mangadap.proc.reductionassessments module¶

Class that performs a number of assessments of a DRP file needed for handling of the data by the DAP. These assessments need only be done once per DRP data file.

Revision history¶

24 Mar 2016: Implementation begun by K. Westfall (KBW)

11 May 2016: (KBW) Switch to using pydl.goddard.astro.airtovac instead of internal function

19 May 2016: (KBW) Added loggers and quiet keyword arguments to ReductionAssessment, removed verbose

23 Feb 2017: (KBW) Use DAPFitsUtil read and write functions.

27 Feb 2017: (KBW) Use DefaultConfig.

17 May 2017: (KBW) Added ability to use a response function for the flux statistics.

class mangadap.proc.reductionassessments.ReductionAssessment(method_key, drpf, pa=0.0, ell=0.0, method_list=None, dapsrc=None, dapver=None, analysis_path=None, directory_path=None, output_file=None, hardcopy=True, symlink_dir=None, clobber=False, checksum=False, loggers=None, quiet=False)[source]¶

Bases: object

Object used to perform and store assessments of a DRP file needed for handling of the data by the DAP. These assessments need only be done once per DRP data file.

See compute() for the provided data.

Parameters:

method_key (str) – Keyword selecting the assessment method to use.
drpf (mangadap.drpfits.DRPFits) – DRP file (object) to use for the assessments.
pa (float) – (Optional) On-sky position angle of the major axis used to calculate elliptical, semi-major-axis coordinates, defined as the angle from North through East and denoted $\phi_0$. Default is 0.0.
ell (float) – (Optional) Ellipticity defined as $\varepsilon=1-b/a$, based on the semi-minor to semi-major axis ratio ($b/a$) of the isophotal ellipse used to calculate elliptical, semi-major-axis coordinates. Default is 0.0.
method_list (list) – (Optional) List of ReductionAssessmentDef objects that define the parameters required to perform the assessments of the DRP file. The method_key must select one of these objects. Default is to construct list using available_reduction_assessments().
dapver (str) – (Optional) DAP version, which is used to define the default DAP analysis path. Default is defined by mangadap.config.defaults.default_dap_version()
analysis_path (str) – (Optional) The path to the top level directory containing the DAP output files for a given DRP and DAP version. Default is defined by mangadap.config.defaults.default_analysis_path().
directory_path (str) – (Optional) The exact path for the output file. Default is defined by mangadap.config.defaults.default_dap_common_path().
output_file (str) – (Optional) The name of the file for the computed assessments. The full path of the output file will be directory_path/output_file. Default is defined by mangadap.config.defaults.default_dap_file_name().
hardcopy (bool) – (Optional) Flag to write the data to a fits file. Default is True.
symlink_dir (str) – (Optional) Create a symlink to the file in this directory. Default is for no symlink.
clobber (bool) – (Optional) If the output file already exists, this will force the assessments to be redone and the output file to be overwritten. Default is False.
checksum (bool) – (Optional) Compare the checksum when reading the data.
loggers (list) – (Optional) List of logging.Logger objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output(). Default is no logging.
quiet (bool) – (Optional) Suppress all terminal and logging output. Default is False.

method¶

Parameters defining the method to use for the reduction assessments.

Type:	`ReductionAssessmentDef`

drpf¶

DRP file (object) with which the template library is associated for analysis

Type:	`mangadap.drpfits.DRPFits`

pa¶

On-sky position angle of the major axis used to calculate elliptical, semi-major-axis coordinates, defined as the angle from North through East and denoted $\phi_0$.

Type:	float

ell¶

Ellipticity defined as $\varepsilon=1-b/a$, based on the semi-minor to semi-major axis ratio ($b/a$) of the isophotal ellipse used to calculate elliptical, semi-major-axis coordinates.

Type:	float

directory_path¶

The exact path for the output file. Default is defined by mangadap.config.defaults.default_dap_common_path().

Type:	str

output_file¶

The name of the file for the computed assessments. The full path of the output file will be directory_path/output_file. Default is defined by _set_paths().

Type:	str

hardcopy¶

Flag to keep a hardcopy of the data by writing the data to a fits file.

Type:	bool

symlink_dir¶

Symlink created to the file in this directory

Type:	str

hdu¶

HDUList with the data, with columns as described above.

Type:	astropy.io.fits.hdu.hdulist.HDUList

correlation¶

Covariance matrix for the mean flux measurements, if calculated.

Type:	`mangadap.util.covariance.Covariance`

loggers¶

List of logging.Logger objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output().

Type:	list

quiet¶

Suppress all terminal and logging output.

Type:	bool

_define_method(method_key, method_list=None, dapsrc=None)[source]¶

Select the assessment method from the provided list. Used to set method; see mangadap.proc.util.select_proc_method().

Parameters:

method_key (str) – Keyword of the selected method. Available methods are provided by available_reduction_assessments()
method_list (list) – (Optional) List of ReductionAssessmentDef objects that define the parameters required to assess the reduced data.
dapsrc (str) – (Optional) Root path to the DAP source directory. If not provided, the default is defined by mangadap.config.defaults.dap_source_dir().

_initialize_primary_header(hdr=None)[source]¶

_per_spectrum_dtype()[source]¶: Construct the record array data type for the output fits extension.

_set_paths(directory_path, dapver, analysis_path, output_file)[source]¶

Set the I/O paths. Used to set directory_path and output_file. If not provided, the defaults are set using, respectively, mangadap.config.defaults.default_dap_common_path() and mangadap.config.defaults.default_dap_file_name().

Parameters:	directory_path (str) – The exact path to the DAP reduction assessments file. See `directory_path`. dapver (str) – DAP version. analysis_path (str) – The path to the top-level directory containing the DAP output files for a given DRP and DAP version. output_file (str) – The name of the file with the reduction assessments. See `compute()`.

compute(drpf, pa=None, ell=None, dapver=None, analysis_path=None, directory_path=None, output_file=None, hardcopy=True, symlink_dir=None, clobber=False, loggers=None, quiet=False)[source]¶

Compute and output the main data products. The list of HDUs are:

PRIMARY : Empty apart from the header information.

SPECTRUM : Extension with the main, per-spectrum measurements; see below.

CORREL : The correlation matrix between the SIGNAL measurements provided in the SPECTRUM extension. The format of this extension is identical to the nominal output of the mangadap.util.covariance.Covariance object; see mangadap.util.covariance.Covariance.write().

The SPECTRUM extension contains the following columns:

DRP_INDEX : Array coordinates in the DRP file; see mangadap.drpfits.DRPFits.spatial_index. For RSS files, this is a single integer; for CUBE files, it is a vector of two integers.

SKY_COO : On-sky X and Y coordinates. Coordinates are sky-right offsets from the object center; i.e., positive X is along the direction of positive right ascension. See mangadap.drpfits.DRPFits.mean_sky_coordinates.

ELL_COO : Elliptical (semi-major axis) radius and azimuth angle from N through East with respect to the photometric position angle; based on the provided ellipticity parameters. See mangadap.util.geometry.SemiMajorAxisCoo.

FGOODPIX : Fraction of good pixels in each spectrum.

MINEQMAX : Flag that min(flux) = max(flux) in the spectrum; i.e., the spaxel has no data.

SIGNAL, VARIANCE, SNR : Per pixel means of the flux, flux variance, and signal-to-noise. The VARIANCE and SNR columns use the inverse variance provided by the DRP. See mangadap.drpfits.DRPFits.flux_stats().

Parameters:

drpf (mangadap.drpfits.DRPFits) – DRP file (object) to use for the assessments.
pa (float) – (Optional) On-sky position angle of the major axis used to calculate elliptical, semi-major-axis coordinates, defined as the angle from North through East and denoted $\phi_0$. Default is 0.0.
ell (float) – (Optional) Ellipticity defined as $\varepsilon=1-b/a$, based on the semi-minor to semi-major axis ratio ($b/a$) of the isophotal ellipse used to calculate elliptical, semi-major-axis coordinates. Default is 0.0.
dapver (str) – (Optional) DAP version, which is used to define the default DAP analysis path. Default is defined by mangadap.config.defaults.default_dap_version()
analysis_path (str) – (Optional) The path to the top level directory containing the DAP output files for a given DRP and DAP version. Default is defined by mangadap.config.defaults.default_analysis_path().
directory_path (str) – (Optional) The exact path for the output file. Default is defined by mangadap.config.defaults.default_dap_common_path().
output_file (str) – (Optional) The name of the file for the computed assessments. The full path of the output file will be directory_path/output_file. Default is defined by mangadap.config.defaults.default_reduction_assessments_file().
hardcopy (bool) – (Optional) Flag to write the data to a fits file. Default is True.
symlink_dir (str) – (Optional) Create a symlink to the file in this directory. Default is for no symlink.
clobber (bool) – (Optional) If the output file already exists, this will force the assessments to be redone and the output file to be overwritten. Default is False.
loggers (list) – (Optional) List of logging.Logger objects to log progress; ignored if quiet=True. Default is no logging.
quiet (bool) – (Optional) Suppress all terminal and logging output. Default is False.

Raises:

ValueError – Raise if no DRPFits object is provided or if the output file is undefined.

static default_paths(plate, ifudesign, method_key, directory_path=None, drpver=None, dapver=None, analysis_path=None, output_file=None)[source]¶

Set the default directory and file name for the output file.

Parameters:	plate (int) – Plate number of the observation. ifudesign (int) – IFU design number of the observation. method_key (str) – Keyword designating the method used for the reduction assessments. directory_path (str) – (Optional) The exact path to the DAP reduction assessments file. Default set by `mangadap.config.defaults.default_dap_common_path()`. drpver (str) – (Optional) DRP version. Default set by `mangadap.config.defaults.default_drp_version()`. dapver (str) – (Optional) DAP version. Default set by `mangadap.config.defaults.default_dap_version()`. analysis_path (str) – (Optional) The path to the top-level directory containing the DAP output files for a given DRP and DAP version. Default set by `mangadap.config.defaults.default_analysis_path()`. output_file (str) – (Optional) The name of the file with the reduction assessments. Default set by `mangadap.config.defaults.default_dap_file_name()`.
Returns:	Two strings with the path for the output file and the name of the output file.
Return type:	str

file_name()[source]¶: Return the name of the output file.

file_path()[source]¶: Return the full path to the output file.

info()[source]¶

class mangadap.proc.reductionassessments.ReductionAssessmentDef(key=None, waverange=None, response_func=None, covariance=False)[source]¶

Bases: mangadap.par.parset.KeywordParSet

Class with parameters used to define how the reduction assessments are performed. At the moment this is just a set of parameters that define how the S/N is calculated.

See mangadap.par.parset.ParSet for attributes.

Todo

Allow for different ways of calculating covariance?

The defined parameters are:

Key	Type	Description
`key`	str	Keyword to distinguish the assessment method.
`waverange`	ndarray, list	A two-element vector with the starting and ending wavelength (angstroms in vacuum) within which to calculate the signal-to-noise
`response_func`	ndarray, list	A two-column array with a response function to use for the S/N calculation. The columns must br the wavelength and amplitude of the response function, respectively.
`covariance`	bool	Type of covariance measurement to produce.

mangadap.proc.reductionassessments.available_reduction_assessments(dapsrc=None)[source]¶

Return the list of available reduction assessment methods. To get a list of default methods provided by the DAP do:

from mangadap.proc.reductionassessments import available_reduction_assessments
rdx_methods = available_reduction_assessments()
print(rdx_methods)

Each element in the rdx_methods list is an instance of ReductionAssessmentDef, which is printed using the ParSet base class representation function.

New methods can be included by adding ini config files to $MANGADAP_DIR/python/mangadap/config/reduction_assessments. See an example file at $MANGADAP_DIR/python/mangadap/config/example_ini/example_reduction_assessment_config.ini.

Parameters:	dapsrc (str) – (Optional) Root path to the DAP source directory (i.e., $MANGADAP_DIR). If not provided, the default is defined by `mangadap.config.defaults.dap_source_dir()`.
Returns:	A list of `ReductionAssessmentDef()` objects, each defining a separate assessment method.
Return type:	list
Raises:	`NotADirectoryError` – Raised if the provided or default dapsrc is not a directory. `OSError/IOError` – Raised if no reduction assessment configuration files could be found. `KeyError` – Raised if the assessment method keywords are not all unique. `NameError` – Raised if either ConfigParser or ExtendedInterpolation are not correctly imported. The latter is a Python 3 only module!

mangadap.proc.reductionassessments.validate_reduction_assessment_config(cnfg)[source]¶

Validate the mangadap.util.parser.DefaultConfig object that provides the reduction-assessment method parameters.

Parameters:	cnfg (`mangadap.util.parser.DefaultConfig`) – Object with the reduction-assessment method parameters needed by `mangadap.proc.reductionassessments.ReductionAssessmentDef`.
Returns:	Booleans that specify how the reduction assessment should be constructed. The flags specify to use (1) the wavelength range, (2) a bandpass filter parameter file, or (3) a file with a filter response function.
Return type:	bool
Raises:	`KeyError` – Raised if required keyword does not exist. `ValueError` – Raised if keys have unacceptable values. `FileNotFoundError` – Raised if a file is specified but could not be found.