New Features 🚀
- Heterogeneous Background Tissue
- Muscle tissue can be created with noise/blobs or structured heterogeneity
- This can be used for e.g. blood volume fraction or oxygenation
- For further information consider the [heterogeneous tissue example](https://github.com/IMSY-DKFZ/simpa/blob/main/simpa_examples/minimal_optical_simulation_heterogeneous_tissue.py)
- Benchmarking
- It is now possible to benchmark your simulations with the profile decorator
- For further information consider the [benchmarking documentation](https://simpa.readthedocs.io/en/main/bench_link.html)
- Better reproducibility by including exact versions/commit hashes in the SIMPA output
- Faster simulations by GPU support
Breaking Changes ðŸ›
- Pathmanager
The naming convention for the directory in which output files are stored was changed from `SIMPA_OUTPUT_PATH` to `SIMPA_OUTPUT_DIRECTORY`
- Module names
Some names of modules and especially adapters were changed in order to have a more consistent naming scheme. Please adapt your simulation scripts accordingly!
What's Changed
* T118 fix device positioning by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/119
* Merge develop into main by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/122
* Offer option to resample to power of 2 in bandpass filter by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/125
* Update InVision device parameters by jgroehl in https://github.com/IMSY-DKFZ/simpa/pull/130
* Added butterworth bandpass filter by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/121
* Rounding issues in reconstruction by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/135
* Merge T139_AnisotropyBug into develop by mschllnbrg in https://github.com/IMSY-DKFZ/simpa/pull/140
* T139 anisotropy bug by jgroehl in https://github.com/IMSY-DKFZ/simpa/pull/141
* Check if key is set before accessing it by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/138
* Rounding fov also in cropping component, fixes 134 by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/137
* Fixed test that would have detected 139 by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/143
* Fixes 142 by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/148
* Fixed detector positioning in msot acuity echo by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/149
* Develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/150
* Run Tests on push and pull request to develop as well. by jgroehl in https://github.com/IMSY-DKFZ/simpa/pull/151
* Add version number in hdf5 by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/147
* Implemented 144, partial volume via settings by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/145
* T152 notify cpu reconstruction by Holzwarth69126 in https://github.com/IMSY-DKFZ/simpa/pull/153
* T128 bf component settings bug and T127 Reconstruction volume dimensions not mandatory by Holzwarth69126 in https://github.com/IMSY-DKFZ/simpa/pull/133
* Update README.md by chiarasfour in https://github.com/IMSY-DKFZ/simpa/pull/161
* Citation of SIMPA paper by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/167
* Develop merge by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/170
* T152 processing unit by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/169
* T77 off by one error by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/174
* T187 bump jdata version by leoyala in https://github.com/IMSY-DKFZ/simpa/pull/188
* T187 bump jdata version (188) by leoyala in https://github.com/IMSY-DKFZ/simpa/pull/190
* T191 numpy types by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/196
* Develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/197
* Improve performance and reduce memory use of mcx io by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/224
* Bump markdown-it-py from 2.1.0 to 2.2.0 by dependabot in https://github.com/IMSY-DKFZ/simpa/pull/213
* Add pre-commit hooks to the repo by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/212
* Develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/225
* T206 io bottleneck by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/207
* T202 head and neck by mschllnbrg in https://github.com/IMSY-DKFZ/simpa/pull/203
* Create template for pull requests by seitela in https://github.com/IMSY-DKFZ/simpa/pull/210
* Update issue templates by seitela in https://github.com/IMSY-DKFZ/simpa/pull/209
* Merge develop into main by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/230
* T199: using rfft and window function correction (considering edge cases) by cbender98 in https://github.com/IMSY-DKFZ/simpa/pull/200
* T217 GaussianBeam bug + focal length by faberno in https://github.com/IMSY-DKFZ/simpa/pull/218
* Develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/231
* Structure creation on GPU by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/175
* speed up `assert_array_well_defined()` by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/238
* Improve generate_mcx_bin_input performance by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/236
* Fix relative path issue in reconstruction_module_time_reversal_adapter.py matlab command by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/235
* T239 wavelength independent volume creation by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/240
* don't run pypi publish action on forks by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/244
* Reduce gpu ram use in EllipticalTubularStructure by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/242
* Create simulation volumes on the GPU by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/243
* Specify mc2 output file format for mcx by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/246
* Use gpu for noise generation if available by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/253
* Update develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/267
* Use mcx SLIT source for MSOTAcuity and MSOTInvision sources by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/266
* Merge develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/268
* Merge fix for 273 from develop by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/274
* Changing operation to make it compatible with M1 Macbooks by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/289
* T291 image heterogeneity by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/295
* T285 vessel structure to torch by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/287
* Minimal optical simulation example and diffuse reflectance by leoyala in https://github.com/IMSY-DKFZ/simpa/pull/263
* KWave adapter rotation bug fix by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/270
* Update test_vesseltree.py by jgroehl in https://github.com/IMSY-DKFZ/simpa/pull/298
* Add profile decorator to simpa utils by lkeegan in https://github.com/IMSY-DKFZ/simpa/pull/241
* PathManager refactoring by leoyala in https://github.com/IMSY-DKFZ/simpa/pull/296
* T279 planar illumination geometry by RecurvedBow in https://github.com/IMSY-DKFZ/simpa/pull/282
* Fix test_instantiate_when_file_is_in_simpa_home by faberno in https://github.com/IMSY-DKFZ/simpa/pull/281
* added missing spacing to error message by faberno in https://github.com/IMSY-DKFZ/simpa/pull/250
* raise valueerror if interpolated wavelengths are out of range and wri… by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/310
* Fixed time spacing bug in reconstruction convenience function by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/261
* Saving norm in a variable named norm_direction_vector_mm by Kamkarl in https://github.com/IMSY-DKFZ/simpa/pull/247
* FIX issue with SPIE link check by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/320
* Replace scipy.interp2d by scipy.RegularGridInterpolator by faberno in https://github.com/IMSY-DKFZ/simpa/pull/312
* T314 remove fillers by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/315
* switch to setuptools by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/306
* Setuptools version can be extracted from simpa.__version__ by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/322
* Update documentation by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/308
* Added function for general tissue definition from optical parameters … by RecurvedBow in https://github.com/IMSY-DKFZ/simpa/pull/326
* Refactored component settings and torch device by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/309
* fix tests by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/328
* Disabled autopep8 formatting of relative import lines by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/331
* T180 refactoring tissue lib by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/321
* T180 Refactoring by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/183
* + RingIlluminationGeometry by RecurvedBow in https://github.com/IMSY-DKFZ/simpa/pull/293
* T333 new documentation by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/336
* T338 msot acuity usable for hetero tissues by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/341
* T339 specific hetero by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/340
* T350 hetero segmentation by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/351
* T300 benchmarking by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/313
* Add installed simpa version in hdf5 files by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/325
* Change folder name for pre commit configs by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/335
* Additional executable flags by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/311
* T105 overview manual test by cbender98 in https://github.com/IMSY-DKFZ/simpa/pull/318
* T115 include bvf by jnoelke in https://github.com/IMSY-DKFZ/simpa/pull/182
* T367 plot bvf by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/368
* Fix ignored acoustical_simulation_3d by faberno in https://github.com/IMSY-DKFZ/simpa/pull/251
* T154 heterogeneous tissue by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/290
* refine benchmarking scripts by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/369
* Refactored (base) classes from init.py into separate files by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/360
* Update segmentation loader to have reasonable values by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/366
* T66 docs for tags and settings by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/355
* T 371 segmentation loader with multiple wavelengths by frisograce in https://github.com/IMSY-DKFZ/simpa/pull/372
* Include environment variables in path manager order by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/347
* Use same FOV definition within different reconstructions by TomTomRixRix in https://github.com/IMSY-DKFZ/simpa/pull/181
* T378 2D vs 3D example by jgroehl in https://github.com/IMSY-DKFZ/simpa/pull/379
* T317 refactor point source manual test by cbender98 in https://github.com/IMSY-DKFZ/simpa/pull/385
* Merge develop into main by kdreher in https://github.com/IMSY-DKFZ/simpa/pull/383
**Full Changelog**: https://github.com/IMSY-DKFZ/simpa/commits/v1.0.0