source: trunk @ 7581

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Diff Rev Age Author Log Message
(edit) @7581   9 years melissa Prevent extra Plane(Timing).ExposureTime attributes from being populated.
(edit) @7580   9 years melissa The JPEG-2000 writer can now use lossy or lossless compression. Closes …
(edit) @7579   9 years melissa Prevent potential AIOOB.
(edit) @7571   9 years melissa Populate all of the wells, even if no image data is associated with them.
(edit) @7570   9 years melissa Sanitize the XML before we parse it.
(edit) @7568   9 years melissa Initial version of Metamorph TIFF HCS support.
(edit) @7564   9 years hinerm Added a "dist" target to the bf-cpp project. Functionally identical to …
(edit) @7562   9 years hinerm Modified the dist target for BF-ITK to no longer copy unnecessary files on …
(edit) @7561   9 years melissa Tweaked MetamorphReader's isThisType to prevent it from picking up files …
(edit) @7560   9 years melissa Tweaked well name detection so that column indexes can only contain at …
(edit) @7559   9 years melissa Clarified CLASSPATH requirements.
(edit) @7558   9 years melissa Added some documentation on file export/conversion.
(edit) @7557   9 years hinerm Forward port from branch 4.2 changes - mistakenly committed to a branch …
(edit) @7554   9 years curtis Add variable for controlling number of channels.
(edit) @7553   9 years melissa Prevent an NPE when attempting to stitch datasets that aren't stitchable. …
(edit) @7552   9 years melissa Group together separate blocks of pixels that belong to the same stack. …
(edit) @7551   9 years melissa Fixed various metadata population problems when working with multi-file …
(edit) @7544   9 years melissa Fixed channel name and wavelength population. See  omero:#3865.
(edit) @7543   9 years melissa One more adjustment to SizeX/SizeY calculations. See #643.
(edit) @7541   9 years melissa Parse valid bits per pixel from Slidebook files. Closes #626.
(edit) @7538   9 years melissa Set 'falseColor' to true, so that lookup tables are not improperly …
(edit) @7535   9 years melissa Fixed plane index in status bar. Closes #637.
(edit) @7528   9 years melissa Corrected pixel type for 32-bit images, as Andor/Fluoview assumes that all …
(edit) @7522   9 years melissa Make primitive type static variables volatile.
(edit) @7514   9 years melissa Fixed indexed flag and LUT parsing. Closes #633.
(edit) @7513   9 years hinerm Enhanced ant dist script to copy BioFormatsIO.dll to the dist directory.
(edit) @7508   9 years melissa Fixed NPE.
(edit) @7502   9 years melissa Don't overwrite existing image names.
(edit) @7500   9 years melissa Search more thoroughly for image descriptions. Image descriptions are no …
(edit) @7496   9 years curtis Fix signedness averaging problem with convertTo8Bit method.
(edit) @7494   9 years curtis Fix problem where custom LUTs override grayscale mode. This happened …
(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 …
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