augmentrum 0.0.1__tar.gz

augmentrum-0.0.1/LICENSE

@@ -0,0 +1,202 @@
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+   Copyright 2026 J. T. LaMaster, J. P. Merkofer, K. C. Igwe
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augmentrum-0.0.1/MANIFEST.in

@@ -0,0 +1,10 @@
+include README.md
+include LICENSE
+recursive-include augmentrum *.py
+recursive-include augmentrum/resources/scans *
+recursive-include assets/figures *.png *.jpg *.svg
+recursive-exclude * __pycache__
+recursive-exclude * *.pyc
+recursive-exclude * *.pyo
+recursive-exclude * .DS_Store
+prune data

augmentrum-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: augmentrum
+Version: 0.0.1
+Summary: A Data Augmentation Package for MR Spectroscopy
+Author-email: "John T. LaMaster" <jlamaste@gmail.com>, "Julian P. Merkofer" <j.p.merkofer@tue.nl>, "Kay C. Igwe" <kci2104@columbia.edu>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/julianmer/Augmentrum
+Project-URL: Documentation, https://github.com/julianmer/Augmentrum#readme
+Project-URL: Repository, https://github.com/julianmer/Augmentrum
+Project-URL: Bug Tracker, https://github.com/julianmer/Augmentrum/issues
+Keywords: MRS,spectroscopy,data augmentation,medical imaging,machine learning
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: torch>=1.10.0
+Requires-Dist: fsl-mrs>=2.1.0
+Requires-Dist: nifti-mrs>=0.1.0
+Requires-Dist: spec2nii>=0.6.0
+Requires-Dist: torchkbnufft>=1.3.0
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: matplotlib>=3.4.0
+Requires-Dist: shutup>=0.2.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Provides-Extra: jax
+Requires-Dist: jax>=0.4.0; extra == "jax"
+Requires-Dist: jaxlib>=0.4.0; extra == "jax"
+Provides-Extra: keras
+Requires-Dist: keras>=3.0.0; extra == "keras"
+Provides-Extra: all
+Requires-Dist: tensorflow>=2.8.0; extra == "all"
+Requires-Dist: keras>=3.0.0; extra == "all"
+Requires-Dist: jax>=0.4.0; extra == "all"
+Requires-Dist: jaxlib>=0.4.0; extra == "all"
+Dynamic: license-file
+
+<div align="center">
+  <img src="assets/figures/logo.png" alt="Augmentrum Logo" width="100" style="margin-bottom: -10px;"/>
+  <h1 style="margin-top: 5px; margin-bottom: 5px;">Augmentrum</h1>
+  <p style="margin-top: 0px;"><em>A Data Augmentation Package for MR Spectroscopy</em></p>
+  
+  [![PyPI version](https://badge.fury.io/py/augmentrum.svg)](https://badge.fury.io/py/augmentrum)
+  [![Python](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/)
+  [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](LICENSE)
+  [![ISMRM 2026](https://img.shields.io/badge/ISMRM-Abstract%20%2305685-lightgrey.svg)](https://submissions.mirasmart.com/ISMRM2026/Itinerary/PresentationDetail.aspx?evdid=1450)
+</div>
+
+---
+
+## Overview
+**Augmentrum** is a modular Python framework designed to help researchers with limited *in-vivo* MRS data create diverse, physically consistent datasets through flexible augmentation. It supports **k-space resampling**, **coil and average sampling**, **signal-level perturbations**, and **synthetic artifact generation**, expanding both synthetic and *in-vivo* data in a realistic and controlled manner.
+
+<div align="center">
+  <img src="assets/figures/overview.png" alt="Augmentrum Pipeline Overview" width="800"/>
+</div>
+
+Built for data-driven MRS applications, Augmentrum streamlines the integration of data augmentation into existing workflows. It operates on the **NIfTI-MRS** standard, making it compatible with any acquisition format. Simply load your data as NIfTI (using `spec2nii` if needed) and apply either predefined augmentation settings or build a custom pipeline by combining modules. Each augmentation can be parameterized or used with default ranges to populate a dense and diverse dataset environment.
+
+From MRSI reconstruction and acquisition variability to spectral perturbations and artifact synthesis, Augmentrum handles it all in a **modular**, **flexible**, and **easy-to-use** structure. Dataloaders allow **on-the-fly augmentation** for deep learning backends such as **PyTorch**, **TensorFlow**, **Keras**, and **JAX**, enabling robust training beyond static datasets.
+
+> **Note:** Augmentrum is currently in **alpha development**. It is an active research framework and may undergo changes as modules and interfaces evolve.
+
+---
+
+## Features
+- Modular augmentation across time, frequency, and k-space domains
+- Physically valid transformations for realistic variability
+- Native NIfTI-MRS I/O and metadata tracking
+- Customizable pipelines with user-defined parameters
+- On-the-fly augmentation for machine learning workflows
+
+---
+
+## Installation
+```bash
+pip install augmentrum
+```
+or from source:
+```bash
+git clone https://github.com/julianmer/Augmentrum.git
+cd Augmentrum
+pip install -e .
+```
+
+---
+
+## Quick Start
+```python
+from augmentrum import Augmentrum
+
+data   # list of NIfTI-MRS files
+water   # list of corresponding water reference files (optional)
+
+# initialize Augmentrum with data and optional water references
+augmenter = Augmentrum(
+    data=data, 
+    water=water, 
+    
+    # custom pipeline example
+    pipeline = [
+        'coil_sampling',
+        'average_sampling',
+        'processing',
+        'line_broadening',
+        'baseline',
+        'noise',
+    ],
+    
+    # general settings
+    batch_size=16,
+    backend='pytorch',  # or 'tensorflow', 'keras', 'jax', 'numpy'
+)
+
+# get a dataloader for PyTorch with on-the-fly augmentation
+train_data = augmenter.dataloader()
+```
+
+---
+
+## Module Reference & Backend Support
+
+Every module is called as `module(nifti_plus, water)`.  When a backend is not
+natively supported, the base class automatically routes the call through the
+NIfTI-list path and returns the result in the original backend format —
+no manual conversion needed.
+
+| Module | Modes / Methods                                         | NIfTI | NumPy | PyTorch | TensorFlow | JAX | Keras |
+|:---|:--------------------------------------------------------|:-----:|:---:|:---:|:---:|:---:|:---:|
+| `AmplitudeScaling` | uniform, normal                                         |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `Apodization` | exponential, truncate                                   |   ✓   | ✓† | ✓† | ✓† | ✓† | ✓† |
+| `ArtificialPeaks` | Lorentzian, Gaussian, Voigt                             |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `BaselineAugmentation` | random_walk, bspline, polynomial                        |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `CoilAverageSampler` | random, deterministic                                   |   ✓   | ~ | ~ | ~ | ~ | ~ |
+| `EddyCurrent` | synthetic, water                                        |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `FrequencyShift` | —                                                       |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `GaussianNoise` | sigma, sigma_frac, snr, snr_db                          |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `KspaceReconstructor` | NUFFT + density compensation                            |   —   | — | ✓ | — | — | — |
+| `LineBroadening` | lorentzian, gaussian, voigt                             |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `NIfTI_RawProcessor` | coil combination, alignment, averaging, ECC, phase/freq |   ✓   | ~ | ~ | ~ | ~ | ~ |
+| `PhaseShift` | zero_order, first_order                                 |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `ResidualWater` | —                                                       |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `SpatialAugmentations` | 2-D / 3-D affine, flip, zoom, shear                     |  ✓ ‡  | ✓ ‡ | ✓ | ~ | ~ | ~ |
+| `SpuriousEchoes` | replica, hybrid                                         |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `ZeroFill` | pad FID to target length                                |   ✓   | ✓† | ✓† | ✓† | ✓† | ✓† |
+
+**✓** native — data tensor stays in the target framework throughout.  
+**~** automatic — the base class routes the call through the NIfTI-list path; the result is returned in the original backend format. Functional, but not natively differentiable.  
+**—** not supported / not applicable.
+
+> **†** `Apodization[truncate]` and `ZeroFill` both change `N_PTS`. Because `target_pts` / `n_pts` is a module-level scalar, the **same length is applied uniformly to every batch member** — the output is still a uniform tensor. On non-NIfTI backends the base class detects the shape change, rebuilds each NIfTI_MRS object at the new length, and emits a `RuntimeWarning`.
+
+> **‡** `SpatialAugmentations` uses `F.grid_sample` (PyTorch) internally; NIfTI-list and NumPy inputs are converted to PyTorch for processing and converted back. TensorFlow, JAX, and Keras are handled by the base-class automatic routing (~).
+
+
+---
+
+## Contact
+
+For questions, issues, or collaborations:
+
+- **GitHub Issues**: [github.com/julianmer/Augmentrum/issues](https://github.com/julianmer/Augmentrum/issues)
+- **Email**: jlamaste@gmail.com, j.p.merkofer@tue.nl, kci2104@columbia.edu
+
+---
+
+## Citation
+J. T. LaMaster, J. P. Merkofer, K. C. Igwe, "Augmentrum: A Data Augmentation Package for MR Spectroscopy", _International Society for Magnetic Resonance in Medicine (ISMRM)_, Abstract #05685, Cape Town, South Africa, 2026.
+
+---
+
+<div align="center">
+  <sub>Built with ❤️ for the MRS community</sub>
+</div>

augmentrum-0.0.1/README.md

@@ -0,0 +1,137 @@
+<div align="center">
+  <img src="assets/figures/logo.png" alt="Augmentrum Logo" width="100" style="margin-bottom: -10px;"/>
+  <h1 style="margin-top: 5px; margin-bottom: 5px;">Augmentrum</h1>
+  <p style="margin-top: 0px;"><em>A Data Augmentation Package for MR Spectroscopy</em></p>
+  
+  [![PyPI version](https://badge.fury.io/py/augmentrum.svg)](https://badge.fury.io/py/augmentrum)
+  [![Python](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/)
+  [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](LICENSE)
+  [![ISMRM 2026](https://img.shields.io/badge/ISMRM-Abstract%20%2305685-lightgrey.svg)](https://submissions.mirasmart.com/ISMRM2026/Itinerary/PresentationDetail.aspx?evdid=1450)
+</div>
+
+---
+
+## Overview
+**Augmentrum** is a modular Python framework designed to help researchers with limited *in-vivo* MRS data create diverse, physically consistent datasets through flexible augmentation. It supports **k-space resampling**, **coil and average sampling**, **signal-level perturbations**, and **synthetic artifact generation**, expanding both synthetic and *in-vivo* data in a realistic and controlled manner.
+
+<div align="center">
+  <img src="assets/figures/overview.png" alt="Augmentrum Pipeline Overview" width="800"/>
+</div>
+
+Built for data-driven MRS applications, Augmentrum streamlines the integration of data augmentation into existing workflows. It operates on the **NIfTI-MRS** standard, making it compatible with any acquisition format. Simply load your data as NIfTI (using `spec2nii` if needed) and apply either predefined augmentation settings or build a custom pipeline by combining modules. Each augmentation can be parameterized or used with default ranges to populate a dense and diverse dataset environment.
+
+From MRSI reconstruction and acquisition variability to spectral perturbations and artifact synthesis, Augmentrum handles it all in a **modular**, **flexible**, and **easy-to-use** structure. Dataloaders allow **on-the-fly augmentation** for deep learning backends such as **PyTorch**, **TensorFlow**, **Keras**, and **JAX**, enabling robust training beyond static datasets.
+
+> **Note:** Augmentrum is currently in **alpha development**. It is an active research framework and may undergo changes as modules and interfaces evolve.
+
+---
+
+## Features
+- Modular augmentation across time, frequency, and k-space domains
+- Physically valid transformations for realistic variability
+- Native NIfTI-MRS I/O and metadata tracking
+- Customizable pipelines with user-defined parameters
+- On-the-fly augmentation for machine learning workflows
+
+---
+
+## Installation
+```bash
+pip install augmentrum
+```
+or from source:
+```bash
+git clone https://github.com/julianmer/Augmentrum.git
+cd Augmentrum
+pip install -e .
+```
+
+---
+
+## Quick Start
+```python
+from augmentrum import Augmentrum
+
+data   # list of NIfTI-MRS files
+water   # list of corresponding water reference files (optional)
+
+# initialize Augmentrum with data and optional water references
+augmenter = Augmentrum(
+    data=data, 
+    water=water, 
+    
+    # custom pipeline example
+    pipeline = [
+        'coil_sampling',
+        'average_sampling',
+        'processing',
+        'line_broadening',
+        'baseline',
+        'noise',
+    ],
+    
+    # general settings
+    batch_size=16,
+    backend='pytorch',  # or 'tensorflow', 'keras', 'jax', 'numpy'
+)
+
+# get a dataloader for PyTorch with on-the-fly augmentation
+train_data = augmenter.dataloader()
+```
+
+---
+
+## Module Reference & Backend Support
+
+Every module is called as `module(nifti_plus, water)`.  When a backend is not
+natively supported, the base class automatically routes the call through the
+NIfTI-list path and returns the result in the original backend format —
+no manual conversion needed.
+
+| Module | Modes / Methods                                         | NIfTI | NumPy | PyTorch | TensorFlow | JAX | Keras |
+|:---|:--------------------------------------------------------|:-----:|:---:|:---:|:---:|:---:|:---:|
+| `AmplitudeScaling` | uniform, normal                                         |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `Apodization` | exponential, truncate                                   |   ✓   | ✓† | ✓† | ✓† | ✓† | ✓† |
+| `ArtificialPeaks` | Lorentzian, Gaussian, Voigt                             |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `BaselineAugmentation` | random_walk, bspline, polynomial                        |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `CoilAverageSampler` | random, deterministic                                   |   ✓   | ~ | ~ | ~ | ~ | ~ |
+| `EddyCurrent` | synthetic, water                                        |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `FrequencyShift` | —                                                       |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `GaussianNoise` | sigma, sigma_frac, snr, snr_db                          |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `KspaceReconstructor` | NUFFT + density compensation                            |   —   | — | ✓ | — | — | — |
+| `LineBroadening` | lorentzian, gaussian, voigt                             |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `NIfTI_RawProcessor` | coil combination, alignment, averaging, ECC, phase/freq |   ✓   | ~ | ~ | ~ | ~ | ~ |
+| `PhaseShift` | zero_order, first_order                                 |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `ResidualWater` | —                                                       |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `SpatialAugmentations` | 2-D / 3-D affine, flip, zoom, shear                     |  ✓ ‡  | ✓ ‡ | ✓ | ~ | ~ | ~ |
+| `SpuriousEchoes` | replica, hybrid                                         |   ✓   | ✓ | ✓ | ✓ | ✓ | ✓ |
+| `ZeroFill` | pad FID to target length                                |   ✓   | ✓† | ✓† | ✓† | ✓† | ✓† |
+
+**✓** native — data tensor stays in the target framework throughout.  
+**~** automatic — the base class routes the call through the NIfTI-list path; the result is returned in the original backend format. Functional, but not natively differentiable.  
+**—** not supported / not applicable.
+
+> **†** `Apodization[truncate]` and `ZeroFill` both change `N_PTS`. Because `target_pts` / `n_pts` is a module-level scalar, the **same length is applied uniformly to every batch member** — the output is still a uniform tensor. On non-NIfTI backends the base class detects the shape change, rebuilds each NIfTI_MRS object at the new length, and emits a `RuntimeWarning`.
+
+> **‡** `SpatialAugmentations` uses `F.grid_sample` (PyTorch) internally; NIfTI-list and NumPy inputs are converted to PyTorch for processing and converted back. TensorFlow, JAX, and Keras are handled by the base-class automatic routing (~).
+
+
+---
+
+## Contact
+
+For questions, issues, or collaborations:
+
+- **GitHub Issues**: [github.com/julianmer/Augmentrum/issues](https://github.com/julianmer/Augmentrum/issues)
+- **Email**: jlamaste@gmail.com, j.p.merkofer@tue.nl, kci2104@columbia.edu
+
+---
+
+## Citation
+J. T. LaMaster, J. P. Merkofer, K. C. Igwe, "Augmentrum: A Data Augmentation Package for MR Spectroscopy", _International Society for Magnetic Resonance in Medicine (ISMRM)_, Abstract #05685, Cape Town, South Africa, 2026.
+
+---
+
+<div align="center">
+  <sub>Built with ❤️ for the MRS community</sub>
+</div>

augmentrum-0.0.1/augmentrum/__init__.py

@@ -0,0 +1,23 @@
+"""
+Augmentrum - A Data Augmentation Package for MR Spectroscopy
+
+A modular Python framework designed to help researchers with limited in-vivo MRS data
+create diverse, physically consistent datasets through flexible augmentation.
+"""
+
+__version__ = "0.0.1"
+__author__ = "John T. LaMaster, Julian P. Merkofer, Kay C. Igwe"
+__email__ = "j.p.merkofer@tue.nl"
+
+# Main API
+from augmentrum.core import Augmentrum, NIfTI_MRS_Plus, Backend, BaseModule, AugmentationPipeline
+
+__all__ = [
+    "__version__",
+    "Augmentrum",
+    "NIfTI_MRS_Plus",
+    "Backend",
+    "BaseModule",
+    "AugmentationPipeline",
+]
+

augmentrum-0.0.1/augmentrum/augmentation/__init__.py

@@ -0,0 +1,32 @@
+"""
+Augmentation modules for MRS data.
+"""
+
+from augmentrum.augmentation.gaussian_noise import GaussianNoise
+from augmentrum.augmentation.line_broadening import LineBroadening
+from augmentrum.augmentation.baseline_augmentation import BaselineAugmentation
+from augmentrum.augmentation.residual_water import ResidualWater
+from augmentrum.augmentation.spurious_echoes import SpuriousEchoes
+from augmentrum.augmentation.artificial_peaks import ArtificialPeaks
+from augmentrum.augmentation.eddy_current import EddyCurrent
+from augmentrum.augmentation.apodization import Apodization
+from augmentrum.augmentation.phase_frequency import PhaseShift, FrequencyShift
+from augmentrum.augmentation.amplitude_scaling import AmplitudeScaling
+from augmentrum.augmentation.spatial_augmentations import SpatialAugmentations
+from augmentrum.augmentation.zero_fill import ZeroFill
+
+__all__ = [
+    'GaussianNoise',
+    'LineBroadening',
+    'BaselineAugmentation',
+    'ResidualWater',
+    'SpuriousEchoes',
+    'ArtificialPeaks',
+    'EddyCurrent',
+    'Apodization',
+    'PhaseShift',
+    'FrequencyShift',
+    'AmplitudeScaling',
+    'SpatialAugmentations',
+    'ZeroFill',
+]