sommerc/develop

CellH5 reader update and CellH5Writer

804ef5aeaaea6ac2d4fdde6a60326515f91ead84 authored over 9 years ago by Melissa Linkert <[email protected]>

travis: Drop OpenJDK6

e26c72619a9ee234964b180809562009eb0db5a5 authored over 9 years ago by Roger Leigh <[email protected]>

Cleanup/remove OMERO layer components

These components come from the time where Bio-Formats was managed as a
submodule of OMERO. As we...

38a4dae8c233c442fe4b61e04632d74c1a56771a authored over 9 years ago by Sebastien Besson <[email protected]>

merge with upstream

80860ed54510a0f836c843c3b56bafb331ac8a15 authored over 9 years ago by Christoph Sommer <[email protected]>