brainscore-vision 2.1__tar.gz → 2.2.2__tar.gz

brainscore_vision-2.2.2/PKG-INFO

@@ -0,0 +1,153 @@
+Metadata-Version: 2.1
+Name: brainscore_vision
+Version: 2.2.2
+Summary: The Brain-Score library enables model comparisons to behavioral and neural experiments
+License: 
+        MIT License
+        
+        Copyright (c) 2017, Martin Schrimpf and Jon Prescott-Roy
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+        
+        
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2
+Requires-Dist: brainscore-core
+Requires-Dist: result-caching
+Requires-Dist: importlib-metadata<5
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: opencv-python
+Requires-Dist: h5py
+Requires-Dist: tqdm
+Requires-Dist: gitpython
+Requires-Dist: fire
+Requires-Dist: jupyter
+Requires-Dist: pybtex
+Requires-Dist: peewee
+Requires-Dist: psycopg2-binary
+Requires-Dist: networkx
+Requires-Dist: eva-decord
+Requires-Dist: psutil
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest_check; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Requires-Dist: torch; extra == "test"
+Requires-Dist: torchvision; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+
+[![Build Status](https://app.travis-ci.com/brain-score/vision.svg?token=vqt7d2yhhpLGwHsiTZvT&branch=master)](https://app.travis-ci.com/brain-score/vision)
+[![Documentation Status](https://readthedocs.org/projects/brain-score/badge/?version=latest)](https://brain-score.readthedocs.io/en/latest/?badge=latest)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) 
+
+Brain-Score is a platform to evaluate computational models of brain function 
+on their match to brain measurements in primate vision. 
+The intent of Brain-Score is to adopt many (ideally all) the experimental benchmarks in the field
+for the purpose of model testing, falsification, and comparison.
+To that end, Brain-Score operationalizes experimental data into quantitative benchmarks 
+that any model candidate following the [`BrainModel`](brainscore_vision/model_interface.py) interface can be scored on.
+
+Note that you can only access a limited set of public benchmarks when running locally. To score a model on all benchmarks, submit it via the [brain-score.org website](http://www.brain-score.org).
+
+See the [documentation](https://brain-score.readthedocs.io) for more details, e.g. for submitting a [model](https://brain-score.readthedocs.io/en/latest/modules/model_tutorial.html) or [benchmark](https://brain-score.readthedocs.io/en/latest/modules/benchmark_tutorial.html) to Brain-Score. For a step-by-step walkthrough on submitting models to the Brain-Score website, see these [web tutorials](https://www.brain-score.org/tutorial/).
+
+See these [code examples](https://github.com/brain-score/vision/blob/master/examples) on scoring models, retrieving data, using and defining benchmarks and metrics.
+These [previous examples](https://github.com/brain-score/candidate_models/blob/master/examples/score-model.ipynb) might be helpful, but their usage has been deprecated after the 2.0 update.
+
+Brain-Score is made by and for the community. 
+To contribute, please [send in a pull request](https://github.com/brain-score/vision/pulls).
+
+
+## Local installation
+
+You will need Python = 3.11 and pip >= 18.1.
+
+`pip install git+https://github.com/brain-score/vision.git`
+
+Test if the installation is successful by scoring a model on a public benchmark:
+
+```python
+from brainscore_vision.benchmarks import public_benchmark_pool
+
+benchmark = public_benchmark_pool['dicarlo.MajajHong2015public.IT-pls']
+model = my_model()
+score = benchmark(model)
+
+# >  <xarray.Score ()>
+# >  array(0.07637264)
+# >  Attributes:
+# >  Attributes:
+# >      error:                 <xarray.Score ()>\narray(0.00548197)
+# >      raw:                   <xarray.Score ()>\narray(0.22545106)\nAttributes:\...
+# >      ceiling:               <xarray.DataArray ()>\narray(0.81579938)\nAttribut...
+# >      model_identifier:      my-model
+# >      benchmark_identifier:  dicarlo.MajajHong2015public.IT-pls
+```
+
+Some steps may take minutes because data has to be downloaded during first-time use.
+
+## Environment Variables
+
+| Variable               | Description                                                                                                                           |
+|------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
+| RESULTCACHING_HOME     | directory to cache results (benchmark ceilings) in, `~/.result_caching` by default (see https://github.com/brain-score/result_caching) |
+
+
+## License
+
+MIT license
+
+
+## Troubleshooting
+
+<details>
+<summary>`ValueError: did not find HDF5 headers` during netcdf4 installation</summary>
+pip seems to fail properly setting up the HDF5_DIR required by netcdf4.
+Use conda: `conda install netcdf4`
+</details>
+
+<details>
+<summary>repeated runs of a benchmark / model do not change the outcome even though code was changed</summary>
+results (scores, activations) are cached on disk using https://github.com/mschrimpf/result_caching.
+Delete the corresponding file or directory to clear the cache.
+</details>
+
+
+## CI environment
+
+Add CI related build commands to `test_setup.sh`. The script is executed in CI environment for unittests.
+
+
+## References
+
+If you use Brain-Score in your work, please cite 
+["Brain-Score: Which Artificial Neural Network for Object Recognition is most Brain-Like?"](https://www.biorxiv.org/content/10.1101/407007v2) (technical) and 
+["Integrative Benchmarking to Advance Neurally Mechanistic Models of Human Intelligence"](https://www.cell.com/neuron/fulltext/S0896-6273(20)30605-X) (perspective) 
+as well as the respective benchmark sources.
+
+```bibtex
+@article{SchrimpfKubilius2018BrainScore,
+  title={Brain-Score: Which Artificial Neural Network for Object Recognition is most Brain-Like?},
+  author={Martin Schrimpf and Jonas Kubilius and Ha Hong and Najib J. Majaj and Rishi Rajalingham and Elias B. Issa and Kohitij Kar and Pouya Bashivan and Jonathan Prescott-Roy and Franziska Geiger and Kailyn Schmidt and Daniel L. K. Yamins and James J. DiCarlo},
+  journal={bioRxiv preprint},
+  year={2018},
+  url={https://www.biorxiv.org/content/10.1101/407007v2}
+}
+
+@article{Schrimpf2020integrative,
+  title={Integrative Benchmarking to Advance Neurally Mechanistic Models of Human Intelligence},
+  author={Schrimpf, Martin and Kubilius, Jonas and Lee, Michael J and Murty, N Apurva Ratan and Ajemian, Robert and DiCarlo, James J},
+  journal={Neuron},
+  year={2020},
+  url={https://www.cell.com/neuron/fulltext/S0896-6273(20)30605-X}
+}
+```

brainscore_vision-2.2.2/README.md

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+[![Build Status](https://app.travis-ci.com/brain-score/vision.svg?token=vqt7d2yhhpLGwHsiTZvT&branch=master)](https://app.travis-ci.com/brain-score/vision)
+[![Documentation Status](https://readthedocs.org/projects/brain-score/badge/?version=latest)](https://brain-score.readthedocs.io/en/latest/?badge=latest)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) 
+
+Brain-Score is a platform to evaluate computational models of brain function 
+on their match to brain measurements in primate vision. 
+The intent of Brain-Score is to adopt many (ideally all) the experimental benchmarks in the field
+for the purpose of model testing, falsification, and comparison.
+To that end, Brain-Score operationalizes experimental data into quantitative benchmarks 
+that any model candidate following the [`BrainModel`](brainscore_vision/model_interface.py) interface can be scored on.
+
+Note that you can only access a limited set of public benchmarks when running locally. To score a model on all benchmarks, submit it via the [brain-score.org website](http://www.brain-score.org).
+
+See the [documentation](https://brain-score.readthedocs.io) for more details, e.g. for submitting a [model](https://brain-score.readthedocs.io/en/latest/modules/model_tutorial.html) or [benchmark](https://brain-score.readthedocs.io/en/latest/modules/benchmark_tutorial.html) to Brain-Score. For a step-by-step walkthrough on submitting models to the Brain-Score website, see these [web tutorials](https://www.brain-score.org/tutorial/).
+
+See these [code examples](https://github.com/brain-score/vision/blob/master/examples) on scoring models, retrieving data, using and defining benchmarks and metrics.
+These [previous examples](https://github.com/brain-score/candidate_models/blob/master/examples/score-model.ipynb) might be helpful, but their usage has been deprecated after the 2.0 update.
+
+Brain-Score is made by and for the community. 
+To contribute, please [send in a pull request](https://github.com/brain-score/vision/pulls).
+
+
+## Local installation
+
+You will need Python = 3.11 and pip >= 18.1.
+
+`pip install git+https://github.com/brain-score/vision.git`
+
+Test if the installation is successful by scoring a model on a public benchmark:
+
+```python
+from brainscore_vision.benchmarks import public_benchmark_pool
+
+benchmark = public_benchmark_pool['dicarlo.MajajHong2015public.IT-pls']
+model = my_model()
+score = benchmark(model)
+
+# >  <xarray.Score ()>
+# >  array(0.07637264)
+# >  Attributes:
+# >  Attributes:
+# >      error:                 <xarray.Score ()>\narray(0.00548197)
+# >      raw:                   <xarray.Score ()>\narray(0.22545106)\nAttributes:\...
+# >      ceiling:               <xarray.DataArray ()>\narray(0.81579938)\nAttribut...
+# >      model_identifier:      my-model
+# >      benchmark_identifier:  dicarlo.MajajHong2015public.IT-pls
+```
+
+Some steps may take minutes because data has to be downloaded during first-time use.
+
+## Environment Variables
+
+| Variable               | Description                                                                                                                           |
+|------------------------|---------------------------------------------------------------------------------------------------------------------------------------|
+| RESULTCACHING_HOME     | directory to cache results (benchmark ceilings) in, `~/.result_caching` by default (see https://github.com/brain-score/result_caching) |
+
+
+## License
+
+MIT license
+
+
+## Troubleshooting
+
+<details>
+<summary>`ValueError: did not find HDF5 headers` during netcdf4 installation</summary>
+pip seems to fail properly setting up the HDF5_DIR required by netcdf4.
+Use conda: `conda install netcdf4`
+</details>
+
+<details>
+<summary>repeated runs of a benchmark / model do not change the outcome even though code was changed</summary>
+results (scores, activations) are cached on disk using https://github.com/mschrimpf/result_caching.
+Delete the corresponding file or directory to clear the cache.
+</details>
+
+
+## CI environment
+
+Add CI related build commands to `test_setup.sh`. The script is executed in CI environment for unittests.
+
+
+## References
+
+If you use Brain-Score in your work, please cite 
+["Brain-Score: Which Artificial Neural Network for Object Recognition is most Brain-Like?"](https://www.biorxiv.org/content/10.1101/407007v2) (technical) and 
+["Integrative Benchmarking to Advance Neurally Mechanistic Models of Human Intelligence"](https://www.cell.com/neuron/fulltext/S0896-6273(20)30605-X) (perspective) 
+as well as the respective benchmark sources.
+
+```bibtex
+@article{SchrimpfKubilius2018BrainScore,
+  title={Brain-Score: Which Artificial Neural Network for Object Recognition is most Brain-Like?},
+  author={Martin Schrimpf and Jonas Kubilius and Ha Hong and Najib J. Majaj and Rishi Rajalingham and Elias B. Issa and Kohitij Kar and Pouya Bashivan and Jonathan Prescott-Roy and Franziska Geiger and Kailyn Schmidt and Daniel L. K. Yamins and James J. DiCarlo},
+  journal={bioRxiv preprint},
+  year={2018},
+  url={https://www.biorxiv.org/content/10.1101/407007v2}
+}
+
+@article{Schrimpf2020integrative,
+  title={Integrative Benchmarking to Advance Neurally Mechanistic Models of Human Intelligence},
+  author={Schrimpf, Martin and Kubilius, Jonas and Lee, Michael J and Murty, N Apurva Ratan and Ajemian, Robert and DiCarlo, James J},
+  journal={Neuron},
+  year={2020},
+  url={https://www.cell.com/neuron/fulltext/S0896-6273(20)30605-X}
+}
+```

brainscore_vision-2.2.2/brainscore_vision/benchmarks/coggan2024_behavior/__init__.py

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+# Created by David Coggan on 2024 06 25
+
+from brainscore_vision import benchmark_registry
+from .benchmark import (
+    Coggan2024_behavior_ConditionWiseAccuracySimilarity)
+
+benchmark_registry['tong.Coggan2024_behavior-ConditionWiseAccuracySimilarity'] = (
+    Coggan2024_behavior_ConditionWiseAccuracySimilarity)
+

brainscore_vision-2.2.2/brainscore_vision/benchmarks/coggan2024_behavior/test.py

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+# Created by David Coggan on 2024 06 26
+
+import pytest
+from pytest import approx
+from brainscore_vision import benchmark_registry, load_benchmark
+from brainscore_vision import load_model
+
+
+def test_benchmark_registry():
+    assert ('tong.Coggan2024_behavior-ConditionWiseAccuracySimilarity' in
+            benchmark_registry)
+
+@pytest.mark.private_access
+def test_benchmarks():
+    benchmark = load_benchmark(
+        'tong.Coggan2024_behavior-ConditionWiseAccuracySimilarity')
+    model = load_model('alexnet')
+    result = benchmark(model)
+    assert result.values == approx(0.1318, abs=.001)
+
+

brainscore_vision-2.2.2/brainscore_vision/benchmarks/coggan2024_fMRI/__init__.py

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+# Created by David Coggan on 2024 06 25
+
+from brainscore_vision import benchmark_registry
+from .benchmark import (
+    Coggan2024_V1,
+    Coggan2024_V2,
+    Coggan2024_V4,
+    Coggan2024_IT,
+)
+
+benchmark_registry['tong.Coggan2024_fMRI.V1-rdm'] = Coggan2024_V1
+benchmark_registry['tong.Coggan2024_fMRI.V2-rdm'] = Coggan2024_V2
+benchmark_registry['tong.Coggan2024_fMRI.V4-rdm'] = Coggan2024_V4
+benchmark_registry['tong.Coggan2024_fMRI.IT-rdm'] = Coggan2024_IT
+

brainscore_vision-2.2.2/brainscore_vision/benchmarks/coggan2024_fMRI/test.py

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+# Created by David Coggan on 2024 06 26
+
+import pytest
+from pytest import approx
+from brainscore_vision import benchmark_registry, load_benchmark
+from brainscore_vision import load_model
+
+
+@pytest.mark.parametrize('region', ['V1', 'V2', 'V4', 'IT'])
+def test_benchmark_registry(region):
+    assert f'tong.Coggan2024_fMRI.{region}-rdm' in benchmark_registry
+
+
+@pytest.mark.parametrize('region', ['V1', 'V2', 'V4', 'IT'])
+def test_benchmarks(region):
+    expected_score = dict(
+        V1=0.0182585,
+        V2=0.3352083,
+        V4=0.3008136,
+        IT=0.4486508)[region]
+    model = load_model('alexnet')
+    benchmark = load_benchmark(f'tong.Coggan2024_fMRI.{region}-rdm')
+    score = benchmark(model)
+    assert score.values == approx(expected_score, abs=.005)
+