Utility Functions

Welcome to the documentation for the ‘wifes_utils.py’ module, which contains a number of utility functions for WiFeS data.

pywifes.wifes_utils.arguments()

Report current functions source file and as-called arguments.

Adapted from http://kbyanc.blogspot.com/2007/07/python-aggregating-function-arguments.html

pywifes.wifes_utils.copy_files(src_dir_path, destination_dir_path, filenames)

Copy files from the source directory to the destination directory.

Parameters:

  • src_dir_path (str) – The path to the source directory.

  • destination_dir_path (str) – The path to the destination directory.

  • filenames (list) – A list of filenames to be copied.

Raises:

Exception – If there is an error while copying the files.

pywifes.wifes_utils.fits_scale_from_bitpix(bitpix)

Map common BITPIX header value to astropy.io.fits ‘scale’ argument.

pywifes.wifes_utils.get_associated_calib(metadata, this_fn, type)

Get the associated calibration file for a given data file.

Parameters:

  • metadata (dict) – The metadata dictionary containing information about the observations.

  • this_fn (str) – The filename of the data file for which to find the associated calibration file.

  • type (str) – The type of calibration file to search for.

Returns:

The filename of the associated calibration file if found, or False if not found.

Return type:

str or bool

pywifes.wifes_utils.get_file_names(src_dir_path, glob_pattern)

Get the names of files in a directory that match a given search query in a glob pattern. Does not search in subfolders.

Parameters:

  • src_dir_path (str) – The path to the source directory.

  • glob_pattern (str) – The glob pattern (search query) to match the filenames.

Returns:

A list of filenames that match the glob pattern.

Return type:

list

pywifes.wifes_utils.get_full_obs_list(metadata, exclude=None)

Get the full observation list from the given metadata.

Parameters:

  • metadata (dict) – A dictionary containing metadata information.

  • exclude (list) – A list of imagetypes to exclude from the returned observation list. Default: None.

Returns:

The full observation list.

Return type:

list

pywifes.wifes_utils.get_primary_sci_obs_list(metadata)

Get the list of primary science observations from the metadata.

Parameters:

metadata (dict) – The metadata containing information about the observations.

Returns:

The list of primary science observations.

Return type:

list

pywifes.wifes_utils.get_primary_std_obs_list(metadata, stdtype='all')

Get the list of primary standard observations based on the given metadata and type.

Parameters:

  • metadata (dict) – The metadata containing information about the observations.

  • stdtype (str, optional) – The type of standard star observations to include in the list. Options: ‘all’, ‘telluric’, ‘flux’. Default: ‘all’.

Returns:

The list of primary standard observations.

Return type:

list

Raises:

ValueError – If the standard star type is not understood.

pywifes.wifes_utils.get_sci_obs_list(metadata)

Get a list of science observations from the metadata.

Parameters:

metadata (dict) – The metadata containing information about the observations.

Returns:

A list of science observation filenames.

Return type:

list

pywifes.wifes_utils.get_sky_obs_list(metadata)

Get a list of sky observations from the metadata.

Parameters:

metadata (dict) – The metadata containing information about the observations.

Returns:

A list of sky observation filenames.

Return type:

list

pywifes.wifes_utils.get_std_obs_list(metadata, type='all')

Get a list of standard observations.

Parameters:

  • metadata (-) – The metadata containing information about the observations.

  • type (-) – The type of observations to include in the list. Options: ‘all’, ‘flux’, ‘telluric’. Default: ‘all’.

Returns:

- std_obs_list – A list of standard observation filenames.

Return type:

list

pywifes.wifes_utils.hl_envelopes_idx(s, dmin=1, dmax=1, split=False, as_bool=False)

Inputs:

s1d-array

data signal from which to extract high and low envelopes

dmin, dmaxint, optional

size of chunks, use this if the size of the input signal is too big

splitbool, optional

if True, split the signal in half along its mean, might help to generate the envelope in some cases

as_boolbool, optional

whether to return boolean arrays indicating if each element is a min or max value

Output: lmin, lmax : low/high envelope idx of input signal s, or if as_bool=True, then boolean arrays where min/max

Adapted from https://stackoverflow.com/questions/34235530/how-to-get-high-and-low-envelope-of-a-signal/60402647#60402647

pywifes.wifes_utils.is_halfframe(inimg, data_hdu=0)

Report whether this exposure (filename or HDUList) is a half-frame (a.k.a. Stellar mode) image.

pywifes.wifes_utils.is_nodshuffle(inimg)

Report whether this exposure is a Nod & Shuffle frame.

pywifes.wifes_utils.is_standard(inimg, data_hdu=0)

Report whether this exposure is a Nod & Shuffle frame.

pywifes.wifes_utils.is_subnodshuffle(inimg, data_hdu=0)

Report whether this exposure is a SubNodAndShuffle frame.

pywifes.wifes_utils.is_taros(inimg)

Report whether this exposure was taken with TAROS. Useful for determining whether last slit of half-frame readouts is truncated.

pywifes.wifes_utils.load_config_file(filename)

Load a configuration file in JSON5 format.

Parameters:

filename (str) – The name of the configuration file.

Returns:

A dictionary containing the loaded configuration data.

Return type:

dict

pywifes.wifes_utils.move_files(src_dir_path, destination_dir_path, filenames)

Move files from the source directory to the destination directory.

Parameters:

  • src_dir_path (str) – The path of the source directory.

  • destination_dir_path (str) – The path of the destination directory.

  • filenames (list of str) – The list of filenames to be moved.

Raises:

Exception – If an error occurs while moving the files.

pywifes.wifes_utils.nan_helper(y)

Helper to handle indices and logical indices of NaNs.

Input:

  • y, 1d numpy array with possible NaNs

Output:

  • nans, logical indices of NaNs

  • index, a function, with signature indices= index(logical_indices), to convert logical indices of NaNs to ‘equivalent’ indices

Example

>>> # linear interpolation of NaNs
>>> nans, x= nan_helper(y)
>>> y[nans]= numpy.interp(x(nans), x(~nans), y[~nans])

https://stackoverflow.com/questions/6518811/interpolate-nan-values-in-a-numpy-array

pywifes.wifes_utils.set_header(filename, kw, kw_value, data_hdu=0)