v1.0.0🌈

Changes

• Merge develop into main @kdreher (#383)
• T317 refactor point source manual test @cbender98 (#385)
• T378 2D vs 3D example @jgroehl (#379)
• Use same FOV definition within different reconstructions @TomTomRixRix (#181)
• Include environment variables in path manager order @TomTomRixRix (#347)
• T 371 segmentation loader with multiple wavelengths @frisograce (#372)
• Refactored (base) classes from init.py into separate files @TomTomRixRix (#360)
• refine benchmarking scripts @frisograce (#369)
• Fix ignored acoustical_simulation_3d @faberno (#251)
• T115 include bvf @jnoelke (#182)
• T105 overview manual test @cbender98 (#318)
• Additional executable flags @TomTomRixRix (#311)
• Change folder name for pre commit configs @jnoelke (#335)
• Add installed simpa version in hdf5 files @jnoelke (#325)
• T350 hetero segmentation @frisograce (#351)
• T338 msot acuity usable for hetero tissues @frisograce (#341)
• T333 new documentation @frisograce (#336)
• • RingIlluminationGeometry @RecurvedBow (#293)
• Disabled autopep8 formatting of relative import lines @TomTomRixRix (#331)
• fix tests @jnoelke (#328)
• Refactored component settings and torch device @TomTomRixRix (#309)
• Added function for general tissue definition from optical parameters … @RecurvedBow (#326)
• Update documentation @jnoelke (#308)
• switch to setuptools @jnoelke (#306)
• T314 remove fillers @frisograce (#315)
• Replace scipy.interp2d by scipy.RegularGridInterpolator @faberno (#312)
• FIX issue with SPIE link check @jnoelke (#320)
• Saving norm in a variable named norm_direction_vector_mm @Kamkarl (#247)
• Fixed time spacing bug in reconstruction convenience function @TomTomRixRix (#261)
• raise valueerror if interpolated wavelengths are out of range and wri… @jnoelke (#310)
• added missing spacing to error message @faberno (#250)
• Fix test_instantiate_when_file_is_in_simpa_home @faberno (#281)
• T279 planar illumination geometry @RecurvedBow (#282)
• PathManager refactoring @leoyala (#296)
• Add profile decorator to simpa utils @lkeegan (#241)
• Update test_vesseltree.py @jgroehl (#298)
• Minimal optical simulation example and diffuse reflectance @leoyala (#263)
• T285 vessel structure to torch @frisograce (#287)
• T291 image heterogeneity @frisograce (#295)
• Changing operation to make it compatible with M1 Macbooks @frisograce (#289)
• Merge fix for #273 from develop @kdreher (#274)
• Merge develop @kdreher (#268)
• Use mcx SLIT source for MSOTAcuity and MSOTInvision sources @lkeegan (#266)
• Update develop @kdreher (#267)
• Use gpu for noise generation if available @lkeegan (#253)
• Specify mc2 output file format for mcx @lkeegan (#246)
• Create simulation volumes on the GPU @lkeegan (#243)
• Reduce gpu ram use in EllipticalTubularStructure @lkeegan (#242)
• don't run pypi publish action on forks @lkeegan (#244)
• T239 wavelength independent volume creation @kdreher (#240)
• Fix relative path issue in reconstruction_module_time_reversal_adapter.py matlab command @lkeegan (#235)
• Improve generate_mcx_bin_input performance @lkeegan (#236)
• speed up assert_array_well_defined() @lkeegan (#238)
• Structure creation on GPU @TomTomRixRix (#175)
• Develop @kdreher (#231)
• T217 GaussianBeam bug + focal length @faberno (#218)
• T199: using rfft and window function correction (considering edge cases) @cbender98 (#200)
• Merge develop into main @kdreher (#230)
• Update issue templates @seitela (#209)
• T202 head and neck @mschllnbrg (#203)
• T206 io bottleneck @jnoelke (#207)
• Develop @kdreher (#225)
• Add pre-commit hooks to the repo @TomTomRixRix (#212)
• Bump markdown-it-py from 2.1.0 to 2.2.0 @dependabot (#213)
• Improve performance and reduce memory use of mcx io @lkeegan (#224)
• Develop @kdreher (#197)
• T191 numpy types @kdreher (#196)
• T187 bump jdata version (#188) @leoyala (#190)
• T187 bump jdata version @leoyala (#188)
• T77 off by one error @TomTomRixRix (#174)
• T152 processing unit @TomTomRixRix (#169)
• Develop merge @kdreher (#170)
• Citation of SIMPA paper @TomTomRixRix (#167)
• Update README.md @chiarasfour (#161)
• T128 bf component settings bug and T127 Reconstruction volume dimensions not mandatory @Holzwarth69126 (#133)
• T152 notify cpu reconstruction @Holzwarth69126 (#153)
• Implemented #144, partial volume via settings @jnoelke (#145)
• Add version number in hdf5 @jnoelke (#147)
• Run Tests on push and pull request to develop as well. @jgroehl (#151)
• Develop @kdreher (#150)
• Fixed detector positioning in msot acuity echo @kdreher (#149)
• Fixes #142 @kdreher (#148)
• Fixed test that would have detected #139 @kdreher (#143)
• Merge T139_AnisotropyBug into develop @mschllnbrg (#140)
• Rounding issues in reconstruction @TomTomRixRix (#135)
• Update InVision device parameters @jgroehl (#130)
• Offer option to resample to power of 2 in bandpass filter @TomTomRixRix (#125)
• Merge develop into main @kdreher (#122)
• T118 fix device positioning @kdreher (#119)

🚀 Features

• T66 docs for tags and settings @frisograce (#355)
• T154 heterogeneous tissue @frisograce (#290)
• T367 plot bvf @frisograce (#368)
• T300 benchmarking @frisograce (#313)
• T339 specific hetero @frisograce (#340)
• T180 refactoring tissue lib @frisograce (#321)
• Create template for pull requests @seitela (#210)
• Added butterworth bandpass filter @TomTomRixRix (#121)

🐛 Bug Fixes

• Update segmentation loader to have reasonable values @frisograce (#366)
• KWave adapter rotation bug fix @TomTomRixRix (#270)
• Rounding fov also in cropping component, fixes #134 @TomTomRixRix (#137)
• Check if key is set before accessing it @TomTomRixRix (#138)
• T139 anisotropy bug @jgroehl (#141)