sciinstitute / scirun

SCIRun is a Problem Solving Environment, for modeling, simulation and visualization of scientific problems. This is version 5, the upgraded version of SCIRun v4.

SCIRun 5

Contents

• SCIRun 5
  • Summary
  • Goals
  • Documentation
    • Build
    • Python API
  • Questions and Answers
  • License and Credits

Summary

Warning!	SCIRun 5 is beta software, you may use for real science but beware of instability.

Goals

SCIRun 5 is a complete rewrite of the GUI front end and graphical components of SCIRun 4, including a more stable and efficient middle layer, with support for Python scripting.

Documentation

For documentation, please see: https://scirun.readthedocs.io/en/latest/

Build

Please see https://scirun.readthedocs.io/en/latest/start/build.html

Python API

Please see https://scirun.readthedocs.io/en/latest/user_doc/python.html

Example Data

Please see: https://github.com/CIBC-Internal/SCIRunTestData

Or, for the older dataset: https://www.sci.utah.edu/releases/scirun_v4.7/SCIRunData_4.7_20160120_data.zip https://www.sci.utah.edu/releases/scirun_v4.7/SCIRunData_4.7_20160120_data.tgz

Questions and Answers

For help, check out the discussion page: https://github.com/SCIInstitute/SCIRun/discussions.

License and Credits

For more information, please see: http://software.sci.utah.edu

The MIT License

Copyright (c) 2023 Scientific Computing and Imaging Institute, University of Utah.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

scirun's Issues

SCIRun Command Queue

To implement command line parameter actions.

Generalizes #130, will deliver after.

Bug: Load network file did not clear existing network.

Module: Eigen solvers

GUI will be similar to SolveLinearSystem, but just provide Eigen's built-in solvers for now.

Some GUI improvements:

• Use text box for error entry.
• Use spinner for max iterations.

Command line options

Integrate boost.ProgramOptions, with this initial set of command line options:

• < file >
  • loads a network file
• -e < file >
  • loads a network file and runs it
• -E < file >
  • loads a network file, runs it, quits

Basic logging architecture

First pick a library: boost.Log, Pantheios?

Logging should be available everywhere.

Module: CreateMatrix

Basic implementation: dialog is there, just grab the string from the text editor and dump it into a matrix, send it out the one matrix output port.

Move connection verification to Domain layer; emit success/failure signal.

C++11 changes

1. boost::shared_ptr -> std::shared_ptr

Code Review: FFP Code in SCIRun 4

Go in depth with some of the current code.

More serialization unit testing is needed.

Tests for bad input, for instance.

Integrate Python: Scripting and Programmability

This is the full headless-mode deliverable. Comes after #179, #180, #266, #299, as well as #176.

Module: "find all files referred to in this network with this path relative to network file"

Need to prototype this idea.

Spire-based ViewScene/ViewWindow

Tuvok will come later.

Add Eigen to the build

Fix build warnings in VC10: Windows DLL related ones

Mostly the C4251/4275s.

Save network file from GUI

Be able to save out a network file using boost.Serialization. Must contain:
--module description list
--connection list
--module positions in the window
--module state

Make debug build work.

Need to include debug versions of boost libs and point to them using the right cmake function. This will be somewhat moot when boost is built as an external alongside SCIRun as it is currently in v4.

Code Review: Service/Middle Layer

8/17: Library organization and naming.
8/24: Discussed State and came up with GlobalStateManager, ModuleVariable.
8/31: Boost library usage.

Build Shared Libs should be on by default

Error reporting: global

Where should the top-level try-catch block go? For instance, if there is an error saving out the network file, somewhere that should be caught and reported.

Investigate GraphViz usage for Network Editor

Eigen integration: Sparse Matrix type

Will inherit from Eigen's class as with DenseMatrix.

Module Widget: resize based on title string

Test case is EvaluateLinearAlgebra*nary modules.

Improve Module::get_input/send_output

Need to access by port name; add option check and maybe a null check; provide casting via template somehow.

Sample networks

Once save/load works, provide lots of sample networks.

Bug: connection delete from GUI is not working the first time.

You need to delete a connection 3-4 times for it to be actually deleted.

Separate Interface_Modules by category

Beautify Module Widget on Mac

When input and output ports are present, the middle buttons get squished.

Clean up duplication.

Run SIMIAN!
http://www.harukizaemon.com/simian/

Eigen integration: Dense Matrix type

Code Review: Overview of OpenGL Code in SCIRun 4

High-level overview with code examples. Include broad categories of what can stay, what should go, what's good and bad, etc.

Global State Manager

Needs a new category. Start by stamping out classes based on diagram from 8/24 meeting.

Load network file into GUI

Once a network file can be saved, be able to load one in, with modules/state/position exactly the same as when saved.

Fix OpenSUSE build; test out build on Ubuntu, etc.

Clean up duplication in test code.

Directory/Namespace changes

Move things to (with matching namespaces):

src/Core/
src/Core/Algorithms
src/Dataflow/Network
src/Dataflow/Engine
src/Dataflow/State
src/Dataflow/Network/Serialization
src/Dataflow/State/Serialization
src/Modules/

Error reporting: modules

When an algorithm or module needs to stop with an error, SCIRun 4 supplies an error() function that will end up as a red button with the error message in the GUI. We need something similar.

Save/Load/SaveAs Buttons in a toolbar

Doxygen documentation

Generate Doxygen documentation.

Eigen integration: Expose basic Eigen functionality

Meet with users to look at graphics examples

@cbrightsci will meet with:

• Moritz (@moritzdannhauer): 4th floor office
• Josh Blauer: 4th floor north side lab
• Jess Tate (@jessdtate): 4th floor south side lab
• Brett (@zaracay): 3rd floor north side lab

Design: New Renderer and Geometry Datatype

Create new Executable project with just scirun/main

Should have no Qt dependency. Check out Seg3D's structure.

Right-click in network editor on top of module should select that module.

Right now right click brings up a context menu for whatever module happens to be selected; it's confusing.

Matrix reading code has issues

It's too brittle, can't handle newlines very well. I'd like to redo it so that the format has [nrows,ncolumns] at the top of the file; should also speed up reading.

Code Review: Unit Testing

Go over some current tests, look at coverage, brainstorm test cases for the next milestone.

GUI Connection z-level needs work.

Should copy SCIRun 4's approach for now: modules always above connections.

Code Review: Directory/Namespace structure

Fix broken unit tests

Some tests crash on non-Windows platforms; others are in a "TODO" state.

Eigen Library Training