ecg-records 0.1.0__tar.gz

ecg_records-0.1.0/CHANGELOG.md

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+# Changelog — ecg-records
+
+All notable changes to the `ecg-records` distribution (import name `ecgfeat`).
+The ECG Record *schema* is versioned separately (see `schema_version` in every
+record); this file tracks the package.
+
+## [Unreleased]
+
+## [0.1.0] - 2026-09-24
+
+First release of the redesigned library (previously the unpublished
+`ecgfeat-dxl-inspired` 0.1.0 working tree).
+
+### Added
+- **ECG Record** (schema `1.0.0`): `ecg_record`, `ecg_prepare` / `ecg_measure` /
+  `ecg_emit`, `load_record`, `validate_record`, `dumps_record`, `query_measurement`,
+  `query_many`, `select_measurements`, `resolve_address`, `iter_leads`, `iter_beats`,
+  profiles `summary` / `all` / `debug`, canonical addresses
+  `ecg-record:<record_id>@<schema_version>#<RFC 6901 pointer>`, and three explicit
+  absence states (plain null, `unmeasurable(reason)`, `not_applicable(reason)`,
+  with a lossless per-field default state).
+- Packaged JSON Schema and validation-evidence registry
+  (`ecgfeat/schemas/ecg-record/1.0/`); strict reading rejects validation claims
+  above the registry. Every published field is `unvalidated` in this release.
+- Verified NPZ sidecar for dense matrices (`serialize_record(..., sidecar_uri=...)`,
+  CLI `measure --sidecar`), deterministic bytes, SHA-256 and identity bound.
+- `ecg-record` command line: `measure`, `validate`, `query`, `resolve`, `select`, `batch`.
+- Record-based plotting in `ecgfeat.viz`: `plot_record`, `plot_beat`,
+  `plot_beat_all_leads`, `plot_representative_beat`, `plot_quality_summary`, all
+  taking `(signal, record)` and returning `(Figure, axes)` through the
+  object-oriented Matplotlib API; the signal is checked against the record's
+  raw-signal SHA-256. `import ecgfeat` never imports Matplotlib.
+- Extras: `viz` (Matplotlib, for `ecgfeat.viz`), `interpret` (installs `ecginterpret`),
+  `performance` (Numba), `wfdb`.
+
+### Changed
+- Extraction runs as an explicit staged pipeline (input, quality, ventricular,
+  beats, delineation, atrial, measurement, finalize) with pacing, QT,
+  applicability and lead-integrity policy objects. Measurements are unchanged:
+  legacy output is byte-identical to the pre-migration baseline on 1,063 golden
+  records from seven public datasets.
+- Engine modules are private (`ecgfeat._engine`); interpretation moved to the
+  `ecginterpret` distribution; the legacy `ECGFeatures` plots moved to
+  `ecgfeat.viz.legacy`.
+- Published records never contain an impossible fiducial order or a negative
+  interval: such cells are `unmeasurable(fiducial_order_violation)` /
+  `unmeasurable(negative_interval)` instead of failing the whole record.
+
+### Deprecated
+- `ecgfeat.ECGFeatureExtractor` / `ecgfeat.api`, `ecgfeat.to_dict` and the
+  `ecgfeat.export` entry points, top-level `interpret`, `plot_*`,
+  `ecgfeat.visualize`, `load_wfdb_mat`, `parse_wfdb_header`, and the old
+  private module paths.
+  They warn on use and are removed no earlier than 0.3.0; `ecgfeat.compat`
+  is the explicit legacy contract meanwhile.
+
+### Known limitations
+- No published field has an approved evidence manifest yet (all `unvalidated`).
+- P-wave delineation is the weakest endpoint in the repository benchmarks.
+- ECG Record 1.0 publishes a compact subset of the engine's measurements;
+  `ecginterpret.interpret_record` therefore needs the raw signal.

ecg_records-0.1.0/LICENSE

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ecg_records-0.1.0/MANIFEST.in

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+include CHANGELOG.md
+include LICENSE
+prune tests
+global-exclude *.py[cod]
+global-exclude __pycache__
+include NOTICE

ecg_records-0.1.0/NOTICE

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+ecg-records
+Copyright 2026 humansys-lab and contributors
+
+Licensed under the Apache License, Version 2.0 (see LICENSE).
+https://github.com/humansys-lab/ECG-feature-extraction-
+
+Research and engineering software; not a medical device.

ecg_records-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ecg-records
+Version: 0.1.0
+Summary: Versioned ECG Record extraction, measurement and plotting (research and engineering software; not a medical device)
+Author: humansys-lab
+Maintainer: humansys-lab
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/humansys-lab/ECG-feature-extraction-
+Project-URL: Repository, https://github.com/humansys-lab/ECG-feature-extraction-
+Project-URL: Issues, https://github.com/humansys-lab/ECG-feature-extraction-/issues
+Project-URL: Documentation, https://github.com/humansys-lab/ECG-feature-extraction-/tree/main/docs/site
+Project-URL: Changelog, https://github.com/humansys-lab/ECG-feature-extraction-/blob/main/feature_extraction/CHANGELOG.md
+Keywords: ecg,electrocardiography,signal-processing,delineation,physionet,visualization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+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: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Typing :: Typed
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: scipy<2,>=1.11
+Provides-Extra: viz
+Requires-Dist: matplotlib<4,>=3.7; extra == "viz"
+Provides-Extra: interpret
+Requires-Dist: ecginterpret<1,>=0.1; extra == "interpret"
+Provides-Extra: performance
+Requires-Dist: numba<0.67,>=0.59; extra == "performance"
+Provides-Extra: wfdb
+Requires-Dist: wfdb<5,>=4.1; extra == "wfdb"
+Provides-Extra: dev
+Requires-Dist: build<2,>=1.2; extra == "dev"
+Requires-Dist: hypothesis<7,>=6.100; extra == "dev"
+Requires-Dist: import-linter<3,>=2; extra == "dev"
+Requires-Dist: jsonschema<5,>=4.22; extra == "dev"
+Requires-Dist: pytest<10,>=8; extra == "dev"
+Requires-Dist: twine<7,>=5; extra == "dev"
+Dynamic: license-file
+
+# ecg-records
+
+`ecg-records` measures 12-lead (or 1–8-channel) ECG signals and emits a small,
+versioned JSON document, the **ECG Record**: fiducials, intervals,
+amplitudes, areas, quality and provenance in raw-sample coordinates, with
+explicit units, an explicit reason for every missing value, a stable address
+for every value, and a per-field validation status. The Python import name is
+`ecgfeat`.
+
+> This software is research and engineering software. It is not a medical
+> device and is not intended to diagnose, treat, cure, or prevent disease.
+> Outputs require independent validation for the intended use and must not be
+> used as a substitute for professional medical judgment.
+
+The measurement pipeline (signal quality, multilead QRS detection, beat
+grouping, representative beats, delineation) is inspired by publicly
+documented 12-lead measurement practice. It is not a reproduction of any
+proprietary product.
+
+## Install
+
+```bash
+pip install ecg-records                  # measurements and ECG Records (NumPy, SciPy)
+pip install "ecg-records[performance]"   # optional Numba acceleration
+pip install "ecg-records[wfdb]"          # WFDB readers
+pip install "ecg-records[viz]"           # plotting with ecgfeat.viz (adds Matplotlib)
+pip install "ecg-records[interpret]"     # rule-based interpretation (ecginterpret)
+```
+
+Python 3.10–3.13. The core package depends only on NumPy and SciPy.
+
+## Measure
+
+```python
+import numpy as np
+from ecgfeat import ecg_record, dumps_record
+
+leads = ["I", "II", "III", "aVR", "aVL", "aVF", "V1", "V2", "V3", "V4", "V5", "V6"]
+signal = np.load("ecg.npy")        # shape (12, n_samples), channel-major, millivolts
+record = ecg_record(signal, sampling_rate=500, lead_names=leads)   # profile="summary"
+with open("ecg.record.json", "wb") as handle:
+    handle.write(dumps_record(record))
+```
+
+Rows must be named explicitly; for fewer than 12 channels pass
+`input_mode="limited"` (axis and formal QT are then `not_applicable`, raw
+measurements stay available). Profiles: `summary` (default; under 24,000 bytes
+for a 10 s, 12-lead, 10-beat record), `all` (every published measurement) and
+`debug`. Dense matrices can move to a verified NPZ sidecar with
+`serialize_record(record, sidecar_uri="ecg.dense.npz")`.
+
+## Read and query
+
+Reading records needs no NumPy, SciPy or plotting code:
+
+```python
+from ecgfeat import load_record, query_measurement, resolve_address
+
+record = load_record("ecg.record.json")              # strict validation by default
+qrs = query_measurement(record, "qrs_duration_ms", lead="V1", beat=3)
+qrs.value, qrs.unit, qrs.absence, qrs.validation.tier, str(qrs.address)
+# absence: None (measured), NullAbsence, UnmeasurableAbsence(reason) or NotApplicableAbsence(reason)
+
+address = f"ecg-record:{record.record_id}@{record.schema_version}#/measurements/global/heart_rate_bpm/values"
+resolve_address(record, address).value
+```
+
+Addresses follow `ecg-record:<record_id>@<schema_version>#<RFC 6901 pointer>`.
+The JSON Schema and the validation-evidence registry ship in the package
+(`ecgfeat/schemas/ecg-record/1.0/`).
+
+## Plot
+
+Plotting ships in this package as `ecgfeat.viz`; only Matplotlib is optional
+(`pip install "ecg-records[viz]"`). `import ecgfeat` never imports Matplotlib,
+and `pyplot` is never used.
+
+```python
+from ecgfeat.viz import plot_beat, plot_record
+
+fig, axes = plot_record(signal, record, leads=["II", "V1", "V5"],
+                        start_s=1.0, end_s=4.0, annotations="all")
+fig.savefig("record.png", dpi=150)
+fig, ax = plot_beat(signal, record, beat=3, lead="II")
+```
+
+`plot_beat_all_leads`, `plot_representative_beat` and `plot_quality_summary`
+work the same way. Every function takes `(signal, record)` and returns
+`(figure, axes)`. `signal` must be the exact array that produced the record:
+its SHA-256 is checked against `/artifacts/raw_signal/sha256`, and a mismatch
+raises `ecgfeat.viz.VisualizationInputError` (an `ECGInputError`). Pass
+`figure=` to draw into an existing `Figure` or `SubFigure`. Every added artist
+carries a `gid` starting with `ecgfeat.viz:`.
+
+## Command line
+
+```bash
+ecg-record measure signal.npy --sampling-rate 500 --lead-names I II III aVR aVL aVF V1 V2 V3 V4 V5 V6 -o rec.json
+ecg-record validate rec.json
+ecg-record query rec.json qrs_duration_ms --lead V1 --beat 3
+ecg-record batch manifest.jsonl --output-dir out --jobs 4
+```
+
+## Validation status
+
+Every published field carries a validation status taken from the shipped
+validation-evidence registry. In schema 1.0.0 **every field is
+`unvalidated`**: benchmark history exists for several endpoints, but no field
+has an approved evidence manifest yet, and a status can only be raised by
+citing one. The four-class ST morphology is deliberately not published (it was
+never validated and is anti-correlated with ischemia).
+
+## Versions and compatibility
+
+- The package version and the ECG Record schema version are independent. This
+  release writes schema `1.0.0` and reads schema major `1`, tolerating
+  additive fields from later minors.
+- Legacy APIs (`ECGFeatureExtractor`, `to_dict`, `interpret`, `plot_*`,
+  `ecgfeat.visualize`, the legacy result dataclasses) remain for a
+  compatibility window. Legacy
+  functions emit `ECGDeprecationWarning` on use; `ecgfeat.compat` provides the
+  exact legacy contract without warnings. Removal is no earlier than 0.3.0.