pyNIBS 0.2024.8__py3-none-any.whl → 0.2026.1__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 (101) hide show
  1. pynibs/__init__.py +26 -14
  2. pynibs/coil/__init__.py +6 -0
  3. pynibs/{coil.py → coil/coil.py} +213 -543
  4. pynibs/coil/export.py +508 -0
  5. pynibs/congruence/__init__.py +4 -1
  6. pynibs/congruence/congruence.py +37 -45
  7. pynibs/congruence/ext_metrics.py +40 -11
  8. pynibs/congruence/stimulation_threshold.py +1 -2
  9. pynibs/expio/Mep.py +120 -370
  10. pynibs/expio/__init__.py +10 -0
  11. pynibs/expio/brainsight.py +34 -37
  12. pynibs/expio/cobot.py +25 -25
  13. pynibs/expio/exp.py +10 -7
  14. pynibs/expio/fit_funs.py +3 -0
  15. pynibs/expio/invesalius.py +70 -0
  16. pynibs/expio/localite.py +190 -91
  17. pynibs/expio/neurone.py +139 -0
  18. pynibs/expio/signal_ced.py +345 -2
  19. pynibs/expio/visor.py +16 -15
  20. pynibs/freesurfer.py +34 -33
  21. pynibs/hdf5_io/hdf5_io.py +149 -132
  22. pynibs/hdf5_io/xdmf.py +35 -31
  23. pynibs/mesh/__init__.py +1 -1
  24. pynibs/mesh/mesh_struct.py +77 -92
  25. pynibs/mesh/transformations.py +121 -21
  26. pynibs/mesh/utils.py +191 -99
  27. pynibs/models/_TMS.py +2 -1
  28. pynibs/muap.py +1 -2
  29. pynibs/neuron/__init__.py +10 -0
  30. pynibs/neuron/models/mep.py +566 -0
  31. pynibs/neuron/neuron_regression.py +98 -8
  32. pynibs/optimization/__init__.py +12 -2
  33. pynibs/optimization/{optimization.py → coil_opt.py} +157 -133
  34. pynibs/optimization/multichannel.py +1174 -24
  35. pynibs/optimization/workhorses.py +7 -8
  36. pynibs/regression/__init__.py +4 -2
  37. pynibs/regression/dual_node_detection.py +229 -219
  38. pynibs/regression/regression.py +92 -61
  39. pynibs/roi/__init__.py +4 -1
  40. pynibs/roi/roi_structs.py +19 -21
  41. pynibs/roi/{roi.py → roi_utils.py} +56 -33
  42. pynibs/subject.py +24 -14
  43. pynibs/util/__init__.py +20 -4
  44. pynibs/util/dosing.py +4 -5
  45. pynibs/util/quality_measures.py +39 -38
  46. pynibs/util/rotations.py +116 -9
  47. pynibs/util/{simnibs.py → simnibs_io.py} +29 -19
  48. pynibs/util/{util.py → utils.py} +20 -22
  49. pynibs/visualization/para.py +4 -4
  50. pynibs/visualization/render_3D.py +4 -4
  51. pynibs-0.2026.1.dist-info/METADATA +105 -0
  52. pynibs-0.2026.1.dist-info/RECORD +69 -0
  53. {pyNIBS-0.2024.8.dist-info → pynibs-0.2026.1.dist-info}/WHEEL +1 -1
  54. pyNIBS-0.2024.8.dist-info/METADATA +0 -723
  55. pyNIBS-0.2024.8.dist-info/RECORD +0 -107
  56. pynibs/data/configuration_exp0.yaml +0 -59
  57. pynibs/data/configuration_linear_MEP.yaml +0 -61
  58. pynibs/data/configuration_linear_RT.yaml +0 -61
  59. pynibs/data/configuration_sigmoid4.yaml +0 -68
  60. pynibs/data/network mapping configuration/configuration guide.md +0 -238
  61. pynibs/data/network mapping configuration/configuration_TEMPLATE.yaml +0 -42
  62. pynibs/data/network mapping configuration/configuration_for_testing.yaml +0 -43
  63. pynibs/data/network mapping configuration/configuration_modelTMS.yaml +0 -43
  64. pynibs/data/network mapping configuration/configuration_reg_isi_05.yaml +0 -43
  65. pynibs/data/network mapping configuration/output_documentation.md +0 -185
  66. pynibs/data/network mapping configuration/recommendations_for_accuracy_threshold.md +0 -77
  67. pynibs/data/neuron/models/L23_PC_cADpyr_biphasic_v1.csv +0 -1281
  68. pynibs/data/neuron/models/L23_PC_cADpyr_monophasic_v1.csv +0 -1281
  69. pynibs/data/neuron/models/L4_LBC_biphasic_v1.csv +0 -1281
  70. pynibs/data/neuron/models/L4_LBC_monophasic_v1.csv +0 -1281
  71. pynibs/data/neuron/models/L4_NBC_biphasic_v1.csv +0 -1281
  72. pynibs/data/neuron/models/L4_NBC_monophasic_v1.csv +0 -1281
  73. pynibs/data/neuron/models/L4_SBC_biphasic_v1.csv +0 -1281
  74. pynibs/data/neuron/models/L4_SBC_monophasic_v1.csv +0 -1281
  75. pynibs/data/neuron/models/L5_TTPC2_cADpyr_biphasic_v1.csv +0 -1281
  76. pynibs/data/neuron/models/L5_TTPC2_cADpyr_monophasic_v1.csv +0 -1281
  77. pynibs/tests/data/InstrumentMarker20200225163611937.xml +0 -19
  78. pynibs/tests/data/TriggerMarkers_Coil0_20200225163443682.xml +0 -14
  79. pynibs/tests/data/TriggerMarkers_Coil1_20200225170337572.xml +0 -6373
  80. pynibs/tests/data/Xdmf.dtd +0 -89
  81. pynibs/tests/data/brainsight_niiImage_nifticoord.txt +0 -145
  82. pynibs/tests/data/brainsight_niiImage_nifticoord_largefile.txt +0 -1434
  83. pynibs/tests/data/brainsight_niiImage_niifticoord_mixedtargets.txt +0 -47
  84. pynibs/tests/data/create_subject_testsub.py +0 -332
  85. pynibs/tests/data/data.hdf5 +0 -0
  86. pynibs/tests/data/geo.hdf5 +0 -0
  87. pynibs/tests/test_coil.py +0 -474
  88. pynibs/tests/test_elements2nodes.py +0 -100
  89. pynibs/tests/test_hdf5_io/test_xdmf.py +0 -61
  90. pynibs/tests/test_mesh_transformations.py +0 -123
  91. pynibs/tests/test_mesh_utils.py +0 -143
  92. pynibs/tests/test_nnav_imports.py +0 -101
  93. pynibs/tests/test_quality_measures.py +0 -117
  94. pynibs/tests/test_regressdata.py +0 -289
  95. pynibs/tests/test_roi.py +0 -17
  96. pynibs/tests/test_rotations.py +0 -86
  97. pynibs/tests/test_subject.py +0 -71
  98. pynibs/tests/test_util.py +0 -24
  99. /pynibs/{regression/score_types.py → neuron/models/m1_montbrio.py} +0 -0
  100. {pyNIBS-0.2024.8.dist-info → pynibs-0.2026.1.dist-info/licenses}/LICENSE +0 -0
  101. {pyNIBS-0.2024.8.dist-info → pynibs-0.2026.1.dist-info}/top_level.txt +0 -0
pynibs/__init__.py CHANGED
@@ -1,28 +1,31 @@
1
- from .tensor_scaling import rescale_lambda_centerized_workhorse
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- from .tensor_scaling import rescale_lambda_centerized
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- from .models import *
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+ __all__ = ["coil", "expio", "freesurfer", "hdf5_io", "mesh", "models", "neuron", "optimization", "regression", "roi",
2
+ "subject", "tensor_scaling", "tensor_scaling", "tms_pulse", "util", "visualization"]
3
+
4
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  from .hdf5_io import *
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- from .coil import *
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- from .expio import *
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- from .util import *
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+ from .subject import *
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+ from .visualization import *
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+ from .freesurfer import *
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8
  from .hdf5_io import *
9
9
  from .optimization import *
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- from .freesurfer import *
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  from .roi import *
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  from .subject import *
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- from .neuron import *
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- from .mesh import *
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- from .regression import *
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- from .visualization import *
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- from .tms_pulse import *
18
12
 
19
13
  try:
20
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  from .pckg import libeep
21
15
  except (ImportError, SyntaxError):
22
16
  pass
23
17
 
24
-
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- __version__ = "0.2024.8"
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+ _lazy_modules = {
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+ "coil": "pynibs.coil",
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+ "expio": "pynibs.expio",
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+ "mesh": "pynibs.mesh",
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+ "models": "pynibs.models",
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+ "neuron": "pynibs.neuron",
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+ "regression": "pynibs.regression",
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+ 'visualization': "pynibs.visualization",
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+ "util":"pynibs.util"
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+ }
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+ __version__ = "0.2026.1"
26
29
 
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  # when pipped, datadir is under pynibs
28
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  __testdatadir__ = os.path.join(os.path.dirname(__file__), '..', 'tests', 'data')
@@ -32,3 +35,12 @@ if not os.path.exists(__testdatadir__):
32
35
  __datadir__ = os.path.join(os.path.dirname(__file__), 'data')
33
36
  if not os.path.exists(__testdatadir__):
34
37
  warnings.warn(f"Cannot find pynibs.__testdatadir__='{__testdatadir__}'")
38
+
39
+
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+ def __getattr__(name):
41
+ if name in _lazy_modules:
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+ import importlib
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+ mod = importlib.import_module(_lazy_modules[name])
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+ globals()[name] = mod # cache so future accesses skip __getattr__
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+ return mod
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+ raise AttributeError(f"module {__name__!r} has no attribute {name}")
pynibs/coil/__init__.py ADDED
@@ -0,0 +1,6 @@
1
+ """
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+ All functions to operate on TMS coils go here, for example to create ``.xdmf`` files to visualize coil positions.
3
+ """
4
+
5
+ from .coil import *
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+ from .export import *