augmentrum 0.0.1__py3-none-any.whl

augmentrum/utils/tensor_ops.py

@@ -0,0 +1,203 @@
+####################################################################################################
+#                                        tensor_ops.py                                             #
+####################################################################################################
+#                                                                                                  #
+# Authors: J. P. Merkofer (j.p.merkofer@tue.nl)                                                    #
+#                                                                                                  #
+# Created: 2026-03-27                                                                              #
+#                                                                                                  #
+# Purpose: Backend-agnostic tensor operations for MRS signal processing.                           #
+#                                                                                                  #
+# Follows the zea philosophy: write once, works with any backend.                                  #
+# Detects the array library from the tensor type and dispatches                                    #
+# to numpy / torch / jax transparently.  No keras dependency.                                      #
+#                                                                                                  #
+# Module authors just write:                                                                       #
+#     from augmentrum.utils.tensor_ops import fft, ifft, fftshift, ifftshift                       #
+#                                                                                                  #
+#     spectrum = fftshift(ifft(fid))   # works with ANY tensor type                                #
+#     fid_out  = fft(ifftshift(spectrum))                                                          #
+#                                                                                                  #
+# The dispatch happens *once* per call inside these helpers — callers never                        #
+# need to check tensor types themselves.                                                           #
+#                                                                                                  #
+####################################################################################################
+
+import numpy as np
+
+
+# ============================================================================
+# Backend detection
+# ============================================================================
+
+def _is_torch(x):
+    """True if *x* is a PyTorch tensor."""
+    return type(x).__module__.split(".")[0] == "torch"
+
+
+def _is_jax(x):
+    """True if *x* is a JAX array."""
+    return type(x).__module__.split(".")[0] in ("jax", "jaxlib")
+
+
+def _is_tf(x):
+    """True if *x* is a TensorFlow tensor."""
+    return type(x).__module__.split(".")[0] == "tensorflow"
+
+
+# ============================================================================
+# Complex FFT / IFFT
+#
+# All three backends (numpy, torch >= 1.7, jax) support native complex-valued
+# FFT with the same semantics, so we just dispatch to the right module.
+# No need for the keras (real, imag)-tuple workaround.
+# ============================================================================
+
+def fft(x):
+    """Complex-to-complex FFT along the last axis (any backend).
+
+    MRS convention: ``fft`` maps *spectrum -> FID*.
+
+    Args:
+        x: Complex tensor of any shape.
+
+    Returns:
+        Complex tensor with the same shape as *x*.
+    """
+    if _is_torch(x):
+        import torch
+        return torch.fft.fft(x)
+    if _is_jax(x):
+        import jax.numpy as jnp
+        return jnp.fft.fft(x)
+    return np.fft.fft(x)
+
+
+def ifft(x):
+    """Complex-to-complex inverse FFT along the last axis (any backend).
+
+    MRS convention: ``ifft`` maps *FID -> spectrum*.
+
+    Args:
+        x: Complex tensor of any shape.
+
+    Returns:
+        Complex tensor with the same shape as *x*.
+    """
+    if _is_torch(x):
+        import torch
+        return torch.fft.ifft(x)
+    if _is_jax(x):
+        import jax.numpy as jnp
+        return jnp.fft.ifft(x)
+    return np.fft.ifft(x)
+
+
+# ============================================================================
+# fftshift / ifftshift
+#
+# numpy / jax use ``axes=`` keyword; torch uses ``dim=``.
+# ============================================================================
+
+def fftshift(x, axis=-1):
+    """Shift zero-frequency component to the centre (like ``np.fft.fftshift``).
+
+    Args:
+        x: Tensor of any shape.
+        axis: Axis (or axes) along which to shift.
+
+    Returns:
+        Shifted tensor.
+    """
+    if _is_torch(x):
+        import torch
+        return torch.fft.fftshift(x, dim=axis)
+    if _is_jax(x):
+        import jax.numpy as jnp
+        return jnp.fft.fftshift(x, axes=axis)
+    return np.fft.fftshift(x, axes=axis)
+
+
+def ifftshift(x, axis=-1):
+    """Inverse of :func:`fftshift` (like ``np.fft.ifftshift``).
+
+    Args:
+        x: Tensor of any shape.
+        axis: Axis (or axes) along which to shift.
+
+    Returns:
+        Shifted tensor.
+    """
+    if _is_torch(x):
+        import torch
+        return torch.fft.ifftshift(x, dim=axis)
+    if _is_jax(x):
+        import jax.numpy as jnp
+        return jnp.fft.ifftshift(x, axes=axis)
+    return np.fft.ifftshift(x, axes=axis)
+
+
+# ============================================================================
+# Conversion helpers
+# ============================================================================
+
+def to_numpy(x):
+    """Convert *any* backend tensor to a NumPy ``ndarray``.
+
+    Handles PyTorch ``.detach().cpu()`` and JAX/TF device arrays
+    transparently.
+
+    Args:
+        x: Tensor or array.
+
+    Returns:
+        ``numpy.ndarray``
+    """
+    if isinstance(x, np.ndarray):
+        return x
+    if _is_torch(x):
+        return x.detach().cpu().numpy()
+    # JAX, TF, and anything with __array__ protocol
+    return np.asarray(x)
+
+
+def match_backend(param, ref):
+    """Convert a NumPy parameter array to the same backend as *ref*.
+
+    This is the key helper for the "auto-promote" pattern.  Augmentation
+    modules generate envelopes / noise / phase ramps as lightweight NumPy
+    arrays, then call::
+
+        result = data_tensor * match_backend(envelope_np, data_tensor)
+
+    This avoids the known issue where ``torch.Tensor * np.ndarray`` can
+    fail when ``requires_grad=True`` (numpy tries to call ``__array__``
+    on the grad-enabled tensor via ufunc dispatch).
+
+    For NumPy-to-NumPy this is a no-op (zero cost).
+
+    Args:
+        param: Parameter array (typically numpy).
+        ref:   Reference tensor whose backend we want to match.
+
+    Returns:
+        ``param`` converted to the same framework as ``ref``.
+    """
+    if isinstance(param, np.ndarray):
+        if isinstance(ref, np.ndarray):
+            return param                             # no-op: numpy handles mixed dtypes
+        if _is_torch(ref):
+            import torch
+            return torch.as_tensor(param, device=ref.device)
+        if _is_jax(ref):
+            import jax.numpy as jnp
+            return jnp.array(param)
+        if _is_tf(ref):
+            import tensorflow as tf
+            # TF is strict: complex64 tensor * complex128 constant raises.
+            # Cast param to match ref's dtype before wrapping.
+            return tf.constant(param, dtype=ref.dtype)
+    # Already same backend, or unknown → return as-is
+    return param
+
+

augmentrum-0.0.1.dist-info/METADATA

@@ -0,0 +1,189 @@
+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>

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augmentrum-0.0.1.dist-info/licenses/LICENSE

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+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
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augmentrum-0.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+augmentrum