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BH-Molecule CLI Commands

The BH-Molecule package provides CLI tools for generating/plotting model spectra and for running BH batch fitting on VIS-1.33 m FITS data.

Installation

To use the commands, you need to install the package. See the Installation section.

Batch fitting (FITS data):

  • bh batch — run BH batch fitting from a YAML config (single file or folder)

Model spectrum generation:

  • bh-spectra
  • bh-spectra-csv
  • bh-spectra-plot

Batch fitting: bh batch

Run BH batch fitting on VIS-1.33 m FITS data using a YAML config. Supports a single FITS file or a folder of .fits files. Frame and channel selection can be automatic (signal detection) or specified in the config.

bh batch --config fit_v3.yaml

Options:

Option Description
--config (Required) Path to YAML config file.
--run-fit-limit N Run only the first N fits (after frame/channel selection) for quick pipeline testing. Default: no limit (full batch).

Example (limited run for testing):

bh batch --config fit_v3.yaml --run-fit-limit 5

With --run-fit-limit 5, the pipeline runs the same steps (selection, fitting, saving CSV, curves, grid plots, per-fit figures) but only for the first 5 (frame, channel) pairs. Output structure and filenames are unchanged; only fewer fits are executed.

Config file (YAML): Must contain either folder (path to directory of .fits files) or fits_file / fits (path to a single FITS). Other keys are passed as batch options, e.g. cw, scale, out_dir, dark_frame, time_range, background_frames, band, threshold_sigma, bounds, fitter_kwargs, frames, channels. See Instruments and calibration and the batch workflow for details.

Common Parameters

All three commands share a set of parameters controlling the generated spectrum:

Parameter Type Default Description
--xmin float 432.8 Minimum wavelength in nm
--xmax float 434.2 Maximum wavelength in nm
--points int 4000 Number of wavelength points
--C float 1.0 Concentration factor
--T_rot float 2000.0 Rotational temperature in K
--dx float 0.0 Wavelength shift in nm
--w_inst float 0.02 Instrumental FWHM in nm
--base float 0.0 Baseline offset
--I_R7 float 0.5 Intensity of R₇ branch line
--I_R8 float 0.3 Intensity of R₈ branch line

Generate Spectrum Data

bh-spectra

Generates model spectrum and saves it as a compressed NumPy file (.npz).

bh-spectra --C 5.0 --T_rot 3500 --out spectrum.npz

Options:

  • --out: Output file name (default: spectrum.npz)

Example:

bh-spectra --xmin 433.0 --xmax 434.0 --points 2000 --C 2.0 --T_rot 2500 --out my_spectrum.npz

bh-spectra-csv

Same as bh-spectra but outputs a CSV file instead of NumPy.

bh-spectra-csv --C 5.0 --T_rot 3500 --out spectrum.csv

Options:

  • --out: Output CSV filename (default: spectrum.csv)

The resulting CSV will have columns:

  • x — Wavelength (nm)
  • y — Intensity (a.u.)

Plot Spectrum

Generates and displays a spectrum plot using Matplotlib.

bh-spectra-plot --C 5.0 --T_rot 3500

Additional options:

  • --save: Save plot to file (e.g. plot.png)
  • --dpi: Resolution when saving (default: 100)
  • --figsize: Width and height in inches (default: 10 6)

Example Workflow

  1. Generate spectrum data 

    bh-spectra --C 4.0 --T_rot 3200 --out data.npz

  2. Export same parameters to CSV 

    bh-spectra-csv --C 4.0 --T_rot 3200 --out data.csv

  3. Visualize spectrum 

    bh-spectra-plot --C 4.0 --T_rot 3200 --save plot.png --dpi 200

Notes

  • The BH-Spectra CLI tools (bh-spectra, bh-spectra-csv, bh-spectra-plot) are based on the BHModel class and use molecular constants loaded via load_v00_wavelengths().
  • Adjusting C, T_rot, and w_inst has the most visible effect on spectrum shape.
  • The bh batch command uses run_bh_batch / run_folder_batch from the package; --run-fit-limit limits the number of fits per run for workflow testing without changing output structure or filenames.