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Add support for loading meshes with trials #87

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Add support for loading meshes with trials #87

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NicerNewerCar
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@NicerNewerCar NicerNewerCar commented Feb 27, 2023 •
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  • Added Mesh Class
  • Added Distance field kernel for distance field calculations
    • Will be called during the loading of a trial if OpenCL is the rendering backend
  • Added new keyword Mesh to the config file
  • Support for STL and VRML files
  • Loaded into facet representation (3 points and a normal)
  • Example config file
mayaCam_csv \WN00105\Data_XROMM\xr_pre_cube_2_817_cam01_MayaCam.csv
mayaCam_csv \WN00105\Data_XROMM\xr_pre_cube_2_817_cam02_MayaCam.csv
CameraRootDir \WN00105\XMA_UND\xr_flx_ext_cam01UND
CameraRootDir \WN00105\XMA_UND\xr_flx_ext_cam02UND
VolumeFile \WN00105\Models\rad\rad_dcm_cropped.tif
VolumeFlip 0 0 0
VoxelSize 0.390625 0.390625 0.625
#Mesh \WN00105\Models\WN00105_trimesh\AUT_rad.wrl
Mesh \WN00105\Models\WN00105_trimesh\stl\AUT_rad.stl
VolumeFile \WN00105\Models\mc3\mc3_dcm_cropped.tif
VolumeFlip 0 0 0
VoxelSize 0.390625 0.390625 0.625
#Mesh \WN00105\Models\WN00105_trimesh\AUT_mc3.wrl
Mesh \WN00105\Models\WN00105_trimesh\stl\AUT_mc3.stl
RenderResolution 512 512
OptimizationOffsets 0.1 0.1 0.1 0.1 0.1 0.1

@amymmorton
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Successful load (added Mesh to config file) but expected some visual display.. how are the mesh files viewed?

jcfr
jcfr reviewed Mar 6, 2023
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If code for reading STL/VRML/... existings in ITK or VTK, it may be sensible to "vendorize" it. (see vtkSTLReader, vtkSTLWriter, ...)

libautoscoper/CMakeLists.txt Outdated Show resolved Hide resolved
libautoscoper/src/Mesh.cpp Outdated Show resolved Hide resolved
libautoscoper/src/Mesh.cpp Outdated Show resolved Hide resolved
libautoscoper/src/Mesh.cpp Outdated Show resolved Hide resolved
libautoscoper/src/Mesh.cpp Outdated Show resolved Hide resolved
libautoscoper/src/PSO.cpp Outdated Show resolved Hide resolved
libautoscoper/src/PSO.cpp Outdated Show resolved Hide resolved
libautoscoper/src/Tracker.cpp Outdated Show resolved Hide resolved
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@NicerNewerCar
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@jcfr
Re: viewing the mesh
Looks like I will need to add some OpenCL code to the View::Render method to get the meshes onto the screen. Do you have any recommendations for methods to render the triangular meshes into the 2D buffer?

Re: output
Should I pivot to exporting the rotated meshes as stls rather than the csvs of rotations/translations?

@NicerNewerCar NicerNewerCar force-pushed the mesh-representation branch 2 times, most recently from ed86711 to 952e728 Compare April 5, 2023 14:21
@NicerNewerCar NicerNewerCar mentioned this pull request Apr 5, 2023
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@NicerNewerCar NicerNewerCar marked this pull request as draft April 6, 2023 14:34
@NicerNewerCar NicerNewerCar force-pushed the mesh-representation branch 4 times, most recently from 0f1ddd9 to ef21f0f Compare April 17, 2023 16:13
@NicerNewerCar NicerNewerCar requested a review from jcfr April 17, 2023 17:07
@NicerNewerCar NicerNewerCar marked this pull request as ready for review April 17, 2023 17:07
@NicerNewerCar NicerNewerCar mentioned this pull request Jun 1, 2023
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Closing this in favor of #128

@NicerNewerCar NicerNewerCar deleted the mesh-representation branch June 5, 2023 13:46
jcfr added a commit to jcfr/SlicerAutoscoperM that referenced this pull request Jun 23, 2023
@jcfr
ENH: Update Autoscoper
29d753b 
Highlighted Autoscoper changes:

* Fix trailing comma when saving single volume tracking data so that the file
  can be loaded by other CVS reader (e.g numpy)
  Before:
    X_data, Y_data, Z_data, YAW_data, PITCH_data, ROLL_data,
  After:
    X_data, Y_data, Z_data, YAW_data, PITCH_data, ROLL_data
  See pull request BrownBiomechanics/Autoscoper#130

* Documentation updates

* Update sources to explicitly reference "std" namespace.

* Add support for 3D kernels (Kernel::block3d and Kernel::grid3d).
  Not yet used. It was originally integrated to support the computation
  of "Distance field" in pull request BrownBiomechanics/Autoscoper#87
  (Add support for loading meshes with trials) which was closed in favor
  of BrownBiomechanics/Autoscoper#128 (Add Collision Detection)

List of Autoscoper changes:

$ git shortlog 60b3d6ec0..b29d30f51 --no-merges
Anthony Lombardi (20):
      ENH: Update OpenCL wrapper to support 3D kernels (PR-113)
      DOC: Fix typos in PyAutoscoper docstrings
      DOC: Set up Markdown Sphinx docs
      DOC: Add Documentation for PyAutoscoper
      DOC: Add About Autoscoper section to RTD
      DOC: Add getting started and user interface to RTD
      DOC: Add MATLAB socket control docs to RTD
      DOC: Add dev guide to RTD
      DOC: Update the license info on the home page
      DOC: Add UI description
      DOC: Add instructions for remote GPU access
      DOC: Add tutorials for sample and custom data
      DOC: Add file specifications
      ENH: Add .readthedocs.yaml to install required packages
      ENH: Make content take up 100% of the screen width
      DOC: Add tutorial for filters
      DOC: Update History and Getting Started
      DOC: Update README for PyAutoscoper to point to RTD
      DOC: Add tutorial descriptions and reference on getting started
      BUG: Fix trailing comma when saving single volume tracking data

Jean-Christophe Fillion-Robin (24):
      STYLE: Update "line-length" black settings from 88 to 120
      DOC: Add top-level license based on source file headers
      DOC: Update README adding a "License" section along with historical notes
      STYLE: Update black version specified in pre-commit config
      COMP: Update pre-commit config to ensure black always uses expected settings
      COMP: Explicitly reference "std" namespace
      DOC: Consistently add an empty line between header and content
      DOC: Strip trailing white spaces
      DOC: Add dedicated "About" top-level section
      DOC: Move SampleData description in "Getting Started"
      DOC: Move "Advanced Topics" after "User Interface" and "Tutorials"
      DOC: Fix headers in CONTRIBUTING document
      DOC: Fix cross-references warnings
      DOC: Update configuration removing invalid options
      DOC: Fix formatting of "Example" in "Camera Calibration File Format"
      DOC: Update "Getting Started" to fix reference to sample data
      ENH: Update NewTrialDialog UI file to use "OK" instead of "Ok"
      DOC: Fix miscellaneous typos
      DOC: Update PyAutoscoper document to use back-ticks around method names
      DOC: Tweak formatting of "Loading and Tracking Data" tutorial
      DOC: Use "AutoscoperM" instead of SAM in "Loading Custom Data" tutorial
      DOC: Ensure "Tutorials" are complete by relying on implicit link text
      STYLE: Remove obsolete comments from autoscoper/CMakeLists.txt
      COMP: Set autoscoper_set_env.sh permission flags only if configuring script
@jcfr jcfr mentioned this pull request Jun 23, 2023
Merged
jcfr added a commit to BrownBiomechanics/SlicerAutoscoperM that referenced this pull request Jun 23, 2023
@jcfr
ENH: Update Autoscoper
26cb5e1 
Highlighted Autoscoper changes:

* Fix trailing comma when saving single volume tracking data so that the file
  can be loaded by other CVS reader (e.g numpy)
  Before:
    X_data, Y_data, Z_data, YAW_data, PITCH_data, ROLL_data,
  After:
    X_data, Y_data, Z_data, YAW_data, PITCH_data, ROLL_data
  See pull request BrownBiomechanics/Autoscoper#130

* Documentation updates

* Update sources to explicitly reference "std" namespace.

* Add support for 3D kernels (Kernel::block3d and Kernel::grid3d).
  Not yet used. It was originally integrated to support the computation
  of "Distance field" in pull request BrownBiomechanics/Autoscoper#87
  (Add support for loading meshes with trials) which was closed in favor
  of BrownBiomechanics/Autoscoper#128 (Add Collision Detection)

List of Autoscoper changes:

$ git shortlog 60b3d6ec0..b29d30f51 --no-merges
Anthony Lombardi (20):
      ENH: Update OpenCL wrapper to support 3D kernels (PR-113)
      DOC: Fix typos in PyAutoscoper docstrings
      DOC: Set up Markdown Sphinx docs
      DOC: Add Documentation for PyAutoscoper
      DOC: Add About Autoscoper section to RTD
      DOC: Add getting started and user interface to RTD
      DOC: Add MATLAB socket control docs to RTD
      DOC: Add dev guide to RTD
      DOC: Update the license info on the home page
      DOC: Add UI description
      DOC: Add instructions for remote GPU access
      DOC: Add tutorials for sample and custom data
      DOC: Add file specifications
      ENH: Add .readthedocs.yaml to install required packages
      ENH: Make content take up 100% of the screen width
      DOC: Add tutorial for filters
      DOC: Update History and Getting Started
      DOC: Update README for PyAutoscoper to point to RTD
      DOC: Add tutorial descriptions and reference on getting started
      BUG: Fix trailing comma when saving single volume tracking data

Jean-Christophe Fillion-Robin (24):
      STYLE: Update "line-length" black settings from 88 to 120
      DOC: Add top-level license based on source file headers
      DOC: Update README adding a "License" section along with historical notes
      STYLE: Update black version specified in pre-commit config
      COMP: Update pre-commit config to ensure black always uses expected settings
      COMP: Explicitly reference "std" namespace
      DOC: Consistently add an empty line between header and content
      DOC: Strip trailing white spaces
      DOC: Add dedicated "About" top-level section
      DOC: Move SampleData description in "Getting Started"
      DOC: Move "Advanced Topics" after "User Interface" and "Tutorials"
      DOC: Fix headers in CONTRIBUTING document
      DOC: Fix cross-references warnings
      DOC: Update configuration removing invalid options
      DOC: Fix formatting of "Example" in "Camera Calibration File Format"
      DOC: Update "Getting Started" to fix reference to sample data
      ENH: Update NewTrialDialog UI file to use "OK" instead of "Ok"
      DOC: Fix miscellaneous typos
      DOC: Update PyAutoscoper document to use back-ticks around method names
      DOC: Tweak formatting of "Loading and Tracking Data" tutorial
      DOC: Use "AutoscoperM" instead of SAM in "Loading Custom Data" tutorial
      DOC: Ensure "Tutorials" are complete by relying on implicit link text
      STYLE: Remove obsolete comments from autoscoper/CMakeLists.txt
      COMP: Set autoscoper_set_env.sh permission flags only if configuring script
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@NicerNewerCar @amymmorton @jcfr