simnibs-reader 0.1.0__tar.gz

simnibs_reader-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Hippolyte Dreyfus, ICM Frontlab CDPR
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

simnibs_reader-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: simnibs-reader
+Version: 0.1.0
+Summary: Lightweight reader for SimNIBS output directories (segmentation, simulation, optimization)
+License: MIT License
+        
+        Copyright (c) 2026 Hippolyte Dreyfus, ICM Frontlab CDPR
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: nibabel>=5.0
+Requires-Dist: nilearn>=0.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Requires-Dist: mkdocs-jupyter; extra == "docs"
+Provides-Extra: opti
+Requires-Dist: h5py>=3.0; extra == "opti"
+Dynamic: license-file
+
+-doit récupérer toute la logique d'input contenu dans io_pipeline de simnibs-analyze pour la réinjecter ensuite sous forme d'une dépdance propre.
+
+
+# simnibs-reader
+
+Python API for easy access of simnibs results with 3 level of organization.
+
+
+**Simnibs-bids-structure :**
+
+A standardization of the name of the simnibs folders (with bids logic) for multi-simulation/optimiation experiments... check if this is a commun use or not ? because it could lead to overuseof "simulation" rather than "optimization" expe... So what could be the real usecase of this ?
+
+(TO DECIDE : hierarchy of simnibs simulation parameters : electrodes_currents_conductivities (see Simnibs Data Structures)
+
+
+**Description of the files accessible in a folder of simnibs results:**
+
+*Folder type : simulation folder / optimization folder /m2m folder*
+
+- les resultats E-nifti en particulier
+- les surfaces ?
+- dans m2m... les fichiers de preparation de simulations (pour pouvoir spécialisé la simulation)
+
+**Description of the variables extractable , for each files :**
+
+--> For each nifti file produced:
+
+1- ROI-based easy querying [IMPORTANT : Checker le tool qui permet de creer des ROIs aisement (en native comme en mni)]
+
+2- postprocessing filters (to check si ça doit rester dans analyze ou si c'est necessairement dans le reader !?)
+
+3- metrics extractions
+
+- efield-niftii specific : mean
+- label_preps specific : total amount of a specific label + width / length measure (check the nilearn tool for this)
+
+--> other type of file ?
+
+
+This querying tool allows both "a la volée python traitement" ou des save propres de metrics utile pour des analyses futures.

simnibs_reader-0.1.0/README.md

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+-doit récupérer toute la logique d'input contenu dans io_pipeline de simnibs-analyze pour la réinjecter ensuite sous forme d'une dépdance propre.
+
+
+# simnibs-reader
+
+Python API for easy access of simnibs results with 3 level of organization.
+
+
+**Simnibs-bids-structure :**
+
+A standardization of the name of the simnibs folders (with bids logic) for multi-simulation/optimiation experiments... check if this is a commun use or not ? because it could lead to overuseof "simulation" rather than "optimization" expe... So what could be the real usecase of this ?
+
+(TO DECIDE : hierarchy of simnibs simulation parameters : electrodes_currents_conductivities (see Simnibs Data Structures)
+
+
+**Description of the files accessible in a folder of simnibs results:**
+
+*Folder type : simulation folder / optimization folder /m2m folder*
+
+- les resultats E-nifti en particulier
+- les surfaces ?
+- dans m2m... les fichiers de preparation de simulations (pour pouvoir spécialisé la simulation)
+
+**Description of the variables extractable , for each files :**
+
+--> For each nifti file produced:
+
+1- ROI-based easy querying [IMPORTANT : Checker le tool qui permet de creer des ROIs aisement (en native comme en mni)]
+
+2- postprocessing filters (to check si ça doit rester dans analyze ou si c'est necessairement dans le reader !?)
+
+3- metrics extractions
+
+- efield-niftii specific : mean
+- label_preps specific : total amount of a specific label + width / length measure (check the nilearn tool for this)
+
+--> other type of file ?
+
+
+This querying tool allows both "a la volée python traitement" ou des save propres de metrics utile pour des analyses futures.

simnibs_reader-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "simnibs-reader"
+version = "0.1.0"
+description = "Lightweight reader for SimNIBS output directories (segmentation, simulation, optimization)"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+
+dependencies = [
+    "nibabel>=5.0",
+    "nilearn>=0.10",
+    "numpy>=1.24",
+    "pandas>=2.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov",
+    "ruff",
+]
+docs = [
+    "mkdocs-material",
+    "mkdocstrings[python]",
+    "mkdocs-jupyter",
+]
+
+opti = [
+    "h5py>=3.0",
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["simnibs_reader*"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"

simnibs_reader-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

simnibs_reader-0.1.0/simnibs_reader/__init__.py

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+"""
+simnibs-reader
+==============
+
+Lightweight reader for SimNIBS output directories.
+
+Quick start
+-----------
+>>> import simnibs_reader as snr
+>>> sim = snr.simulation("path/to/simulation_folder")
+>>> sim.magnE.data  # lazy-loaded NIfTI array
+"""
+
+from __future__ import annotations
+
+from .core.simulation import SimulationResult
+from .core.segmentation import SegmentationResult
+from .core.optimization import OptimizationResult
+
+__version__ = "0.1.0"
+
+
+# ── Public factory functions ──────────────────────────────────────────────
+
+
+def simulation(path: str) -> SimulationResult:
+    """Load a SimNIBS simulation output folder.
+
+    Parameters
+    ----------
+    path : str or Path
+        Path to the simulation directory (contains ``mni_volumes/``,
+        ``subject_volumes/``, ``fields_summary.txt``, etc.).
+    """
+    return SimulationResult(path)
+
+
+def segmentation(path: str) -> SegmentationResult:
+    """Load a SimNIBS head-model folder (``m2m_<subID>``).
+
+    Parameters
+    ----------
+    path : str or Path
+        Path to the ``m2m_*`` directory produced by ``charm`` / ``headreco``.
+    """
+    return SegmentationResult(path)
+
+
+def optimization(path: str) -> OptimizationResult:
+    """Load a SimNIBS optimization / leadfield folder.
+
+    Parameters
+    ----------
+    path : str or Path
+        Path to the optimization output directory.
+    """
+    return OptimizationResult(path)