aztools.misc

Miscellaneous Utilities

Functions

split_array(arr, length, *args[, strict])	Split an array arr to segments of length length.
group_array(arr[, by_n, bins])	Group elements of array arr given one of the criterion
write_pha_spec(bin1, bin2, arr, err, stem, **kwargs)	Write some data array to pha file so it can be
write_2d_veusz(fname, arr[, xcent, ycent, append])	Write a 2d array to a file for veusz viewing
set_fancy_plot()	Some settings for plt that make nicer plots
sync_lcurve(lc_list[, tbase])	Synchronize a list of arrays or LCurves
lcurve_to_segments(lcurves, seglen[, strict])	Split an LCurve or a list of them to segments.
read_fits_lcurve(fits_file, **kwargs)	Read a light cuurve from fits file
run_cmd_line_tool(cmd[, env, allow_fail, logfile])	Run a command line tool
add_spectra(speclist, outfile, **kwargs)	Call addspec to combine spectra.
parallelize(func[, use_irun])	A wrapper to make a function run in parallel

Module Contents

split_array(arr: numpy.ndarray, length: int, *args, strict: bool = False, **kwargs)

Split an array arr to segments of length length.

Parameters:

• arr (np.ndarray) – The array to be split.

• length (int) – The desired length of the segments

• strict (bool) – If True, force all segments to have length length. Some data may be discarded

• split (any other arrays similar to arr to be)

Keywords

overlap: int

number < length of overlap between segments.

split_at_gaps: bool

Split at non-finite values. Default True.

min_seg_length: int.

Minimum seg length to keep. Used when strict=False

approx: int

length is used as an approximation.

returns:

A tuple with

rtype:

(result, indx, …{other arrays if given})

group_array(arr: numpy.ndarray, by_n: numpy.ndarray | list = None, bins: numpy.ndarray | list = None, **kwargs)

Group elements of array arr given one of the criterion

Parameters:

• arr (np.ndarray) – The array to be grouped. Assumed 1d.

• by_n (np.ndarray or list) – [nstart, nfac] creates a new groupd at [nstart, nstart*nfac, nstart*nfac^2 …]

• bins (np.ndarray or list) – A list of bin boundaries. Values outside these bins are discarded

• Keywords

• --------

• do_unique (bool) – if True, the groupping is done for the unique values.

• min_per_bin (int) – The minimum number of elements per bin.

write_pha_spec(bin1: list | numpy.ndarray, bin2: list | numpy.ndarray, arr: numpy.ndarray, err: numpy.ndarray, stem: str, **kwargs)

Write some data array to pha file so it can be used inside xspec

Parameters:

• bin1 (list of np.ndarray.) – The lower boundaries of bins

• bin2 (list of np.ndarray.) – The upper boundaries of bins

• arr (np.ndarray) – The array of data values to be written.

• err (np.ndarray) – The array of measurement error corresponding to arr.

• Keywords

• --------

• stem (str:) – Stem name for the output spectra -> {stem}.pha|rsp

write_2d_veusz(fname: str, arr: numpy.ndarray, xcent: numpy.ndarray = None, ycent: numpy.ndarray = None, append: bool = False)

Write a 2d array to a file for veusz viewing

Parameters:

• fname (str) – The name of file to write.

• arr (np.ndarray) – The array to write, its shape is (len(xcent), len(ycent))

• xcent (np.ndarray:) – Central points of X-axis.

• ycent (np.ndarray:) – Central points of Y-axis.

• append (bool) – Append to file? Default=False

set_fancy_plot()

Some settings for plt that make nicer plots

sync_lcurve(lc_list: list | numpy.ndarray, tbase: numpy.ndarray = None)

Synchronize a list of arrays or LCurves

Parameters:

• lc_list (list) – A list of arrays or a list of LCurve objects. if arrays, the shape is (nlcurve, 3 (or 4 with fexp), ntime). The 3 is for (time, rate, rerr)

• tbase (np.ndarray) – The time array to use for reference. If not given, use the intersection of all time arrays

Return type:

a list of sync’ed arrays/light curves

lcurve_to_segments(lcurves, seglen: float, strict: bool = False, **kwargs)

Split an LCurve or a list of them to segments. Useful to be used with calculate_psd|lag etc.

Parameters:

• lcurves (LCurve) – an LCurve or a list of them

• seglen (float) – segment length in seconds.

• strict (bool) – force all segments to have length length. Some data may be discarded

• Keywords

• --------

• uneven (The light curves are uneven, so the splitting produces) – segments that have the same number of points. Default: False

• split_array (**other arguments to be passed to)

Returns:

• rate, rerr, time, seg_idx

• seg_idx is the indices used to create the segments.

read_fits_lcurve(fits_file: str, **kwargs)

Read a light cuurve from fits file

Parameters:

• fits_file (str) – Name of the fits file.

• Keywords

• --------

• min_exp (float) – minimum fractional exposure to allow. Default 0.0 for all

• rate_tbl (str or int) – Name or number of hdu that contains the light curve data. Default: RATE

• rate_col (str or int) – Name or number of rate column. Default: RATE

• time_col (str or int) – Name or number of time column. Default: TIME

• rerr_col (str or int) – Name or number of rerr column. Default: ERROR

• fexp_col (str or int) – Name or number of the fracexp column. Default: FRACEXP

• gti_table (str or int) – Name or number of gti extension hdu. Default: GTI

• dt_key (str or int) – Name of time sampling keyword in header. Default: TIMEDEL

• gti_skip (float) – How many seconds to skip at the gti boundaries. Default: 0

• verbose (bool) – Print progress

Returns:

lcurve_data (shape

Return type:

4,nt containing, time, rate, rerr, fexp), deltat

run_cmd_line_tool(cmd: str, env: dict = None, allow_fail: bool = True, logfile: str = None)

Run a command line tool

Parameters:

• cmd (str) – The command string to be run where the parameters are in the string

• env (dict) – Dictionary of environment variables to be used by the task

• allow_fail (bool) – If True and the task fails, return without raising an exception

• logfile (str) – File name to long output/error to. If None, no logs are produced

add_spectra(speclist: list, outfile: str, **kwargs)

Call addspec to combine spectra.

do it multiple times if num of spectra above kwargs[‘nmax’]

Parameters:

• speclist (list) – list of the names of the spectral files to be added

• outfile (str) – output name root

• Keywords

• ---------

• nmax (int) – add a maximum of nmax spectra at a time

• (qaddrmf (other parameters for addspec)

• qsubback

• clobber)

parallelize(func, use_irun=True)

A wrapper to make a function run in parallel

Parameters:

• func (method) – The method to parallelize. It can have any args or kwargs.

• use_irun (bool) – If True, pass a keyword argument irun as int to func that holds the call number in the sequence of parallel calls. See description of the returned function below

Returns:

• return a method with parameters that are lists of args/kwargs

• to be passed to func. The returned method takes these special kwargs