github.com/ome/ome-model commits | Ecosyste.ms: OpenCollective

cpp: bioformats: Add basic model sanity checking and correction to MetadataTools

6f56e576700244349d7b4db3b73ebf5334668986 authored almost 10 years ago

cpp: bioformats: Correct EffectiveSizeC and ImageCount calculations in FormatWriter detail

c76b829cf55bbdb077920a29bc815a89ec967e0c authored almost 10 years ago

cpp: bioformats: FormatWriter::setId always compares canonicalised paths

27f6c3eeb39c7ff3d3c80e81eee257df060e0d0a authored almost 10 years ago

cpp: bioformats: FormatReader::setId always compares canonicalised paths

7e25c6b86261e763a1dcdb8a4e12f020aa41f716 authored almost 10 years ago

cpp: bioformats: Correct warning in OMETIFFReader.h

cbd215b7b799f157187e32474a9f7c1b85f3e1ca authored almost 10 years ago

cpp: bioformats: Correct OMETIFFReader description

fc244b8338ff19cb2c0382d9394755b2d7c48ec1 authored almost 10 years ago

Update POM version numbers to 5.1.2-SNAPSHOT

f13b2366c7a7d0f4d7dba88e4d8324a96965c4b1 authored almost 10 years ago

Merge pull request #1747 from melissalinkert/5.1.1-version

Update POM version numbers to 5.1.1

7e58cc7c8afdc5e5020ec32e2b11d44302e6858e authored almost 10 years ago

Merge branch 'develop' of github.com:openmicroscopy/bioformats into develop

255da4bf9bf6dfd231b40c853841f6a93b095f48 authored almost 10 years ago

travis: Switch from saucy to trusty

saucy has been removed from the mirrors and was no longer supported.

b60fc2ab49b563c1bd80a5c2ff555f58a12a6793 authored almost 10 years ago

Merge pull request #1749 from rleigh-dundee/cpp-tiffwriter-fixes

C++: Reader and writer channel-related fixes

0ccfb2e7dead62de3717fd06cf7148b726aa9ecc authored almost 10 years ago

cpp: bioformats: Restore FormatReader::getOptimalTile*

Added back with caveats documented.

b77cb6da53627ad69bd8245dd342f268d8cae0e0 authored almost 10 years ago

cpp: bioformats: Update FormatWriter channel range comments

9b5a6c3f067b8be070fbf7daea6fcc28ce8715fb authored almost 10 years ago

cpp: bioformats: Update FormatReader channel range comments

15dbbe07861c58e4483d96f0614744c6e73226b2 authored almost 10 years ago

Merge branch 'develop' of github.com:openmicroscopy/bioformats into develop

b19ef13c6521608c36fdaee5ab3f570e6b058e54 authored almost 10 years ago

Merge pull request #1730 from mtbc/Vector-cleanup

clean up older Java code

4a78c89ce81d65f9430a1d8bb1e4af06fbf2f162 authored almost 10 years ago

cpp: bioformats: tiff: Handle interleaved property when reading IFD

b3edb954a318bd2b09a7699e0bbfdc99dc6cf529 authored almost 10 years ago

merge 1

56f8e23cb0e96553ece2c9ef7fb9bcff82c8e521 authored almost 10 years ago

cpp: test: Improve MinimalTIFFWriter interleaved testing

5c8cc5e4269486de43635cfa39b9edd534e61af1 authored almost 10 years ago

cpp: bioformats: LookupTable methods match openBytes/saveBytes for consistency

9e130c7d05b2e80ac3a0da87cd58d3944caf6c4e authored almost 10 years ago

cpp: bioformats: Drop FormatReader channel argument defaults

Since using the defaults inappropriately could cause serious
problems, it's best to always requi...

c4dc5ad82aa7542c54b75f8dd61ee6d0be360224 authored almost 10 years ago

cpp: bioformats: Make plane and series indices more self-describing

9b7af2fbc1b3f4a995c628cff34f2ab0a0a8cc06 authored almost 10 years ago

cpp: bioformats: Correct broken subchannel assumptions

Correct for both TIFF readers and writers. openBytes and
saveBytes can now handle transfer of R...

3faa776976ce16660d2fca4af2dc5c1bb7c8488b authored almost 10 years ago

cpp: bioformats: Add interleaved property and methods to FormatWriter

f8a16c1e77d54f3d89a31831c1ef0c525dc716ca authored almost 10 years ago

cpp: bioformats: tiff: Set SOFTWARE tag when writing an IFD

9a977251503c44ec24f20da60cbf3ff403f79996 authored almost 10 years ago

cpp: bioformats: MetadataTools effective size C is always > 0

f0382f220d0db09aaa094e6489826daf96494eaa authored almost 10 years ago

Update POM version numbers to 5.1.1

427f78fe83867c6adb442f9ec222420647c53ebc authored almost 10 years ago

cpp: bioformats: Correct and extend BigTIFF warnings and support

- Expose optional BigTIFF flag in the writer interface.
- Use optional state to correct warning ...

23e8c9d20a79c6acb5b0c94c2f4e29ba39e93151 authored almost 10 years ago

cpp: bioformats: Correct MinimalTIFFWriter BigTIFF checks

e6007a620744415e814858efdeae714e18d9522e authored almost 10 years ago

cpp: bioformats: Add TIFF writer

f1b503f528ce4861e9920029f432c9332319ea4c authored almost 10 years ago

cpp: bioformats: Add helper methods to FormatWriter implementation

Add methods to get dimension sizes etc. to match FormatReader,
but obtain from MetadataRetrieve....

60dd23dc533ed0865bc490adfecdf9683038143d authored almost 10 years ago

cpp: bioformats: Add plane methods to FormatWriter and clean up

Add getPlane and setPlane methods, equivalent to getSeries and
setSeries. These are used to ens...

7dd807cfc5c328b48dc8120c8421ff1a165b5d79 authored almost 10 years ago

cpp: test: Split TIFF sample discovery from tiff tests

This permits the samples to be reused in other tests.

48724aa6ce29c839608aa1658bade459dcf62f58 authored almost 10 years ago

cpp: bioformats: tiff: Move and add utility functions to Util

- Move makeCoreMetadata from IFD to Util.
- Add getCoreMetadata and setCoreMetadata to get CoreM...

9288360fcfac64519da52eb518a3bd42f45438ca authored almost 10 years ago

cpp: bioformats: Add pixel size methods to MetadataTools

Use to compute maximum potential storage sizes for series' in
the MetadataStore. The intended u...

1f22150d72252e3859a1aea3c4805ea5f7cb3eca authored almost 10 years ago

cpp: MetadataTools: Allow filling of MetadataStore directly from CoreMetadata

Primarily useful for testing where the FormatReader API isn't used
to set up the MetadataStore.

74a47ccbc42faa5b90a4feb39760501e63e3c814 authored almost 10 years ago

cpp: bioformats: tiff: Add methods for BitsPerSample

b92d260309036665d10c5cf0c75c1b5d70e438a2 authored almost 10 years ago

cpp: bioformats: Drop FormatWriter SaveSeries sentry

Since writers may have strict ordering requirements, it doesn't
make sense to be able to freely ...

3460a436a496a575c99c37073c5c6f1208188dc5 authored almost 10 years ago

cpp: bioformats: Add MergeSubchannelVisitor helper

This is to allow recombining of separate subchannels into a
VariantPixelBuffer with multiple sub...

a3cb1ff4e788b2ab3db205ae764f731be3218cbd authored almost 10 years ago

cpp: bioformats: Add significant bit sizes to PixelProperties

Unlike the existing size properties which reflect the in-memory
type storage size, this represen...

4107a7a24a90b35708a4e17302d82048e46609b3 authored almost 10 years ago

cpp: bioformats: Add storage_size_type

Unlike dimension_size_type, this is a 64-bit quantity to handle
any file offset and multiplicati...

2d8434b4415e5e3127a6e4ca2aa4ff92d401706d authored almost 10 years ago

cpp: bioformats: CopySubchannelVisitor uses planar pixel layout

While there's only one subchannel so planar or interleaved subchannels
actually have identical s...

9feaf78431e1d4fe8f792a6d9d82480c4c53b469 authored almost 10 years ago

cpp: bioformats: Correct FormatReader documentation comment

5b208a586d854ef9037e5a2c6af928b30072a828 authored almost 10 years ago

cpp: bioformats: Add IFD::readImage overloads for subchannel

ff43bbbb16ccafce51e4e839a8b7c464730f9277 authored almost 10 years ago

cpp: bioformats: Document bigTIFF extensions in MinimalTIFFReader

cbbc2d1523444f48398a5caf4a00c56302c7c18f authored almost 10 years ago

cpp: bioformats: Add TIFF codec support

af1a21c9e611470562340122f2161e80d294e721 authored almost 10 years ago

Merge pull request #1705 from rleigh-dundee/build-docs-refactor

Refactor sphinx ant build and add cmake build

e72261ea13c6e3a78755109e9a4aefdaf13da749 authored almost 10 years ago

prevent utests/test.mdb from confusing git

suggested by @melissalinkert

72690eb5db268d995fa7f8ffc542568aead34179 authored almost 10 years ago

cmake: Move sphinx build rules to docs/sphinx

488d9eb9807ea888b711ad3cf63698b4c2e07fcf authored almost 10 years ago

docs: Install doxygen docs and adjust user manual install directory

e8676e6a6df332d7434914ad97cf7abd02bf6829 authored almost 10 years ago

cmake: Correct flake8 warnings in python helpers

6ccf8b5ff87678303617e7af502f11a016a632db authored almost 10 years ago

Merge pull request #1704 from rleigh-dundee/cpp-test-travis

cpp: test: Delete generated test files to conserve disc space

a608e1e4f43fed04bdaf0bcf3a901ae2799a650f authored almost 10 years ago

docs: Don't pass unsettable options with sphinx-build -D

Options set with -D don't get set unless whitelisted and then don't take effect
until after conf...

9455f54574e45a69b7668021dc6c3fa27478232b authored almost 10 years ago

cmake: Introspect sphinx configuration and add sphinx man target

004ee8aa445813f361231133dcec1418244914b9 authored almost 10 years ago

cmake: Build and install sphinx HTML and PDF manuals

2321bc04cfe19b09c9b3448db5148eca37c20b43 authored almost 10 years ago

cpp: test: Delete generated test files to conserve disc space

be53dbe6f20510f3982b4635c92b47d33403726c authored almost 10 years ago

Update POM version numbers to 5.1.1-SNAPSHOT

e4d4a22d39ff5680e34b4e448fbb1e5bf422c346 authored almost 10 years ago

Merge pull request #1698 from melissalinkert/5.1.0-final-version

Update POM version numbers for 5.1.0

69fca821efa478de6a752e167b76552ab6ea2954 authored almost 10 years ago

Merge pull request #1694 from melissalinkert/private-javadoc

Display private fields and methods in Javadocs

a07942b90d8cce67716baac04f24c5ecc53a252f authored almost 10 years ago

Update POM version numbers for 5.1.0

897624b34e9be17bb47f6ae2b227fa2d7ddd50ac authored almost 10 years ago

Update POM version numbers to 5.1.0-SNAPSHOT

88b456b2203b1d439603546a12ea6a99cd98c59b authored almost 10 years ago

Update POM version numbers to 5.1.0-rc2

5dab4688aa40522d08b65f77ca6007eac2fd28b6 authored almost 10 years ago

Fix Javadoc warnings

a84ca69e48dbd6c8fd63e893805277522b99192e authored almost 10 years ago

Merge pull request #1691 from melissalinkert/5.1.0-snapshot

Update POM version numbers to 5.1.0-SNAPSHOT

8e1e91e01716559d5aec2f59f16215cae4ed44f4 authored almost 10 years ago

Merge pull request #1689 from rleigh-dundee/cmake-pathconfig

cmake: Add Bio-Formats-specific paths to cache to allow user configuration

c07a07b1ac44a16ab3c1bc462f2fc2f758eea5b3 authored almost 10 years ago

Update POM version numbers to 5.1.0-SNAPSHOT

d76dd33ee2adc9bed35297f38ec74d34360d69a0 authored almost 10 years ago

Merge pull request #1667 from melissalinkert/5.1.0-version

Update POM version numbers to 5.1.0-rc1

d64fa3cfc3d1efa5c2c1285e65147d7a87b8494d authored almost 10 years ago

Merge remote-tracking branch 'origin/develop' into 5.1.0-version

Conflicts:
pom.xml

6c2e8354f061316aab2f21f1fff59d0e1ff234da authored almost 10 years ago

Update copyright headers

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

Generated by BIOFORMATS-5.1-latest-co...

1011b3b23dc61e5cf585e84f53cf48cfdd1f16a7 authored almost 10 years ago

Merge pull request #1684 from ctrueden/devel/units-api

Improve the units API

f26c5dbec85b48151a72229feb05c6972bb6c0cc authored almost 10 years ago

cmake: Add Bio-Formats-specific paths to cache to allow user configuration

a9a23f2b7adc0a0e9f4a670622760f38cbe7430f authored almost 10 years ago

Merge pull request #1678 from jburel/inputstream

Input stream

7954ab10f0a08c7428414d77b94333dd2ee7c5db authored almost 10 years ago

Merge pull request #1683 from rleigh-dundee/doc-cpp-examples2

C++: Add FormatReader section to tutorial

d9509edc03e6144ec027abc276bd315e33d54e01 authored almost 10 years ago

Merge pull request #1664 from rleigh-dundee/git-error

build: Use long and short git revisions

8c2e9cf5afbbe8193986cec8778cc2ce9e974cf9 authored almost 10 years ago

cpp: cmake: Special-case bf-test shell wrapper rootdir determination for empty path

8835f5fb470f768fe9510bf2d24ecb4b94b80369 authored almost 10 years ago

Add missing @Override annotations

760fad2ed032449f527b4fe504334a35ad8b310e authored almost 10 years ago

Quantity: add common subclass methods

This is very convenient when coding API against Quantity variables
without knowing their type; o...

d7608fe88865ac4958dcc01299a52be6467b9308 authored almost 10 years ago

Remove unused imports

1ae394ce03097345063f60573fed27a74e5fd529 authored almost 10 years ago

cpp: Document ome::bioformats::in namespace

76394364134133b827610692db8aeae994782965 authored almost 10 years ago

docs: Add C++ FormatReader example

ff08913b75dfb80fa5244293b366992437a6b791 authored almost 10 years ago

Merge pull request #1675 from rleigh-dundee/doc-cpp-examples

C++: Add metadata examples to tutorial

a5408df11304ba0c55f1d3f5c7fcbb3b10945b72 authored almost 10 years ago

Throw exception.

b6135d32ad6e8343d775657e7f9e0500053ee5a1 authored almost 10 years ago

docs: Add pixel buffer section to the tutorial

aacbb76a86d078cb7258b74d2b0caca28e05fe2d authored almost 10 years ago

Close input stream

8cf3035eb128dfc22357c21b47edf53e6b82bfe2 authored almost 10 years ago

cpp: Add examples

1146517af29d9f74c4e28a36e7601b3475538d23 authored almost 10 years ago

cpp: bioformats: Use validate argument in MetadataTools getOMEXML

1195330000d4f6ea322f9ea9b2d4999491c6c37e authored almost 10 years ago

Pinhole and wavelength were wrongly reset.

1e66648f09eb9f7a9ee733022f0576def4cc6b51 authored almost 10 years ago

Merge pull request #1668 from jburel/xslt-map-unit-fix

Fix transforms

183a2cb8ccb75d3aa721193200b18a4de8f885ce authored almost 10 years ago

Merge pull request #1622 from joshmoore/unit-conv-2

Unit conversions (XSD from sympy)

0114e9bcecb3b49fa5b9fd9c176108fc3941dfcb authored almost 10 years ago

Merge pull request #1670 from rleigh-dundee/cpp-ometiff-fixes

C++: Small fixes for the OME-TIFF reader

5a7e54ed444303ed169333380c74e27f75eba82f authored almost 10 years ago

Merge pull request #1672 from rleigh-dundee/cpp-viewer-pan

cpp: qtwidgets: Correct camera pan direction in GLView2D

3c81f6df0ccfb175eabff35eff0779040152ed5f authored almost 10 years ago

Merge pull request #1669 from qidane/correct-catalog

Correct the 2008-02 catalog

6c22c8873c1850bba297d89d9eb3204e310892d2 authored almost 10 years ago

Fix typo error.

7a462077d1c213b17b36965ef287572a0cc1c7f4 authored almost 10 years ago

Add missing metadata.

9c757ef702d66938d62a06b2d99d79c51c7cbca7 authored almost 10 years ago

Use more direct transform paths

bace5419a965230039be1610b7841030f896007c authored almost 10 years ago

Merge pull request #1632 from qidane/raise-the-bar

Adding bar to units

58418814b773906790530f229d332a695adddac5 authored almost 10 years ago

Remove commented out lines.

94b37726200079feb1db2b6f602d546eb04828f6 authored almost 10 years ago

Merge pull request #2 from qidane/round-not-strip

Round dont strip floats to ints

cb47d6821e28e6495d060822de7781ffa4b0eee7 authored almost 10 years ago

Round dont strip floats to ints

5827c4d018f6dd0132b0851dbd3b1b471917df90 authored almost 10 years ago

cpp: qtwidgets: Correct camera pan direction in GLView2D

7efc32fa7b7c5eee69f0d72defd0e64a90d927d2 authored almost 10 years ago