PixTable¶

class mpdaf.drs.PixTable(filename, xpos=None, ypos=None, lbda=None, data=None, dq=None, stat=None, origin=None, weight=None, primary_header=None, save_as_ima=True, wcs=Unit("pix"), wave=Unit("Angstrom"), unit_data=Unit("ct"))[source]¶

Bases: object

PixTable class.

This class manages input/output for MUSE pixel table files. The FITS file is opened with memory mapping. Just the primary header and table dimensions are loaded. The methods get_xpos, get_ypos, get_lambda, get_data, get_dq, get_stat and get_origin must be used to get columns data.

Parameters:

filename : str

The FITS file name. None by default.

Attributes

filename	(str) The FITS file name. None if any.
primary_header	(`astropy.io.fits.Header`) The primary header.
nrows	(int) Number of rows.
nifu	(int) Number of merged IFUs that went into this pixel table.
wcs	(`astropy.units.Unit`) Type of spatial coordinates of this pixel table (u.pix, u.deg or u.rad)
wave	(`astropy.units.Unit`) Type of spectral coordinates of this pixel table
ima	(bool) If True, pixtable is saved as multi-extension FITS image instead of FITS binary table.

Attributes Summary

`fluxcal`	If True, this pixel table was flux-calibrated.
`projection`	Return the projection type.
`skysub`	If True, this pixel table was sky-subtracted.

Methods Summary

`copy`()	Copy PixTable object in a new one and returns it.
`divide_slice_median`(skyref, pixmask)
`extract`([filename, sky, lbda, ifu, sl, ...])	Extracts a subset of a pixtable using the following criteria:
`extract_from_mask`(mask)	Return a new pixtable extracted with the given mask.
`get_column`(name[, ksel])	Load a column and return it.
`get_data`([ksel, unit])	Load the data column and return it.
`get_dq`([ksel])	Load the dq column and return it.
`get_exp`()	Load the exposure numbers and return it as a column.
`get_keyword`(key)	Return the keyword value corresponding to key, adding the keyword prefix (`'HIERARCH ESO DRS MUSE PIXTABLE'`).
`get_lambda`([ksel, unit])	Load the lambda column and return it.
`get_origin`([ksel])	Load the origin column and return it.
`get_pos_sky`([xpos, ypos])	Return the absolute position on the sky in degrees/pixel.
`get_stat`([ksel, unit])	Load the stat column and return it.
`get_weight`([ksel])	Load the weight column and return it.
`get_xpos`([ksel, unit])	Load the xpos column and return it.
`get_ypos`([ksel, unit])	Load the ypos column and return it.
`info`()	Print information.
`mask_column`([maskfile])	Compute the mask column corresponding to a mask file.
`origin2coords`(origin)	Converts the origin value and returns (ifu, slice, ypix, xpix).
`origin2ifu`(origin)	Converts the origin value and returns the ifu number.
`origin2slice`(origin)	Converts the origin value and returns the slice number.
`origin2xoffset`(origin[, ifu, sli])	Converts the origin value and returns the x coordinates offset.
`origin2xpix`(origin[, ifu, sli])	Converts the origin value and returns the x coordinates.
`origin2ypix`(origin)	Converts the origin value and returns the y coordinates.
`reconstruct_det_image`([xstart, ystart, ...])	Reconstructs the image on the detector from the pixtable.
`reconstruct_det_waveimage`()	Reconstructs an image of wavelength values on the detector from the pixtable.
`select_exp`(exp, col_exp)	Return a mask corresponding to given exposure numbers.
`select_ifus`(ifus[, origin])	Return a mask corresponding to given ifus.
`select_lambda`(lbda[, unit])	Return a mask corresponding to the given wavelength range.
`select_sky`(sky)	Return a mask corresponding to the given aperture on the sky
`select_slices`(slices[, origin])	Return a mask corresponding to given slices.
`select_stacks`(stacks[, origin])	Return a mask corresponding to given stacks.
`select_xpix`(xpix[, origin])	Return a mask corresponding to given detector pixels.
`select_ypix`(ypix[, origin])	Return a mask corresponding to given detector pixels.
`selfcalibrate`([pixmask, corr_clip, logfile])	Correct the background level of the slices.
`set_column`(name, data[, ksel])	Set a column (or a part of it).
`set_data`(data[, ksel, unit])	Set data column (or a part of it).
`set_dq`(dq[, ksel])	Set dq column (or a part of it).
`set_keyword`(key, val)	Set the keyword value corresponding to key, adding the keyword prefix (`'HIERARCH ESO DRS MUSE PIXTABLE'`).
`set_lambda`(lbda[, ksel, unit])	Set lambda column (or a part of it).
`set_origin`(origin[, ksel])	Set origin column (or a part of it).
`set_stat`(stat[, ksel, unit])	Set stat column (or a part of it).
`set_weight`(weight[, ksel])	Set weight column (or a part of it).
`set_xpos`(xpos[, ksel, unit])	Set xpos column (or a part of it).
`set_ypos`(ypos[, ksel, unit])	Set ypos column (or a part of it).
`sky_ref`([pixmask, dlbda, nmax, nclip, ...])	Compute the reference sky spectrum using sigma clipped median.
`subtract_slice_median`(skyref, pixmask)
`write`(filename[, save_as_ima])	Save the object in a FITS file.

Attributes Documentation

fluxcal¶: If True, this pixel table was flux-calibrated.

projection¶

Return the projection type.

‘positioned’ for positioned pixtables
‘projected’ for reduced pixtables

skysub¶: If True, this pixel table was sky-subtracted.

Methods Documentation

copy()[source]¶: Copy PixTable object in a new one and returns it.

divide_slice_median(skyref, pixmask)[source]¶

extract(filename=None, sky=None, lbda=None, ifu=None, sl=None, xpix=None, ypix=None, exp=None, stack=None, method='and')[source]¶

Extracts a subset of a pixtable using the following criteria:

aperture on the sky (center, size and shape)
wavelength range
IFU numbers
slice numbers
detector pixels
exposure numbers
stack numbers

The arguments can be either single value or a list of values to select multiple regions.

Parameters:

filename : str

The FITS filename used to save the resulted object.

sky : (float, float, float, char)

(y, x, size, shape) extract an aperture on the sky, defined by a center (y, x) in degrees/pixel, a shape (‘C’ for circular, ‘S’ for square) and size (radius or half side length) in arcsec/pixels.

lbda : (float, float)

(min, max) wavelength range in angstrom.

ifu : int or list

IFU number.

sl : int or list

Slice number on the CCD.

xpix : (int, int) or list

(min, max) pixel range along the X axis

ypix : (int, int) or list

(min, max) pixel range along the Y axis

exp : list of int

List of exposure numbers

stack : list of int

List of stack numbers

method : ‘and’ or ‘or’

Logical operation used to merge the criteria

Returns:

out : PixTable

extract_from_mask(mask)[source]¶

Return a new pixtable extracted with the given mask.

Parameters:

mask : numpy.ndarray

Mask (array of bool).

Returns:

out : PixTable

get_column(name, ksel=None)[source]¶

Load a column and return it.

Parameters:

name : str or attribute

Name of the column.

ksel : output of np.where

Elements depending on a condition.

Returns:

out : numpy.array

get_data(ksel=None, unit=None)[source]¶

Load the data column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

Unit of the returned data.

Returns:

out : numpy.array

get_dq(ksel=None)[source]¶

Load the dq column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

Returns:

out : numpy.array

get_exp()[source]¶

Load the exposure numbers and return it as a column.

Returns:	out : numpy.memmap

get_keyword(key)[source]¶

Return the keyword value corresponding to key, adding the keyword prefix ('HIERARCH ESO DRS MUSE PIXTABLE').

Parameters:

key : str

Keyword.

Returns:

out : keyword value

get_lambda(ksel=None, unit=None)[source]¶

Load the lambda column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

Unit of the returned data.

Returns:

out : numpy.array

get_origin(ksel=None)[source]¶

Load the origin column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

Returns:

out : numpy.array

get_pos_sky(xpos=None, ypos=None)[source]¶

Return the absolute position on the sky in degrees/pixel.

Parameters:

xpos : numpy.array

xpos values

ypos : numpy.array

ypos values

Returns:

xpos_sky, ypos_sky : numpy.array, numpy.array

get_stat(ksel=None, unit=None)[source]¶

Load the stat column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

Unit of the returned data.

Returns:

out : numpy.array

get_weight(ksel=None)[source]¶

Load the weight column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

Returns:

out : numpy.array

get_xpos(ksel=None, unit=None)[source]¶

Load the xpos column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

Unit of the returned data.

Returns:

out : numpy.array

get_ypos(ksel=None, unit=None)[source]¶

Load the ypos column and return it.

Parameters:

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

Unit of the returned data.

Returns:

out : numpy.array

info()[source]¶: Print information.

mask_column(maskfile=None)[source]¶

Compute the mask column corresponding to a mask file.

Parameters:

maskfile : str

Path to a FITS image file with WCS information, used to mask out bright continuum objects present in the FoV. Values must be 0 for the background and >0 for objects.

Returns:

out : mpdaf.drs.PixTableMask

origin2coords(origin)[source]¶

Converts the origin value and returns (ifu, slice, ypix, xpix).

Parameters:

origin : int

Origin value.

Returns:

out : (int, int, float, float)

origin2ifu(origin)[source]¶

Converts the origin value and returns the ifu number.

Parameters:

origin : int

Origin value.

Returns:

out : int

origin2slice(origin)[source]¶

Converts the origin value and returns the slice number.

Parameters:

origin : int

Origin value.

Returns:

out : int

origin2xoffset(origin, ifu=None, sli=None)[source]¶

Converts the origin value and returns the x coordinates offset.

Parameters:

origin : int

Origin value.

Returns:

out : float

origin2xpix(origin, ifu=None, sli=None)[source]¶

Converts the origin value and returns the x coordinates.

Parameters:

origin : int

Origin value.

Returns:

out : float

origin2ypix(origin)[source]¶

Converts the origin value and returns the y coordinates.

Parameters:

origin : int

Origin value.

Returns:

out : float

reconstruct_det_image(xstart=None, ystart=None, xstop=None, ystop=None)[source]¶

Reconstructs the image on the detector from the pixtable.

The pixtable must concerns only one IFU, otherwise an exception is raised.

Returns:	out : `Image`

reconstruct_det_waveimage()[source]¶

Reconstructs an image of wavelength values on the detector from the pixtable. The pixtable must concerns only one IFU, otherwise an exception is raised.

Returns:	out : `Image`

select_exp(exp, col_exp)[source]¶

Return a mask corresponding to given exposure numbers.

Parameters:

exp : list of int

List of exposure numbers

Returns:

out : array of bool

mask

select_ifus(ifus, origin=None)[source]¶

Return a mask corresponding to given ifus.

Parameters:

ifu : int or list

IFU number.

Returns:

out : array of bool

mask

select_lambda(lbda, unit=Unit("Angstrom"))[source]¶

Return a mask corresponding to the given wavelength range.

Parameters:

lbda : (float, float)

(min, max) wavelength range in angstrom.

unit : astropy.units.Unit

Unit of the wavelengths in input.

Returns:

out : array of bool

mask

select_sky(sky)[source]¶

Return a mask corresponding to the given aperture on the sky (center, size and shape)

Parameters:

sky : (float, float, float, char)

(y, x, size, shape) extract an aperture on the sky, defined by a center (y, x) in degrees/pixel, a shape (‘C’ for circular, ‘S’ for square) and size (radius or half side length) in arcsec/pixels.

Returns:

out : array of bool

mask

select_slices(slices, origin=None)[source]¶

Return a mask corresponding to given slices.

Parameters:

slices : list of int

Slice number on the CCD.

Returns:

out : array of bool

mask

select_stacks(stacks, origin=None)[source]¶

Return a mask corresponding to given stacks.

Parameters:

stacks : list of int

Stacks numbers (1,2,3 or 4)

Returns

——-

out : array of bool

mask

select_xpix(xpix, origin=None)[source]¶

Return a mask corresponding to given detector pixels.

Parameters:

xpix : list

[(min, max)] pixel range along the X axis

Returns:

out : array of bool

mask

select_ypix(ypix, origin=None)[source]¶

Return a mask corresponding to given detector pixels.

Parameters:

ypix : list

[(min, max)] pixel range along the Y axis

Returns:

out : array of bool

mask

selfcalibrate(pixmask=None, corr_clip=15.0, logfile=None)[source]¶

Correct the background level of the slices.

This requires a Pixtable that is not sky-subtracted. It uses the mean sky level as a reference, and compute a multiplicative correction to apply to each slice to bring its background level to the reference one.

A mask of sources can be provided. A PixTableMask must be computed from a 2D mask file with mask_column. This mask will be merged with the ‘DQ’ column from the pixtable.

The method works on wavelength bins, defined in mpdaf.drs.pixtable.SKY_SEGMENTS. These bins have been chosen so that their edges do not fall on a sky line, with a 200A to 300A width. They can also be modified (by setting a new list to this global variable).

Then, the algorithm can be summarized as follow:

- foreach lambda bin:
    - foreach ifu:
        - foreach slice:
            - foreach pixel:
                - compute the mean flux
            - compute the median flux of the slice
        - compute the median flux of the ifu
        - foreach slice:
            - if too few points, use the mean ifu flux
    - compute the total mean flux

    - foreach ifu:
        - foreach slice:
            - compute the correction: total_flux / slice_flux
        - compute the mean and stddev of the corrections
        - for slices where |correction - mean| > corr_clip*std_dev:
            - use the mean ifu correction: total_flux / ifu_flux

- foreach ifu:
    - foreach slice:
        - foreach lambda bin:
            - reject spikes in the correction curves, using
              a comparison with the correction from the next and
              previous lambda bin.

Parameters:

pixmask : mpdaf.drs.PixTableMask

Column corresponding to a mask file (previously computed by mask_column).

corr_clip : float

Clipping threshold for slice corrections in one IFU.

logfile : str

Path to a file to which the log will be written.

Returns:

out : mpdaf.drs.PixTableAutoCalib

set_column(name, data, ksel=None)[source]¶

Set a column (or a part of it).

Parameters:

name : str or attribute

Name of the column.

data : numpy.array

data values

ksel : output of np.where

Elements depending on a condition.

set_data(data, ksel=None, unit=None)[source]¶

Set data column (or a part of it).

Parameters:

data : numpy.array

data values

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

unit of the data column in input.

set_dq(dq, ksel=None)[source]¶

Set dq column (or a part of it).

Parameters:

dq : numpy.array

dq values

ksel : output of np.where

Elements depending on a condition.

set_keyword(key, val)[source]¶

Set the keyword value corresponding to key, adding the keyword prefix ('HIERARCH ESO DRS MUSE PIXTABLE').

Parameters:

key : str

Keyword.

val : str or int or float

Value.

set_lambda(lbda, ksel=None, unit=None)[source]¶

Set lambda column (or a part of it).

Parameters:

lbda : numpy.array

lbda values

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

unit of the lambda column in input.

set_origin(origin, ksel=None)[source]¶

Set origin column (or a part of it).

Parameters:

origin : numpy.array

origin values

ksel : output of np.where

Elements depending on a condition.

set_stat(stat, ksel=None, unit=None)[source]¶

Set stat column (or a part of it).

Parameters:

stat : numpy.array

stat values

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

unit of the stat column in input.

set_weight(weight, ksel=None)[source]¶

Set weight column (or a part of it).

Parameters:

weight : numpy.array

weight values

ksel : output of np.where

Elements depending on a condition.

set_xpos(xpos, ksel=None, unit=None)[source]¶

Set xpos column (or a part of it).

Parameters:

xpos : numpy.array

xpos values

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

unit of the xpos column in input.

set_ypos(ypos, ksel=None, unit=None)[source]¶

Set ypos column (or a part of it).

Parameters:

ypos : numpy.array

ypos values

ksel : output of np.where

Elements depending on a condition.

unit : astropy.units.Unit

unit of the ypos column in input.

sky_ref(pixmask=None, dlbda=1.0, nmax=2, nclip=5.0, nstop=2, lmin=None, lmax=None)[source]¶

Compute the reference sky spectrum using sigma clipped median.

Algorithm from Kurt Soto (kurt.soto@phys.ethz.ch)

Parameters:

pixmask : mpdaf.drs.PixTableMask

Column corresponding to a mask file (previously computed by mask_column).

dlbda : double

Wavelength step in angstrom

nmax : int

Maximum number of clipping iterations

nclip : float or (float,float)

Number of sigma at which to clip. Single clipping parameter or lower/upper clipping parameters

nstop : int

If the number of not rejected pixels is less than this number, the clipping iterations stop.

Returns:

out : Spectrum

subtract_slice_median(skyref, pixmask)[source]¶

write(filename, save_as_ima=True)[source]¶

Save the object in a FITS file.

Parameters:

filename : str

The FITS filename.

save_as_ima : bool

If True, pixtable is saved as multi-extension FITS image instead of FITS binary table.