nifti2bids 0.0.9__tar.gz → 0.1.0__tar.gz

{nifti2bids-0.0.9 → nifti2bids-0.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nifti2bids
-Version: 0.0.9
+Version: 0.1.0
 Summary: Post-hoc BIDS conversion toolkit for NIfTI datasets without original DICOMs.
 Author-email: Donisha Smith <dsmit420@jhu.edu>
 License-Expression: MIT
@@ -45,7 +45,7 @@ Dynamic: license-file
 [![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-py/badge/?version=latest)](http://nifti2bids.readthedocs.io/en/latest/?badge=latest)
+[![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.

{nifti2bids-0.0.9 → nifti2bids-0.1.0}/README.md

@@ -7,7 +7,7 @@
 [![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-py/badge/?version=latest)](http://nifti2bids.readthedocs.io/en/latest/?badge=latest)
+[![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.

nifti2bids-0.1.0/nifti2bids/__init__.py

@@ -0,0 +1,20 @@
+"""
+Post-hoc BIDS conversion toolkit for NIfTI datasets without original DICOMs.
+----------------------------------------------------------------------------
+Documentation can be found at https://nifti2bids.readthedocs.io.
+
+Submodules
+----------
+bids -- Operations related to initializing and creating BIDs compliant files
+
+io -- Generic operations related to loading NIfTI data
+
+logging -- Set up a logger using ``RichHandler`` as the default handler if a root or
+module specific handler is not available
+
+metadata -- Operations related to extracting metadata information from NIfTI images
+
+simulate -- Simulate a basic NIfTI image for testing purposes
+"""
+
+__version__ = "0.1.0"

nifti2bids-0.0.9/nifti2bids/io.py → nifti2bids-0.1.0/nifti2bids/bids.py

@@ -1,139 +1,9 @@
-"""Module for input/output operations."""
-
-import glob, json, os, shutil
+import os, json
 from typing import Optional
 
-import nibabel as nib
-
-
-def load_nifti(
-    nifti_file_or_img: str | nib.nifti1.Nifti1Image,
-) -> nib.nifti1.Nifti1Image:
-    """
-    Loads a NIfTI image.
-
-    Loads NIfTI image when not a ``Nifti1Image`` object or
-    returns the image if already loaded in.
-
-    Parameters
-    ----------
-    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
-        Path to the NIfTI file or a NIfTI image.
-
-    Returns
-    -------
-    nib.nifti1.Nifti1Image
-        The loaded in NIfTI image.
-    """
-    nifti_img = (
-        nifti_file_or_img
-        if isinstance(nifti_file_or_img, nib.nifti1.Nifti1Image)
-        else nib.load(nifti_file_or_img)
-    )
-
-    return nifti_img
-
-
-def compress_image(nifti_file: str, remove_src_file: bool = False) -> None:
-    """
-    Compresses a ".nii" image to a ".nii.gz" image.
-
-    Parameters
-    ----------
-    nifti_file: :obj:`str`
-        Path to the NIfTI image.
-
-    remove_src_file: :obj:`bool`
-        Deletes the original source image file.
-
-    Returns
-    -------
-    None
-    """
-    img = nib.load(nifti_file)
-    nib.save(img, nifti_file.replace(".nii", ".nii.gz"))
-
-    if remove_src_file:
-        os.remove(nifti_file)
-
-
-def glob_contents(src_dir: str, pattern: str) -> list[str]:
-    """
-    Use glob to get contents with specific patterns.
-
-    Parameters
-    ----------
-    src_dir: :obj:`str`
-        The source directory.
-
-    ext: :obj:`str`
-        The extension.
-
-    Returns
-    -------
-    list[str]
-        List of contents with the pattern specified by ``pattern``.
-    """
-    return glob.glob(os.path.join(src_dir, f"*{pattern}"))
-
-
-def get_nifti_header(nifti_file_or_img):
-    """
-    Get header from a NIfTI image.
-
-    Parameters
-    ----------
-    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
-        Path to the NIfTI file or a NIfTI image.
-
-    Returns
-    -------
-    nib.nifti1.Nifti1Image
-        The header from a NIfTI image.
-    """
-    return load_nifti(nifti_file_or_img).header
-
-
-def get_nifti_affine(nifti_file_or_img):
-    """
-    Get the affine matrix from a NIfTI image.
-
-    Parameters
-    ----------
-    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
-        Path to the NIfTI file or a NIfTI image.
-
-    Returns
-    -------
-    nib.nifti1.Nifti1Image
-        The header from a NIfTI image.
-    """
-    return load_nifti(nifti_file_or_img).affine
-
+import pandas as pd
 
-def _copy_file(src_file: str, dst_file: str, remove_src_file: bool) -> None:
-    """
-    Copy a file and optionally remove the source file.
-
-    Parameters
-    ----------
-    src_file: :obj:`str`
-        The source file to be copied
-
-    dst_file: :obj:`str`
-        The new destination file.
-
-    remove_src_file: :obj:`bool`
-        Delete the source file if True.
-
-    Returns
-    -------
-    None
-    """
-    shutil.copy(src_file, dst_file)
-
-    if remove_src_file:
-        os.remove(src_file)
+from nifti2bids.io import _copy_file, glob_contents
 
 
 def create_bids_file(
@@ -285,3 +155,36 @@ def save_dataset_description(dataset_description: dict[str, str], dst_dir: str)
         os.path.join(dst_dir, "dataset_description.json"), "w", encoding="utf-8"
     ) as f:
         json.dump(dataset_description, f)
+
+
+def create_participant_tsv(
+    bids_dir: str, save_df: bool = False, return_df: bool = True
+) -> pd.DataFrame | None:
+    """
+    Creates a basic participant dataframe for the "participants.tsv" file.
+
+    Parameters
+    ----------
+    bids_dir: :obj:`str`
+        The root of BIDS compliant directory.
+
+    save_df: :obj:`bool`, bool=False
+        Save the dataframe to the root of the BIDS compliant directory.
+
+    return_df: :obj:`str`
+        Whether or not to return the dataframe.
+
+    Returns
+    -------
+    pd.DataFrame or None
+        The dataframe if ``return_df`` is True.
+    """
+    participants = [
+        os.path.basename(folder) for folder in glob_contents(bids_dir, "*sub-*")
+    ]
+    df = pd.DataFrame({"participant_id": participants})
+
+    if save_df:
+        df.to_csv(os.path.join(bids_dir, "participants.tsv"), sep="\t", index=None)
+
+    return df if return_df else None

nifti2bids-0.1.0/nifti2bids/io.py

@@ -0,0 +1,135 @@
+"""Module for input/output operations."""
+
+import glob, os, shutil
+
+import nibabel as nib
+
+
+def load_nifti(
+    nifti_file_or_img: str | nib.nifti1.Nifti1Image,
+) -> nib.nifti1.Nifti1Image:
+    """
+    Loads a NIfTI image.
+
+    Loads NIfTI image when not a ``Nifti1Image`` object or
+    returns the image if already loaded in.
+
+    Parameters
+    ----------
+    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
+        Path to the NIfTI file or a NIfTI image.
+
+    Returns
+    -------
+    nib.nifti1.Nifti1Image
+        The loaded in NIfTI image.
+    """
+    nifti_img = (
+        nifti_file_or_img
+        if isinstance(nifti_file_or_img, nib.nifti1.Nifti1Image)
+        else nib.load(nifti_file_or_img)
+    )
+
+    return nifti_img
+
+
+def compress_image(nifti_file: str, remove_src_file: bool = False) -> None:
+    """
+    Compresses a ".nii" image to a ".nii.gz" image.
+
+    Parameters
+    ----------
+    nifti_file: :obj:`str`
+        Path to the NIfTI image.
+
+    remove_src_file: :obj:`bool`
+        Deletes the original source image file.
+
+    Returns
+    -------
+    None
+    """
+    img = nib.load(nifti_file)
+    nib.save(img, nifti_file.replace(".nii", ".nii.gz"))
+
+    if remove_src_file:
+        os.remove(nifti_file)
+
+
+def glob_contents(src_dir: str, pattern: str) -> list[str]:
+    """
+    Use glob to get contents with specific patterns.
+
+    Parameters
+    ----------
+    src_dir: :obj:`str`
+        The source directory.
+
+    ext: :obj:`str`
+        The extension.
+
+    Returns
+    -------
+    list[str]
+        List of contents with the pattern specified by ``pattern``.
+    """
+    return glob.glob(os.path.join(src_dir, f"*{pattern}"))
+
+
+def get_nifti_header(nifti_file_or_img):
+    """
+    Get header from a NIfTI image.
+
+    Parameters
+    ----------
+    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
+        Path to the NIfTI file or a NIfTI image.
+
+    Returns
+    -------
+    nib.nifti1.Nifti1Image
+        The header from a NIfTI image.
+    """
+    return load_nifti(nifti_file_or_img).header
+
+
+def get_nifti_affine(nifti_file_or_img):
+    """
+    Get the affine matrix from a NIfTI image.
+
+    Parameters
+    ----------
+    nifti_file_or_img: :obj:`str` or :obj:`Nifti1Image`
+        Path to the NIfTI file or a NIfTI image.
+
+    Returns
+    -------
+    nib.nifti1.Nifti1Image
+        The header from a NIfTI image.
+    """
+    return load_nifti(nifti_file_or_img).affine
+
+
+def _copy_file(src_file: str, dst_file: str, remove_src_file: bool) -> None:
+    """
+    Copy a file and optionally remove the source file.
+
+    Parameters
+    ----------
+    src_file: :obj:`str`
+        The source file to be copied
+
+    dst_file: :obj:`str`
+        The new destination file.
+
+    remove_src_file: :obj:`bool`
+        Delete the source file if True.
+
+    Returns
+    -------
+    None
+    """
+    shutil.copy(src_file, dst_file)
+
+    if remove_src_file:
+        os.remove(src_file)

nifti2bids-0.0.9/nifti2bids/utils.py → nifti2bids-0.1.0/nifti2bids/metadata.py

@@ -3,12 +3,12 @@
 import datetime, os, re
 from typing import Any, Literal, Optional
 
-import nibabel as nib, numpy as np, pandas as pd
+import nibabel as nib, numpy as np
 
 from ._exceptions import SliceAxisError, DataDimensionError
 from ._decorators import check_all_none
-from .io import load_nifti, get_nifti_header, glob_contents
-from .logger import setup_logger
+from .io import load_nifti, get_nifti_header
+from .logging import setup_logger
 
 LGR = setup_logger(__name__)
 
@@ -418,7 +418,7 @@ def is_valid_date(date_str: str, date_fmt: str) -> bool:
 
     Example
     -------
-    >>> from nifti2bids.utils import is_valid_date
+    >>> from nifti2bids.metadata import is_valid_date
     >>> is_valid_date("241010", "%y%m%d")
         True
     """
@@ -451,7 +451,7 @@ def get_date_from_filename(filename: str, date_fmt: str) -> str | None:
 
     Example
     -------
-    >>> from nifti2bids.utils import get_date_from_filename
+    >>> from nifti2bids.metadata import get_date_from_filename
     >>> get_date_from_filename("101_240820_mprage_32chan.nii", "%y%m%d")
         "240820"
     """
@@ -469,22 +469,6 @@ def get_date_from_filename(filename: str, date_fmt: str) -> str | None:
     return date_str
 
 
-def create_participant_tsv(bids_dir: str) -> None:
-    """
-    Creates a participant TSV file.
-
-    Parameters
-    ----------
-    bids_dir: :obj:`str`
-        The BIDS compliant directory.
-    """
-    participants = [
-        os.path.basename(folder) for folder in glob_contents(bids_dir, "*sub-*")
-    ]
-    df = pd.DataFrame({"participant_id": participants})
-    df.to_csv(os.path.join(bids_dir, "participants.tsv"), sep="\t", index=None)
-
-
 def get_entity_value(filename: str, entity: str) -> str | None:
     """
     Gets entity value of a BIDS compliant filename.
@@ -504,7 +488,7 @@ def get_entity_value(filename: str, entity: str) -> str | None:
 
     Example
     -------
-    >>> from nifti2bids.utils import get_entity_value
+    >>> from nifti2bids.metadata import get_entity_value
     >>> get_entity_value("sub-01_task-flanker_bold.nii.gz", "task")
         "flanker"
     """
@@ -536,7 +520,7 @@ def infer_task_from_image(
     Example
     -------
     >>> from nifti2bids.io import simulate_nifti_image
-    >>> from nifti2bids.utils import infer_task_from_image
+    >>> from nifti2bids.metadata import infer_task_from_image
     >>> img = simulate_nifti_image((100, 100, 100, 260))
     >>> volume_to_task_map = {300: "flanker", 260: "nback"}
     >>> infer_task_from_image(img, volume_to_task_map)

{nifti2bids-0.0.9 → nifti2bids-0.1.0}/nifti2bids.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nifti2bids
-Version: 0.0.9
+Version: 0.1.0
 Summary: Post-hoc BIDS conversion toolkit for NIfTI datasets without original DICOMs.
 Author-email: Donisha Smith <dsmit420@jhu.edu>
 License-Expression: MIT
@@ -45,7 +45,7 @@ Dynamic: license-file
 [![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-py/badge/?version=latest)](http://nifti2bids.readthedocs.io/en/latest/?badge=latest)
+[![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.

{nifti2bids-0.0.9 → nifti2bids-0.1.0}/nifti2bids.egg-info/SOURCES.txt

@@ -5,17 +5,19 @@ nifti2bids/__init__.py
 nifti2bids/_decorators.py
 nifti2bids/_exceptions.py
 nifti2bids/_helpers.py
+nifti2bids/bids.py
 nifti2bids/io.py
-nifti2bids/logger.py
+nifti2bids/logging.py
+nifti2bids/metadata.py
 nifti2bids/simulate.py
-nifti2bids/utils.py
 nifti2bids.egg-info/PKG-INFO
 nifti2bids.egg-info/SOURCES.txt
 nifti2bids.egg-info/dependency_links.txt
 nifti2bids.egg-info/requires.txt
 nifti2bids.egg-info/top_level.txt
+tests/test_bids.py
 tests/test_decorators.py
 tests/test_io.py
-tests/test_logger.py
-tests/test_simulate.py
-tests/test_utils.py
+tests/test_logging.py
+tests/test_metadata.py
+tests/test_simulate.py

nifti2bids-0.1.0/tests/test_bids.py

@@ -0,0 +1,70 @@
+import glob, os
+
+import pandas as pd, pytest
+
+from nifti2bids.bids import (
+    create_bids_file,
+    create_participant_tsv,
+    create_dataset_description,
+    save_dataset_description,
+)
+
+
+@pytest.mark.parametrize("dst_dir, remove_src_file", ([None, True], [True, False]))
+def test_create_bids_file(nifti_img_and_path, tmp_dir, dst_dir, remove_src_file):
+    """Test for ``create_bids_file``."""
+    _, img_path = nifti_img_and_path
+    dst_dir = None if not dst_dir else os.path.join(tmp_dir.name, "test")
+    if dst_dir:
+        os.makedirs(dst_dir)
+
+    bids_filename = create_bids_file(
+        img_path,
+        subj_id="01",
+        desc="bold",
+        remove_src_file=remove_src_file,
+        dst_dir=dst_dir,
+        return_bids_filename=True,
+    )
+    assert bids_filename
+    assert os.path.basename(bids_filename) == "sub-01_bold.nii"
+
+    if dst_dir:
+        dst_file = glob.glob(os.path.join(dst_dir, "*nii"))[0]
+        assert os.path.basename(dst_file) == "sub-01_bold.nii"
+
+        src_file = glob.glob(os.path.join(os.path.dirname(img_path), "*.nii"))[0]
+        assert os.path.basename(src_file) == "img.nii"
+    else:
+        files = glob.glob(os.path.join(os.path.dirname(img_path), "*.nii"))
+        assert len(files) == 1
+        assert os.path.basename(files[0]) == "sub-01_bold.nii"
+
+
+def test_create_dataset_description():
+    """Test for ``create_dataset_description``."""
+    dataset_desc = create_dataset_description(dataset_name="test", bids_version="1.2.0")
+    assert dataset_desc.get("Name") == "test"
+    assert dataset_desc.get("BIDSVersion") == "1.2.0"
+
+
+def test_save_dataset_description(tmp_dir):
+    """Test for ``save_dataset_description``."""
+    dataset_desc = create_dataset_description(dataset_name="test", bids_version="1.2.0")
+    save_dataset_description(dataset_desc, tmp_dir.name)
+    files = glob.glob(os.path.join(tmp_dir.name, "*.json"))
+    assert len(files) == 1
+    assert os.path.basename(files[0]) == "dataset_description.json"
+
+
+def test_create_participant_tsv(tmp_dir):
+    """Test for ``create_participant_tsv``."""
+    os.makedirs(os.path.join(tmp_dir.name, "sub-01"))
+    df = create_participant_tsv(tmp_dir.name, save_df=True, return_df=True)
+    assert isinstance(df, pd.DataFrame)
+
+    filename = os.path.join(tmp_dir.name, "participants.tsv")
+    assert os.path.isfile(filename)
+
+    df = pd.read_csv(filename, sep="\t")
+    assert df["participant_id"].values[0] == "sub-01"

nifti2bids-0.1.0/tests/test_io.py

@@ -0,0 +1,48 @@
+import glob, os
+import nibabel as nib, pandas as pd, pytest
+import nifti2bids.io as bids_io
+
+
+def test_compress_image(nifti_img_and_path):
+    """Test for ``compress_image``."""
+    _, img_path = nifti_img_and_path
+
+    files = glob.glob(os.path.join(os.path.dirname(img_path), "*"))
+    assert len(files) == 1
+
+    file = files[0]
+    assert file.endswith(".nii")
+
+    bids_io.compress_image(img_path, remove_src_file=True)
+
+    files = glob.glob(os.path.join(os.path.dirname(img_path), "*"))
+    assert len(files) == 1
+
+    file = files[0]
+    assert file.endswith(".nii.gz")
+
+
+def test_load_nifti(nifti_img_and_path):
+    """Test for ``load_nifti``."""
+    img, img_path = nifti_img_and_path
+    assert isinstance(bids_io.load_nifti(img), nib.nifti1.Nifti1Image)
+    assert isinstance(bids_io.load_nifti(img_path), nib.nifti1.Nifti1Image)
+
+
+def test_glob_contents(nifti_img_and_path):
+    """Test for ``glob_contents``"""
+    _, img_path = nifti_img_and_path
+    files = bids_io.glob_contents(os.path.dirname(img_path), pattern=".nii")
+    assert len(files) == 1
+
+
+def test_get_nifti_header(nifti_img_and_path):
+    """Test for ``get_nifti_header``."""
+    img, _ = nifti_img_and_path
+    assert isinstance(bids_io.get_nifti_header(img), nib.nifti1.Nifti1Header)
+
+
+def test_get_nifti_affine(nifti_img_and_path):
+    """Test for ``get_nifti_affine``."""
+    img, _ = nifti_img_and_path
+    assert bids_io.get_nifti_affine(img).shape == (4, 4)

nifti2bids-0.0.9/tests/test_logger.py → nifti2bids-0.1.0/tests/test_logging.py

@@ -2,7 +2,7 @@ import logging
 
 import rich
 
-from nifti2bids.logger import setup_logger, _add_default_handler
+from nifti2bids.logging import setup_logger, _add_default_handler
 
 
 def test_setup_logger(caplog):

nifti2bids-0.0.9/tests/test_utils.py → nifti2bids-0.1.0/tests/test_metadata.py

@@ -1,6 +1,5 @@
-import os
-import nibabel as nib, numpy as np, pandas as pd, pytest
-import nifti2bids.utils as bids_utils
+import nibabel as nib, numpy as np, pytest
+import nifti2bids.metadata as bids_meta
 
 
 @pytest.mark.parametrize("return_header", (False, True))
@@ -10,14 +9,14 @@ def test_get_hdr_metadata(nifti_img_and_path, return_header):
     img.header["slice_end"] = 100
 
     if return_header:
-        slice_end, hdr = bids_utils.get_hdr_metadata(
+        slice_end, hdr = bids_meta.get_hdr_metadata(
             metadata_name="slice_end",
             nifti_file_or_img=img,
             return_header=return_header,
         )
         assert isinstance(hdr, nib.nifti1.Nifti1Header)
     else:
-        slice_end = bids_utils.get_hdr_metadata(
+        slice_end = bids_meta.get_hdr_metadata(
             metadata_name="slice_end",
             nifti_file_or_img=img,
             return_header=return_header,
@@ -31,23 +30,23 @@ def test_determine_slice_axis(nifti_img_and_path):
     img, _ = nifti_img_and_path
 
     with pytest.raises(ValueError):
-        bids_utils.determine_slice_axis(img)
+        bids_meta.determine_slice_axis(img)
 
     # Subtract one to convert to index
     img.header["slice_end"] = img.get_fdata().shape[2] - 1
-    assert bids_utils.determine_slice_axis(img) == 2
+    assert bids_meta.determine_slice_axis(img) == 2
 
 
 def test_get_n_volumes(nifti_img_and_path):
     """Test for ``get_n_volumes``."""
     img, _ = nifti_img_and_path
-    assert bids_utils.get_n_volumes(img) == 5
+    assert bids_meta.get_n_volumes(img) == 5
 
     from nifti2bids.simulate import simulate_nifti_image
     from nifti2bids._exceptions import DataDimensionError
 
     with pytest.raises(DataDimensionError):
-        bids_utils.get_n_volumes(simulate_nifti_image((10, 10, 10)))
+        bids_meta.get_n_volumes(simulate_nifti_image((10, 10, 10)))
 
 
 def test_get_n_slices(nifti_img_and_path):
@@ -59,23 +58,23 @@ def test_get_n_slices(nifti_img_and_path):
     img.header["slice_end"] = img.get_fdata().shape[2] - 1
 
     with pytest.raises(SliceAxisError):
-        bids_utils.get_n_slices(img, slice_axis="x")
+        bids_meta.get_n_slices(img, slice_axis="x")
 
-    assert bids_utils.get_n_slices(img, slice_axis="z") == img.header["slice_end"] + 1
-    assert bids_utils.get_n_slices(img) == img.header["slice_end"] + 1
+    assert bids_meta.get_n_slices(img, slice_axis="z") == img.header["slice_end"] + 1
+    assert bids_meta.get_n_slices(img) == img.header["slice_end"] + 1
 
 
 def test_get_tr(nifti_img_and_path):
     """Test for ``get_tr``."""
     img, _ = nifti_img_and_path
     img.header["pixdim"][4] = 2.3
-    assert bids_utils.get_tr(img) == 2.3
-    assert not isinstance(bids_utils.get_tr(img), np.floating)
-    assert not isinstance(bids_utils.get_tr(img), np.integer)
+    assert bids_meta.get_tr(img) == 2.3
+    assert not isinstance(bids_meta.get_tr(img), np.floating)
+    assert not isinstance(bids_meta.get_tr(img), np.integer)
 
     img.header["pixdim"][4] = 0
     with pytest.raises(ValueError):
-        bids_utils.get_tr(img)
+        bids_meta.get_tr(img)
 
 
 @pytest.mark.parametrize("slice_acquisition_method", ("sequential", "interleaved"))
@@ -88,21 +87,21 @@ def test_create_slice_timing(slice_acquisition_method):
     img.header["slice_end"] = 3
 
     if slice_acquisition_method == "sequential":
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=True,
         )
         assert slice_timing_dict == [0, 0.5, 1, 1.5]
 
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=False,
         )
         assert slice_timing_dict == [1.5, 1, 0.5, 0]
     else:
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=True,
@@ -110,7 +109,7 @@ def test_create_slice_timing(slice_acquisition_method):
         )
         assert slice_timing_dict == [0, 1, 0.5, 1.5]
 
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=False,
@@ -118,7 +117,7 @@ def test_create_slice_timing(slice_acquisition_method):
         )
         assert slice_timing_dict == [1.5, 0.5, 1, 0]
 
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=True,
@@ -126,7 +125,7 @@ def test_create_slice_timing(slice_acquisition_method):
         )
         assert slice_timing_dict == [1, 0, 1.5, 0.5]
 
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=False,
@@ -135,7 +134,7 @@ def test_create_slice_timing(slice_acquisition_method):
         assert slice_timing_dict == [0.5, 1.5, 0, 1]
 
     with pytest.raises(ValueError):
-        slice_timing_dict = bids_utils.create_slice_timing(
+        slice_timing_dict = bids_meta.create_slice_timing(
             nifti_file_or_img=img,
             slice_acquisition_method=slice_acquisition_method,
             ascending=False,
@@ -148,49 +147,38 @@ def test_is_3d_img(nifti_img_and_path):
     from nifti2bids.simulate import simulate_nifti_image
 
     img = simulate_nifti_image((10, 10, 10))
-    assert bids_utils.is_3d_img(img)
+    assert bids_meta.is_3d_img(img)
 
     img, _ = nifti_img_and_path
-    assert not bids_utils.is_3d_img(img)
+    assert not bids_meta.is_3d_img(img)
 
 
 def test_get_scanner_info(nifti_img_and_path):
     """Test for ``get_scanner_info``."""
     img, _ = nifti_img_and_path
     with pytest.raises(ValueError):
-        bids_utils.get_scanner_info(img)
+        bids_meta.get_scanner_info(img)
 
     img.header["descrip"] = "Philips Ingenia Elition X 5.7.1"
-    manufacturer_name, model_name = bids_utils.get_scanner_info(img)
+    manufacturer_name, model_name = bids_meta.get_scanner_info(img)
     assert manufacturer_name == "Philips"
     assert model_name == "Ingenia Elition X 5.7.1"
 
 
 def test_get_date_from_filename():
     """Test for ``get_date_from_filename``."""
-    date = bids_utils.get_date_from_filename("101_240820_mprage_32chan.nii", "%y%m%d")
+    date = bids_meta.get_date_from_filename("101_240820_mprage_32chan.nii", "%y%m%d")
     assert date == "240820"
 
-    date = bids_utils.get_date_from_filename("101_mprage_32chan.nii", "%y%m%d")
+    date = bids_meta.get_date_from_filename("101_mprage_32chan.nii", "%y%m%d")
     assert not date
 
 
-def test_create_participant_tsv(tmp_dir):
-    """Test for ``get_date_from_filename``."""
-    os.makedirs(os.path.join(tmp_dir.name, "sub-01"))
-    bids_utils.create_participant_tsv(tmp_dir.name)
-    filename = os.path.join(tmp_dir.name, "participants.tsv")
-    assert os.path.isfile(filename)
-
-    df = pd.read_csv(filename, sep="\t")
-    assert df["participant_id"].values[0] == "sub-01"
-
-
 def test_get_entity_value():
     """Test for ``get_entity_value``."""
     filename = "sub-01_task-test_bold.nii.gz"
-    assert bids_utils.get_entity_value(filename, "task") == "test"
-    assert not bids_utils.get_entity_value(filename, "ses")
+    assert bids_meta.get_entity_value(filename, "task") == "test"
+    assert not bids_meta.get_entity_value(filename, "ses")
 
 
 def test_infer_task_from_image(nifti_img_and_path):
@@ -199,4 +187,4 @@ def test_infer_task_from_image(nifti_img_and_path):
 
     volume_to_task_map = {5: "flanker", 10: "nback"}
 
-    assert bids_utils.infer_task_from_image(img, volume_to_task_map) == "flanker"
+    assert bids_meta.infer_task_from_image(img, volume_to_task_map) == "flanker"

nifti2bids-0.0.9/nifti2bids/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.0.9"

nifti2bids-0.0.9/tests/test_io.py

@@ -1,99 +0,0 @@
-import glob, os
-import nibabel as nib, pytest
-import nifti2bids.io as bids_io
-
-
-def test_compress_image(nifti_img_and_path):
-    """Test for ``compress_image``."""
-    _, img_path = nifti_img_and_path
-
-    files = glob.glob(os.path.join(os.path.dirname(img_path), "*"))
-    assert len(files) == 1
-
-    file = files[0]
-    assert file.endswith(".nii")
-
-    bids_io.compress_image(img_path, remove_src_file=True)
-
-    files = glob.glob(os.path.join(os.path.dirname(img_path), "*"))
-    assert len(files) == 1
-
-    file = files[0]
-    assert file.endswith(".nii.gz")
-
-
-def test_load_nifti(nifti_img_and_path):
-    """Test for ``load_nifti``."""
-    img, img_path = nifti_img_and_path
-    assert isinstance(bids_io.load_nifti(img), nib.nifti1.Nifti1Image)
-    assert isinstance(bids_io.load_nifti(img_path), nib.nifti1.Nifti1Image)
-
-
-def test_glob_contents(nifti_img_and_path):
-    """Test for ``glob_contents``"""
-    _, img_path = nifti_img_and_path
-    files = bids_io.glob_contents(os.path.dirname(img_path), pattern=".nii")
-    assert len(files) == 1
-
-
-def test_get_nifti_header(nifti_img_and_path):
-    """Test for ``get_nifti_header``."""
-    img, _ = nifti_img_and_path
-    assert isinstance(bids_io.get_nifti_header(img), nib.nifti1.Nifti1Header)
-
-
-def test_get_nifti_affine(nifti_img_and_path):
-    """Test for ``get_nifti_affine``."""
-    img, _ = nifti_img_and_path
-    assert bids_io.get_nifti_affine(img).shape == (4, 4)
-
-
-@pytest.mark.parametrize("dst_dir, remove_src_file", ([None, True], [True, False]))
-def test_create_bids_file(nifti_img_and_path, tmp_dir, dst_dir, remove_src_file):
-    """Test for ``create_bids_file``."""
-    _, img_path = nifti_img_and_path
-    dst_dir = None if not dst_dir else os.path.join(tmp_dir.name, "test")
-    if dst_dir:
-        os.makedirs(dst_dir)
-
-    bids_filename = bids_io.create_bids_file(
-        img_path,
-        subj_id="01",
-        desc="bold",
-        remove_src_file=remove_src_file,
-        dst_dir=dst_dir,
-        return_bids_filename=True,
-    )
-    assert bids_filename
-    assert os.path.basename(bids_filename) == "sub-01_bold.nii"
-
-    if dst_dir:
-        dst_file = glob.glob(os.path.join(dst_dir, "*nii"))[0]
-        assert os.path.basename(dst_file) == "sub-01_bold.nii"
-
-        src_file = glob.glob(os.path.join(os.path.dirname(img_path), "*.nii"))[0]
-        assert os.path.basename(src_file) == "img.nii"
-    else:
-        files = glob.glob(os.path.join(os.path.dirname(img_path), "*.nii"))
-        assert len(files) == 1
-        assert os.path.basename(files[0]) == "sub-01_bold.nii"
-
-
-def test_create_dataset_description():
-    """Test for ``create_dataset_description``."""
-    dataset_desc = bids_io.create_dataset_description(
-        dataset_name="test", bids_version="1.2.0"
-    )
-    assert dataset_desc.get("Name") == "test"
-    assert dataset_desc.get("BIDSVersion") == "1.2.0"
-
-
-def test_save_dataset_description(tmp_dir):
-    """Test for ``save_dataset_description``."""
-    dataset_desc = bids_io.create_dataset_description(
-        dataset_name="test", bids_version="1.2.0"
-    )
-    bids_io.save_dataset_description(dataset_desc, tmp_dir.name)
-    files = glob.glob(os.path.join(tmp_dir.name, "*.json"))
-    assert len(files) == 1
-    assert os.path.basename(files[0]) == "dataset_description.json"