Difference between revisions of "MIPAV change list"

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== Version 5.x.x change list ==
+
== Version 7.x.x change list ==
 
+
=== 5.3.1 (5/12/2011) ===
+
 
+
* VOIs and paint
+
** Improved the memory usage of VOIs.
+
 
+
* Image views and visualization
+
** Modified multi-histogram blending in the GPU volume renderer.
+
** Added keyboard shortcut ('s') to save the GPU volume renderer view to a .jpg file.
+
 
+
* Miscellaneous
+
** Fixed a an issue with the Image overlay preferences.
+
** Fixed a case-sensitivity issue when (re-)installing plugins on some OSes.
+
** Improved error handling during plugin installation.
+
 
+
** Added the ability to start up ImageJ from MIPAV and transfer images between the two programs.
+
** Added the ability to open ImageJ plugins from MIPAV.
+
** Added the ability to compile and run plugins for MIPAV and ImageJ from within MIPAV.
+
  
=== 5.3.0 (5/9/2011) ===
+
=== 7.0.1 (4/5/2013) ===
  
 
* File handling
 
* File handling
** DICOM: Fixed an issue reading in DICOM images.
+
** DICOM: When trying to open an image with a Transfer Syntax UID that indicates that it is a compressed DICOM, but with an image tag length that implies that it is not compressed, try reading it in without decompression.
** XML: Added Unsigned Integer type to Image XML schema.
+
** DICOM: Fixed a problem in the DICOMDIR browser that prevented it from opening.
** AVI: Removed MSVC, CVID and MJPEG codec support.
+
** Fixed a problem in the Open sequence tool with the use of progress bars that caused crashes for some file formats (this means that there are no progress bars when opening the sequence).
** MATLAB: Improved memory management during zlib decompression.
+
** FITS: Corrected writing of resolutions.
+
** Improved handling of (0028,0030) tags in DICOM and GE Signa 4/5X.
+
** GE Signa 4X: Added write support.
+
** GE Signa 4X: Added anonymization support.
+
** GE Signa 5X: Added write support.
+
** GE Signa 5X: Added anonymization support.
+
** Improved the Open image sequence tool.
+
** MINC2: '''Writing of Minc2 files is currently not supported.  Additionally, some Minc2 files which perform rescaling are not currently read in correctly.'''
+
  
 
* Algorithms and utilities
 
* Algorithms and utilities
** Fixed a bug in the handling of complex data in the FFT algorithm.
+
** Added new utility for correction of non-helical CT gantry tilt correction.
** Added a checkbox to the FFT algorithm to produce an complex inverse image.
+
** Fixed some issues running the Prostate segementation algorithm on some systems.
** Added ability to perform forward FFT on complex images.
+
** The DialogDefaultsInterface has been added back. JDialogBase now implements this interface and provides default versions of the loadDefaults() and saveDefaults() methods.
** The Crop utility now works with complex images.
+
** The Add margins utility now works with complex images.
+
** Added K-means tool.
+
** Improved 3D to 4D conversion utility operation.
+
** Fixed a bug in the Generate grid utility.
+
** Added a new utility to convert 4D images to multiple 3D volumes.
+
** Removed the following algorithms for licensing reasons: XcosmEM, DenoisingBLS_GSM, DQED and Trilateral filter.
+
** Added 4D Image calculator utility.
+
** Fixed an output problem in the Transform algorithm.
+
** Fixed updating of file infos of non-DICOM images with scanner transformation matrices when algorithms or utilities complete.
+
** Added JOCL/OpenCL implementation of the FFT algorithm (only for power-of-two-sized images).
+
** Added utility to concatenate multiple 2D images into a 3D volume.
+
  
 
* VOIs and paint
 
* VOIs and paint
** Made Select all VOIs action scriptable.
+
** The backspace key now behaves the same as delete when working with VOIs to delete points or entire curves (which fixes issues with using an Apple keyboard on Windows).
** Fixed a problem in paint brush display for some image resolutions.
+
** Improved error reporting if a VOI will not load into an image.
+
** Fixed reading of some VOI files.
+
** Fixed the recording of shortcuts for VOIs and the execution of VOI-related shortcuts.
+
** Added the ability to create multiple levelset/livewire VOIs by holding down the Shift key.
+
** Improved handling of very long text in the text annotation VOIs.
+
  
 
* Image views and visualization
 
* Image views and visualization
** Fixed display of complex images if Magnitude is selected as a display option.
+
** Added better handling of when the GPU volume renderer when the videocard doesn't support the required OpenGL or GLSL version.
** Using the arrow keys in the Tri-planar view now moves the crosshairs accordingly.
+
** When opening the renderer, apply the LUT that is already set for the image.
** Added the ability to sync images slice number when doing linked scrolling.
+
** Fixed Tri-planar frame linking.
+
** Made it so that if imageB radio button is selected on the main controls, then when you launch the Histo LUT, the imageB tab is selected.
+
** Fixed the quickLUT operation for 4D images.
+
** Added an option so that user can open images in tiled fashion.
+
  
 
* Miscellaneous
 
* Miscellaneous
** '''MIPAV now ships and uses a new version of JOGL from jogamp (0.9-283).'''  Additionally, we now package JOCL in the MIPAV installer.
+
** Fixed some issues with scripting plugins that have JDialog in their name.
** Fixed ModelStorageBase DataType enum so UINTEGER is the 15th in order.
+
** PlugInAlgorithm plugins now are displayed even when no image is open (but are disabled).
** The Image attributes dialog Apply button now properly saves all changes made on any of its tabs regardless of which one is currently selected.
+
** Fixed some issues in handling command line arguments that start with two dashes instead of one.
** Some minor bug fixes to the slice/time slider appearance.
+
** Added buildSlider() method to GuiBuilder.
** Added ability to run MIPAV in headless-compliant mode using the command line option '-headless'.
+
** Auto-restart of MIPAV after a memory change on Windows is no longer supported.
** Improved parsing of command line arguments.
+
** MIPAV is now started the same way on 32 and 64 bit systems.  Shortcuts to start with or without a debugging window are now installed.
** Added MIPAV version to the main title bar.
+
  
=== 5.2.1 (2/10/2011) ===
+
=== 7.0.0 (3/22/2013) ===
 +
 
 +
Updated the JREs and libraries distributed with MIPAV.  On Windows and Linux, the JRE installed is based on version 1.7.0_17.  The installed native libraries used are the same, except for Jogamp, which is now the Jogamp JOGL/JOCL release from 2012-11-01.
  
 
* File handling
 
* File handling
** Analyze: Improved display of location 112 information.
+
** PARREC: Fixed bug reading orientations and FOV from some files.
** Matlab: Images now only load with log mag display if it is set in the preferences.
+
** PARREC: Fixed reading of 4th dim unit of measure and resolution.
** Vista: Added reading and writing support for the Vista file format.
+
** PARREC: Added patient name reading and included it in file header dialog information.
** Interfile: Fixed a problem reading some truncated files.
+
** PARREC: When reading sagittal files for sliceAngle and offCentre arrays put minus signs in front of sliceAngle[2] and offCentre[2] to reflect change from RL in PARREC to LR in MIPAV.
** PSD: Fixed support for Photoshop PSD files.
+
** Added support for reading AFNI matrix (.1D file) to TransMatrix.
** Improved handling of the absence of the HDF5 libraries when trying to detect an unknown file.
+
** Allowed ViewImageFileFilter to be extended, added .1d file format to list, made accept() method insensitive to capitalization differences.
 +
** ViewImageFileFilter now explicitly implements java.io.FileFilter to improve performance.
 +
** DICOM: Fixed the reading of some chunked DICOM encapsulated lossless JPEG files.
 +
** DICOM: Added a dictionary of private tags, which supplies them with names in the view header dialog.
 +
** DICOM: Fixed error reading some images that included an icon image in a sequence tag.
 +
** DICOM: Changed tag reading to assume that finding 0028,0008 - Number of Frames means that the DICOM is multi-frame.  Before, a 0002,0002 - Media Storage SOP Class UID that indicated enhanced MR, CT or XA was required.  This caused a problem for a multi-frame OCT dataset from JHU.
 +
** DICOM: Changed error message when the slice data extents are 0.  Indicate that there was a problem in reading extents/image data, not that we think it's a spectroscopy dataset.
 +
** Added TrackVis file support.
 +
** AFNI: Added afni implementation of subBrick names and statistical distributions.
 +
** Implemented ability to programmatically read in just the header of most images, those images where this is not possible print out that information to the Preferences.debug output and return null.
  
 
* Algorithms and utilities
 
* Algorithms and utilities
** Added more customization options to Talairach transform utility.
+
** Added Multi-exponential to Time fitting Systems analysis tool.
** In the transform algorithm, fixed the setting of (0020, 0032) tag when the transform alters the number of slices in a 3D volume.
+
** The Time fitting tool can now use a custom DICOM tag for the time values.
 +
** In the utility Match images, fixed a bug in the handling of when the images' units of measure are unknown or do not match.
 +
** Added Spectral clustering tool to Systems analysis.
 +
** K-means algorithm no longer trys to read text points file twice.
 +
** Added Spatial color compactness algorithm to Segmentation menu.
 +
** Added OpenCL-based image Deconvolution algorithm.
 +
** Fixed OAR3D transformation directory saving logic.
 +
** Subset image now transfers LUT to result image.
 +
** In Transformation algorithm, fixed readTransformMatrixFile() to work with 4D images.
 +
** Fixed a number of issues in scripting with filters that now support opencl processing.  Some algorithms didn't properly set up the params or use them when trying to run the algorithm.  GaussianBlur didn't record at all when run using opencl.
 +
** Fixed the Median algorithm progress bar.
  
 
* VOIs and paint
 
* VOIs and paint
** Corrected a number of area/volume/conversion measurements.
+
** Fixed a bug handling VOI stats on 2d images.
** Added the ability to show/hide a VOI's bounding box from the right click menu.
+
** Fixed a bug displaying VOI statistics results table for color images.
** Fixed a bug in saving VOI state.
+
** Fixed a bug in the livewire VOI tool.
+
** Improved memory management when performing multiple VOI undo/redo actions.
+
  
 
* Image views and visualization
 
* Image views and visualization
** Improved the display of complex image data values.
+
** Major updates to the GPU volume renderer.  Changed supported version of OpenGL to 3 core profile and GLSL to shading language 330.  These changes should fix the GPU renderer on MacOS 10.7 and above.
 +
** Fixed mouse wheel scrolling in the GPU renderer on Macs.
 +
** Removed a number of old, unused GLSL shaders.
 +
** Updated the WildMagic library: Changed Vector2f, Vector3f, Vector4f, Vector2d, Vector3d, Vector4d, Matrix2f, Matrix3f, Matrix3d, Matrix4f so that most functions return 'this', enabling chaining of multiple vector or matrix operations. The original functions were deprecated and the new functions now begin with a lower-case letter. All classes using Vector3f and Matrix3f were also updated to use the non-deprecated functions.
 +
** GPU renderer now supports displaying a grayscale image and a color image at the same time.
 +
** Fixed some issues with loading and changing the inital display/lut method.  Removed 'Default' option, but left in support for that value when reading in legacy files.
 +
** Fixed auto-loading of saved win/level (first and last point of transfer function were being set up incorrectly).
 +
** TransferFunction methods to remove points now return the removed points.
 +
** Added t-score LUT option that mimics AFNI.
 +
** Fixed a minor bug in the Zoom dialog.
  
 
* Miscellaneous
 
* Miscellaneous
** Added a number of enumerations for units of measure. The unit of measure static ints are deprecated, but will not be removed for the foreseeable future.
+
** Fixed the Report bug button.
** Fixed a problem with the slice slider display under some circumstances.
+
** Added button to the MIPAV options dialog to reset all values to defaults.
 +
** Fixed a number of installer-related issues on multiple platforms.
 +
** Added ability to change the Java look and feel in the MIPAV options.
 +
** Added preference for using DICOM ordering when opening AFNI files in the MIPAV options dialog.
 +
** Added preference for automatically using LUTs stored in images in the MIPAV options dialog.
 +
** In TransMatrixd, changed routine name from transformAsPoint3Df to transformAsPoint3Dd.
 +
** Fixed minor bugs in ModelImage methods: set(int[], Number), set(int[], boolean), set(int[], byte), set(int[], short), set(int[], int), set(int[], long), set(int[], float), and set(int[], double).
 +
** Changed a number of methods and fields in file- and view-related classes to protected.
 +
** Improved display of toolbar buttons on Macs.
  
=== 5.2.0 (1/21/2011) ===
 
  
* File handling
+
== Version 6.x.x change list ==
** 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
+
=== 6.0.1 (11/14/2012) ===
** 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
+
* File handling
** Fixed some issues with choosing custom VOI colors.
+
** Changed start location in FileRawChunk.readImage to long instead of int to support reading some large files. This affected a number of different file format readers.
** 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
 
* Image views and visualization
** The GPU volume renderer no longer requires images to be resized to a power to two in each dimension.
+
** Updated the multi-histogram display. Fixed the display panel gradient mag. graph. Added a 'window' option for the triangle widget by moving the green control point up/down. Fixed reload error when the renderer is closed and then opened again. Fixed save / load file bug for triangle widget.
** 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 a new default lookup table/transfer function option that mimics the behavior of ImageJ.
** 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) ===
+
=== 6.0.0 (11/7/2012) ===
  
* Algorithms and utilities
+
'''MIPAV is now open source!'''  See the [http://mipav.cit.nih.gov/license/license.html license information] for details.
** 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
 
* File handling
** PARREC: Improved reader support of some axis orientations.
+
** Added basic support for dragging-and-dropping directories, single files and multifile images into MIPAV.
** DICOM: Fixed DICOMDIR preview and opening of images.
+
** DICOM: Fixed reading of some files with private tags that resemble the image tag pattern.
** DICOM: Fixed a problem writing the q and s matrices of NIFTI images out to DICOM format.
+
** DICOM: Fixed an issue reading some enhanced DICOM tag sequences.
** DICOM: Added a better error message when trying to open an unsupported DICOM spectroscopy file.
+
** DICOM: Added support for writing enhanced MR, CT and XA.
** NIFTI: Fixed reading of some files with Nifti extensions stored with gz/zip/bz2 compression.
+
** DICOM: Fixed an issue reading tags in some boolean images.
** NIFTI: Corrected some Y-axis origin and matrix issues when reading NIFTI images that need to be flipped.
+
** DICOM: Fixed handling of a number of tags in the 0018 group when reading and writing images.
** NIFTI: Improved orientation support when writing to NIFTI from DICOM.
+
** DICOM: In writeMultiFrameImage in "0028,0010" bitsPerPixel = 16 rather than source image bitsPerPixel value so that it always reflects the short data in the written file.
** 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.
+
** DICOM: Fixed display of min and max values for color images in the file header dialog.
** ANALYZE: Improved memory usage when reading and writing binary files.
+
** DICOM: Fixed an issue reading image data when no pixel padding was specified.
** Added a better error message when trying to load an XML Image header as a VOI and vice versa.
+
** DICOM: Added support for writing multiframe ushort, ARGB and ARGB_ushort data types.
** Fixed an error when creating a blank image.
+
** DICOM: Added support for writing ARGB_ushort data types.
 +
** TIFF: Added support for reading in ImageJ ROIs stored in TIFF header.
 +
** TIFF: 4D TIFF data is written out as a set of 3D files now.
 +
** RAW: Fixed issue writing out 4D volume as 3D files.
 +
** RAW: Fixed issue reading boolean image.
 +
** ANALYZE: Fixed an issue reading some boolean images.
 +
** PARREC: Fixed resolution calculation for some images.
 +
** PARREC: Fixed processing of angulation midslice in parrec images.
 +
** PARREC: Added slice/offcenter loading for any orientation.
 +
** PARREC: Added support for reading/writing 4D data as multifile.
 +
** Added new Spar file format support.
 +
** MINC2: Fixed progress bar issue and added better support for saving image subsets (either 3D or 4D).
 +
** MINC2: Improved support for reading 3D and 4D images with some orientation/image data settings.
 +
** MINC: Added support for writing 2D and 4D images.
 +
** MINC: Added support for multifile datasets.
 +
** INTERFILE: Added multifile support.
 +
** Fixed getting image unit from abbreviation.
 +
** NIFTI: For Preferences.PREF_FLIP_NIFTI_READ the default preferences has been changed form true to false.
  
 
* Algorithms and utilities
 
* Algorithms and utilities
** OAR algorithms now can be performed with a non-orthogonal Powell's method (by default orthogonal line minimization is used).
+
** Added a new system for saving/loading algorithm and utility defaults automatically to JDialogBase.  The old interface was renamed to LegacyDialogDefaultsInterface and was deprecated.  As part of this, dialogs that want to have this behavior should call super.actionPerformed(event) when the event is not handled in the subclass actionPerformed().  The new system also adds the ability to save/load parameters to different profiles.
** The Fuzzy C-Means algorithm now produces a NIFTI result image when run on a NIFTI source image.
+
** Added Locally linear embedding algorithm.
** Fixed the updating of NIFTI matrices in the Flip utility.
+
** In DTI importer, corrected anatomy fat shift options.
** Fixed the updating of NIFTI matrices in the Reorient utility.
+
** OAR algorithms now save interpolation, resolutions, dims, transformVOIs, clip and pad in matrix file.
** Fixed progress bar for Anisotropic diffusion algorithm.
+
** Transformation algorithm now reads the additional matrix file parameters if they are found.
** Added Mosaic to 3D volume utility.
+
** Switched many registration and transformation algorithms to use doubles instead of floats.
** Fixed a bug in the Crop using VOI utility.
+
** Sped up the nearest neighbor operations in the Transformation algorithm.
 +
** Added new Time fitting algorithm to the Systems analysis menu.
 +
** Removed the Skeletonize3D algorithm.
  
 
* VOIs and paint
 
* VOIs and paint
** '''Added many more VOI bug fixes and improvements related to the new VOI subsystem.'''
+
** Fixed handling of VOI bounding box checkbox in VOI properties dialog.
** Added a preferences file settings for changing the paint opacity.
+
** Fixed some issues grouping VOI contours.
** Added 2x2 brush to the set of default paint brushes.
+
** Added Ctrl key angle modification for line VOIs.
 +
** Allowed line, protractor, and point vois to save in voxel coordinates.
 +
** Now able to do image statistics without having a VOI present from the VOI properties dialog.
 +
** Fixed an issue converting between VOI and mask and back again.
  
 
* Image views and visualization
 
* Image views and visualization
** Fixed image overlay display bug.
+
** Added Bicubic image interpolation mode to image display.
** Added ability to jump to specific coordinates in the Tri-planar view.
+
** Made a number of improvements to the Custom zoom dialog.
** Added tab to the Tri-planar view for Scanner RAS coordinates.
+
** Fixed J3D surface volume calculation.
** Added the ability to pan around the image when the scrollbars are visible via dragging the image while holding the Shift key.
+
** Fixed bug in the slices panel for the GPU renderer.
 +
** Fixed a number of VOI issues in the GPU renderer and in surface extraction.
 +
** Created new method for image display, default transfer function now has a min/max set at the 5/95 percentiles of an image.
 +
** Added new option to the MIPAV options dialog that allows for selection of how the initial LUT for an image should be constructed.
 +
** Made a number of fixes and additions (including a triangle widget and widget save/load) to the GPU renderer multi histogram tool.
  
 
* Miscellaneous
 
* Miscellaneous
** Removed missing preferences file warning dialog when running MIPAV from JWS.
+
** Added a new integrated bug reporting button (only works from within NIH - fixed in a future version).
** Added "Close all images" item to the File menu.
+
** Added the ability to drag menus out of the main MIPAV menu to separate windows.
** 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).
+
** In TransMatrix, a new version of saveMatrix can store other transform variables in addition to the TransMatrix.  A new version of readMatrix can read these variables. The variables are interp, oXres, oYres, oZres, oXdim, oYdim, oZdim, tVOI, clip, and pad.
** Added a better error message when trying to run non-generic plugins from the command line.
+
** Removed mipav help jar and the MipavUtil.showHelp() method that used it.  MipavUtil.showWebHelp() should now be used to show wiki-based help pages instead of the jar-based help.
  
=== 5.0.0 (07/09/2010) ===
+
== Version 5.x.x change list ==
  
* '''MIPAV now requires Java 1.6 or higher to run.'''
+
[[MIPAV change list 5.x.x]]
  
* 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).
 
  
 
== Version 4.x.x change list ==
 
== Version 4.x.x change list ==

Latest revision as of 16:08, 8 April 2013

Version 7.x.x change list

7.0.1 (4/5/2013)

  • File handling
    • DICOM: When trying to open an image with a Transfer Syntax UID that indicates that it is a compressed DICOM, but with an image tag length that implies that it is not compressed, try reading it in without decompression.
    • DICOM: Fixed a problem in the DICOMDIR browser that prevented it from opening.
    • Fixed a problem in the Open sequence tool with the use of progress bars that caused crashes for some file formats (this means that there are no progress bars when opening the sequence).
  • Algorithms and utilities
    • Added new utility for correction of non-helical CT gantry tilt correction.
    • Fixed some issues running the Prostate segementation algorithm on some systems.
    • The DialogDefaultsInterface has been added back. JDialogBase now implements this interface and provides default versions of the loadDefaults() and saveDefaults() methods.
  • VOIs and paint
    • The backspace key now behaves the same as delete when working with VOIs to delete points or entire curves (which fixes issues with using an Apple keyboard on Windows).
  • Image views and visualization
    • Added better handling of when the GPU volume renderer when the videocard doesn't support the required OpenGL or GLSL version.
    • When opening the renderer, apply the LUT that is already set for the image.
  • Miscellaneous
    • Fixed some issues with scripting plugins that have JDialog in their name.
    • PlugInAlgorithm plugins now are displayed even when no image is open (but are disabled).
    • Fixed some issues in handling command line arguments that start with two dashes instead of one.
    • Added buildSlider() method to GuiBuilder.
    • Auto-restart of MIPAV after a memory change on Windows is no longer supported.
    • MIPAV is now started the same way on 32 and 64 bit systems. Shortcuts to start with or without a debugging window are now installed.

7.0.0 (3/22/2013)

Updated the JREs and libraries distributed with MIPAV. On Windows and Linux, the JRE installed is based on version 1.7.0_17. The installed native libraries used are the same, except for Jogamp, which is now the Jogamp JOGL/JOCL release from 2012-11-01.

  • File handling
    • PARREC: Fixed bug reading orientations and FOV from some files.
    • PARREC: Fixed reading of 4th dim unit of measure and resolution.
    • PARREC: Added patient name reading and included it in file header dialog information.
    • PARREC: When reading sagittal files for sliceAngle and offCentre arrays put minus signs in front of sliceAngle[2] and offCentre[2] to reflect change from RL in PARREC to LR in MIPAV.
    • Added support for reading AFNI matrix (.1D file) to TransMatrix.
    • Allowed ViewImageFileFilter to be extended, added .1d file format to list, made accept() method insensitive to capitalization differences.
    • ViewImageFileFilter now explicitly implements java.io.FileFilter to improve performance.
    • DICOM: Fixed the reading of some chunked DICOM encapsulated lossless JPEG files.
    • DICOM: Added a dictionary of private tags, which supplies them with names in the view header dialog.
    • DICOM: Fixed error reading some images that included an icon image in a sequence tag.
    • DICOM: Changed tag reading to assume that finding 0028,0008 - Number of Frames means that the DICOM is multi-frame. Before, a 0002,0002 - Media Storage SOP Class UID that indicated enhanced MR, CT or XA was required. This caused a problem for a multi-frame OCT dataset from JHU.
    • DICOM: Changed error message when the slice data extents are 0. Indicate that there was a problem in reading extents/image data, not that we think it's a spectroscopy dataset.
    • Added TrackVis file support.
    • AFNI: Added afni implementation of subBrick names and statistical distributions.
    • Implemented ability to programmatically read in just the header of most images, those images where this is not possible print out that information to the Preferences.debug output and return null.
  • Algorithms and utilities
    • Added Multi-exponential to Time fitting Systems analysis tool.
    • The Time fitting tool can now use a custom DICOM tag for the time values.
    • In the utility Match images, fixed a bug in the handling of when the images' units of measure are unknown or do not match.
    • Added Spectral clustering tool to Systems analysis.
    • K-means algorithm no longer trys to read text points file twice.
    • Added Spatial color compactness algorithm to Segmentation menu.
    • Added OpenCL-based image Deconvolution algorithm.
    • Fixed OAR3D transformation directory saving logic.
    • Subset image now transfers LUT to result image.
    • In Transformation algorithm, fixed readTransformMatrixFile() to work with 4D images.
    • Fixed a number of issues in scripting with filters that now support opencl processing. Some algorithms didn't properly set up the params or use them when trying to run the algorithm. GaussianBlur didn't record at all when run using opencl.
    • Fixed the Median algorithm progress bar.
  • VOIs and paint
    • Fixed a bug handling VOI stats on 2d images.
    • Fixed a bug displaying VOI statistics results table for color images.
  • Image views and visualization
    • Major updates to the GPU volume renderer. Changed supported version of OpenGL to 3 core profile and GLSL to shading language 330. These changes should fix the GPU renderer on MacOS 10.7 and above.
    • Fixed mouse wheel scrolling in the GPU renderer on Macs.
    • Removed a number of old, unused GLSL shaders.
    • Updated the WildMagic library: Changed Vector2f, Vector3f, Vector4f, Vector2d, Vector3d, Vector4d, Matrix2f, Matrix3f, Matrix3d, Matrix4f so that most functions return 'this', enabling chaining of multiple vector or matrix operations. The original functions were deprecated and the new functions now begin with a lower-case letter. All classes using Vector3f and Matrix3f were also updated to use the non-deprecated functions.
    • GPU renderer now supports displaying a grayscale image and a color image at the same time.
    • Fixed some issues with loading and changing the inital display/lut method. Removed 'Default' option, but left in support for that value when reading in legacy files.
    • Fixed auto-loading of saved win/level (first and last point of transfer function were being set up incorrectly).
    • TransferFunction methods to remove points now return the removed points.
    • Added t-score LUT option that mimics AFNI.
    • Fixed a minor bug in the Zoom dialog.
  • Miscellaneous
    • Fixed the Report bug button.
    • Added button to the MIPAV options dialog to reset all values to defaults.
    • Fixed a number of installer-related issues on multiple platforms.
    • Added ability to change the Java look and feel in the MIPAV options.
    • Added preference for using DICOM ordering when opening AFNI files in the MIPAV options dialog.
    • Added preference for automatically using LUTs stored in images in the MIPAV options dialog.
    • In TransMatrixd, changed routine name from transformAsPoint3Df to transformAsPoint3Dd.
    • Fixed minor bugs in ModelImage methods: set(int[], Number), set(int[], boolean), set(int[], byte), set(int[], short), set(int[], int), set(int[], long), set(int[], float), and set(int[], double).
    • Changed a number of methods and fields in file- and view-related classes to protected.
    • Improved display of toolbar buttons on Macs.


Version 6.x.x change list

6.0.1 (11/14/2012)

  • File handling
    • Changed start location in FileRawChunk.readImage to long instead of int to support reading some large files. This affected a number of different file format readers.
  • Image views and visualization
    • Updated the multi-histogram display. Fixed the display panel gradient mag. graph. Added a 'window' option for the triangle widget by moving the green control point up/down. Fixed reload error when the renderer is closed and then opened again. Fixed save / load file bug for triangle widget.
    • Added a new default lookup table/transfer function option that mimics the behavior of ImageJ.

6.0.0 (11/7/2012)

MIPAV is now open source! See the license information for details.

  • File handling
    • Added basic support for dragging-and-dropping directories, single files and multifile images into MIPAV.
    • DICOM: Fixed reading of some files with private tags that resemble the image tag pattern.
    • DICOM: Fixed an issue reading some enhanced DICOM tag sequences.
    • DICOM: Added support for writing enhanced MR, CT and XA.
    • DICOM: Fixed an issue reading tags in some boolean images.
    • DICOM: Fixed handling of a number of tags in the 0018 group when reading and writing images.
    • DICOM: In writeMultiFrameImage in "0028,0010" bitsPerPixel = 16 rather than source image bitsPerPixel value so that it always reflects the short data in the written file.
    • DICOM: Fixed display of min and max values for color images in the file header dialog.
    • DICOM: Fixed an issue reading image data when no pixel padding was specified.
    • DICOM: Added support for writing multiframe ushort, ARGB and ARGB_ushort data types.
    • DICOM: Added support for writing ARGB_ushort data types.
    • TIFF: Added support for reading in ImageJ ROIs stored in TIFF header.
    • TIFF: 4D TIFF data is written out as a set of 3D files now.
    • RAW: Fixed issue writing out 4D volume as 3D files.
    • RAW: Fixed issue reading boolean image.
    • ANALYZE: Fixed an issue reading some boolean images.
    • PARREC: Fixed resolution calculation for some images.
    • PARREC: Fixed processing of angulation midslice in parrec images.
    • PARREC: Added slice/offcenter loading for any orientation.
    • PARREC: Added support for reading/writing 4D data as multifile.
    • Added new Spar file format support.
    • MINC2: Fixed progress bar issue and added better support for saving image subsets (either 3D or 4D).
    • MINC2: Improved support for reading 3D and 4D images with some orientation/image data settings.
    • MINC: Added support for writing 2D and 4D images.
    • MINC: Added support for multifile datasets.
    • INTERFILE: Added multifile support.
    • Fixed getting image unit from abbreviation.
    • NIFTI: For Preferences.PREF_FLIP_NIFTI_READ the default preferences has been changed form true to false.
  • Algorithms and utilities
    • Added a new system for saving/loading algorithm and utility defaults automatically to JDialogBase. The old interface was renamed to LegacyDialogDefaultsInterface and was deprecated. As part of this, dialogs that want to have this behavior should call super.actionPerformed(event) when the event is not handled in the subclass actionPerformed(). The new system also adds the ability to save/load parameters to different profiles.
    • Added Locally linear embedding algorithm.
    • In DTI importer, corrected anatomy fat shift options.
    • OAR algorithms now save interpolation, resolutions, dims, transformVOIs, clip and pad in matrix file.
    • Transformation algorithm now reads the additional matrix file parameters if they are found.
    • Switched many registration and transformation algorithms to use doubles instead of floats.
    • Sped up the nearest neighbor operations in the Transformation algorithm.
    • Added new Time fitting algorithm to the Systems analysis menu.
    • Removed the Skeletonize3D algorithm.
  • VOIs and paint
    • Fixed handling of VOI bounding box checkbox in VOI properties dialog.
    • Fixed some issues grouping VOI contours.
    • Added Ctrl key angle modification for line VOIs.
    • Allowed line, protractor, and point vois to save in voxel coordinates.
    • Now able to do image statistics without having a VOI present from the VOI properties dialog.
    • Fixed an issue converting between VOI and mask and back again.
  • Image views and visualization
    • Added Bicubic image interpolation mode to image display.
    • Made a number of improvements to the Custom zoom dialog.
    • Fixed J3D surface volume calculation.
    • Fixed bug in the slices panel for the GPU renderer.
    • Fixed a number of VOI issues in the GPU renderer and in surface extraction.
    • Created new method for image display, default transfer function now has a min/max set at the 5/95 percentiles of an image.
    • Added new option to the MIPAV options dialog that allows for selection of how the initial LUT for an image should be constructed.
    • Made a number of fixes and additions (including a triangle widget and widget save/load) to the GPU renderer multi histogram tool.
  • Miscellaneous
    • Added a new integrated bug reporting button (only works from within NIH - fixed in a future version).
    • Added the ability to drag menus out of the main MIPAV menu to separate windows.
    • In TransMatrix, a new version of saveMatrix can store other transform variables in addition to the TransMatrix. A new version of readMatrix can read these variables. The variables are interp, oXres, oYres, oZres, oXdim, oYdim, oZdim, tVOI, clip, and pad.
    • Removed mipav help jar and the MipavUtil.showHelp() method that used it. MipavUtil.showWebHelp() should now be used to show wiki-based help pages instead of the jar-based help.

Version 5.x.x change list

MIPAV change list 5.x.x


Version 4.x.x change list

MIPAV change list 4.x.x


Version 3.x.x change list

MIPAV change list 3.x.x


Version 2.x change list

MIPAV change list 2.x


Version 1.xx change list

MIPAV change list 1.xx


Pre-1.0 change list

MIPAV change list pre-1.0