pypeit.core.pydl module

class pypeit.core.pydl.TraceSet(*args, **kwargs)[source]

Bases: object

Implements the idea of a trace set.

func

Name of function type used to fit the trace set.

Type: str

xmin

Minimum x value.

Type: float-like

xmax

Maximum x value.

Type: float-like

coeff

Coefficients of the trace set fit.

Type: array-like

nTrace

Number of traces in the object.

Type: int

ncoeff

Number of coefficients of the trace set fit.

Type: int

xjumplo

Jump value, for BOSS readouts.

Type: float-like

xjumphi

Jump value, for BOSS readouts.

Type: float-like

xjumpval

Jump value, for BOSS readouts.

Type: float-like

lower

used for robust_polyfit_djs If set, reject points with data < model - lower * sigma.

Type: int or float, optional

upper

used for robust_polyfit_djs If set, reject points with data > model + upper * sigma.

Type: int or float, optional

outmask

When initialized with x,y positions, this contains the rejected points.

Type: array-like

yfit

When initialized with x,y positions, this contains the fitted y values.

Type: array-like

pypeitFits

Holds a list of pypeit.fitting.PypeItFit fits

Type: list

property has_jump: True if jump conditions are set.

property nx: Number of x values.

property xRange: Range of x values.

property xmid: Midpoint of x values.

xnorm(xinput, jump)[source]

Convert input x coordinates to normalized coordinates suitable for input to special polynomials.

Parameters

xinput (array-like) – Input coordinates.
jump (bool) – Set to True if there is a jump.

Returns

Normalized coordinates.

Return type

array-like

xy(xpos=None, ignore_jump=False)[source]

Convert from a trace set to an array of x,y positions.

Parameters

xpos (array-like, optional) – If provided, evaluate the trace set at these positions. Otherwise the positions will be constructed from the trace set object iself.
ignore_jump (bool, optional) – If True, ignore any jump information in the tset object

Returns

The x, y positions.

Return type

tuple() of array-like

class pypeit.core.pydl.chunks(ra, dec, minSize)[source]

Bases: object

chunks class

Functions for creating and manipulating spherical chunks are implemented as methods on this class.

assign(ra, dec, marginSize)[source]: Take the objects and the chunks (already defined in the constructor) and assign the objects to the appropriate chunks, with some leeway given by the parameter marginSize. Basically, at the end, each chunk should be associated with a list of the objects that belong to it.

chunkfriendsoffriends(ra, dec, chunkList, linkSep)[source]: Does friends-of-friends on the ra, dec that are defined by chunkList.

cosDecMin(i)[source]: Frequently used utility function.

friendsoffriends(ra, dec, linkSep)[source]: Friends-of-friends using chunked data.

get(ra, dec)[source]: Find the chunk to which a given point belongs.

getbounds(ra, dec, marginSize)[source]: Find the set of chunks a point (with margin) belongs to.

getraminmax(ra, raOffset)[source]: Utility function used by rarange.

rarange(ra, minSize)[source]

Finds the offset which yields the smallest raRange & returns both.

Notes

Warning

This is not (yet) well-defined for the case of only one point.

pypeit.core.pydl.djs_laxisgen(dims, iaxis=0)[source]

Returns an integer array where each element of the array is set equal to its index number along the specified axis.

Parameters

dims (list) – Dimensions of the array to return.
iaxis (int, optional) – Index along this dimension.

Returns

An array of indexes with dtype=int32.

Return type

numpy.ndarray

Raises

ValueError – If iaxis is greater than or equal to the number of dimensions.

Notes

For two or more dimensions, there is no difference between this routine and djs_laxisnum().

Examples

>>> from pydl.pydlutils.misc import djs_laxisgen
>>> print(djs_laxisgen([4,4]))
[[0 0 0 0]
 [1 1 1 1]
 [2 2 2 2]
 [3 3 3 3]]

pypeit.core.pydl.djs_laxisnum(dims, iaxis=0)[source]

Returns an integer array where each element of the array is set equal to its index number in the specified axis.

Parameters

dims (list) – Dimensions of the array to return.
iaxis (int, optional) – Index along this dimension.

Returns

An array of indexes with dtype=int32.

Return type

numpy.ndarray

Raises

ValueError – If iaxis is greater than or equal to the number of dimensions, or if number of dimensions is greater than three.

Notes

For two or more dimensions, there is no difference between this routine and djs_laxisgen().

Examples

>>> from pydl.pydlutils.misc import djs_laxisnum
>>> print(djs_laxisnum([4,4]))
[[0 0 0 0]
 [1 1 1 1]
 [2 2 2 2]
 [3 3 3 3]]

pypeit.core.pydl.djs_maskinterp(yval, mask, xval=None, axis=None, const=False)[source]

Interpolate over masked pixels in a vector, image or 3-D array.

Parameters

yval (numpy.ndarray) – The input values
mask (numpy.ndarray) – The mask
xval (numpy.ndarray, optional) – If set, use these x values, otherwise use an array
axis (int, optional) – Must be set if yval has more than one dimension. If set to zero, interpolate along the first axis of the array, if set to one, interpolate along the second axis of the array, and so on.
const (bool, optional) – This value is passed to a helper function, djs_maskinterp1.

Returns

The interpolated array.

Return type

numpy.ndarray

pypeit.core.pydl.djs_maskinterp1(yval, mask, xval=None, const=False)[source]

Interpolate over a masked, 1-d array.

Parameters

yval (numpy.ndarray) – The input values.
mask (numpy.ndarray) – The mask.
xval (numpy.ndarray, optional) – If set, use these x values, otherwise use an array.
const (bool, optional) – If set to True, bad values around the edges of the array will be set to a constant value. Because of the default behavior of numpy.interp(), this value actually makes no difference in the output.

Returns

The yval array with masked values replaced by interpolated values.

Return type

numpy.ndarray

pypeit.core.pydl.djs_reject(data, model, outmask=None, inmask=None, invvar=None, lower=None, upper=None, percentile=False, maxdev=None, maxrej=None, groupdim=None, groupsize=None, groupbadpix=False, grow=0, sticky=False, use_mad=False)[source]

Routine to reject points when doing an iterative fit to data.

Parameters

data (numpy.ndarray) – The data
model (numpy.ndarray) – The model, must have the same number of dimensions as data.
outmask (numpy.ndarray, optional) – Output mask, generated by a previous call to djs_reject. If sticky=True, then bad points accumulate in this mask between calls. Otherwise, this mask is only used to determine if the rejection iterations are complete (e.g. to set qdone). Although this parameter is technically optional, it will almost always be set. If not supplied, this mask will be initialized to a mask that masks nothing and qdone will always be returned as True.
inmask (numpy.ndarray, optional) – Input mask. Bad points are marked with a value that evaluates to False. Must have the same number of dimensions as data. Points masked as bad “False” in the inmask will also always evaluate to “False” in the outmask
invvar (numpy.ndarray, optional) – Inverse variance of the data, used to reject points based on the values of upper and lower.
lower (int or float, optional) – If set, reject points with data < model - lower * sigm, where sigma = 1.0/sqrt(invvar)
upper (int or float, optional) – If set, reject points with data > model + upper * sigma, where sigma = 1.0/sqrt(invvar)
maxdev (int or float, optional) – If set, reject points with abs(data-model) > maxdev. It is permitted to set all three of lower, upper and maxdev.
maxrej (int or numpy.ndarray, optional) – Maximum number of points to reject in this iteration. If groupsize or groupdim are set to arrays, this should be an array as well.
groupdim (class: int) – Dimension along which to group the data; set to 1 to group along the 1st dimension, 2 for the 2nd dimension, etc. If data has shape [100,200], then setting GROUPDIM=2 is equivalent to grouping the data with groupsize=100. In either case, there are 200 groups, specified by [*,i]. NOT WELL TESTED IN PYTHON!
groupsize (class: int) – If this and maxrej are set, then reject a maximum of maxrej points per group of groupsize points, where the grouping is performed in the along the dimension of the data vector. (For use in curve fitting, one probably wants to make sure that data is sorted according to the indpeendent variable. For multi-dimensional arrays where one desires this grouping along each dimension, then groupdim should be set. If groupdim is also set, then this specifies sub-groups within that.
groupbadpix (bool, optional) – If set to True, consecutive sets of bad pixels are considered groups, overriding the values of groupsize.
grow (int, optional, default = 0) – If set to a non-zero integer, N, the N nearest neighbors of rejected pixels will also be rejected.
sticky (bool, optional) – If set to True then points rejected in outmask from a previous call to djs_reject are kept rejected. If set to False, if a fit (model) changes between iterations, points can alternate from being rejected to not rejected.
use_mad – It set to True, compute the median of the maximum absolute deviation between the data and use this for the rejection instead of the default which is to compute the standard deviation of the yarray - modelfit. Note that it is not possible to specify use_mad=True and also pass in values invvar, and the code will return an error if this is done.

Returns

outmask (np.ndarray, boolean) – mask where rejected data values are False
qdone (boolean) – a value set to “True” if djs_reject believes there is no further rejection to be done. This will be set to “False” if the points marked as rejected in the outmask have changed. It will be set to “True” when the same points are rejected in outmask as from a previous call. It will also be set to “False” if model is set to None. Recall that outmask is also an optional input parameter. If it is not set, then qdone will simply return true, so outmask needs to be input from the previous iteration for the routine to do something meaningful.

Raises

ValueError – If dimensions of various inputs do not match.

pypeit.core.pydl.func_fit(x, y, ncoeff, invvar=None, function_name='legendre', ia=None, inputans=None, inputfunc=None)[source]

Fit x, y positions to a functional form.

Parameters

x (array-like) – X values (independent variable).
y (array-like) – Y values (dependent variable).
ncoeff (int) – Number of coefficients to fit.
invvar (array-like, optional) – Weight values; inverse variance.
function_name (str, optional) – Function name, default ‘legendre’.
ia (array-like, optional) – An array of bool of length ncoeff specifying free (True) and fixed (False) parameters.
inputans (array-like, optional) – An array of values of length ncoeff specifying the values of the fixed parameters.
inputfunc (array-like, optional) – Multiply the function fit by these values.

Returns

Fit coefficients, length ncoeff; fitted values.

Return type

tuple() of array-like

Raises

KeyError – If an invalid function type is selected.
ValueError – If input dimensions do not agree.

pypeit.core.pydl.gcirc(ra1, dec1, ra2, dec2, units=2)[source]

Computes rigorous great circle arc distances.

Parameters

ra1 (float or array-like) – RA and Dec of two points.
dec1 (float or array-like) – RA and Dec of two points.
ra2 (float or array-like) – RA and Dec of two points.
dec2 (float or array-like) – RA and Dec of two points.
units ({ 0, 1, 2 }, optional) –
- units = 0: everything is already in radians
- units = 1: RA in hours, dec in degrees, distance in arcsec.
- units = 2: RA, dec in degrees, distance in arcsec (default)

Returns

The angular distance. Units of the value returned depend on the input value of units.

Return type

float or array-like

Notes

The formula below is the one best suited to handling small angular separations. See: http://en.wikipedia.org/wiki/Great-circle_distance

class pypeit.core.pydl.groups(coordinates, distance, separation='euclid')[source]

Bases: object

Group a set of objects (a list of coordinates in some space) based on a friends-of-friends algorithm

static euclid(x1, x2)[source]: Pythagorean theorem in Euclidean space with arbitrary number of dimensions.

static sphereradec(x1, x2)[source]: Separation of two points on a 2D-sphere, assuming they are in longitude-latitude or right ascension-declination form. Assumes everything is already in radians.

pypeit.core.pydl.spheregroup(ra, dec, linklength, chunksize=None)[source]

Perform friends-of-friends grouping given ra/dec coordinates.

Parameters

ra (numpy.ndarray) – Arrays of coordinates to group in decimal degrees.
dec (numpy.ndarray) – Arrays of coordinates to group in decimal degrees.
linklength (float) – Linking length for the groups in decimal degrees.
chunksize (float, optional) – Break up the sphere into chunks of this size in decimal degrees.

Returns

A tuple containing the group number of each object, the multiplicity of each group, the first member of each group, and the next member of the group for each object.

Return type

tuple()

Raises

msgs.error – If the array of coordinates only contains one point.

Notes

It is important that chunksize >= 4 * linklength. This is enforced.

Warning

Behavior at the poles is not well tested.

pypeit.core.pydl.spherematch(ra1, dec1, ra2, dec2, matchlength, chunksize=None, maxmatch=1)[source]

Match points on a sphere.

Parameters

ra1 (numpy.ndarray) – The sets of coordinates to match. Assumed to be in decimal degrees
dec1 (numpy.ndarray) – The sets of coordinates to match. Assumed to be in decimal degrees
ra2 (numpy.ndarray) – The sets of coordinates to match. Assumed to be in decimal degrees
dec2 (numpy.ndarray) – The sets of coordinates to match. Assumed to be in decimal degrees
matchlength (float) – Two points closer than this separation are matched. Assumed to be in decimal degrees.
chunksize (float, optional) – Value to pass to chunk assignment.
maxmatch (int, optional) – Allow up to maxmatch matches per coordinate. Default 1. If set to zero, All possible matches will be returned.

Returns

A tuple containing the indices into the first set of points, the indices into the second set of points and the match distance in decimal degrees.

Return type

tuple()

Notes

If you have sets of coordinates that differ in size, call this function with the larger list first. This exploits the inherent asymmetry in the underlying code to reduce memory use.

Warning

Behavior at the poles is not well tested.

pypeit.core.pydl.traceset2xy(tset, xpos=None, ignore_jump=False)[source]

Convert from a trace set to an array of x,y positions.

Parameters

tset (TraceSet) – A TraceSet object.
xpos (array-like, optional) – If provided, evaluate the trace set at these positions. Otherwise the positions will be constructed from the trace set object iself.
ignore_jump (bool, optional) – If True, ignore any jump information in the tset object

Returns

The x, y positions.

Return type

tuple() of array-like

pypeit.core.pydl.xy2traceset(xpos, ypos, **kwargs)[source]

Convert from x,y positions to a trace set.

Parameters

xpos (array-like) – X,Y positions corresponding as [nx,Ntrace] arrays.
ypos (array-like) – X,Y positions corresponding as [nx,Ntrace] arrays.
invvar (array-like, optional) – Inverse variances for fitting.
func (str, optional) – Function type for fitting; defaults to ‘legendre’.
ncoeff (int, optional) – Number of coefficients to fit. Defaults to 3.
xmin (float, optional) – Explicitly set minimum and maximum values, instead of computing them from xpos.
xmax (float, optional) – Explicitly set minimum and maximum values, instead of computing them from xpos.
maxiter (int, optional) – Maximum number of rejection iterations; set to 0 for no rejection; default to 10.
inmask (array-like, optional) – Mask set to 1 for good points and 0 for rejected points; same dimensions as xpos, ypos. Points rejected by inmask are always rejected from the fits (the rejection is “sticky”), and will also be marked as rejected in the outmask attribute.
ia (array-like, optional) – These arguments will be passed to func_fit().
inputans (array-like, optional) – These arguments will be passed to func_fit().
inputfunc (array-like, optional) – These arguments will be passed to func_fit().
xjumplo (float, optional) – x position locating start of an x discontinuity
xjumphi (float, optional) – x position locating end of that x discontinuity
xjumpval (float, optional) – magnitude of the discontinuity “jump” between those bounds (previous 3 keywords motivated by BOSS 2-phase readout)

Returns

A TraceSet object.

Return type

TraceSet