lcmodel-wrapper 0.1.2__tar.gz → 0.2.0__tar.gz

lcmodel_wrapper-0.2.0/LICENSE

@@ -0,0 +1,202 @@
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lcmodel_wrapper-0.2.0/LICENSE.lcmodel

@@ -0,0 +1,39 @@
+LCModel license
+===============
+
+This project (PyLCModel / lcmodel_wrapper) is a Python wrapper. It does NOT
+contain the original LCModel program in its own copyright. LCModel is a separate
+work distributed under the BSD 3-Clause License reproduced below. When the
+wrapper downloads, builds, or otherwise redistributes the LCModel executable or
+its Fortran source, the following license and notice apply to that component.
+
+Copyright (c) 1992-2021, Stephen Provencher
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ 1. Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+
+ 3. Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Reference: S.W. Provencher (1993) Magn. Reson. Med. 30, 672-679.
+LCModel home page: https://s-provencher.com/lcmodel.shtml

lcmodel_wrapper-0.2.0/MANIFEST.in

@@ -0,0 +1,4 @@
+include LICENSE
+include LICENSE.lcmodel
+include NOTICE
+include README.md

lcmodel_wrapper-0.2.0/NOTICE

@@ -0,0 +1,34 @@
+PyLCModel (lcmodel_wrapper)
+Copyright (c) 2024 Julian P. Merkofer and contributors
+
+This product is licensed under the Apache License, Version 2.0 (see LICENSE).
+
+------------------------------------------------------------------------------
+Third-party components
+------------------------------------------------------------------------------
+
+LCModel
+  LCModel is NOT part of this project's copyright. It is a separate program by
+  Dr. Stephen Provencher, distributed under the BSD 3-Clause License
+  (Copyright (c) 1992-2021, Stephen Provencher). See LICENSE.lcmodel for the
+  full text. This wrapper can download, build, or run the LCModel executable,
+  but does not claim any rights over it.
+  Home page: https://s-provencher.com/lcmodel.shtml
+
+LCModel compiled binaries
+  Pre-compiled LCModel binaries are obtained on demand from the community
+  collection at https://github.com/schorschinho/LCModel (maintained by
+  Georg Oeltzschner et al.). Individual builds were contributed by:
+    - macOS Catalina (Intel)   - Georg Oeltzschner
+    - macOS Monterey (M1)      - Bethany A. Stennett
+    - macOS Sequoia (M4)       - Julian P. Merkofer
+    - Windows 10 (x86_64)      - Georg Oeltzschner
+    - Linux (x86_64)           - Will Foran
+  The BSD 3-Clause LCModel license (LICENSE.lcmodel) applies to these binaries.
+
+Other referenced tools (not bundled)
+  - Augmentrum (https://github.com/julianmer/Augmentrum) - NIfTI-MRS augmentation
+  - MRS-Basis-Set-Conversion-Toolbox
+    (https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox) - basis set
+    conversion reference
+  - Osprey (https://github.com/schorschinho/osprey) - control/basis tooling

lcmodel_wrapper-0.2.0/PKG-INFO

@@ -0,0 +1,141 @@
+Metadata-Version: 2.4
+Name: lcmodel_wrapper
+Version: 0.2.0
+Summary: Lightweight Python wrapper for LCModel MRS fitting
+Author-email: Julian Merkofer <j.p.merkofer@tue.nl>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/julianmer/PyLCModel
+Project-URL: Repository, https://github.com/julianmer/PyLCModel
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: LICENSE.lcmodel
+License-File: NOTICE
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.10
+Requires-Dist: nibabel>=4.0
+Requires-Dist: nifti-mrs>=1.0
+Provides-Extra: test
+Requires-Dist: pandas>=1.4; extra == "test"
+Requires-Dist: openpyxl>=3.0; extra == "test"
+Dynamic: license-file
+
+<div align="center">
+  <img src="https://raw.githubusercontent.com/julianmer/PyLCModel/main/assets/logo_grey.png" alt="PyLCModel Logo" width="160"/>
+  <h1 style="margin-top:-10px; margin-bottom: 5px;">PyLCModel</h1>
+  <p style="margin-top: 0px;"><em>A lightweight Python wrapper for LCModel spectral fitting in MR spectroscopy</em></p>
+
+  [![PyPI version](https://badge.fury.io/py/lcmodel-wrapper.svg)](https://pypi.org/project/lcmodel-wrapper/)
+  [![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/)
+  [![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](LICENSE)
+</div>
+
+**PyLCModel** is a lightweight Python wrapper that streamlines the use of [LCModel](https://s-provencher.com/lcmodel.shtml) for least-squares spectral fitting in MRS. It automates control-file generation, handles flexible data input, manages the LCModel executable for you, and parses the output (with single- and multi-core processing).
+
+---
+
+## Features
+
+- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, build from source, or your own path); nothing is bundled in the wheel.
+- **Flexible input** — NumPy arrays, NIfTI-MRS, jMRUI text, and LCModel `.RAW`, in time or frequency domain.
+- **Automated control files** — generated to match your data, or templated from an existing one.
+- **Basis conversion (experimental)** — jMRUI, FSL-MRS, LCModel `.RAW`, and Osprey/FID-A basis sets to `.basis`.
+- **Batch fitting** — single- or multi-core, with full output parsing (concentrations, CRLBs, QC, fitted series).
+
+---
+
+## Installation
+
+### From PyPI
+```bash
+pip install lcmodel-wrapper
+```
+Enter your API token:
+
+### From Source
+```bash
+git clone https://github.com/julianmer/PyLCModel.git
+cd PyLCModel
+pip install -e .
+```
+
+---
+
+## How the LCModel binary is handled
+
+The LCModel program is **not** part of this package and is **not** shipped in the wheel. On first use, the binary is resolved in this order:
+
+1. an explicit `path2exec="/path/to/lcmodel"` you pass to `PyLCModel`,
+2. a previously cached download/build (under `~/.cache/lcmodel_wrapper`, or `%LOCALAPPDATA%` on Windows; override with `LCMODEL_CACHE_DIR`),
+3. a download of the matching binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
+4. a build from the LCModel Fortran source via `gfortran` (source fetched on demand).
+
+There is no git submodule and no bundled `lcmodel/` folder — keeping both the repository and the PyPI wheel small.
+
+---
+
+## Getting Started
+
+```python
+from lcmodel_wrapper import PyLCModel
+
+# Initialize the wrapper with your basis set (the LCModel binary is resolved automatically)
+lcmodel = PyLCModel(path2basis="/path/to/your/basis_set.basis")
+
+# `data` can be a NumPy array of FIDs (time domain), a NIfTI-MRS path, etc.
+concentrations, crlbs = lcmodel(data)
+
+print("Fitted Metabolite Concentrations:", concentrations)
+print("CRLBs:", crlbs)
+```
+
+Frequency-domain input or a custom executable:
+```python
+lcmodel = PyLCModel(
+    path2basis="/path/to/basis.basis",
+    domain="freq",                 # pass spectra instead of FIDs
+    path2exec="/path/to/lcmodel",  # optional: use your own binary
+)
+```
+
+Experimental basis conversion (other formats -> `.basis`):
+```python
+# Auto-detect the source format (jMRUI/AQSES/QUEST .txt folder, FSL-MRS .json folder,
+# LCModel .RAW folder, or Osprey/FID-A .mat):
+lcmodel = PyLCModel(path2basis="/path/to/basis_folder", convert_basis=True)
+
+# ...or force a format and supply parameters the source does not carry:
+lcmodel = PyLCModel(
+    path2basis="/path/to/raw_folder",
+    convert_basis=True,
+    basis_format="raw",          # "jmrui" | "fsl" | "raw" | "mat"
+    bandwidth=4000, central_freq=123.25,
+)
+
+# Or convert directly without fitting:
+from lcmodel_wrapper import convert_to_basis
+convert_to_basis("/path/to/jmrui_folder", out_path="out.basis")
+```
+> Basis conversion is **experimental** and not validated. For a dedicated, more complete tool, see the [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox).
+
+---
+
+## Licensing
+
+This wrapper (the Python code) is released under the **Apache License 2.0** (see [LICENSE](LICENSE)).
+
+**LCModel itself is a separate program** by Dr. Stephen Provencher, distributed under the **BSD 3-Clause License** (see [LICENSE.lcmodel](LICENSE.lcmodel)). This package does not bundle LCModel; when it downloads, builds, or runs the LCModel executable, that BSD-3-Clause license and the attributions in [NOTICE](NOTICE) apply. See the [LCModel home page](https://s-provencher.com/lcmodel.shtml) for details.
+
+---
+
+## Acknowledgements
+
+- LCModel binaries: [schorschinho/LCModel](https://github.com/schorschinho/LCModel) (Georg Oeltzschner and contributors)
+- Basis conversion reference: [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox) (Kay Igwe)
+- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Pyhton tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+
+---
+
+<div align="center">
+  <sub>Built with ❤️ for the MRS community</sub>
+</div>

lcmodel_wrapper-0.2.0/README.md

@@ -0,0 +1,119 @@
+<div align="center">
+  <img src="https://raw.githubusercontent.com/julianmer/PyLCModel/main/assets/logo_grey.png" alt="PyLCModel Logo" width="160"/>
+  <h1 style="margin-top:-10px; margin-bottom: 5px;">PyLCModel</h1>
+  <p style="margin-top: 0px;"><em>A lightweight Python wrapper for LCModel spectral fitting in MR spectroscopy</em></p>
+
+  [![PyPI version](https://badge.fury.io/py/lcmodel-wrapper.svg)](https://pypi.org/project/lcmodel-wrapper/)
+  [![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/)
+  [![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](LICENSE)
+</div>
+
+**PyLCModel** is a lightweight Python wrapper that streamlines the use of [LCModel](https://s-provencher.com/lcmodel.shtml) for least-squares spectral fitting in MRS. It automates control-file generation, handles flexible data input, manages the LCModel executable for you, and parses the output (with single- and multi-core processing).
+
+---
+
+## Features
+
+- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, build from source, or your own path); nothing is bundled in the wheel.
+- **Flexible input** — NumPy arrays, NIfTI-MRS, jMRUI text, and LCModel `.RAW`, in time or frequency domain.
+- **Automated control files** — generated to match your data, or templated from an existing one.
+- **Basis conversion (experimental)** — jMRUI, FSL-MRS, LCModel `.RAW`, and Osprey/FID-A basis sets to `.basis`.
+- **Batch fitting** — single- or multi-core, with full output parsing (concentrations, CRLBs, QC, fitted series).
+
+---
+
+## Installation
+
+### From PyPI
+```bash
+pip install lcmodel-wrapper
+```
+Enter your API token:
+
+### From Source
+```bash
+git clone https://github.com/julianmer/PyLCModel.git
+cd PyLCModel
+pip install -e .
+```
+
+---
+
+## How the LCModel binary is handled
+
+The LCModel program is **not** part of this package and is **not** shipped in the wheel. On first use, the binary is resolved in this order:
+
+1. an explicit `path2exec="/path/to/lcmodel"` you pass to `PyLCModel`,
+2. a previously cached download/build (under `~/.cache/lcmodel_wrapper`, or `%LOCALAPPDATA%` on Windows; override with `LCMODEL_CACHE_DIR`),
+3. a download of the matching binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
+4. a build from the LCModel Fortran source via `gfortran` (source fetched on demand).
+
+There is no git submodule and no bundled `lcmodel/` folder — keeping both the repository and the PyPI wheel small.
+
+---
+
+## Getting Started
+
+```python
+from lcmodel_wrapper import PyLCModel
+
+# Initialize the wrapper with your basis set (the LCModel binary is resolved automatically)
+lcmodel = PyLCModel(path2basis="/path/to/your/basis_set.basis")
+
+# `data` can be a NumPy array of FIDs (time domain), a NIfTI-MRS path, etc.
+concentrations, crlbs = lcmodel(data)
+
+print("Fitted Metabolite Concentrations:", concentrations)
+print("CRLBs:", crlbs)
+```
+
+Frequency-domain input or a custom executable:
+```python
+lcmodel = PyLCModel(
+    path2basis="/path/to/basis.basis",
+    domain="freq",                 # pass spectra instead of FIDs
+    path2exec="/path/to/lcmodel",  # optional: use your own binary
+)
+```
+
+Experimental basis conversion (other formats -> `.basis`):
+```python
+# Auto-detect the source format (jMRUI/AQSES/QUEST .txt folder, FSL-MRS .json folder,
+# LCModel .RAW folder, or Osprey/FID-A .mat):
+lcmodel = PyLCModel(path2basis="/path/to/basis_folder", convert_basis=True)
+
+# ...or force a format and supply parameters the source does not carry:
+lcmodel = PyLCModel(
+    path2basis="/path/to/raw_folder",
+    convert_basis=True,
+    basis_format="raw",          # "jmrui" | "fsl" | "raw" | "mat"
+    bandwidth=4000, central_freq=123.25,
+)
+
+# Or convert directly without fitting:
+from lcmodel_wrapper import convert_to_basis
+convert_to_basis("/path/to/jmrui_folder", out_path="out.basis")
+```
+> Basis conversion is **experimental** and not validated. For a dedicated, more complete tool, see the [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox).
+
+---
+
+## Licensing
+
+This wrapper (the Python code) is released under the **Apache License 2.0** (see [LICENSE](LICENSE)).
+
+**LCModel itself is a separate program** by Dr. Stephen Provencher, distributed under the **BSD 3-Clause License** (see [LICENSE.lcmodel](LICENSE.lcmodel)). This package does not bundle LCModel; when it downloads, builds, or runs the LCModel executable, that BSD-3-Clause license and the attributions in [NOTICE](NOTICE) apply. See the [LCModel home page](https://s-provencher.com/lcmodel.shtml) for details.
+
+---
+
+## Acknowledgements
+
+- LCModel binaries: [schorschinho/LCModel](https://github.com/schorschinho/LCModel) (Georg Oeltzschner and contributors)
+- Basis conversion reference: [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox) (Kay Igwe)
+- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Pyhton tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+
+---
+
+<div align="center">
+  <sub>Built with ❤️ for the MRS community</sub>
+</div>

lcmodel_wrapper-0.2.0/lcmodel_wrapper/__init__.py

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+"""PyLCModel - a lightweight Python wrapper for the LCModel MRS fitting tool.
+
+LCModel itself is a separate program by Dr. Stephen Provencher, distributed under the
+BSD 3-Clause License (see LICENSE.lcmodel). This package only wraps it.
+"""
+
+from .core import PyLCModel
+from .basis import read_basis, LCModelBasis
+from .convert import ensure_basis, convert_to_basis, detect_format
+from . import binaries, io, control, coord, convert
+
+__all__ = [
+    "PyLCModel",
+    "read_basis",
+    "LCModelBasis",
+    "ensure_basis",
+    "convert_to_basis",
+    "detect_format",
+    "binaries",
+    "io",
+    "control",
+    "coord",
+    "convert",
+]

lcmodel_wrapper-0.2.0/lcmodel_wrapper/basis.py

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+####################################################################################################
+#                                            basis.py                                              #
+####################################################################################################
+#                                                                                                  #
+# Authors: J. P. Merkofer (j.p.merkofer@tue.nl)                                                    #
+#                                                                                                  #
+# Created: 26/06/26                                                                                #
+#                                                                                                  #
+# Purpose: Lightweight parser for LCModel ".basis" files. Replaces the previous dependency on       #
+#          fsl_mrs for reading basis metadata. It extracts only what the wrapper needs to build    #
+#          control files and to align fitted concentrations: the field strength (HZPPPM), dwell       #
+#          time (BADELT), number of points (NDATAB) and the ordered metabolite names (METABO).     #
+#                                                                                                  #
+####################################################################################################
+
+import os
+import re
+from dataclasses import dataclass, field
+from typing import List, Optional
+
+
+#*************************#
+#   basis data container  #
+#*************************#
+@dataclass
+class LCModelBasis:
+    """Metadata parsed from an LCModel ".basis" file."""
+
+    path: str
+    central_freq: Optional[float] = None   # HZPPPM, field strength in MHz
+    dwell: Optional[float] = None           # BADELT, dwell time in seconds
+    n_points: Optional[int] = None          # NDATAB, number of complex points
+    echo_time: Optional[float] = None       # ECHOT, echo time
+    names: List[str] = field(default_factory=list)   # METABO entries, in file order
+
+    @property
+    def bandwidth(self) -> Optional[float]:
+        """Spectral bandwidth in Hz (1 / dwell)."""
+        if self.dwell in (None, 0):
+            return None
+        return 1.0 / self.dwell
+
+    @property
+    def n_metabs(self) -> int:
+        return len(self.names)
+
+
+#***********************************#
+#   parse a single namelist value   #
+#***********************************#
+def _find_scalar(text: str, key: str):
+    """Return the first numeric scalar assigned to "key" (e.g. "HZPPPM = 123.26")."""
+    m = re.search(rf"{key}\s*=\s*([-+0-9.eEdD]+)", text)
+    if not m:
+        return None
+    raw = m.group(1).replace("D", "E").replace("d", "e")
+    try:
+        return float(raw)
+    except ValueError:
+        return None
+
+
+#******************#
+#   read a basis   #
+#******************#
+def read_basis(path: str) -> LCModelBasis:
+    """Parse an LCModel ".basis" file and return an LCModelBasis.
+
+    Only the header namelists and the "METABO" names are read; the (large) numeric
+    basis vectors are skipped for speed.
+    """
+    if not os.path.isfile(path):
+        raise FileNotFoundError(f"Basis file not found: {path}")
+
+    basis = LCModelBasis(path=os.path.abspath(path))
+
+    with open(path, "r", errors="ignore") as fh:
+        header_lines = []
+        for line in fh:
+            header_lines.append(line)
+            # "METABO" lines are sparse; keep scanning the whole file for them.
+            # Match exactly "METABO =" (not "METABO_CONTAM" / "METABO_SINGLET").
+            m = re.match(r"\s*METABO\s*=\s*'(.*?)'", line)
+            if m:
+                basis.names.append(m.group(1).strip())
+
+        header = "".join(header_lines[:200])   # scalars live near the top
+
+    basis.central_freq = _find_scalar(header, "HZPPPM")
+    basis.dwell = _find_scalar(header, "BADELT")
+    basis.echo_time = _find_scalar(header, "ECHOT")
+    ndatab = _find_scalar(header, "NDATAB")
+    basis.n_points = int(ndatab) if ndatab is not None else None
+
+    if not basis.names:
+        raise ValueError(
+            f"No METABO entries found in basis file: {path}. "
+            "Is this a valid LCModel .basis file?"
+        )
+    return basis