pisces-lite 3.0.0__tar.gz

pisces_lite-3.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Arcascope Inc
+
+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.

pisces_lite-3.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pisces-lite
+Version: 3.0.0
+Summary: ML-backend-agnostic core supporting data set discovery, loading, common spectrogram/PSD-based processing, and CV scoring.
+Author-email: Arcascope Inc <support@arcascope.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Arcascope/pisces-lite
+Project-URL: Repository, https://github.com/Arcascope/pisces-lite
+Project-URL: Issues, https://github.com/Arcascope/pisces-lite/issues
+Keywords: sleep,actigraphy,accelerometer,spectrogram,wearables
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: pandas
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Provides-Extra: proc
+Requires-Dist: arcascope-senpy==4.0.3; extra == "proc"
+Provides-Extra: jax
+Requires-Dist: arcascope-senpy[jax]==4.0.3; extra == "jax"
+Dynamic: license-file
+
+# pisces-lite
+
+ML-backend-agnostic core for wearable sleep data: dataset discovery and loading,
+accelerometer-to-spectrogram processing, cross-validation splitting, and metrics
+logging. It carries no model framework, though there is a JAX-accelerated option
+for the `[jax]` extra components.
+
+## Install
+
+```bash
+pip install pisces-lite
+```
+
+Python 3.12+. To do the processing yourself rather than read a prebuilt feature
+cache, install an extra — see [Optional extras](#optional-extras). The `proc`
+and `jax` extras require a Python version the compiled backend publishes wheels
+for (currently 3.12–3.14):
+
+```bash
+pip install "pisces-lite[proc]"
+```
+
+## Getting started
+
+```python
+from pisces_lite.datasets import DataSetObject, load_subject
+
+# Discover datasets laid out as <dataset>/cleaned_<feature>/<subject>.csv
+data_sets = DataSetObject.find_data_sets("data/")
+ds = data_sets["mydata"]
+
+# Load one subject: (accelerometer, PSG) frames with standardised columns
+subject = load_subject(ds, ds.ids[0])
+```
+
+Datasets are described by an optional `data_set.json` next to the data; it sets
+per-feature timestamp units, accelerometer scaling, PSG stage mappings, CSV
+delimiters, and subject-id patterns. Non-standard layouts can ship a
+`pisces_lite_adapter.py` exposing `load_data_sets(root, **kwargs)`.
+
+Configure the processing pipeline and turn raw accelerometer into spectrograms:
+
+```python
+from pisces_lite.proc import ProcessingConfig
+
+config = ProcessingConfig.from_dict({"type": "nufft", "fs": 32.0})
+X = config.apply(accel_array)   # (T, F) or (T, F, C) with spectral_channels
+```
+
+Split subjects and score folds:
+
+```python
+from pisces_lite.cv import CVConfig, iter_folds
+from pisces_lite.metrics import MetricsConfig, MetricsLogger
+
+cv = CVConfig(mode="loso", train_sets=["mydata"], test_sets=["mydata"])
+for fold in iter_folds(cv, data_sets):
+    ...  # train on fold.train_subjects, evaluate fold.test_subjects
+```
+
+## Optional extras
+
+The base install never pulls a C++ toolchain. Add an extra only when you need
+the processing pipeline itself.
+
+| Extra | Install | What it adds | Use when |
+|---|---|---|---|
+| `proc` | `pip install "pisces-lite[proc]"` | `arcascope-senpy` (import name `senpy`; compiled pybind11 + finufft), the CPU `streaming`/`cpu` NUFFT backends | You are turning raw accelerometer data into spectrograms |
+| `jax` | `pip install "pisces-lite[jax]"` | `arcascope-senpy[jax]` and JAX, adding the `jax` NUFFT backend | You want GPU-batched spectrogram extraction |
+| `dev` | `pip install "pisces-lite[dev]"` | `pytest` | You are running the test suite |
+
+Working from a prebuilt feature cache — a training or inference host that only
+reads `cv`, `metrics`, `model_io`, and `ProcessingConfig` — needs no extra.
+`pisces_lite.proc` resolves its pipeline classes lazily, so importing a
+`ProcessingConfig` does not import `senpy`; touching a pipeline class without
+the extra raises a clear error naming the extra to install.

pisces_lite-3.0.0/README.md

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+# pisces-lite
+
+ML-backend-agnostic core for wearable sleep data: dataset discovery and loading,
+accelerometer-to-spectrogram processing, cross-validation splitting, and metrics
+logging. It carries no model framework, though there is a JAX-accelerated option
+for the `[jax]` extra components.
+
+## Install
+
+```bash
+pip install pisces-lite
+```
+
+Python 3.12+. To do the processing yourself rather than read a prebuilt feature
+cache, install an extra — see [Optional extras](#optional-extras). The `proc`
+and `jax` extras require a Python version the compiled backend publishes wheels
+for (currently 3.12–3.14):
+
+```bash
+pip install "pisces-lite[proc]"
+```
+
+## Getting started
+
+```python
+from pisces_lite.datasets import DataSetObject, load_subject
+
+# Discover datasets laid out as <dataset>/cleaned_<feature>/<subject>.csv
+data_sets = DataSetObject.find_data_sets("data/")
+ds = data_sets["mydata"]
+
+# Load one subject: (accelerometer, PSG) frames with standardised columns
+subject = load_subject(ds, ds.ids[0])
+```
+
+Datasets are described by an optional `data_set.json` next to the data; it sets
+per-feature timestamp units, accelerometer scaling, PSG stage mappings, CSV
+delimiters, and subject-id patterns. Non-standard layouts can ship a
+`pisces_lite_adapter.py` exposing `load_data_sets(root, **kwargs)`.
+
+Configure the processing pipeline and turn raw accelerometer into spectrograms:
+
+```python
+from pisces_lite.proc import ProcessingConfig
+
+config = ProcessingConfig.from_dict({"type": "nufft", "fs": 32.0})
+X = config.apply(accel_array)   # (T, F) or (T, F, C) with spectral_channels
+```
+
+Split subjects and score folds:
+
+```python
+from pisces_lite.cv import CVConfig, iter_folds
+from pisces_lite.metrics import MetricsConfig, MetricsLogger
+
+cv = CVConfig(mode="loso", train_sets=["mydata"], test_sets=["mydata"])
+for fold in iter_folds(cv, data_sets):
+    ...  # train on fold.train_subjects, evaluate fold.test_subjects
+```
+
+## Optional extras
+
+The base install never pulls a C++ toolchain. Add an extra only when you need
+the processing pipeline itself.
+
+| Extra | Install | What it adds | Use when |
+|---|---|---|---|
+| `proc` | `pip install "pisces-lite[proc]"` | `arcascope-senpy` (import name `senpy`; compiled pybind11 + finufft), the CPU `streaming`/`cpu` NUFFT backends | You are turning raw accelerometer data into spectrograms |
+| `jax` | `pip install "pisces-lite[jax]"` | `arcascope-senpy[jax]` and JAX, adding the `jax` NUFFT backend | You want GPU-batched spectrogram extraction |
+| `dev` | `pip install "pisces-lite[dev]"` | `pytest` | You are running the test suite |
+
+Working from a prebuilt feature cache — a training or inference host that only
+reads `cv`, `metrics`, `model_io`, and `ProcessingConfig` — needs no extra.
+`pisces_lite.proc` resolves its pipeline classes lazily, so importing a
+`ProcessingConfig` does not import `senpy`; touching a pipeline class without
+the extra raises a clear error naming the extra to install.

pisces_lite-3.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pisces-lite"
+version = "3.0.0"
+description = "ML-backend-agnostic core supporting data set discovery, loading, common spectrogram/PSD-based processing, and CV scoring."
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Arcascope Inc", email = "support@arcascope.com" }]
+requires-python = ">=3.12"
+keywords = ["sleep", "actigraphy", "accelerometer", "spectrogram", "wearables"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering",
+]
+
+# senpy is deliberately NOT here. It is a compiled extension (pybind11 +
+# finufft) and is only ever used by pisces_lite.proc, which turns raw
+# accelerometer data into spectrograms. A consumer working from an already
+# built feature cache -- a training or inference host -- imports cv, metrics,
+# model_io and ProcessingConfig but never calls into proc, so making it a hard
+# dependency forced a C++ toolchain into images that had nothing to compile.
+# Install "pisces-lite[proc]" to do the processing itself.
+dependencies = [
+    "matplotlib",
+    "numpy",
+    "scipy",
+    "scikit-learn",
+    "pandas",
+    "seaborn",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+dev = ["pytest"]
+# The processing pipeline: pisces_lite.proc's runtime backend.
+# The distribution is named `arcascope-senpy`; its import name is `senpy`.
+# (There is an unrelated `senpy` project on PyPI, hence the prefixed name.)
+proc = [
+    "arcascope-senpy==4.0.3",
+]
+# proc on a JAX NUFFT backend. Superset of [proc]; arcascope-senpy[jax] covers it.
+jax = [
+    "arcascope-senpy[jax]==4.0.3",
+]
+
+[project.urls]
+Homepage = "https://github.com/Arcascope/pisces-lite"
+Repository = "https://github.com/Arcascope/pisces-lite"
+Issues = "https://github.com/Arcascope/pisces-lite/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]

pisces_lite-3.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pisces_lite-3.0.0/src/pisces_lite/cv/__init__.py

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+"""Cross-validation orchestration (framework-agnostic).
+
+Two modes:
+
+- ``loso`` — leave-one-subject-out across the union of ``test_sets``.
+- ``transfer`` — train once on ``train_sets``, evaluate every subject in
+  ``test_sets`` (which must be disjoint from ``train_sets``).
+
+Both modes hold out ``validation_sets`` from training. See
+:class:`CVConfig` for the exact invariants.
+"""
+from pisces_lite.cv.config import CVConfig, CVMode
+from pisces_lite.cv.fold import Fold, SubjectRef, iter_folds
+
+__all__ = ["CVConfig", "CVMode", "Fold", "SubjectRef", "iter_folds"]

pisces_lite-3.0.0/src/pisces_lite/cv/config.py

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+"""CVConfig: cross-validation splitting configuration (no ML-framework deps)."""
+from __future__ import annotations
+
+import json
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import List, Literal, Optional
+
+
+CVMode = Literal["loso", "transfer"]
+
+
+@dataclass
+class CVConfig:
+    """Subject-splitting configuration.
+
+    Modes:
+      - ``loso`` (leave-one-subject-out): requires ``test_sets ⊆ train_sets``.
+        Iterates over every subject in the union of ``test_sets``, holding one
+        out per fold; trains on the remaining pooled train subjects (minus any
+        validation subjects). Produces N folds, N models.
+      - ``transfer``: requires ``train_sets ∩ test_sets = ∅``. Trains one
+        model on the pooled train subjects, evaluates every subject in the
+        union of ``test_sets``. Produces 1 fold, 1 model, |test| evaluations.
+
+    In both modes, ``train_sets ∩ validation_sets`` must be empty at the
+    dataset level; validation subjects are always excluded from training.
+    """
+
+    mode: CVMode
+    train_sets: List[str]
+    test_sets: List[str]
+    validation_sets: List[str] = field(default_factory=list)
+    max_folds: Optional[int] = None
+
+    @classmethod
+    def from_json(cls, path: "Path | str") -> "CVConfig":
+        with open(path) as f:
+            return cls.from_dict(json.load(f))
+
+    @classmethod
+    def from_dict(cls, d: dict) -> "CVConfig":
+        known = {f for f in cls.__dataclass_fields__}
+        return cls(**{k: v for k, v in d.items() if k in known})
+
+    def validate(self) -> None:
+        """Raise ValueError on any invariant violation."""
+        train = set(self.train_sets)
+        test = set(self.test_sets)
+        val = set(self.validation_sets)
+
+        if not train:
+            raise ValueError("CVConfig: train_sets is empty")
+        if not test:
+            raise ValueError("CVConfig: test_sets is empty")
+
+        overlap = train & val
+        if overlap:
+            raise ValueError(
+                f"CVConfig: train_sets and validation_sets overlap on "
+                f"{sorted(overlap)}; validation must be a held-out dataset"
+            )
+
+        if self.mode == "loso":
+            extras = test - train
+            if extras:
+                raise ValueError(
+                    f"CVConfig(mode='loso'): requires test_sets ⊆ train_sets; "
+                    f"found in test_sets but not train_sets: {sorted(extras)}. "
+                    f"If you intended to train on {sorted(train)} and test on "
+                    f"disjoint datasets, use mode='transfer'."
+                )
+        elif self.mode == "transfer":
+            overlap = train & test
+            if overlap:
+                raise ValueError(
+                    f"CVConfig(mode='transfer'): requires train_sets ∩ "
+                    f"test_sets = ∅; overlap: {sorted(overlap)}. "
+                    f"If you intended leave-one-subject-out within that "
+                    f"overlap, use mode='loso'."
+                )
+        else:
+            raise ValueError(
+                f"CVConfig: mode must be 'loso' or 'transfer', got {self.mode!r}"
+            )

pisces_lite-3.0.0/src/pisces_lite/cv/fold.py

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+"""Fold iteration over datasets according to a CVConfig."""
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Dict, Iterable, Iterator, List, NamedTuple, Sequence, Union
+
+from pisces_lite.cv.config import CVConfig
+
+
+class SubjectRef(NamedTuple):
+    """A reference to one subject. Cheap; consumers pass through ``load_subject``."""
+
+    dataset_name: str
+    subject_id: str
+
+
+@dataclass(frozen=True)
+class Fold:
+    """One fold of a CV run.
+
+    For ``mode='transfer'``, always ``fold_id=0`` and ``total_folds=1``.
+    For ``mode='loso'``, ``fold_id`` ranges ``0..total_folds-1`` and each fold
+    holds out exactly one ``test_subjects`` entry.
+    """
+
+    fold_id: int
+    total_folds: int
+    mode: str
+    description: str
+    train_subjects: List[SubjectRef]
+    val_subjects: List[SubjectRef]
+    test_subjects: List[SubjectRef]
+
+
+DatasetsArg = Union[Dict[str, "object"], Sequence["object"]]
+
+
+def _datasets_by_name(datasets: DatasetsArg) -> Dict[str, "object"]:
+    if isinstance(datasets, dict):
+        return datasets
+    return {d.name: d for d in datasets}
+
+
+def _subjects_from(
+    set_names: Iterable[str],
+    by_name: Dict[str, "object"],
+    exclude: Iterable[SubjectRef] = (),
+) -> List[SubjectRef]:
+    excluded = set(exclude)
+    out: List[SubjectRef] = []
+    for name in set_names:
+        ds = by_name[name]
+        for sid in ds.ids:
+            ref = SubjectRef(name, sid)
+            if ref in excluded:
+                continue
+            out.append(ref)
+    return sorted(out)
+
+
+def _require_all_loaded(cv_config: CVConfig, by_name: Dict[str, "object"]) -> None:
+    needed = set(cv_config.train_sets) | set(cv_config.test_sets) | set(cv_config.validation_sets)
+    missing = needed - set(by_name)
+    if missing:
+        raise KeyError(
+            f"iter_folds: datasets referenced by CVConfig are not loaded: "
+            f"{sorted(missing)}. Loaded: {sorted(by_name)}"
+        )
+
+
+def iter_folds(cv_config: CVConfig, datasets: DatasetsArg) -> Iterator[Fold]:
+    """Yield one :class:`Fold` per CV split, dispatching on ``cv_config.mode``.
+
+    ``datasets`` may be a list of ``DataSetObject`` or a pre-built ``{name: ds}``
+    mapping. The caller is responsible for calling ``parse_data`` on each
+    dataset before passing it here.
+    """
+    cv_config.validate()
+    by_name = _datasets_by_name(datasets)
+    _require_all_loaded(cv_config, by_name)
+
+    val_subjects = _subjects_from(cv_config.validation_sets, by_name)
+
+    if cv_config.mode == "transfer":
+        train_subjects = _subjects_from(
+            cv_config.train_sets, by_name, exclude=val_subjects
+        )
+        test_subjects = _subjects_from(cv_config.test_sets, by_name)
+        yield Fold(
+            fold_id=0,
+            total_folds=1,
+            mode="transfer",
+            description=(
+                f"transfer: 1 model on {len(train_subjects)} train subj "
+                f"from {list(cv_config.train_sets)} → "
+                f"{len(test_subjects)} test subj "
+                f"from {list(cv_config.test_sets)} "
+                f"(val: {len(val_subjects)})"
+            ),
+            train_subjects=train_subjects,
+            val_subjects=val_subjects,
+            test_subjects=test_subjects,
+        )
+        return
+
+    # LOSO
+    test_pool = _subjects_from(
+        cv_config.test_sets, by_name, exclude=val_subjects
+    )
+    train_pool = _subjects_from(
+        cv_config.train_sets, by_name, exclude=val_subjects
+    )
+
+    total = len(test_pool)
+    if cv_config.max_folds is not None:
+        test_pool = test_pool[: cv_config.max_folds]
+
+    for i, held_out in enumerate(test_pool):
+        train_subjects = [s for s in train_pool if s != held_out]
+        yield Fold(
+            fold_id=i,
+            total_folds=total,
+            mode="loso",
+            description=(
+                f"LOSO fold {i + 1}/{total}: holding out "
+                f"{held_out.subject_id} from {held_out.dataset_name} "
+                f"({len(train_subjects)} train subj, "
+                f"{len(val_subjects)} val subj)"
+            ),
+            train_subjects=train_subjects,
+            val_subjects=val_subjects,
+            test_subjects=[held_out],
+        )

pisces_lite-3.0.0/src/pisces_lite/datasets/__init__.py

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+"""Multi-feature sleep-study dataset loading.
+
+Datasets are described by a per-dataset :class:`DataSetConfig` parsed from
+``data_set.json`` rather than sniffed from the dataset name.
+"""
+from pisces_lite.datasets.constants import (
+    ACC_HZ,
+    DELTA_T_COL,
+    END_HZ,
+    MINIMUM_ACCEL_SAMPLES_PER_PSG,
+    MINUTES_TO_SECONDS,
+    PSG_CLASS_TO_NAME,
+    PSG_COL,
+    PSG_DT,
+    PSG_MAPPING_5C,
+    PSG_MAPPING_DREAMT,
+    PSG_MAPPING_NO_N4,
+    PSG_MAPPING_PRESETS,
+    PSG_MAPPING_WEAVER,
+    PSG_5C_MAPPING_TO_WLDR,
+    PSG_5C_MAPPING_TO_WNR,
+    PSG_5C_MAPPING_TO_WS,
+    PSG_MASK,
+    PSG_STAGING_LEGEND,
+    SET_NAMES_PRETTY,
+    SLEEP_CLASS_LABEL,
+    TIMESTAMP_COL,
+    WAKE_CLASS_LABEL,
+    WALCH_PSG_LABELS,
+    X_COL,
+    Y_COL,
+    Z_COL,
+    get_class_names,
+)
+from pisces_lite.datasets.config import (
+    AccelConfig,
+    CSVConfig,
+    DataSetConfig,
+    PSGConfig,
+    SubjectData,
+    TimestampConfig,
+    load_subject,
+)
+from pisces_lite.datasets.adapters import (
+    DEFAULT_ADAPTER_FILENAME,
+    DataSetAdapter,
+    import_adapter_module,
+    load_data_sets_from_adapter,
+    normalize_data_sets,
+)
+from pisces_lite.datasets.data_set_object import DataSetObject, get_subject_data
+from pisces_lite.datasets.id_extraction import IdExtractor, SimplifiablePrefixTree
+from pisces_lite.datasets.loading import determine_header_rows_and_delimiter
+from pisces_lite.datasets.processing import (
+    align_trim,
+    calculate_binary_activity,
+    mask_data,
+    psg_map,
+    psg_to_sleep_wake,
+    rescale_spectrogram,
+)
+
+__all__ = [
+    "ACC_HZ",
+    "AccelConfig",
+    "CSVConfig",
+    "DEFAULT_ADAPTER_FILENAME",
+    "DELTA_T_COL",
+    "DataSetAdapter",
+    "DataSetConfig",
+    "DataSetObject",
+    "PSGConfig",
+    "SubjectData",
+    "TimestampConfig",
+    "load_subject",
+    "END_HZ",
+    "IdExtractor",
+    "MINIMUM_ACCEL_SAMPLES_PER_PSG",
+    "MINUTES_TO_SECONDS",
+    "PSG_CLASS_TO_NAME",
+    "PSG_COL",
+    "PSG_DT",
+    "PSG_MAPPING_5C",
+    "PSG_MAPPING_DREAMT",
+    "PSG_MAPPING_NO_N4",
+    "PSG_MAPPING_PRESETS",
+    "PSG_MAPPING_WEAVER",
+    "PSG_5C_MAPPING_TO_WLDR",
+    "PSG_5C_MAPPING_TO_WNR",
+    "PSG_5C_MAPPING_TO_WS",
+    "PSG_MASK",
+    "PSG_STAGING_LEGEND",
+    "SET_NAMES_PRETTY",
+    "SLEEP_CLASS_LABEL",
+    "SimplifiablePrefixTree",
+    "TIMESTAMP_COL",
+    "WAKE_CLASS_LABEL",
+    "WALCH_PSG_LABELS",
+    "X_COL",
+    "Y_COL",
+    "Z_COL",
+    "align_trim",
+    "calculate_binary_activity",
+    "determine_header_rows_and_delimiter",
+    "get_class_names",
+    "get_subject_data",
+    "import_adapter_module",
+    "load_data_sets_from_adapter",
+    "mask_data",
+    "normalize_data_sets",
+    "psg_map",
+    "psg_to_sleep_wake",
+    "rescale_spectrogram",
+]