nifti-finder 0.1.0

nifti-finder - Navigate neuroimaging datasets across multiple data structures

nifti-finder

Navigate neuroimaging datasets (and more) with simple file explorers and filters. Optimized for NIfTI workflows but flexible enough for any file type by adjusting filename patterns.

• Python: >= 3.10
• License: Apache 2.0

Installation

pip install nifti-finder
# or from source
pip install -e .

Example usage

Explore NIfTI files with nested structure

from nifti_finder.explorers import NiftiExplorer

# Default: finds all .nii and .nii.gz files
explorer = NiftiExplorer()

for path in explorer.scan("/path/to/dataset"):
    print(path)

Track subject-level progress in BIDS-style datasets

from nifti_finder.explorers import NiftiExplorer
from nifti_finder.filters import ExcludeFileSuffix

from your_package import preprocess

explorer = NiftiExplorer(
    stage_1_pattern="sub-*",
    stage_2_pattern="**/anat/*T1w.nii*",
)

for path in explorer.scan("/path/to/dataset", progress=True, desc="Subjects"):
    preprocess(path)

Output:

Subjects:  50%|███████████████████▌               | 30/60 [00:15<00:15,  2.00 it/s]

Require a segmentation mask in a parallel labels/ tree

from nifti_finder.explorers import NiftiExplorer
from nifti_finder.filters import IncludeIfFileExists

from your_package import preprocess

explorer = NiftiExplorer(
    stage_1_pattern="sub-*",
    stage_2_pattern="**/anat/*T1w.nii*",
    filters=[
        IncludeIfFileExists(
            filename_pattern="*seg*",
            search_in="/labels",
            mirror_relative_to="/path/to/dataset",
        )
    ],
)

for path in explorer.scan("/path/to/dataset"):
    preprocess(path)

Extra functionality

Use with non-NIfTI files (e.g., JSON)

from nifti_finder import NiftiExplorer, AllPurposeFileExplorer

explorer = NiftiExplorer(stage_1_pattern="sub-*", stage_2_pattern="**/*.json")
for p in explorer.scan("/path/to/bids", progress=True, desc="Subjects"):
    print(p)

Explorers support multiple patterns and filters, but will traverse once per pattern.

General-purpose exploration

If you don’t want to assume any nested (subject/... or dataset/subject/...) hierarchy, use AllPurposeFileExplorer for flexible scanning.

from nifti_finder.explorers import AllPurposeFileExplorer

explorer = AllPurposeFileExplorer(pattern="*.json")

for path in explorer.scan("/path/to/dataset"):
    print(path)

Materializing Results

Both NiftiExplorer and AllPurposeExplorer provide convenience methods to turn the streaming output of scan() into concrete Python data structures.

This is useful when you want:

• A list of paths (with optional sorting, deduplication, or limiting)
• A single path (first match)
• A quick boolean check
• A count
• Iteration in batches

from nifti_finder.explorers import NiftiExplorer

explorer = NiftiExplorer(stage_1_pattern="sub-*", stage_2_pattern="**/anat/*T1w.nii*")
paths = explorer.list("/path/to/dataset", sort=True, unique=True)

Filtering

Both NiftiExplorer and AllPurposeExplorer allow include/exclude filters to refine results.

from nifti_finder.explorers import AllPurposeFileExplorer
from nifti_finder.filters import (
    IncludeExtension, ExcludeDirPrefix, IncludeIfFileExists
)

explorer = AllPurposeFileExplorer(
    pattern="**/*.nii*",
    filters=[
        ExcludeFileSuffix("preprocessed"),              # drop already preprocessed files
        ExcludeDirPrefix("bad"),                        # drop 'bad' files
        IncludeIfFileExists(filename_pattern="*mask*"), # keep if a brain mask exists in same directory
    ],
    logic="AND",                                        # combination logic
)

for path in explorer.scan("/path/to/dataset"):
    print(path)

Filters can by dynamically adjusted.

explorer.add_filters(ExcludeFileSuffix("mask"))
explorer.remove_filters(ExcludeFileSuffix("mask"))
explorer.clear_filters()

Filters can be composed together to get their own combination logic.

from nifti_finder.filters import ComposeFilter, ExcludeFilePrefix

suffix_filter = ComposeFilter(
    filters=[ExcludeFileSuffix("bet"), ExcludeFileSuffix("mask")],
    logic="OR"
)
prefix_filter = ComposeFilter(
    filters=[ExcludeFileSuffix("pet"), ExcludeFileSuffix("dwi")],
    logic="OR"
)
filename_filter = ComposeFilter(
    filters=[suffix_filter, prefix_filter],
    logic="AND"
)
explorer.add_filters(filename_filter)

API Overview

• Explorers
  • BasicFileExplorer - pattern-only scanning (any structure).
  • TwoStageFileExplorer - pattern-only scanning with progress tracking (nested structure).
  • AllPurposeFileExplorer - pattern scanning + filters (any dataset structure)
  • NiftiExplorer - pattern scanning (preconfigured for NIfTI) + filters + progress tracking (nested structure)
• Filters (selected)
  • Include/Exclude: Extension, FilePrefix, FileSuffix, FileRegex, DirectoryPrefix/Suffix/Regex, IfFileExists

Development

# Setup
pip install -e .[test]

# Run tests
pytest -q

Why nifti-finder?

• Simple patterns for fast discovery
• Composable filters for precise control
• Flexible traversal with progress tracking for common neuroimaging layouts
• Works for any file types (not just NIfTI) by changing patterns