pyNIBS 0.2024.8__tar.gz → 0.2026.1__tar.gz

pynibs-0.2026.1/PKG-INFO

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: pyNIBS
+Version: 0.2026.1
+Summary: A python toolbox to conduct non-invasive brain stimulation (NIBS) experiments.
+Author: Konstantin Weise, Ole Numssen, Benjamin Kalloch
+Maintainer-email: Konstantin Weise <weise@cbs.mpg.de>, Ole Numssen <numssen@cbs.mpg.de>
+License: GPL3
+Project-URL: Home, https://gitlab.gwdg.de/tms-localization/pynibs
+Project-URL: Docs, https://pynibs.readthedocs.io/
+Project-URL: Twitter, https://www.twitter.com/num_ole
+Project-URL: Bluesky, https://bsky.app/profile/numole.bsky.social
+Project-URL: Download, https://pypi.org/project/pynibs/
+Keywords: NIBS,non-invasive brain stimulation,TMS,FEM
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cython>=0.29.20
+Requires-Dist: h5py>=2.10.0
+Requires-Dist: lmfit
+Requires-Dist: matplotlib>=3.2.1
+Requires-Dist: meshio
+Requires-Dist: nibabel>=3.0.2
+Requires-Dist: nilearn>=0.6.2
+Requires-Dist: numpy<2
+Requires-Dist: ortools
+Requires-Dist: pandas>=1.0.3
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: scikit-learn>=0.22.1
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: scikit-image
+Requires-Dist: setuptools>=49.1.0
+Requires-Dist: tqdm>=4.45.0
+Requires-Dist: trimesh>=3.8.11
+Requires-Dist: transformations
+Requires-Dist: fslpy
+Requires-Dist: pygpc>=0.4.1
+Requires-Dist: uncertainties
+Requires-Dist: asteval
+Requires-Dist: jsonschema
+Requires-Dist: tables
+Requires-Dist: vtk
+Requires-Dist: rtree
+Requires-Dist: tvb-gdist
+Dynamic: license-file
+
+# pyNIBS
+Preprocessing, postprocessing, and analyses routines for non-invasive brain stimulation experiments.
+
+[![Latest Release](https://gitlab.gwdg.de/tms-localization/pynibs/-/badges/release.svg)](https://gitlab.gwdg.de/tms-localization/pynibs)
+[![Documentation](https://readthedocs.org/projects/pynibs/badge/)](https://pynibs.readthedocs.io/)
+[![pipeline status](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/pipeline.svg)](https://gitlab.gwdg.de/tms-localization/pynibs/commits/master)
+[![coverage report](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/coverage.svg)](https://tms-localization.pages.gwdg.de/pynibs)
+
+![](https://gitlab.gwdg.de/uploads/-/system/project/avatar/9753/Fig_4.png?width=128)
+
+`pyNIBS` provides the functions to allow **cortical mappings** with transcranial magnetic stimulation (TMS) via **functional analysis**. `pyNIBS` is developed to work with [SimNIBS](http://www.simnibs.org), i.e. SimNIBS' meshes and FEM results can directly be used.
+ Currently, [SimNIBS >=4.0](https://github.com/simnibs/simnibs/releases/latest) is supported.
+
+See the [documentation](https://pynibs.readthedocs.io/) for package details and our [protocol](https://doi.org/10.1038/s41596-022-00776-6) publication for a extensive usage examples. Free view only version of the paper: https://t.co/uv7CmVw6tp.
+
+## Installation
+Via PiP:
+
+``` bash
+pip install pynibs
+```
+
+Or clone the source repository and install the development branch for the most recent version:
+
+``` bash
+git clone https://gitlab.gwdg.de/tms-localization/pynibs
+cd pynibs
+git checkout dev
+pip install -e .
+```
+
+See [here](https://gitlab.gwdg.de/tms-localization/papers/tmsloc_proto/-/blob/2aec4763edf17e7a2ac604403287bc7fb10285ff/README.md) for more detailed installation instructions.
+
+To import CED Signal EMG data use the `export to .mat` feature of Signal. 
+To read `.cfs` files exported with CED Signal you might need to [manually](HOW_TO_INSTALL_BIOSIG.txt) compile the libbiosig package.
+
+
+## Bugs
+For sure. Please open an [issue](https://gitlab.gwdg.de/tms-localization/pynibs/-/issues) or feel free to file a PR.
+
+
+## Citation
+Please cite _Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage, 245, 118654. doi:[10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)_ when using this toolbox in your research.
+
+
+## References
+  - Weise*, K., Numssen*, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. *NeuroImage*, 209, 116486. doi: [10.1016/j.neuroimage.2019.116486](https://doi.org/10.1016/j.neuroimage.2019.116486)
+  - Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage*, 245, 118654. doi: [10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)
+  - Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen°, G., Knösche°, T. R. (2023). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi: [10.1038/s41596-022-00776-6](https://doi.org/10.1038/s41596-022-00776-6) 
+  - Jing, Y., Numssen, O., Weise, K., Kalloch, B., Buchberger, L., Haueisen, J., Hartwigsen, G., Knösche, T. (2023). Modeling the Effects of Transcranial Magnetic Stimulation on Spatial Attention. *Physics in Medicine & Biology*. doi: [10.1088/1361-6560/acff34](https://doi.org/10.1088/1361-6560/acff34)
+  - Numssen*, O., Kuhnke*, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106) 
+  - Numssen, O., Martin, S., Williams, K., Knösche, T. R., & Hartwigsen, G. (2024). Quantification of subject motion during TMS via pulsewise coil displacement. *Brain Stimulation, 17*(5), 1045–1047. doi: [10.1016/j.brs.2024.08.009](https://doi.org/10.1016/j.brs.2024.08.009) 
+  - Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025). Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds. *Brain Stimulation, 18*(2), 280–286. doi: [10.1016/j.brs.2025.02.007](https://doi.org/10.1016/j.brs.2025.02.007)
+  - Jing, Y., Numssen, O., Hartwigsen, G., Knösche, T. R., & Weise, K. (2024). Effects of Electric Field Direction on TMS-based Motor Cortex Mapping. *bioRxiv*. doi: [10.1101/2024.12.10.627753](https://doi.org/10.1101/2024.12.10.627753) 
+  - Numssen*, O., Martin*, C. W., Worbs, T., Thielscher, A., Weise, K., & Knösche, T. R. (2025). Optimizing and assessing multichannel TMS focality. *bioRxiv*. doi: [10.1101/2025.09.19.677136](https://doi.org/10.1101/2025.09.19.677136)

{pyNIBS-0.2024.8 → pynibs-0.2026.1}/README.md

@@ -9,7 +9,7 @@ Preprocessing, postprocessing, and analyses routines for non-invasive brain stim
 ![](https://gitlab.gwdg.de/uploads/-/system/project/avatar/9753/Fig_4.png?width=128)
 
 `pyNIBS` provides the functions to allow **cortical mappings** with transcranial magnetic stimulation (TMS) via **functional analysis**. `pyNIBS` is developed to work with [SimNIBS](http://www.simnibs.org), i.e. SimNIBS' meshes and FEM results can directly be used.
- Currently, [SimNIBS 3.2.6](https://github.com/simnibs/simnibs/releases/tag/v3.2.6) and [SimNIBS >=4.0](https://github.com/simnibs/simnibs/releases/latest) are supported.
+ Currently, [SimNIBS >=4.0](https://github.com/simnibs/simnibs/releases/latest) is supported.
 
 See the [documentation](https://pynibs.readthedocs.io/) for package details and our [protocol](https://doi.org/10.1038/s41596-022-00776-6) publication for a extensive usage examples. Free view only version of the paper: https://t.co/uv7CmVw6tp.
 
@@ -45,7 +45,11 @@ Please cite _Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche,
 
 ## References
   - Weise*, K., Numssen*, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. *NeuroImage*, 209, 116486. doi: [10.1016/j.neuroimage.2019.116486](https://doi.org/10.1016/j.neuroimage.2019.116486)
-  - Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage*, 245, 118654. doi:[10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)
-  - Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen°, G., Knösche°, T. R. (2023). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi:[10.1038/s41596-022-00776-6](https://doi.org/10.1038/s41596-022-00776-6) 
+  - Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage*, 245, 118654. doi: [10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)
+  - Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen°, G., Knösche°, T. R. (2023). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi: [10.1038/s41596-022-00776-6](https://doi.org/10.1038/s41596-022-00776-6) 
   - Jing, Y., Numssen, O., Weise, K., Kalloch, B., Buchberger, L., Haueisen, J., Hartwigsen, G., Knösche, T. (2023). Modeling the Effects of Transcranial Magnetic Stimulation on Spatial Attention. *Physics in Medicine & Biology*. doi: [10.1088/1361-6560/acff34](https://doi.org/10.1088/1361-6560/acff34)
-  - Numssen, O., Kuhnke, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106) 
+  - Numssen*, O., Kuhnke*, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106) 
+  - Numssen, O., Martin, S., Williams, K., Knösche, T. R., & Hartwigsen, G. (2024). Quantification of subject motion during TMS via pulsewise coil displacement. *Brain Stimulation, 17*(5), 1045–1047. doi: [10.1016/j.brs.2024.08.009](https://doi.org/10.1016/j.brs.2024.08.009) 
+  - Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025). Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds. *Brain Stimulation, 18*(2), 280–286. doi: [10.1016/j.brs.2025.02.007](https://doi.org/10.1016/j.brs.2025.02.007)
+  - Jing, Y., Numssen, O., Hartwigsen, G., Knösche, T. R., & Weise, K. (2024). Effects of Electric Field Direction on TMS-based Motor Cortex Mapping. *bioRxiv*. doi: [10.1101/2024.12.10.627753](https://doi.org/10.1101/2024.12.10.627753) 
+  - Numssen*, O., Martin*, C. W., Worbs, T., Thielscher, A., Weise, K., & Knösche, T. R. (2025). Optimizing and assessing multichannel TMS focality. *bioRxiv*. doi: [10.1101/2025.09.19.677136](https://doi.org/10.1101/2025.09.19.677136)

pynibs-0.2026.1/pyNIBS.egg-info/PKG-INFO

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: pyNIBS
+Version: 0.2026.1
+Summary: A python toolbox to conduct non-invasive brain stimulation (NIBS) experiments.
+Author: Konstantin Weise, Ole Numssen, Benjamin Kalloch
+Maintainer-email: Konstantin Weise <weise@cbs.mpg.de>, Ole Numssen <numssen@cbs.mpg.de>
+License: GPL3
+Project-URL: Home, https://gitlab.gwdg.de/tms-localization/pynibs
+Project-URL: Docs, https://pynibs.readthedocs.io/
+Project-URL: Twitter, https://www.twitter.com/num_ole
+Project-URL: Bluesky, https://bsky.app/profile/numole.bsky.social
+Project-URL: Download, https://pypi.org/project/pynibs/
+Keywords: NIBS,non-invasive brain stimulation,TMS,FEM
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cython>=0.29.20
+Requires-Dist: h5py>=2.10.0
+Requires-Dist: lmfit
+Requires-Dist: matplotlib>=3.2.1
+Requires-Dist: meshio
+Requires-Dist: nibabel>=3.0.2
+Requires-Dist: nilearn>=0.6.2
+Requires-Dist: numpy<2
+Requires-Dist: ortools
+Requires-Dist: pandas>=1.0.3
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: scikit-learn>=0.22.1
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: scikit-image
+Requires-Dist: setuptools>=49.1.0
+Requires-Dist: tqdm>=4.45.0
+Requires-Dist: trimesh>=3.8.11
+Requires-Dist: transformations
+Requires-Dist: fslpy
+Requires-Dist: pygpc>=0.4.1
+Requires-Dist: uncertainties
+Requires-Dist: asteval
+Requires-Dist: jsonschema
+Requires-Dist: tables
+Requires-Dist: vtk
+Requires-Dist: rtree
+Requires-Dist: tvb-gdist
+Dynamic: license-file
+
+# pyNIBS
+Preprocessing, postprocessing, and analyses routines for non-invasive brain stimulation experiments.
+
+[![Latest Release](https://gitlab.gwdg.de/tms-localization/pynibs/-/badges/release.svg)](https://gitlab.gwdg.de/tms-localization/pynibs)
+[![Documentation](https://readthedocs.org/projects/pynibs/badge/)](https://pynibs.readthedocs.io/)
+[![pipeline status](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/pipeline.svg)](https://gitlab.gwdg.de/tms-localization/pynibs/commits/master)
+[![coverage report](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/coverage.svg)](https://tms-localization.pages.gwdg.de/pynibs)
+
+![](https://gitlab.gwdg.de/uploads/-/system/project/avatar/9753/Fig_4.png?width=128)
+
+`pyNIBS` provides the functions to allow **cortical mappings** with transcranial magnetic stimulation (TMS) via **functional analysis**. `pyNIBS` is developed to work with [SimNIBS](http://www.simnibs.org), i.e. SimNIBS' meshes and FEM results can directly be used.
+ Currently, [SimNIBS >=4.0](https://github.com/simnibs/simnibs/releases/latest) is supported.
+
+See the [documentation](https://pynibs.readthedocs.io/) for package details and our [protocol](https://doi.org/10.1038/s41596-022-00776-6) publication for a extensive usage examples. Free view only version of the paper: https://t.co/uv7CmVw6tp.
+
+## Installation
+Via PiP:
+
+``` bash
+pip install pynibs
+```
+
+Or clone the source repository and install the development branch for the most recent version:
+
+``` bash
+git clone https://gitlab.gwdg.de/tms-localization/pynibs
+cd pynibs
+git checkout dev
+pip install -e .
+```
+
+See [here](https://gitlab.gwdg.de/tms-localization/papers/tmsloc_proto/-/blob/2aec4763edf17e7a2ac604403287bc7fb10285ff/README.md) for more detailed installation instructions.
+
+To import CED Signal EMG data use the `export to .mat` feature of Signal. 
+To read `.cfs` files exported with CED Signal you might need to [manually](HOW_TO_INSTALL_BIOSIG.txt) compile the libbiosig package.
+
+
+## Bugs
+For sure. Please open an [issue](https://gitlab.gwdg.de/tms-localization/pynibs/-/issues) or feel free to file a PR.
+
+
+## Citation
+Please cite _Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage, 245, 118654. doi:[10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)_ when using this toolbox in your research.
+
+
+## References
+  - Weise*, K., Numssen*, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. *NeuroImage*, 209, 116486. doi: [10.1016/j.neuroimage.2019.116486](https://doi.org/10.1016/j.neuroimage.2019.116486)
+  - Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage*, 245, 118654. doi: [10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)
+  - Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen°, G., Knösche°, T. R. (2023). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi: [10.1038/s41596-022-00776-6](https://doi.org/10.1038/s41596-022-00776-6) 
+  - Jing, Y., Numssen, O., Weise, K., Kalloch, B., Buchberger, L., Haueisen, J., Hartwigsen, G., Knösche, T. (2023). Modeling the Effects of Transcranial Magnetic Stimulation on Spatial Attention. *Physics in Medicine & Biology*. doi: [10.1088/1361-6560/acff34](https://doi.org/10.1088/1361-6560/acff34)
+  - Numssen*, O., Kuhnke*, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106) 
+  - Numssen, O., Martin, S., Williams, K., Knösche, T. R., & Hartwigsen, G. (2024). Quantification of subject motion during TMS via pulsewise coil displacement. *Brain Stimulation, 17*(5), 1045–1047. doi: [10.1016/j.brs.2024.08.009](https://doi.org/10.1016/j.brs.2024.08.009) 
+  - Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025). Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds. *Brain Stimulation, 18*(2), 280–286. doi: [10.1016/j.brs.2025.02.007](https://doi.org/10.1016/j.brs.2025.02.007)
+  - Jing, Y., Numssen, O., Hartwigsen, G., Knösche, T. R., & Weise, K. (2024). Effects of Electric Field Direction on TMS-based Motor Cortex Mapping. *bioRxiv*. doi: [10.1101/2024.12.10.627753](https://doi.org/10.1101/2024.12.10.627753) 
+  - Numssen*, O., Martin*, C. W., Worbs, T., Thielscher, A., Weise, K., & Knösche, T. R. (2025). Optimizing and assessing multichannel TMS focality. *bioRxiv*. doi: [10.1101/2025.09.19.677136](https://doi.org/10.1101/2025.09.19.677136)

{pyNIBS-0.2024.8 → pynibs-0.2026.1}/pyNIBS.egg-info/SOURCES.txt

@@ -3,28 +3,6 @@ README.md
 pyproject.toml
 requirements.txt
 setup.cfg
-setup.py
-data/configuration_exp0.yaml
-data/configuration_linear_MEP.yaml
-data/configuration_linear_RT.yaml
-data/configuration_sigmoid4.yaml
-data/network mapping configuration/configuration guide.md
-data/network mapping configuration/configuration_TEMPLATE.yaml
-data/network mapping configuration/configuration_for_testing.yaml
-data/network mapping configuration/configuration_modelTMS.yaml
-data/network mapping configuration/configuration_reg_isi_05.yaml
-data/network mapping configuration/output_documentation.md
-data/network mapping configuration/recommendations_for_accuracy_threshold.md
-data/neuron/models/L23_PC_cADpyr_biphasic_v1.csv
-data/neuron/models/L23_PC_cADpyr_monophasic_v1.csv
-data/neuron/models/L4_LBC_biphasic_v1.csv
-data/neuron/models/L4_LBC_monophasic_v1.csv
-data/neuron/models/L4_NBC_biphasic_v1.csv
-data/neuron/models/L4_NBC_monophasic_v1.csv
-data/neuron/models/L4_SBC_biphasic_v1.csv
-data/neuron/models/L4_SBC_monophasic_v1.csv
-data/neuron/models/L5_TTPC2_cADpyr_biphasic_v1.csv
-data/neuron/models/L5_TTPC2_cADpyr_monophasic_v1.csv
 pyNIBS.egg-info/PKG-INFO
 pyNIBS.egg-info/SOURCES.txt
 pyNIBS.egg-info/dependency_links.txt
@@ -32,12 +10,14 @@ pyNIBS.egg-info/not-zip-safe
 pyNIBS.egg-info/requires.txt
 pyNIBS.egg-info/top_level.txt
 pynibs/__init__.py
-pynibs/coil.py
 pynibs/freesurfer.py
 pynibs/muap.py
 pynibs/subject.py
 pynibs/tensor_scaling.py
 pynibs/tms_pulse.py
+pynibs/coil/__init__.py
+pynibs/coil/coil.py
+pynibs/coil/export.py
 pynibs/congruence/__init__.py
 pynibs/congruence/congruence.py
 pynibs/congruence/ext_metrics.py
@@ -49,7 +29,9 @@ pynibs/expio/brainvis.py
 pynibs/expio/cobot.py
 pynibs/expio/exp.py
 pynibs/expio/fit_funs.py
+pynibs/expio/invesalius.py
 pynibs/expio/localite.py
+pynibs/expio/neurone.py
 pynibs/expio/signal_ced.py
 pynibs/expio/visor.py
 pynibs/hdf5_io/__init__.py
@@ -64,10 +46,12 @@ pynibs/models/__init__.py
 pynibs/neuron/__init__.py
 pynibs/neuron/neuron_regression.py
 pynibs/neuron/util.py
+pynibs/neuron/models/m1_montbrio.py
+pynibs/neuron/models/mep.py
 pynibs/optimization/__init__.py
+pynibs/optimization/coil_opt.py
 pynibs/optimization/multichannel.py
 pynibs/optimization/opt_mep.py
-pynibs/optimization/optimization.py
 pynibs/optimization/workhorses.py
 pynibs/pckg/__init__.py
 pynibs/pckg/biosig/biosig4c++-1.9.5.src_fixed.tar.gz
@@ -76,16 +60,15 @@ pynibs/pckg/libeep/pyeep.so
 pynibs/regression/__init__.py
 pynibs/regression/dual_node_detection.py
 pynibs/regression/regression.py
-pynibs/regression/score_types.py
 pynibs/roi/__init__.py
-pynibs/roi/roi.py
 pynibs/roi/roi_structs.py
+pynibs/roi/roi_utils.py
 pynibs/util/__init__.py
 pynibs/util/dosing.py
 pynibs/util/quality_measures.py
 pynibs/util/rotations.py
-pynibs/util/simnibs.py
-pynibs/util/util.py
+pynibs/util/simnibs_io.py
+pynibs/util/utils.py
 pynibs/visualization/__init__.py
 pynibs/visualization/para.py
 pynibs/visualization/plot_2D.py
@@ -95,20 +78,12 @@ tests/test_elements2nodes.py
 tests/test_mesh_transformations.py
 tests/test_mesh_utils.py
 tests/test_nnav_imports.py
+tests/test_opt_coil.py
+tests/test_opt_mtms.py
+tests/test_optimization_multichannel.py
 tests/test_quality_measures.py
 tests/test_regressdata.py
 tests/test_roi.py
 tests/test_rotations.py
 tests/test_subject.py
-tests/test_util.py
-tests/data/InstrumentMarker20200225163611937.xml
-tests/data/TriggerMarkers_Coil0_20200225163443682.xml
-tests/data/TriggerMarkers_Coil1_20200225170337572.xml
-tests/data/Xdmf.dtd
-tests/data/brainsight_niiImage_nifticoord.txt
-tests/data/brainsight_niiImage_nifticoord_largefile.txt
-tests/data/brainsight_niiImage_niifticoord_mixedtargets.txt
-tests/data/create_subject_testsub.py
-tests/data/data.hdf5
-tests/data/geo.hdf5
-tests/test_hdf5_io/test_xdmf.py
+tests/test_util.py

{pyNIBS-0.2024.8 → pynibs-0.2026.1}/pyNIBS.egg-info/requires.txt

@@ -5,8 +5,8 @@ matplotlib>=3.2.1
 meshio
 nibabel>=3.0.2
 nilearn>=0.6.2
-numpy<=2.0.0
-ortools<=9.1.9490
+numpy<2
+ortools
 pandas>=1.0.3
 pyyaml>=5.3.1
 scikit-learn>=0.22.1
@@ -15,11 +15,13 @@ scikit-image
 setuptools>=49.1.0
 tqdm>=4.45.0
 trimesh>=3.8.11
-tvb_gdist
+transformations
 fslpy
+pygpc>=0.4.1
 uncertainties
 asteval
 jsonschema
 tables
 vtk
-fmm3dpy
+rtree
+tvb-gdist

pynibs-0.2026.1/pynibs/__init__.py

@@ -0,0 +1,46 @@
+__all__ = ["coil", "expio", "freesurfer", "hdf5_io", "mesh", "models", "neuron", "optimization", "regression", "roi",
+           "subject", "tensor_scaling", "tensor_scaling", "tms_pulse", "util", "visualization"]
+
+from .hdf5_io import *
+from .subject import *
+from .visualization import *
+from .freesurfer import *
+from .hdf5_io import *
+from .optimization import *
+from .roi import *
+from .subject import *
+
+try:
+    from .pckg import libeep
+except (ImportError, SyntaxError):
+    pass
+
+_lazy_modules = {
+    "coil": "pynibs.coil",
+    "expio": "pynibs.expio",
+    "mesh": "pynibs.mesh",
+    "models": "pynibs.models",
+    "neuron": "pynibs.neuron",
+    "regression": "pynibs.regression",
+    'visualization': "pynibs.visualization",
+    "util":"pynibs.util"
+}
+__version__ = "0.2026.1"
+
+# when pipped, datadir is under pynibs
+__testdatadir__ = os.path.join(os.path.dirname(__file__), '..', 'tests', 'data')
+__datadir__ = os.path.join(os.path.dirname(__file__), '..', 'data')
+if not os.path.exists(__testdatadir__):
+    __testdatadir__ = os.path.join(os.path.dirname(__file__), 'tests', 'data')
+    __datadir__ = os.path.join(os.path.dirname(__file__), 'data')
+if not os.path.exists(__testdatadir__):
+    warnings.warn(f"Cannot find pynibs.__testdatadir__='{__testdatadir__}'")
+
+
+def __getattr__(name):
+    if name in _lazy_modules:
+        import importlib
+        mod = importlib.import_module(_lazy_modules[name])
+        globals()[name] = mod  # cache so future accesses skip __getattr__
+        return mod
+    raise AttributeError(f"module {__name__!r} has no attribute {name}")

pynibs-0.2026.1/pynibs/coil/__init__.py

@@ -0,0 +1,6 @@
+"""
+All functions to operate on TMS coils go here, for example to create ``.xdmf`` files to visualize coil positions.
+"""
+
+from .coil import *
+from .export import *