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TODO.md

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User Requests

  • General

    • key parameters in networks, environment need to be findable and available in UI

    • expose network XML, or at least key network info (modules, file paths, gui vars...)

      • better network parameter editing
      • maybe a network wizard?
      • show what files are being used, network file name

    • more example nets

    • more documentation, more sample networks (very useful for demonstrating module functionality)

    • search modules, networks for keywords

      • see Matlab descriptors at the top of source files as an example
      • when searching for modules, can we have the option of searching within the module text (i.e. search module GUI component names, variable names etc.)

    • port colors: change intensities, not just colors

      • get updated palette from Nathan

    • standardize field names etc.

      • i.e. interpolation: source -> target, object -> target, source -> object

    • support for transparent background in images or movies (image library)

    • image or movie resolution options (can we generate higher resolution images than displayed?)

    • first time use window

    • Nifti reader for SCIRun

    • STL file support

    • Add preset location for saving SCIRun network files

    • Parser modules need better error reporting

    • Actually implement ColorMap2DSemantics module

    • list field properties

    • if statement module

    • SCIRun should be able to read "obj" format meshes

    • Simple importer for 1D colormaps

  • UI

    • collapse network preview window

    • side pane to expose some module parameters

      • expose important dataset parameters too (size, dims, data info etc.)

    • easier way to do notes

      • copy notes with modules
      • easy way to edit or clear notes
      • easy way to manipulate note location
      • render text on top of pipes

    • better graph layout algorithms?

      • look into graphviz, others?
      • line up modules
      • expose-like (OS X)

    • Add GUI element for indicating result of "Clear Output" button of module CollectMatrices

    • Add string port to Read / Write Nrrd

    • Add support for newer Matlab file format

    • Add cylinder to vector glyph types

    • ShowMatrix module should detect matrix dimensions

    • IO plugin for Meshalyzer binary mesh format

    • IO plugin for a binary node index matrix

  • Networks

    • halt network without killing SCIRun

  • Subnets

    • subnets must work (currently broken) - should be an easy select and create operation in GUI

    • better views for subnets: dockable widgets, tabs etc.

    • duplicate entire subnet

    • import network into other network

      • choice to import as subnet or register network
      • choice to save subnet as separate file

Qt Migration

  • Basic GUI Redesign

    • Determine overall look and feel.

      • Background color of network editor
      • Placement of main window widgets--match current design at first?

    • Redesigning major parts of the main window.

      • Menu bar
      • Context menus
      • Toolbars
      • Status bar
      • Configuration panel
      • Module Search
      • Module progress indicators
      • Module general settings: port caching, info on ports, general info: available in "drawer" subwidget
      • Tooltips
      • Command window

    • CIBC:Documentation:SCIRun:DevTasks:SCIRunGuiFeatureList

  • Major Development Milestones

    • All menu options/preferences work
    • Can walk through entire SCIRun tutorial!

  • IO

    • is there a way we can display a brief blurb describing file importer and exporter plugin information (i.e. show a short description of the file types supported, file extensions etc.)?

  • Graphics and Visualization

    • Be able to select or click on objects in renderer and get information i.e. node index, position etc.

  • OpenGL

    • move all OpenGL code into Core (and intermediate layer as needed)

  • Externals

    • verify that libpng and zlib are still needed, if so, update
    • better XML parsing library (libxml2 is overly complex and buggy)

  • Build

    • merge all generated headers into a single generated header file

  • Testing

    • Add regression testing feature to diff numerical output, either through text files or of matrix objects directly.

  • Core

    • Isosurface algorithm is very slow and should be rewritten

  • Error Handling and Exceptions

    • SCIRun exceptions could use an overhaul.

    • SCIRun assertions could also use an overhaul.

    • The same kind of assertions need to be used throughout the code. Currently, we're using:

      • assert from cassert
      • SCIRun's custom ASSERT macros
      • Boost static assert (perhaps it would be best to replace all other asserts with Boost assert utilities?)

  • Modules

    • Possible Problem Modules

      • ShowMatrix: this module should be completely rewritten
      • CreateMatrix: bug #327
      • GeneratePointSamplesFromFieldOrWidget: spinner boxes in both tabs are not editable. This is really annoying if one wants to generate a large number of samples.
      • GeneratePointSamplesFromField: The execution pattern for this module should be improved. Also, SCIRun test networks are using GeneratePointSamplesFromFieldOrWidget, so there are no tests for this module.
      • CreateAndEditColorMap: the GUI is not very usable and can be difficult to navigate.

    • Module Improvements

      • See if it's possible to encapsulate common functionality in Matlab Importer modules in a parent class. Same with Exporter modules.

Known Bugs

  • Duplicated modules in networks
  • Adjusting current displayed slice in ShowTextureSlices
  • Connecting module after disabling and enabling can crash SCIRun
  • Row indices not displayed for newly created rows in CreateMatrix
  • Error reading fields created using older SCIRun versions
  • BioTensor crashes on Windows
  • BioTensor fails on OS X Snow Leopard
  • SCIRun crashes when applying colormap to field from OBJ file
  • InsertHexVolSheetAlongSurface gets invalid indices, doesn't converge
  • changing light direction for volume rendering is broken
  • closing the ViewWindow causes a crash
  • Crash while not SCIRun is idle
  • Create module skeleton creates bad CMake files
  • Crash: replacing port on ShowTextureSlices
  • Dipole does not change orientation after edit
  • X11 crash when loading network
  • SCIRun Matlab field exported by SCIRun cannot be read by SCIRun
  • Incorrect rendering when network executed on startup
  • Installer install path defaults to previously installed path
  • UnuAxInfo should show current axis attributes
  • Disabled modules execute during regression testing
  • File dialog selection gets reset
  • Showfield does not update appropriately.
  • ShowAndEditCameraWidget hangs SCIRun
  • Regression tests timeout before loading network
  • Networks that hang on execution in regression testing mode fail to output image.
  • scirun hangs while viewing extracted isosurface
  • ResampleRegularMesh module missing resampling kernel options
  • CalculateFieldDataMetric Integral option broken
  • Cannot change field type in CreateParameterBundle module GUI
  • CreateAndEditColormap SegFault
  • Segfault caused by key/button click on widget
  • Matlab file text field gets cleared on execute in ExportDatatypesToMatlab
  • Transparency not supported in ExtractIsosurface geometry output
  • RemoveZerosFromMatrix module is broken
  • RemoveZeroRowsAndColumns module does not remove zero columns
  • GenerateLinearSegments output field has geometry size 0
  • CreateAndEditColorMap hangs on execution
  • ExtractIsosurface module geometry ignores opacity
  • SolveLinearSystem Jacobi method does not converge when used with AddKnownsToLinearSystem
  • ShowField crashes if attempting to display data value text in a field with no data
  • ShowTextureSlices crashes when its output port is used more than once.
  • InsertHexVolSheet creates invalid elements
  • ExtractIsosurface creates crossing elements
  • RefineMesh local refinement bug
  • FairMesh should check for and report crossing elements
  • ConvertColorMap2ToNrrd always fails on assert
  • EvaluateLinAlgUnary writes to invalid SparseMatrix location
  • Setting SparseMatrix entries to same constant fails with EvaluateLinAlgUnary
  • Review OptimizeConductivities module to make sure it works as expected.
  • OptimizeDipole sample networks hang
  • ViewScene record movie fails silently if path doesn't exist
  • torso-tank-bem.srn network fails if cage is moved
  • ExportNrrdsToMatlab doens't preserve header information
  • ViewSlices module not ported properly from SCIRun 3

Resolved Bugs

  • SCIRun crashes when you write a movie to a directory where you do not have the permission to.
  • libxml2 does not resolve local DTD path
  • SCIRun module GeneratePlanarElectrode causes SCIRun to crash when loading.
  • ShowAndEditCameraWidget UI is broken
  • Changing spaces in OS X 10.6.3 logs user out
  • Seg3D freezes when using 'Save Volume'
  • MatlabInterface broken in SCIRun OS X app
  • Tcl/Tk interpreter crashes on startup on Ubuntu 11
  • Problem reading Seg3D2 segmentations (.nrrds) into SCIRun
  • ExportFieldsToMatlab executes when disabled
  • Record movie causes SCIRun to hang
  • Memory leaks in BuildFEGridMapping algorithm
  • CollectMatrices does not detect new inputs
  • Missing parser documentation in CreateFieldData Medium
  • String port input does not update parser module expression
  • Deleting CreateAndEditColorMap2D from network crashes SCIRun.
  • SolveLinearSystem graph does not show the current iteration
  • ExportMatricesToMatlab file path error on Windows
  • GetNetworkFileName does not update when network is cleared.
  • Tcl/Tk GUI code cannot handle infinite floating point values
  • Deleting swatches from CreateAndEditColorMap2D's UI crashes SCIRun.
  • Issues with ConvertMatricesToMesh module: GUI
  • Issues with ConvertMatricesToMesh module: C++
  • Script tab in ReadField does not work
  • Closing rendering window crashes X11 in XQuartz 2.7.x
  • Crash when displaying text in LatVol (duplicate)
  • SparseRowMatrix::put cannot put values in matrix if number of non-zero values 0
  • Visualization test networks hang on Ubuntu when executed on startup
  • TriSurf mesh get_edges with nodes argument broken