Timeline


and

05/05/10:

17:18 Changeset [6242] by curtis
Specify a pixel type for the importer tests.
16:40 Changeset [6241] by melissa
Updated Bio-Formats utils to use new MetadataStore/MetadataRetrieve.
16:10 Changeset [6240] by curtis
Initial version of some simple tests for Bio-Formats Importer.
16:10 Changeset [6239] by curtis
Minor progress on Bio-Formats Importer refactoring.
16:09 Changeset [6238] by curtis
Add toplevel utility method for obtaining ImagePlus from path string.
16:08 Changeset [6237] by curtis
Temporarily disable bf-ice and ome-notes components in dependency checker.
16:07 Changeset [6236] by curtis
Add a hack to skip file existence check for .fake files.
16:07 Changeset [6235] by curtis
Add ome-xml.jar to Eclipse classpath, hopefully as a temporary workaround.
14:28 Changeset [6234] by melissa
* Fixed compile errors introduced in r6230. * Added transformations from …
13:24 Ticket #490 (Add support for PDS files) created by melissa
See files in data/pds/.
11:34 Changeset [6233] by melissa
Populate original metadata using StructuredAnnotations.
10:30 Changeset [6232] by melissa
OME-XML generation should work now.

05/04/10:

20:41 Changeset [6231] by melissa
Added loci.formats.ome.OMEXMLMetadataImpl, which should have been in …
20:26 Changeset [6230] by melissa
Updated to new MetadataStore/MetadataRetrieve APIs. This may temporarily …
17:23 Changeset [6229] by curtis
Minor progress on Bio-Formats plugins refactoring. * Reorganize some …
17:03 Changeset [6228] by curtis
Change certain logger warnings to debug instead, to avoid extraneous …
16:58 Changeset [6227] by curtis
Fix problems with available() and readString(int). Fixes an indirect bug …
12:22 Changeset [6226] by callan
Re-run of code generation ( ome-xml:r585).
05:09 Changeset [6225] by andrew
Adding code for Metadata Store test cases in Instrument, Plate and ROI.

05/03/10:

18:09 Changeset [6224] by curtis
Better error output for scan-deps.
17:43 Changeset [6223] by curtis
Temporary fix for compile errors.
17:27 Changeset [6222] by melissa
Ported r6221 to 4.1 branch.
17:27 Changeset [6221] by melissa
Fixed Nikon type, compression, and image count detection bugs.
17:26 Changeset [6220] by curtis
Open sliced images as hyperstacks by default.
17:25 Changeset [6219] by curtis
Fix Slicer plugin.
13:47 Changeset [6218] by melissa
* Cache previously opened LSM plane if channels are being split. * …
12:10 Changeset [6217] by melissa
Reduced Zeiss LSM IFD parsing time.
12:05 Changeset [6216] by callan
Enabling check of abstract-proprietary type counts. (At the moment only …
12:04 Changeset [6215] by callan
Re-run of code generation ( ome-xml:r584).
11:00 Changeset [6214] by callan
Updated test cases from Andrew and a couple more passing with some changes …
10:32 Changeset [6213] by callan
IMetadata getter test cases.
09:44 Changeset [6212] by callan
Test case updates from Andrew.
09:09 Changeset [6211] by callan
Initial commit of IMetadata mock. Passes initial Image test cases.
09:03 Changeset [6210] by callan
Re-run of code generation ( ome-xml:r583).
05:34 Changeset [6209] by callan
Moved test cases to a mock based foundation.

04/30/10:

18:33 Changeset [6208] by curtis
Minor fix to showinf output.
15:09 Ticket #489 (Andor TIFF timestamps are missing or incorrect) created by melissa
[…] See files in data/andor/pariksheet.
14:06 Ticket #488 (Add support for OpenEXR files) created by melissa
See data in data/openexr/ and  http://www.openexr.com/.
13:58 Changeset [6207] by melissa
Fixed parsing of ND filter from log file.
10:54 Changeset [6206] by callan
OME XML metadata implementation. Re-run of code generation ( ome-xml:r582).

04/29/10:

12:54 Changeset [6205] by melissa
Prevent NPE if ROI file is missing.
11:59 Changeset [6204] by callan
Initial version of OME XML metadata and updated metadata store and …
10:57 Changeset [6203] by melissa
Removed SPA-LEED reader, which hasn't yet been committed.
10:41 Changeset [6202] by callan
Re-run of code generation ( ome-xml:r579).
03:53 Changeset [6201] by callan
Reverting changes to Eclipse settings.
03:52 Changeset [6200] by callan
Removed erroneous classes from the OMERO schema.

04/28/10:

10:16 Changeset [6199] by callan
Metadata store and retrieve interfaces for examination and testing. Re-run …

04/27/10:

14:01 Changeset [6198] by melissa
Tweaked matching priorities so that reordering works again.
13:16 Changeset [6197] by melissa
* Added Molecular Imaging and JPK readers. See #412. * Minor cleanup in …
04:37 Changeset [6196] by callan
Move to use primitives for NonNegativeInteger, PositiveInteger and …
03:16 Changeset [6195] by callan
All tests passing. Re-run of code generation ( ome-xml:r554).

04/26/10:

16:03 Changeset [6194] by callan
Re-run of code generation ( ome-xml:r552).
13:51 Changeset [6193] by melissa
Added RHK Technologies reader. See #412.
12:45 Changeset [6192] by curtis
Fix classpath problem with Windows batch files.
12:11 Changeset [6191] by melissa
Added SBIG reader and fixed a NIfTI type detection bug. See #412.

04/25/10:

13:46 Changeset [6190] by melissa
* Updated remaining readers to respect MetadataOptions. * Added bounds …

04/24/10:

19:25 Changeset [6189] by curtis
Fix for NullPointerException, courtesy of Lee Kamentsky.

04/23/10:

15:46 Changeset [6188] by melissa
* Updated a few more readers to respect MetadataOptions. * Fixed a couple …
14:51 Changeset [6187] by curtis
Add dist-bftools target for creating bftools.zip.
14:04 Changeset [6186] by curtis
Simple utility for printing out Java system properties.
12:41 Changeset [6185] by callan
Re-run of code generation ( ome-xml:r544)
12:20 Changeset [6184] by callan
Re-run of code generation ( ome-xml:r543)
11:41 Changeset [6183] by callan
Re-run of code generation ( ome-xml:r542)
11:38 Changeset [6182] by curtis
Fix up logging with Bio-Formats command line tools. This removes the hard …
11:09 Changeset [6181] by callan
Re-run of code generation ( ome-xml:r541)
10:47 Changeset [6180] by callan
Re-run of code generation ( ome-xml:r540)
10:15 Changeset [6179] by callan
Re-run of code generation ( ome-xml:r539)
07:24 Changeset [6178] by callan
Foundation for reference handling support. ( ome-xml:r536) Fixed a few …
03:28 Changeset [6177] by callan
Fixed some typos.

04/22/10:

11:53 Changeset [6176] by melissa
Added a few more Annotation test.
11:40 Changeset [6175] by callan
Re-run of code generation ( ome-xml:r527)
11:29 Changeset [6174] by callan
Re-run of code generation ( ome-xml:r526)
11:16 Changeset [6173] by callan
Add support for binary file schema. ( ome-xml:r525)
10:52 Changeset [6172] by callan
Re-run of code generation ( ome-xml:r525)
10:36 Changeset [6171] by callan
References going OUT. ( ome-xml:r523)
10:24 Changeset [6170] by melissa
Added a few Annotation tests.
06:29 Changeset [6169] by callan
Re-run of code generation ( ome-xml:r522)
06:25 Changeset [6168] by callan
Updated with extended test case and namespace support (fixes SPW, ROI and …

04/21/10:

16:58 Changeset [6167] by curtis
Add a very simple log4j configuration file for use with various main …
16:58 Changeset [6166] by curtis
Tweak (irrelevant) "External libraries" build directory.
15:11 Changeset [6165] by curtis
Fix up Eclipse classpaths: * Use build-eclipse instead of build/classes …
14:37 Changeset [6164] by melissa
Ported a few channel splitting fixes from trunk.
11:31 Changeset [6163] by curtis
Quick, sloppy launcher files for flow cytometry app.
11:04 Changeset [6162] by melissa
Fixed NPE.
10:33 Changeset [6161] by callan
Few more OTF properties (critically no objective settings) to add to …
10:28 Changeset [6160] by callan
Adjusted test case dependency slightly to get a little better coverage …
10:16 Changeset [6159] by melissa
Added tests for Dichroic, Filter, FilterSet, and OTF.
09:23 Changeset [6158] by callan
Updated with new code generation. (OME-XML Subversion revision 518)
05:51 Changeset [6157] by callan
Passing tests for <Detector/>, <LightSource/> and its sub-classes. Type …

04/20/10:

19:47 Changeset [6156] by melissa
Updated several more readers to respect MetadataOptions.
16:37 Changeset [6155] by curtis
Various cleanup and refactoring progress. * Progress on Bio-Formats …
16:34 Changeset [6154] by curtis
Create only one codec per instance of NativeND2Reader. This change avoids …
16:25 Changeset [6153] by curtis
Construct JAI ImageIO service only once per JPEG2000Codec instance.
15:18 Changeset [6152] by melissa
Changed some of the ServiceFactory logging from 'warn' to 'debug'.
14:55 Changeset [6151] by melissa
Added a couple of object linkage tests. Note that Detector creation …
12:32 Changeset [6150] by callan
Updated to new infrastructure. (OME-XML Subversion revision 510)
12:09 Changeset [6149] by melissa
Added ROI population test.
11:59 Changeset [6148] by melissa
Updated the remainder of the SXM readers to respect MetadataOptions.
10:36 Changeset [6147] by melissa
Added minimal Plate object and a few tests for Instrument and Plate …
10:03 Changeset [6146] by callan
Added object creation for the Instrument hierarchy.
09:57 Changeset [6145] by callan
Make object creation a little more flexible in the test case.
09:51 Changeset [6144] by callan
Made whitespace and style conform to LOCI guidelines.
07:46 Changeset [6143] by callan
Full in/out support and test cases for 2010-04 working copy schema …

04/19/10:

16:07 Changeset [6142] by curtis
Fix a stupid mistake.
15:56 Changeset [6141] by curtis
Use generics where appropriate; fix miscellaneous warnings and issues.
14:53 Changeset [6140] by melissa
Updated more readers to respect MetadataOptions.
13:49 Changeset [6139] by melissa
Fixed a couple of bugs that prevented Nikon images with more than one …
13:27 Changeset [6138] by callan
Committed actual class files for r6137 from 201004 code generation.
13:13 Changeset [6137] by callan
Re-arranged enumeration locations, split between ome-xml and bio-formats …
12:18 Changeset [6136] by callan
Enumeration types from the latest working copy schema (OME-XML Subversion …
10:51 Changeset [6135] by bselinsky
cheap compilation and run scripts
10:39 Changeset [6134] by bselinsky
updates for creating cmake files

04/18/10:

19:47 Changeset [6133] by curtis
Fix some minor unchecked warnings.

04/16/10:

20:17 Changeset [6132] by curtis
More progress on Bio-Formats Importer refactoring. Not totally happy …
17:43 Changeset [6131] by curtis
More progress on Bio-Formats Importer. Probably breaks some options.
15:34 Changeset [6130] by curtis
Progress on Bio-Formats Importer refactoring.

04/15/10:

17:05 Changeset [6129] by melissa
Updated more readers to respect MetadataOptions, and added some TIFF IFD …
14:37 Changeset [6128] by curtis
Fix some Eclipse warnings, clean up imports, minor progress on Importer …

04/14/10:

16:47 Changeset [6127] by melissa
Updated a few more readers to respect MetadataOptions.
11:56 Changeset [6126] by melissa
Fixed bug that caused a bunch of extra garbage bytes to be written to the …
11:50 Changeset [6125] by curtis
Improve robustness of color map parsing.
11:49 Changeset [6124] by curtis
Add explicit bounds checking to unpackBytes. Makes for nicer error …
11:12 Changeset [6123] by melissa
Hopefully fixed XML parsing problems introduced in r6000.

04/13/10:

16:21 Changeset [6122] by melissa
Set physical Z size, even if instrument data is not present.
16:01 Ticket #455 (Add support for Zip files with multiple entries) closed by melissa
fixed: (In [6121]) Preliminary support for reading Zip files with multiple …
16:01 Changeset [6121] by melissa
Preliminary support for reading Zip files with multiple entries. Closes …
15:05 Changeset [6120] by curtis
Remove tabs.
14:54 Changeset [6119] by curtis
Add note about alternate location for compiled class files.
12:22 Changeset [6118] by melissa
* Updated a few more readers to respect MetadataOptions. * Added utility …

04/12/10:

18:04 Changeset [6117] by melissa
* Updated Imaris readers to respect MetadataOptions. * Fixed a couple of …
15:44 Changeset [6116] by melissa
Updated a few more readers to respect MetadataOptions.
10:31 Ticket #484 (Investigate usage of FileChannel.map(...)) closed by melissa
fixed: See r6093 and r6100.
09:30 Changeset [6115] by bselinsky
Add Usage Messages and error handling

04/09/10:

15:37 Changeset [6114] by curtis
Begin rearranging some code.
14:27 Changeset [6113] by melissa
Fixed various whitespace issues in AmiraParameters, and updated a few more …
12:55 Changeset [6112] by melissa
Updated several readers to respect MetadataOptions.
09:59 Changeset [6111] by melissa
Fixed how channel indices are reset.
09:41 Changeset [6110] by bselinsky
add jar file support
09:40 Changeset [6109] by bselinsky
add jar file support
09:09 Ticket #487 (Add support for ECAT7 files) created by melissa
See examples files in data/ecat7/mark/.

04/08/10:

16:29 Changeset [6108] by melissa
Fixed a couple of TIFF export bugs.
14:34 Changeset [6107] by melissa
Make sure that all RandomAccessInputStreams are closed.
14:29 Changeset [6106] by bselinsky
add dependency lift file
14:08 Changeset [6105] by melissa
Prevent Image.CreationDate and PlaneTiming.DeltaT from being populated …
11:35 Changeset [6104] by melissa
* Make sure that DV log files are detected regardless of the …
11:25 Changeset [6103] by bselinsky
Adding options flags
11:23 Changeset [6102] by bselinsky
Adding option flags
10:40 Changeset [6101] by bselinsky
new
05:52 Changeset [6100] by callan
Moved byte buffer map() vs. allocate() to a static block and the state …

04/07/10:

17:22 Changeset [6099] by melissa
* Fixed a DICOM offset bug. * Prevent Packbits codec from seeking past the …
14:36 Changeset [6098] by melissa
* Allow the comment delimiter to be changed in IniParser. * Fixed a whole …

04/06/10:

21:51 Changeset [6097] by melissa
Fixed NPE.
18:59 Changeset [6096] by melissa
Moved plane index parsing; this substantially reduces parsing time.
13:35 Changeset [6095] by melissa
Cleaned up BD Pathway reader a bit; the reader now parses more metadata …
11:10 Changeset [6094] by melissa
* Prevent Leica reader from reading beyond the end of the file. * Fixed a …
10:29 Changeset [6093] by callan
Added byte buffer provider to compartmentalize the usage of map() vs. …
02:50 Changeset [6092] by callan
Removed an unused import and fixed a potential null pointer exception as …
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