Vtkski development

2010-11-08T15:43:51Z

Enodwell:

==Documentation for vtkski==

On-line documentation for vtkski is available at http://mike.kin.ucalgary.ca/vtkski/ .

==Building vtkski==

See [[Bone lab libraries#Build Instructions]] .

==Checklist for new vtkski classes==

* Select a category for your new class, for example 'IO', and put your source files in that directory.
* Modify the CmakeLists.txt file in that directory to add your new source files to the list of source files.
* Build vtkski and make sure that your class compiles.
* Refer to [[Creating VTK Classes]] for important coding style tips.
* Add your class, with a brief description, to [[Class List for vtkski]].

For help writing VTK classes, refer to the book "VTK User's Guide", Part III, "Developer's Guide". There are a couple of copies in the lab.

Eric To Do

2010-11-05T17:24:32Z

Enodwell:

==Soon==

Update FAIM / VTK installation instructions.

Put faim To Do list on trac.

Aluminum foam: need to rotate and trim this model.

Build ParaView 3.8.1 with mpi support.

Investigate load times for AIM files in ParaView.

FAIM: make sure that force constraints are correct. (Need to have vtkskiFiniteElementModel generator that applies constant body force?? or pressure??)

Material models: need string constants instead of integer constants (possibly they exist already for C++, but need Python versions.)

FAIM: all output to current directory.

Bending test: does not work very well for data sets with large offset (i.e. test25a.aim). Solution: Need to be able to specify not just neutral axis angle, but entire neutral axis vector. Also, probably want one surface fixed, and the other surface to have force conditions.

comparative functional tests (ie. compared to a previously-run functional test). Sharing a common base test class with compare_to_fe_by_assembly. This would be useful for multithreaded vs. singlethreaded.

faim: svn revision number (then report this in functional tests)

functional tests: anisotropic

functional tests: multithreaded solutions

functional tests: a test case for rotated tests (i.e., same thing, but rotated so along x,y,z axes). Or alternatively just apply force along different axis.

functional tests: force constraints

faim: transverse constraints for standard tests. i.e. pivot points.

faim: license file

faim: cmake installation to destination

faim: compare speed of new build to old build.

Backup drive.

Gaussian Filter in ParaView is working? not really - maybe in 3.8.1?

Test network speed between mighty-mac and mike .

AIMSimilarityRegistration.cxx : working?

AppPointPicker (name??) works on OS-X?

vtkski: test installation.

vtkTensorOfInertia:
# get principle axes
# accept weights (as pointer) - or use scalars as default??
# test cases
# treat voxels as boxes instead of points
# accept UnstructuredGrid input (someday)

Carolyn : list of programs.

Add section to wiki about:
1. Basic CMake usage
2. common development directories (/usr. /opt, etc...)

Try build of vtkski/ParaView with spaces in directory names.

ParaView build with vtkski included, Windows.

Binary build of vtkski? (Including all Applications.)

Westgrid account.

Make OrientationParameters a class (in vtkMeshGenerator).

Take Scoliosis thesis to Ivan.

vtkImageToMesh: Need to return some sort of structure that stores (1) the integer location of nodes, (2) sets of nodes on surfaces. Maybe just (1) for vtkImageToMesh, stored as a DataArray on the points. The (2) could be generated in vtkGenerateMesh??

Functional tests for vtkMeshGenerator (or maybe they are unit tests).

vtkMeshModel: Create Functions AddSingleConstraint. This will add a single displacement/force constraint. Possibly there will be a dedicated named selection for all of these.

Faim memory:
* reporting
* limiting (e.g. faim -memlimit 4GB somemodel.inp)
* estimating (e.g. faim -estimate somemodel.inp)

vtkskiMeshModel : no longer separately encode Restraints and Displacements (Restraints are just 0-valued Displacements).

compile AIX for OS-X .

==Medium Term==

Move ifdutil out of faim tree to common. Rename it n88util.

Error handling for vtkski: Go through everything and make sure that return values are actually handled (ug).

Migrate high priority vtkMy apps with ITK.

Migrate high priority vtkMy apps with Qt.

Find out why vtkImagePurify appears to do nothing.

Find out why vtkFairSmooth appears to do nothing.

Analytic expression for orthotropic element stiffness matrix elements.

Work out boundary values that arise from integration by parts in analytic expression for element stiffness matrix elements.

Get test data for aimpack_test?

MeshGenerator: split into
# Generic Mesh Generator (no boundary conditions)
# Standard Models Generator (probably a base class and subclasses)

Split faim FE solver and analysis into two separate programs.

Make sure that all Test programs can be run unmodified when moved out of the vtkski source tree.

DOxygen documentation for itkski

Fix up itkAIMImageIO.

itk Reader/Writer for AIM (and remove VTK dependencies for apps that use only this VTK item).

Submit conf_parser to boost??

Change all vtkski / Applications to use boost::program_options

Revision number in main page of vtkski doxygen documentation.

Evaluate possible speed gain of eliminating device syncs in faim/GPU.

Evaluate double-precision speed of faim on Westgrid hardware.

Make a vtkFAIMInputReader class.

Compile faim on WestGrid.

Move plane intersection functions out of vtkMeshGenerator into their own filter(s).

faim: accelerate post-processing

Rewrite faim in C++.

vtkski: cmake copy all headers to 'include' directory in build directory.

==Someday==

mighty-mac and mavis: reconfigure disks into a single striped RAID array (hence users don't have to think about using /Volumes/localdata).

FAIM: Ever need models with 64 bit indexing?? (i.e. more than 2^32 nodes or elements)

FAIM: km generation should be function (or even better, class) - should allow two flavors:
# S&G style numerical integration
# my analytic expression

CPU affinity for multithreading in FAIM (NUMA)

MPI solver for faim

FAIM: partitioner based on 3D geometry (ie. noninductive sets based on 27 nearest neighbours + center).

Paraview: Create Mesh Model (including custom constraints) within ParaView

CMake: Install destination for vtkski, etc....

CMake: Binary Installer for vtkski, etc...

ParaView: Registraion Plugins (a modification of one of http://paraview.org/Wiki/User_Created_Plugins ?)

Speed tests for ifdutil and faim in general.

==Random Ideas==

New file format for faim. Either a more robust text format (with optional binary sections), or something like NetCDF/HDF5.

Eric To Do

2010-11-05T16:58:00Z

Enodwell:

==Soon==

Put faim To Do list on trac.

Aluminum foam: need to rotate and trim this model.

Build ParaView 3.8.1 with mpi support.

Investigate load times for AIM files in ParaView.

FAIM: make sure that force constraints are correct. (Need to have vtkskiFiniteElementModel generator that applies constant body force?? or pressure??)

Material models: need string constants instead of integer constants (possibly they exist already for C++, but need Python versions.)

FAIM: all output to current directory.

Bending test: does not work very well for data sets with large offset (i.e. test25a.aim). Solution: Need to be able to specify not just neutral axis angle, but entire neutral axis vector. Also, probably want one surface fixed, and the other surface to have force conditions.

comparative functional tests (ie. compared to a previously-run functional test). Sharing a common base test class with compare_to_fe_by_assembly. This would be useful for multithreaded vs. singlethreaded.

faim: svn revision number (then report this in functional tests)

functional tests: anisotropic

functional tests: multithreaded solutions

functional tests: a test case for rotated tests (i.e., same thing, but rotated so along x,y,z axes). Or alternatively just apply force along different axis.

functional tests: force constraints

faim: transverse constraints for standard tests. i.e. pivot points.

faim: license file

faim: cmake installation to destination

faim: compare speed of new build to old build.

Backup drive.

Gaussian Filter in ParaView is working? not really - maybe in 3.8.1?

Test network speed between mighty-mac and mike .

AIMSimilarityRegistration.cxx : working?

AppPointPicker (name??) works on OS-X?

vtkski: test installation.

vtkTensorOfInertia:
# get principle axes
# accept weights (as pointer) - or use scalars as default??
# test cases
# treat voxels as boxes instead of points
# accept UnstructuredGrid input (someday)

Carolyn : list of programs.

Add section to wiki about:
1. Basic CMake usage
2. common development directories (/usr. /opt, etc...)

Try build of vtkski/ParaView with spaces in directory names.

ParaView build with vtkski included, Windows.

Binary build of vtkski? (Including all Applications.)

Westgrid account.

Make OrientationParameters a class (in vtkMeshGenerator).

Take Scoliosis thesis to Ivan.

vtkImageToMesh: Need to return some sort of structure that stores (1) the integer location of nodes, (2) sets of nodes on surfaces. Maybe just (1) for vtkImageToMesh, stored as a DataArray on the points. The (2) could be generated in vtkGenerateMesh??

Functional tests for vtkMeshGenerator (or maybe they are unit tests).

vtkMeshModel: Create Functions AddSingleConstraint. This will add a single displacement/force constraint. Possibly there will be a dedicated named selection for all of these.

Faim memory:
* reporting
* limiting (e.g. faim -memlimit 4GB somemodel.inp)
* estimating (e.g. faim -estimate somemodel.inp)

vtkskiMeshModel : no longer separately encode Restraints and Displacements (Restraints are just 0-valued Displacements).

compile AIX for OS-X .

==Medium Term==

Move ifdutil out of faim tree to common. Rename it n88util.

Error handling for vtkski: Go through everything and make sure that return values are actually handled (ug).

Migrate high priority vtkMy apps with ITK.

Migrate high priority vtkMy apps with Qt.

Find out why vtkImagePurify appears to do nothing.

Find out why vtkFairSmooth appears to do nothing.

Analytic expression for orthotropic element stiffness matrix elements.

Work out boundary values that arise from integration by parts in analytic expression for element stiffness matrix elements.

Get test data for aimpack_test?

MeshGenerator: split into
# Generic Mesh Generator (no boundary conditions)
# Standard Models Generator (probably a base class and subclasses)

Split faim FE solver and analysis into two separate programs.

Make sure that all Test programs can be run unmodified when moved out of the vtkski source tree.

DOxygen documentation for itkski

Fix up itkAIMImageIO.

itk Reader/Writer for AIM (and remove VTK dependencies for apps that use only this VTK item).

Submit conf_parser to boost??

Change all vtkski / Applications to use boost::program_options

Revision number in main page of vtkski doxygen documentation.

Evaluate possible speed gain of eliminating device syncs in faim/GPU.

Evaluate double-precision speed of faim on Westgrid hardware.

Make a vtkFAIMInputReader class.

Compile faim on WestGrid.

Move plane intersection functions out of vtkMeshGenerator into their own filter(s).

faim: accelerate post-processing

Rewrite faim in C++.

vtkski: cmake copy all headers to 'include' directory in build directory.

==Someday==

mighty-mac and mavis: reconfigure disks into a single striped RAID array (hence users don't have to think about using /Volumes/localdata).

FAIM: Ever need models with 64 bit indexing?? (i.e. more than 2^32 nodes or elements)

FAIM: km generation should be function (or even better, class) - should allow two flavors:
# S&G style numerical integration
# my analytic expression

CPU affinity for multithreading in FAIM (NUMA)

MPI solver for faim

FAIM: partitioner based on 3D geometry (ie. noninductive sets based on 27 nearest neighbours + center).

Paraview: Create Mesh Model (including custom constraints) within ParaView

CMake: Install destination for vtkski, etc....

CMake: Binary Installer for vtkski, etc...

ParaView: Registraion Plugins (a modification of one of http://paraview.org/Wiki/User_Created_Plugins ?)

Speed tests for ifdutil and faim in general.

==Random Ideas==

New file format for faim. Either a more robust text format (with optional binary sections), or something like NetCDF/HDF5.

Eric To Do

2010-11-05T16:47:45Z

Enodwell:

==Soon==

Put faim To Do list on trac.

Aluminum foam: need to rotate and trim this model.

FAIM input file: Fixed: change so just record columns of (index, axis)

Build ParaView 3.8.1 with mpi support.

Investigate load times for AIM files in ParaView.

FAIM: make sure that force constraints are correct. (Need to have vtkskiFiniteElementModel generator that applies constant body force?? or pressure??)

Material models: need string constants instead of integer constants (possibly they exist already for C++, but need Python versions.)

FAIM: all output to current directory.

Bending test: does not work very well for data sets with large offset (i.e. test25a.aim). Solution: Need to be able to specify not just neutral axis angle, but entire neutral axis vector. Also, probably want one surface fixed, and the other surface to have force conditions.

comparative functional tests (ie. compared to a previously-run functional test). Sharing a common base test class with compare_to_fe_by_assembly. This would be useful for multithreaded vs. singlethreaded.

faim: svn revision number (then report this in functional tests)

functional tests: anisotropic

functional tests: multithreaded solutions

functional tests: a test case for rotated tests (i.e., same thing, but rotated so along x,y,z axes). Or alternatively just apply force along different axis.

functional tests: force constraints

faim: transverse constraints for standard tests. i.e. pivot points.

faim: license file

faim: cmake installation to destination

faim: compare speed of new build to old build.

Backup drive.

Gaussian Filter in ParaView is working? not really - maybe in 3.8.1?

Test network speed between mighty-mac and mike .

AIMSimilarityRegistration.cxx : working?

AppPointPicker (name??) works on OS-X?

vtkski: test installation.

vtkTensorOfInertia:
# get principle axes
# accept weights (as pointer) - or use scalars as default??
# test cases
# treat voxels as boxes instead of points
# accept UnstructuredGrid input (someday)

Carolyn : list of programs.

Add section to wiki about:
1. Basic CMake usage
2. common development directories (/usr. /opt, etc...)

Try build of vtkski/ParaView with spaces in directory names.

ParaView build with vtkski included, Windows.

Binary build of vtkski? (Including all Applications.)

Westgrid account.

Make OrientationParameters a class (in vtkMeshGenerator).

Take Scoliosis thesis to Ivan.

vtkImageToMesh: Need to return some sort of structure that stores (1) the integer location of nodes, (2) sets of nodes on surfaces. Maybe just (1) for vtkImageToMesh, stored as a DataArray on the points. The (2) could be generated in vtkGenerateMesh??

Functional tests for vtkMeshGenerator (or maybe they are unit tests).

vtkMeshModel: Create Functions AddSingleConstraint. This will add a single displacement/force constraint. Possibly there will be a dedicated named selection for all of these.

Faim memory:
* reporting
* limiting (e.g. faim -memlimit 4GB somemodel.inp)
* estimating (e.g. faim -estimate somemodel.inp)

vtkskiMeshModel : no longer separately encode Restraints and Displacements (Restraints are just 0-valued Displacements).

compile AIX for OS-X .

==Medium Term==

Move ifdutil out of faim tree to common. Rename it n88util.

Error handling for vtkski: Go through everything and make sure that return values are actually handled (ug).

Migrate high priority vtkMy apps with ITK.

Migrate high priority vtkMy apps with Qt.

Find out why vtkImagePurify appears to do nothing.

Find out why vtkFairSmooth appears to do nothing.

Analytic expression for orthotropic element stiffness matrix elements.

Work out boundary values that arise from integration by parts in analytic expression for element stiffness matrix elements.

Get test data for aimpack_test?

MeshGenerator: split into
# Generic Mesh Generator (no boundary conditions)
# Standard Models Generator (probably a base class and subclasses)

Split faim FE solver and analysis into two separate programs.

Make sure that all Test programs can be run unmodified when moved out of the vtkski source tree.

DOxygen documentation for itkski

Fix up itkAIMImageIO.

itk Reader/Writer for AIM (and remove VTK dependencies for apps that use only this VTK item).

Submit conf_parser to boost??

Change all vtkski / Applications to use boost::program_options

Revision number in main page of vtkski doxygen documentation.

Evaluate possible speed gain of eliminating device syncs in faim/GPU.

Evaluate double-precision speed of faim on Westgrid hardware.

Make a vtkFAIMInputReader class.

Compile faim on WestGrid.

Move plane intersection functions out of vtkMeshGenerator into their own filter(s).

faim: accelerate post-processing

Rewrite faim in C++.

vtkski: cmake copy all headers to 'include' directory in build directory.

==Someday==

mighty-mac and mavis: reconfigure disks into a single striped RAID array (hence users don't have to think about using /Volumes/localdata).

FAIM: Ever need models with 64 bit indexing?? (i.e. more than 2^32 nodes or elements)

FAIM: km generation should be function (or even better, class) - should allow two flavors:
# S&G style numerical integration
# my analytic expression

CPU affinity for multithreading in FAIM (NUMA)

MPI solver for faim

FAIM: partitioner based on 3D geometry (ie. noninductive sets based on 27 nearest neighbours + center).

Paraview: Create Mesh Model (including custom constraints) within ParaView

CMake: Install destination for vtkski, etc....

CMake: Binary Installer for vtkski, etc...

ParaView: Registraion Plugins (a modification of one of http://paraview.org/Wiki/User_Created_Plugins ?)

Speed tests for ifdutil and faim in general.

==Random Ideas==

New file format for faim. Either a more robust text format (with optional binary sections), or something like NetCDF/HDF5.