nutate 0.1.0__tar.gz

nutate-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+  workflow_call:  # the release workflow runs the tests first
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: pyvista/setup-headless-display-action@v5
+      - run: pip install -e ".[dev]"
+      - run: ruff check .
+      - run: pytest -v

nutate-0.1.0/.github/workflows/release.yml

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+name: Release
+
+# Push a tag vX.Y.Z matching the version in pyproject.toml: the tests run, then the package
+# is built, published to PyPI (trusted publishing, no token) and attached to a GitHub release.
+
+on:
+  push:
+    tags: ["v*"]
+
+jobs:
+  test:
+    uses: ./.github/workflows/ci.yml
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+      - name: Check the tag matches the package version
+        run: |
+          version=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")
+          if [ "${GITHUB_REF_NAME#v}" != "$version" ]; then
+            echo "::error::tag $GITHUB_REF_NAME does not match version $version in pyproject.toml"
+            exit 1
+          fi
+      - run: python -m pip install build twine
+      - run: python -m build
+      - run: twine check --strict dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: [test, build]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: dist/*

nutate-0.1.0/.gitignore

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+output/
+.venv/
+__pycache__/
+*.egg-info
+.idea/
+.DS_Store
+.superpowers/
+dist/
+build/

nutate-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here. The format follows
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and versions follow
+[Semantic Versioning](https://semver.org/).
+
+## [0.1.0] - 2026-10-19
+
+First release.
+
+### Added
+
+- Rotating-frame Bloch simulation of any pulse sequence for many offsets at once, stepped
+  with the exact SU(2) propagator; phase cycling and drive (B1) amplitude scaling.
+- Pulses as a waveform normalised to 1 plus its Rabi frequency: `nt.waveform` from
+  amplitude and phase or I and Q, with `rabi` or the hard 90° length `t90`; `nt.delay` for
+  free precession.
+- `nt.run`: one call from a pulse or sequence to a Bloch-sphere video, a still, B1
+  robustness figures (offset × B1 map, surface, phase sensitivity) or interactive windows.
+- Rendering with PyVista to MP4/GIF and PNG or an interactive viewer: arrows or ribbons,
+  fading trails, drive amplitude and phase insets, light and dark themes, orbiting camera.
+- Optional pulse families: `nutate.pulses.swept_frequency` (chirps, hyperbolic-secant
+  pulses, CHORUS, phase correction) and `nutate.pulses.composite` (composite pulses and
+  presets).
+
+[0.1.0]: https://github.com/mforoozandeh/nutate/releases/tag/v0.1.0

nutate-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: Nutate
+abstract: Bloch simulations of any pulse sequence rendered as 3D Bloch-sphere videos.
+authors:
+  - family-names: Foroozandeh
+    given-names: Mohammadali
+license: Apache-2.0
+repository-code: https://github.com/mforoozandeh/nutate
+version: 0.1.0

nutate-0.1.0/LICENSE

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nutate-0.1.0/NOTICE

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+Nutate — Copyright 2026 Mohammadali Foroozandeh

nutate-0.1.0/PKG-INFO

@@ -0,0 +1,211 @@
+Metadata-Version: 2.5
+Name: nutate
+Version: 0.1.0
+Summary: Bloch simulations of any pulse sequence rendered as 3D Bloch-sphere videos
+Project-URL: Homepage, https://github.com/mforoozandeh/nutate
+Project-URL: Repository, https://github.com/mforoozandeh/nutate
+Project-URL: Issues, https://github.com/mforoozandeh/nutate/issues
+Project-URL: Changelog, https://github.com/mforoozandeh/nutate/blob/main/CHANGELOG.md
+Author: Mohammadali Foroozandeh
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: Bloch simulation,Bloch sphere,EPR,ESR,NMR,magnetic resonance,pulse,qubit,visualization
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.11
+Requires-Dist: imageio-ffmpeg>=0.6
+Requires-Dist: imageio>=2.31
+Requires-Dist: matplotlib>=3.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: pyvista>=0.45
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Nutate
+
+Bloch simulations of any pulse sequence, rendered as 3D Bloch-sphere videos.
+
+![A composite pulse on the Bloch sphere](https://raw.githubusercontent.com/mforoozandeh/nutate/main/docs/media/composite.webp)
+
+Full-quality video (1080p):
+
+https://github.com/user-attachments/assets/1848f607-e421-4923-b198-bb7745c69010
+
+Nutate takes any pulse, given as a waveform (amplitude and phase, or I and Q) with its
+duration and Rabi frequency, whether it drives nuclear spins (NMR), electron spins (EPR/ESR)
+or a qubit. It simulates the Bloch vector in the rotating frame for many offsets at once,
+renders the trajectories with [PyVista](https://pyvista.org) as MP4/GIF videos, PNG stills
+or an interactive viewer, and maps robustness to drive (B1) amplitude errors. Optional pulse
+families (chirps, hyperbolic-secant pulses, CHORUS, composite pulses) live in
+`nutate.pulses`.
+
+## Install
+
+```bash
+pip install nutate
+```
+
+Python ≥ 3.11. Video encoding uses the ffmpeg binary bundled with `imageio-ffmpeg`; no
+system ffmpeg or LaTeX needed.
+
+## Quickstart
+
+A generator makes the pulse: a waveform normalised to 1 plus its duration and Rabi frequency
+ν1 (the drive amplitude, RF or MW, at waveform value 1). `nt.run` simulates it and writes
+the video and/or the B1 robustness figures.
+
+```python
+import nutate as nt
+from nutate.pulses.swept_frequency import chirp
+
+pulse = chirp(10e-3, 20e3, 500, smoothing=10)  # pulse.amp (peak 1), .phase, .duration, .rabi
+nt.run(pulse, 10e3, still=True, b1=True, out="output", name="chirp")
+# output/chirp.mp4, chirp.png, chirp_b1_map.png, chirp_b1_surface.png, chirp_b1_phase.png
+```
+
+Units are SI throughout (seconds, hertz, radians); arguments in degrees end in `_deg`.
+
+The package core holds the pulse type, `nt.waveform` (your own arrays) and `nt.delay` (free
+precession). Pulse families live in `nutate.pulses`:
+
+- `nutate.pulses.swept_frequency`: `chirp`, `hs`, `chorus` (a list including its delay),
+  `CHORUS_CYCLE`, `phase_correction` and `chorus_phase_correction`
+- `nutate.pulses.composite`: `composite` (a list, one pulse per element) and `PRESETS`
+
+`pulse.with_rabi(ν1)` changes the Rabi frequency and keeps the waveform.
+
+### Your own waveform
+
+`nt.waveform` turns arrays from any other generator (an optimiser, a shape tool) into a
+pulse: amplitude and phase, or I and Q, normalised to 1. `rabi` is the Rabi frequency in
+Hz, or give `t90`, the hard 90° pulse length (`rabi = 1/(4·t90)`). Slight overshoot above 1
+is simulated as given; a peak above 1.5 is an error.
+
+```python
+p1 = nt.waveform(amp, phase, duration=2e-3, rabi=15e3)  # or phase_deg=...
+p2 = nt.waveform(i=I, q=Q, duration=1e-3, t90=10e-6)
+result = nt.run([p1, p2], 300e3, b1=True, out="output", name="my_pulse")
+```
+
+### Sequences and delays
+
+A sequence is a list, played back to back. Put `nt.delay(duration, n_steps)` between
+pulses for free precession (no drive); `n_steps` sets how finely the delay is sampled, i.e.
+how smoothly the video shows it.
+
+```python
+sequence = [p1, nt.delay(500e-6, 100), p2]  # p1, 500 µs of free precession, then p2
+nt.run(sequence, 300e3, out="output", name="echo")
+```
+
+### `nt.run` options
+
+- Offsets span `±bandwidth/2`: `n_offsets` (31) for the video, `b1_offsets` (101) for the
+  B1 map. Or pass `offsets=` (Hz) for both.
+- `video` (on), `still` (last frame as PNG), `b1` (off), `show` (interactive windows
+  instead of files). Pulses in a list play back to back; `phase_cycle=` is passed through.
+- `video_options` go to `nt.render`; those that apply also go to the still and the viewer:
+  - `offsets`: draw only `k` evenly spaced offsets, or given indices
+  - `mode`: `"arrows"`, `"ribbon"` (a curve through all tips) or `"both"`
+  - `trail`: fading tip trails, as a fraction of the sequence
+  - `inset` / `inset_phase`: drive amplitude (and phase) vs time with a moving cursor
+  - `theme`: `"light"` (default) or `"dark"`
+  - `camera=nt.Camera(orbit=90)`, `style=nt.Style(...)` (colours, sizes, font), `duration`,
+    `size`
+- B1 figures plot `−My` by default; `component="z"` for inversion. `b1_scales` (0.5–1.5) and
+  `rabi_ref` (the highest ν1, for the `Δ/Ω1(0)` axis) can be changed.
+- The result holds the trajectory, the B1 map, the phase sensitivity and the files written.
+
+### Lower level
+
+```python
+import numpy as np
+
+traj = nt.simulate([pulse], offsets=np.linspace(-5e3, 5e3, 31))
+nt.render(traj, "chirp.mp4", duration=12)
+```
+
+`nt.snapshot(...)` writes a PNG still; `nt.show(traj)` opens an interactive window with a
+time slider. `nt.plot_profiles(traj)` and `nt.plot_map(traj)` make the 2D excitation
+profile and time–offset map plots.
+
+### B1 robustness
+
+```python
+pulse = nt.waveform([1.0], [0.0], duration=10e-6, t90=10e-6)  # hard 90°, ν1 = 25 kHz
+offsets = np.linspace(-100e3, 100e3, 101)  # Δ/Ω1(0) from −4 to 4
+scales = np.linspace(0.5, 1.5, 101)  # Ω1 / Ω1(0)
+bmap = nt.b1_map([pulse], offsets, scales)
+nt.plot_b1_map(bmap, "y", sign=-1)  # contours over Δ/Ω1(0) × Ω1/Ω1(0)
+nt.plot_b1_map(bmap, "y", sign=-1, surface=True)
+nt.plot_b1_phase(scales, nt.b1_phase_sensitivity([pulse], scales))
+```
+
+Sequences whose phase varies quickly across the band, such as a single chirp, need dense
+offsets; `examples/b1_chirp.py` uses 1000, as the original script did.
+
+`simulate(..., b1=...)` scales every drive amplitude (one factor, or one per offset);
+`simulate_final` returns only the final states, which keeps large grids small in memory.
+`nutate.pulses.swept_frequency.phase_correction(sequence, bandwidth, ...)` fits the
+first-chirp phase correction for any CHORUS-like sequence.
+
+## Examples
+
+Each script generates its pulses and passes them to `nt.run`. Video scripts write
+`output/<name>.mp4` and `.png`; the `b1_*` scripts (and `waveform.py`) write
+`output/<name>_b1_map.png`, `_b1_surface.png` and `_b1_phase.png`. To change what they
+produce, edit the `nt.run` call: `show=True` for interactive windows, `out=` for another
+folder, `video_options={"theme": "dark"}` for a dark video.
+
+| Example | Shows |
+|---|---|
+| [`examples/chirp.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/chirp.py) | linear chirp excitation |
+| [`examples/chirp_rewind.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/chirp_rewind.py) | a chirp, then an ideal rewind of its quadratic phase |
+| [`examples/hard_pulse.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/hard_pulse.py) | a hard 90° pulse over a wide offset range |
+| [`examples/composite.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/composite.py) | a composite pulse (preset 9 on a 10 µs 90° pulse) |
+| [`examples/chorus.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/chorus.py) | CHORUS with phase correction, plus excitation profiles |
+| [`examples/compressed_chorus_epr.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/compressed_chorus_epr.py) | compressed CHORUS for EPR, plus a time–offset map and phase paths |
+| [`examples/waveform.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/waveform.py) | your own I/Q arrays (a shifted Gaussian 90°): video, still and B1 figures |
+| [`examples/b1_hard.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_hard.py) | B1 map and phase sensitivity: hard 90° pulse |
+| [`examples/b1_composite.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_composite.py) | B1 map and phase sensitivity: composite pulses |
+| [`examples/b1_chirp.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_chirp.py) | B1 map and phase sensitivity: single chirp |
+| [`examples/b1_double_chirp.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_double_chirp.py) | B1 map and phase sensitivity: double chirp |
+| [`examples/b1_chorus.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_chorus.py) | B1 map and phase sensitivity: CHORUS |
+| [`examples/b1_abstruse.py`](https://github.com/mforoozandeh/nutate/blob/main/examples/b1_abstruse.py) | B1 map and phase sensitivity: ABSTRUSE (hyperbolic-secant pulses) |
+
+## Conventions
+
+- Rotating frame, no relaxation; initial magnetization `(0, 0, 1)`.
+- Each step rotates the magnetization by `+α = 2π·sqrt(Ω² + Δ²)·dt` (right-handed) about
+  `n = (sinθ cosφ, sinθ sinφ, cosθ)` with `θ = atan2(Ω, Δ)`, for drive amplitude `Ω`
+  (waveform × ν1), phase `φ` and offset `Δ` — i.e. `Rz(φ)·Ry(θ)·Rz(α)·Ry(−θ)·Rz(−φ)`. So an
+  on-resonance 90° pulse with phase 0 takes `z → −y`.
+- Profile phase is `angle(My + i·Mx)`.
+
+## Headless rendering
+
+Videos are rendered off-screen. On a server without a display, VTK needs an off-screen
+OpenGL context (OSMesa/EGL or a virtual display); see the off-screen rendering notes in the
+[PyVista documentation](https://docs.pyvista.org).
+
+## Citation
+
+If you use `nutate` in published work, please cite it; see [`CITATION.cff`](https://github.com/mforoozandeh/nutate/blob/main/CITATION.cff).
+
+## License
+
+Apache License 2.0 — see [`LICENSE`](https://github.com/mforoozandeh/nutate/blob/main/LICENSE) and [`NOTICE`](https://github.com/mforoozandeh/nutate/blob/main/NOTICE).