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
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nimare/resources/__init__.py ADDED
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+ """Resources for NiMARE."""
nimare/resources/atlases/Harvard-Oxford-LICENSE ADDED
@@ -0,0 +1,93 @@
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+ FMRIB Software Library, Release 6.0 (c) 2018, The University of Oxford
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+ (the "Software")
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+
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+ The Software remains the property of Oxford University Innovation
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+ ("the University").
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+
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+ The Software is distributed "AS IS" under this Licence solely for
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+ non-commercial use in the hope that it will be useful, but in order
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+ that the University as a charitable foundation protects its assets for
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+ the benefit of its educational and research purposes, the University
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+ makes clear that no condition is made or to be implied, nor is any
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+ warranty given or to be implied, as to the accuracy of the Software,
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+ or that it will be suitable for any particular purpose or for use
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+ under any specific conditions. Furthermore, the University disclaims
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+ all responsibility for the use which is made of the Software. It
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+ further disclaims any liability for the outcomes arising from using
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+ the Software.
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+
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+ The Licensee agrees to indemnify the University and hold the
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+ No part of the Software may be reproduced, modified, transmitted or
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+ without the express permission of the University. The permission of
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+ You are not permitted under this Licence to use this Software
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+ commercially. Use for which any financial return is received shall be
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+ University Innovation ("OUI"), the technology transfer company of the
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+ University, to negotiate a licence. Contact details are:
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+ fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
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+
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+
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+ -------------------------------------------------------------------
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+
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+ The Standard Space Atlases
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+
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+ The Cerebellum, Harvard-Oxford, JHU, Juelich, Striatum and Thalamus atlases,
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+ whilst not being the property of Oxford, are released under the terms of the
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+ main FSL licence above, at the request of their owners. These atlases
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+ should therefore not be used for commercial purposes; for such
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+ purposes please contact the primary co-ordinator for the relevant
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+ atlas:
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+
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+ Harvard-Oxford: steve@fmrib.ox.ac.uk
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+ JHU: susumu@mri.jhu.edu
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+ Juelich: S.Eickhoff@fz-juelich.de
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+ Thalamus: behrens@fmrib.ox.ac.uk
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+ Cerebellum: j.diedrichsen@bangor.ac.uk
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+ Striatum: andri.tziortzi@gmail.com
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+
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+ -------------------------------------------------------------------
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+
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+ FSLView
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+
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+ FSLView sources are released under the terms of the GPLv2
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+ (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html). FSLView
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+ binaries use Qt (http://qt.nokia.com) which is released under LGPLv2.1.
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+ The FSLView binaries are released under the GPL, with the added
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+ exception that we also give permission to link this program with the Qt
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+ non-commercial edition, and distribute the resulting executable,
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+ without including the source code for the Qt non-commercial edition in
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+ the source distribution.
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+
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+ FSLView is distributed "AS IS" under this Licence in the hope that it
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+ will be useful, but in order that the University as a charitable
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+ foundation protects its assets for the benefit of its educational and
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+ research purposes, the University makes clear that no condition is
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+ made or to be implied, nor is any warranty given or to be implied, as
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+ to the accuracy of the Software, or that it will be suitable for any
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+ particular purpose or for use under any specific conditions.
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+ Furthermore, the University disclaims all responsibility for the use
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+ which is made of the Software. It further disclaims any liability for
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+ the outcomes arising from using the Software.
nimare/resources/database_file_manifest.json ADDED
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+ {
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+ "coordinates": "data-neurosynth_version-3_coordinates.tsv.gz",
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+ "metadata": "data-neurosynth_version-3_metadata.tsv.gz",
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+ "features": [
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+ {
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+ "features": "data-neurosynth_version-3_vocab-terms_source-abstract_type-tfidf_features.npz",
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+ "vocabulary": "data-neurosynth_version-3_vocab-terms_vocabulary.txt"
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+ }
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+ ]
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+ },
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+ {
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+ "coordinates": "data-neurosynth_version-4_coordinates.tsv.gz",
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+ "metadata": "data-neurosynth_version-4_metadata.tsv.gz",
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+ "features": [
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+ {
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+ "features": "data-neurosynth_version-4_vocab-terms_source-abstract_type-tfidf_features.npz",
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+ "vocabulary": "data-neurosynth_version-4_vocab-terms_vocabulary.txt"
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+ }
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+ ]
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+ },
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+ {
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+ "coordinates": "data-neurosynth_version-5_coordinates.tsv.gz",
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+ "metadata": "data-neurosynth_version-5_metadata.tsv.gz",
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+ "features": [
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+ {
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+ "features": "data-neurosynth_version-5_vocab-terms_source-abstract_type-tfidf_features.npz",
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+ "vocabulary": "data-neurosynth_version-5_vocab-terms_vocabulary.txt"
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+ }
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+ ]
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+ },
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+ {
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+ "coordinates": "data-neurosynth_version-6_coordinates.tsv.gz",
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+ "metadata": "data-neurosynth_version-6_metadata.tsv.gz",
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+ "features": [
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+ {
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+ "features": "data-neurosynth_version-6_vocab-terms_source-abstract_type-tfidf_features.npz",
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+ "vocabulary": "data-neurosynth_version-6_vocab-terms_vocabulary.txt"
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+ },
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+ {
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+ "features": "data-neurosynth_version-6_vocab-LDA50_source-abstract_type-weight_features.npz",
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+ "vocabulary": "data-neurosynth_version-6_vocab-LDA50_vocabulary.txt",
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+ "keys": "data-neurosynth_version-6_vocab-LDA50_keys.tsv",
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+ "metadata": "data-neurosynth_version-6_vocab-LDA50_metadata.json"
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+ },
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+ {
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+ "features": "data-neurosynth_version-6_vocab-LDA100_source-abstract_type-weight_features.npz",
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+ "vocabulary": "data-neurosynth_version-6_vocab-LDA100_vocabulary.txt",
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+ "keys": "data-neurosynth_version-6_vocab-LDA100_keys.tsv",
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+ "metadata": "data-neurosynth_version-6_vocab-LDA100_metadata.json"
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+ },
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+ {
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+ "features": "data-neurosynth_version-6_vocab-LDA200_source-abstract_type-weight_features.npz",
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+ "vocabulary": "data-neurosynth_version-6_vocab-LDA200_vocabulary.txt",
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+ "keys": "data-neurosynth_version-6_vocab-LDA200_keys.tsv",
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+ "metadata": "data-neurosynth_version-6_vocab-LDA200_metadata.json"
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+ },
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