TransformJ: Release Notes

2.8.0, September 17, 2010

• The plugins now require ImageJ 1.44a and ImageScience 2.4.0 or higher.
• As of this version the plugins are now also distributed as part of Fiji.
• As of this version the source code of all the classes is included in the jar-files.
• All plugins in the package can now deal with the HyperStack and CompositeImage types.
• Changed the prefix "TJ" to the full package name "TransformJ" in the naming of all plugins.
• Removed the "About" and "Website" menu items but kept them as part of the "Panel".
• Added an option to the "Options" dialog to enable or disable progress indication.
• The progress bar now indicates the status of the complete process rather than subprocesses.
• The dialogs of the "Crop" and "Mirror" plugins now show only the relevant dimensions.
• Improved the way in which the "Shift" plugin deals with values at the image boundaries.
• Renamed the "Shift" plugin to "Translate" in line with more conventional terminology.
• Replaced the "F1" key by a "Browse" button in the "Affine" dialog for file opening.
• Added a "Create" button to the "Affine" dialog for (re)creating matrix files.
• Added the "TransformJ Matrix" plugin for creating or modifying matrix files.
• The positions of all plugin dialogs are now remembered during an ImageJ session.

2.7.1, November 8, 2008

• The plugins now require Java 1.5 and ImageJ 1.41g or higher.
• Updated all plugins to work with the latest ImageScience API.
• Renamed the "Debug messenging" option to "Log messaging".
• Added an option to close input images after transforming.
• Replaced "ch" (the channel index) to "c" in all dialogs.

2.7.0, July 16, 2007

• The package now requires ImageJ 1.38x and Java 1.4 or higher.
• Replaced function calls that were deprecated in Java 1.5.
• Made the package compliant with Image5D version 1.1.7.
• Added version checking of the ImageJ and ImageScience libraries.
• Added utility classes and reorganized code to reduce code duplication in the package.
• Added a plugin class that shows basic information about the package.
• Added a plugin class that opens the default browser showing the TransformJ website.
• Added menu item ImageJ > Help > About Plugins > TransformJ...
• Reorganized the plugin button layouting in the panel.
• Added an option to adopt brightness/contrast from input images.
• Corrected wrong error message when running out of memory.

2.6.0, March 23, 2006

• The program is now distributed as a single jar-file to facilitate installation. Before installing the new version, you should delete all of the following files and folders of older versions (note that not all of these may have been present in all older versions, so please check carefully whether these indeed belong to your version of TransformJ or to some other package):

     ImageJ
       |- TJOptions.dat        (file)
       |- plugins
             |- Basics         (folder)
             |- BasicsJ        (folder)
             |- TransformJ     (folder)
             |- imagescience   (folder)
  

• The dialogs are now all based on ImageJ's GenericDialog. As a consequence, they can no longer be left open all the time. In order to still have quick access to the different plugins, a panel has been added which will stay open until the user closes it explicitly.
• The interface of some dialogs has changed (see the online manual for details). This may require revision of some macros. Also note that all plugins are now fully macroable and that previous synchronization problems should have been solved.
• The package is now fully 5D compatible. If Image5D is installed, result images with a size larger than 1 in the t- or ch-dimension are displayed in an Image5D window. If it is not installed, result images are displayed as usual.
• Options are no longer stored in a separate file (TJOptions.dat) but in ImageJ's preferences file (IJ_Prefs.txt).
• Indexing for the z-, t-, and ch-dimension in the Crop and Embed plugins is now compatible with ImageJ. That is to say, it starts at 1 rather than 0 (as opposed to the x- and y-dimension).

2.5.0, October 22, 2003

• All plugin classes of the package are now macroable.

2.4.0, October 8, 2003

• The code has been adapted to work with a new version of my Basics package, which has been split into two packages: images and utilities.
• The convolution operations in the Affine, Rotate, Scale, and Shift algorithms have been optimized by a slightly more efficient implementation of the interpolation kernels. The effects on the computation times turn out to be marginal though.
• It is no longer possible to apply the Affine, Rotate, Scale, and Shift plugins to indexed color images, since it doesn't make any sense to interpolate color indices.
• Error messages are now displayed in a window with title "TransformJ: Error" instead of the standard ImageJ message window.

2.3.1, March 10, 2003

• Improved the progress indication by lowering the priority of the threads in which the computations are carried out.

2.3.0, October 12, 2002

• The classes containing the actual algorithms have been split off and now form a separate package, called Transforms.
• Some of the methods have been synchronized so as to avoid possible collisions in the case of simultaneous calls from different threads.
• Minor changes in and reorganization of the options-related classes.
• The BasicsJ package, now called Basics, has been extended and improved.

2.2.0, April 6, 2002

• All classes of a more general nature have been split off from the original package and now form a separate package, BasicsJ. The classes containing the actual transformation algorithms now depend solely on the latter package. This makes it easier for anyone interest in using these algorithms in other Java-based environments, since in that case only the BasicsJ classes need to be rewritten.
• The image classes, now in BasicsJ, have been rewritten so as to have an interface that is completely independent of the environment in which the classes are used. The transformation and accompanying plugin classes have been adapted accordingly.
• All dialogs in the package are now modeless, meaning that they can be left open as long as the user desires without blocking input to other dialogs. This should facilitate repetitive application of the plugins, to different images or with different settings.
• The options, as specified in the options dialog, can now be saved to disk. When the plugin is started, it first checks if there is an options file on disk and if so, it will load it. This makes it easier for users to adapt the behavior of the package to their wishes.
• The Chunk plugin has been renamed to Crop, a more common name for the kind of operation it performs.
• Some minor changes have been introduced in the naming of the windows displaying the images resulting from the different plugins. Minor changes have also been made to some of the labels in the dialogs.

2.1.0, November 14, 2001

• The Affine, Rotate, Scale, and Shift plugins have been redesigned and are now considerably less memory demanding, especially when dealing with 8-bit, 16-bit, and RGB-color images.
• The Embed plugin has been extended to support clamping of the input image as a form of filling the remainder.
• All plugins now also generate status messages. Especially for the separable algorithms, this should make it more clear what the progress bar is actually indicating.

2.0.0, October 9, 2001

• There is now an ImageJ-dedicated version for each of the main functional classes in the package (those corresponding to an ImageJ plugin), which makes the use of the package under ImageJ much faster and less memory demanding.
• It is now possible to create instances of the OptionsDialog class with a user-specified name. This allows for re-use of the class by other packages with the same global options as the TransformJ package.
• The Chunk plugin now checks if there exists a rectangular region of interest for the selected image or stack. If so, it will automatically adjust the parameters in the dialog to it.
• Solved the problem that when transforming an image or stack while re-using the original window for displaying, the window title is not adjusted to the new image title.
• Solved the problem that when transforming a stack while re-using the original window for displaying, the scroll-bar does not correspond to the current slice displayed. The scroll-bar is now always reset to the first slice.
• Solved the problem that when transforming an image or stack of type 8-bit color, the window displaying the result has no scroll-bar.
• Fixed two bugs in the Scale class. In the previous version, when scaling four-dimensional (4D) RGB images, only the volume at t=0 was considered. Also, when scaling 2D images of any type in the z-dimension using an interpolation type other than nearest-neighbor interpolation, the resulting image was zero everywhere.
• Fixed bug in the Embed plugin class. In the previous version, the plugin gave the erroneous title "Chunk of ..." instead of "Embedded version of ..." to the resulting image. A similar copy-and-paste bug has been fixed in the Rotate class, which gave the message "Checking arguments for resizing" instead of "Checking arguments for rotation" at start-up.

1.0.2, September 24, 2001

• The version number now appears in the first line of the debug messages generated by each of the main functional classes in the package, that is, those corresponding to an ImageJ plugin class.

1.0.1, September 20, 2001

• When using the package under ImageJ, invalid arguments in the dialogs now result only in an error-box and not also in an IllegalArgumentException.

1.0.0, September 19, 2001

• First release.