History of Changes

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Version 1.4.7 (December 2007)

environment

  • add Added GUI to change plot types. 4 plot types are available: Line, Symbol, Histogram, and Column. Issue [1569325]. (SM)
  • add Added Welcome screen (currently set to CESE survey). (SM)
  • fix Fixed empty printing under certain conditions. (SM)
  • fix Fixed Lock Record action not staying locked. (SM)
  • update Improved performance in plot legend. (SM)
  • update Changed the default directory location to "My Documents/cese-1.4" in Windows. (SM)

Version 1.4.6 (February 2007)

environment

  • add Much better feedback on status of simulation in case of continuous or infinite simulation runs. Issue [1572373]. (SM)
  • add Added options to highlight parameters that were changed during the simulation run. Issue [1572375]. (SM)
  • add Added visual hint when model parameters were changed either manually, or due to simulation. This reminds user to save the parameters. Issue [1572375]. (SM)
  • add Added Report Bug command to the Help menu. Calls web browser and opens bug tracker page. Issue [1569324]. (SM)
  • add Added Print Options dialog (available via Print Preview) to change visual parameters of the printout. Issues [1569322, 1569321]. (SM)
  • add Added a number of additional options to printouts, including print legend, title of Results View window being printed, print data and time, footer comment. Issues [1569322, 1569321]. (SM)
  • add Added export of plots to SVG (Scalable Vector Graphics) format using Apache Batik. (SM)
  • fix Simulation Options dialog does not lose the number of simulations when Single iteration is selected. (SM)
  • fix Refactored data exports for various formats into the separate package. (SM)
  • fix Fixed rendering of plots when data was changed in the table. Issue [1569316]. (SM)
  • fix Fixed rendering of plots when window changed size and plot was not visible. Issue [1569319]. (SM)
  • fix Fixed Print Preview and export of results to PNG and SVG formats when plot view was not available. Issue [1569314]. (SM)
  • update Model export does not create Results View when export selection is empty. Changed the logic of window creation to be faster and more reliable. Issues [1572377, 1572372]. (SM)
  • update Replaced dependence on Apache Xalan with a built-in Java 1.5 jaxp, reduced the size of distribution package. (SM)
  • update Model info was changed to make clamped variable selection persistent between model parameters changes, filterings, and loads. Issue [1572163]. (SM)

models

  • update Models were recompiled using Java 1.5 compilation target. (SM)

Version 1.4.5 (September 2006)

environment

  • add Massive fixes for mutithreading. Resolved known conflicts between worker and interface (event) threads. (SM)
  • add Show update manager when a new version is available for download. (SM)
  • add Added "Save Parameters As" action for specifying parameters file name, and turned "Save Parameters" into simplified quick save. (SM)
  • add Added recent parameters and record file lists in submenus. (SM)
  • add Added table for cursors analysis data (tab "Cursors" at the bottom of each Results window) and commands "Append Cursor Data" and "Replace Cursor Data" to add analysis results to the table. (SM)
  • add "Link to partner" option for cursors - move a pair of cursors together. (SM)
  • add Autoscroll for cursors - view is scrolled when cursor is moved out of the current zoom range. (SM)
  • add Added Window list dialog to window list submenu when there are >10 windows on desktop. (SM)
  • add Autoscale for Y axis in data view. (SM)
  • fix Allowed block selection for data tables (simulation data and cursor data). (SM)
  • fix Fixed cursors appearance on different look and feels. Make MacOS X and Windows users happy. Issue [979177]. (SM)
  • fix Fixed cursors popup menu toggle actions. (SM)
  • fix Prevent cursor flicker when scrolling data view vertically. (SM)
  • fix Fixed NPE-s in the model manager dialog. (SM)
  • fix Additional optimizations in data view and axis. (SM)
  • fix Much faster plots, optimization achieved by precalculating point threshold before main plot loop. (SM)
  • fix Cleaned up JavaDoc warnings in the Ant build. (SM)
  • update CESE has switched to JDK/JRE 1.5.0 or above. Compilation warnings have been fixed and many libraries updated. Make sure to upgrade your Java runtime. (SM)
  • update Click on data table header selects column. (SM)
  • update Cursor horizontal positions are set to use double precision - much more accurate measurements now possible. (SM)

Version 1.4.4 (August 2006)

environment

  • add Generated native Windows .exe launcher using launch4j. (SM)
  • add Refactored simulation history. History, display tree selection, and .mdl file name is preserved when models are changed via model selector. (SM)
  • add Major usability change: model is not reset to the intial state when changed via Model Selector. This makes it easier to switch between models without loosing their state. (SM)
  • add Sweep title in the Legend displays model name. (SM)
  • add Results View title is set to the model name to improve usability. (SM)
  • add Results View title can be edited. (SM)
  • add Added splashscreen to give feedback during startup. (SM)
  • fix Much faster Print Preview. (SM)
  • fix Reduction in data view memory consumption, and improved performance. (SM)
  • fix Major improvements in data axis performance and reduction in memory consumption, especially when scrolling and at high zoom. (SM)
  • fix Replaced rssutil with rome for fetching rss streams. (SM)
  • fix Increased allocated memory size to 512 Mb to prevent OutOfMemory errors. (SM)
  • update Improved update manager with changelog support. (SM)
  • update Separated Results View number and title. (SM)
  • update Increased maximum zoom range to 0.001. (SM)

Version 1.4.3 (May 2006)

environment

  • fix Accommodates changes in CVS environment at Sourceforge.net. (SM)

Version 1.4.2 (February 2006)

commands

  • add Add a magical variable "record". Its value is initialized with the current record number, useful for calculating e.g., deltas in IVs and such. See ik1_iv.rec for example. (SM)

environment

  • add Added column (bar) and histogram plots. For column plot the fill attribute is available for modification/selection from the indexed pallette. (SM)
  • add Table that contains simulation results is now editable. Plot is re-rendered automatically when data are modified. (SM)
  • add Automatically set cursors into the data lock mode when channel is selected. (SM)
  • add Persistent display of cursor value during dragging. (SM)
  • add Data axis now has tooltip showing current range and units. (SM)
  • add Visually indicate zoom bounds on axis when zooming with mouse in view. (SM)
  • add Option to Zoom to cursors 1..2 range in data view. (SM)
  • add Task progress bar displays a list of current tasks in a tooltip. (SM)
  • fix Do not display cursor y values when selected channel is an "x-channel". (SM)
  • fix More robust handling of visualization of invalid data. (SM)
  • fix Major performance improvement for channel selection with mouse click. (SM)
  • update Report model autoinstallation in task progress bar. (SM)
  • update Data cursors code cleanup. (SM)

Version 1.4.1 (January 2006)

environment

  • add Plots are assigned individually for each channel instead of one per DataView. This should permit composition of different plots in one view. (SM)
  • fix Minor bugfixes. (SM)
  • update Scatter plot symbols are cached in static array. (SM)
  • update Selected channel indicated by thicker line/symbol instead of color (less confusing). (SM)

Version 1.4.0 (August 2005)

commands

  • add Added a new clamp segment command: "waveform". It loads a column of ASCII data from an external file and uses the data to create an arbitrary clamping command. Requested by Dr. David Van Wagoner. (SM)
  • update Main menu has been changed to move everything related to clamping into a separate category "Records". (SM)

environment

  • add Added option to check for software updates online. CESE checks the SourceForge file releases RSS feed and informs user whether new releases are available for download. (SM)
  • add Added simulation history. CESE now keeps a history of all simulation runs for the current model and allows to go back to the previous run if necessary. This helps to correct errors in user input without restarting simulations from the beginning. Original idea by Dr. Frank Starmer. (SM)
  • add Convenience Zoom In/Zoom Out x2 commands in axis and data view. (SM)
  • add All parameters setup in the Simulation Options dialog are now stored in the property file and retrieved when CESE restarts. (SM)
  • add Added an option to turn beeping after simulation off. (SM)
  • add During the first run CESE clones all the parameter, model, result, records, and cellml directories to the user home directory. This allows us to separate the system-wide CESE installation and personal user settings that are now stored on a per-user basis. (SM)
  • fix CESE now works when installed in a directory, containing space(s) in its name (such as "Program Files" on Windows). (SM)
  • update Calculate and display deltas for x and y values in the cursor pair. (SM)
  • update Load models on a separate thread to improve startup time. (SM)
  • update As a result of implementation of a new rendering pipeline, cursors performance was improved as well. The responsiveness of the cursors dragging does not depend on the number of data traces (channels) in the window anymore. (SM)
  • update Data visualization engine has been upgraded to utilize a new rendering pipeline. We now render data to the offscreen buffer. All the subsequent redrawing are updated from that buffer. This should improve the redraw performance by several fold, depending on the usage pattern. (SM)

Version 1.3.4 (February 2005)

commands

  • add "Single-click clamp mode": switch to the clamp mode automatically, after opening of the record file. (SM)
  • add "Single-click clamp mode": mark the clamped variables in the model property table based on the information in the record file. (SM)
  • add "Single-click clamp mode": limit the range of the possible record numbers to the number of groups in the current record file. (SM)

environment

  • add Warn if no variables are selected in the display tree. (SM)
  • add Error dialogs display the exception stack trace for debugging and error reporting. (SM)
  • add Model parameters can be exported to a table of ASCII data. (SM)
  • fix Minor bugfixes. (SM)

models

  • add Stimulation parameters and BCL can now be clamped in models. Useful for simulation of restitution curves. (SM)

Version 1.3.3 (October 2004)

environment

  • add Build system can now update CESE from CVS source code. (SM)
  • add Result View content can be exported to the PNG image file. This is a convenient way to create screenshots of the result data. (SM)
  • fix Printing of data plots now works properly. The fix for this problem is related to the work done on plot scaling. Plotting now properly supports high-resolution graphics devices, such as printers. (SM)
  • fix Improved data axis code. (SM)
  • fix Fixed lockup problem in the data view. (SM)
  • update Major rewrite of the Print Preview dialog. Implemented correct zooming using the off-screen image. (SM)
  • update Changed the way scaling transform works in plots. Custom line width and attributes can now be implemented. (SM)
  • update Storage model has been improved to better support batch channel inserts. Performance of the data export was improved as the result of the changes. (SM)

models

  • add Added the FitzHugh-Nagumo (1961) Model. (SM)
  • fix Removed singularities in the Hodgkin-Huxley, Beeler-Reuter, and Luo-Rudy I model formulations. (FS)
  • fix Fixed repolarisation problem in the Puglisi-Bers Model. (SM)

Version 1.3.2 (September 2004)

environment

  • add Added background task progress notification mechanism. (SM)
  • add Beginning of unit test support. Tests are located in $CESE_HOME/tests directory. (SM)
  • fix Fixed warnings related to unused variables and static access. (SM)
  • update Data analysis routines (Build I-V, Basic Statistics, Channel Average) have been converted to background tasks with proper notification. (SM)
  • update Updated Record Editor. (SM)
  • update Updated JavaHelp documentation. (SM)

models

  • add Models are now being built using the Ant script. (SM)
  • fix Removed singularities in the Luo-Rudy II model formulation. (FS)
  • fix Fixed time step and experiment time in the Hodgkin-Huxley Model. (SM)
  • update Model source code was moved to $CESE_HOME/models directory. This is was done to cleanly separate models and the environment. (SM)

Version 1.3.1 (June 2004)

environment

  • fix Fixed CESE on non-English default locales. (SM)
  • fix Fixed CESE on MacOS X. Issue [979177]. (SM)

models

  • add Added the Hodgkin-Huxley (1952) Model. (SM)
  • update Updated to the recent MathML-X stylesheet. (SM)

Version 1.3 (May 2004)

environment

  • add Eclipse Team Set allows rapid project/CVS setup in Eclipse IDE. (SM)
  • add Ant build script should make source compilation and JavaDoc generation a snap. (SM)
  • add NetCDF export. (SM)
  • add Model Manager dialog with Install Model/Remove model, etc functions. This is a beginning of the CellML conversion GUI too. (SM)
  • update Updated JavaHelp documentation. (SM)
  • update Work to make CESE Tiger (1.5)-ready. (SM)

models

  • add Preliminary support for conversion of CellML models into the CESE/JavaBeans-compatible Java source code. (SM)

Version 1.2 (Nov 2003)

commands

  • fix Improvements to the clamping code -- we now explicitely specify what variable to clamp in record files. This eliminates ambiguity of the old clamping routines. (SM)

environment

  • add Further code refactoring -- all CESE classes were moved to com.javable.cese.* packages. These include templates for AP models and data exports. (SM)
  • add Cursors were added -- this permits selection of the region of interest (ROI) and data measurement similar to Axon Clampfit. Expect more features and performance rewrite of cursors in the next release(s). (SM)
  • add A number of analysis routines were added -- Build I-V (current-voltage relationships and data extraction), Basic Statistics (including peak and slope values extraction), Channel Averaging. Note that CESE remains to be mainly simulation control package, you should consider using commercial data analysis software for any complicated data processing. (SM)
  • add Sweep manipulations using Sweep Selector -- similar to the Axon Clampfit, only better :). (SM)
  • fix Scatter plot type was finalized. (SM)
  • fix Lots of bugfixes. (SM)
  • update Feature update release -- lots of new features added/updated, most notably cursors and data analysis routines. (SM)
  • update Initial (and still incomplete) JavaHelp documentation/manual. (SM)

Version 1.1 (Aug 2000)

commands

  • add A simple XML Editor is bundled (thanks to the great guys at CERN). Both components of the clamping protocols (records and signals) can be created in this editor (you still need to know what you are doing, though). (SM)
  • add Records can be tested before usage. (SM)
  • fix Clamp signal framework was finalized (or I just gave up). (SM)

environment

  • add Added support for pluggable plots -- different types of plots can be combined in a single view. Line plot is still the only one that used, and beta-version of scatter plot is ready. More plot-types are underway (or implement your own). (SM)
  • add Zoom out is implemented. (SM)
  • add Views and axis now have context menus (right mouse button click). (SM)
  • add Views and axis properties can be changed in correspondent dialogs. (SM)
  • add Print Preview dialog. (SM)
  • add Data can be exported into the delimited ASCII and ATF (Axon Text Files) -- you can import your simulation results into the Axon ClampFit now. (SM)
  • add Simulation dialog is added (it is possible to start a set of simulations with a single click on Start Simulation button -- useful for I-Vs). (SM)
  • add Improved About dialog :) (SM)
  • fix Plotting framework was refactored and moved into the separate package (com.javable.dataview). It's made complitely independent from the rest of the program and can be reused in any project that requires 2D plotting abilities. (SM)
  • fix Plotting framework now relies on standard JDK classes more. (SM)
  • fix How channel stores the data and how it stores all visual attributes is now separated using the Decorator pattern. (SM)
  • fix Dramatic increase in the plotting performance (Java2D + smarter use of clipping). (SM)
  • fix Lots of smaller fixes/improvements that I forgot about. (SM)
  • update This is a first release that is targeted to the general audience. Most of the core components were rewritten and this should provide a stable platform for future updates. Markovian models framework is not final (need a better way of handling models with several Markovian currents) -- you've been warned. (SM)
  • update Major rewrite of the JavaBean editors/properties framework. It's now much more flexible and is able to provide access to any Java class (in 1.0.2 support was limited to the primitive types, boolean and String). (SM)
  • update Plotting now utilizes Java2D framework (using Graphics2D everywhere). This allows better hardware acceleration (especially in the upcoming JDK1.4), and full access to the Java2D advanced plotting features (antialiasing, clipping, alpha channel, fancy strokes and fills, etc.). (SM)

models

  • add Main template class for models (com.javable.cese.templates.AbstractAPModel) got Runge-Kutta-Felhberg 5th order ODE solver. This means that all your models can now get access to this solver (simply override derivative() method in your class and call doMarkovian() once at the every simulation step). It's here mainly for Markovian models (unless you can come up with a better use). (SM)

Version 1.0.2 (Sep 1999)

environment

  • update This is the first limited "proof of concept" public release of CESE. Most of the critical features were implemented in this version, but framework was not flexible enough which resulted in the major code rewrite in v. 1.1. (SM)
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