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/tests/data/InstrumentMarker20200225163611937.xml DELETED
@@ -1,19 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <InstrumentMarkerList coordinateSpace="RAS">
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- <!--All positions are saved in the coordinate system of the corresponding medical data.
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- NIfTI image data are recommended using RAS system (x-axis increases from the left hand side to the right hand side of the patient,
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- y-axis increases from the posterior side to the anterior side of the patient and z-axis increases from the feet toward the head of the patient).-->
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- <InstrumentMarker alwaysVisible="false" index="0" selected="true">
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- <Marker additionalInformation="" color="#ff0000" description="test" set="true">
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- <Matrix4D data00="0.9013614031176984"
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- data01="0.2983920094889285" data02="-0.3138959024047658"
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- data03="-71.18429093438886" data10="0.38530408399367894"
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- data11="-0.8834528036471245"
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- data12="0.26659466328018544" data13="-79.95375674706612"
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- data20="-0.1977604402582455"
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- data21="-0.3612397546019023"
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- data22="-0.9112724377855788" data23="38.69342634326524"
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- data30="0.0" data31="0.0" data32="0.0" data33="1.0"/>
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- </Marker>
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- </InstrumentMarker>
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- </InstrumentMarkerList>
pynibs/tests/data/TriggerMarkers_Coil0_20200225163443682.xml DELETED
@@ -1,14 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <TriggerMarkerList coordinateSpace="RAS" isOnlineReading="false" startTime="16:34:43.636">
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- <!--All positions are saved in the coordinate system of the corresponding medical data.
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- NIfTI image data are recommended using RAS system (x-axis increases from the left hand side to the right hand side of the patient,
5
- y-axis increases from the posterior side to the anterior side of the patient and z-axis increases from the feet toward the head of the patient).-->
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- <ResponseParameters selectedResponseChannel="0">
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- <responseDescription id="response" maxValue="51200.0"
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- minValue="-51200.0" name="Response" unit="uV"/>
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- <responseDescription id="valueA" maxValue="200.0" minValue="0.0"
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- name="Value A (di/dt)" unit="A/us"/>
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- <responseDescription id="amplitudeA" maxValue="100.0"
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- minValue="0.0" name="Amplitude A" unit="%"/>
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- </ResponseParameters>
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- </TriggerMarkerList>