20:06 Changeset [2287] by chris
Notebook: support for multiple pixels in weird order should be in place I …
19:37 Changeset [2286] by chris
Notebook: added capacity to find lowest ID number in pixels. no longer …
19:30 Changeset [2285] by chris
Notebook: Adding support for multiple pixel thumbnails, commiting what I …
15:41 Changeset [2284] by sorber
New classes for drawing polylines. Typos and small changes.
14:31 Changeset [2283] by curtis
Fix critical OME-TIFF conversion bug (insert required TiffData element).
14:11 Changeset [2282] by sorber
Fixed bug which allowed multiple freeforms to become selected as each was …
14:10 Changeset [2281] by curtis
Nicer error message when ij.jar is not found.
14:07 Changeset [2280] by curtis
Better error messages in testRead if OME-XML generation fails (in …
14:05 Changeset [2279] by curtis
Nicer error message if QTJava is not found.
14:02 Changeset [2278] by curtis
Update JAR classpaths.
13:42 Changeset [2277] by curtis
Better exceptions when libraries are missing.
13:42 Changeset [2276] by melissa
Instantiate OMEReader directly if we are downloading from OME (since …
13:30 Changeset [2275] by curtis
Remove OMEReader from the readers list -- easier than wrapping all …
13:25 Changeset [2274] by curtis
Throw a nicer exception if OME-Java is not present.
13:25 Changeset [2273] by curtis
Be more aggressive about trapping ND2 exceptions when the jai_imageio.jar …
12:56 Changeset [2272] by curtis
Fix compile error.
08:20 Changeset [2271] by melissa
Fixed compile error.


17:08 Changeset [2270] by chris
Notebook: 1) delete old tif file if it exists before using TiffWriter to …
16:56 Changeset [2269] by chris
Notebook: more efficient saving of tiff files through TiffWriter instead …
16:42 Changeset [2268] by curtis
Use getChildNodes instead of old getChildren signature.
16:42 Changeset [2267] by curtis
Switch to new setPixels signature.
16:40 Changeset [2266] by curtis
Change method signatures from OMEXMLNode.getChildren to …
16:32 Changeset [2265] by curtis
Change setPixels to have separate Image and Pixels indices.
15:38 Changeset [2264] by curtis
Better internal ID generation (based on element names instead of global).
14:28 Changeset [2263] by curtis
Assume links starting with http: are web links rather than internal.
14:20 Changeset [2262] by curtis
Fix Windows browser launching.


16:58 Changeset [2261] by curtis
Rearrange GUI to accommodate interactive color table; add ability to …
16:25 Changeset [2260] by nor
fixed improper sizeC value
15:24 Changeset [2259] by sorber
Cleaned up logic of mouseDown method
14:56 Changeset [2258] by melissa
Fixed bug - close() didn't reset image counter.
09:31 Changeset [2257] by melissa
Fixed channel min/max computation and retrieval for RGB TIFFs.


12:54 Changeset [2256] by callan
* Absolves the responsibility of handling min/max calculation from the …


13:54 Changeset [2255] by melissa
* Fixed OIB axis size bug. * Fixed NPEs caused by …
13:15 Changeset [2254] by sorber
No more single-node freeforms. They are either never constructed or …
12:36 Changeset [2253] by melissa
Fixed core metadata. BMP, MNG, EPS, PICT, PNG, JPG, and ImageJ-supported …
11:58 Changeset [2252] by melissa
Better handling of ignoreColorTable flag - fixes files in data/leica/joel.
09:53 Changeset [2251] by melissa
Don't display OME password in the status bar. Changed login dialog to …


19:24 Changeset [2250] by sorber
Added additional getDistSegWt method to accept double precision arrays.
19:18 Changeset [2249] by sorber
Changed FreeformTool to use pixel coordinates instead of domain …
18:10 Changeset [2248] by chris
Notebook: Capability to merge saved versions of companion and original …
17:07 Changeset [2247] by chris
Notebook: Capable now of saving wierd formats (if they're openable by …
14:06 Changeset [2246] by sorber
Misc small changes: removed visible flag from TransientSelect Box, …
10:27 Changeset [2245] by melissa
Fixed scanline padding problem with RGB AVI files.
08:53 Changeset [2244] by melissa
Updated exporter plugin to (hopefully) work with macros.


18:02 Changeset [2243] by chris
Notebook: Companion files and merging completely in place, should work …
17:52 Changeset [2242] by curtis
2007 Feb 7 release of LOCI Tools.
17:52 Changeset [2241] by curtis
2007 Feb 7 release of LOCI Tools.
17:51 Changeset [2240] by curtis
2007 Feb 7 release of LOCI Tools.
17:51 Changeset [2239] by curtis
2007 Feb 7 release of LOCI Tools.
17:50 Changeset [2238] by curtis
2007 Feb 7 release of LOCI Tools.
17:50 Changeset [2237] by curtis
2007 Feb 7 release of LOCI Tools.
17:49 Changeset [2236] by curtis
2007 Feb 7 release of LOCI Tools.
17:49 Changeset [2235] by curtis
2007 Feb 7 release of LOCI Tools.
17:48 Changeset [2234] by curtis
Relative paths are screwed up.
17:47 Changeset [2233] by curtis
2007 Feb 7 release of LOCI Tools.
17:46 Changeset [2232] by curtis
Add tags and branches directories.
17:25 Changeset [2231] by curtis
Include loci.ome.upload and loci.ome.util package trees in VisBio and LOCI …
17:24 Changeset [2230] by curtis
Change loci.ome package references to loci.ome.util.
17:20 Changeset [2229] by curtis
Fix package statements; ignore *.class files.
17:11 Changeset [2228] by curtis
Move OME helper classes into OME utility package.
17:10 Changeset [2227] by curtis
OME utility classes package.
15:18 Changeset [2226] by curtis
Turn off debugging flag.
15:11 Changeset [2225] by curtis
Add release date to what's new file.
15:10 Changeset [2224] by curtis
Tweak comment.
14:55 Changeset [2223] by curtis
Add OMEXMLNode.getChildren() method.
14:08 Changeset [2222] by melissa
Set value of BigEndian to false.
10:08 Changeset [2221] by melissa
Added note about new RandomAccessStream feature.
09:59 Changeset [2220] by melissa
Attempt to free up some memory.
09:36 Changeset [2219] by melissa


11:17 Changeset [2218] by curtis
Fix NumberFormatException bug; eliminate catch-all exception handling.
11:13 Changeset [2217] by curtis
Use Double.parseDouble instead of Integer.parseInt during metadata …
11:04 Changeset [2216] by curtis
Fix StringIndexOutOfBoundsException and NullPointerException in …
10:57 Changeset [2215] by curtis
Fix NullPointerException in LeicaReader.isThisType.


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.
Note: See TracTimeline for information about the timeline view.