ftmwpipeline 0.1.0b1__tar.gz

ftmwpipeline-0.1.0b1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Kyle N. Crabtree
+
+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.

ftmwpipeline-0.1.0b1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ftmwpipeline
+Version: 0.1.0b1
+Summary: A Python package for FTMW spectroscopy signal processing and peak fitting
+Author-email: "Kyle N. Crabtree" <kncrabtree@ucdavis.edu>
+Maintainer-email: "Kyle N. Crabtree" <kncrabtree@ucdavis.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/kncrabtree/ftmwpipeline
+Project-URL: Documentation, https://ftmwpipeline.readthedocs.io/
+Project-URL: Repository, https://github.com/kncrabtree/ftmwpipeline.git
+Project-URL: Bug Tracker, https://github.com/kncrabtree/ftmwpipeline/issues
+Keywords: spectroscopy,FTMW,signal-processing,peak-fitting,scientific-computing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: h5py>=3.1.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: threadpoolctl>=3.0.0
+Requires-Dist: blackchirp>=0.1.0rc2
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: isort>=5.10.0; extra == "dev"
+Requires-Dist: flake8>=5.0.0; extra == "dev"
+Requires-Dist: Flake8-pyproject>=1.2.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: pre-commit>=2.15.0; extra == "dev"
+Requires-Dist: build>=1.0.0; extra == "dev"
+Requires-Dist: twine>=4.0.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=5.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.0.0; extra == "docs"
+Provides-Extra: notebook
+Requires-Dist: jupyter>=1.0.0; extra == "notebook"
+Requires-Dist: ipywidgets>=7.6.0; extra == "notebook"
+Requires-Dist: ipykernel>=6.0.0; extra == "notebook"
+Dynamic: license-file
+
+# ftmwpipeline
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.9%2B-blue.svg)](pyproject.toml)
+
+A Python package for FTMW (Fourier Transform Microwave) spectroscopy signal
+processing and peak fitting — from a raw free-induction decay to a fitted line
+list with honest uncertainties.
+
+The design goal is a **statistically faithful** measurement, not just a
+plausible-looking spectrum:
+
+- **Unbiased spectrum.** The canonical Fourier transform is computed with no
+  apodization, time-domain windowing, or zero-padding. Those operations trade
+  frequency resolution, bias the line shape, and interpolate bins so the noise
+  and χ² statistics no longer mean what they should. Keeping the transform
+  native-length preserves resolution and the line shape, and keeps the per-bin
+  statistics valid for everything downstream.
+- **Rigorous from noise to fit.** A region-aware, per-bin noise estimate sets
+  detection thresholds; lines are fit in the time domain over finite-duration
+  windows; and fitted parameters carry uncertainties propagated **with their
+  correlations**, not as independent error bars. A reported precision reflects
+  what the data actually constrains.
+- **Reproducible and portable.** Each experiment is one self-contained `.ftmw`
+  file. Given the file and a compatible package version, the analysis
+  reproduces the same result on any machine — no external preset or side
+  artifact can silently change it.
+- **One analysis, three interfaces.** A command-line interface, an
+  object-oriented `Pipeline` class, and a stateless functional API are thin
+  wrappers over one implementation and produce numerically identical results;
+  use whichever fits your workflow.
+
+## Installation
+
+`ftmwpipeline` is currently in open beta. To install,
+
+```bash
+pip install --pre ftmwpipeline
+```
+
+This pulls in the scientific Python stack (NumPy, SciPy, Matplotlib, pandas,
+h5py) and the `blackchirp` loader dependency. Testing and documentation tooling
+are available as extras (`[dev]`, `[docs]`).
+
+To work from a clone, install in editable mode — directly with pip, or via the
+provided conda environment files:
+
+```bash
+pip install -e ".[dev]"
+# or
+conda env create -f environment-dev.yml && conda activate ftmwpipeline-dev
+```
+
+## Quick start
+
+Process a raw experiment end to end in one command:
+
+```bash
+ftmwpipeline run path/to/experiment/ --output exp.ftmw --trim 26500:40000
+```
+
+`--trim` selects the active spectral band (MHz). The same build from Python,
+through the class API:
+
+```python
+from ftmwpipeline import Pipeline
+
+result = Pipeline.build("path/to/experiment/", trim=(26500, 40000), output="exp.ftmw")
+pipe = Pipeline.open(result["pipeline_file"])
+print(pipe.info())   # provenance, completed stages, next available stages
+```
+
+or driven stage by stage, with the same calls available on the functional API
+(`import ftmwpipeline.api as ftmw`):
+
+```python
+pipe = Pipeline.create("exp.ftmw", source="path/to/experiment/")
+pipe.compute_ft(trim=(26500, 40000))
+pipe.estimate_noise()
+pipe.calibrate_tau()
+pipe.detect_peaks()
+pipe.assign_windows()
+pipe.fit_peaks()
+```
+
+At the command line each stage runs with the object-verb grammar
+(`<stage> run` / `<stage> show`):
+
+```bash
+ftmwpipeline data import  exp.ftmw path/to/experiment/
+ftmwpipeline ft run       exp.ftmw --trim 26500:40000
+ftmwpipeline noise run    exp.ftmw
+ftmwpipeline tau run      exp.ftmw
+ftmwpipeline peaks run    exp.ftmw
+ftmwpipeline windows run  exp.ftmw
+ftmwpipeline fit run      exp.ftmw
+ftmwpipeline report run   exp.ftmw --output-dir report
+```
+
+## Documentation
+
+Full documentation — installation, a worked quickstart on bundled example data,
+a guide to each pipeline stage, and the CLI/API reference — is at
+[ftmwpipeline.readthedocs.io](https://ftmwpipeline.readthedocs.io/).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

ftmwpipeline-0.1.0b1/README.md

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+# ftmwpipeline
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.9%2B-blue.svg)](pyproject.toml)
+
+A Python package for FTMW (Fourier Transform Microwave) spectroscopy signal
+processing and peak fitting — from a raw free-induction decay to a fitted line
+list with honest uncertainties.
+
+The design goal is a **statistically faithful** measurement, not just a
+plausible-looking spectrum:
+
+- **Unbiased spectrum.** The canonical Fourier transform is computed with no
+  apodization, time-domain windowing, or zero-padding. Those operations trade
+  frequency resolution, bias the line shape, and interpolate bins so the noise
+  and χ² statistics no longer mean what they should. Keeping the transform
+  native-length preserves resolution and the line shape, and keeps the per-bin
+  statistics valid for everything downstream.
+- **Rigorous from noise to fit.** A region-aware, per-bin noise estimate sets
+  detection thresholds; lines are fit in the time domain over finite-duration
+  windows; and fitted parameters carry uncertainties propagated **with their
+  correlations**, not as independent error bars. A reported precision reflects
+  what the data actually constrains.
+- **Reproducible and portable.** Each experiment is one self-contained `.ftmw`
+  file. Given the file and a compatible package version, the analysis
+  reproduces the same result on any machine — no external preset or side
+  artifact can silently change it.
+- **One analysis, three interfaces.** A command-line interface, an
+  object-oriented `Pipeline` class, and a stateless functional API are thin
+  wrappers over one implementation and produce numerically identical results;
+  use whichever fits your workflow.
+
+## Installation
+
+`ftmwpipeline` is currently in open beta. To install,
+
+```bash
+pip install --pre ftmwpipeline
+```
+
+This pulls in the scientific Python stack (NumPy, SciPy, Matplotlib, pandas,
+h5py) and the `blackchirp` loader dependency. Testing and documentation tooling
+are available as extras (`[dev]`, `[docs]`).
+
+To work from a clone, install in editable mode — directly with pip, or via the
+provided conda environment files:
+
+```bash
+pip install -e ".[dev]"
+# or
+conda env create -f environment-dev.yml && conda activate ftmwpipeline-dev
+```
+
+## Quick start
+
+Process a raw experiment end to end in one command:
+
+```bash
+ftmwpipeline run path/to/experiment/ --output exp.ftmw --trim 26500:40000
+```
+
+`--trim` selects the active spectral band (MHz). The same build from Python,
+through the class API:
+
+```python
+from ftmwpipeline import Pipeline
+
+result = Pipeline.build("path/to/experiment/", trim=(26500, 40000), output="exp.ftmw")
+pipe = Pipeline.open(result["pipeline_file"])
+print(pipe.info())   # provenance, completed stages, next available stages
+```
+
+or driven stage by stage, with the same calls available on the functional API
+(`import ftmwpipeline.api as ftmw`):
+
+```python
+pipe = Pipeline.create("exp.ftmw", source="path/to/experiment/")
+pipe.compute_ft(trim=(26500, 40000))
+pipe.estimate_noise()
+pipe.calibrate_tau()
+pipe.detect_peaks()
+pipe.assign_windows()
+pipe.fit_peaks()
+```
+
+At the command line each stage runs with the object-verb grammar
+(`<stage> run` / `<stage> show`):
+
+```bash
+ftmwpipeline data import  exp.ftmw path/to/experiment/
+ftmwpipeline ft run       exp.ftmw --trim 26500:40000
+ftmwpipeline noise run    exp.ftmw
+ftmwpipeline tau run      exp.ftmw
+ftmwpipeline peaks run    exp.ftmw
+ftmwpipeline windows run  exp.ftmw
+ftmwpipeline fit run      exp.ftmw
+ftmwpipeline report run   exp.ftmw --output-dir report
+```
+
+## Documentation
+
+Full documentation — installation, a worked quickstart on bundled example data,
+a guide to each pipeline stage, and the CLI/API reference — is at
+[ftmwpipeline.readthedocs.io](https://ftmwpipeline.readthedocs.io/).
+
+## License
+
+MIT — see [LICENSE](LICENSE).

ftmwpipeline-0.1.0b1/pyproject.toml

@@ -0,0 +1,195 @@
+[build-system]
+requires = ["setuptools>=77.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ftmwpipeline"
+dynamic = ["version"]
+description = "A Python package for FTMW spectroscopy signal processing and peak fitting"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    {name = "Kyle N. Crabtree", email = "kncrabtree@ucdavis.edu"}
+]
+maintainers = [
+    {name = "Kyle N. Crabtree", email = "kncrabtree@ucdavis.edu"}
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+keywords = ["spectroscopy", "FTMW", "signal-processing", "peak-fitting", "scientific-computing"]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.21.0",
+    "scipy>=1.7.0",
+    "matplotlib>=3.5.0",
+    "pandas>=1.3.0",
+    "h5py>=3.1.0",
+    "pyyaml>=6.0",
+    "tqdm>=4.60.0",
+    # Cross-backend BLAS/OpenMP thread limiting for the Stage 5 fork pool: the
+    # workers must run single-threaded BLAS to avoid N-workers x M-threads
+    # oversubscription, and threadpoolctl re-limits the already-loaded runtime
+    # (OpenBLAS / MKL / BLIS / Accelerate) at fork time -- an env var cannot,
+    # the backend reads it only at init, which has already happened.
+    "threadpoolctl>=3.0.0",
+    # 0.1.0rc2+ (the 2.0 pre-release line) exposes BCFTMW.get_fid /
+    # BCFid.is_lower_sideband and the version-tolerant enum parsing the
+    # Blackchirp loader delegates to. The stable 0.0.11 release predates them.
+    "blackchirp>=0.1.0rc2",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-xdist>=3.0.0",
+    "black>=22.0.0",
+    "isort>=5.10.0",
+    "flake8>=5.0.0",
+    # Lets flake8 read the [tool.flake8] config from pyproject.toml (flake8 does
+    # not read pyproject natively), so local and CI linting agree.
+    "Flake8-pyproject>=1.2.0",
+    "mypy>=1.0.0",
+    "pre-commit>=2.15.0",
+    # Release tooling: build sdist/wheel and validate the package metadata.
+    "build>=1.0.0",
+    "twine>=4.0.0",
+]
+docs = [
+    "sphinx>=5.0.0",
+    "sphinx-rtd-theme>=1.0.0",
+]
+notebook = [
+    "jupyter>=1.0.0",
+    "ipywidgets>=7.6.0",
+    "ipykernel>=6.0.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/kncrabtree/ftmwpipeline"
+Documentation = "https://ftmwpipeline.readthedocs.io/"
+Repository = "https://github.com/kncrabtree/ftmwpipeline.git"
+"Bug Tracker" = "https://github.com/kncrabtree/ftmwpipeline/issues"
+
+[project.scripts]
+ftmwpipeline = "ftmwpipeline.cli:main"
+
+[tool.setuptools.dynamic]
+version = {attr = "ftmwpipeline.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+ftmwpipeline = ["presets/*.yaml"]
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+addopts = [
+    "-ra",
+    "--strict-markers",
+    "--strict-config",
+    "--cov=ftmwpipeline",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+    "--cov-report=xml",
+]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+    "unit: marks tests as unit tests",
+    "performance: marks tests as performance benchmarks",
+]
+
+[tool.coverage.run]
+source = ["src/ftmwpipeline"]
+omit = [
+    "*/tests/*",
+    "*/test_*",
+    "setup.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if __name__ == .__main__.:",
+    "class .*\\bProtocol\\):",
+    "@(abc\\.)?abstractmethod",
+]
+
+[tool.black]
+line-length = 88
+target-version = ['py39', 'py310', 'py311', 'py312']
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+line_length = 88
+known_first_party = ["ftmwpipeline"]
+
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503", "E501"]
+exclude = [".git", "__pycache__", "build", "dist", ".eggs"]
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+disallow_untyped_decorators = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+
+[[tool.mypy.overrides]]
+module = [
+    "scipy.*",
+    "matplotlib.*",
+    "h5py.*",
+    "pandas.*",
+    "blackchirp.*",
+    "threadpoolctl.*",
+]
+ignore_missing_imports = true

ftmwpipeline-0.1.0b1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

ftmwpipeline-0.1.0b1/src/ftmwpipeline/__init__.py

@@ -0,0 +1,79 @@
+"""
+FTMW Pipeline - A Python package for FTMW spectroscopy signal processing and peak fitting.
+
+This package provides tools for processing Fourier Transform Microwave (FTMW)
+spectroscopy data, including baseline estimation, peak detection, window assignment,
+and advanced fitting algorithms.
+"""
+
+__version__ = "0.1.0b1"
+__author__ = "Kyle N. Crabtree"
+
+# Functional API - can be imported as "import ftmwpipeline.api as ftmw"
+from ftmwpipeline import api
+
+# Core data structures
+from ftmwpipeline.core.data_structures import (
+    FID,
+    ComplexFT,
+    FIDProcessingParameters,
+    FittedPeak,
+    FittingResult,
+    FitWindow,
+    FixedContributor,
+    FTMWData,
+    Peak,
+    PeakClassification,
+    Sideband,
+    SpectralWindow,
+    WindowPlan,
+)
+
+# Main pipeline interface
+from ftmwpipeline.pipeline import Pipeline
+
+__all__ = [
+    # Version info
+    "__version__",
+    "__author__",
+    # Core data structures
+    "FTMWData",
+    "FID",
+    "ComplexFT",
+    "SpectralWindow",
+    "Peak",
+    "FittedPeak",
+    "FittingResult",
+    "FIDProcessingParameters",
+    "PeakClassification",
+    "Sideband",
+    "FixedContributor",
+    "FitWindow",
+    "WindowPlan",
+    # Main pipeline interface
+    "Pipeline",
+    # Functional API module
+    "api",
+]
+
+# Package-level configuration
+import logging
+
+# Configure default logging
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+# Optional imports with graceful fallbacks
+try:
+    import matplotlib
+
+    _HAS_MATPLOTLIB = True
+except ImportError:
+    _HAS_MATPLOTLIB = False
+
+# Package metadata
+PACKAGE_INFO = {
+    "name": "ftmwpipeline",
+    "version": __version__,
+    "description": "FTMW spectroscopy signal processing and peak fitting",
+    "has_matplotlib": _HAS_MATPLOTLIB,
+}

ftmwpipeline-0.1.0b1/src/ftmwpipeline/__main__.py

@@ -0,0 +1,10 @@
+"""
+Enables running ftmwpipeline as a module with python -m ftmwpipeline
+"""
+
+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

ftmwpipeline-0.1.0b1/src/ftmwpipeline/_internal/__init__.py

@@ -0,0 +1,19 @@
+"""
+Internal shared implementations for ftmwpipeline.
+
+This module contains the core implementation functions that are shared between
+the three interfaces: CLI commands, Pipeline class, and functional API.
+
+The functions in this module are considered internal and should not be imported
+directly by users. Instead, they should use one of the public interfaces:
+
+- CLI: ftmwpipeline command-line interface
+- Pipeline class: from ftmwpipeline import Pipeline
+- Functional API: import ftmwpipeline as ftmw
+
+Architecture:
+- stage0_impl.py: Data import and FID visualization implementations
+- stage1_impl.py: FT processing and spectrum visualization implementations
+- stage2_impl.py: Noise estimation and visualization implementations (future)
+- shared_utils.py: Common utilities used across pipeline stages
+"""