nimare 0.4.2rc4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (119) hide show
  1. benchmarks/__init__.py +0 -0
  2. benchmarks/bench_cbma.py +57 -0
  3. nimare/__init__.py +45 -0
  4. nimare/_version.py +21 -0
  5. nimare/annotate/__init__.py +21 -0
  6. nimare/annotate/cogat.py +213 -0
  7. nimare/annotate/gclda.py +924 -0
  8. nimare/annotate/lda.py +147 -0
  9. nimare/annotate/text.py +75 -0
  10. nimare/annotate/utils.py +87 -0
  11. nimare/base.py +217 -0
  12. nimare/cli.py +124 -0
  13. nimare/correct.py +462 -0
  14. nimare/dataset.py +685 -0
  15. nimare/decode/__init__.py +33 -0
  16. nimare/decode/base.py +115 -0
  17. nimare/decode/continuous.py +462 -0
  18. nimare/decode/discrete.py +753 -0
  19. nimare/decode/encode.py +110 -0
  20. nimare/decode/utils.py +44 -0
  21. nimare/diagnostics.py +510 -0
  22. nimare/estimator.py +139 -0
  23. nimare/extract/__init__.py +19 -0
  24. nimare/extract/extract.py +466 -0
  25. nimare/extract/utils.py +295 -0
  26. nimare/generate.py +331 -0
  27. nimare/io.py +635 -0
  28. nimare/meta/__init__.py +39 -0
  29. nimare/meta/cbma/__init__.py +6 -0
  30. nimare/meta/cbma/ale.py +951 -0
  31. nimare/meta/cbma/base.py +947 -0
  32. nimare/meta/cbma/mkda.py +1361 -0
  33. nimare/meta/cbmr.py +970 -0
  34. nimare/meta/ibma.py +1683 -0
  35. nimare/meta/kernel.py +501 -0
  36. nimare/meta/models.py +1199 -0
  37. nimare/meta/utils.py +494 -0
  38. nimare/nimads.py +492 -0
  39. nimare/reports/__init__.py +24 -0
  40. nimare/reports/base.py +664 -0
  41. nimare/reports/default.yml +123 -0
  42. nimare/reports/figures.py +651 -0
  43. nimare/reports/report.tpl +160 -0
  44. nimare/resources/__init__.py +1 -0
  45. nimare/resources/atlases/Harvard-Oxford-LICENSE +93 -0
  46. nimare/resources/atlases/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz +0 -0
  47. nimare/resources/database_file_manifest.json +142 -0
  48. nimare/resources/english_spellings.csv +1738 -0
  49. nimare/resources/filenames.json +32 -0
  50. nimare/resources/neurosynth_laird_studies.json +58773 -0
  51. nimare/resources/neurosynth_stoplist.txt +396 -0
  52. nimare/resources/nidm_pain_dset.json +1349 -0
  53. nimare/resources/references.bib +541 -0
  54. nimare/resources/semantic_knowledge_children.txt +325 -0
  55. nimare/resources/semantic_relatedness_children.txt +249 -0
  56. nimare/resources/templates/MNI152_2x2x2_brainmask.nii.gz +0 -0
  57. nimare/resources/templates/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz +0 -0
  58. nimare/resources/templates/tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz +0 -0
  59. nimare/resources/templates/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz +0 -0
  60. nimare/resources/templates/tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz +0 -0
  61. nimare/results.py +225 -0
  62. nimare/stats.py +276 -0
  63. nimare/tests/__init__.py +1 -0
  64. nimare/tests/conftest.py +229 -0
  65. nimare/tests/data/amygdala_roi.nii.gz +0 -0
  66. nimare/tests/data/data-neurosynth_version-7_coordinates.tsv.gz +0 -0
  67. nimare/tests/data/data-neurosynth_version-7_metadata.tsv.gz +0 -0
  68. nimare/tests/data/data-neurosynth_version-7_vocab-terms_source-abstract_type-tfidf_features.npz +0 -0
  69. nimare/tests/data/data-neurosynth_version-7_vocab-terms_vocabulary.txt +100 -0
  70. nimare/tests/data/neurosynth_dset.json +2868 -0
  71. nimare/tests/data/neurosynth_laird_studies.json +58773 -0
  72. nimare/tests/data/nidm_pain_dset.json +1349 -0
  73. nimare/tests/data/nimads_annotation.json +1 -0
  74. nimare/tests/data/nimads_studyset.json +1 -0
  75. nimare/tests/data/test_baseline.txt +2 -0
  76. nimare/tests/data/test_pain_dataset.json +1278 -0
  77. nimare/tests/data/test_pain_dataset_multiple_contrasts.json +1242 -0
  78. nimare/tests/data/test_sleuth_file.txt +18 -0
  79. nimare/tests/data/test_sleuth_file2.txt +10 -0
  80. nimare/tests/data/test_sleuth_file3.txt +5 -0
  81. nimare/tests/data/test_sleuth_file4.txt +5 -0
  82. nimare/tests/data/test_sleuth_file5.txt +5 -0
  83. nimare/tests/test_annotate_cogat.py +32 -0
  84. nimare/tests/test_annotate_gclda.py +86 -0
  85. nimare/tests/test_annotate_lda.py +27 -0
  86. nimare/tests/test_dataset.py +99 -0
  87. nimare/tests/test_decode_continuous.py +132 -0
  88. nimare/tests/test_decode_discrete.py +92 -0
  89. nimare/tests/test_diagnostics.py +168 -0
  90. nimare/tests/test_estimator_performance.py +385 -0
  91. nimare/tests/test_extract.py +46 -0
  92. nimare/tests/test_generate.py +247 -0
  93. nimare/tests/test_io.py +240 -0
  94. nimare/tests/test_meta_ale.py +298 -0
  95. nimare/tests/test_meta_cbmr.py +295 -0
  96. nimare/tests/test_meta_ibma.py +240 -0
  97. nimare/tests/test_meta_kernel.py +209 -0
  98. nimare/tests/test_meta_mkda.py +234 -0
  99. nimare/tests/test_nimads.py +21 -0
  100. nimare/tests/test_reports.py +110 -0
  101. nimare/tests/test_stats.py +101 -0
  102. nimare/tests/test_transforms.py +272 -0
  103. nimare/tests/test_utils.py +200 -0
  104. nimare/tests/test_workflows.py +221 -0
  105. nimare/tests/utils.py +126 -0
  106. nimare/transforms.py +907 -0
  107. nimare/utils.py +1367 -0
  108. nimare/workflows/__init__.py +14 -0
  109. nimare/workflows/base.py +189 -0
  110. nimare/workflows/cbma.py +165 -0
  111. nimare/workflows/ibma.py +108 -0
  112. nimare/workflows/macm.py +77 -0
  113. nimare/workflows/misc.py +65 -0
  114. nimare-0.4.2rc4.dist-info/LICENSE +21 -0
  115. nimare-0.4.2rc4.dist-info/METADATA +124 -0
  116. nimare-0.4.2rc4.dist-info/RECORD +119 -0
  117. nimare-0.4.2rc4.dist-info/WHEEL +5 -0
  118. nimare-0.4.2rc4.dist-info/entry_points.txt +2 -0
  119. nimare-0.4.2rc4.dist-info/top_level.txt +2 -0
@@ -0,0 +1,124 @@
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+ Metadata-Version: 2.1
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+ Name: nimare
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+ Version: 0.4.2rc4
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+ Summary: NiMARE: Neuroimaging Meta-Analysis Research Environment
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+ Home-page: https://github.com/neurostuff/NiMARE
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+ Author: NiMARE developers
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+ Author-email: tsalo006@fiu.edu
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+ Maintainer: Taylor Salo
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+ Maintainer-email: tsalo006@fiu.edu
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+ License: MIT
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Environment :: Console
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Topic :: Scientific/Engineering
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+ Requires-Python: >=3.8
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: cognitiveatlas>=0.1.11
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+ Requires-Dist: fuzzywuzzy
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+ Requires-Dist: jinja2
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+ Requires-Dist: joblib>=1.3.0
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+ Requires-Dist: matplotlib>=3.6.0
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+ Requires-Dist: nibabel>=3.2.0
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+ Requires-Dist: nilearn!=0.10.3,>=0.10.1
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+ Requires-Dist: numba>=0.57.0
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+ Requires-Dist: numpy>=1.22
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+ Requires-Dist: pandas>=2.0.0
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+ Requires-Dist: patsy
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+ Requires-Dist: plotly
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+ Requires-Dist: pymare>=0.0.8
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+ Requires-Dist: pyyaml
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+ Requires-Dist: requests
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+ Requires-Dist: ridgeplot
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+ Requires-Dist: scikit-learn>=1.0.0
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+ Requires-Dist: scipy>=1.6.0
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+ Requires-Dist: sparse>=0.13.0
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+ Requires-Dist: statsmodels!=0.13.2
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+ Requires-Dist: tqdm
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+ Requires-Dist: importlib-resources; python_version < "3.9"
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+ Provides-Extra: all
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+ Requires-Dist: indexed-gzip>=1.4.0; extra == "all"
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+ Requires-Dist: torch>=2.0; extra == "all"
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+ Requires-Dist: m2r2; extra == "all"
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+ Requires-Dist: matplotlib; extra == "all"
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+ Requires-Dist: mistune; extra == "all"
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+ Requires-Dist: pillow; extra == "all"
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+ Requires-Dist: recommonmark; extra == "all"
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+ Requires-Dist: seaborn; extra == "all"
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+ Requires-Dist: sphinx>=3.5; extra == "all"
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+ Requires-Dist: sphinx-argparse; extra == "all"
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+ Requires-Dist: sphinx-copybutton; extra == "all"
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+ Requires-Dist: sphinx-gallery; extra == "all"
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+ Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "all"
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+ Requires-Dist: sphinxcontrib-bibtex; extra == "all"
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+ Requires-Dist: sphinxcontrib-mermaid; extra == "all"
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+ Requires-Dist: docutils<0.21,>=0.18.1; extra == "all"
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+ Requires-Dist: coverage; extra == "all"
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+ Requires-Dist: coveralls; extra == "all"
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+ Requires-Dist: flake8-black; extra == "all"
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+ Requires-Dist: flake8-docstrings; extra == "all"
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+ Requires-Dist: flake8-isort; extra == "all"
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+ Requires-Dist: pytest; extra == "all"
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+ Requires-Dist: pytest-cov; extra == "all"
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+ Provides-Extra: cbmr
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+ Requires-Dist: torch>=2.0; extra == "cbmr"
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+ Provides-Extra: doc
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+ Requires-Dist: m2r2; extra == "doc"
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+ Requires-Dist: matplotlib; extra == "doc"
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+ Requires-Dist: mistune; extra == "doc"
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+ Requires-Dist: pillow; extra == "doc"
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+ Requires-Dist: recommonmark; extra == "doc"
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+ Requires-Dist: seaborn; extra == "doc"
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+ Requires-Dist: sphinx>=3.5; extra == "doc"
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+ Requires-Dist: sphinx-argparse; extra == "doc"
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+ Requires-Dist: sphinx-copybutton; extra == "doc"
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+ Requires-Dist: sphinx-gallery; extra == "doc"
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+ Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "doc"
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+ Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
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+ Requires-Dist: sphinxcontrib-mermaid; extra == "doc"
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+ Requires-Dist: docutils<0.21,>=0.18.1; extra == "doc"
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+ Provides-Extra: gzip
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+ Requires-Dist: indexed-gzip>=1.4.0; extra == "gzip"
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+ Provides-Extra: minimum
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+ Requires-Dist: matplotlib==3.6.0; extra == "minimum"
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+ Requires-Dist: nibabel==4.0.0; extra == "minimum"
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+ Requires-Dist: nilearn==0.10.1; extra == "minimum"
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+ Requires-Dist: numpy==1.22; extra == "minimum"
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+ Requires-Dist: pandas==2.0.0; extra == "minimum"
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+ Requires-Dist: pymare==0.0.8; extra == "minimum"
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+ Requires-Dist: scikit-learn==1.0.0; extra == "minimum"
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+ Requires-Dist: scipy==1.6.0; extra == "minimum"
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+ Requires-Dist: seaborn==0.13.0; extra == "minimum"
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+ Provides-Extra: tests
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+ Requires-Dist: coverage; extra == "tests"
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+ Requires-Dist: coveralls; extra == "tests"
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+ Requires-Dist: flake8-black; extra == "tests"
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+ Requires-Dist: flake8-docstrings; extra == "tests"
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+ Requires-Dist: flake8-isort; extra == "tests"
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+ Requires-Dist: pytest; extra == "tests"
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+ Requires-Dist: pytest-cov; extra == "tests"
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+
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+ # NiMARE
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+
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+ NiMARE (Neuroimaging Meta-Analysis Research Environment) is a Python
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+ package for coordinate-based and image-based meta-analysis of
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+ neuroimaging data.
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+
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+ # License
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+
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+ `NiMARE` is licensed under the terms of the MIT license. See the file
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+ \'LICENSE\' for information on the history of this software, terms &
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+ conditions for usage, and a DISCLAIMER OF ALL WARRANTIES.
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+
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+ All trademarks referenced herein are property of their respective
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+ holders.
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+
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+ Copyright (c) 2018\--, NiMARE developers
@@ -0,0 +1,119 @@
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+ benchmarks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ benchmarks/bench_cbma.py,sha256=fg_EER8hohi6kD1Hno_uXsFntKuCLTvseu-6OqkHkoU,1382
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+ nimare/__init__.py,sha256=HHIq3EimSZSf3zJSDwuTjBig1GbRwHGYfRLSqI3yleE,802
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+ nimare/_version.py,sha256=-_XjBHi6NWmhzi6JM6lRzA_-9vJ61UHSP66mEa1jicw,500
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+ nimare/base.py,sha256=9DlcRB2mW759p7XqpKG3wRE-MmPsEPiYTbq6V1Yile4,7826
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+ nimare/cli.py,sha256=Zvy5jN2KopH_MBke-gm8A0DbBZmIFGvnE1tjhbYib9I,3695
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+ nimare/correct.py,sha256=2eI0jR6_odND-2CzSlaxRU2um6ccLSapd7ERAYteBnE,17110
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+ nimare/dataset.py,sha256=LmjDE1GQ3ud33l3plvms_Uv8GB9_Xb-6kPtkIV2eYTw,24650
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+ nimare/diagnostics.py,sha256=sCatkXUM9rvrY9MMz6Q66njWSiWGifWwSNEMu3ldnVs,20263
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+ nimare/estimator.py,sha256=DtsSIyPDrKkpi-KNv2m-cZMvJO7CCfHLXHRhCT73sbY,5063
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+ nimare/generate.py,sha256=L4_c2sLAlF7XDKTm-3q4oOx8pLID2NaxG9YET5KSIZw,12475
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+ nimare/io.py,sha256=iNejkAclJh6u6_zGa_9sg1u4YBO02fho0quKyycDUTQ,25831
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+ nimare/nimads.py,sha256=Wxz7b_O0f8DEXb2NNlOuJkEcfGKbH-wGwLkoZhdU8sY,16277
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+ nimare/results.py,sha256=7szcyR6PkZAXBqbIGGWrw1nW9j9QCdpdl4MxUK_1Wzc,8190
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+ nimare/stats.py,sha256=XhXfFj6KHTPVSTXhbEid0qt8HLqJD82Bl5T23qmaf40,10098
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+ nimare/transforms.py,sha256=_kZO8N3IEHxd6Ir4IcewZtkWHpFknnjEnjsaD9b-1pg,30136
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+ nimare/utils.py,sha256=BJOOKgQuubamE0RBMJVubggQfaPgIH9wZ9Oou9DKvbU,46936
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+ nimare/annotate/__init__.py,sha256=hTla1yFYTJ8PDjm72ReeHa3qf0Que50Ww0fqz3Z86JI,434
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+ nimare/annotate/cogat.py,sha256=xzrepAuTkRenbECn4XYwgyul45r0tIMxCDKQV_ZFVb8,7457
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+ nimare/annotate/gclda.py,sha256=P2OQjuJn3DX0GVPte_VIVZf0LfO-yE_OhLbs6DwMaHQ,42592
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+ nimare/annotate/lda.py,sha256=iacqOHPMYnSSetplKiKbGQLbk66v_fx-wNLBUmyT3Zo,5576
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+ nimare/annotate/text.py,sha256=qjBgaNAlNtmo-z8xzqaYlvHZTXKrAZSXCxqFRot5vvc,2426
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+ nimare/annotate/utils.py,sha256=ZJPoS-UVa9svZuv6owcnZIy_Cl-Oxgf15I2-FbS0sx0,3051
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+ nimare/decode/__init__.py,sha256=Yp5NOijtD2Y3_sYTIarcqYIA3smFegk50k5azog8XsU,703
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+ nimare/decode/base.py,sha256=PFhlsXm-28A20XPWa4cJ42uF6cjYX0NFJpxucyIk0v4,4372
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+ nimare/decode/continuous.py,sha256=Wef_dCyI4avYjZoAdlRZdfxQva_LDOhDhq1tQtr3je0,16996
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+ nimare/decode/discrete.py,sha256=jr0CjbE4TUjHASXwWzYEqugoFNqyRgdep1AK30YMKYo,28217
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+ nimare/decode/encode.py,sha256=DcrwWSPIo_viACdSizOXzI_w9_cVP3Xj6b_xMNhNqXk,4554
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+ nimare/decode/utils.py,sha256=tpsHxhaeG3ZVcTLviWfAhVlW_Gp1_Fvsw7EEF1Q1y9M,1288
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+ nimare/extract/__init__.py,sha256=0dnoq_Lryti2Zy1tVlILjojvPpx1j3gqN8ARw9ELP5w,383
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+ nimare/extract/extract.py,sha256=GAh_Kkjvfoj-H5MjHYZbBYqS3GGfkMr5EbpeIg60zSE,17080
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+ nimare/extract/utils.py,sha256=yGhfnz_OBSJLO7BjgnX0D_PwBMJzXB5Bb3_BgyqEnvE,8994
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+ nimare/meta/__init__.py,sha256=vkXIPdEFmg81EIeVRmblbQynCHQY2ivf3AJjLiCJ_uc,816
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+ nimare/meta/cbmr.py,sha256=h9CNMHW4KUh-YQYyGDRzqPN7G1tkHYAhrSgxrP8E61s,47769
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+ nimare/meta/ibma.py,sha256=qVw3ZhOlK6hgTdZZwa7TPDpfrGLf52dN00wH2Gw-Z8c,65442
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+ nimare/meta/kernel.py,sha256=5wN-6dbLkzqQ0WUSTrC0DJPSbbyGiZCls9M_TAYhNGY,19169
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+ nimare/meta/models.py,sha256=0QPlQTjWaNTeI8qTX-DHMXVjQSRD72SfJ2RZIYBZnCg,47054
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+ nimare/meta/utils.py,sha256=fvnFz4ek8APjQHhYBS441WYXE1N9huHaTiOO0Bvui4Q,18083
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+ nimare/meta/cbma/__init__.py,sha256=bWLrv5tL03U2ITttnnz3yerbg74w44qkZgdy32QMhqQ,219
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+ nimare/meta/cbma/ale.py,sha256=ZNjXC4MXhfSHvrTRppY04NkGtz_Iri696k5QMuBog7o,39273
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+ nimare/meta/cbma/mkda.py,sha256=V5vSQodiLZoZhkYPhous0a_-1pZoRjAIL8gmGyyoezc,60397
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+ nimare/reports/__init__.py,sha256=zGfrOPlMq2lTorKNEpyPblArFCnsvz3dRsvOHy_Ciag,428
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+ nimare/reports/figures.py,sha256=MCsjDR53475Jz1_anktKvNOh0qUNPMx-dfvP6Vy0uUc,19783
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+ nimare/resources/__init__.py,sha256=huwax0KmUCfwVlxSRYS0qwmEzaAcNkNnpNbKp1K0n1E,28
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+ nimare/resources/database_file_manifest.json,sha256=gn9aXERthi0KYzdI5cvYKcVXWG-BLa2BKNq-r2nQJAI,7441
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+ nimare/resources/english_spellings.csv,sha256=w3CW1d2-_gCuwzB_b1YETGorg3Uvxa_sqmsaLPU81VY,38750
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+ nimare/resources/filenames.json,sha256=eDSbduIwHXXTDVKoi8Ha27vK5U4dEiFyCefDa6bizg0,890
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+ nimare/resources/neurosynth_laird_studies.json,sha256=hUqLogxCLtLSTuQvXXoPvX4A3v7GJWg2ZynkEuMgsfw,3259995
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+ nimare/resources/neurosynth_stoplist.txt,sha256=UXkljEEDmHlTAcgj_2yMvWrGx-TcE2Fq03NhZ42JXBg,2606
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+ nimare/resources/nidm_pain_dset.json,sha256=GgbnFrd5dbCB82OHuF8d24e3Z2jy6d1U0kWnIKccM78,40052
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+ nimare/resources/references.bib,sha256=wAKWftdiAC-PqjY5rCu1Xgn_Hp53sSCp9B95G1tNJx0,20511
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+ nimare/resources/semantic_knowledge_children.txt,sha256=6cwfiV4wobblI2srW7xQldLAvhirwTkUFv_hyFutnTc,6417
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+ nimare/resources/semantic_relatedness_children.txt,sha256=WS2CsyLd-266D5CRV1r9bF4oNSlW3YdVTzUgH9lvN7E,4870
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+ nimare