Release Notes (Detailed) for SCIRun Version 1.24.1 (Full Release)
March 9, 2005
Note: The release notes from the previous 1.24.0b (Beta) release
contain a list of the majority of updates for the 1.24 release.
Please refer to those notes if you need a comprehensive list of
updates from the 1.24 version of SCIRun.
Content:H1,H2
New Modules
SCIRun Modules (Category in parentheses)
- BuildMappingMatrix (FieldsData) - Was BuildInterpMatrix
- ApplyMappingMatrix (FieldsData) - Was ApplyInterpMatrix
- DirectMapping (FieldsData) - Was DirectInterpolate
- MatrixInfo (Math) - Information about a SCIRun matrix.
- EditColorMap2D (Visualization) - Was EditTransferFunc2
Teem Modules (Category in parentheses)
- NrrdSetupTexture (NrrdData) - More efficiently building volume rendering data.
BioPSE Modules (Category in parentheses)
- ApplyFEMElectrodeSource (Forward) - Split 'electrode set' mode of ApplyFEMCurrentSource into separate module.
Module Enhancements
SCIRun Modules (Category in parentheses)
- Add Generation output to the various Info modules.
- ClipByFunction (FieldsCreate) - Fix compilation for gcc 3.4 (u0-u5 templating issue).
- GatherFields (FieldsCreate) - Add support for elem data copying.
- GatherFields (FieldsCreate) - Fix crash bug when no valid input fields are present.
- SampleField (FieldsCreate) - Lower the max number of samples to 201 on rake slider.
- BuildMappingMatrix (FieldsData) - Reenable parallel interpolation.
- ChangeFieldBasis (FieldsData) - Emit identity mapping if basis is same.
- ChangeFieldBasis (FieldsData) - Fix backwards compatability bug.
- FieldMeasures (FieldsOther) - Add error checking and fix normals.
- LinAlgUnary (Math) - Added support for SparseRowMatrices.
- LinAlgBinary (Math) - Added support for SparseRowMatrices.
- Viewer (Render) - Check for stereo support before using it in the viewer, bug #2478.
- Viewer (Render) - Fix 'Use Global Controls' button on Viewer items, bug #2431.
- Isosurface (Visualization) - Filter out degenerate output elements when isosurfacing, bug #2468.
- EditColorMap2D (Visualization) - load/save use cmap2 format, not .xff files
- EditColorMap2D (Visualization) - fix endian bug in ppm thumbnail images on macs
- TransformMesh (modules with scrolling text dialog) - UI comes back to the size the user specifies
Teem Modules (Category in parentheses)
- Upgraded many Unu and Tend modules to work with new Teem, 1.8.0.
- NrrdToField (Converters) - Now handles PointCloud points only case.
- NrrdToField (Converters) - Fix gcc 3.4 compilation (reorder includes).
- UnuFlip (UnuAToM) - Maintains axis min/max for flipped axis.
- UnuCmedian (UnuAToM) - Module now caches.
Insight Modules (Category in parentheses)
- ImageToField (Converters) - Bounding box and number of samples now set correctly.
- BinaryThresholdImageFilter (Filters) - Initialize lower threshold to be lower than upper threshold.
BioPSE Modules (Category in parentheses)
- ApplyFEMCurrentSource (Forward) - Changed to use a Mapping Matrix instead of an Interpolant Field.
Deprecated Modules
SCIRun Modules (Category in parentheses)
- BuildInterpolant (FieldsData) - Use BuildMappingMatrix instead.
- BuildInterpMatrix (FieldsData) - Use BuildMappingMatrix instead.
- Interp2TransferMatrix (FieldsOther) - Use BuildMappingMatrix instead.
- ApplyInterpolant (FieldsData) - Use ApplyMappingMatrix instead.
- ApplyInterpMatrix (FieldsData) - Use ApplyMappingMatrix instead.
- DirectInterpolate (FieldsData) - Use DirectMapping instead.
- EditTransferFunc2 (Visualization) - Use EditColorMap2D instead.
Power App Enhancements
Power App (Package in parentheses)
- Help and about now work for all Power Apps.
- BioTensor (Teem) - Now saves out glyph normalize scale.
- BioTensor (Teem) - Autoviews correctly when loading tensors directly.
- BioTensor (Teem) - Bug fixed when user selects Execute mutliple times during load process.
- BioTensor (Teem) - Coloring planes, isosurfaces, glyphs and fibers and switching between all of these color methods now works.
- BioImage (Teem) - Handles reseting of crops and resamples correctly when loading a saved sesssion as well as the filter type of a resample filter.
- BioImage (Teem) - 'incr' call fixed when adding filters to the history.
- BioImage (Teem) - Proper ViewSlices orientations now set when loading a session.
- BioImage (Teem) - Progress indicator now works for loading large datasets.
- BioImage (Teem) - Hide/Show icons reversed in filter history.
- BioImage (Teem) - Uses correct paths to data directory.
- BioImage (Teem) - References to Cmedain changed to Median Filtering.
- BioImage (Teem) - Scroll wheel now works in history frame.
- BioImage (Teem) - Now uses a RescaleColorMap module for volume rendering for machines that do not support shaders.
- BioImage (Teem) - Now handles loading different datasets.
- BioImage (Teem) - Allow user to change color of 2D text.
- BioImage (Teem) - Allow user to turn 2D text on or off.
- BioImage (Teem) - Updated tutorial figures.
- BioImage (EditColorMap2d) - Allow user to paint directly in EditColorMap2D window when paint widget is selected.
- BioImage (EditColorMap2d) - Widgets now save the value range in which they were created.
- BioImage (EditColorMap2d) - Add 'X' Delete button to widgets to quickly delete widgets.
- BioImage (EditColorMap2d) - Fix un-necessary multiple redraws of volume rendering when moving widgets.
- BioImage (EditColorMap2d) - Paint strokes scale with window zoom level.
- BioImage (EditColorMap2d) - Swatches save to ~/SCIRun/Colormaps directory
- BioImage (ViewSlices) - Toggle button to display Anatomical or Cartesian Coordinates in Orientation labels
- BioImage (ViewSlices) - Real-time update of volume rendering transfer function when painting.
- BioImage (ViewSlices) - Over and Under Layers while painting volume rendering transfer function.
- BioImage (ViewSlices) - Add 'Show Transfer Function in 2D' checkbutton.
- BioImage (ViewSlices) - Autoviewing of 2D slice windows.
- BioImage (ViewSlices) - Gradient Threshold slider masks paint in low gradient areas.
- BioImage (ViewSlices) - Add lighting to 2D slices in 3D window
- BioImage (ViewSlices) - Change Window Width and Window Level to handle floating point value ranges.
- BioImage (ViewSlices) - Disable painting when cropping.
- BioImage (ViewSlices) - Remove padding for cropping as eye now shows correct data.
- BioImage (ViewSlices) - Fix display of data that was flipped by unu flip before loading.
- BioImage (ViewSlices) - Change Zoom to be up/left is zoom out and down/right is zoom in to be consistent with 3D window.
- BioImage (Viewer) - Fix 3D autoview when loading a dataset for the first time.
- BioImage (GUI) - Move eye radio button to between filters and automatically update when changing eye.
- BioImage (GUI) - Automatic Re-Orginization of filters in Network Editor
- BioImage (GUI) - Crop filter has number spinners for changing bounds with mouse.
- BioImage (GUI) - Add 'Show 2D Crop Region' checkbutton for crop filter to toggle display of crop region of interest.
- BioImage (GUI) - Autoload corresponding .cmap2 file when loading all nrrds (not just distributed datasets).
- BioImage - Fix connections between filters when inserting/deleting image processing filters.
- BioImage - Gracefully refuse to load non-3D datasets.
- All PowerApps (Teem) - changed the label of Nrrd file reader to reflect ability to read in generic raster data, such as .vff and .vol
Infrastructure Enhancements
- Fix permissions of SCIRun/src/include/sci_gl.h and SCIRun/src/include/sci_glx.h that were causing compiles to fail.
- Fixed how we build tensors from eigenvectors/eigenvalues
(had been missing a transpose).
- Add double and float types to PropertyManager so that all options in NrrdSetProperty work.
- Add SparseRowMatrix multiply.
- Fixed crash bug in SparseRowMatrix::submatrix.
- Cleaned up matrix classes.
- Change Matrix::get to return value rather than reference.
- Use copy_properties instead of unsafe typecast in teem modules.
- Cleanup Thread_pthreads.cc, do proper pthread error checking (not errno).
- Templatize Import/Export ExecConverter code to reduce redundancy.
- Throw error on invalid get_iport(string) or get_oport(string). Remove much redundant error checking code from modules.
- Add data_size() function to the Field class.
- Simplify update_progress interface.
- Add new send command to Mailbox class so that we don't spam redraw events on viewer expose and resize.
- Use dynamic test for shader support in volume code.
- Add support for get_normals to ImageMesh and StructQuadSurfMeshes.
- Use std::vector for all Mesh::get_neighbors. Cannot guarantee an upper bound on neighbor size so fixed-sized arrays won't work.
- Work around bad parsing of exponents in our tcl expscale widget. %d will not read integers with a leading zero as it thinks they are octal. However %.0f works.
- Wrap up OpenGL shader problems to avoid backwards linking compatability problems.
- Create virtual destructor for GeomColormapInterface.
- Use const references for Masked*Field indices where appropriate.
- Fix volume rendering transparency on apples with unsupported hardware.
- Change FreeType texture to render to 1 channel to save texture memory
- Change name of base RPMs from SCIRun to SCIRunBioPSE
- Major re-factoring of SCIRun->Render->ViewSlices to use function pointers for common tasks
- Re-Layout of BioImage underlying network makes network debugging easier.
- Throttle ViewSlices redraw loop if mouse is not in GL window.
- Fix bug rendering ViewSlices slice positions in wrong locaiton on first draw.
- Print name of mutex when displaying error about destroying locked mutex.
- Fix bug that was creating new widgets in EditColorMap2D off-screen
- Added 'bool GuiVar::changed()' method that return true if the TCL var has changed. Useful for determining if re-execution is necessary.
- Fix bug that was disabling hardware widget rasterizaiton in EditColorMap2D.
- Flip input nrrd in Y in Teem->Converters->NrrdToColorMap2.
- Added methods GuiArgs::get_int() & GuiArgs::get_double(), that automatically convert TCL arguments to tcl_command to their numeric representation and handle error checking too.
- Added versioning of .scirunrc file. Prompts user to copy .scirunrc file if version of SCIRun is newer than the version the users .scirunrc file was written for.
- Bug #2535. Fix duplicating module on subnet.
- Bug #2536: Support for dopuble-quote character '"' in Tooltips.
- Clear EditColorMap2d undo stack when loading new .cmap2 file
- Package RPMS and OSX binary release with ITK 2.0.0.
- Add button 'New ViewSlices Window' to open multiple ViewSlices GL windows for one module
- Bug #2031, update wording and numbering of viewer windows in menus.
Environment Variables
- SCIRUN_RCFILE_VERSION - Allows versioning of .scirunrc file.
- SCIRUN_DISABLE_SHADERS - Manually disables GL ARB fragment shaders for debugging.
GUI Enhancements
- Cleaned up and simplified the 'Component Wizard' (for new module creation).
Documentation
- Added a Graphics Card and Accelerated Driver section to the FAQ
Data Sets
- There is .cmap2 file for each dataset in the volume/
directory, which are the default cmap in BioImage when viewing
the respective datasets.
- There are .jpg files for each dataset in the volume/
directory that show a screenshot of the volume rendered in BioImage.
Known Bugs