Release Notes - SCIRun Version 1.22 - July 14, 2004

Data Sets

• New "Matlab" directory containing geometry.mat and timeseries.mat used in the MatlabInterface sample nets to demonstrate capabilities of new MatlabInterface modules.

New Modules

SCIRun Modules (Category in parentheses)

• NodeGradient (FieldsData) module for computing gradients of node centered LatVolFields.
• ApplyInterpMatrix (FieldsGeometry) module interpolates the Source field onto the geometry of the Destination field using the Interpolant matrix to do the projection.
• ToStructured (FieldsGeometry) module for converting from regular lattices to structured grids.

Teem Modules (Category in parentheses)

• All Unu and Tend modules have been wrapped.
• Add ImageMagick based ImageImporter and ImageExporter (DataIO) modules.
• MatrixToNrrd (DataIO) - converts a SCIRun Matrix to nrrds.
• NrrdToMatrix (DataIO) - converts 1D and Nrrds to a SCIRun Matrix.
• MRITissueClassifier (Segmentation) module to support Tolga Tasdizen's research.

MatlabInterface Modules (Category in parentheses)

• MatlabMatricesReader (DataIO) - reads a matrix from a MATLAB file.
• MatlabNrrdsReader (DataIO) - reads a matrix from a MATLAB .mat file and exports it as a Nrrd.
• MatlabFieldsReader (DataIO) - reads a SCIRun field from a MATLAB file. The module requires that the data in the MATLAB file is formatted according to the guidelines described in the documentation.
• MatlabMatricesWriter (DataIO) - saves a SCIRun matrix in a MATLAB .mat file.
• MatlabNrrdsWriter (DataIO) - saves a SCIRun NRRD object into a MATLAB .mat file.

Module Enhancements

SCIRun Modules (Category in parentheses)

• Added '?' button to open module help.
• Changed readers and writers to have a Set, Execute, Cancel an Find button. Set will change the module's filename, and exit the UI without executing the module. Execute will set the filenam, execute the module, and close the UI.
• All "Choose" modules have a "Use first valid" checkbox which causes the module to iterate over its connected inputs and use the first valid data.
• Regular Meshes now display formatted printing of Cell, Node, and Face indices in ShowField, Probe, and FieldInfo modules.
• SampleField (FieldsCreate) module now has ring on 3D gauge widget to set number of samples interactively.
• Added VCR buttons to MatrixSelectVector (Math) UI
• Ability to link a viewer's ViewWindows so that interaction in one window, will be duplicated in other ViewWindows.
• Added Viewer's ViewWindow->View... entries to get view from other active ViewWindows.
• Added Viewer's ViewWindow->View...->'Track Viewer Window 0' option to forward mouse events from view window 0.
• Fix saving of Viewer Window variables.
• Save the current visual in the Viewer module.
• Fix ViewWindow inertia mode lockup on Fedora Core 2.
• Viewer lights saved properly.
• MPEG movie recording can save to a path other than the working directory.
• Fix ViewWindow crash bug when autoviewing on single point.
• Change ManageFieldData to preserve field data type if possible.
• Change ClipField to ignore widget if there is a clip mesh.
• Add interpolant matrix output support to the ClipByFunction, FieldBoundary, IsoClip, Isosurface, FieldBoundary, and ChangeFieldDataAt modules.
• Replace TetVolMesh::Node::array_type with a statically allocated stack vector for performance enhancement.
• Support for edge emphasis of superquadratic tensors in ShowField.
• Use fabs for vector->rgb conversion in ShowField.
• Support eigenvector generation for tensor visualization within ShowField.
• Performance enhancements for StreamLines module.
• More efficient IsoClip find_ functions.
• Add normals option to the FieldMeasures module.
• ClipField saves widget positions now.
• Fix Unstructure (FieldsGeometry) to preseve node ordering in scanline orientation.
• Fix uninitialized sigma crash in ScalarFieldStats.
• Fix Isosurface-quadtypeface.net crash bug associated with ImageMesh::get_neighbors().
• Fix const DenseMatrix compilation error.
• Fix TransformData3 compilation failure if third field type was different than others.
• Use safe_normalize when computing TriSurfMesh normals, fixes degenerate triangle crash.
• Wrap instanced dynamic compilation classes differently to fix include crash in ClipByFunction, LinAlgUnary, LinAlgBinary.

BioPSE Modules

• Major speedup to ModifyConductivites (Modeling) by moving create_entires outside inner loop.
• Fix SetupFEMatrix crashing if data not at elements, report error instead.
• Added splash screen image for BioFEM.

Teem Modules (Category in parentheses)

• Using Teem 1.7
• Teem Unu Modules Categorized - The Unu modules were distributed into the subcategories UnuAtoM and UnuNtoZ to make finding specific modules easier.
• Kind axis information added to nrrds.
• Fix NrrdToField to take in 3 nrrds (Points, Connectivity, Data) and be able to create, structured, unstructured, or regular fields.
• FieldToNrrd can produce 3 nrrds (Points, Connectivity, Data).
• DicomToNrrd changed to DicomNrrdReader.
• AnalyzeToNrrd changed to AnalyzeNrrdReader.
• Added VCR buttons to NrrdSelectTime (NrrdData) UI.
• BioTensor now has the ability to save out computed tensors.
• Optimizations in BioTensor in order to use less memory.
• Use GuiFilename for filenames instead of GuiString in NrrdReader and NrrdWriter.

Insight Modules (Category in parentheses)

• FieldToImage, ImageToField, NrrdToImage, and ImageToNrrd now work on Vector images.

Deprecated Modules

SCIRun Modules (Category in parentheses)

• Deprecate BioPSE/Forward/SphereModel module, use SCIRun/FieldsCreate/ClipByFunction instead.
• Deprecate TransformVectorData and TransformScalarData, use TransformData instead.

Fusion Modules (Category in parentheses)

• NrrdFieldConverter module retired. Now use Teem's NrrdToField module which has the same functionality. SCIRun will automatically instantiate Teem's NrrdToField module when networks ask for a Fusion NrrdFieldConverter module.

Infrastructure Enhancements

• Replace TetVolMesh::Node::array_type with a statically allocated stack vector for performance enhancement.
• Multiple Notes windows can now be opened at the same time allowing for cut/paste operations.
• New progress bar shows accurate status of loading .net file or PowerApp initialization.
• Module help is now viewed in full HTML format. User is prompted to choose HTML browswer.
• The license has changed to the MIT License.
• Added exertior product to ColumnMatrix.
• TetVolMesh::refine_elements and refine_elements_levels added for tet refinement.
• Use const reference for GenericField::value() functions.
• Fix GeomCones polycount.
• More efficient GeomCones using GL_QUAD_STRIPS.
• Remove unused GUI elements from 3D Widget options.
• Fix broken io for all Struct*Mesh types.
• Fix thread lock problem for RHE and probably RH9.0.
• Change port disconnect behavior such that disconnecting a running module doesn't deadlock.
• Deprecate Core/Math/function parsing in favor of dynamically compiled C++ code. This was used by the ClipByFunction, LinAlgBinary and LinAlgUnary modules.
• Change Connection Blocking to internally Delete connections while keeping GUI representation up.
• Add Module::presave() callback to give modules a chance to copy all state to GuiVars before their state is written to TCL script.
• Change Mesh::get_weights() functions to use static array for weights.
• Implement LatVolMesh::get_cells for nodes.
• Change Mesh::locate to use const references where possible.
• Add node_reserve and elem_reserve functions to meshes.
• Add debugging asserts to set_value and value calls for fields.
• Use unsigned int as under_type for all meshes.
• Add module runtimes to regression output.
• Use lessthan function for map<> when hash_map not defined.
• Use a better string hash function, use X31 hash.
• Lock PropertyManager more agressively, add copy_properties function.
• Fix typo that was causing dynamic compliation directory to always default to ~/SCIRun/on-the-fly-libs//
• Add MakeReal function that converts double numbers that are: +infinity to max double, -infinity to min double, and NaN to 0. Used only for sending values to the TCL interpreter.
• Change widget_moved(int) method to widget_moved(int,BaseWidget*) signature to allow callback to determine which widget was moved
• Send return value back to TCL when calling [netedit sci_system].
• Removed redundant GuiContext::getSub/setSub methods. Use subVar to create sub-contexts instead.
• Add 'bool GuiSingle::valid()' method to return true if variable exists in TCL scope and is of correct type.
• Evaluate floating point numbers using TCL's 'expr' command to pare down redundant 0's after decimal place.
• Added TCL function initGlobal that will assign a value to a global variable if and only if that variable does not already exist.
• Add TCLInterface::complete_command that returns true if str is a complete TCL script with matching braces.
• Added TCL proc envBool to query the boolean status of an environemnt variable.
• Use Core/Util/Enviroment.h to provide universal environment that works on SGIs, Mac G5's, and Linux.
• In TCL, Use [netedit getenv VARNAME], and [netedit setenv VARNAME VALUE] to interface with environment variables.
• Move some code from SCIRun/src/Dataflow/GUI/Module.tcl out into SCIRun/src/Dataflow/GUI/Port.tcl and SCIRun/src/Dataflow/GUI/Connection.tcl.
• Added procedure genSubnetScript - the core of the network writing algorithm.
• Always send floating point numbers to TCL with a decimal in them so TCL wont cast them to an integer.
• Handle bad values (like inf) better when writing floating point values to networks.

Environment Variables

• Added environment variable SCIRUN_NET_SUBSTITUTE_DATADIR. If true, .nets will automatically substitute SCIRUN_DATA and SCIRUN_DATASET.
• Added environment variable SCIRUN_FAST_QUIT. If true, will not ask user to save before exiting scirun.
• Added environment variable SCIRUN_REGRESSION_TESTING_TIMEOUT. Set to number of seconds before regression test kills SCIRun.
• Added environment variable SCIRUN_HIDE_PROGRESS. If true, all progress bars are hidden. Renamed environment variable SCI_NOSPLASH to SCIRUN_NOSPLASH to be consistent with naming scheme.
• Renamed environment variable SCI_CONFIRM_OVERWRITE to SCIRUN_CONFIRM_OVERWRITE to be consistent with naming scheme.
• Move NEED_ATI_CARD_FIX define to SCIRUN_DRAWARRAYS_DISABLE environment variable.
• Don't ask multiple times about SCIRUN_DATA and SCIRUN_DATASET when loading subnets or a network with multiple sourceSettingsFile calls.
• Add SCIRUN_NOCLEANUPCOMPILE environment variable for debugging dynamically compiled code.
• Removed environment variables PSE_DATA and SCI_DATA.

Network Editor Enhancements

• Saving .net files re-written to be much faster for large networks.
• When writing networks, save out really large numbers in Scientific Notation.
• Added 'Duplicate' option to module menu. Also copies over all associated GUI settings for total duplication of module state.
• Added 'Insert Module' option to connection menu. Inserts module directly into the connections path.
• Added 'Replace' option to module menu. Replaces the module with another one, keeping its connections intact.
• Networks now save out all open ViewWindows and their size and position.
• Allow user re-sizing of panes in main network editor window.
• Added feature of moving by grabbing a connection.
• Added 'SR' button to Subnet Icons to access the Sub-Network Editor.
• Sub-Networks have been revamped to embed their information in the main .net file.
• Sub-Networks retain the old functionality with the 'On Disk' option to have the subnet files be saved seperately from the .net file.
• Subnets have been revamped to embed their information in the main .net file.
• Subnets retain to 'On Disk' option to have the subnet files be saved seperately or as templates.
• All .nets residing in SCIRun/src/Subnets and ~/SCIRun/Subnets/*.net are automatically loaded as templates.
• Added Control-Qtt> keyboard shortcut to quit.
• Fix deletion of dynamic ports.
• Show error when .net files attempt to create connections between ports of different types.
• Added black and white icons to SCIRun Network Editor and module GUIs.
• Connection tracing draws faster.
• Expand Network Information to store creation time and date per Sub-Network.
• Resize module icons when their name has changed.
• Move subnet editor ports right a few pixels.
• Fix bug writing out notes colors.
• Fix TCL error when choosing cancel on setting notes text color.
• Fix reseting notes text color.
• Fix crash when deleting modules with connections to themselves.
• Fix 'Expand Subnet' option for Sub-Network Icons.
• Fix error when removing ports with multiple viewers.
• Register all GUI variables with TCL for saving nets with TCL proc initVarStates.
• Mini network editor view now always displays correctly.
• Don't save invalid connections.
• Rewrite isaDefaultValue to vastly speedup writing of large network files.
• Arrow keys to scroll Sub-Network Editor. Must right-click in canvas to focus first.