MIPAV change list

• 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.

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.

• 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.

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.

MIPAV change list 5.x.x

MIPAV change list 4.x.x

MIPAV change list 3.x.x

MIPAV change list 2.x

MIPAV change list 1.xx

MIPAV change list pre-1.0