pyNIBS 0.2024.8__py3-none-any.whl

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  1. pyNIBS-0.2024.8.dist-info/LICENSE +623 -0
  2. pyNIBS-0.2024.8.dist-info/METADATA +723 -0
  3. pyNIBS-0.2024.8.dist-info/RECORD +107 -0
  4. pyNIBS-0.2024.8.dist-info/WHEEL +5 -0
  5. pyNIBS-0.2024.8.dist-info/top_level.txt +1 -0
  6. pynibs/__init__.py +34 -0
  7. pynibs/coil.py +1367 -0
  8. pynibs/congruence/__init__.py +15 -0
  9. pynibs/congruence/congruence.py +1108 -0
  10. pynibs/congruence/ext_metrics.py +257 -0
  11. pynibs/congruence/stimulation_threshold.py +318 -0
  12. pynibs/data/configuration_exp0.yaml +59 -0
  13. pynibs/data/configuration_linear_MEP.yaml +61 -0
  14. pynibs/data/configuration_linear_RT.yaml +61 -0
  15. pynibs/data/configuration_sigmoid4.yaml +68 -0
  16. pynibs/data/network mapping configuration/configuration guide.md +238 -0
  17. pynibs/data/network mapping configuration/configuration_TEMPLATE.yaml +42 -0
  18. pynibs/data/network mapping configuration/configuration_for_testing.yaml +43 -0
  19. pynibs/data/network mapping configuration/configuration_modelTMS.yaml +43 -0
  20. pynibs/data/network mapping configuration/configuration_reg_isi_05.yaml +43 -0
  21. pynibs/data/network mapping configuration/output_documentation.md +185 -0
  22. pynibs/data/network mapping configuration/recommendations_for_accuracy_threshold.md +77 -0
  23. pynibs/data/neuron/models/L23_PC_cADpyr_biphasic_v1.csv +1281 -0
  24. pynibs/data/neuron/models/L23_PC_cADpyr_monophasic_v1.csv +1281 -0
  25. pynibs/data/neuron/models/L4_LBC_biphasic_v1.csv +1281 -0
  26. pynibs/data/neuron/models/L4_LBC_monophasic_v1.csv +1281 -0
  27. pynibs/data/neuron/models/L4_NBC_biphasic_v1.csv +1281 -0
  28. pynibs/data/neuron/models/L4_NBC_monophasic_v1.csv +1281 -0
  29. pynibs/data/neuron/models/L4_SBC_biphasic_v1.csv +1281 -0
  30. pynibs/data/neuron/models/L4_SBC_monophasic_v1.csv +1281 -0
  31. pynibs/data/neuron/models/L5_TTPC2_cADpyr_biphasic_v1.csv +1281 -0
  32. pynibs/data/neuron/models/L5_TTPC2_cADpyr_monophasic_v1.csv +1281 -0
  33. pynibs/expio/Mep.py +1518 -0
  34. pynibs/expio/__init__.py +8 -0
  35. pynibs/expio/brainsight.py +979 -0
  36. pynibs/expio/brainvis.py +71 -0
  37. pynibs/expio/cobot.py +239 -0
  38. pynibs/expio/exp.py +1876 -0
  39. pynibs/expio/fit_funs.py +287 -0
  40. pynibs/expio/localite.py +1987 -0
  41. pynibs/expio/signal_ced.py +51 -0
  42. pynibs/expio/visor.py +624 -0
  43. pynibs/freesurfer.py +502 -0
  44. pynibs/hdf5_io/__init__.py +10 -0
  45. pynibs/hdf5_io/hdf5_io.py +1857 -0
  46. pynibs/hdf5_io/xdmf.py +1542 -0
  47. pynibs/mesh/__init__.py +3 -0
  48. pynibs/mesh/mesh_struct.py +1394 -0
  49. pynibs/mesh/transformations.py +866 -0
  50. pynibs/mesh/utils.py +1103 -0
  51. pynibs/models/_TMS.py +211 -0
  52. pynibs/models/__init__.py +0 -0
  53. pynibs/muap.py +392 -0
  54. pynibs/neuron/__init__.py +2 -0
  55. pynibs/neuron/neuron_regression.py +284 -0
  56. pynibs/neuron/util.py +58 -0
  57. pynibs/optimization/__init__.py +5 -0
  58. pynibs/optimization/multichannel.py +278 -0
  59. pynibs/optimization/opt_mep.py +152 -0
  60. pynibs/optimization/optimization.py +1445 -0
  61. pynibs/optimization/workhorses.py +698 -0
  62. pynibs/pckg/__init__.py +0 -0
  63. pynibs/pckg/biosig/biosig4c++-1.9.5.src_fixed.tar.gz +0 -0
  64. pynibs/pckg/libeep/__init__.py +0 -0
  65. pynibs/pckg/libeep/pyeep.so +0 -0
  66. pynibs/regression/__init__.py +11 -0
  67. pynibs/regression/dual_node_detection.py +2375 -0
  68. pynibs/regression/regression.py +2984 -0
  69. pynibs/regression/score_types.py +0 -0
  70. pynibs/roi/__init__.py +2 -0
  71. pynibs/roi/roi.py +895 -0
  72. pynibs/roi/roi_structs.py +1233 -0
  73. pynibs/subject.py +1009 -0
  74. pynibs/tensor_scaling.py +144 -0
  75. pynibs/tests/data/InstrumentMarker20200225163611937.xml +19 -0
  76. pynibs/tests/data/TriggerMarkers_Coil0_20200225163443682.xml +14 -0
  77. pynibs/tests/data/TriggerMarkers_Coil1_20200225170337572.xml +6373 -0
  78. pynibs/tests/data/Xdmf.dtd +89 -0
  79. pynibs/tests/data/brainsight_niiImage_nifticoord.txt +145 -0
  80. pynibs/tests/data/brainsight_niiImage_nifticoord_largefile.txt +1434 -0
  81. pynibs/tests/data/brainsight_niiImage_niifticoord_mixedtargets.txt +47 -0
  82. pynibs/tests/data/create_subject_testsub.py +332 -0
  83. pynibs/tests/data/data.hdf5 +0 -0
  84. pynibs/tests/data/geo.hdf5 +0 -0
  85. pynibs/tests/test_coil.py +474 -0
  86. pynibs/tests/test_elements2nodes.py +100 -0
  87. pynibs/tests/test_hdf5_io/test_xdmf.py +61 -0
  88. pynibs/tests/test_mesh_transformations.py +123 -0
  89. pynibs/tests/test_mesh_utils.py +143 -0
  90. pynibs/tests/test_nnav_imports.py +101 -0
  91. pynibs/tests/test_quality_measures.py +117 -0
  92. pynibs/tests/test_regressdata.py +289 -0
  93. pynibs/tests/test_roi.py +17 -0
  94. pynibs/tests/test_rotations.py +86 -0
  95. pynibs/tests/test_subject.py +71 -0
  96. pynibs/tests/test_util.py +24 -0
  97. pynibs/tms_pulse.py +34 -0
  98. pynibs/util/__init__.py +4 -0
  99. pynibs/util/dosing.py +233 -0
  100. pynibs/util/quality_measures.py +562 -0
  101. pynibs/util/rotations.py +340 -0
  102. pynibs/util/simnibs.py +763 -0
  103. pynibs/util/util.py +727 -0
  104. pynibs/visualization/__init__.py +2 -0
  105. pynibs/visualization/para.py +4372 -0
  106. pynibs/visualization/plot_2D.py +137 -0
  107. pynibs/visualization/render_3D.py +347 -0
pynibs/congruence/__init__.py ADDED
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+ """
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+ :py:class:`pynibs.congruence` holds the initial congruence factor implementation as described in Weise, Numssen, et al., 2020 [1]_.
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+ This code is mainly stored here for reproducibility reasons. The current approach (Numssen et al., 2021; [2]_) uses
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+ the :py:class:`pynibs.regression` methods.
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+
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+ References
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+ ----------
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+ .. [1] Weise, K., Numssen, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020).
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+ A novel approach to localize cortical TMS effects. Neuroimage, 209, 116486.
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+ .. [2] Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021).
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+ Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage, 245, 118654.
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+ """
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+ from .congruence import *
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+ from .ext_metrics import *
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+ from .stimulation_threshold import *