25194239086

Committed 26 Apr 2026 08:07PM UTC coverage: 61.697% (-28.8%) from 90.54%

Build # 25194239086

Build Type

push

github

Committed by

jameswilburlewis

Commit Message

Added test for loading Cluster CODIF differential energy flux

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0 of 7 new or added lines in 1 file covered. (0.0%)

19460 existing lines in 418 files now uncovered.

30204 of 48955 relevant lines covered (61.7%)

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100.0

/pyspedas/tplot_tools/tplot_math/tdeflag.py

"""
Removes NaNs and other flags.

Notes
----
Allowed wildcards are ? for a single character, * from multiple characters.
Similar to tdeflag.pro in IDL SPEDAS, but now a wrapper for deflag.py

"""
import logging
import pyspedas
from pyspedas.tplot_tools import tnames, deflag

def tdeflag(names,
            flag=None,
            method='remove_nan',
            newname=None,
            suffix=None,
            overwrite=None,
            fillval=None
):
    """
    Replaces FLAGs in arrays with interpolated or other values.

    Parameters
    ----------
    names: str/list of str
        List of tplot variables names to deflag (wildcards accepted)
    flag: float, int, or list
        Value or values to be treated as flags
    method: str, optional
        Method to apply.
        If None,then flagged values are replaced with NaN
        Other options 'repeat' (repeat last good value), 
        'linear' (interpolate linearly over gap).
        'replace' replaces flagged value with a fill value, which can be set using the 
                  keyword 'fillval' (default is to use NaN)
        Option 'remove_nan' removes time intervals with NaN values
        Default: 'remove_nan'
    newname: str/list of str, optional
        List of new names for tplot variables.
        If '', then tplot variables are replaced.
        Default: None. If not specified then a suffix is applied.
    suffix: str, optional
        A suffix to apply.
        Default: '-deflag'.
    overwrite: bool, optional
        Replace the existing tplot name.
        Default: None
    fillval: int, float (optional)
        Value to use as replacement if method='replace'

    Returns
    -------
    list of str
        List of tplot variables created or altered by tdeflag

    Examples
    --------

    >>> import pyspedas
    >>> pyspedas.store_data('d', data={'x':[2,5,8,11,14,17,21], 'y':[[1,1],[2,2],[100,4],[4,90],[5,5],[6,6],[7,7]]})
    >>> # Remove any instances of [100,90,7,2,57] from 'd', store in 'e'.
    >>> pyspedas.deflag('d',[100,90,7,2,57],newname='e')
    >>> d_deflagged = pyspedas.get_data('e')
    >>> print(d_deflagged)
    """

    old_names = tnames(names)

    if len(old_names) < 1:
        logging.error('tdeflag: No valid tplot names were provided.')
        return None

    if suffix is None:
        suffix = '-deflag'

    if overwrite is not None:
        n_names = old_names
    elif newname is None:
        n_names = [s + suffix for s in old_names]
    else:
        n_names = newname

    if isinstance(n_names, str):
        n_names = [n_names]

    if len(n_names) != len(old_names):
        n_names = [s + suffix for s in old_names]
        logging.info('input newname has incorrect number of elements')

    for i in range(len(old_names)):
        deflag(old_names[i], flag, newname=n_names[i], method=method, fillval=fillval)
        logging.info('tdeflag was applied to: ' + n_names[i])

    return n_names

1	"""
2	Removes NaNs and other flags.
3
4	Notes
5	----
6	Allowed wildcards are ? for a single character, * from multiple characters.
7	Similar to tdeflag.pro in IDL SPEDAS, but now a wrapper for deflag.py
8
9	"""
10	import logging	3✔
11	import pyspedas	3✔
12	from pyspedas.tplot_tools import tnames, deflag	3✔
13
14	def tdeflag(names,	3✔
15	flag=None,
16	method='remove_nan',
17	newname=None,
18	suffix=None,
19	overwrite=None,
20	fillval=None
21	):
22	"""
23	Replaces FLAGs in arrays with interpolated or other values.
24
25	Parameters
26	----------
27	names: str/list of str
28	List of tplot variables names to deflag (wildcards accepted)
29	flag: float, int, or list
30	Value or values to be treated as flags
31	method: str, optional
32	Method to apply.
33	If None,then flagged values are replaced with NaN
34	Other options 'repeat' (repeat last good value),
35	'linear' (interpolate linearly over gap).
36	'replace' replaces flagged value with a fill value, which can be set using the
37	keyword 'fillval' (default is to use NaN)
38	Option 'remove_nan' removes time intervals with NaN values
39	Default: 'remove_nan'
40	newname: str/list of str, optional
41	List of new names for tplot variables.
42	If '', then tplot variables are replaced.
43	Default: None. If not specified then a suffix is applied.
44	suffix: str, optional
45	A suffix to apply.
46	Default: '-deflag'.
47	overwrite: bool, optional
48	Replace the existing tplot name.
49	Default: None
50	fillval: int, float (optional)
51	Value to use as replacement if method='replace'
52
53	Returns
54	-------
55	list of str
56	List of tplot variables created or altered by tdeflag
57
58	Examples
59	--------
60
61	>>> import pyspedas
62	>>> pyspedas.store_data('d', data={'x':[2,5,8,11,14,17,21], 'y':[[1,1],[2,2],[100,4],[4,90],[5,5],[6,6],[7,7]]})
63	>>> # Remove any instances of [100,90,7,2,57] from 'd', store in 'e'.
64	>>> pyspedas.deflag('d',[100,90,7,2,57],newname='e')
65	>>> d_deflagged = pyspedas.get_data('e')
66	>>> print(d_deflagged)
67	"""
68
UNCOV 69	old_names = tnames(names)	2✔
70
UNCOV 71	if len(old_names) < 1:	2✔
UNCOV 72	logging.error('tdeflag: No valid tplot names were provided.')	2✔
UNCOV 73	return None	2✔
74
UNCOV 75	if suffix is None:	2✔
UNCOV 76	suffix = '-deflag'	2✔
77
UNCOV 78	if overwrite is not None:	2✔
UNCOV 79	n_names = old_names	2✔
UNCOV 80	elif newname is None:	2✔
UNCOV 81	n_names = [s + suffix for s in old_names]	1✔
82	else:
UNCOV 83	n_names = newname	2✔
84
UNCOV 85	if isinstance(n_names, str):	2✔
UNCOV 86	n_names = [n_names]	2✔
87
UNCOV 88	if len(n_names) != len(old_names):	2✔
UNCOV 89	n_names = [s + suffix for s in old_names]	1✔
UNCOV 90	logging.info('input newname has incorrect number of elements')	1✔
91
UNCOV 92	for i in range(len(old_names)):	2✔
UNCOV 93	deflag(old_names[i], flag, newname=n_names[i], method=method, fillval=fillval)	2✔
UNCOV 94	logging.info('tdeflag was applied to: ' + n_names[i])	2✔
95
UNCOV 96	return n_names	2✔

spedas / pyspedas / 25194239086

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