nimare 0.4.2__py3-none-any.whl

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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 +667 -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 +294 -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-0.4.2.dist-info/LICENSE +21 -0
  115. nimare-0.4.2.dist-info/METADATA +124 -0
  116. nimare-0.4.2.dist-info/RECORD +119 -0
  117. nimare-0.4.2.dist-info/WHEEL +5 -0
  118. nimare-0.4.2.dist-info/entry_points.txt +2 -0
  119. nimare-0.4.2.dist-info/top_level.txt +2 -0
nimare/resources/filenames.json ADDED
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+ {
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+ "name": "nimare",
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+ "entities": [
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+ {
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+ "name": "datatype",
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+ "pattern": "([a-zA-Z0-9]+)[_.]"
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+ },
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+ {
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+ "name": "description",
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+ "pattern": "[_/\\\\]+desc-([a-zA-Z0-9]+)"
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+ },
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+ {
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+ "name": "level",
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+ "pattern": "[_/\\\\]+level-([a-zA-Z]+)"
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+ },
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+ {
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+ "name": "correction",
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+ "pattern": "[_/\\\\]+corr-([A-Z]+)"
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+ },
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+ {
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+ "name": "method",
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+ "pattern": "[_/\\\\]+method-([a-zA-Z0-9]+)"
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+ },
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+ {
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+ "name": "extension",
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+ "pattern": "[._]*[a-zA-Z0-9]*?(\\.[^/\\\\]+)$"
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+ }
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+ ],
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+ "default_path_patterns": [
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+ "{datatype<{datatype}>}[_desc-{description}][_level-{level<cluster|voxel>}][_corr-{correction<FDR|FWE>}][_method-{method}]{extension<.nii|.nii.gz|.json>|.nii.gz}"
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+ ]
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+ }