Implement rudimentary citation system #68
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giovannivolpe
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* Feature: ComplexGaussian * Add distributed to base class * More robust index handling * Correctly broadcast arithmetic operators * lower case function * convert to new syntax * Add dependencies * introduce benchmarking * Add config object * Allow init with cupy * hide _update methods * Benchmark on gpu vs cpu * Implement mie on gpu * Implement brightfield on gpu * Bigfix Clip * Coerce inputs before method to ensure all is on same devicc * Allow gpu * Implement conditional features * Enable memory growth * More tests * format input after properties * Merge CappedContinuousGenerator into ContinuousGenerator * Update benchmarks using groups * Include banchmark command * Significant speedup by not copying array * Enable benchmark * Specialcase creating Image with another Image * Don't return depadding * Minor bugfixes * Request pixel radius * Support adding preprocessing to model * Implement autotracker * Implement autotracker * base multiparticle autotracking implementation * Correcting loss and data generation * Make labels array before indexing * Include new models implementation * Defining center in terms of center of mass * Single particle tracking tests * Single particle tests * Addded rotational consistency loss * Allow definition of number of symmetries * Sorting imports * Added documentation * Delete legacy examples * Get z directly * Linting improvements * Autotrack multiply by symmetries * Allow different modes * Implement rotational consistency * alpha release version * Orientation training notebook * Fixing positioning of complex images * Add rnn * remove cappedcontinuousgenerator * removed vscode settings * Remove logging * allow image of tuples * Made fluorescence compatible with gpu * Fetch z-position of fields via get_property * Update README.md * add cgan model * add pcgan model * add documentation for cgan * add documentation for pcgan and evaluate the perceptual model definition * all layers in perceptual discriminator are now frozen * update documentation * Check for nans in pupil * Fixed bug where array is not converted to cpu * Don't correct prediction * Added OneOf and OneOfDict * Add resolve arguments to property-list * Facilitate external control of key * Initialize before adding deps * OneOf should not be distributed * Ensure key is propagated to properties * correctly return modified properties * Add unit tests for OneOf and OneOfDict * Correct error with array function * Ensure code runs without cupy * Add sizing and notebooks * Implement rudimentary citation system * elementwise test fix * Remove center_crop * Implement rudimentary citation system (#68) * citation as static property * Fix convolutional loss * Fix brughtfield pupil * Reduced memory allocation in brightfield * Remove unused context definition * Load copy of default unit definitions without Printing group * Use with-statement to set context * Change conversions * Create default definition file * Set context outside conversion table * remove print * Implemented tests for base models * Update autotracking * allow registered configs * sizing * Implement pytorch style generator * Patch weird interaction with np.ma.ravel * Example showcasing how to usse pytorch with deeptrack * tutorial for experimental data * optmized loss calculation * Reformat model structure * version bump * Fix shape prediction shape bug * Better saving/loading * better indexing * latest * Allow generator kwargs * Correct generator output * Correct generator output * Run notebook * Fix Average * Optimized autotracker speed * Implement equivariances * update example * typo fix * Check for data size first * Wait at start of on_epoch_end * Invalidate entire DataList * un-name unused kwargs * Fix interaction between repeat and sequence * version bump * Set default z-offset unit to meters * Update autotracking example * restructure examples * Delete autotrack-examples directory Move example * Update python-app.yml * Remove plotting * rerun notebooks * chore: make docs * add dep to pint * allow user-defined normalization layers * Avoid optional dependencies * avoid optional dependencies and improve documentation * Update layers.py * Update test_layers.py * Update layers.py * Vastly simplified logic in code * Use weakref to avoid dependency explosion * rename replicate_index to _ID * linting improvements * Add multi-head attention layers * Update test_layers.py * Allow use of unit for resolution * remove test code * 11.5 pypi fix * Update layers.py * Update layers.py * Create gnns/layers.py * Update test_layers.py * Update test_layers.py * Update python-app.yml * Update python-app.yml * Update test_layers.py * Update python-app.yml * Update python-app.yml * Update layers.py * Update layers.py * v2.0.11.3 (#61) (#92) * Fixed bug: Edge case of incorrect positioning of scatterer. Co-authored-by: BenjaminMidtvedt <41636530+BenjaminMidtvedt@users.noreply.github.com> * Update gans * Update gnn layers and fix bugs related to non-accessible trainable parameters * Move layer functions to utils.py * Update test_layers.py * Update utils.py * Add reuse and fix off by one error in flips * Cap poisson to avoid lam too large error * Make generator not stall on out_of_data * move lodestar examples * correctly import gans * fix bug with reuse with lists * Fix LoadImage extra dimensions * LoadImage and Poisson bug fixes * update examples to v2.1 * Accidental import of value * rename to lodestar * rename folder * rename folder * rename to lodestar * ignore datasets * failed run * better run * version bump * don't pass batch_size to model.fit * improve plotting * Create embeddings.py * Add TransformerEncoder * Update test_layers.py * Update layers.py * Create __init__.py * Update __init__.py * Update layers.py * Create gnns/models * Update layers.py * Update __init__.py * Update layers.py * fix polarization calculation * Delete 04. building_complex_pipelines copy.ipynb * Delete 05. making_timeseries.ipynb * Remove legacy functions * Update README.md * fix minor bug * Update README.md * Update README.md * Update README.md * Update logo.png * Update README.md * Update README.md * Update generators.py Make generator compatible with 2.0 syntax Co-authored-by: Benjamin Midtvedt <benmid@student.chalmers.se> Co-authored-by: BenjaminMidtvedt <41636530+BenjaminMidtvedt@users.noreply.github.com> Co-authored-by: JesusPinedaC <jesus.pineda@physics.gu.se> Co-authored-by: Jesús Pineda <36273229+JesusPinedaC@users.noreply.github.com>
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Implements a recursive way of getting relevant citations for any deeptrack object. To add ones own citation, the following syntax is suggested:
Where ParentDeepTrackObject is any deeptrack object (such as Feature or KerasModel).
For function-wrapped initialisers (How many network architectures are implemented currently), we provide the decorator
@with_citation. Example is provided for the unet:Currently, the bibtex is not parsed in any way, and no validation of the correctness of the grammar is provided. I propose that such additions are to be implemented in the future if deemed relevant.
To recursively retrieve all citations of a deeptrack object (and its dependencies), we provide the utility method
obj.get_citations(). This returns a set of unique citations that can be iterated over and printed: