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Revision Author Date Message Commit Date
6ff9ef5 [maven-release-plugin] prepare release imagej-omero-0.3.3 22 November 2015, 03:05:01 UTC
fcf871b Avoid imagej-legacy-related class loading problems We really need to address #52 though, to stop worrying about this stuff. 22 November 2015, 02:44:38 UTC
1780361 POM: bump parent to pom-imagej 14.0.0 21 November 2015, 04:55:55 UTC
44f895d POM: Update developers and contributors See: http://imagej.net/Team 12 November 2015, 21:15:08 UTC
4b20c54 POM: add more precise URL 12 November 2015, 21:15:04 UTC
129dd47 POM: remove obsolete mailing list entry We use the ImageJ forum now: http://forum.imagej.net/ 12 November 2015, 13:56:38 UTC
6adb519 POM: bump pom-imagej parent to 13.3.0 12 November 2015, 13:55:50 UTC
a14594a Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 09 June 2015, 14:26:02 UTC
23ef342 Update to OMERO 5.1.2 This also rolls back the JRE requirement to 1.6, since the omero-client 5.1.2 artifact is compatible with Java 6 again. Well, sort of -- it has some Java 7-specific dependencies, but we can tell the Maven Enforcer plugin to ignore those. 08 June 2015, 17:52:48 UTC
e7101ec OMEROFormatTest: Stick to one context With imagej-legacy on the classpath, context creation needs to be handled carefully. By using a single context we avoid potential race conditions. Closes #61 02 June 2015, 18:49:04 UTC
bcb0a50 Get rid of IJ1 macro version of Rename Image While the ImageJ Legacy layer provides a script language plugin for IJ1 macros, they are fundamentally limited and dare I say problematic when it comes to OMERO server side execution. In particular, when running headless, the ij.WindowManager does not track open image windows, so calls like selectImage and selectWindow seem not to work. At least, ij.ImagePlus inputs are somehow not available as arguments to the selectImage macro function. I fixed several minor problems in various components relating to the functioning of macros in this way, but the IJ1 macro logic is very complex, suffusing much of the IJ1 core with macro-related case logic. For now, I give up on supporting IJ1 macros from OMERO server side. Instead, let's ensure all the examples are non-macro-based script languages, to avoid the associated pitfalls. I filed issue #62 to document this limitation, though fixing it is extremely low priority. 02 June 2015, 15:04:35 UTC
0108b96 Add working script to correct uneven background 02 June 2015, 14:07:47 UTC
fa399d3 ModuleAdapter: handle null outputs better Let's explicitly warn about them. And let's also not try to feed them to OMERO. This avoids the following lovely beast: omero.ApiUsageException: null at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_11] at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_11] at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_11] at java.lang.reflect.Constructor.newInstance(Constructor.java:408) ~[na:1.8.0_11] at java.lang.Class.newInstance(Class.java:433) ~[na:1.8.0_11] at IceInternal.BasicStream.createUserException(BasicStream.java:2615) ~[omero-client-5.1.1-ice35.jar:na] at IceInternal.BasicStream.access$300(BasicStream.java:12) ~[omero-client-5.1.1-ice35.jar:na] at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099) ~[omero-client-5.1.1-ice35.jar:na] at IceInternal.BasicStream.throwException(BasicStream.java:2077) ~[omero-client-5.1.1-ice35.jar:na] at IceInternal.Outgoing.throwUserException(Outgoing.java:538) ~[omero-client-5.1.1-ice35.jar:na] at omero.api._ISessionDelM.setOutput(_ISessionDelM.java:979) ~[omero-client-5.1.1-ice35.jar:na] at omero.api.ISessionPrxHelper.setOutput(ISessionPrxHelper.java:3148) ~[omero-client-5.1.1-ice35.jar:na] at omero.api.ISessionPrxHelper.setOutput(ISessionPrxHelper.java:3120) ~[omero-client-5.1.1-ice35.jar:na] at omero.client.setOutput(client.java:1142) ~[omero-client-5.1.1-ice35.jar:na] at net.imagej.omero.ModuleAdapter.launch(ModuleAdapter.java:141) ~[imagej-omero-0.3.1.jar:0.3.1] 01 June 2015, 23:00:54 UTC
0970a3d Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 29 May 2015, 19:11:25 UTC
d10c7d5 Merge pull request #59 from imagej/enable-min-max Reenable min/max for OMERO script parameters 29 May 2015, 19:08:36 UTC
94e3927 Reenable min/max for OMERO script parameters They were disabled due to a bug in SciJava Common: non-numeric parameters -- particularly string parameters -- had their min and max set to the empty string, due to how Java annotation types work. The relevant upstream is: scijava/scijava-common@d5b58e4a4d29518523de83c6e1c08a1eca7a11d6 29 May 2015, 18:58:48 UTC
7daebd7 POM: bump to pom-imagej 8.0.1 This brings in important bug-fixes from scijava-common and scifio. 29 May 2015, 18:58:41 UTC
5d6dcd2 Add test drive class for OpenImageFromOMERO 21 May 2015, 19:59:18 UTC
f442eba ScriptGenerator: make script location configurable Previously, ImageJ script wrappers always went to lib/scripts/imagej. With this change, you can pass "--namespace foo" and it will generate the scripts to lib/scripts/foo instead. This feature, together with its judicious use in relation to multiple ImageJ installations, resolves #15. 21 May 2015, 04:45:46 UTC
fa5e0d3 ScriptGenerator: parse args more flexibly First, we check for -- prefix. If found, we parse known args, or issue an error if the arg is unknown. We also use loop over the index explicitly, so that we can parse multi-term args some day. 21 May 2015, 04:44:02 UTC
3b5c51c README.md: use OMERO-5.1, not OMERO-5.0 We do leave a mention of the old OMERO-5.0 update site, although further updates are not currently planned to that update site. In the future, if and when the OMERO API continues to evolve and break backwards compatibility again, we'll have to consider whether to start maintaining multiple integration branches for ImageJ-OMERO. But not yet. 20 May 2015, 19:50:43 UTC
fd23287 Make the installer use OMERO 5.1, not 5.0 The master branch currently tracks OMERO 5.1.x. For the moment, I am avoiding complexifying things by having separate topic branches for 5.0.x vs. 5.1.x; rather, the OMERO-5.0 update site is (at least for the moment) deprecated in favor of OMERO-5.1. 20 May 2015, 19:50:43 UTC
64bddc4 Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 20 May 2015, 19:07:05 UTC
fac85be Populate the actual number of channels, not just 1 This fixes #55 (and hence also #31 and #47). 20 May 2015, 18:44:21 UTC
4f779f4 Fix stupid bug introduced in e4401c45de04c9de9eb8e002d398b8f73ee8325a Eclipse refactoring is pretty great... but not THAT great. You still have to actually use your variables. 20 May 2015, 17:22:21 UTC
cdf0b77 Upgrade to OMERO 5.1.x API This updates the OMERO client library to 5.1.1 with Ice 3.5. It makes the necessary code changes to account for backwards incompatibilities in the API from 5.0.x. While at it, we populate units from OMERO into the ImageJ axis data structures. 18 May 2015, 21:11:07 UTC
6db6898 OMEROFormatTest: remove unnecessary import 18 May 2015, 21:11:07 UTC
e4401c4 OMEROSession: be defensive about too-large axes 15 May 2015, 19:40:08 UTC
6ee9da1 POM: make a property for the OMERO version 15 May 2015, 16:29:38 UTC
7fb8435 POM: tidy up order of configuration blocks Accomplished using: mvn tidy:pom 15 May 2015, 16:28:13 UTC
15125ab POM: remove obsolete scifio-omero dependency 13 May 2015, 02:20:23 UTC
6597b45 README.md: shorten section header 29 April 2015, 22:14:00 UTC
7e3e3ca Update license headers This was accomplished using: mvn license:update-file-header 29 April 2015, 21:49:14 UTC
dc32c96 Move io.scif.omero classes to net.imagej.omero Now everything has the same package prefix. 29 April 2015, 21:48:37 UTC
92e470d README.md: merge in & tweak scifio-omero's README 29 April 2015, 21:45:40 UTC
61ac41c README.md: use better project URLs 29 April 2015, 21:45:29 UTC
ef2ef68 Merge in POM elements from scifio-omero This also bumps the SNAPSHOT version to 0.3.0, due to the magnitude of the reorganization. 29 April 2015, 21:40:39 UTC
93be746 Merge scifio-omero project with imagej-omero Having two projects was confusing. Having one is simpler. Originally, the idea was that scifio-omero was the "low level SCIFIO-only" stuff, but SCIFIO is now built on ImageJ Common. So actually, the only extra dependency that imagej-omero brought to the table was imagej-legacy (and with it, ij). But we'll fix that (see #52), and then the dependencies will be identical. So having two separate repos makes much less sense. The merge was accomplished easily using the "-X ours" option. Closes #51. 29 April 2015, 21:40:12 UTC
1c9728d Move ImageJ-OMERO commands to their own package This renames commands: * net.imagej.omero.OpenFromOMERO -> net.imagej.omero.commands.OpenImageFromOMERO * net.imagej.omero.SaveToOMERO -> net.imagej.omero.commands.SaveImageToOMERO Note that both the package name _and_ class name changed. This was done to facilitate the addition of more commands, such as OpenTableFromOMERO and SaveTableToOMERO. 29 April 2015, 21:31:00 UTC
cd94870 DefaultOMEROService: shorten toArray helper method 29 April 2015, 21:30:53 UTC
68f5c93 DefaultOMEROService: make helper functions static 29 April 2015, 21:30:32 UTC
6bf38a8 DefaultOMEROService: fix package of ColorRGB 29 April 2015, 21:30:19 UTC
901cd5c POM: add missing net.imagej:ij dependency We depend on it directly, so should declare it directly. 29 April 2015, 21:30:12 UTC
74e4bb2 README.md: link Jenkins badge to the job 29 April 2015, 19:43:57 UTC
a6ebcc3 README.md: link Jenkins badge to the job 29 April 2015, 19:43:04 UTC
2f184ed README.md: add Jenkins build status badge 29 April 2015, 04:03:49 UTC
ba10803 README.md: add Jenkins build status badge 29 April 2015, 04:00:00 UTC
c60f04d Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 17 April 2015, 20:37:20 UTC
9efa45a Temporarily disable unit tests They fail intermittently on the ImageJ Jenkins server, preventing release. Unfortunately, they do not fail in any other scenario I can find, nor do they fail reliably. They weren't testing much anyway, so let's disable them for the moment, to have a reproducible build. 17 April 2015, 20:35:34 UTC
6beda40 Revert "Bump to next development cycle" This reverts commit 93717e3f7f4c7088a49e05629d356eaec268201c. The release failed again, due to spuriously failing unit tests. One more try... 17 April 2015, 20:35:34 UTC
b856707 POM: drop support for OMERO 4.4 It is bad to have different dependencies declared in different profiles. And we are developing against OMERO5. So let's just use OMERO5 as the one true dependency here. See also: https://github.com/scifio/scifio-omero/commit/2817fed37eae4b824028e042f7e583c881d5b24b 17 April 2015, 20:29:36 UTC
93717e3 Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 17 April 2015, 20:29:24 UTC
a93605e Bump pom-imagej parent to 7.0.0 This updates the Bio-Formats version to 5.1.0, so we should probably update the omero-client version to 5.1.0 here as well. But there will be substantial complications there, so that's a problem for another commit! 17 April 2015, 20:24:41 UTC
7cbc2fc Revert "Bump to next development cycle" This reverts commit 44876a27312a05ac0a01a07f3bdcbc2eafd4357e. The first 0.8.0 release attempt was unsuccessful for some reason. 17 April 2015, 20:19:27 UTC
a685199 README.md: use shorter URLs for ImageJ web pages 17 April 2015, 18:16:56 UTC
d7217e5 README.md: remove obsolete instructions It is no longer necessary to switch to modern mode. The plugins work just fine in the legacy UI. 17 April 2015, 18:15:53 UTC
25da580 run-class: fix comment 17 April 2015, 16:07:31 UTC
44876a2 Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 15 April 2015, 19:51:42 UTC
c02f347 Bump pom-scifio parent to 7.0.0 This updates the Bio-Formats version to 5.1.0, so we should probably update the omero-client version to 5.1.0 here as well. But there will be substantial complications there, so that's a problem for another commit! 15 April 2015, 19:30:34 UTC
dd8783d POM: tweak dependency category 26 February 2015, 23:14:31 UTC
9d3c0ec Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 26 February 2015, 14:29:14 UTC
bd26dc8 Bump to pom-imagej 5.12.0 Update to latest parent pom. 26 February 2015, 14:27:44 UTC
558cf09 OpenFromOMERO: load planes on demand only This makes use of SCIFIO's awesome cell-driven image opener, to cache planes on demand. This is how ImageJ-OMERO used to work for larger images, before we backed off on the heuristic such that cells are chosen less often. 18 February 2015, 17:35:25 UTC
cea1570 README.md: tweak CLI for System Information The file on disk now has an underscore instead of a space. 18 February 2015, 17:13:01 UTC
22c0308 OMEROFormat: generalize zct helper method This is a first step toward addressing the FIXME of moving the routine's more general aspects into a core SCIFIO utility class somewhere. Thanks to Mark Hiner for the suggestions. 18 February 2015, 16:24:47 UTC
a5bfc20 Organize imports 18 February 2015, 16:24:45 UTC
0d254d5 Tweak project description in license headers This project is only for OMERO servers (not the old OME Perl server). 10 February 2015, 17:05:02 UTC
cdb10c5 POM: split up dependencies into more sections This is more consistent with other SciJava software project POMs. 10 February 2015, 17:05:02 UTC
e39f339 Eliminate deprecated DatasetService I/O calls That logic moved into SCIFIO, in the DatasetIOService. 10 February 2015, 16:11:10 UTC
07951a3 DefaultOMEROService: organize imports 10 February 2015, 16:10:59 UTC
112e153 Bump to latest pom-scifio parent 10 February 2015, 16:05:42 UTC
11276fd Bump to latest pom-imagej parent 10 February 2015, 16:04:11 UTC
f738e61 Update the example scripts, adding a few more 26 January 2015, 14:59:38 UTC
2f88b86 scripts/README.md: clarify script installation 26 January 2015, 14:50:59 UTC
751bb57 Update copyright for 2015 22 January 2015, 08:43:07 UTC
139b8b9 Update license project and organization name 22 January 2015, 08:42:40 UTC
55863d1 Add LICENSE.txt 22 January 2015, 08:37:18 UTC
7c0ee0d Happy New Year 2015! 16 January 2015, 23:03:34 UTC
9deecf1 Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 07 January 2015, 20:21:38 UTC
e882ae2 Replace net.imglib2.meta imports Updated to use the appropriate net.imagej import. 07 January 2015, 20:18:57 UTC
cc022d3 Bump to latest parent pom Updated to pom-scifio 5.2.0 07 January 2015, 20:13:26 UTC
00fafec Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 04 November 2014, 21:54:28 UTC
79a5b78 POM: bump to pom-imagej 5.0 This restructures the parent POM dependency management, and inherits the latest dependency versions. It also makes the necessary code changes to adjust for backwards incompatibilities in the imagej-common API. 04 November 2014, 21:53:00 UTC
dbc7333 Bump to next development cycle Signed-off-by: Jenkins <jenkins@imagej.net> 04 November 2014, 19:13:08 UTC
0103d2a Bump to latest parent pom Updated to pom-scifio 5.0 Replcaed imglib2-meta dependency with imagej-common. 04 November 2014, 19:11:44 UTC
bac02b5 Merge branch 'reduce-deps' This eliminates the dependency on the toplevel net.imagej:imagej artifact, which cuts the dependency footprint by ~50%. 31 October 2014, 18:00:28 UTC
05ff723 POM: remove no-longer-used net.imagej:imagej dep This reduces the dependency graph of imagej-omero by half! (from 106 to 56 artifacts) 31 October 2014, 17:59:41 UTC
969e170 Remove superfluous Main class It was useful for testing, but dragged in a dependency on net.imagej:imagej. 31 October 2014, 17:56:39 UTC
c6676cb Eliminate usages of net.imagej.ImageJ This change is in preparation for reducing the dependencies of the imagej-omero component. While net.imagej:imagej is very convenient as a starting point and for casual developers, for robust library components like imagej-omero it makes more sense to do the dependencies properly, declaring only those dependencies which are actually needed. 31 October 2014, 17:53:45 UTC
2d0b45f Merge branch 'module-order' Closes #21. 12 September 2014, 22:32:30 UTC
9ed3df6 Add unit tests for ScriptGenerator In particular, this tests that the scripts are generated in the expected directory structure, with the correct number of prepended 0xfeff Unicode characters, so that they will be sorted properly in the OMERO menus. 12 September 2014, 22:32:25 UTC
10c1a5d ScriptGenerator: generate scripts in menu order Rather than iterating over all modules from the module service directly, we now use the menu structure obtained from the menu service. This approach gives us the menus ordered by weight, so that we can write out the script files in that same order, by prepending the file names with the Unicode 0xfeff character ("ZERO WIDTH NO-BREAK SPACE"). 12 September 2014, 22:32:19 UTC
55aa130 POM: bump to pom-imagej 2.51 This updates to scijava-common 2.33.0, with some needed bug-fixes. 12 September 2014, 22:27:14 UTC
4bd5e35 DefaultOMEROService: add TODO reminder 04 September 2014, 17:29:53 UTC
df9ee0c DefaultOMEROService: use ConvertService API The ConversionUtils#convert methods are now deprecated. Pay no attention to the resemblance to org.scriptframework.core.convert.ConversionService! 16 August 2014, 20:14:48 UTC
28a4069 ScriptGenerator: simplify expression 16 August 2014, 20:11:12 UTC
bb4f408 ScriptGenerator: remove superfluous parameter 16 August 2014, 20:11:04 UTC
74f9d80 OpenFromOMERO: remove unneeded import 16 August 2014, 20:10:49 UTC
91614a0 ModuleAdapter: improve version detection This uses the new SJC Versioned interface rather than hardcoding the versioning algorithm. 16 August 2014, 20:08:09 UTC
f316483 POM: bump to pom-imagej 2.47 This bumps scijava-common to 2.30.0, which includes the new Versioned interface for better versioning of SciJava modules. 16 August 2014, 20:06:37 UTC
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