Timeline


and

11/05/07:

18:59 Changeset [3343] by melissa
Removed unnecessary getIFDs call.
11:25 Changeset [3342] by melissa
Giving lse.xml file to BioRadReader will now open entire dataset.
09:30 Changeset [3341] by melissa
Fixed interleaving bug for real this time.
09:26 Changeset [3340] by melissa
Fixed interleaving bug.
09:02 Changeset [3339] by melissa
Don't try to decompress more bytes than are needed.

11/02/07:

19:08 Ticket #210 (Better file stitching in BioradReader) closed by melissa
fixed: Done in r3338. If an lse.xml file is present, the appropriate .pic files …
14:13 Changeset [3338] by melissa
Find and group PIC files if lse.xml companion file is present.
11:23 Changeset [3337] by melissa
CustomImage can now merge up to 4 channels.
10:48 Ticket #211 (Add ImageJ plugin that merges/colorizes channels) created by melissa
At some point, the importer's merging and colorizing logic should get …

11/01/07:

09:52 Changeset [3336] by melissa
Make sure PixelSizeZ is always parsed, even if SizeZ == 1.
09:44 Ticket #210 (Better file stitching in BioradReader) created by melissa
BioradReader should check the companion files to more accurately detect …

10/31/07:

15:31 Ticket #209 (OME download is broken) created by curtis
The latest version of VisBio fails to download from an OME server, due to …
12:07 Changeset [3335] by melissa
Don't throw an exception if a Z stamp is encountered when we are expecting …
11:55 Changeset [3334] by melissa
More reliable pixel size parsing.
08:04 Ticket #207 (Slicer plugin throws an exception when there is no active image) closed by melissa
fixed: Fixed in r3333.
08:03 Changeset [3333] by melissa
Slicer now implements PlugInFilter, preventing an exception when there are …

10/30/07:

15:21 Ticket #208 (Add information about format versions to web site) created by curtis
The Bio-Formats web site should provide information about which file …
14:47 Ticket #207 (Slicer plugin throws an exception when there is no active image) created by curtis
The Slicer plugin implements PlugIn, which means currently it throws an …
13:22 Ticket #206 (Color merge throws an exception) closed by melissa
fixed: Fixed in r3330.
13:11 Changeset [3332] by melissa
Catch UnsupportedClassVersionError when creating ReflectedUniverse - this …
13:08 Changeset [3331] by melissa
Catch EOFException when parsing image files.
13:03 Changeset [3330] by melissa
Fixed merging bug.
10:49 Changeset [3329] by melissa
Calculate pixel sizes if they aren't stored explicitly.
08:50 Changeset [3328] by melissa
Make sure pixel sizes get reset; check for invalid min/max values before …
08:04 Changeset [3327] by melissa
Set pixel type correctly for signed images.

10/29/07:

10:39 Changeset [3326] by curtis
No more need for omebf script.
10:37 Ticket #206 (Color merge throws an exception) created by curtis
The option to "Merge channels to RGB" can throw an exception. For example, …
10:06 Ticket #205 (Window titles can become too long) closed by melissa
fixed: Fixed in r3325. The window title is now file name plus the series name …
10:05 Changeset [3325] by melissa
Better string trimming.
10:01 Changeset [3324] by melissa
Make sure that window titles are <= 128 chars.
09:33 Changeset [3323] by melissa
Populate PixelSize*, if values exist in metadata; better parsing of …

10/26/07:

15:22 Changeset [3322] by melissa
Fixed endianness.
14:56 Changeset [3321] by melissa
* Removed a bunch of unnecessary axis size calculation logic from …
13:38 Ticket #205 (Window titles can become too long) created by curtis
The Importer plugin currently uses the full path name, plus the image …
13:31 Changeset [3320] by melissa
Multiple series are now correctly detected; replaced evil axis …
12:53 Changeset [3319] by curtis
Remove unnecessary imports.
11:28 Changeset [3318] by curtis
Typo.
11:24 Changeset [3317] by curtis
Workaround for XML parsing bug with SAX on Windows and Mac OS X.
08:52 Changeset [3316] by melissa
Reorganized MetadataStore population logic - calls to setLogicalChannel …
07:36 Changeset [3315] by melissa
Temporary hack to unbreak openBytes(int, byte[]).

10/25/07:

16:10 Changeset [3314] by curtis
Remove unnecessary import.
16:10 Changeset [3313] by curtis
Print exceptions to Results window rather than with IJ.showMessage or …
15:25 Changeset [3312] by curtis
Remove references to the optional loci.formats.tools package.
15:01 Changeset [3311] by melissa
Removed unnecessary import statements.
14:49 Changeset [3310] by curtis
Add NetCDF libraries to build properties.
13:13 Ticket #178 (Add support for Imaris 5.5) closed by melissa
fixed: Done in r3309.
13:12 Changeset [3309] by melissa
Added support for Imaris 5.5 (HDF-based).
07:47 Changeset [3308] by melissa
Implemented openBytes(int).
07:45 Changeset [3307] by melissa
Added command-line flags to ImageConverter (-merge, -separate, -stitch, …

10/24/07:

16:17 Changeset [3306] by curtis
Fix problem with LuraWave compression.

10/23/07:

13:29 Ticket #202 (Create "Bio-Formats Stack Splitter" plugin) closed by melissa
fixed: Done in r3305.
10:02 Ticket #200 (Split channels option divides image planes across the wrong dimension when ...) closed by melissa
fixed: Fixed in r3305 with addition of stack slicing plugin.
09:52 Changeset [3305] by melissa
Added stack slicing plugin, which replaces the channel splitting logic in …
08:15 Changeset [3304] by melissa
Better indexed color support in Zeiss LSM.

10/22/07:

09:07 Changeset [3303] by melissa
Minor adjustment to offset calculation.

10/19/07:

10:54 Changeset [3302] by melissa
Set indexed = false if the lookup table is too small.

10/18/07:

13:56 Changeset [3301] by melissa
Temporarily commented out Cinepak logic.
13:42 Changeset [3300] by melissa
Changed TiffIFDEntry's 'offset' field to 'long'; calls to …
13:09 Changeset [3299] by melissa
Alpha channel is now handled correctly.
10:43 Changeset [3298] by melissa
Fixed filename parsing logic.
08:27 Changeset [3297] by melissa
Fixed openBytes(int, byte[]) so it no longer returns all zeros.

10/17/07:

15:10 Changeset [3296] by curtis
Print a message if no TIFF comment is found, rather than throwing an …
14:14 Changeset [3295] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3294] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3293] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3292] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3291] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3290] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3289] by melissa
2007 Oct 17 release of LOCI Tools
14:14 Changeset [3288] by melissa
2007 Oct 17 release of LOCI Tools
14:08 Changeset [3287] by melissa
Updated what's new for today's release.
14:04 Ticket #196 (ZVI reader sometimes reverses Z and T dimensions) closed by melissa
fixed: Fixed in r3286.
14:03 Changeset [3286] by melissa
Fixed Z/T reversal.
10:11 Changeset [3285] by melissa
If bmpColorsUsed == 0, set it to 2bitsPerPixel.
10:05 Ticket #203 (Some PICT files have incorrect pixel type) closed by melissa
fixed: Fixed in r3284.
10:05 Changeset [3284] by melissa
Corrected pixel type for 5-5-5 RGB data.
09:34 Changeset [3283] by melissa
Make sure elementLength/compression indicators are reset.
08:37 Changeset [3282] by melissa
Fixed case logic for setting pixel scale value.
08:02 Changeset [3281] by melissa
Finished logic to correctly handle signed data.

10/16/07:

12:38 Changeset [3280] by melissa
Correctly handle signed data.
11:39 Ticket #204 (Support lossless JPEG in DICOM reader) created by melissa
DicomReader currently supports lossy (conventional) JPEG, but not lossless …
11:10 Changeset [3279] by melissa
* Added new API method to loci.formats.codec.Codec to allow decompressing …
10:17 Ticket #203 (Some PICT files have incorrect pixel type) created by melissa
8-bit files in data/pict/brian/images/ (e.g. RED.PCT) should have pixel …
08:22 Changeset [3278] by melissa
Fixed indexed to RGB conversion.

10/15/07:

15:26 Ticket #202 (Create "Bio-Formats Stack Splitter" plugin) created by curtis
To my knowledge, there is no easy way within ImageJ to split out a …
14:45 Ticket #201 (Improve configuration file generator) created by melissa
When writing configuration files, loci.formats.test.ReaderTest should only …
12:41 Ticket #200 (Split channels option divides image planes across the wrong dimension when ...) created by curtis
This command works as expected: […] But this one causes the channels to …
12:33 Changeset [3277] by curtis
Fix problems with duplicate macro options.
10:21 Changeset [3276] by melissa
* Fixed bug with "open each channel in new window" + "specify range". * …

10/14/07:

11:09 Ticket #199 (Fix exception with new OIB files) created by melissa
data/fv1000/aryeh/1h_after_pdt.oib and data/fv1000/aryeh/control_test.oib …
11:03 Ticket #197 (Bio-Formats Importer fails with indexed images) closed by melissa
fixed: Fixed in r3275.
11:02 Changeset [3275] by melissa
Fixed ZCT calculation for indexed color images.

10/13/07:

13:25 Ticket #198 (OME-TIFF files fail with Bio-Formats Importer plugin) closed by melissa
fixed: Fixed in r3274.
13:25 Changeset [3274] by melissa
Don't need to manually prepend directory name to file name.

10/12/07:

16:42 Ticket #198 (OME-TIFF files fail with Bio-Formats Importer plugin) created by curtis
When importing OME-TIFF files to ImageJ using the Bio-Formats Importer …
16:40 Ticket #197 (Bio-Formats Importer fails with indexed images) created by curtis
Attempting to import an indexed color image with the Bio-Formats Importer …
15:56 Ticket #196 (ZVI reader sometimes reverses Z and T dimensions) created by curtis
The dataset in data/zeiss-zvi/monica/Monica_elegans_movie.zvi has 14 …
15:30 Changeset [3273] by curtis
Fix little bug in arg parsing.
13:04 Changeset [3272] by melissa
More tiling/BigTIFF fixes.
11:33 Changeset [3271] by melissa
Corrected image count calculation if we have indexed color planes.
09:03 Ticket #158 (Add support for BigTiff) closed by melissa
fixed: Complete in r3270.
08:46 Changeset [3270] by melissa
Fixed tiling bug and added remaining BigTIFF types.

10/11/07:

15:17 Changeset [3269] by melissa
Initial implementation of BigTIFF.
14:32 Changeset [3268] by melissa
Removed several hacks that added an extra blank channel if C == 2.
14:31 Ticket #195 (Cannot construct 2-channel images with ImageTools) closed by melissa
fixed: Fixed in r3267. Solution was to add new 2-component ColorSpace …
13:45 Changeset [3267] by melissa
Added new ColorSpace for 2-channel images; updated ImageTools accordingly.
12:46 Changeset [3266] by melissa
Fixed plane number -> IFD mapping for primary file.
12:23 Changeset [3265] by curtis
Clean up and debug image construction methods.
12:22 Changeset [3264] by curtis
Use BYTES_PER_ENTRY instead of hardcoded 12 where relevant.
12:20 Changeset [3263] by curtis
Rename "used" to "usedFiles" so it is easier to search.
10:51 Changeset [3262] by curtis
Remove unnecessary imports.
09:49 Changeset [3261] by melissa
Only parse the primary file once.
09:26 Changeset [3260] by curtis
TiffComment now has a trivial implementation thanks to …
09:17 Changeset [3259] by curtis
* Add TiffTools.getComment convenience method. * Some efficiency …
08:27 Changeset [3258] by melissa
Removed option to force compatible pixel type.

10/10/07:

17:26 Changeset [3257] by curtis
Standardize getPixels methods to use a single sample model checker method …
17:23 Ticket #195 (Cannot construct 2-channel images with ImageTools) created by curtis
Currently, ImageTools throws an exception when you attempt to create a …
15:12 Changeset [3256] by curtis
Comment out reference to broken makeType method.
15:10 Changeset [3255] by curtis
Comment out reference to broken makeType method.
15:09 Changeset [3254] by curtis
Fix getPixels implementations to never use makeType, and get rid of …
13:52 Ticket #170 (Investigate ImageJ's VirtualStack objects) closed by melissa
fixed: In order to create a VirtualStack, each plane of the dataset must be …
12:33 Ticket #175 (More cohesive floating point image support) closed by melissa
fixed: As of r3253, all byte array to float array conversions are done using …
12:24 Changeset [3253] by melissa
All byte array to float array conversions are now handled by …
11:19 Changeset [3252] by melissa
Fixed bug in fake rows per strip calculation.
10:54 Ticket #192 (Default implementation for saveBytes) closed by melissa
fixed: Completed in r3251. In order to use saveBytes, a valid MetadataRetrieve …
10:52 Changeset [3251] by melissa
Added default saveBytes implementations. To use saveBytes, a …

10/09/07:

23:58 Ticket #194 (Investigate usage of JMF library) created by curtis
The [ http://java.sun.com/products/java-media/jmf/index.jsp Java Media …
15:06 Changeset [3250] by curtis
Disable editing of file path text boxes for now.
15:04 Ticket #193 (Test omeul with OME 2.6.1) created by curtis
The client-side OME upload functionality provided by the omeul script has …
14:35 Changeset [3249] by melissa
Fixed pixel type mismatch.
14:06 Ticket #192 (Default implementation for saveBytes) created by curtis
Adding a default implementation for the FormatWriter.saveBytes methods …
13:57 Changeset [3248] by melissa
Fixed series/currentSeries typo; update file map along with IFD map.
13:39 Ticket #159 (Add support for compressed ZVI images) closed by melissa
fixed: Finished in r3247.
13:38 Changeset [3247] by melissa
Added support for JPEG-compressed ZVI images.
13:17 Changeset [3246] by melissa
Fixed one last bug.
12:55 Changeset [3245] by melissa
Parse XML using SAX.
11:16 Ticket #191 (3-view) created by curtis
(From Matt Conklin) It may be useful to generate a "3-view" of the plot. …
11:16 Ticket #190 (Export to spreadsheet) created by curtis
(From Matt Conklin) It would be great to get the data seamlessly into a …
11:15 Ticket #189 (Save/export to figure file) created by curtis
(From Matt Conklin) Saving/exporting the plot into a figure making …
11:15 Ticket #188 (Overlapping line and surface plots) created by curtis
(From Matt Conklin) Overlapping the line plots of the data over the …
10:40 Ticket #187 (Model some data for testing) created by curtis
To verify the accuracy and proper behavior of Slim Plotter's algorithms, …
10:38 Ticket #186 (Plot chi-squared error graphically) created by curtis
It is currently possible to plot the exponential curve fit results …
10:26 Ticket #185 (Plot system response data graphically) created by curtis
To give the user a better idea of exactly what is being done by the …
10:20 Ticket #184 (Additional logic for handling background issues) created by curtis
When fitting exponential curves, the c value represents the background. …
09:51 Ticket #183 (Devise a scheme to embed calibration information into the SDT format) created by curtis
As mentioned in tickets #84 and #135, we need to embed calibration …

10/08/07:

14:02 Ticket #176 (ImageJ stack ordering broken) closed by melissa
fixed: Fixed in r3244.
13:58 Changeset [3244] by melissa
Added option to open each plane in a separate window; fixed CustomImage …
12:27 Changeset [3243] by curtis
Echo status message events to the ImageJ status bar.
12:18 Changeset [3242] by curtis
Add Javadoc for getReorderedIndex.
12:14 Changeset [3241] by curtis
Another status message, indicating parsing of each constituent OME-TIFF …
12:08 Changeset [3240] by curtis
Add status message for each TIFF file checked.
12:08 Ticket #182 (Fix bug with >2GB LIF files) closed by melissa
fixed: Fixed in r3239.
12:07 Changeset [3239] by melissa
Fixed bug with >2GB files.
11:56 Ticket #182 (Fix bug with >2GB LIF files) created by melissa
Leica LIF files larger than 2GB throw the following exception: […]
11:53 Changeset [3238] by melissa
Improved logic for mapping plane numbers to IFDs - scrambled TiffData …
11:38 Ticket #171 (Improve OME-TIFF grouping logic) closed by curtis
fixed: Melissa has improved the OME-TIFF reader's file grouping logic and fixed …
11:34 Ticket #181 (Investigate LSM data with nonstandard LZW compression) created by curtis
The LSM files in data/zeiss-lsm/tom have problems being decoded properly …
11:25 Ticket #180 (AVI codecs supported by NIS Elements) created by melissa
The following AVI codecs are supported by NIS Elements: * Cinepak * …
11:24 Ticket #179 (Add support for compressed LIM files) created by melissa
Pixels in a LIM file can be compressed using a proprietary lossless …
11:22 Ticket #178 (Add support for Imaris 5.5) created by melissa
Need to obtain sample data by installing latest Imaris version; add …
11:18 Ticket #177 (Additional plugin options) created by melissa
Two new ImageJ plugin features have been requested: 1. Open each plane …
11:13 Ticket #176 (ImageJ stack ordering broken) created by melissa
When other options (e.g. "merge channels to RGB") are checked, the …
10:54 Ticket #175 (More cohesive floating point image support) created by curtis
Currently Bio-Formats has duplicate implementations of byte-array-to-float …
10:44 Ticket #174 (Investigate usage of Sanselan image library) created by curtis
A new pure Java image library has recently been released called …
10:40 Ticket #173 (Standard way to "fail through" to another reader) created by curtis
In some cases, there are multiple readers that can ostensibly support a …
10:32 Ticket #172 (Better usage of JAI Image I/O Tools) created by curtis
Bio-Formats currently uses the [ https://jai-imageio.dev.java.net/ JAI …
10:06 Changeset [3237] by melissa
Fixed sizeC calculation for RGBA TIFFs.
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