MIPAV change list

Version 5.x.x change list

5.2.0 (1/21/2011)

File handling
- DICOM: Added support for Siemens mosaic image private tags.
- DICOM: Fixed a bug in the reading of some 4D enhanced DICOM files.
- JPEG/GIF/other: Added support for writing out a number of non-medical image formats when the image is not contained within an image frame.
- MATLAB: Added support for Matlab .mat files.
- Analyze: Fixed image file checking routine issue.
- Minc: 64-bit Mac versions of the jHDF libraries are not currently available. Fixed the handling of not finding the libraries when trying to determine the type of a given file.
- Bruker: Fixed some problems in the selection of data files and added support for more fields.
- LIFF: Removed support for LZO compressed LIFF files.
- Removed DCCIE conversion code.

Algorithms and utilities
- Fixed memory leak in Insert slice utility.
- Restructured a number of base mathematical classes to use different b-spline, optimization and integration routines.
- Added extended precision versions of a number of mathematical classes.
- Improved performance of VOI landmark registration with new VOI system.
- The RGB to gray utility now properly updates the (0028,0002) and (0028,0004) DICOM tags to match the image data, if run on a DICOM image.
- Added Complex concatenation utility.
- Added Complex to real conversion utility.
- Added more options to Maximum intensity projection algorithm.
- The Flip and Reorient utilities now correctly update the matrix and origin of DICOM and NIFTI files.
- Fixed two errors in level eight of OAR 3.5D registration. OAR 3.5D should be used instead of the now-removed TSOAR.
- Linked in a working version of the Diffusion levelset ITK method. Also, added geodesic active contour and threshold level set filters.
- Made ITK levelset filter algorithms scriptable and compatible with JIST.
- Fixed a bug in handling some Afni files using the ACPC dialog.
- Fixed a problem handling VOIs confined to one slice in the Watershed algorithm.

VOIs and paint
- Fixed some issues with choosing custom VOI colors.
- Fixed VOI colors when using the Preset hue and New VOI buttons.
- Fixed VOI colors when using Load all VOIs from...
- Fixed a problem when generating VOI stats with no VOI selected.
- Fixed an issue handling unaffected curves during VOI splitting.
- Improved the bounding-box scaling of VOI contours.
- Added optional <Comment> field to text annotation files (.lbl).
- Added a tool to "manually" evolve 2D VOI boundaries. The user can specify the amount to shrink/grow a contour in image units (i.e., mm).
- Added the ability to convert point VOIs to mask images, in addition to the other VOI types.
- The VOI statistics generator has been modified to make it extensible by plugins.
- Fixed issues with the VOI statistics generator in some situations.
- Added the ability to exclude some intensity ranges from VOI statistics calculation.
- Added VOI logical operations utility (replaces 'Allow VOI holes' option).
- Fixed a problem with the VOI livewire's determining when to finish VOI construction.
- Fixed VOI contour point deletion while holding down the shift key.
- Added ability to create circles using the VOI ellipse tool while holding down the CTRL key. The circle diameter can also be directly edited by the user by right clicking.
- Added ability to create squares using the VOI rectangle tool while holding down the CTRL key. The square length can also be directly edited by the user by right clicking.

Image views and visualization
- The GPU volume renderer no longer requires images to be resized to a power to two in each dimension.
- The GPU volume renderer now calculates the gradient magnitude and laplace images on-demand (on checking the grad mag check box or the multi-histogram check box).
- Added the ability to link scrolling of images of unequal dimensions.
- Added a + bi and re^itheta displays for complex data when dragging in the image.
- The surface colors in the volume renderers should now exactly match the colors used for VOIs (based on the striped LUT).
- Fixed bugs in DTI visualization framework. Systems analysis - DTI now works as expected.

5.1.1 (9/20/2010)

Algorithms and utilities
- OAR 3D now defaults to parallel operation, unless the non-orthogonal option is enabled.
- Increased the parallelization of the OAR 3D algorithm.

VOIs and paint
- Continued to make bug fixes and improvements to the VOI components (most importantly, fixed point dragging and statistics generation bugs).
- Added optional <comment> tag to the voi and voi_coord XML structures.

5.1.0 (9/15/2010)

File handling
- PARREC: Improved reader support of some axis orientations.
- DICOM: Fixed DICOMDIR preview and opening of images.
- DICOM: Fixed a problem writing the q and s matrices of NIFTI images out to DICOM format.
- DICOM: Added a better error message when trying to open an unsupported DICOM spectroscopy file.
- NIFTI: Fixed reading of some files with Nifti extensions stored with gz/zip/bz2 compression.
- NIFTI: Corrected some Y-axis origin and matrix issues when reading NIFTI images that need to be flipped.
- NIFTI: Improved orientation support when writing to NIFTI from DICOM.
- NIFTI: Added improved NIFTI header extension support. There is now no limit on the number of extensions. Added ecodes for MIND, AFNI, ascii, and Caret extensions. Improved display of extensions in header dialog.
- ANALYZE: Improved memory usage when reading and writing binary files.
- Added a better error message when trying to load an XML Image header as a VOI and vice versa.
- Fixed an error when creating a blank image.

Algorithms and utilities
- OAR algorithms now can be performed with a non-orthogonal Powell's method (by default orthogonal line minimization is used).
- The Fuzzy C-Means algorithm now produces a NIFTI result image when run on a NIFTI source image.
- Fixed the updating of NIFTI matrices in the Flip utility.
- Fixed the updating of NIFTI matrices in the Reorient utility.
- Fixed progress bar for Anisotropic diffusion algorithm.
- Added Mosaic to 3D volume utility.
- Fixed a bug in the Crop using VOI utility.

VOIs and paint
- Added many more VOI bug fixes and improvements related to the new VOI subsystem.
- Added a preferences file settings for changing the paint opacity.
- Added 2x2 brush to the set of default paint brushes.

Image views and visualization
- Fixed image overlay display bug.
- Added ability to jump to specific coordinates in the Tri-planar view.
- Added tab to the Tri-planar view for Scanner RAS coordinates.
- Added the ability to pan around the image when the scrollbars are visible via dragging the image while holding the Shift key.

Miscellaneous
- Removed missing preferences file warning dialog when running MIPAV from JWS.
- Added "Close all images" item to the File menu.
- Added -pluginDir command line argument to allow the user to specify a place in addition to $HOME/mipav/plugins/ that should be searched for plugins to be included in the Plugin menu (this location should also be included in the Java Classpath).
- Added a better error message when trying to run non-generic plugins from the command line.

5.0.0 (07/09/2010)

MIPAV now requires Java 1.6 or higher to run.

File handling
- NRRD: Fixed bug writing the header for 4D images.
- DICOM: Fixed file pointer boundary condition check for some DICOM files.
- DICOM: Improved read/write compatibility for some DICOM files.
- DICOM: Fixed handling of DICOM dictionary entries with wildcard element numbers (related to DICOM overlays and curves).
- DICOM: Fixed an issue opening images as multifile when the file names were just numbers without a file extension or non-numeric prefix.
- DICOM: Fixed problem saving orientation matrix for some 4D files.
- DICOM: Improved updating of (0020,0032) and image origin when writing to disk.
- DICOM: Fixed a problem converting points to/from scanner space.
- DICOM: Fixed file separator character and character alignment bug in DICOM DIR utility.
- NIFTI: Eliminated extra disk write when saving nii.gz/zip/bz2 files.
- NIFTI: Fixed writing of nii.gz/zip/bz2 files via a script.
- NIFTI: If writing a DICOM image as NIFTI, the tag (0020,0037) is used to fill the rotation matrix if none was specifically set by the user.
- NIFTI: Fixed qmat and smat replacement from the Image attributes dialog.
- NIFTI: Added very basic support for reading header extensions.
- MINC: Eliminated extra disk write when saving mnc.gz/zip/bz2 files.
- MINC: Fixed some issues converting DICOM tags stored in Minc2 files when writing out to DICOM (private and sequence tags stored in the Minc2 as byte arrays are still discarded and big endian encoding is assumed).
- MINC: Added support for 4D Minc2 images.
- MINC: Fixed reading/writing of Minc2 files with data scaling.
- PARREC: Added read support for volumes where the 4D dataset is sorted by volume, instead of by slice.
- Fixed writing of unsigned integer data in a number of formats.
- Fixed boolean support for a number of file formats.
- Improved performance of a number of image data reader methods, which has sped up compressed file reading considerably.
- Removed the option to save a MIPAV XML header when writing out Analyze files.
- Fixed some instances where FileUtility methods were not properly trimming white space from file names and paths.

Algorithms and utilities
- Despot algorithms renamed to Tre, with improved 4D processing, parallelism, scripting and JIST support.
- Improvements to SM2 algorithm.
- Improvements to Thin plate spline registration.
- Improvements to Constrained non-linear fitting algorithm.
- Image calculator modified to allow n-1 dimensional images to be selected for the multiplication operation only. Also, fixed spacing of image names and radio buttons.
- Correlation ratio now selected as default OAR/BSpline registration cost function for all grayscale images.
- Removed a number of algorithms and utilities from the source tree that were no longer being used.
- Fixed a problem in Talairach transform where the origin was not being updated properly and axis orientations when going from acpc to orig or tlrc to orig were not correct.
- Added JIST support to most algorithms and utilities. Some of the more complex algorithms are not supported, yet.
- The Convert type utility now has the option to retain the same file info header as the original image for some file formats.
- Fixed a bug in the Swap dims utility when exchanging dims 1 and 4.
- The Add margins utility and Transform algorithm now properly update the DICOM extent tags (0028,0010) and (0028,0011)
- Added inverse (1/intensity) operation to Image math utility. If intensity is 0, the pixel is set to Float.NaN.

VOIs and paint
- Changed underlying VOI structures to better support 3D. Many VOI-related features are now available from the Triplanar and GPU-based Volume renderer views. A number of VOI methods have been deprecated (or removed, if deprecation was not an option). If you have plugins that use the VOI system, you will want to test to ensure compatibility.
- Added toolbar buttons for 3D VOI intersection and union.
- Saving VOIs no longer causes the DICOM matrix to be saved as well for some images.
- Improved data output along with the VOI boundary intensity graph.
- Writing of .voi files is no longer allowed. They can still be opened to allow for backward compatibility. Users should write out all VOIs in XML format.
- Added coordinate-space element to voi.xsd and text.xsd to better support switching between saving voxel and scanner coordinates.

Image views and visualization
- Fixed image linking in the Triplanar view.
- Improved Triplanar view support for 4D volumes.

Miscellaneous
- Removed the option to show platform dependent file chooser dialogs.
- Refactored slice, time and imageA/B blending sliders to be more consistent.
- Removed SwingWorker version 3 in favor of using the Java 1.6 SwingWorker.
- Fixed quick list problem that sometimes caused the wrong file to be opened.
- Moved MipavMath class to package gov.nih.mipav.util.
- Refactored contents of gov.nih.mipav.util package to remove unused classes and create new ones as needed (ArrayUtil, ThreadUtil).