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Add initial 3d support to GUI and Pixel simulator #850

Merged
merged 1 commit into from May 25, 2023
Merged

Add initial 3d support to GUI and Pixel simulator #850

merged 1 commit into from May 25, 2023

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lkeegan
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@lkeegan lkeegan commented Jan 4, 2023 •
edited

  • Add basic 3d objects (thin wrappers extending previous 2d Qt objects)
    • Voxel: QPoint + z-index
    • VoxelF: QPointF + double for z
    • Volume: QSize + z size
    • VolumeF: QSizeF + double for z
    • ImageStack: vector of QImages, one for each z-slice
  • Replace all (x,y) QImages with (x,y,z) ImageStacks
  • add 3d versions of image utils
    • add VoxelFlattener: 3d equivalent of QPointFlattener
    • add VoxelIndexer: 3d equivalent of QPointIndexer
  • extend Compartment, Membrane, Field to 3d
    • QPoint -> Voxel
    • QImage -> ImageStack
    • QSize -> Volume
    • Compartment
      • add up_z(), dn_z()
      • extend fill missing by dilation to 3d
    • Membrane
      • add iteration of z-pairs to existing x,y-pairs, extend iteration over entire ImageStack
  • import analytic geometry from sbml as 3d ImageStack
  • sme (python bindings)
    • add z dimension to all image arrays
    • update docstrings
    • migrate tests from unittest to pytest
  • Pixel 2d -> 3d
    • Add z term to diffusion
    • Add z to x,y species for spatially-dependent reaction terms
    • resolves Pixel 3d-support #835
  • QLabelMouseTracker
  • MainWindow
    • add z-slider
    • sets z-slice for whole GUI (excluding dialogs)
  • DialogAnalytic, DialogConcentrationImage, DialogGeometryImage
    • QImage -> ImageStack
    • add z-sliders to QLabelMouseTracker
  • add 3d diffusion model to example models
  • add test of simulation of 3d diffusion model
  • mesh generation is disabled for images with more than 1 z-slice
  • ModelGeometry.getPhysicalPoint() now returns location of centre of supplied voxel
  • initModelData now catches runtime_errors and sets an error message to be displayed in GUI
    • ModelSpecies now throws if a species compartment is a membrane instead of segfaulting

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codecov bot commented Jan 4, 2023 •
edited

Codecov Report

Merging #850 (e99cab4) into main (782cb3c) will increase coverage by 0.14%.
The diff coverage is 91.74%.

❗ Current head e99cab4 differs from pull request most recent head c6c0370. Consider uploading reports for the commit c6c0370 to get more accurate results

@@            Coverage Diff             @@
##             main     #850      +/-   ##
==========================================
+ Coverage   89.73%   89.87%   +0.14%     
==========================================
  Files         135      142       +7     
  Lines       12944    13166     +222     
==========================================
+ Hits        11615    11833     +218     
- Misses       1329     1333       +4
Flag Coverage Δ
cli 26.08% <27.28%> (-1.34%) ⬇️
core 53.98% <59.21%> (-0.86%) ⬇️
gui 71.20% <72.96%> (-0.15%) ⬇️
mainwindow 42.97% <42.56%> (-0.92%) ⬇️
sme 32.47% <39.06%> (+0.10%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
benchmark/bench.hpp 0.00% <0.00%> (ø)
benchmark/benchmark.cpp 0.00% <0.00%> (ø)
core/common/include/sme/utils.hpp 68.00% <ø> (+68.00%) ⬆️
core/common/src/utils.cpp 100.00% <ø> (ø)
core/mesh/src/boundaries_bench.cpp 0.00% <0.00%> (ø)
core/mesh/src/interior_point_bench.cpp 0.00% <0.00%> (ø)
core/mesh/src/line_simplifier_bench.cpp 0.00% <0.00%> (ø)
core/mesh/src/mesh_bench.cpp 0.00% <0.00%> (ø)
core/mesh/src/triangulate_bench.cpp 0.00% <0.00%> (ø)
core/model/include/sme/model.hpp 0.00% <ø> (ø)
... and 52 more

... and 18 files with indirect coverage changes

@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch 8 times, most recently from dfc749c to 68e249b Compare January 10, 2023 10:48
@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch 5 times, most recently from 47a3a7a to aaf64c4 Compare March 3, 2023 11:12
@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch from 18c6b8e to c97ce67 Compare March 9, 2023 15:23
@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch from c97ce67 to e99cab4 Compare March 28, 2023 09:35
@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch 2 times, most recently from afe26a7 to 5400210 Compare April 28, 2023 12:16
@lkeegan
Add initial 3d support to GUI and Pixel simulator
c6c0370 
- Add basic 3d objects (thin wrappers extending previous 2d Qt objects)
  - Voxel: QPoint + z-index
  - VoxelF: QPointF + double for z
  - Volume: QSize + z size
  - VolumeF: QSizeF + double for z
  - ImageStack: vector of QImages, one for each z-slice
- Replace all (x,y) QImages with (x,y,z) ImageStacks
- add 3d versions of image utils
  - add VoxelFlattener: 3d equivalent of QPointFlattener
  - add VoxelIndexer: 3d equivalent of QPointIndexer
- extend Compartment, Membrane, Field to 3d
  - QPoint -> Voxel
  - QImage -> ImageStack
  - QSize -> Volume
  - Compartment
    - add up_z(), dn_z()
    - extend fill missing by dilation to 3d
  - Membrane
    - add iteration of z-pairs to existing x,y-pairs, extend iteration over entire ImageStack
- import analytic geometry from sbml as 3d ImageStack
- sme (python bindings)
  - add z dimension to all image arrays
  - update docstrings
  - migrate tests from unittest to pytest
- Pixel 2d -> 3d
  - Add z term to diffusion
  - Add z to x,y species for spatially-dependent reaction terms
  - resolves #835
- QLabelMouseTracker
  - can set the z slice
  - can connect a QSlider to set them
  - resolves #836
- MainWindow
  - add z-slider
  - sets z-slice for whole GUI (excluding dialogs)
- DialogAnalytic, DialogConcentrationImage, DialogGeometryImage
  - QImage -> ImageStack
  - add z-sliders to QLabelMouseTracker
- add 3d diffusion model to example models
- add test of simulation of 3d diffusion model
- mesh generation is disabled for images with more than 1 z-slice
- ModelGeometry.getPhysicalPoint() now returns location of *centre* of supplied voxel
- initModelData now catches runtime_errors and sets an error message to be displayed in GUI
  - ModelSpecies now throws if a species compartment is a membrane instead of segfaulting
@lkeegan lkeegan force-pushed the fix_836_z_slider_qlabelmousetracker branch from 5400210 to c6c0370 Compare May 25, 2023 09:13
@lkeegan lkeegan changed the title WIP 3d support Add initial 3d support to GUI and Pixel simulator May 25, 2023
@sonarcloud
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sonarcloud bot commented May 25, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 41 Code Smells

94.9% 94.9% Coverage
0.0% 0.0% Duplication

@lkeegan lkeegan merged commit 689e066 into main May 25, 2023
18 checks passed
@lkeegan lkeegan deleted the fix_836_z_slider_qlabelmousetracker branch May 25, 2023 10:23
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QLabelMouseTracker 3d support Pixel 3d-support
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@lkeegan