18:09 Changeset [2214] by chris
oops, forgot to add the new Merger file.
18:08 Changeset [2213] by chris
Notebook: Added merger gui and some logic, but no merging actually takes …
14:54 Changeset [2212] by curtis
Use FormatReader.debug in ReaderTest.
13:25 Changeset [2211] by melissa
Main method should construct a new Base64Encoder.
08:30 Changeset [2210] by melissa
Fixed memory issue with file cache.
07:55 Changeset [2209] by melissa
Tweaked dimension ordering.


17:56 Changeset [2208] by chris
Notebook: ability to save ".meta" extension companion OME-xml files added.
17:36 Changeset [2207] by chris
MetadataNotebook: New logic for opening files, independent of file …
16:56 Changeset [2206] by chris
fixed bug where metadata not displayed when filestitching
16:53 Changeset [2205] by curtis
Fix compile error.
16:48 Changeset [2204] by curtis
Remove bounds sanity checking from file pattern (until after the release).
16:48 Changeset [2203] by curtis
List of what's new for the forthcoming release.
16:01 Changeset [2202] by curtis
Remove debugging statements.
16:00 Changeset [2201] by curtis
Fix bug in domainToPixel (use 0 instead of Double.NaN for missing axes).
15:35 Changeset [2200] by melissa
Added logic to RandomAccessStream that keeps track of how many files we …
15:23 Changeset [2199] by curtis
Totally untested new domainToPixel method.
14:12 Changeset [2198] by curtis
Add toString method for Location.
12:33 Changeset [2197] by melissa
Added some logic to deal with datasets like …
09:32 Changeset [2196] by melissa
Close abandoned open files.
08:58 Changeset [2195] by melissa
Use new ConfigEntry class to store data from a config file (instead of …


18:10 Changeset [2194] by curtis
Fix possible NullPointerException (maybe?).
15:43 Changeset [2193] by chris
Build used files list lazily, to avoid calling initFile on every …
14:16 Changeset [2192] by chris
Be more thorough catching problems with loading reader classes; print …


16:58 Changeset [2191] by sorber
16:48 Changeset [2190] by sorber
Disable text field and fill checkbox for non-text, non-fillable objs.
15:01 Changeset [2189] by curtis
Use dashes rather than colons in log file.
14:55 Changeset [2188] by curtis
Tweak javadocs.
13:33 Changeset [2187] by curtis
First cut at making ND2 work without JAI Image I/O Tools in classpath.
13:04 Changeset [2186] by melissa
Added note on new close(boolean) method and unit testing.
12:53 Changeset [2185] by melissa
Disable more options during conversion. NOTE: r2183 actually contains …
12:15 Changeset [2184] by melissa
Gracefully handle canceled OMETablePanel.
11:48 Changeset [2183] by melissa
Added OME image browser to VisBio. Also moved much of the connection and …
09:11 Changeset [2182] by melissa
* Added new API method to IFormatReader - "void close(boolean)" - if the …


15:56 Changeset [2181] by curtis
Soften "You need to install..." messages a little.
15:49 Changeset [2180] by curtis
Use readFully instead of read, where appropriate.
15:44 Changeset [2179] by curtis
Only check for a JPEG-2000 reader once.
15:20 Changeset [2178] by curtis
Update copyrights: changes for 2007, add missing authors, tweak some …
15:06 Changeset [2177] by curtis
Add main method, shell script, and batch file for testing Bio-Formats …
14:31 Changeset [2176] by melissa
Pass currentId to getMetadataStore to avoid infinite recursion.
14:15 Changeset [2175] by melissa
Close opened header files.
14:04 Changeset [2174] by curtis
Use com.sun.media.imageio.disableCodecLib instead of …
13:53 Changeset [2173] by curtis
Set system property to force pure Java JPEG-2000 instead of native codec.
12:42 Changeset [2172] by melissa
Don't catch Throwable; only set the noPOI flag if ReflectedUniverse …
10:33 Changeset [2171] by melissa
Close files opened by isThisType.


16:48 Changeset [2170] by sorber
Enabled dragging multiple objects.
16:48 Changeset [2169] by melissa
Moved used files logic, so as not to interfere with image count …
16:32 Changeset [2168] by melissa
Hopefully fixed FileStitcher to retrieve used files list from each …
15:56 Changeset [2167] by melissa
Corrected inaccuracy in getUsedFiles.
13:51 Changeset [2166] by melissa
Removed debugging statement (oops).
13:50 Changeset [2165] by melissa
Make sure we use the absolute path to the root data directory.
13:32 Changeset [2164] by sorber
Added method to convert from domain to pixel coordinates


14:58 Changeset [2163] by nor
Added JPEGCompressor.java using the Compressor interface, removed …
10:47 Changeset [2162] by curtis
Remove explicit garbage collection call.
10:46 Changeset [2161] by curtis
Tweak documentation.
10:02 Changeset [2160] by melissa
Add configuration files as they're found.
07:35 Changeset [2159] by melissa
Fixed remainder of cases where files were opened using the relative path …


15:00 Changeset [2158] by melissa
Added new command line option to ReaderTest that automatically generates …
10:36 Changeset [2157] by melissa
Fix to allow filenames with spaces - requires filename to be enclosed in …
10:15 Changeset [2156] by melissa
Reworked configuration file structure for testing framework. Instead of …


13:23 Changeset [2155] by melissa
Removed Plane2D - the same functionality is provided by BufferedImages.
10:36 Changeset [2154] by melissa
Obey the dataset ID, if specified. If the dataset ID is not null, then …
10:01 Changeset [2153] by melissa
Cleaned up ZVI metadata - string values are no longer truncated.
08:44 Changeset [2152] by melissa
Make sure series names show up in series chooser dialog.


15:30 Changeset [2151] by melissa
Added OME-CA files to bad files list.
15:27 Changeset [2150] by melissa
Changed initFile to check if id is the array returned by …
13:23 Changeset [2149] by melissa
Fixed bug causing two images to be created.
12:40 Changeset [2148] by melissa
Call initFile with the absolute path name.
12:17 Changeset [2147] by melissa
Fixed to allow arguments with escaped spaces.
12:16 Changeset [2146] by melissa
- Updated ImageUploader to use loci.ome.upload API. - Updated OMEImage to …
12:11 Changeset [2145] by melissa
Fixed NullPointerException.
08:30 Changeset [2144] by melissa
Fixed off-by-one bug in initMetadata; tweaked initFile to return if the …


16:37 Changeset [2143] by curtis
Update handling of null sizeC (if Leica TIFF is given as id); add more …
16:14 Changeset [2142] by curtis
Hardcode reader name in initFile debugging statements.
16:08 Changeset [2141] by curtis
Add new "insane" debugging level that prints every debugging message as a …
14:53 Changeset [2140] by curtis
More comments.
14:51 Changeset [2139] by curtis
Tweak a comment.
14:49 Changeset [2138] by curtis
Update bad files list again, this time with comments.
14:43 Changeset [2137] by curtis
Allow blank lines and comments in bad files list.
14:35 Changeset [2136] by curtis
Add some more files to the ignore list.
14:27 Changeset [2135] by melissa
Fixed NullPointerException with stitched files.
14:26 Changeset [2134] by curtis
In testRead, only print effective sizeC if it differes from normal sizeC.
14:12 Changeset [2133] by curtis
Turn on metadata filtering for ImageJ importer plugin.
14:10 Changeset [2132] by curtis
Add metadata filtering logic. A metadata entry is filtered out as invalid …
13:46 Changeset [2131] by curtis
Add methods for toggling metadata filtering. Reorganize metadata …
13:28 Changeset [2130] by melissa
I'm an idiot, we really do want to use the effective sizeC...but it should …
13:23 Changeset [2129] by melissa
Make sure the id map is not null.
12:57 Changeset [2128] by melissa
Use real sizeC when computing indices (not effective sizeC).
12:48 Changeset [2127] by curtis
Add Location(File) constructor; readd FilePattern.findPattern(File).
11:49 Changeset [2126] by melissa
Improved support for renamed LEI and TIFF files.


12:30 Changeset [2125] by sorber
Text rendering toggles off while selecting multiple overlays.
12:28 Changeset [2124] by curtis
Remove executable property from batch files.
11:50 Changeset [2123] by sorber
Removed auto-padding feature. Zero-area objects now disappear on mouseUp.
11:31 Changeset [2122] by melissa
Updated to reflect FileWrapper rename, id mapping API change, and new …
11:05 Changeset [2121] by melissa
Make sure the MetadataStore is up-to-date. This fixes a bug where the …
10:26 Changeset [2120] by melissa
Fixed calibration issue.
09:25 Changeset [2119] by melissa
* Fixed how importer handles files with sizeC > 4. * Fixed bugs in …


16:59 Changeset [2118] by melissa
Use Location.getMappedId.
16:41 Changeset [2117] by melissa
Replaced FileWrapper logic with new Location class. This provides an API …
15:08 Changeset [2116] by curtis
Change getZCTCoords calls to new signature.
13:52 Changeset [2115] by sorber
Added dynamic list refreshing when selecting overlays with a …
13:51 Changeset [2114] by sorber
Fixed bug caused by zero-area boxes and ovals. Zero-area OverlayBox's and …
13:17 Changeset [2113] by melissa
Added feature to stitch series with the same dimensions.
10:53 Changeset [2112] by melissa
Fixed bug that caused all Pixels elements to be placed under the first …
10:25 Changeset [2111] by melissa
Make sure pixel arrays are the correct size.
10:02 Changeset [2110] by melissa
Various bugfixes.


14:13 Changeset [2109] by curtis
Better population of core metadata into table for multi-series datasets.
14:00 Changeset [2108] by curtis
Integrate last two versions of Importer properly (oops).
13:56 Changeset [2107] by curtis
Add display option to show metadata only (no pixels).
13:14 Changeset [2106] by curtis
Better dimensionality info in multiple series chooser; migrate sizeC logic …
11:40 Changeset [2105] by melissa
Parse pixel sizes from Gatan files.
10:12 Changeset [2104] by melissa
Fixed Zeiss ZVI metadata.
09:38 Changeset [2103] by melissa
Fixed compiler error.
09:33 Changeset [2102] by curtis
Fix bug with getIndex and getZCTCoords for RGB=true with SizeC>4.
09:15 Changeset [2101] by sorber
Note about shift key
07:57 Changeset [2100] by melissa
Added make, model, and document name tags to metadata hashtable.
07:56 Changeset [2099] by melissa
Prepend series name to each key in metadata hashtable.


17:12 Changeset [2098] by sorber
Help and screenshot for overlaysHelp and screenshot for overlaysHelp and …
15:34 Changeset [2097] by curtis
Add option to disable texture mapping.
15:00 Changeset [2096] by curtis
Fix most lines greater than 80 chars.
14:50 Changeset [2095] by curtis
Change mouseDown/Up/Drag API to include coordinates in pixel coordinate …
14:36 Changeset [2094] by sorber
Changes to mouse logic for simultaneous L and R mouse clicks


14:12 TracTicketsCustomFields created by trac
14:12 WikiDeletePage created by trac
14:12 TracBackup created by trac
14:12 TracTickets created by trac
14:12 TracInstall created by trac
14:12 TracTimeline created by trac
14:12 TracRss created by trac
14:12 WikiPageNames created by trac
14:12 TracImport created by trac
14:12 TracFastCgi created by trac
14:12 TracIni created by trac
14:12 WikiRestructuredText created by trac
14:12 TracPermissions created by trac
14:12 TracSupport created by trac
14:12 WikiHtml created by trac
14:12 TracSyntaxColoring created by trac
14:12 TracModPython created by trac
14:12 WikiFormatting created by trac
14:12 TracBrowser created by trac
14:12 WikiRestructuredTextLinks created by trac
14:12 TracNotification created by trac
14:12 TracUnicode created by trac
14:12 TracAccessibility created by trac
14:12 TracEnvironment created by trac
14:12 TracReports created by trac
14:12 WikiMacros created by trac
14:12 TracCgi created by trac
14:12 CamelCase created by trac
14:12 WikiProcessors created by trac
14:12 TracSearch created by trac
14:12 TracQuery created by trac
14:12 WikiStart created by trac
14:12 TracLogging created by trac
14:12 SandBox created by trac
14:12 TracStandalone created by trac
14:12 TracLinks created by trac
14:12 TracPlugins created by trac
14:12 TracRoadmap created by trac
14:12 RecentChanges created by trac
14:12 TracUpgrade created by trac
14:12 TracChangeset created by trac
14:12 TracAdmin created by trac
14:12 TracGuide created by trac
14:12 TitleIndex created by trac
14:12 TracWiki created by trac
14:12 TracInterfaceCustomization created by trac
14:12 WikiNewPage created by trac


17:12 Changeset [2093] by nor
Moving Nikon over to Compressor interface
16:39 Changeset [2092] by nor
Update for Packbits Compressor
16:38 Changeset [2091] by nor
16:38 Changeset [2090] by nor
Update for PackbitsCompressor
16:38 Changeset [2089] by nor
Moving Packbits over to Compressor interface
15:28 Changeset [2088] by curtis
Use getCurrentFile instead of raw ID for metadata window title.
15:26 Changeset [2087] by curtis
Use getCurrentFile instead of raw ID when possible for window title.
15:12 Changeset [2086] by melissa
Save previous server and user name; use these as the default when logging …
15:00 Changeset [2085] by melissa
* Fixed a bug in the importer that caused remote import + stitched files …
14:54 Changeset [2084] by curtis
Change "Filename" metadata parameter name to "OME address" or "URL" …
14:45 Changeset [2083] by nor
- Added AdobeDeflateCompressor.java as part of the files using Compressor …
14:25 Changeset [2082] by curtis
Make filename the first piece of metadata in the table.
14:17 Changeset [2081] by curtis
14:16 Changeset [2080] by curtis
Separate local file, OME server, and Internet into separate plugin …
14:10 Changeset [2079] by melissa
Fixed bug with long directory listings.
13:01 Changeset [2078] by melissa
Tweaked RAUrl and several readers to provide better support for reading …
12:44 Changeset [2077] by nor
Corrected typo (LZW->LZO)
12:38 Changeset [2076] by nor
- Modified to use LZOCompressor as part of Compressor interface changes. - …
12:36 Changeset [2075] by nor
Javadoc fix (removed @param from method with no params)
12:35 Changeset [2074] by nor
Style fix…
12:28 Changeset [2073] by nor
Moving loci.formats.Compression.lzoUncompress to the Compressor interface.


12:22 Changeset [2072] by curtis
Fill in tooltips for min and max color value sliders.
09:00 Changeset [2071] by nor
Changes to API and "Object-orientation" due to BaseCompressor.java, also …
08:59 Changeset [2070] by nor
Base Compressor class, providing default implementations for several …
08:57 Changeset [2069] by nor
Style fixes, bug fixes (thanks Curtis!)


18:25 Changeset [2068] by curtis
Add min and max color scaling for intensity plot.
16:23 Changeset [2067] by melissa
Finally fixed bug in RGB conversion.
14:03 Changeset [2066] by nor
changed to use Base64Encode class with Compressor interface
13:58 Changeset [2065] by nor
Windows batch files for useful testing utilities.
13:56 Changeset [2064] by melissa
Copied server sanity logic from …
13:48 Changeset [2063] by nor
Style fixes
13:44 Changeset [2062] by nor
Add test method
13:40 Changeset [2061] by nor
Encoder for Base64 using the Compressor interface
11:04 Changeset [2060] by nor
Updated to use LZWCompressor.
10:52 Changeset [2059] by melissa
Improved RGB stack handling, so min/max adjustment is done before RGB …
10:48 Changeset [2058] by nor
Implements LZW compression using the Compressor interface.
10:47 Changeset [2057] by nor
Compression interface, for implementing various compression schemes such …
10:41 Changeset [2056] by nor
Style changes
10:09 Changeset [2055] by melissa
Be more flexible about how server name is specified - fill in " http://" …
10:02 Changeset [2054] by melissa
Star out password field in login box.
09:59 Changeset [2053] by melissa
Added new IFormatReader API method: String getCurrentFile(). If you need …
08:46 Changeset [2052] by melissa
* Fixed memory bug in Zeiss LSM. * Fixed bug with 2-channel BufferedImage …


14:37 Changeset [2051] by melissa
Fix display issue with 16 and 32 bit data (fixes Glen MacDonald's OIF …
13:00 Changeset [2050] by melissa
Fixed LIF reader to label the first series correctly.
12:30 Changeset [2049] by melissa
* Fixed several bugs in ND2 reader * Tweaked OMEReader.initFile to allow …


18:22 Changeset [2048] by curtis
Pass Z and T sizes properly to View5D.
17:56 Changeset [2047] by curtis
Avoid problem with java.awt.SplashScreen in Java 1.6.
13:49 Changeset [2046] by melissa
* Added options to importer to allow downloading from OME or other …
10:19 Changeset [2045] by melissa
Added OMEReader, a subclass of FormatReader for reading OME images. …


16:34 Changeset [2044] by nor
Added comment to BitBuffer.java
16:19 Changeset [2043] by nor
added skipBits(long bits) method.


16:40 Changeset [2042] by curtis
Update release date.
16:33 Changeset [2041] by curtis
Use new FormatReader.setDebug method instead of setting flag directly.
16:32 Changeset [2040] by curtis
Add accessor methods for debug and debugLevel parameters.
16:10 Changeset [2039] by curtis
Style fixes.
16:08 Changeset [2038] by sorber
(removed print statements)
15:51 Changeset [2037] by curtis
Avoid shadowed fields.
15:49 Changeset [2036] by curtis
15:49 Changeset [2035] by curtis
15:48 Changeset [2034] by curtis
Avoid using deprecated readLine method (just throw IOException, since …
15:44 Changeset [2033] by curtis
Eliminate totally squashed exceptions (print stack trace if debug flag is …
15:43 Changeset [2032] by sorber
Dynamic selection of multiple objects with TransientSelectBox
15:08 Changeset [2031] by melissa
Only print stack traces if the 'debug' flag is set.
12:27 Changeset [2030] by melissa
* Added feature to read files over HTTP. * Updated "what's new" list
09:22 Changeset [2029] by melissa
Tweaked isThisType(String, boolean) to check if there is an XML file in …


21:55 Changeset [2028] by nor
Added comments, test method
21:54 Changeset [2027] by nor
Added write(String bitString) method
17:33 Changeset [2026] by chris
Browser: 1) references to getSizeC() in CacheManager changed to …
17:27 Changeset [2025] by curtis
First cut at disallowing mutually exclusive import options.
17:12 Changeset [2024] by sorber
Added shading to TransientSelectBox (rgb -> rgba for all OverlayObjects' …
16:59 Changeset [2023] by chris
Browser: 1) Better support for cache/no cache, but RAM thing isn't there …
16:06 Changeset [2022] by chris
Browser: 1) changed all references to filestitcher in cachemanager to be …
15:24 Changeset [2021] by chris
Browser: 1) OptionsWindow now functional for both FileStitcher and …
15:10 Changeset [2020] by curtis
Fix problem where dev-compile always compiled all files.
14:45 Changeset [2019] by curtis
Fix bug where background slice loading thread took 100% CPU.
14:36 Changeset [2018] by curtis
Fix bug where "View stack with" preference was not properly set to old …
14:04 Changeset [2017] by chris
Browser: 1) something here must have changed, but I forget at this point. …
13:48 Changeset [2016] by melissa
* Force LeicaReader.initFile to close open files. * Make sure ReaderTest …
13:15 Changeset [2015] by chris
Browser: 1) annoying ass debug messages quashed!
13:12 Changeset [2014] by chris
Browser: 1)reverted getTempSlice(index) to functional method.
13:08 Changeset [2013] by curtis
One email link that Melissa missed.
12:51 Changeset [2012] by chris
Browser: 1) Multiple threads being created is fixed... now there's only …
11:37 Changeset [2011] by melissa
Tweaked support for planar TIFF files (fixes issue with 2-channel LSM …
10:02 Changeset [2010] by melissa
* Tweaked OIB and OIF metadata parsing so that the output looks the same. …


15:49 Changeset [2009] by chris
Browser: 1) fixed it so that random filepatterns will be displayed as per …
14:33 Changeset [2008] by melissa
Allow file name switching.
14:30 Changeset [2007] by chris
Browser: 1) fixed bug that index of image was off by -1 2) fixed indicator …
13:49 Changeset [2006] by melissa
Fix to allow file name switching.
13:05 Changeset [2005] by chris
Fix previous getEffectiveSizeC fix.
12:54 Changeset [2004] by melissa
More changes to allow file name switching.
12:42 Changeset [2003] by chris
Clean up getEffectiveSizeC implementations.
12:10 Changeset [2002] by melissa
Fixed to allow the output file name to be changed before the last plane …
12:01 Changeset [2001] by melissa
Added close method to IFormatWriter API; tweaked most readers to either …
11:51 Changeset [2000] by melissa
Fixed bug in isThisType.
10:53 Changeset [1999] by chris
PrairieReader: 1) reverted code around line 214 back to what it was …
10:45 Changeset [1998] by chris
PrairieReader: 1) slight fix to avoid infinite loop I created around line …
10:35 Changeset [1997] by chris
PrairieReader: 1) added code at line 214 to preclude the substring method …
09:11 Changeset [1996] by melissa
Added support for Prairie TIFF files.
Note: See TracTimeline for information about the timeline view.