pyNIBS 0.2024.8__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 (107) hide show
  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
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+ pynibs/data/configuration_exp0.yaml,sha256=oIGzghlgQjTYwf72LAgMcsPjGidc4CD4RTkFYbYlq2U,2841
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+ pynibs/data/configuration_sigmoid4.yaml,sha256=xb12PD5TMH1Va2E1u9aoEJejvmTa22JE84ZeVnhs3uc,3748
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+ pynibs/data/network mapping configuration/configuration_TEMPLATE.yaml,sha256=JgziyZ-bePmTXubJFPC7QOsKEFV8wx293SPrQJa5Lxo,2233
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+ pynibs/data/network mapping configuration/output_documentation.md,sha256=hWau9A_6BCUwpuv1Aauuxbs9qKc-vwmICVMRBBQXK1I,11169
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+ pynibs/data/neuron/models/L23_PC_cADpyr_biphasic_v1.csv,sha256=RU5zp35iIMk8zwVYeVoY35wot92SbBG6tCHVjzvLKTU,30471
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+ pynibs/data/neuron/models/L4_LBC_biphasic_v1.csv,sha256=G-35zjTIsGW4tvvzxgFQfTd1VQNZN---YpFa4AHKEAc,37927
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+ pynibs/data/neuron/models/L4_NBC_biphasic_v1.csv,sha256=RjETfsuR5Q6irNWLaEPwymZoSqyPLp8JfCd7MVEv_Gc,37777
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+ pynibs/data/neuron/models/L4_NBC_monophasic_v1.csv,sha256=M2a61JDUYqWQTBampNK-lZM_yW0RR9yjsh_VkvWg-Yg,37552
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+ pynibs/data/neuron/models/L4_SBC_biphasic_v1.csv,sha256=BH2oR57W9G0X9H6FvC3XDfgmphs-nALtBpEbL5G3W2g,37578
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+ pynibs/data/neuron/models/L4_SBC_monophasic_v1.csv,sha256=_Ullq-xwsGgrQUO2uUImK0auxuLUzEo1DHOC4UmH0aE,37530
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+ pynibs/expio/Mep.py,sha256=zgqGanj4P2AaHE6Z1UO2U8an6CctWtHCq0fE06eZ9Ms,57018
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+ pynibs/expio/localite.py,sha256=3FKAIKzEbgRznzsZ7wEhpgEhWb5QkHfQnasxMdqKo4w,81602
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+ pynibs/expio/visor.py,sha256=ca6trT9OXcGu5tdYnqx43EAi7No7j2uHGltqzvAodiA,23772
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+ pynibs/hdf5_io/__init__.py,sha256=nI4CnHWW6O45AoTYBV7bYqI_9G7EPd3IE5ILHGL7TPE,519
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+ pynibs/hdf5_io/xdmf.py,sha256=1IvpyFnb_fDClBrpt8v7P1SOD7qtfqZ_nPZ-SYiiNL0,67767
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+ pynibs/mesh/__init__.py,sha256=CJUPqvhjQGYY49vQ4N8kPUh29XP_m00VNp1A6AwnyyQ,78
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+ pynibs/mesh/transformations.py,sha256=DeR2zPk_2TotJIxWU5MRtQoRU7oEQgGuhdM0-d8GaTY,34586
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+ pynibs/mesh/utils.py,sha256=6NaiAB_aRR57xopyMdt1OcKxLf0eSpe0DKj-Lyh_Yus,41915
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+ pynibs/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ pynibs/neuron/__init__.py,sha256=M03aDpT-q4Bkk8_hKy6oGZCQK8cJIqm9VWG9h0W7kuY,53
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+ pynibs/neuron/neuron_regression.py,sha256=cG3q-RV_XJ_rV1cgDJyF2nNh3oqPrJx6PvuC8hIPAO0,12275
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+ pynibs/neuron/util.py,sha256=g5EEtHGkLqw-OgMGmF6uPH_xGf0eK7NrQGCws6MNqmg,1524
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+ pynibs/optimization/__init__.py,sha256=M6RzMbgBnv78b9didBEyuSsroKFZ5WhvQDDOmICU-kA,165
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+ pynibs/tests/data/brainsight_niiImage_niifticoord_mixedtargets.txt,sha256=U9Nu9zrSTBQoT06BsL2yRBFtbg-HRhxxs5c2grPw8wU,6678
89
+ pynibs/tests/data/create_subject_testsub.py,sha256=6g9qg8UkfOvUfzci53BjjYQurFxbCwGX5w-y-QbzKaA,18775
90
+ pynibs/tests/data/data.hdf5,sha256=v7-bryLXD1vC6MaeDn7RRiOBixvbqOFvQVOR-dD4sFA,129968
91
+ pynibs/tests/data/geo.hdf5,sha256=vJmeL5ZVHcQdyOXVmhR8gU1IblLfil9R_wFcC_HZ7sk,2625592
92
+ pynibs/tests/test_hdf5_io/test_xdmf.py,sha256=prkjZjkSPBGOlkcBuzHZt1NWjXNXPNjj66nhmFOROuw,2009
93
+ pynibs/util/__init__.py,sha256=I-64wp5bAf3wk1u8BnyFCrclCZlJeuK9V7emFTH9I6k,100
94
+ pynibs/util/dosing.py,sha256=KqtLJvi9Z93tUy8sH3JDSdNGQspeD5ePLtcW9ochktc,9236
95
+ pynibs/util/quality_measures.py,sha256=f13RU8bYog32A98V1R7jsU0seldnRQ5VGIcxlKJQr54,21686
96
+ pynibs/util/rotations.py,sha256=Mkre2YdCyNOoVY7dJM3iWBSzYcptjWxPQgStbLl3z8M,9133
97
+ pynibs/util/simnibs.py,sha256=K6kQXYHvOZYUPMUivhWtgouXkdOLeW6D9dIF8ngBSrI,31635
98
+ pynibs/util/util.py,sha256=XA_p1PEM3OgSXxdSQpplCexpEBO4F_aeQg0I-2LKOjo,20484
99
+ pynibs/visualization/__init__.py,sha256=K3uGzZBM3plKsVGkGZ0bb0-oLRfT8l5PQIqTkTwfVmE,48
100
+ pynibs/visualization/para.py,sha256=lnyWph3DpLtgc2ef8tovSlTTEjBFRzaWP8ycSti5NkM,185081
101
+ pynibs/visualization/plot_2D.py,sha256=rcCgVilMqCqJceHXMvwwo05OrxwYcuQv6lAA2TDKFn4,5139
102
+ pynibs/visualization/render_3D.py,sha256=YaW_-cgrH7UrSqspWekZMG3__lKbsFEF6uiF3O8dbxM,14871
103
+ pyNIBS-0.2024.8.dist-info/LICENSE,sha256=GkQ9UpUz_pzXqfniZT3PopCfmi1K2wSZpiIqcHnMbMA,32476
104
+ pyNIBS-0.2024.8.dist-info/METADATA,sha256=DZiMkI6qHoZ_h6WJF0VDN28COZAJz9kty-5j-H3jGzk,43182
105
+ pyNIBS-0.2024.8.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
106
+ pyNIBS-0.2024.8.dist-info/top_level.txt,sha256=9ZHaYB8yuIaluoqNxocpuDPbJak9szUD0bESYmGZpgQ,7
107
+ pyNIBS-0.2024.8.dist-info/RECORD,,
@@ -0,0 +1,5 @@
1
+ Wheel-Version: 1.0
2
+ Generator: bdist_wheel (0.42.0)
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any
5
+
@@ -0,0 +1 @@
1
+ pynibs
pynibs/__init__.py ADDED
@@ -0,0 +1,34 @@
1
+ from .tensor_scaling import rescale_lambda_centerized_workhorse
2
+ from .tensor_scaling import rescale_lambda_centerized
3
+ from .models import *
4
+ from .hdf5_io import *
5
+ from .coil import *
6
+ from .expio import *
7
+ from .util import *
8
+ from .hdf5_io import *
9
+ from .optimization import *
10
+ from .freesurfer import *
11
+ from .roi import *
12
+ from .subject import *
13
+ from .neuron import *
14
+ from .mesh import *
15
+ from .regression import *
16
+ from .visualization import *
17
+ from .tms_pulse import *
18
+
19
+ try:
20
+ from .pckg import libeep
21
+ except (ImportError, SyntaxError):
22
+ pass
23
+
24
+
25
+ __version__ = "0.2024.8"
26
+
27
+ # when pipped, datadir is under pynibs
28
+ __testdatadir__ = os.path.join(os.path.dirname(__file__), '..', 'tests', 'data')
29
+ __datadir__ = os.path.join(os.path.dirname(__file__), '..', 'data')
30
+ if not os.path.exists(__testdatadir__):
31
+ __testdatadir__ = os.path.join(os.path.dirname(__file__), 'tests', 'data')
32
+ __datadir__ = os.path.join(os.path.dirname(__file__), 'data')
33
+ if not os.path.exists(__testdatadir__):
34
+ warnings.warn(f"Cannot find pynibs.__testdatadir__='{__testdatadir__}'")