Timeline


and

10/27/06:

14:26 Changeset [1695] by curtis
Tweak.
13:43 Changeset [1694] by curtis
Add note indicating date of first official release.
13:42 Changeset [1693] by curtis
Add the last couple of release notes to the "What's new" document.
13:41 Changeset [1692] by curtis
Comment out Repository injection.
13:31 Changeset [1691] by sorber
loci.visbio.util.MathUtil I split getDistance(double[] a, double[] b, …
12:39 Changeset [1690] by curtis
Add "tools" task for building a JAR file containing many LOCI tools plus …
10:45 Changeset [1689] by melissa
Added "whats-new.txt".
07:53 Changeset [1688] by melissa
Temporarily commented out Nikon compression logic.

10/26/06:

15:52 Changeset [1687] by curtis
Progress on OMEIS/Bio-Formats command line utility.
14:12 Changeset [1686] by melissa
Construct a separate legacy ZVI reader for each normal reader.
14:07 Changeset [1685] by curtis
No need to override mapId for QTReader.
14:02 Changeset [1684] by curtis
Make mapIds work when delegating to legacy readers.
13:11 Changeset [1683] by melissa
Make sure native QT and ZVI readers propagate their state to the legacy …

10/25/06:

14:46 Changeset [1682] by curtis
Flesh out the getMappedId note a little bit.
14:41 Changeset [1681] by curtis
Fix bug when reading OME-XML images with height > width.
12:21 Changeset [1680] by melissa
Fixed endianness bug in OMEXMLReader - the endianness flag was being reset …
08:44 Changeset [1679] by melissa
Added getMappedId(String) to "getting started" guide.

10/24/06:

16:26 Changeset [1678] by curtis
Use mapping API for OmeisImporter.importIds.
16:13 Changeset [1677] by curtis
Use new mapId method for testIds.
15:49 Changeset [1676] by curtis
Move ImageReader-specific file format detection logic into …
15:46 Changeset [1675] by curtis
Tweak isThisType and javadoc.
15:46 Changeset [1674] by curtis
Tweak javadoc.
15:12 Changeset [1673] by curtis
1) Use "getMappedId(id)" instead of "id" everywhere the file is …
14:39 Changeset [1672] by curtis
Call mapped id getter 'getMappedId' instead of 'getActualFilename'; use …
14:27 Changeset [1671] by curtis
1) Add IFormatHandler.mapId(String, String) and …
13:55 Changeset [1670] by curtis
Tweak isThisType(String, boolean) documentation.
13:34 Changeset [1669] by curtis
Fix documentation typo.
13:04 Changeset [1668] by curtis
Progress on Bio-Formats/OMEIS command line utility.
08:39 Changeset [1667] by curtis
Script for launching OmeisImporter from the command line.
08:30 Changeset [1666] by melissa
Fixed FormatReader.testRead to handle files that begin with "-".

10/23/06:

17:41 Changeset [1665] by curtis
Begin work on command line OME importer that works in conjunction with …
15:49 Changeset [1664] by curtis
Remove illegal @author tags in methods.
15:48 Changeset [1663] by curtis
Fix documentation.

10/20/06:

18:01 Changeset [1662] by curtis
Rename decode method to more descriptive base64Decode.
17:35 Changeset [1661] by curtis
Bugfixes.
16:11 Changeset [1660] by curtis
Fix file pattern detection; report whether OME-TIFF comment was saved.
16:01 Changeset [1659] by curtis
No more need to specify number of time points (but still allowed).
08:48 Changeset [1658] by melissa
- Added a 'close' flag to most methods in OME upload API; this allows the …

10/19/06:

15:38 Changeset [1657] by curtis
Use setVisible(true) instead of deprecated show().
14:45 Changeset [1656] by curtis
Slim Plotter now uses Bio-Formats library externally.
14:44 Changeset [1655] by curtis
Minor tweaks.
14:30 Changeset [1654] by curtis
Use Bio-Formats (SDTReader) to read header information. Add Export button …
14:23 Changeset [1653] by curtis
A few minor edits.
14:23 Changeset [1652] by curtis
Change "-ignore" flag to "-nocolors".
13:57 Changeset [1651] by curtis
Make all fields public.
13:31 Changeset [1650] by melissa
Tweaked OME upload API.
12:05 Changeset [1649] by melissa
Fixed SizeC detection in OIFReader.
08:08 Changeset [1648] by melissa
Removed some unnecessary variables from AliconaReader.
08:01 Changeset [1647] by melissa
Added "getting started" guide that describes the basics of writing a new …
07:58 Changeset [1646] by melissa
Added draft of new OME uploader API.
07:51 Changeset [1645] by melissa
- Added support for Alicona AL3D - Added option to ignore color tables …

10/18/06:

10:27 Changeset [1644] by curtis
Use loci.formats.in package instead of loci.formats for readers.
10:25 Changeset [1643] by curtis
Rename script to something that doesn't conflict with GNU/Linux so much.
10:03 Changeset [1642] by melissa
Better dimension detection for OIF files.
09:51 Changeset [1641] by melissa
Fixed plane ordering in OIBReader.
08:14 Changeset [1640] by melissa
Better metadata parsing in LIFReader.

10/17/06:

15:27 Changeset [1639] by curtis
Remove IFormatReader.getImages(String) method; tweak documentation.
14:25 Changeset [1638] by curtis
Add -nometa flag for suppressing output of non-core metadata.
14:05 Changeset [1637] by curtis
Change file stitcher prefix detection to be case insensitive.
14:04 Changeset [1636] by curtis
Style fixes.

10/16/06:

16:10 Changeset [1635] by curtis
First cut at bugfix for FileStitcher when wrapping another ReaderWrapper …
12:29 Changeset [1634] by chris
Browser: 1) CacheManager Options gui in the options window now completely …

10/13/06:

17:46 Changeset [1633] by chris
Browser: 1) Added gui for cache managing controls. Not yet functional.
08:52 Changeset [1632] by melissa
Changed series chooser dialog in ImageJ importer.

10/12/06:

16:20 Changeset [1631] by chris
Browser: 1) all RECT_MODE type cachemanaging schemes implemented. this …
15:27 Changeset [1630] by curtis
No need for canDoStacks to throw IOException.
15:19 Changeset [1629] by curtis
Style fixes.
15:01 Changeset [1628] by curtis
Add support for removing consecutive blank lines.
14:45 Changeset [1627] by curtis
Include root java folder in classpath.
14:02 Changeset [1626] by curtis
Better style check script.
13:51 Changeset [1625] by curtis
Ignore .class files.
13:50 Changeset [1624] by curtis
Include jar-checks in jars target.
13:50 Changeset [1623] by curtis
Add About dialog for loci.checks package.
13:44 Changeset [1622] by curtis
Better docs target; fix javadoc warnings.
13:00 Changeset [1621] by melissa
Fixed memory issue in GatanReader.
12:57 Changeset [1620] by melissa
Fixed some lingering memory leaks.
12:51 Changeset [1619] by curtis
Add package for LOCI custom Checkstyle checks.
12:51 Changeset [1618] by curtis
Documentation tweak.
12:50 Changeset [1617] by curtis
Tweak comment.
12:08 Changeset [1616] by melissa
- Make sure ImageJ always applies custom calibrations, if available. - …
10:37 Changeset [1615] by curtis
Style fixes.
10:33 Changeset [1614] by curtis
Fix author tags.
10:33 Changeset [1613] by curtis
Add import order check.
10:21 Changeset [1612] by curtis
Whitespace.
10:00 Changeset [1611] by curtis
Implement getCompressionTypes and setCompression for ImageWriter.

10/11/06:

19:15 Changeset [1610] by melissa
Fixed most pixel type mismatches.
15:08 Changeset [1609] by curtis
Add IFormatWriter interface, similar to IFormatReader. Clean up and …
13:33 Changeset [1608] by sorber
You can now redraw interior segments of a freeform overlay, but only …
11:59 Changeset [1607] by melissa
Fixed some stuff in ZVI readers. Also fixed a major bug in patched …
10:30 Changeset [1606] by curtis
Add pixel type reporting to image viewer status bar.
10:29 Changeset [1605] by curtis
Add pixel type mismatch checking to testRead.
10:03 Changeset [1604] by curtis
Fix pixel type.
10:03 Changeset [1603] by curtis
Whitespace.

10/10/06:

16:22 Changeset [1602] by curtis
Rely on external jars for MovieStitcher.jar, instead of bundling …
16:21 Changeset [1601] by curtis
Allow any format of input movies (instead of just QuickTime and TIFF).
15:27 Changeset [1600] by curtis
Fix MovieStitcher targets; eliminate some hardcoding from build.xml.
15:23 Changeset [1599] by curtis
Tweak application description.
14:55 Changeset [1598] by curtis
Add FileStitcher constructor signature allowing ids to be patterns rather …
14:27 Changeset [1597] by curtis
Eliminate jikes warning.
12:59 Changeset [1596] by melissa
Fixed reported issue with opening ZVI files in ImageJ. This includes …
12:24 Changeset [1595] by curtis
Update build rules to reflect loci.apps.qt -> loci.apps.stitcher change.
12:17 Changeset [1594] by curtis
Rename QT Converter to Movie Stitcher to reflect an increase in …
12:16 Changeset [1593] by curtis
Move loci.apps.qt package to loci.apps.stitcher in anticipation of name …

10/09/06:

16:53 Changeset [1592] by sorber
A variety of changes to OverlayObject, OverlayFreeform, & FreeformTool to …
15:04 Changeset [1591] by curtis
Add support for fill option for freeform lines.
09:35 Changeset [1590] by curtis
Remove debugging statement.
09:21 Changeset [1589] by melissa
- Close files in LeicaReader.openBytes and LeicaReader.openImage - …

10/06/06:

15:53 Changeset [1588] by curtis
Fix ClassCastException in FileStitcher.
12:07 Changeset [1587] by curtis
Latest ImageJ/HandleExtraFileTypes/Bio-Formats integration from Wayne.
08:33 Changeset [1586] by melissa
Fixed ImageJ importer to work with files in data/fv1000/marc.

10/05/06:

14:47 Changeset [1585] by melissa
Made a slight change to ImageJ plugin that should free up some memory. …
08:53 Changeset [1584] by melissa
Temporarily reverted NikonReader.
08:50 Changeset [1583] by melissa
Pad thumbnails to 128x128 by default.
08:49 Changeset [1582] by melissa
Fixed bugs in thumbnail creation.

10/04/06:

17:30 Changeset [1581] by curtis
Comment out calls to getChannelGlobal methods for now.
17:29 Changeset [1580] by curtis
Tweaks.
17:29 Changeset [1579] by curtis
Fix bug in global minimum and maximum assignment.
14:41 Changeset [1578] by curtis
Support for canceled flag with HandleExtraFileTypes to detect if user …
14:40 Changeset [1577] by curtis
Little utility for combining TIFFs (workaround for WiscScan bug + crash).
14:27 Changeset [1576] by melissa
- Removed getChannelGlobalMinimum and getChannelGlobalMaximum from …
11:36 Changeset [1575] by melissa
Fixed a critical bug in ZeissZVIReader.
11:27 Changeset [1574] by melissa
- Removed autoscaling logic from ChannelMerger. - Moved scanData method …
11:23 Changeset [1573] by melissa
- Override getChannelGlobalMinimum and getChannelGlobalMaximum where …
09:45 Changeset [1572] by curtis
Eliminate jikes warnings; whitespace.
09:34 Changeset [1571] by curtis
No need to catch FormatException upon FileStitcher construction anymore.
09:31 Changeset [1570] by curtis
Fix separate reader per file option.
09:24 Changeset [1569] by curtis
Remove needless FormatException from ReaderWrapper and subclass …
09:14 Changeset [1568] by curtis
No need for true flag for FileStitcher construction in testRead.
09:10 Changeset [1567] by melissa
Default to using multiple readers in FileStitcher.

10/03/06:

16:49 Changeset [1566] by chris
browser: 1) CROSS_MODE entirely implemented for all combinations of axes …
14:41 Changeset [1565] by curtis
Fix compile error.
13:39 Changeset [1564] by melissa
Added logic to FileStitcher that allows one reader per file. Changed …
12:42 Changeset [1563] by melissa
Tweaked FormatReader.openThumbImage
12:41 Changeset [1562] by melissa
Changed signature of ImageTools.scale to "void scale(BufferedImage, int, …
12:18 Changeset [1561] by melissa
Fixed dimension order in ChannelSeparator; fixed pixel type in …
12:00 Changeset [1560] by melissa
Fixed a bug in BaseTiffReader - openBytes didn't properly handle multiple …
12:00 Changeset [1559] by melissa
- Fixed native QuickTime reader to handle random access of RLE planes. - …
11:59 Changeset [1558] by curtis
Synchronize every call to the same format reader object.
11:16 Changeset [1557] by curtis
Do some array wrapping, and ignore LITTLE_ENDIAN fake IFD tag, when …
11:09 Changeset [1556] by melissa
Fixed ClassCastException in ChannelSeparator; dimension order is still …
00:26 Changeset [1555] by curtis
Add -thumbs option to read thumbnails instead of full size pixels.
00:07 Changeset [1554] by curtis
Fix bug with ImagePlus object having no corresponding ImageStack, …

10/02/06:

18:06 Changeset [1553] by curtis
Cut down on new instances of ImageReader; close files after reading.
17:34 Changeset [1552] by chris
Browser: 1) comments added 2) ImagePlus is no longer a stack, so there's …
13:28 Changeset [1551] by chris
CacheManager: 1) getMix() method fixed so that SURROUND_FIRST mode …
12:17 Changeset [1550] by melissa
Fixed "open channels in separate windows" option in ImageJ plugin (for …
09:57 Changeset [1549] by curtis
Add default constructor around a new ImageReader.
09:50 Changeset [1548] by melissa
Fixed native ZVI reader to delegate properly if a POI-related error …
08:52 Changeset [1547] by melissa
Fixed outstanding bugs in LeicaReader. Also fixed a bug in the import …
08:03 Changeset [1546] by melissa
Fixed PICT reader to play nicely with ImageJ. New PICT file works now.
07:51 Changeset [1545] by melissa
Improved memory usage in POI-based readers.

09/29/06:

16:58 Changeset [1544] by curtis
Add library check for forms-1.0.4.jar; use BoxLayout for exporter plugin.
16:17 Changeset [1543] by melissa
Close files in PerkinElmer reader.
16:11 Changeset [1542] by curtis
Add core metadata (SizeX/Y/Z/C/T, IsRGB, etc.) to metadata table window.
16:10 Changeset [1541] by curtis
Add static getPixelTypeString method for converting from pixel type …
15:54 Changeset [1540] by curtis
Default merge to off, split windows to true.
15:48 Changeset [1539] by curtis
Fix calibration if values are not found.
15:43 Changeset [1538] by curtis
SDT reader works.
14:58 Changeset [1537] by melissa
Force Perkin-Elmer files to be ordered numerically rather than …
14:45 Changeset [1536] by curtis
Whitespace.
13:01 Changeset [1535] by curtis
ZVI files must end in .zvi, because otherwise related OLE-based formats …
12:39 Changeset [1534] by curtis
Tweak documentation.
11:42 Changeset [1533] by melissa
- Finally added support for 16-bit palette color TIFFs. - End of line …
10:31 Changeset [1532] by melissa
Fixed option to open channels in separate windows.
10:16 Changeset [1531] by melissa
Use IFormatReader objects instead of FormatReader objects.
10:15 Changeset [1530] by melissa
Changed ChannelSeparator and FileStitcher to use new ReaderWrapper class. …
10:08 Changeset [1529] by melissa
fixed LeicaReader.isThisType(String, boolean) to fail more quickly if the …
09:03 Changeset [1528] by melissa
fixed ChannelMerger bug

09/28/06:

18:44 Changeset [1527] by curtis
New ChannelMerger that extends ReaderWrapper. Still has bugs.
18:09 Changeset [1526] by curtis
Fix Wayne's issue with Bio-Formats and HandleExtraFileTypes; clean up …
11:25 Changeset [1525] by melissa
fixed Metamorph bug
11:00 Changeset [1524] by curtis
Move ZVI and OIB back to "POI readers" section.
08:36 Changeset [1523] by melissa
Fixed ChannelSeparator to override initFile(String).
08:25 Changeset [1522] by melissa
removed debugging statements
08:24 Changeset [1521] by melissa
- fixed dimension ordering in SEQ and IPW readers - fixed dimension …

09/27/06:

14:24 Changeset [1520] by melissa
fixed calibration error in LIFReader
14:10 Changeset [1519] by melissa
Added preliminary support for Slidebook files.
10:25 Changeset [1518] by curtis
Add Christopher Peterson to credits in loci_formats.jar About dialog box.
10:08 Changeset [1517] by curtis
Change pixel types to lower case.
09:05 Changeset [1516] by melissa
make sure POI-based readers close their RandomAccessStreams
08:26 Changeset [1515] by melissa
- fixed pixelType population in OpenlabReader - tweaked metadata parsing …
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