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Remove matlab#3183

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Commits on Aug 20, 2016

• Add new infrastructure to test serialization regression

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• Fix writeConfigFile NPE

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• Expand testMemoFileUsage to use the cache directory

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• Refactor testMemoFileUsage reloading step depending on the cache configuration

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• Migrate cache generation to dedicated build target

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Commits on Oct 28, 2017

• Fix classpath for gen-cache target

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• Update testMemoFileUsage to read from both current and cached memo files

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• Add test-memoizer target to run only testMemoFileUsage

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Commits on Nov 20, 2017

• testMemoFileUsage: fail on invalid directory and pass on missing .bfmemo

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Commits on Jan 12, 2018

• Add gen-file-list target to save a list of scanned files

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Commits on Jan 16, 2018

• Update test-automated to accept a testng.file-list argument

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Commits on Feb 5, 2018

• Volocity: expand Image names to include the stack parent name(s)

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Commits on Feb 6, 2018

• Compare Integers with 'equals' instead of '=='

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• Inveon: attempt to find renamed data files

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• Do not allow the header file to be used as the data file

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• Do not require Inveon image files to be detected

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Commits on Feb 7, 2018

• Move Inveon check in testSaneUsedFiles to prevent conflict

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Commits on Feb 26, 2018

• Cellomics: fix indexing when the field counts are variable

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Commits on Apr 18, 2018

• Update POM version numbers to 5.9.0-SNAPSHOT

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• FileStitcher: do not use detected patterns that include missing files

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Commits on Apr 23, 2018

• Merge pull request #3128 from snoopycrimecop/develop/latest/version_bump

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• Zeiss CZI: fix big image edge case when tiling is present but a pyramid is not

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Commits on Apr 24, 2018

• switch modifiers to customary order in NDPISReader

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• switch modifiers to customary order in CellH5Reader

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Commits on Apr 30, 2018

• Merge pull request #3130 from mtbc/static-final

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Commits on May 2, 2018

• test-suite: Add testng.allow-missing property

  

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• test-suite: Pass testng.allow-missing property via ant

  

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• test-suite: Adjust size of test list dynamically

  

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• test-suite: Failing setId is not an error when allowing missing files

  

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• test-suite: Treat present configuration and setId failure as failure

  

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• Log stored OME-XML at TRACE

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• OBF: add FLIM support

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Commits on May 3, 2018

• build: Never run upgrade checker when running unit tests

  

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Commits on May 9, 2018

• TiffParser: Don't add SUBIFDS to main IFD list

  

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• MinimalTiffWriter: Merge SubIFDs into main IFD list if explicitly requested

  

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• MinimalTiffReader: Document mergeSubIFDs

  

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• MinimalTiffReader: Don't reset mergeSubIFDs on close

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• MinimalTiffReader: Add all SubIFDs at once

  

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• TiffParser: Rename getIFDs to getMainIFDs and restore old getIFDs implementation

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• TiffParser: Correct last remaining uses of getIFDs

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• MinimalTiffReader: Make mergeSubIFDs transient

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Commits on May 10, 2018

• test-suite: Configuration: Account for RGB channel count in plane size calculation

  

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• test-suite: FormatReaderTest: Account for Effective SizeC in plane size calculation

  

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• test-suite: FormatReaderTest: Plane size calculation matches that in Configuration

  

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• ci: Simplify ant testing to avoid Travis timeouts

  

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Commits on May 11, 2018

• Merge pull request #3142 from rleigh-codelibre/ci-avoid-upgradecheck

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• Metamorph: override getDomains() to check if the current file has a plate

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Commits on May 28, 2018

• TiffWriter: Add support for DEFLATE (zlib) compression

  

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Commits on May 31, 2018

• Warn if passing metadata with dimensionOrder in bfsave

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• ND2: prevent integer overflow when reading a tile from a large image

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Commits on Jun 5, 2018

• Trestle: ensure consistent ordering of used files

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Commits on Jun 6, 2018

• Memoizer: add generateMemo(String) convenience method

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• Refactor test used by gen-cache target to use

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• Add cachgen command line tool for generating memo files

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• Memoizer: add setReadOnly method

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• Fix configurations for gen-cache and test-memoizer targets

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• Make testMemoFileUsage's Memoizer read-only

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• Merge pull request #3158 from melissalinkert/trestle-used-files

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Commits on Jun 7, 2018

• Merge pull request #3140 from rleigh-codelibre/sync-east-tests

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• Merge remote-tracking branch 'origin/develop' into serialization_tests

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• Fix Metamorph RGB series channel count

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Commits on Jun 8, 2018

• Merge pull request #3160 from jmuhlich/metamorph-series-rgb

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Commits on Jun 11, 2018

• Plugins exporter: Reorder the dimensions

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• GelReader: Don't allow overflow when reading unsigned integer values

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Commits on Jun 12, 2018

• build: Update maven plugin versions

  

  Roger Leigh

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• build: Add xalan.version and use in all poms

  

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• build: Add maven-javadoc-plugin.version

  

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• build: Use maven-enforcer-plugin to enforce maven and java versions

  

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• build: Move lifecycle-mapping to eclipse-specific build profile

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• build: Update m2e lifecycle-mapping plugin versions

  

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• build: Update imagej1 plugin to 1.51r

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• build: Add jaxb-api as test dependency

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• build: Update maven plugin versions (2)

  

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• build: Use maven-enforcer-plugin 3.0.0-M1 for Java 9 support

  

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• ci: Update for maven changes

  

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• Update maven plugin versions

  

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• Update maven plugin versions

  

  Roger Leigh

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• Build javadocs as part of the main build

  

  Roger Leigh

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• gitignore: Ignore IntelliJ IDEA files

  

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• gitignore: Ignore IntelliJ IDEA files

  

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• ci: Only test ant build with JDK8

  

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Commits on Jun 14, 2018

• MetaMorph - Prevent NullPointerException

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• Merge pull request #3165 from rleigh-codelibre/maven-updates-develop

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• Merge pull request #3086 from melissalinkert/cellomics-indexing

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Commits on Jun 15, 2018

• Merge pull request #3163 from rleigh-codelibre/gel-square-conv

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• Merge pull request #3147 from rleigh-codelibre/tiff-parser-backport

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• OIR - Exit while loop if length is 0

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Commits on Jun 17, 2018

• ci: Build with Java 10 on appveyor and travis

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• maven: Update plugin versions

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Commits on Jun 18, 2018

• Update the ImageJ API link for Javadoc crosslinks

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• Merge pull request #3157 from melissalinkert/nd2-tile-overflow-develop

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• LIF: only prioritize C in dimension order if channels are RGB

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• Fix classpaths for gen-file-list, gen-cache, and test-memoizer

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• Merge pull request #3132 from melissalinkert/qa-20612

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Commits on Jun 19, 2018

• Merge pull request #3153 from rleigh-codelibre/tiff-zlib

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• Metamorph: ensure that isHCS is set correctly when MetadataLevel is MINIMUM

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Commits on Jun 20, 2018

• Set HTTPS protocols for running Appveyor on Java 7

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• Only set https.protocols for Java 7 builds

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Commits on Jun 21, 2018

• Pin MAVEN_OPTS https.protocols to Java 7 only

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• Clarify ordering expectation in get*UsedFiles Javadocs

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Commits on Jun 22, 2018

• Remove java 7 from Appveyor

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• Merge pull request #3174 from sbesson/sonatype_tls

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• Fix download URLs in bf.bat and bf.sh

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• Use imagej.net URL for ImageJ Javadoc

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Commits on Jun 25, 2018

• Merge pull request #3176 from melissalinkert/command-line-url

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• Merge pull request #3175 from melissalinkert/getusedfiles-javadoc

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• Merge pull request #3169 from dgault/OIR-PreventInfiniteLoop

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Commits on Jun 26, 2018

• Revert "Use imagej.net URL for ImageJ Javadoc"

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• Merge pull request #3148 from melissalinkert/metamorph-domain-develop

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• Merge pull request #3162 from dgault/plugins-exporter-dimOrder

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• Merge pull request #3063 from melissalinkert/volocity-image-names

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Commits on Jun 27, 2018

• Merge pull request #3064 from melissalinkert/inveon-renamed-file

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• Merge pull request #3141 from melissalinkert/obf-fixes

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• Merge pull request #3173 from melissalinkert/lif-dimension-order

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Commits on Jun 29, 2018

• Rename Memoizer.setReadOnly(boolean) to Memoizer.skipSave(boolean)

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• Also update function description

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• Merge pull request #3170 from rleigh-codelibre/ci-java-10

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• Merge pull request #3156 from jarmond/develop

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Commits on Jul 2, 2018

• Merge pull request #3167 from dgault/metamorph-nullpointer

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• Merge pull request #3129 from melissalinkert/pattern-missing-files

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• Merge pull request #3159 from melissalinkert/serialization_tests

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• Update POM version numbers to 5.9.0

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• Merge pull request #3172 from sbesson/imagej_api_link

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• Merge pull request #3177 from snoopycrimecop/develop/latest/version_bump

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Commits on Jul 3, 2018

• Merge tag 'v5.9.0' into 5.10.0-SNAPSHOT

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• Bump versions to 5.10.0-SNAPSHOT

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Commits on Jul 6, 2018

• Remove Bio-Formats Matlab support

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