Difference between revisions of "MIPAV change list"

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(Created page with '== Version 4.x.x change list == === 4.2.1 (03/02/2009) === * File handling ** Added AVI MJPEG decoder improvements. ** Greatly improved memory usage in PAR/REC file reader. ** ...')
 
(6.0.0 (11/7/2012))
 
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== Version 4.x.x change list ==
+
== Version 7.x.x change list ==
  
=== 4.2.1 (03/02/2009) ===
+
=== 7.0.1 (4/5/2013) ===
  
 
* File handling
 
* File handling
** Added AVI MJPEG decoder improvements.
+
** 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.
** Greatly improved memory usage in PAR/REC file reader.
+
** DICOM: Fixed a problem in the DICOMDIR browser that prevented it from opening.
** Fixed a problem setting the image orientation information in the PAR/REC file reader.
+
** 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).
** Improved memory usage in the Tiff file reader.
+
 
** Adjusted the background coloring of tag groups in the DICOM header dialog.
+
** Private DICOM sequences and private tags within public sequences are no longer shown in the DICOM header dialog unless the user decides to show all private tags.
+
** Added the ability to read DICOM files with an invalid rescaling slope of 0.
+
** Removed code which ignored the DICOM tags for rescaling slope and rescaling intercept for MR modality images.
+
** Changed DICOM data rescaling to round the resulting values instead of casting them to short.
+
** Fixed a number of problems reading DICOM tags stored in Minc2 headers.
+
** Fixed reading of Minc2 modality.
+
** Improved the Minc2 file header information written out to a new file by MIPAV.
+
 
* Algorithms and utilities
 
* Algorithms and utilities
** Added Bilateral and Trilateral filters.
+
** Added new utility for correction of non-helical CT gantry tilt correction.
** Fixed saving of dialog parameters in the Gaussian blur algorithm.
+
** Fixed some issues running the Prostate segementation algorithm on some systems.
** Renamed Histogram matching to Histogram image matching.
+
** The DialogDefaultsInterface has been added back. JDialogBase now implements this interface and provides default versions of the loadDefaults() and saveDefaults() methods.
** Added Histogram slice matching.
+
** Added Histogram slice equalization.
+
** Fixed slice indexing problem in Extract slices utility.
+
** Fixed a bug in the Powell's optimization used by OAR that caused the Midsagittal alignment algorithm to produce incorrect results.
+
* VOIs and Paint
+
** Conversion of VOIs to binary, short and ubyte now copies the transformation matrices and origin from the source image to the generated mask image.
+
** Added the option to use XOR behavior when importing VOIs in the Multi-paint dialog.
+
** Improved error handling when trying to load a VOI into an image where it will not fit.
+
* Image views and visualization
+
** Added updated GLSL volume rendering shaders to the GPU-based volume renderer. These are now used instead of the Cg shaders by default, which adds support for many ATI graphics cards. A number of performance improvements in the shader programs have also been implemented.
+
** Added the ability to read and write ASCII GIFTI surface files (no compression or encoding).
+
* Miscellaneous
+
** Bundled new versions of the Java Runtime Environment (1.6.0_12), Java3D (1.5.2), Jogl (1.1.1) and Cg Toolkit (2.1) on those systems whose installers include a bundled JVM. This appears to have fixed a problem encountered by a number of users running the 32-bit Linux installer.
+
** Fixed handling of OutOfMemoryError when an image is magnified too much.
+
** Added buttons to close all image frames or delete all open images to the Image registry dialog.
+
** Updated HDF-java libraries used to read and write Minc2 files to version 2.5.
+
** Added new MIPAV icon for the Mac OS X release of MIPAV.
+
  
=== 4.2.0 (01/16/2009) ===
+
* 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).
  
* Added Java Web Start Nightly and Release versions of MIPAV to our download page. Java 1.5 or higher must be installed on your system. Minc2 support and the Volume renderer tool are not supported at this time. Using JWS will keep you up to date with the latest version of MIPAV automatically.
 
* File handling
 
** Fixed some minor Analyze format issues (one of which was related to handling the image origin).
 
** Fixed a bug automatically determining the format of .img/.hdr files (Analyze, Nifti, SPM).
 
** Some minor FITS format writing fixes.
 
** Multiple improvements to AVI support.
 
** Fixed an AFNI memory usage issue.
 
** Added JPEG2000 (JP2) support.
 
** Added encapsulated JPEG2000 support to DICOM.
 
** Fixed issue saving from Minc to DICOM (rescaling).
 
** Nifti scanner anatomical transforms are now shown as 'NIFTI Scanner Anatomical' in the Image attributes dialog instead of 'Scanner Anatomical'.
 
** Updated the DICOM dictionary used by MIPAV (1234 new entries, 44 corrected).
 
** Dicom browser automatically parses the selected directory when it is opened.
 
** When viewing the header of a DICOM image, tag groupings are now displayed with alternating blue and green backgrounds. Private tags are shown with a red background.
 
** Some DICOM image header display bugs related to unknown VRs and private tag sequences have been fixed.
 
** Added support for autoconversion of Cheshire float images to short when saving as DICOM.
 
** Fixed an issue in the tag autogeneration in the dialog that appears when saving images as DICOM which caused problems in the MIPAV nightly build.
 
** Added support for data rescaling (from short to float) when reading PARREC images.
 
** Switched a number of file formats to use store separate file information objects for each image slice (behavior was inconsistent previously). AFNI, BFLOAT, BioRad, BRUKER, Cheshire, DM3, FITS, ICS, Interfile, MRC, OSM.
 
** The 3 flipped and unflipped orientations are now supported for SPM (instead of just the 3 unflipped orientations).
 
** Corrected the writing origins of non-SPM files to SPM format.
 
** Fixed a few other orientation-related bugs in the Analyze and SPM format handlers.
 
** SPM files can now be opened from either the .hdr or .img files.
 
** When writing a SPM file, if the origin is within a half pixel of the image center for every dimension, the origin is set to (0,0,0) to designate that the image center is intended to be used.
 
** Removed extra 'All files' file filter from the Save dialog.
 
** When reading an Interfile dataset, MIPAV now tries the default name for the data file if the name indicated in the header's data file line is not present.
 
** MIPAV will now automatically open single-file image datasets ending in .bz2 and .gz by uncompressing them to a customizable temporary directory before reading the image files. Since this only works with single-file formats, only MINC1, MINC2 and .nii NIFTI files are currently supported.
 
** Single-file formats (NIFTI .nii, MINC1 and MINC2) can be written out with gzip or bzip2 compression by adding .gz or .bz2 to the file name in the Save as dialog (e.g., example_image.mnc.gz).
 
** The MIPAV XML file format now supports gzip and bzip2 compression of the raw image data. The image.xsd file has been updated accordingly.
 
* Algorithms and utilities
 
** Fixed issue in Gradient magnitude filter.
 
** Fixed some problems with the Constrained OAR 3D algorithm.
 
** Fixed an issue in the OAR 3D algorithm.
 
** Fixed some issues with the cost functions and optimization algorithms used by the different registration algorithms.
 
** Fixed a bug in the regisration algorithms where the origin and matrices of the registered image where not being set to match those of the reference image.
 
** The Histogram summary algorithm now outputs the mean, standard deviation, median and mode to the Output window's Data tab. Also changed the Data tab output to be more like tab delimited text with column headers at the top.
 
** Fixed a bug in the Haralick texture algorithm with some parameters.
 
** The Haralick texture algorithm no longer requires an unsigned byte image to run.
 
** In the Haralick texture algorithm, data is rescaled if necessary to allow any float and double data and to keep grey level co-occurrence matrix size to between 8 x 8 and 64 x 64.
 
** Added support for color images to the Haralick texture algorithm.
 
** Changed the padding value in the Transform algorithm to a float value to better support its use with floating point datasets (also affects the registration and Match images algorithms).
 
** Added a field to the Transform algorithm that allows the user to specify what value should be used to fill areas in the result image that were out of the bounds of the original image (also used in registration algorithm results).
 
** Added dialog to create morphological foreground and background maps.
 
** Fixed the copying of the source image matrix to the result image in the Insert slice utility.
 
* VOIs and Paint
 
** Fixed an issue with notifying windows listening for paint changes when the Paint grow dialog is being used.
 
** Added some measurements to the VOI properties and VOI statistics generator dialogs:
 
*** - largest line segment completely contained within a VOI slice
 
*** - largest line segment completely contained within a VOI
 
** In the VOI properties and VOI statistics generator dialogs, the center of mass and geometric center are now displayed with the resolutions applied (dim * res) and in scanner coordinates.
 
** Added Shape-based VOI interpolation algorithm.
 
** Added the ability to Save intensities in VOI to..., which produces a comma delimited file.
 
** Added the ability to Merge VOIs.
 
 
* Image views and visualization
 
* Image views and visualization
** More improvements to the GPU Volume renderer
+
** Added better handling of when the GPU volume renderer when the videocard doesn't support the required OpenGL or GLSL version.
** Added the ability to change the slice interval in the Lightbox view.
+
** When opening the renderer, apply the LUT that is already set for the image.
** Fixed a layout issue that prevented the currently displayed slice number from being shown in the Surface plotter view.
+
 
* Scripting
+
** In ChangeName script action, added a 'image_name_action' parameter that can be either 'replace' (the default), 'append' or 'prepend'.
+
** Fixed scripting of Histogram summary algorithm.
+
* Help updates and additions
+
** Updated the 'Retracing a VOI' and 'Annotating with Text' sections.
+
** Updated the 'Supported Formats', 'Image Basics' and 'Quick Start' sections.
+
** Added a 'Haralick Texture' section.
+
 
* Miscellaneous
 
* Miscellaneous
** Fixed some issues with image and global provenance recording and display.
+
** 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.
  
=== 4.1.3 (10/15/2008) ===
+
=== 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
** Added automatic detection of DICOM ver. 2 files without the .dcm extension.
+
** PARREC: Fixed bug reading orientations and FOV from some files.
** Eliminated some memory leaks in the DICOM reader and writer.
+
** 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
 
* Algorithms and utilities
** Added Morphological algorithm support for processing Byte and Short images that have no negative values.
+
** Added Multi-exponential to Time fitting Systems analysis tool.
** Fixed an error that sometimes occurred while running the BET algorithm.
+
** The Time fitting tool can now use a custom DICOM tag for the time values.
* VOIs and Paint
+
** In the utility Match images, fixed a bug in the handling of when the images' units of measure are unknown or do not match.
** When commiting masks for a 4D image, the multipaint dialog has radio options for commiting masks as 3D or 4D; for regular painting in the 2D view and in Tri-planar image, a dialog pops up asking if masks are to be commited in 3D or 4D when trying to commit paint to mask.
+
** Added Spectral clustering tool to Systems analysis.
** Fixed a problem with the Protractor tool in the Tri-planar view.
+
** K-means algorithm no longer trys to read text points file twice.
* Help updates and additions
+
** Added Spatial color compactness algorithm to Segmentation menu.
** Added help topics on the Hough circle, ellipse, line and parabola algorithms.
+
** Added OpenCL-based image Deconvolution algorithm.
* Miscellaneous
+
** Fixed OAR3D transformation directory saving logic.
** Fixed a problem setting the output directory of the generated file when performing a screen capture.
+
** Subset image now transfers LUT to result image.
** Fixed support for printing the contents of the Output window.
+
** 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.
  
=== 4.1.2 (09/12/2008) ===
+
* VOIs and paint
 +
** Fixed a bug handling VOI stats on 2d images.
 +
** Fixed a bug displaying VOI statistics results table for color images.
  
* Fixed a problem with the MIPAV installer which caused the 4.1.1 release for Windows-amd64 systems to fail to start up.
 
* File handling
 
** Fixed an issue with decoding 24-bit CVID AVI files.
 
** Added support for black and white CVID AVI files.
 
* Algorithms and utilities
 
** Fixed a matrix-copying issue when running algorithms and utilities on DICOM images.
 
* VOIs and Paint
 
** More improvements to VOI text annotation.
 
 
* Image views and visualization
 
* Image views and visualization
** Fixed a problem with the GPU renderer on Macintosh systems.
+
** 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.
* Help updates and additions
+
** Fixed mouse wheel scrolling in the GPU renderer on Macs.
** The MIPAV Help system has been changed significantly. Each help topic now contains information on using the component it is associated with and a link to a page on the MIPAV website which has background information for that algorithm or utility. This has significantly reduced the amount of disk space taken up by the MIPAV Help system.
+
** 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
** Fixed a problem which prevented the command line argument usage window from appearing when the -hide command was not used.
+
** 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.
  
=== 4.1.1 (09/08/2008) ===
+
 
 +
== Version 6.x.x change list ==
 +
 
 +
=== 6.0.1 (11/14/2012) ===
  
 
* File handling
 
* File handling
** Cleaned up memory usage of a number of file handlers.
+
** 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.
** Added 8-bit grayscale support to JIMI reader (JPEG, etc).
+
 
** Added support for saving Analyze float images to DICOM.
+
** Fixed an issue with capital letters in file extensions.
+
** PAR/REC files may now be opened by selecting either the .par or .rec file.
+
** Improved SPM file format detection.
+
** Fixed a problem with reading COR files.
+
** Fixed an issue with the VOI file filter.
+
** Changed the saving of 3D DICOM datasets to be done on a slice-by-slice basis to reduce memory usage and prevent problems with large datasets.
+
** Fixed some issues with MINC2-HDF orientations.
+
** Added AVI decoder support for 24-bits-per-pixel CVID files.
+
* Algorithms and utilities
+
** Fixed a number of minor bugs:
+
*** Regularized isotropic diffusion
+
*** Gradient magnitude
+
*** Gaussian blur
+
*** Center of mass
+
*** Watershed
+
*** Edge lapacian
+
*** Image calculator
+
*** Registration patient position
+
*** Registration B-spline
+
*** Registration mosaic
+
*** Registration OAR 2.5D
+
*** Registration TSOAR
+
*** Transform
+
*** Subsample
+
*** Pad
+
** Added the display of the standard deviation when the Image calculator and Bulk image calculator are run.
+
** Added Poisson noise to the Noise generation utility.
+
** Added a utility to swap the 1st and 4th dimensions of a 4D image.
+
** Added a new utility to reorient (and optionally resample) an image (contributed by Pilou Bazin).
+
* VOIs and Paint
+
** Corrected some minor issues with the Multi-paint tools.
+
** Improved memory management while painting, reducing memory creep and removing a garbage collection call performed on 64-bit JVMs.
+
** Livewire VOI now works with color images.
+
** Fixed a Power paint dialog bug.
+
** Fixed a problem with creating custom brushes.
+
** Changed paint behavior so that when the user paints in the main image frame, the paint in the Tri-planar frame is only updated on mouse release.
+
** Fixed a race condition when switching paint colors in the Multi-paint dialog.
+
** Fixed some issues with VOI annotations.
+
** Improved how backing up and reverting to the paint bitmask backup is performed. This significantly improved paint performance with large images on initial mouse press and when undo-ing an action.
+
** Converting a VOI in a 4D dataset to a mask image now produces a 4D volume with the VOI converted on all time slices.
+
 
* Image views and visualization
 
* Image views and visualization
** Improved the surface decimation algorithm.
+
** 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 PLY surface format support.
+
** Added a new default lookup table/transfer function option that mimics the behavior of ImageJ.
** Added the ability to save the current camera and object parameters in the GPU Volume renderer and restore them again later.
+
** Improved surface extraction algorithms to automactially reduce surface complexity.
+
* Scripting
+
** Fixed Transform scripting bug when resampling.
+
** Fixed a scripting issue with the Optimized automatic registration algorithms.
+
** A number of algorithms were being run in a separate thread during script execution (FFT, std dev thresholding, registration OAR 2.5D and 3.5D, background distance map, evaluate mask segmentation, evaluate segmentation, remove t-slices).
+
* Help updates and additions
+
** Muscle segmentation plug-in.
+
** Conformal mapping algorithms.
+
** DICOM query dialog.
+
** DICOM images section.
+
** Wavelet thresholding.
+
** LUT for two images (A and B).
+
** Filters (frequency).
+
** Wavelet BLS GSM.
+
** Talairach transform
+
** Modify graph
+
** Paint grow
+
** 2D B-spline registration
+
** Mosaic registration
+
** Scripting
+
* Miscellaneous
+
** Added menu items Open graph to same frame
+
** MIPAV classes no longer use Java3D vecmath classes. Instead WildMagic vector and matrix classes are now used. Usage of Jama classes has been refactored and the location of the code within the MIPAV classpath has been changed. MIPAV Vector*, Color* and Point* classes have all been removed.
+
** Added -outputDir command line option for selection of the directory where files written out to disk by MIPAV should be located (to be used with scripting).
+
** Changed -dir command line option to -inputDir.
+
** Fixed a problem where an error dialog would sometimes pop-up when running MIPAV with the -hide command line option.
+
  
=== 4.1.0 (06/13/2008) ===
+
=== 6.0.0 (11/7/2012) ===
 +
 
 +
'''MIPAV is now open source!'''  See the [http://mipav.cit.nih.gov/license/license.html license information] for details.
  
 
* File handling
 
* File handling
** Gzipped archives (containing a single file in a format supported by MIPAV) can now be automatically un-archived and opened in MIPAV.
+
** Added basic support for dragging-and-dropping directories, single files and multifile images into MIPAV.
** Improved the processing of determining the file format of files with an unknown or non-existent extension.
+
** DICOM: Fixed reading of some files with private tags that resemble the image tag pattern.
** Fixed a problem where .tiff files would not show up in the Image browser when the TIFF file filter was selected.
+
** DICOM: Fixed an issue reading some enhanced DICOM tag sequences.
** New file formats supported:
+
** DICOM: Added support for writing enhanced MR, CT and XA.
*** BFLOAT
+
** DICOM: Fixed an issue reading tags in some boolean images.
*** LIFF
+
** DICOM: Fixed handling of a number of tags in the 0018 group when reading and writing images.
*** Minc2
+
** 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.
*** STL surface format (.stla and .stlb)
+
** DICOM: Fixed display of min and max values for color images in the file header dialog.
*** VTK surface format
+
** DICOM: Fixed an issue reading image data when no pixel padding was specified.
** File formats with bug fixes or improvements:
+
** DICOM: Added support for writing multiframe ushort, ARGB and ARGB_ushort data types.
*** Analyze
+
** DICOM: Added support for writing ARGB_ushort data types.
*** Biorad
+
** TIFF: Added support for reading in ImageJ ROIs stored in TIFF header.
*** DICOM (UT supported as explicit VR with 32-bit length; reading of critical tags that were incorrectly written)
+
** TIFF: 4D TIFF data is written out as a set of 3D files now.
*** DM3
+
** RAW: Fixed issue writing out 4D volume as 3D files.
*** ICS
+
** RAW: Fixed issue reading boolean image.
*** Minc (slice thickness now saved to the acquisition -- slice_thickness attribute)
+
** ANALYZE: Fixed an issue reading some boolean images.
*** OSM
+
** PARREC: Fixed resolution calculation for some images.
*** PARREC
+
** PARREC: Fixed processing of angulation midslice in parrec images.
*** TIFF
+
** PARREC: Added slice/offcenter loading for any orientation.
* Algorithms
+
** PARREC: Added support for reading/writing 4D data as multifile.
** Added automatic parsing of ITK filter interfaces for access from the Algorithms menu (available only on 32-bit Windows systems, by default).
+
** Added new Spar file format support.
** Image calculator (added color support)
+
** MINC2: Fixed progress bar issue and added better support for saving image subsets (either 3D or 4D).
** Image math (added color support)
+
** MINC2: Improved support for reading 3D and 4D images with some orientation/image data settings.
** Match for reference
+
** MINC: Added support for writing 2D and 4D images.
** Match images
+
** MINC: Added support for multifile datasets.
** Maximum intensity projection (added color support)
+
** INTERFILE: Added multifile support.
** Transform (adjusts units of measure of input image to match reference image)
+
** Fixed getting image unit from abbreviation.
** The Threshold and dual threshold tools now output unsigned byte instead of short masks.
+
** NIFTI: For Preferences.PREF_FLIP_NIFTI_READ the default preferences has been changed form true to false.
** Improved the multi-threaded image convolution support.
+
** Parallelized the Optimized automatic registration algorithm.
+
** Integrated the Talairach transform plugin from JHU Medic into MIPAV.
+
* Utilities
+
** Moved Center of mass from the Algorithms menu to the Utilities menu.
+
** Improved the Center of mass output sent to the Output window's data tab.
+
** Fixed the way that the Rotate utilities handled setting the VR of DICOM image tags.
+
* VOIs and Paint
+
** Fixed a problem with cloning some VOIs.
+
** Fixed some issues with the Livewire VOI tool.
+
* Image views & visualization
+
** Parallelized the Raycast volume renderer.
+
** Many improvements have been made to the GPU-based volume renderer.
+
** Multipaint dialog improvements -- auto-save for multiple masks and keyboard shortcuts that work with the triplanar view.
+
** Changed the paint brush sizing in the triplanar view to be consistent regardless of the image resolution.
+
** Added Paint -> Unsigned byte mask conversion tool.
+
* Scripting
+
** The Transform algorithm now saves the relative path to the transformation matrix file in its script action line, if a file is selected in the dialog.
+
** Added -dir option for setting the default image directory when running scripts from the command line.
+
* Miscellaneous
+
** The MIPAV installer now tries to correct the permissions of file containing memory limit.
+
** Added a checkbox in the MIPAV options dialog for the enabling/disabling of the parallelization of algorithms.
+
** A Capture screen memory leak was fixed.
+
** Many DTI algorithm and visualization improvements have been added.
+
** Moved the keyboard shortcut file (accessory.dirs) from the user.home directory to user.home/mipav.
+
  
=== 4.0.3 (02/29/2008) ===
+
* 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.
  
* File handling
+
* VOIs and paint
** AVI transcoding bug fixed.
+
** Fixed handling of VOI bounding box checkbox in VOI properties dialog.
** Added support for many new variations of the TIFF format.
+
** Fixed some issues grouping VOI contours.
** Fixed some minor issues with the Interfile reader.
+
** Added Ctrl key angle modification for line VOIs.
** Fixed some minor issues in the Afni reader.
+
** Allowed line, protractor, and point vois to save in voxel coordinates.
** Fixed some minor issues in the Analyze reader.
+
** Now able to do image statistics without having a VOI present from the VOI properties dialog.
** Solved a problem in MIPAV's support of NIFTI multifile datasets.
+
** Fixed an issue converting between VOI and mask and back again.
** Added XFM matrix file format support (McGill transforms).
+
** Fixed problem storing very large float or double values into a unsigned integer image buffer.
+
** Fixed NRRD reader progress bar.
+
** The user can now select DICOM tags to save from the Image header dialog (this action is scriptable).
+
** Improved dialog for selection of tags to convert from DICOM to XML.
+
** Fixed a problem encountered reading DICOM files with malformed slice thickness (0018,0050) or slice spacing (0018,0088) tags.
+
** Solved problem reading reading DICOM CT images stored as unsigned short on disk with negative rescaling.
+
** Fixed NRRD matrix and origin orientation problem.
+
** Added option in the MIPAV options to always open img/hdr files as either Analyze/NIFTI/Interfile or to force MIPAV to always prompt the user. This change may cause some temporary problems when scripting the saving of files to these formats with the -hide option.
+
** Modified Par/Rec reader to handle new version of the header file.
+
* Algorithms
+
** Parallelization of Optimized automatic registration, non-linear registration (b-spline and least squares), FFT, and separable convolver-based algorithms to take full advantage of multi-processor and multi-core systems.
+
** Fixed a problem with the Transform algorithm.
+
** Fixed bug in FFT algorithm.
+
** Added beta version of auto-exposure of Insight Toolkit (ITK) filters from within MIPAV.
+
* Utilities
+
** Fixed the Image calculator utility difference and average functions for complex images.
+
** Added an Image calculator - bulk images utility to perform calculations on multiple open images.
+
** Added a utility to calculate an image's center of mass.
+
* VOIs
+
** Added Coefficient of skewness and Coefficient of kurtosis to VOI statistics/properties.
+
** Center of mass has been renamed Geometric center in the VOI statistics/properties.
+
** Fixed display of scanner coordinates for VOI points in the VOI statistics/properties output.
+
** Fixed problem in Rectangle VOI.
+
** Added new button to open VOI properties dialog.
+
* Image views & visualization
+
** GPU renderer (beta) improvements:
+
*** Added support for GLSL programmable shaders.
+
*** Ported volume renderer slice view.
+
*** Fixed miscellaneous bugs.
+
*** Added volume sculpting support.
+
*** Added triangular surface mesh support.
+
*** Improved clipping planes.
+
*** Added ability to paint on surface meshes.
+
** Added new LUT color scheme presets.
+
* Scripting
+
** Added support for graphically selecting transformation matrix files for use when scripting the Transform algorithm (Contributed by Pilou Basin).
+
* Miscellaneous
+
** MIPAV now consistently displays slice positions in a zero-based format.
+
** Plugins can now be run without the rest of the MIPAV interface appearing by using the -p PlugInName command line option with the -hide option.
+
** Added the following help topics:
+
*** Morphological filter
+
*** Skeletonize 3D
+
*** Surface plotter
+
*** Barrel/pincushion distortion correction
+
*** Cumulative histogram
+
*** Image calculator - bulk images
+
*** Creating a self-contained plug-in frame
+
*** Display pixel similarity cost function
+
  
=== 4.0.2 (11/15/2007) ===
+
* 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.
  
* File handling
 
** Added support for writing NRRD files.
 
** Resolved a problem with some 2D Nifti files.
 
** Fixed writing of image matrix to MIPAV XML for 4D+ datasets.
 
** Fixed reading of some (uncompressed, ISFT, LIST, IV32, IV41) AVI files.
 
** Afni reader now allows the time dim to be set to 1.
 
* Algorithms
 
** Fixed Transform algorithm handling of VOIs when 2.5D processing is performed.
 
** Minor bug fixes included for a number of algorithms:
 
*** Extract brain (BET)
 
*** Registration mosaic
 
*** Registration OAR 3D, 3.5D, 4D
 
* Utilities
 
** Merged Pad and Add image margins utilties
 
** Minor bug fixes included for a number of utilities:
 
*** Change type
 
*** Clone
 
*** Crop
 
*** Depth flip
 
*** Image calculator
 
*** Image math
 
*** Maximum intensity projection (MIP)
 
*** Noise
 
*** Quantify mask
 
*** Randomize slice order
 
*** Remove slices
 
*** Replace removed slices
 
* VOIs
 
** Fixed a minor bug in VOI histogram when there is no VOI contour present.
 
** The Livewire dialog now maps the Enter key to the OK button.
 
* Image views & visualization
 
** More Diffusion tensor tool updates.
 
** Continued improvements to the WildMagic GPU-based renderer.
 
* Scripting
 
** Fixed recording and playback of the 'Invert matrix' flag in the Transform dialog.
 
 
* Miscellaneous
 
* Miscellaneous
** Fixed image min/max calculation for boolean images.
+
** Added a new integrated bug reporting button (only works from within NIH - fixed in a future version).
** Added the following help topics:
+
** Added the ability to drag menus out of the main MIPAV menu to separate windows.
*** Background distance map
+
** 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.
*** Close
+
** 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.
*** Delete objects
+
*** Dilate
+
*** Distance map
+
*** Edge laplacian
+
*** Edge NM suppression
+
*** Erode
+
*** Evaluate mask segmentation
+
*** Evaluate segmentation
+
*** Fill objects
+
*** Find edges
+
*** Histogram summary
+
*** ID objects
+
*** Multi-paint
+
*** Open
+
*** Particle analysis
+
*** Power paint
+
*** Skeletonize
+
*** Standard deviation threshold
+
*** Ultimate erode
+
  
=== 4.0.1 (10/12/2007) ===
+
== Version 5.x.x change list ==
  
* File handling
+
[[MIPAV change list 5.x.x]]
** Fixed Image-offset tag value in MIPAV XML files saved from some other formats.
+
** Fixed the XML image header file name set for new images created as a result of some algorithms.
+
** Fixed an error which would occur when writing Dicom images with some types of sequence tags to the MIPAV XML format.
+
** Found and resolved a bug in writing some datasets to the Nifti (.nii) format.
+
** Modified the Minc reader to support 4D volumes.
+
** An optional tag indicating the dataset slice thickness has been added to the MIPAV XML file format specification.
+
** Fixed a problem with handling some version number strings in the NRRD file reader.
+
** The NRRD file format has been added to the Medical file type filter used in the Open and Save image dialogs.
+
* Algorithms
+
** Fixed VOI region processing in multiple algorithms:
+
*** Find edges
+
*** Particle analysis
+
*** Thin
+
*** Prune
+
*** Ultimate erode
+
*** Laplacian
+
** Removed 2.5D processing option from Particle analysis algorithm dialog.
+
** The Extract brain (BET) algorithm now defaults the 'Axial brain orientation' parameter to selected when using an Axial image.
+
** Fixed some data value wrap-around issues when running the Laplacian algorithm. New images generated are now always stored in a float datatype. When replacing the source image, the result data values are scaled to fit within the source image datatype (when necessary).
+
** When running the Frequency filter algorithm with the replace source image option, the image datatype is now forced to float.
+
** Fixed a bug in the Homomorphic frequency filter.
+
** When running the Anisotropic diffusion algorithm with the replace source image option, the result data is rescaled if it does not fit within the source image data range.
+
** Fixed 2.5D VOI region processing for some combinations of images and parameters in the Laplacian algorithm.
+
** Improved the Median filter algorithm dialog and made traditional filtering the default choice.
+
** Fixed the AHE local algorithm progress bar for 2D color images.
+
** Fixed the display of the wavelet image under certain conditions in the Wavelet threshold algorithm.
+
** Removed duplicate data output by the Colocalization regression algorithm.
+
** Fixed a small bug in the subsampling routine of the Entropy minimization algorithm.
+
** When running the Principal components algorithm, the filtered and average destination image values are rescaled if they exceed the image data type range.
+
** Fixed a problem in the Maximum likelihood iterated blind deconvolution algorithm resampling routine.
+
** Fixed a bug in the processing of 2D images with the Two MRI images signal-to-noise ratio algorithm.
+
** The Subsample algorithm now copies over VOIs from the original image to the result volume.
+
** Fixed a few small interface issues in the Transform algorithm dialog.
+
** Fixed the behavior of 2D and 3D B-Spline registration progess bars.
+
** Constrained optimized automatic registration is now disabled for 2D images.
+
* Utilities
+
** Correct image spacing now operates on all image formats, not just MIPAV XML. It also handles situations where correction is not needed more gracefully.
+
* VOIs
+
** Added a VOI splitter tool, which allows the user to divide one VOI into two.
+
** VOI statistic values are now saved in the Parameter set portion of the header of MIPAV XML images.
+
** Added sum intensities to the list of available VOI statistics in the VOI properties dialog and VOI statistics generator.
+
* Paint
+
** The buttons to Hide masks and paint in the Multipaint dialog now update the Tri-Planar view as well.
+
** Added the ability to Lock/Unlock all masks in the Multipaint dialog.
+
** A number of Power paint dialog upgrades have been made:
+
*** Support for color images has been added.
+
*** The Threshold GUI has been changed to spinners.
+
*** Added the ability to use the thresholds during paint growing and dilation.
+
* Image views & visualization
+
** Added support for reading and writing of VTK XML surface files (*.vtp).
+
** Added the ability to adjust the raytracing step size in the GPU-based volume renderer.
+
* Help topic updates and additions
+
** Advanced paint
+
** Edge dection
+
** Histogram tools
+
** Morphology
+
** Segmentation
+
** Utilities
+
* Miscellaneous
+
** Added tools for DTI image segmentation and visualization.
+
** Masks created and placed into the ImageB slot are now named according to the current ImageA volume.
+
** The Insight Toolkit Kit (ITK) dlls distributed with the 32-bit Windows MIPAV installers have been updated to version 3.2.0.
+
  
=== 4.0.0 (09/07/2007) ===
 
  
* File handling
+
== Version 4.x.x change list ==
** Fixed problem reading in multiple matrices in MIPAV's XML image file format.
+
 
** When converting from Minc to DICOM, we now ignore Sequence tags stored within the Minc header since they are generally not stored in a consistent format.
+
[[MIPAV change list 4.x.x]]
** Improved the memory management of the Nifti file reader and writer.
+
** Fixed the saving of orientation and other header information when converting non-Nifti files to the Nifti file format.
+
** Fixed a bug in data type handling for some DICOM files.
+
** Fixed a problem in the PAR/REC file reader.
+
** Fixed a bug in the Afni file reader.
+
** Fixed the image offset value when saving XML files from other image file formats.
+
** Fixed a bug reading in encapsulated DICOM files.
+
* Algorithms
+
** Fixed a memory leak in the Colocalization EM algorithm.
+
** Added option to insert padding into an image before running the Subsample algorithm to make the image extents divisible by the sub-sampling factor.
+
** The Histogram summary now allows the user to specify the summary minimum and maximum.
+
** Fixed a bug in the BET algorithm.
+
** Fixed the Separable edge laplacian algorithm progess bar for 2D images.
+
** Fixed the Auto covariance progress bar.
+
** Fixed the Subsample dialog's expected extents labels for 2D images.
+
** Fixed a problem in the Subsample algorithm's memory management.
+
** Removed the bandpass and bandstop options from the Frequency filter algorithm for Gaussian filters.
+
** Solved a progress bar problem for the Adaptive path smooth algorithm.
+
** Disabled Boundary attenuation algorithm for 2D images.
+
** Fixed a memory management problem in the Coherence enhancing diffusion algorithm.
+
** Added a kernel error check for the separable Gradient magnitude algorithm.
+
** Fixed a bug in processing a VOI region with the Gradient magnitude algorithm.
+
** Fixed a bug in processing a VOI region with the Erode algorithm.
+
** Fixed a bug in processing a VOI region with the Distance map and Background distance map algorithms.
+
* Utilities
+
** Fixed Crop utility when Replace image was selected. Also fixed a memory issue when cropping DICOM images. Fixed a problem with a warning dialog which popped up when no VOIs were selected.
+
** Fixed a bug in the Pad utility's handling of 3D RGB images when Replace image was selected.
+
** Fixed a crash when attempting to run the Rotate utility on 2D, non-DICOM images.
+
** Added the option to threshold an image before generating its Maximum intensity projection using the MIP utility.
+
** The Flip utility no longer displays the option to flip 2D images along the Z axis.
+
** Fixed bounds checking problem in RGB concatenation utility.
+
** The Quantify using mask utility can now be run on RGB images. It also outputs the mean and standard deviation for grayscale or RGB images. The mask can be loaded from a file or from an image frame.
+
* VOIs
+
** Improved the progress bar of the Rubberband livewire VOI tool.
+
** Fixed a bug in the Smooth VOI with the Replace original contour option selected.
+
** When VOI graphs are generated, the mean and standard deviation is now output to the data window.
+
* Image views & visualization
+
** Added a new hardware-shader-based volume rendering system. It is based on a port of the WildMagic libraries to Java. It currently requires a modern Nvidia graphics card and is a beta release.
+
** Fixed initial zoom of Tri-planar view on some datasets.
+
** Fixed a problem with the magnification when the zoom is set below 1x.
+
** Added a new XML surface file format that references a .sur file, which contains the surface mesh data (resulting in faster surface loading).
+
** Improved speed of Talairach Tri-planar view.
+
** Added support for the .vtk legacy surface file format.
+
** Fixed a bug in the saving of VRML and WRL surface file formats.
+
** Added the ability to view surfaces within the volume renderer without viewing an image volume.
+
** Fixed a number of minor bugs in the Java3D volume renderer.
+
* Scripting
+
** Fixed a problem when executing a script with CloseFrame actions from the Run script dialog.
+
* Painting
+
** The Power paint tools are now disabled for 2D images.
+
** Extracting a paint mask to a new image now uses the correct paint intensity.
+
** Fixed problem when collapsing paint and mask layers for RGB images in the Multi-paint dialog.
+
** Fixed an error in the Multi-paint dialog when a RGB imageB is present.
+
** The Paint calculator button now calculates total intensity, mean intensity and standard deviation of the painted region.
+
* Miscellaneous
+
** Added installer support for 64-bit Windows systems.
+
** MIPAV installers for Windows and Linux systems now include Java virtual machine 1.6.0_02, JMF 2.1.1e, Java3D 1.5.1, Jogl 1.1.0 and Nvidia Cg Toolkit 1.5.
+
** Added BIRN data provenance 2.0 support. This information may be tracked globally and for each image. The provenance data can then be saved to an xml format along side an image file (with an .xmp file extension). It records algorithms and utilities applied to an image volume (i.e., the image's history) and information about the version of MIPAV used.
+
** Many improvements and additions have been made to the MIPAV help. A few of the changes include:
+
*** Added Talairach transform topic.
+
*** Added MIP utility topic.
+
*** Updated Quick start chapter.
+
*** Updated Plugins section.
+
*** Updated Dicom browser topic.
+
*** Updated Segmentation topic.
+
** Fixed a problem with the image frame resize handling on some systems.
+
** Fixed some minor problems in the uniform and gaussian random number generators.
+
** Added some SRB security measures:
+
*** 10 SRB login failure lockout.
+
*** 30 minute SRB inactivity auto-logout.
+
*** NDAR privacy notice on successful SRB login.
+
** Removed BIRN Xcede-related features.
+
** Changed PlugInAlgorithm and PlugInView interfaces to remove the ViewUserInterface parameters from their run() methods.
+
  
  

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