nifti2bids 0.1.2__py3-none-any.whl

nifti2bids/simulate.py

@@ -0,0 +1,59 @@
+"""Module for creating simulated data."""
+
+import nibabel as nib, numpy as np
+
+from numpy.typing import NDArray
+
+
+def simulate_nifti_image(
+    img_shape: tuple[int, int, int] | tuple[int, int, int, int], affine: NDArray = None
+) -> nib.Nifti1Image:
+    """
+    Simulates a NIfTI image.
+
+    Parameters
+    ----------
+    img_shape: :obj:`tuple[int, int, int]` or :obj:`tuple[int, int, int, int]`
+        Shape of the NIfTI image.
+
+    affine: :obj:`NDArray`, default=None
+        The affine matrix.
+
+        .. important::
+           If None, creates an identity matrix.
+
+    Returns
+    -------
+    Nifti1Image
+        The NIfTI image with no header.
+    """
+    if affine is None:
+        affine = create_affine(
+            xyz_diagonal_value=1, translation_vector=np.array([0, 0, 0, 1])
+        )
+
+    return nib.Nifti1Image(np.random.rand(*img_shape), affine)
+
+
+def create_affine(xyz_diagonal_value: int, translation_vector: NDArray) -> NDArray:
+    """
+    Generate an 4x4 affine matrix.
+
+    Parameters
+    ----------
+    xyz_diagonal_value: :obj:`int`
+        The value assigned to the diagonal of the affine for x, y, and z.
+
+    translation_vector: :obj:`NDArray`
+        The translation vector/shift from the origin.
+
+    Returns
+    -------
+    NDArray
+        The affine matrix.
+    """
+    affine = np.zeros((4, 4))
+    np.fill_diagonal(affine[:3, :3], xyz_diagonal_value)
+    affine[:, 3:] = translation_vector[:, np.newaxis]
+
+    return affine

nifti2bids-0.1.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: nifti2bids
+Version: 0.1.2
+Summary: Post-hoc BIDS conversion toolkit for NIfTI datasets without original DICOMs.
+Author-email: Donisha Smith <dsmit420@jhu.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://nifti2bids.readthedocs.io
+Project-URL: Github, https://github.com/donishadsmith/nifti2bids
+Project-URL: Issues, https://github.com/donishadsmith/nifti2bids/issues
+Project-URL: Changelog, https://nifti2bids.readthedocs.io/en/stable/changelog.html
+Keywords: python,neuroimaging,fMRI,MRI,BIDS,NIfTI
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows :: Windows 11
+Classifier: Development Status :: 3 - Alpha
+Requires-Python: >=3.10.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26.3
+Requires-Dist: nibabel>=5.0.0
+Requires-Dist: rich>=14.2.0
+Requires-Dist: nilearn>=0.10.4
+Requires-Dist: pandas>=2.1.0
+Provides-Extra: all
+Requires-Dist: nifti2bids[test]; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Dynamic: license-file
+
+# Nifti2Bids
+
+[![Latest Version](https://img.shields.io/pypi/v/nifti2bids.svg)](https://pypi.python.org/pypi/nifti2bids/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/nifti2bids.svg)](https://pypi.python.org/pypi/nifti2bids/)
+[![Source Code](https://img.shields.io/badge/Source%20Code-nifti2bids-purple)](https://github.com/donishadsmith/nifti2bids)
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![Test Status](https://github.com/donishadsmith/nifti2bids/actions/workflows/testing.yaml/badge.svg)](https://github.com/donishadsmith/nifti2bids/actions/workflows/testing.yaml)
+[![codecov](https://codecov.io/gh/donishadsmith/nifti2bids/graph/badge.svg?token=PCJ17NA627)](https://codecov.io/gh/donishadsmith/nifti2bids)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Documentation Status](https://readthedocs.org/projects/nifti2bids/badge/?version=stable)](http://nifti2bids.readthedocs.io/en/stable/?badge=stable)
+
+
+A toolkit for post hoc BIDS-ification NIfTI datasets. Includes utilities for metadata extraction, file renaming, and JSON sidecar generation, designed primarily for datasets where the original DICOMs are unavailable.
+
+## Installation
+To install ``nifti2bids`` use one of the following methods:
+
+### Standard Installation
+```bash
+pip install nifti2bids
+```
+
+### Development Version
+
+```bash
+git clone --depth 1 https://github.com/donishadsmith/nifti2bids/
+cd nifti2bids
+pip install -e .
+```

nifti2bids-0.1.2.dist-info/RECORD

@@ -0,0 +1,14 @@
+nifti2bids/__init__.py,sha256=LQlB2KxI-DGzpPTFTseAr4ZUb3FbuWsd7VVrxrOHt5Q,681
+nifti2bids/_decorators.py,sha256=Ny05P-kn49-fenfHBOCPHkFbYkcMMJrF50Db4KRXOrY,1586
+nifti2bids/_exceptions.py,sha256=Lup5wtAHbUA799MFBAOm4vI1PIl67YRJb2yhtSzMKO0,1245
+nifti2bids/_helpers.py,sha256=GevqfWws98xpJjnyGdCFUFlqFNBMcriH5Kz58XY8Pvw,192
+nifti2bids/bids.py,sha256=qZYbXuHG1EL-wCFNKDscarQUwC1DAKq7Ils3PFl7AS4,5341
+nifti2bids/io.py,sha256=YbjsrLC07Eon17J14RZiKsqhE29eLtqSP86hKk0lZ6o,2907
+nifti2bids/logging.py,sha256=HZ1kEV780e7lVtIUg11RrqY1f6ST8BrdZAXytRInWgQ,1923
+nifti2bids/metadata.py,sha256=9v-Rhzv-xjvgyG3xoA8Gd0-vHnhsSv4tVMpH7a0H6SA,23354
+nifti2bids/simulate.py,sha256=y9tT8FZQ3AwKiBbguaLKLT-_7QC6vDrbsN3SaeYStRg,1461
+nifti2bids-0.1.2.dist-info/licenses/LICENSE,sha256=yCnTvShS6GH1UbLmn2bplwrIaAvbC956sxP5tRJP5OM,1070
+nifti2bids-0.1.2.dist-info/METADATA,sha256=5xDr24mK6t4_noP5nal4Cns7hGwjB1VrzhchXI681VI,3108
+nifti2bids-0.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nifti2bids-0.1.2.dist-info/top_level.txt,sha256=D_dJLgalvEjgKIdUQrhKjKTEd796j1RpDcYAziScNOA,11
+nifti2bids-0.1.2.dist-info/RECORD,,

nifti2bids-0.1.2.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

nifti2bids-0.1.2.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Donisha Smith
+
+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.

nifti2bids-0.1.2.dist-info/top_level.txt

@@ -0,0 +1 @@
+nifti2bids