mangadap.config.manga module

Class defining the I/O configuration for MaNGA files in the DAP.

License

Copyright © 2019, SDSS-IV/MaNGA Pipeline Group

class mangadap.config.manga.MaNGAAnalysisPlan(planlist, cube=None, analysis_path=None)[source]

Bases: AnalysisPlan

Define the analysis plan and output paths for MaNGA data.

This class only redefines the output paths from the base class.

common_path()[source]

Return the path for data common to all plans.

Parameters:

cube (DataCube, optional) – Cube being analyzed. Passed for cube-specific path specification. Not used by this base class.

Returns:

Path object for the “common” output

Return type:

Path

method_path(plan_index=0, qa=False, ref=False)[source]

Return the path for method-specific output.

Parameters:

  • cube (DataCube, optional) – Cube being analyzed. Passed for cube-specific path specification. Not used by this base class.

  • plan_index (int, optional) – The index of the plan. This is used to select the ‘key’ of the analysis plan being used, which is used as the subdirectory for the output.

  • qa (bool, optional) – Flag that the output is specifically quality assessment plots.

  • ref (bool, optional) – Flag that the output is specifically reference data.

Returns:

Path object for the method-specific output

Return type:

Path

Raises:

ValueError – Raised if the plan index is invalid or if both qa and ref are true.

class mangadap.config.manga.MaNGAConfig(plate, ifudesign, mode='CUBE', log=True, drpver=None, redux_path=None, chart_path=None, directory_path=None)[source]

Bases: object

property cfg_root

Generate the root name of the MaNGA DAP configuration and script files.

Returns:

Root name for the DAP file: mangadap-[PLATE]-[IFUDESIGN]-LOG[MODE]

Return type:

str

static check_mode(mode)[source]

Check that the mode is valid.

Valide modes are set by mode_options().

Parameters:

mode (str) – Mode value to check.

Raises:

ValueError – Raised if the mode is undefined.

copy()[source]

Create a deep copy.

static cube_pixelscale()[source]

Return the default pixel scale of the DRP CUBE files in arcsec.

static cube_recenter()[source]

Return the default recentering flag used when regridding the DRP RSS spectra into the CUBE format.

static cube_width_buffer()[source]

Return the default width buffer in pixels used when regridding the DRP RSS spectra into the CUBE format.

static do_not_fit_flags()[source]

Return the maskbit names that should not be fit.

static do_not_stack_flags()[source]

Return the maskbit names that should not be stacked.

static do_not_use_flags()[source]

Return the maskbit names that should not be used.

property file_name
property file_path
classmethod from_config(cfgfile, mode='CUBE')[source]
classmethod from_file(datafile)[source]

Initialize the I/O configuration from the datafile for the DAP to process.

property image_path
instrument = 'manga'
property output_root
static propagate_flags()[source]

Flags that should be propagated from the observed data to the analysis data.

static regrid_rlim()[source]

Return the default limiting radius for the Gaussian kernel used when regridding the DRP RSS spectra into the CUBE format.

static regrid_sigma()[source]

Return the default standard deviation of the Gaussian kernel used when regridding the DRP RSS spectra into the CUBE format.

static spectral_resolution(hdu, ext=None, fill=False, median=False)[source]

Return the spectral resolution for all spectra.

See spectral_resolution_extension() for a description of the precedence used when ext is None.

Parameters:

  • hdu (astropy.io.fits.HDUList) – The opened MaNGA DRP file.

  • ext (str, optional) – Specify the extension with the spectral estimate to use. See spectral_resolution_extension().

  • fill (bool, optional) – Fill masked values by interpolation. Default is to leave masked pixels in returned array.

  • median (bool, optional) – Return a single vector with the median spectral resolution instead of a per spectrum array. When using the SPECRES extension, this just returns the vector provided by the DRP file; when using either of the LSF extensions, this performs a masked median across the array and then interpolates any wavelengths that were masked in all vectors.

Returns:

Returns a str with the name of the extension used for the spectral-resolution measurements and a numpy.ma.MaskedArray with the spectral resolution data. Even if interpolated such that there should be no masked values, the function returns a masked array. Array contains the spectral resolution (\(R = \lambda/\Delta\lambda\)) pulled from the DRP file.

Return type:

tuple

static spectral_resolution_extension(hdu, ext=None)[source]

Determine the spectral resolution channel to use.

Precedence follows this order: LSFPRE, PRESPECRES, LSFPOST, SPECRES.

Parameters:

  • hdu (astropy.io.fits.HDUList) – The opened MaNGA DRP file.

  • ext (str, optional) – Specify the extension with the spectral estimate to use. Should be in None, LSFPRE, PRESPECRES, LSFPOST, or SPECRES. The default is None, which means it will return the extension found first in the order above. None is returned if none of the extensions are present.

Returns:

The name of the preferred extension to use.

Return type:

str

static write_config(ofile, plate, ifudesign, log=True, z=None, vdisp=None, ell=None, pa=None, reff=None, sres_ext=None, sres_fill=None, covar_ext=None, drpver=None, redux_path=None, directory_path=None, overwrite=True)[source]

Write the configuration file that can be used to instantiate a MaNGA data object (mangadap.datacube.manga.MaNGADataCube or mangadap.spectra.manga.MaNGARSS).

See from_config().

Parameters:

  • ofile (str, optional) – Name of the configuration file.

  • plate (int) – Plate number

  • ifudesign (int) – IFU design

  • log (bool, optional) – Use the datacube that is logarithmically binned in wavelength.

  • z (float, optional) – Estimated bulk redshift. If None, some of the DAP analysis modules will fault.

  • vdisp (float, optional) – Estimated velocity dispersion. If None, some of the DAP analysis modules will assume an initial guess of 100 km/s.

  • ell (float, optional) – Characteristic isophotal ellipticity (1-b/a). If None, some of the DAP modules will issue a warning and continue by assuming ell=0.

  • pa (float, optional) – Characteristic isophotal position angle (through E from N). If None, some of the DAP modules will issue a warning and continue by assuming pa=0.

  • reff (float, optional) – Effective (half-light) radius in arcsec. If None, some of the DAP modules will issue a warning and continue by assuming reff=1.

  • sres_ext (str, optional) – The extension to use when constructing the spectral resolution vectors. See spectral_resolution().

  • sres_fill (bool, optional) – Fill masked values by interpolation. Default is to leave masked pixels in returned array.

  • covar_ext (str, optional) – Extension to use as the single spatial correlation matrix for all wavelength channels, read from the DRP file. For generating the covariance matrix directly for an arbitrary wavelength channel using the RSS file, see mangadap.datacube.datacube.DataCube.covariance_matrix().

  • drpver (str, optional) – DRP version, which is used to define the default DRP redux path. Default is defined by mangadap.config.manga.drp_version()

  • redux_path (str, optional) – The path to the top level directory containing the DRP output files for a given DRP version. Default is defined by mangadap.config.manga.drp_redux_path().

  • directory_path (str, optional) – The exact path to the DRP file. Default is defined by mangadap.config.manga.drp_directory_path(). Providing this ignores anything provided for drpver or redux_path.

  • overwrite (bool, optional) – Overwrite any existing parameter file.

mangadap.config.manga.dap_analysis_path(drpver=None, dapver=None)[source]

Return the main output path for the DAP using the environmental variable MANGA_SPECTRO_ANALYSIS.

Parameters:

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • dapver (str, optional) – DAP version. Default is to use dap_version().

Returns:

Path to analysis directory

Return type:

str

mangadap.config.manga.dap_config(plate, ifudesign, drpver=None, dapver=None, analysis_path=None, directory_path=None)[source]

Return the full path to the DAP configuration file.

The configuration file provides the input data necessary to instantiate a mangadap.datacube.manga.MaNGADataCube.

Parameters:

  • plate (int) – Plate number

  • ifudesign (int) – IFU design number

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • dapver (str, optional) – DAP version. Default is to use dap_version().

  • analysis_path (str, optional) – Path to the root analysis directory. Default is to use dap_analysis_path().

  • directory_path (str, optional) – Path to the directory with the DAP output files. Default is to use dap_common_path()

Returns:

Full path to the DAP par file

Return type:

str

mangadap.config.manga.dap_version()[source]

Return the DAP version defined by the environmental variable MANGADAP_VER. If that environmental variable does not exist, mangadap.__version__ is returned.

mangadap.config.manga.dapall_file(drpver=None, dapver=None, analysis_path=None)[source]

Return the path to the DAPall file.

Parameters:

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • dapver (str, optional) – DAP version. Default is to use dap_version().

  • analysis_path (str, optional) – Path to the root analysis directory. Default is to use dap_analysis_path()

Returns:

Full path to the DAPall fits file.

Return type:

str

mangadap.config.manga.drp_directory_path(plate, drpver=None, redux_path=None)[source]

Return the exact directory path with the DRP file.

Parameters:

  • plate (int) – Plate number

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • redux_path (str, optional) – Path to the root reduction directory. Default is to use drp_redux_path().

Returns:

Path to the directory with the 3D products of the DRP

Return type:

str

mangadap.config.manga.drp_finding_chart_path(plate, drpver=None, redux_path=None)[source]

Return the exact directory path with the finding charts for a given plate.

Parameters:

  • plate (int) – Plate number

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • redux_path (str, optional) – Path to the root reduction directory. Default is to use drp_redux_path().

Returns:

Path to the directory with the finding charts.

Return type:

str

mangadap.config.manga.drp_redux_path(drpver=None)[source]

Return the main output path for the DRP products using the environmental variable MANGA_SPECTRO_REDUX.

Parameters:

drpver (str, optional) – DRP version. Default is to use drp_version().

Returns:

Path to reduction directory

Return type:

str

mangadap.config.manga.drp_version()[source]

Return the DRP version defined by the environmental variable MANGADRP_VER.

mangadap.config.manga.drpall_file(drpver=None, redux_path=None)[source]

Return the path to the DRPall file.

Parameters:

  • drpver (str, optional) – DRP version. Default is to use drp_version().

  • redux_path (str, optional) – Path to the root reduction directory. Default is to use drp_redux_path().

Returns:

Full path to the DRPall fits file.

Return type:

str

mangadap.config.manga.manga_fits_root(plate, ifudesign, mode=None)[source]

Generate the main root name for the output MaNGA fits files for a given plate/ifudesign/mode.

Parameters:

  • plate (int) – Plate number

  • ifudesign (int) – IFU design number

  • mode (str, optional) – Mode of the output fits file. Options are: 'LINCUBE', 'LINRSS', 'LOGCUBE', 'LOGRSS', or 'MAPS'. Default is that no mode is included in the name.

Returns:

Root name for a MaNGA fits file: manga-[PLATE]-[IFUDESIGN]-[MODE]

Return type:

str

Raises:

ValueError – Raised if mode is not a valid option.

mangadap.config.manga.parse_plate_ifu_from_file(name)[source]

Parse the plate and ifu numbers from the file name of a MaNGA DRP file.

mangadap.config.manga.photometry_fix_file()[source]

Return the path to the default photometry fix file.

Returns:

Expected path to the photometry-fix parameter file.

Return type:

str

mangadap.config.manga.plate_target_files()[source]

Return the default plateTarget files in mangacore and their associated catalog indices. The catalog indices are determined assuming the file names are of the form:

'plateTargets-{0}.par'.format(catalog_id)
Returns:

Two arrays: the first contains the identified plateTargets files found using the default search string, the second provides the integer catalog index determined for each file.

Return type:

numpy.ndarray

mangadap.config.manga.redshift_fix_file()[source]

Return the path to the default redshift fix file.

Returns:

Expected path to the redshift-fix parameter file.

Return type:

str