spectrumpy-flight 1.1.3

Ground-system decoding, fitting, and visualization tools for the LASP/IMPACT IDEX campaign.

SpectrumPY-Flight

Ground-system decoding, fitting, and visualization tools for the LASP/IMPACT IDEX campaign.

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Overview

SpectrumPY-Flight wraps packet decoding, fitting, and visualization into a single workflow that covers the full time-of-flight (TOF) dust analysis loop:

• Automatic TOF mass spectrometry – Load raw telemetry or oscilloscope captures and generate calibrated mass axes with the Newton-stabilized series expansion implemented in mass_calibration.py and time2mass.py. Interactive stretch-and-shift bootstrapping keeps solutions stable even on faint spectra.【F:src/spectrumpy_flight/docs/time_to_mass_calibration.md†L1-L111】
• Batch processing – Launch the provided shell helpers to ingest new downlinks or laboratory campaigns without touching the GUI, then hand the derived products back to the quicklook tools for inspection.【F:process_packets.sh†L1-L27】【F:process_EM_Data.sh†L1-L37】
• Fit adjustments on demand – Recompute exponential-modified Gaussian (EMG) overlays, tweak lmfit parameters, and persist manual overrides directly inside the Dust Composition workspace.【F:IDEX-quicklook.py†L1056-L1349】【F:dust_composition.py†L1129-L1478】
• Composition identification – Compare detected species to reference libraries, apply relative sensitivity factors, and summarise abundances with ternary diagrams that highlight cometary dust classes and olivine content in real time.【F:dust_composition.py†L3008-L3484】【F:dust_composition.py†L3526-L4023】

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Launch in 10 seconds

python -m spectrumpy_flight.start

The Spectrum Launcher opens immediately and hands off to the Quicklook viewer so you can load telemetry, browse documentation, and export science plots without touching any other scripts.【F:src/spectrumpy_flight/start.py†L1-L7】【F:src/spectrumpy_flight/spectrum_launcher.py†L167-L289】

Installation

Install the published package from PyPI when you want to run SpectrumPY outside the repository checkout:

python -m pip install spectrumpy

The default install remains lightweight so packet analysis scripts such as idex_packet.py and drive_idex_packet.py work on headless hosts without Qt. Add the GUI and SQL helpers in a single step when you want to run the Quicklook tooling:

python -m pip install "spectrumpy[quicklook]"

macOS-specific preparation steps are covered in src/spectrumpy_flight/docs/macos_pip_install.md. The document explains how to prepare Homebrew Python environments, optional extras, and Qt security prompts for first-time launches on Ventura and newer systems.【F:src/spectrumpy_flight/docs/macos_pip_install.md†L1-L83】

Optional extras match the bundled feature sets declared in pyproject.toml. Combine extras when needed (spectrumpy[quicklook,pyqt,gpu,database]) to pull in all secondary dependencies listed in the metadata.【F:pyproject.toml†L32-L52】

Extra	Included dependencies	When to use
quicklook	PySide6 + qtawesome for the Qt GUI, SQLAlchemy + PyMySQL for accelerator matching	Enables the Spectrum Launcher, Quicklook viewer, and other GUI entry points on a clean environment.
pyqt	PyQt6	Swap to the PyQt bindings instead of PySide6 (can be combined with quicklook).
gpu	CuPy	Accelerate packet decoding on CUDA-capable hosts.
database	SQLAlchemy, PyMySQL, MySQL connector	Install database adapters without the GUI stack (used for legacy telemetry archives).

SpectrumPY ships lean wheels so pip install spectrumpy stays well under PyPI's size limits. Sample telemetry captures and pre-generated CDF products remain available in the source repository; download them separately when you need tutorial data.

Command-line entry points

The PyPI package exposes convenience launchers so the most common workflows require no manual path management after installation:

• idex-packet – decode raw packets and emit HDF5 analysis products.
• drive-idex-packet – orchestrate parallel conversions across directories of captures.
• idex-quicklook – open the Qt quicklook viewer directly.
• spectrumpy-start – launch the SpectrumPY welcome screen with automatic oscilloscope ingestion.

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Core capabilities

• Packet decommutation – Decode binary telemetry with the XTCE mission definition and publish structured HDF5/CDF products for analysis.【F:idex_packet.py†L203-L440】【F:science_tool.py†L60-L377】
• Batch processing – Automate pipeline runs for new downlinks or oscilloscope campaigns with the provided shell helpers.【F:process_packets.sh†L1-L27】【F:process_EM_Data.sh†L1-L37】
• Fit adjustment – Refine lmfit overlays inside the GUI, reset overrides, persist overrides to disk, and compare solutions in real time.【F:IDEX-quicklook.py†L1056-L1349】【F:IDEX-quicklook.py†L3520-L3722】
• Noise diagnostics – Launch the dedicated analysis window for Gaussian histograms, FFT spectra, and autocorrelation studies per channel.【F:IDEX-quicklook.py†L2027-L2188】【F:noise_analysis.py†L260-L429】
• Parallel decoding – Scale packet processing across CPU cores with automatic worker discovery, per-job memory limits, and live progress reporting.【F:tools/process_packets_parallel.py†L1-L120】【F:tools/resource_utils.py†L1-L75】
• TOF mass spectrometry – Quantify dust populations with the composition workspace, apply relative sensitivity factors, match library samples, and inspect EMG mass lines in detail.【F:dust_composition.py†L3008-L3484】【F:dust_composition.py†L3526-L4023】

Time-to-mass conversion details

The calibration workflow models the arrival-time series as a polynomial in the reduced coordinate (s = \sqrt{m}):

[ t(s) = t_0 + a_1 s + a_2 s^2 + \cdots + a_K s^K. ]

Least-squares fitting recovers the coefficients (a_k) from calibration lines and the safeguarded Newton inversion maps measured times back to masses while clipping to the instrument range.【F:src/spectrumpy_flight/docs/time_to_mass_calibration.md†L13-L91】

After convergence the squared coordinate yields the final mass axis:

[ m = \left(s^{(n)}\right)^2. ]

These steps are exposed through TOFMassCal and the time2mass.py CLI so that both automated batch runs and interactive GUI sessions share the same well-conditioned calibration pipeline.【F:src/spectrumpy_flight/docs/time_to_mass_calibration.md†L1-L146】

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Performance and parallelization details

idex_packet.py

• GPU-assisted bit unpacking – _bitstring_to_ints converts ASCII bit streams into integers with a fully vectorised NumPy path and an automatic CuPy offload whenever more than 32 000 values are present, falling back seamlessly if GPU execution is unavailable or fails mid-run.【F:idex_packet.py†L96-L125】 The helper keeps allocations contiguous (astype(..., copy=False)) and trims padding without extra passes so the downstream waveform parsing never re-materialises the raw bitstring.【F:idex_packet.py†L96-L125】
• Shared kernels for saturation and SNR detection – Signal-quality metrics (SNR, saturation runs) operate on NumPy arrays with optional GPU execution that mirrors the CPU algorithm: detect_saturation lifts the differencing and run-length detection to CuPy when possible, then reuses the same boolean boundaries to avoid Python loops, while calculate_snr slices baseline windows in-place to minimise temporary buffers.【F:idex_packet.py†L128-L195】
• Rice/Golomb decompression in-stream – RiceGolombDecompressor instances emit fully decompressed traces directly into self.data, eliminating intermediate files for both low- and high-speed telemetry and reusing instrument trigger block counts to size the buffers exactly.【F:idex_packet.py†L941-L979】
• Time-base reuse and deterministic scaling – _build_time_array precomputes high-rate and low-rate time axes once per batch using cached trigger offsets, so waveform analyses (mass fitting, target modelling) only rescale existing arrays instead of rebuilding per channel.【F:idex_packet.py†L1002-L1290】
• Threaded waveform analysis with capped fan-out – write_to_hdf5 packages every (event, channel) pair and submits them to a ThreadPoolExecutor whose worker count is bounded by both the host CPU count and a hard cap of 32, preventing oversubscription when many events are present.【F:idex_packet.py†L1182-L1295】 Each worker returns a structured dictionary that the coordinator consumes sequentially to materialise datasets, guaranteeing that HDF5 writes remain serial while expensive per-channel transforms (mass scaling, EMG fitting, target curve estimation) execute in parallel.【F:idex_packet.py†L1208-L1336】

drive_idex_packet.py

• Parallel process orchestration – The driver discovers extensionless oscilloscope captures, filters out already-converted targets, and farms the remaining workload to a thread-backed execution pool that launches separate idex_packet.py processes so every core handles an independent capture.【F:drive_idex_packet.py†L24-L134】 Logging is performed per job (job_XXXX.(out|err)), enabling high-velocity runs without interleaved stdout noise.【F:drive_idex_packet.py†L51-L71】
• Oversubscription controls – Operator-provided --max-procs bounds the executor fan-out, while build_env injects BLAS/OpenMP thread caps (OMP_NUM_THREADS, OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, NUMEXPR_NUM_THREADS, and Accelerate’s VECLIB_MAXIMUM_THREADS) so the heavy SciPy/Numpy kernels inside each packet conversion cannot oversubscribe cores when dozens of jobs launch at once.【F:drive_idex_packet.py†L39-L134】 Optional niceness further de-prioritises the child processes on POSIX hosts for cooperative scheduling in shared environments.【F:drive_idex_packet.py†L60-L71】
• Resumable workflows – By evaluating destination .h5 existence up front (needs_conversion), the orchestrator skips already processed captures, enabling incremental reruns that immediately converge on the remaining work without repeated scans or redundant CPU time.【F:drive_idex_packet.py†L35-L110】

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Quicklook essentials

Primary windows

• Data Browser – Press Ctrl+B or choose View → Open Data Browser to launch the structure tree for the active event. The viewer exposes every dataset, attribute, and preview panel inside the HDF5/CDF product.【F:IDEX-quicklook.py†L1888-L1964】【F:HDF_View.py†L60-L398】
• Variable Definitions – Use View → Variable Definitions… to open the spreadsheet companion that maps engineering units, calibration spans, and coefficients straight from the official Excel reference.【F:IDEX-quicklook.py†L1888-L1964】【F:IDEX_Definitions_View.py†L1-L199】
• Dust Composition – Click the Dust Composition toolbar button or press Ctrl+D to launch the EMG fitting studio for the current event.【F:IDEX-quicklook.py†L2036-L2083】【F:dust_composition.py†L1-L215】
• Noise Analysis – Use the toolbar button or Ctrl+N to open the diagnostics workspace with histogram, FFT, and autocorrelation summaries for the active channel.【F:IDEX-quicklook.py†L2027-L2188】【F:noise_analysis.py†L260-L429】
• Documentation Center – Hit F1 (or the ? button) to browse the bundled Markdown library without leaving the viewer; Ctrl+F1 jumps directly to the global search panel.【F:IDEX-quicklook.py†L1888-L1964】

Inspect individual mass lines

1. Open the Dust Composition window (Ctrl+D) from the main toolbar.【F:IDEX-quicklook.py†L2036-L2083】
2. Combine the TOF traces if needed, select a region on the stacked plot, and click Add Mass Line to fit a new EMG peak; manual entry is also available through Add Manual Line.【F:dust_composition.py†L1129-L1244】
3. Highlight a row in the Mass Line Fits table and press Inspect Selected to open the zoomed EMG editor with amplitude, μ, σ, λ, and window controls, plus optional HyperEMG/Voigt tails.【F:dust_composition.py†L1188-L1478】
4. Apply relative sensitivity factors (RSFs) or sample library templates to renormalise abundances, adjust parameters, and confirm—tables and ternary summaries refresh immediately.【F:dust_composition.py†L3008-L3484】【F:dust_composition.py†L3526-L4023】

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Packaging quick reference

Shared setup

All platforms use the same PyInstaller spec. Start from a clean Python ≥3.10 environment and install the packaging requirements:

python -m pip install --upgrade pip
pip install -r packaging/packaging-requirements.txt

Then build the application bundle:

pyinstaller --noconfirm packaging/idex_quicklook.spec

【F:packaging/README.md†L26-L55】【F:packaging/idex_quicklook.spec†L1-L89】

macOS

./packaging/macos/create_dmg.sh dist/IDEX-Quicklook.app "IDEX-Quicklook-$(git describe --tags --always)-$(uname -m).dmg"

The script wraps the generated .app into a signed-ready disk image; finish by running your usual codesign and notarization steps.【F:packaging/README.md†L57-L76】

Windows

PyInstaller emits dist/IDEX-Quicklook/IDEX-Quicklook.exe. Compress that folder into a ZIP for delivery, or feed it into your MSI tool of choice, for example:

powershell -Command "Compress-Archive -Path dist/IDEX-Quicklook -DestinationPath IDEX-Quicklook-windows.zip"

Users unzip the archive and launch IDEX-Quicklook.exe directly.【F:packaging/README.md†L78-L88】

Linux

Package the frozen binary as a tarball ready for distribution:

tar -C dist -czf IDEX-Quicklook-linux.tar.gz IDEX-Quicklook

The executable runs without root privileges and extracts its shared libraries on first launch.【F:packaging/README.md†L90-L108】

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Documentation & tutorials

• Quicklook tutorial – Guided walkthrough of the GUI workflow, shortcuts, and recommended analysis order.【F:src/spectrumpy_flight/docs/quicklook_tutorial.md†L1-L123】
• Fitting reference – Deep dive into baseline handling, Data Browser correlations, and variable-definition lookups.【F:src/spectrumpy_flight/docs/fitting_reference.md†L1-L115】
• Packaging playbook – Extended release checklists, validation steps, and troubleshooting strategies for desktop builds.【F:src/spectrumpy_flight/docs/packaging_tutorial.md†L1-L198】
• Olivine metrics – Instructions for running the olivine regression and locating the generated SNR, timing, and saturation reports.【F:src/spectrumpy_flight/docs/olivine_metrics.md†L1-L64】
• Time-to-mass calibration – Polynomial fitting, Newton inversion safeguards, and quick recipes for turning TOF traces into calibrated mass axes.【F:src/spectrumpy_flight/docs/time_to_mass_calibration.md†L1-L146】
• Feature reference – Exhaustive catalogue of launchers, CLIs, shell helpers, and their underlying algorithms with LaTeX formulas and usage examples.【F:src/spectrumpy_flight/docs/feature_reference.md†L1-L195】

Launch the in-app documentation center anytime (F1) to search and read these guides inside the Quicklook viewer.【F:IDEX-quicklook.py†L1888-L1964】

License

This repository is released under the Ayari Public No-Derivatives License (APND) v1.0. You may download and use the software as-is. You may not modify it or distribute modified versions without written permission. See LICENSE.

Citation & DOI

If you use this software in research or a product, please cite it. We archive releases on Zenodo to mint a DOI. You can also download machine-readable metadata from CITATION.cff.

How to cite (example):

Ayari, E. (2025). SpectrumPY-Flight (v1.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.14948734

For convenience, you can embed the DOI badge anywhere documentation is published:

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14948734.svg)](https://doi.org/10.5281/zenodo.14948734)

Contributing

This is a read-only public release. We do not accept external pull requests or patches. Please open an issue for bugs or feature requests. For derivative-use exceptions, contact the author.

Repro/Use

• Clone or download a release tarball.
• Use unmodified sources/binaries as described in the docs.
• Do not redistribute modified versions.