YAML Configuration Reference

3DCubeGen uses YAML configuration files to control LVM cube generation. Two command modes are available: sincube for generating a single cube, and pipecube for batch-processing multiple targets through a pipeline.

Template configuration files are provided in the Configfiles/ directory:

• Configfiles/config_sincube.yml – single-cube mode

• Configfiles/config_pipecube.yml – pipeline mode

sincube Configuration

The sincube section defines parameters for generating a single data cube from one target.

Parameter	Type	Default	Description
survey_type	string	LVM	Survey identifier. Must contain LVM for LVM data.
out_path	string	out_cubes/	Output directory for the generated cube FITS files.
redux_ver	string	1.1.1.dev0	DRP reduction version of the input lvmCFrame files.
redux_dir	string	''	Path to the redux directory. When empty, defaults to <path_sas>/sdsswork/lvm/spectro/redux.
sigm_s	float	32.2	Smoothing kernel size (arcsec) used to reconstruct the cube. This sets the spatial resolution.
pix_s	float	0.0	Output spaxel size (arcsec). When set to 0, it is auto-calculated as 0.75 * sigm_s.
alph_s	float	2.0	Kernel shape factor. A value of 2.0 produces a Gaussian kernel. Values larger than 2 produce a sharper (more top-hat-like) kernel.
flu16	bool	True	If True, output cube flux units are 10-16 erg/s/cm2/A. If False, units are erg/s/cm2/A.
nameF	string	–	Root name for the target. Used as both the output cube filename stem and the exposure list filename (read from pathF + nameF).
use_slitmap	bool	True	Use the astrometry stored in the slitmap header of the RSS files.
pbars	bool	True	Enable or disable progress bars during processing.
spec_range	list	[0, 0]	Spectral range [lambda_min, lambda_max] in Angstroms for the output cube. Set to [0, 0] to use the full spectral range from the input RSS files.
path_sas	string	''	Path to the local SDSS SAS directory. Used only if the SAS_BASE_DIR environment variable is not defined (see SAS Directory Resolution).
basename	string	lvmSFrame-NAME.fits	Template filename of the input RSS files. NAME is replaced at runtime with the exposure number.
errors	bool	True	Enable error propagation. When True, the output cube includes an error extension computed via inverse-variance weighting.
fac_sizeY	float	1.1	Multiplicative factor applied to the field-of-view extent in the Y (declination) direction.
fac_sizeX	float	1.1	Multiplicative factor applied to the field-of-view extent in the X (right ascension) direction.
cent	bool	True	Enable centering of the output field-of-view on the coordinates given by coord_cen.
coord_cen	list	[0, 0]	Central coordinates [RA, Dec] in degrees for the output cube. Used when cent is True.
pathF	string	''	Directory path where the exposure list file is located. The code opens pathF + nameF, so this must end with / if non-empty.

sincube Example

---
sincube:
  - survey_type: LVM
    out_path: out_cubes/
    redux_ver: 1.1.1.dev0
    redux_dir: ''
    sigm_s: 32.2
    pix_s: 0.0
    alph_s: 2
    flu16: True
    nameF: NGC_1234
    use_slitmap: True
    pbars: True
    spec_range: [0, 0]
    path_sas: ''
    basename: lvmSFrame-NAME.fits
    errors: True
    fac_sizeY: 1.1
    fac_sizeX: 1.1
    cent: True
    coord_cen: [180.0, -30.0]
    pathF: exposure_lists/

pipecube Configuration

The pipecube section defines parameters for batch-processing multiple targets. It shares most parameters with sincube but adds pipeline-specific options and uses a predefined kernel type instead of explicit sigm_s/pix_s values.

Parameter	Type	Default	Description
survey_type	string	LVM	Survey identifier. Must contain LVM.
out_path	string	out_cubes/	Base output directory. The pipeline automatically appends <redux_ver>/<type>/ to this path and creates the directory if it does not exist.
redux_ver	string	1.1.1.dev0	DRP reduction version.
redux_dir	string	''	Path to the redux directory. When empty, defaults to <path_sas>/sdsswork/lvm/spectro/redux.
type	string	c	Kernel type code that sets the spatial resolution. See Type-to-parameter mapping below.
flu16	bool	True	Flux unit scaling (same as sincube).
nameL	list	–	List of target names, e.g. [NGC_1234, NGC_5678]. Each name is used to find the corresponding exposure list file at pathF + name.
use_slitmap	bool	True	Use slitmap astrometry.
pbars	bool	True	Enable progress bars.
path_sas	string	''	Local SAS directory path (see SAS Directory Resolution).
basename	string	lvmSFrame-NAME.fits	RSS file template name.
errors	bool	True	Enable error propagation.
fac_sizeY	float	1.1	FoV Y extent factor.
fac_sizeX	float	1.1	FoV X extent factor.
cent	bool	True	Enable FoV centering.
coord_cenL	list	[[0,0]]	List of [RA, Dec] coordinate pairs (degrees), one per target in nameL. Used when cent is True.
pathF	string	''	Directory containing the exposure list files.
mergecube	bool	False	Enable cube merging. When a target has more than 100 exposures, the cube is built in spectral chunks and then co-added.
nsp	int	0	Number of spatial tiles per axis for the merged cube (nsp x nsp grid). Set to 0 or 1 to disable spatial tiling.
cube2rss	bool	True	After cube generation, extract an RSS from the cube.
out_pathrss	string	out_rss/	Base output directory for extracted RSS files. The pipeline appends <redux_ver>/<type>/ automatically.
nproc	int	3	Number of parallel threads for the kernel interpolation.
force_merge	bool	False	When True, skip cube generation and only run the co-addition step. Useful for restarting after a partial run.
index_reset	int	0	Starting index for spectral chunk processing. Set to a non-zero value to resume from a specific chunk after interruption.

pipecube Example

---
pipecube:
  - survey_type: LVM
    out_path: out_cubes/
    redux_ver: 1.1.1.dev0
    redux_dir: ''
    type: c
    flu16: True
    nameL: [NGC_1234, NGC_5678]
    use_slitmap: True
    pbars: True
    path_sas: ''
    basename: lvmSFrame-NAME.fits
    errors: True
    fac_sizeY: 1.1
    fac_sizeX: 1.1
    cent: True
    coord_cenL: [[180.0, -30.0], [200.0, -25.0]]
    pathF: exposure_lists/
    mergecube: False
    nsp: 0
    cube2rss: True
    out_pathrss: out_rss/
    nproc: 3
    force_merge: False
    index_reset: 0

Kernel Type Codes

The pipecube command uses a single-letter type code to select a predefined kernel size. The kernel size (sigm_s) and spaxel size (pix_s) are computed as:

sigm_s = 8.8 * 32 * multiplier    (arcsec)
pix_s  = 8.8 * 0.75 * 32 * multiplier  (arcsec)

where the multiplier depends on the type code:

Code	Multiplier	sigm_s (arcsec)	pix_s (arcsec)
a	16	4505.6	3379.2
b	8	2252.8	1689.6
c	4	1126.4	844.8
d	2	563.2	422.4
e	1	281.6	211.2
f	1/2	140.8	105.6
g	1/4	70.4	52.8
h	1/8	35.2	26.4
i	1/16	17.6	13.2
j	1/32	8.8	6.6

Larger multipliers produce coarser spatial resolution (bigger kernels and spaxels), suitable for large mosaics. Smaller multipliers give finer resolution for individual pointings.

Note

For targets with fewer than 3 exposures, types i and j are automatically upgraded to type h to avoid undersampling.

SAS Directory Resolution

The code resolves the SAS base directory in this order:

1. If the SAS_BASE_DIR environment variable is set, its value is used (with a trailing / appended).

2. Otherwise, the path_sas config parameter is used (with a trailing / appended).

The redux directory is then constructed as:

<SAS_BASE_DIR>/sdsswork/lvm/spectro/redux

unless redux_dir is explicitly set to a non-empty value.

Output Path Construction

sincube: Output files are written directly to out_path.

pipecube: The pipeline appends <redux_ver>/<type>/ to both out_path and out_pathrss. For example, with:

out_path: out_cubes/
out_pathrss: out_rss/
redux_ver: 1.1.1.dev0
type: c

the effective output paths become:

out_cubes/1.1.1.dev0/c/
out_rss/1.1.1.dev0/c/

These directories are created automatically if they do not exist.