source: trunk @ 7493

Revision Log Mode:


Legend:

Added
Modified
Copied or renamed
Diff Rev Age Author Log Message
(edit) @7493   9 years melissa Slightly more robust well name checking.
(edit) @7489   9 years melissa Prevent potential NPE if the "Info" property is not set on the ImagePlus …
(edit) @7488   9 years melissa Sanitize OME-XML before attempting to create a MetadataStore.
(edit) @7487   9 years melissa Use a ConcurrentHashMap instead of a HashMap.
(edit) @7486   9 years melissa Added optional cacheing of directory listings, courtesy of Lee Kamentsky.
(edit) @7485   9 years melissa Escape backslashes when finding a pattern. Closes #634.
(edit) @7484   9 years melissa Various fixes to allow retrieval of pixel data from truncated TIFFs.
(edit) @7483   9 years melissa Fixed a handful of bugs introduced in r7481.
(edit) @7482   9 years melissa Moved 'void setWriteSequentially(boolean)' from TiffWriter to …
(edit) @7481   9 years melissa Expanded special strip unpacking case to allow multiple strips.
(edit) @7480   9 years melissa Set a more reasonable timeout when checking for updates.
(edit) @7478   9 years melissa Added tests for screen detection. Closes #619.
(edit) @7477   9 years melissa Allow sparse plates.
(edit) @7476   9 years melissa Prevent a NPE when calling isThisType on a file with no parent directory.
(edit) @7475   9 years melissa Attach non-well files as companion metadata files.
(edit) @7474   9 years melissa Allow multi-series files to be stitched if the file pattern contains only …
(edit) @7473   9 years melissa Make type detection slightly more restrictive; this should allow the tests …
(edit) @7472   9 years melissa Added more flexible plate/well detection, so that InCell 3000 datasets are …
(edit) @7471   9 years melissa 'bfview' now has the same behavior as 'showinf', except that a deprecation …
(edit) @7470   9 years melissa Allow virtual stacks to be sliced. Closes #580.
(edit) @7469   9 years melissa Removed duplicate variable declaration, which prevented 2008-09 and …
(edit) @7467   9 years melissa Fixed NPE introduced in r7433.
(edit) @7466   9 years melissa Fixed one more IFD caching bug.
(edit) @7465   9 years melissa Fixed how EPS images with two channels are handled. Closes #631.
(edit) @7464   9 years melissa Reset ColorModel after setting the display range; this prevents LUTs from …
(edit) @7463   9 years melissa Preserve user name and emission wavelengths. Closes #632.
(edit) @7462   9 years melissa * Fixed various TIFF-parsing related problems introduced in r7459. * …
(edit) @7461   9 years melissa Fixed a bug in ZipHandle.isZipFile(String) that was introduced in r7460.
(edit) @7460   9 years melissa Updated ZipHandle and ZipReader to use a ZipInputStream instead of a …
(edit) @7459   9 years melissa Fill in IFD values after the IFDs have been parsed, thus reducing the …
(edit) @7458   9 years melissa A few small speed improvements for reading Openlab files.
(edit) @7455   9 years melissa Added initial version of Trestle reader, see #479.
(edit) @7454   9 years melissa Made PGM parsing more flexible, as required for #479.
(edit) @7453   9 years melissa Added methods for retrieving the optimal size of a sub-image. Closes …
(edit) @7452   9 years melissa Fixed .nd/.stk file searching, to prevent problems with multiple …
(edit) @7451   9 years melissa Append 'Z' to the dimension order string when appropriate. See …
(edit) @7449   9 years melissa Added reader for InCell 3000 files. Closes #443.
(edit) @7448   9 years melissa One more fix to 'uiSequenceCount' parsing. This really definitely fixes …
(edit) @7446   9 years melissa Parse and apply LUTs stored in the 'u32OffsetChannelColors' block. See …
(edit) @7443   9 years melissa Use the 'uiSequenceCount' attribute to calculate the image count. Closes …
(edit) @7442   9 years melissa Populate channel colors even if the MetadataLevel is set to MINIMUM. This …
(edit) @7433   9 years melissa Make sure that channel names are populated for screen data.
(edit) @7429   9 years melissa Adjust the number of padding bytes based upon the total number of bytes …
(edit) @7428   9 years melissa * Added setValidBitsPerPixel(int) to IFormatWriter. * Updated ICSWriter to …
(edit) @7427   9 years melissa Catch exception when parsing .mdb files, so that .lsm files can be read …
(edit) @7424   9 years hinerm Enhanced BF-ITK build for windows. The dist target is now specific to a …
(edit) @7418   9 years callan More robust InCellReader XML parsing. (See #623) Specifically handled: * …
(edit) @7417   9 years callan Made InCellReader support a little more generic to accomodate InCell 2000 …
(edit) @7402   9 years melissa Moved missing OME-XML messages into OMEXMLServiceImpl. Closes #604.
(edit) @7401   9 years melissa Override openBytes, so that correct pixels are returned for each series.
(edit) @7400   9 years melissa Added series number to one last failure message.
(edit) @7389   9 years callan Resolve OpenlabReader thread safety as it applies to the internal static …
(edit) @7386   9 years melissa Added some debugging to help track down an FV1000 bug.
(edit) @7384   9 years melissa Fixed well row and column indices, because I obviously didn't read r7379
(edit) @7379   9 years melissa Added better type checking to ScreenReader, so it is now included in …
(edit) @7375   9 years melissa Added more sophisticated image name parsing to OpenlabReader. Closes …
(edit) @7374   9 years melissa Fixed series count population assertBlock's Y offset calculation.
(edit) @7373   9 years melissa Sanitize XML before parsing and prevent XML parsing failures from causing …
(edit) @7372   9 years callan Include series in any failures. (See  omero:#3627)
(edit) @7371   9 years callan Extended OMERO openBytes() test case (See  omero:#3627) * Go through every …
(edit) @7370   9 years melissa Some polishing in ScreenReader. Wells are now sorted correctly and SPW …
(edit) @7357   9 years melissa Make sure references are resolved before resetting an OMEXMLMetadata's …
(edit) @7356   9 years melissa Smarter pixel offset detection for Visitech XYS files.
(edit) @7355   9 years melissa Fixed a handful of problems with reading Amira sub-images.
(edit) @7354   9 years melissa Removed erroneous call to skipBytes, so that sub-images of uncompressed …
(edit) @7353   9 years melissa * Allow the same plane to be read multiple times in succession. * Fixed …
(edit) @7352   9 years melissa Restored getFirst(), getLast(), and getStep() as deprecated methods.
(edit) @7351   9 years melissa Fixed AVI reader to allow a compressed plane to be accessed multiple times …
(edit) @7350   9 years melissa * Reader wrapper implementations that manipulate byte arrays now declare …
(edit) @7349   9 years melissa Added method to AWTImageTools for retrieving subimages. Readers now use …
(edit) @7339   9 years melissa Fixed row reversal to work correctly with sub-images.
(edit) @7338   9 years melissa Updated FEI reader to properly support sub-image reading.
(edit) @7337   9 years melissa Fixed plane size and pixel offset calculations when opening a sub-image.
(edit) @7336   9 years melissa Fixed MD5 calculations for planes whose SizeY is odd.
(edit) @7334   9 years melissa Updated what's new for today's release.
(edit) @7333   9 years melissa Initial version of generic screen reader. It still needs a lot of work, …
(edit) @7319   9 years melissa Added Ant target to run OMERO openBytes tests. To use it: 'ant …
(edit) @7318   9 years melissa ImageTools.splitChannels now takes an extra int parameter that specifies …
(edit) @7317   9 years melissa Make image names more easily identifiable in the original metadata.
(edit) @7316   9 years melissa Return a blank plane if a TIFF file is missing, just like we do with many …
(edit) @7315   9 years callan Script to run OMERO openBytes() tests on a suite of files on Hudson.
(edit) @7314   9 years callan Fix a missing variable initialization in the OMERO openBytes() test case.
(edit) @7313   9 years callan Test.java (from  omero:#3627) port to a full blown TestNG test case also …
(edit) @7312   9 years callan Adding required ome-xml project to the test-suite component Eclipse …
(edit) @7311   9 years melissa A couple of fixes for reading a sub-image of the second channel in 2 …
(edit) @7310   9 years hinerm Added code allowing jar paths and trailing slashes (or absence thereof) on …
(edit) @7309   9 years callan Fix min/max calculation in the "slush" area outside the actual pixel count …
(edit) @7287   9 years melissa Parse some more (undocumented) metadata from STK files, including channel …
(edit) @7286   9 years curtis Fix problem with skipping past EOF.
(edit) @7285   9 years curtis Add compression type to original metadata table.
(edit) @7284   9 years callan Fixed minMaxDone population. Much more thorough test case that includes …
(edit) @7283   9 years callan Solution for minima and maxima calculation when using block based …
(edit) @7282   9 years callan Fix documentation locations and header comment in XML annotation test.
(edit) @7281   9 years hinerm Corrected a missing end brace in the BFITK plug-in code.
(edit) @7280   9 years melissa Close readers left open by the openImage/openSubImage macro functions.
(edit) @7278   9 years melissa Fixed one more typo.
(edit) @7277   9 years curtis Fix typo.
(edit) @7276   9 years curtis Clarify Autoscale help text. These changes are based on updated text …
(edit) @7275   9 years melissa Updated metadata support documentation.
(edit) @7274   9 years melissa Updated version numbers to 4.3-DEV.
Note: See TracRevisionLog for help on using the revision log.