Home > SCIRun/BioPSE 1.24.1 Release Notes

SCIRun/BioPSE/Fusion 1.24.1
Release Notes

(1.24.1 update 3/15/05)

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.

New Modules
Module Enhancements
Deprecated Modules
Power App Enhancements
Infrastructure Enhancements
Environmental Variables
GUI Enhancements
Documentation
Data Sets

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

BioPSE Modules (Category in parentheses)

  • ApplyFEMCurrentSource (Forward) - Changed to use a Mapping Matrix instead of an Interpolant Field.

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.

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 parenthesis)
  • 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.

Please send feedback/improvements specific to the rpm to scirun-users@sci.utah.edu.