nltools 0.6.0.dev0__py3-none-any.whl

nltools/__init__.py

@@ -0,0 +1,55 @@
+"""nltools: a Python toolbox for analyzing neuroimaging data.
+
+Focused on multivariate analyses and built on top of nilearn and scikit-learn,
+nltools provides high-level data classes — `BrainData`, `Adjacency`, and
+`DesignMatrix` — that wrap common neuroimaging workflows, alongside a
+functional core of statistics and algorithms (`nltools.algorithms`) that the
+data classes delegate to.
+"""
+
+__all__ = [
+    "Adjacency",
+    "BrainData",
+    "DesignMatrix",
+    "Roc",
+    "SimulateGrid",
+    "Simulator",
+    "__version__",
+    "concatenate",
+    "get_brainspace",
+    "reset_brainspace",
+    "set_brainspace",
+    "with_brainspace",
+]
+
+from .data import (
+    BrainData,
+    Adjacency,
+    DesignMatrix,
+    Simulator,
+    SimulateGrid,
+    Roc,
+)
+from .data.combine import concatenate
+from .templates import (
+    get_brainspace,
+    set_brainspace,
+    reset_brainspace,
+    with_brainspace,
+)
+from .version import __version__
+
+# Bind the submodules users reach through attribute access (e.g.
+# nltools.datasets, nltools.cross_validation) so no prior explicit
+# `import nltools.datasets` is needed. They are not part of the advertised
+# surface; the names in __all__ above are.
+from . import (  # noqa: F401
+    algorithms,
+    cross_validation,
+    data,
+    datasets,
+    io,
+    mask,
+    plotting,
+    utils,
+)

nltools/algorithms/__init__.py

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+"""nltools.algorithms — the functional core of nltools.
+
+Every user-facing statistical function and algorithm is importable flat from
+here (`from nltools.algorithms import fdr, zscore, isc`), organized into
+focused submodules underneath:
+
+- **corrections**: multiple-comparison corrections (FDR, Holm-Bonferroni, thresholding)
+- **outliers**: outlier detection, winsorizing, z-scoring
+- **signal**: temporal signal processing (resampling, filtering, basis functions)
+- **similarity**: similarity metrics and Fisher transforms
+- **regression**: standalone OLS regression on numpy arrays
+- **alignment**: the `align`/`procrustes` entry points and the shared-response
+  estimators behind them
+- **inference**: permutation tests, bootstrap resampling, and intersubject
+  statistics (ISC/ISFC/ISPS), parallelized across joblib workers
+- **backends**: device selection and memory budgeting for the ridge paths;
+  `check_gpu_available` is how you ask before requesting `device='gpu'`
+
+Ridge regression lives in `nltools.models.Ridge`, which delegates its numerics
+to the Himalaya library and is reached through `BrainData.fit(model='ridge')`.
+"""
+
+__all__ = [
+    "align",
+    "align_states",
+    "calc_bpm",
+    "check_gpu_available",
+    "circle_shift",
+    "compute_searchlight_neighborhoods",
+    "compute_similarity",
+    "correlation_permutation_test",
+    "distance_correlation",
+    "downsample",
+    "fdr",
+    "find_spikes",
+    "fisher_r_to_z",
+    "fisher_z_to_r",
+    "holm_bonf",
+    "isc",
+    "isc_group",
+    "isfc",
+    "isps",
+    "make_cosine_basis",
+    "matrix_permutation_test",
+    "multi_threshold",
+    "one_sample_permutation_test",
+    "phase_randomize",
+    "procrustes",
+    "procrustes_distance",
+    "regress",
+    "threshold",
+    "transform_pairwise",
+    "trim",
+    "two_sample_permutation_test",
+    "upsample",
+    "winsorize",
+    "zscore",
+]
+
+from .alignment import (
+    align,
+    align_states,
+    procrustes,
+    procrustes_distance,
+)
+from .backends import check_gpu_available
+from .corrections import fdr, holm_bonf, multi_threshold, threshold
+from .neighborhoods import compute_searchlight_neighborhoods
+from .inference import (
+    circle_shift,
+    correlation_permutation_test,
+    distance_correlation,
+    matrix_permutation_test,
+    one_sample_permutation_test,
+    phase_randomize,
+    two_sample_permutation_test,
+)
+
+# Imported from the submodule, not the `inference` package namespace: exporting
+# the `isc` *function* there would shadow the `inference.isc` engine *module*.
+from .inference.intersubject import isc, isc_group, isfc, isps
+from .outliers import find_spikes, trim, winsorize, zscore
+from .regression import regress
+from .signal import calc_bpm, downsample, make_cosine_basis, upsample
+from .similarity import (
+    compute_similarity,
+    fisher_r_to_z,
+    fisher_z_to_r,
+    transform_pairwise,
+)

nltools/algorithms/alignment/__init__.py

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+"""Multi-subject functional alignment algorithms.
+
+Algorithms for aligning functional data across subjects:
+
+- **SRM** / **DetSRM**: Shared Response Model (Chen et al. 2015)
+- **align**: whole-brain alignment of a group of subjects, by SRM or by
+  Procrustes-based hyperalignment (Haxby et al. 2011)
+- **procrustes** / **procrustes_distance**: pairwise Procrustes superposition
+  and its permutation test
+- **align_states**: match two sets of state weight maps
+"""
+
+# Internal package: these imports are re-exports for the rest of nltools, not
+# an advertised surface, so there is no `__all__` to mark them as used.
+from .srm import _SRM, _DetSRM  # noqa: F401
+from .procrustes import (  # noqa: F401
+    align,
+    align_states,
+    procrustes,
+    procrustes_distance,
+)