"""
This module provides processing routines for data captured with the LYRA (Lyman
Alpha Radiometer) instrument on Proba-2.
"""
import copy
import csv
import datetime
import sqlite3
from urllib.parse import urljoin
from warnings import warn
import numpy as np
import pandas
from astropy.time import Time
from sunpy.data import cache
from sunpy.time import parse_time
from sunpy.time.time import _variables_for_parse_time_docstring
from sunpy.timeseries import TimeSeries
from sunpy.util.decorators import add_common_docstring
LYTAF_REMOTE_PATH = "http://proba2.oma.be/lyra/data/lytaf/"
__all__ = [
"remove_lytaf_events_from_timeseries",
"get_lytaf_events",
"get_lytaf_event_types",
"split_series_using_lytaf",
"_prep_columns",
"_lytaf_event2string",
"_remove_lytaf_events",
]
[docs]
def remove_lytaf_events_from_timeseries(
ts, artifacts=None, return_artifacts=False, force_use_local_lytaf=False
):
"""
Removes periods of LYRA artifacts defined in LYTAF from a TimeSeries.
Parameters
----------
ts : `sunpy.timeseries.TimeSeries`
artifacts : `list`
Sets the artifact types to be removed. For a list of artifact types
see reference [1]. For example, if a user wants to remove only large
angle rotations, listed at reference [1] as LAR, set artifacts=["LAR"].
The default is that no artifacts will be removed.
return_artifacts : `bool`
Set to True to return a `numpy.recarray` containing the start time, end
time and type of all artifacts removed.
Default=False
force_use_local_lytaf : `bool`
Ensures current local version of lytaf files are not replaced by
up-to-date online versions even if current local lytaf files do not
cover entire input time range etc.
Default=False
Returns
-------
ts_new : `sunpy.timeseries.TimeSeries`
copy of input TimeSeries with periods corresponding to artifacts
removed.
artifact_status : `dict`
List of 4 variables containing information on what artifacts were
found, removed, etc. from the time series.
| **artifact_status["lytaf"]** : `numpy.recarray`
| The full LYRA annotation file for the time series time range
| output by get_lytaf_events().
| **artifact_status["removed"]** : `numpy.recarray`
| Artifacts which were found and removed from from time series.
| **artifact_status["not_removed"]** : `numpy.recarray`
| Artifacts which were found but not removed as they were not
| included when user defined artifacts kwarg.
| **artifact_status["not_found"]** : `list` of strings
| Artifacts listed to be removed by user when defining
| artifacts kwarg which were not found in time series time range.
Notes
-----
This function is intended to take TimeSeries objects as input, but the
deprecated LightCurve is still supported here.
References
----------
[1] http://proba2.oma.be/data/TARDIS
Examples
--------
Remove LARs (Large Angle Rotations) from TimeSeries for 4-Dec-2014:
>>> import sunpy.timeseries as ts
>>> import sunpy.data.sample # doctest: +REMOTE_DATA
>>> from sunkit_instruments.lyra import remove_lytaf_events_from_timeseries
>>> lyrats = ts.TimeSeries(sunpy.data.sample.LYRA_LEVEL3_TIMESERIES, source='LYRA') # doctest: +REMOTE_DATA
>>> ts_nolars = remove_lytaf_events_from_timeseries(lyrats, artifacts=["LAR"]) # doctest: +REMOTE_DATA
To also retrieve information on the artifacts during that day:
>>> ts_nolars, artifact_status = remove_lytaf_events_from_timeseries(
... lyrats, artifacts=["LAR"], return_artifacts=True) # doctest: +REMOTE_DATA
"""
# Remove artifacts from time series
ts_ds = ts.to_dataframe()
data_columns = ts_ds.columns
time, channels, artifact_status = _remove_lytaf_events(
ts_ds.index,
channels=[np.asanyarray(ts_ds[col]) for col in data_columns],
artifacts=artifacts,
return_artifacts=True,
force_use_local_lytaf=force_use_local_lytaf,
)
# Create new copy of timeseries and replace data with
# artifact-free time series.
data = pandas.DataFrame(
index=time, data={col: channels[i] for i, col in enumerate(data_columns)}
)
ts_new = TimeSeries(data, ts.meta)
if return_artifacts:
return ts_new, artifact_status
else:
return ts_new
def _remove_lytaf_events(
time,
channels=None,
artifacts=None,
return_artifacts=False,
filecolumns=None,
force_use_local_lytaf=False,
):
"""
Removes periods of LYRA artifacts from a time series.
This functions removes periods corresponding to certain artifacts recorded
in the LYRA annotation file from an array of times given by the time input.
If a list of arrays of other properties is supplied through the channels
kwarg, then the relevant values from these arrays are also removed. This
is done by assuming that each element in each array supplied corresponds to
the time in the same index in time array. The artifacts to be removed are
given via the artifacts kwarg. The default is "all", meaning that all
artifacts will be removed. However, a subset of artifacts can be removed
by supplying a list of strings of the desired artifact types.
Parameters
----------
time : `numpy.ndarray` of `astropy.time.Time`
Gives the times of the timeseries.
channels : `list` of `numpy.array` convertible to float64.
Contains arrays of the irradiances taken at the times in the time
variable. Each element in the list must have the same number of
elements as time.
artifacts : `list` of strings
Contain the artifact types to be removed. For list of artifact types
see reference [1]. For example, if user wants to remove only large
angle rotations, listed at reference [1] as LAR, let artifacts=["LAR"].
Default=[], i.e. no artifacts will be removed.
return_artifacts : `bool`
Set to True to return a numpy recarray containing the start time, end
time and type of all artifacts removed.
Default=False
filecolumns : `list` of strings
Gives names of columns of any output files produced. Although
initially set to None above, the default is in fact
["time", "channel0", "channel1",..."channelN"]
where N is the number of irradiance arrays in the channels input
(assuming 0-indexed counting).
force_use_local_lytaf : `bool`
Ensures current local version of lytaf files are not replaced by
up-to-date online versions even if current local lytaf files do not
cover entire input time range etc.
Default=False
Returns
-------
clean_time : `numpy.ndarray` of `astropy.time.Time`
time array with artifact periods removed.
clean_channels : `list` ndarrays/array-likes convertible to float64
list of irradiance arrays with artifact periods removed.
artifact_status : `dict`
List of 4 variables containing information on what artifacts were
found, removed, etc. from the time series.
artifact_status["lytaf"] = artifacts found : `numpy.recarray`
The full LYRA annotation file for the time series time range
output by get_lytaf_events().
artifact_status["removed"] = artifacts removed : `numpy.recarray`
Artifacts which were found and removed from from time series.
artifact_status["not_removed"] = artifacts found but not removed :
`numpy.recarray`
Artifacts which were found but not removed as they were not
included when user defined artifacts kwarg.
artifact_status["not_found"] = artifacts not found : `list` of strings
Artifacts listed to be removed by user when defining artifacts
kwarg which were not found in time series time range.
References
----------
[1] http://proba2.oma.be/data/TARDIS
Example
-------
Sample data for example
>>> from sunpy.time import parse_time
>>> from sunkit_instruments.lyra import _remove_lytaf_events
>>> time = parse_time(np.arange('2005-02-01T00:00:00', '2005-02-01T02:00:00',
... dtype='datetime64[m]'))
>>> channel_1 = np.zeros(len(time))+0.4
>>> channel_2 = np.zeros(len(time))+0.1
Remove LARs (Large Angle Rotations) from time series.
>>> time_clean, channels_clean = _remove_lytaf_events(
... time, channels=[channel_1, channel_2], artifacts=['LAR']) # doctest: +SKIP
"""
# Check inputs
if channels and not isinstance(channels, list):
raise TypeError(
f"channels must be None or a list of numpy arrays of dtype 'float64', not {type(channels)}"
)
if not artifacts:
raise ValueError("User has supplied no artifacts to remove.")
if type(artifacts) is str:
artifacts = [artifacts]
if not all(isinstance(artifact_type, str) for artifact_type in artifacts):
raise TypeError("All elements in artifacts must in strings.")
all_lytaf_event_types = get_lytaf_event_types(print_event_types=False)
for artifact in artifacts:
if artifact not in all_lytaf_event_types:
print(all_lytaf_event_types)
raise ValueError(f"{artifact} is not a valid artifact type. See above.")
# Define outputs
clean_time = parse_time(time)
clean_channels = copy.deepcopy(channels)
artifacts_not_found = []
# Get LYTAF file for given time range
lytaf = get_lytaf_events(
time[0], time[-1], force_use_local_lytaf=force_use_local_lytaf
)
# Find events in lytaf which are to be removed from time series.
artifact_indices = np.empty(0, dtype="int64")
for artifact_type in artifacts:
indices = np.where(lytaf["event_type"] == artifact_type)[0]
# If none of a given type of artifact is found, record this
# type in artifact_not_found list.
if len(indices) == 0:
artifacts_not_found.append(artifact_type)
else:
# Else, record the indices of the artifacts of this type
artifact_indices = np.concatenate((artifact_indices, indices))
artifact_indices.sort()
# Remove relevant artifacts from timeseries. If none of the
# artifacts the user wanted removed were found, raise a warning and
# continue with code.
if not len(artifact_indices):
warn("None of user supplied artifacts were found.")
artifacts_not_found = artifacts
else:
# Remove periods corresponding to artifacts from flux and time
# arrays.
bad_indices = np.empty(0, dtype="int64")
all_indices = np.arange(len(time))
for index in artifact_indices:
bad_period = np.logical_and(
time >= lytaf["begin_time"][index].datetime,
time <= lytaf["end_time"][index].datetime,
)
bad_indices = np.append(bad_indices, all_indices[bad_period])
clean_time = np.delete(clean_time, bad_indices)
if channels:
for i, f in enumerate(clean_channels):
clean_channels[i] = np.delete(f, bad_indices)
# If return_artifacts kwarg is True, return a list containing
# information on what artifacts found, removed, etc. See docstring.
if return_artifacts:
artifact_status = {
"lytaf": lytaf,
"removed": lytaf[artifact_indices],
"not_removed": np.delete(lytaf, artifact_indices),
"not_found": artifacts_not_found,
}
# Return values.
if return_artifacts:
if not channels:
return clean_time, artifact_status
else:
return clean_time, clean_channels, artifact_status
else:
if not channels:
return clean_time
else:
return clean_time, clean_channels
[docs]
def get_lytaf_events(
start_time,
end_time,
combine_files=("lyra", "manual", "ppt", "science"),
csvfile=None,
force_use_local_lytaf=False,
):
"""
Extracts combined lytaf file for given time range.
Given a time range defined by start_time and end_time, this function
extracts the segments of each LYRA annotation file and combines them.
Parameters
----------
start_time : `astropy.time.Time` or `str`
Start time of period for which annotation file is required.
end_time : `astropy.time.Time` or `str`
End time of period for which annotation file is required.
combine_files : `tuple` of strings
States which LYRA annotation files are to be combined.
Default is all four, i.e. lyra, manual, ppt, science.
See Notes section for an explanation of each.
force_use_local_lytaf : `bool`
Ensures current local version of lytaf files are not replaced by
up-to-date online versions even if current local lytaf files do not
cover entire input time range etc.
Default=False
Returns
-------
lytaf : `numpy.recarray`
Containing the various parameters stored in the LYTAF files.
Notes
-----
There are four LYRA annotation files which mark different types of events
or artifacts in the data. They are named annotation_suffix.db where
suffix is a variable equalling either lyra, manual, ppt, or science.
annotation_lyra.db : contains entries regarding possible effects to
the data due to normal operation of LYRA instrument.
annotation_manual.db : contains entries regarding possible effects
to the data due to unusual or manually logged events.
annotation_ppt.db : contains entries regarding possible effects to
the data due to pointing or positioning of PROBA2.
annotation_science.db : contains events in the data scientifically
interesting, e.g. GOES flares.
References
----------
Further documentation: http://proba2.oma.be/data/TARDIS
Examples
--------
Get all events in the LYTAF files for January 2014
>>> from sunkit_instruments.lyra import get_lytaf_events
>>> lytaf = get_lytaf_events('2014-01-01', '2014-02-01') # doctest: +SKIP
"""
# Check inputs
# Parse start_time and end_time
start_time = parse_time(start_time)
end_time = parse_time(end_time)
# Check combine_files contains correct inputs
if not all(
suffix in ["lyra", "manual", "ppt", "science"] for suffix in combine_files
):
raise ValueError(
"Elements in combine_files must be strings equalling "
"'lyra', 'manual', 'ppt', or 'science'."
)
# Remove any duplicates from combine_files input
combine_files = list(set(combine_files))
combine_files.sort()
# Convert input times to UNIX timestamp format since this is the
# time format in the annotation files
start_time_uts = (start_time - Time("1970-1-1")).sec
end_time_uts = (end_time - Time("1970-1-1")).sec
# Define numpy record array which will hold the information from
# the annotation file.
lytaf = np.empty(
(0,),
dtype=[
("insertion_time", object),
("begin_time", object),
("reference_time", object),
("end_time", object),
("event_type", object),
("event_definition", object),
],
)
# Access annotation files
for suffix in combine_files:
# Check database files are present
dbname = f"annotation_{suffix}.db"
lytaf_path = cache.download(urljoin(LYTAF_REMOTE_PATH, dbname))
# Open SQLITE3 annotation files
connection = sqlite3.connect(str(lytaf_path))
# Create cursor to manipulate data in annotation file
cursor = connection.cursor()
# Check if lytaf file spans the start and end times defined by
# user. If not, download newest version.
# First get start time of first event and end time of last
# event in lytaf.
cursor.execute(
"select begin_time from event order by begin_time asc " "limit 1;"
)
db_first_begin_time = cursor.fetchone()[0]
db_first_begin_time = datetime.datetime.fromtimestamp(db_first_begin_time)
cursor.execute("select end_time from event order by end_time desc " "limit 1;")
db_last_end_time = cursor.fetchone()[0]
db_last_end_time = datetime.datetime.fromtimestamp(db_last_end_time)
# If lytaf does not include entire input time range...
if not force_use_local_lytaf:
if end_time > db_last_end_time or start_time < db_first_begin_time:
# ...close lytaf file...
cursor.close()
connection.close()
# ...Download latest lytaf file...
lytaf_path = cache.download(
urljoin(LYTAF_REMOTE_PATH, dbname), redownload=True
)
# ...and open new version of lytaf database.
connection = sqlite3.connect(str(lytaf_path))
cursor = connection.cursor()
# Select and extract the data from event table within file within
# given time range
cursor.execute(
"select insertion_time, begin_time, reference_time, "
"end_time, eventType_id from event where end_time >= "
"{} and begin_time <= "
"{}".format(start_time_uts, end_time_uts)
)
event_rows = cursor.fetchall()
# Select and extract the event types from eventType table
cursor.row_factory = sqlite3.Row
cursor.execute("select * from eventType")
eventType_rows = cursor.fetchall()
eventType_id = []
eventType_type = []
eventType_definition = []
for eventType_row in eventType_rows:
eventType_id.append(eventType_row["id"])
eventType_type.append(eventType_row["type"])
eventType_definition.append(eventType_row["definition"])
# Enter desired information into the lytaf numpy record array
for event_row in event_rows:
id_index = eventType_id.index(event_row[4])
lytaf = np.append(
lytaf,
np.array(
(
Time(
datetime.datetime.utcfromtimestamp(event_row[0]),
format="datetime",
),
Time(
datetime.datetime.utcfromtimestamp(event_row[1]),
format="datetime",
),
Time(
datetime.datetime.utcfromtimestamp(event_row[2]),
format="datetime",
),
Time(
datetime.datetime.utcfromtimestamp(event_row[3]),
format="datetime",
),
eventType_type[id_index],
eventType_definition[id_index],
),
dtype=lytaf.dtype,
),
)
# Close file
cursor.close()
connection.close()
# Sort lytaf in ascending order of begin time
np.recarray.sort(lytaf, order="begin_time")
# If csvfile kwarg is set, write out lytaf to csv file
if csvfile:
# Open and write data to csv file.
with open(csvfile, "w") as openfile:
csvwriter = csv.writer(openfile, delimiter=";")
# Write header.
csvwriter.writerow(lytaf.dtype.names)
# Write data.
for row in lytaf:
new_row = []
new_row.append(row[0].strftime("%Y-%m-%dT%H:%M:%S"))
new_row.append(row[1].strftime("%Y-%m-%dT%H:%M:%S"))
new_row.append(row[2].strftime("%Y-%m-%dT%H:%M:%S"))
new_row.append(row[3].strftime("%Y-%m-%dT%H:%M:%S"))
new_row.append(row[4])
new_row.append(row[5])
csvwriter.writerow(new_row)
return lytaf
[docs]
def get_lytaf_event_types(print_event_types=True):
"""
Prints the different event types in the each of the LYTAF databases.
Parameters
----------
print_event_types : `bool`
If True, prints the artifacts in each lytaf database to screen.
Returns
-------
all_event_types : `list`
List of all events types in all lytaf databases.
"""
suffixes = ["lyra", "manual", "ppt", "science"]
all_event_types = []
# For each database file extract the event types and print them.
if print_event_types:
print("\nLYTAF Event Types\n-----------------\n")
for suffix in suffixes:
dbname = f"annotation_{suffix}.db"
# Check database file exists, else download it.
lytaf_path = cache.download(urljoin(LYTAF_REMOTE_PATH, dbname))
# Open SQLITE3 LYTAF files
connection = sqlite3.connect(str(lytaf_path))
# Create cursor to manipulate data in annotation file
cursor = connection.cursor()
cursor.execute("select type from eventType;")
event_types = cursor.fetchall()
all_event_types.append(event_types)
if print_event_types:
print(f"----------------\n{suffix} database\n----------------")
for event_type in event_types:
print(str(event_type[0]))
print(" ")
# Unpack event types in all_event_types into single list
all_event_types = [
event_type[0] for event_types in all_event_types for event_type in event_types
]
return all_event_types
[docs]
def split_series_using_lytaf(timearray, data, lytaf):
"""
Splits LYRA timeseries around locations where "LARs" (and other data
events) are observed.
Parameters
----------
timearray : `numpy.ndarray`
An array of times understood by `sunpy.time.parse_time`.
data : `numpy.ndarray`
An array corresponding to the given time array.
lytaf : `numpy.recarray`
Events obtained from querying the LYTAF database using
`sunkit_instruments.lyra.get_lytaf_events`.
Returns
-------
`list` of `dict`
Each dictionary contains a sub-series corresponding to an interval of
"good data".
"""
n = len(timearray)
mask = np.ones(n)
el = len(lytaf)
# make the input time array a list of Time objects
time_array = [parse_time(tim) for tim in timearray]
# scan through each entry retrieved from the LYTAF database
for j in range(0, el):
# want to mark all times with events as bad in the mask, i.e. = 0
start_dt = lytaf["begin_time"][j]
end_dt = lytaf["end_time"][j]
# find the start and end indices for each event
start_ind = np.searchsorted(time_array, start_dt)
end_ind = np.searchsorted(time_array, end_dt)
# append the mask to mark event as 'bad'
mask[start_ind:end_ind] = 0
diffmask = np.diff(mask)
tmp_discontinuity = np.where(diffmask != 0.0)
# disc contains the indices of mask where there are discontinuities
disc = tmp_discontinuity[0]
if len(disc) == 0:
print(
"No events found within time series interval. " "Returning original series."
)
return [{"subtimes": time_array, "subdata": data}]
# -1 in diffmask means went from good data to bad
# +1 means went from bad data to good
# want to get the data between a +1 and the next -1
# if the first discontinuity is a -1 then the start of the series was good.
if diffmask[disc[0]] == -1.0:
# make sure we can always start from disc[0] below
disc = np.insert(disc, 0, 0)
split_series = []
limit = len(disc)
# now extract the good data regions and ignore the bad ones
for h in range(0, limit, 2):
if h == limit - 1:
# can't index h+1 here. Go to end of series
subtimes = time_array[disc[h] : -1]
subdata = data[disc[h] : -1]
subseries = {"subtimes": subtimes, "subdata": subdata}
split_series.append(subseries)
else:
subtimes = time_array[disc[h] : disc[h + 1]]
subdata = data[disc[h] : disc[h + 1]]
subseries = {"subtimes": subtimes, "subdata": subdata}
split_series.append(subseries)
return split_series
def _lytaf_event2string(integers):
if isinstance(integers, int):
integers = [integers]
out = []
for i in integers:
if i == 1:
out.append("LAR")
if i == 2:
out.append("N/A")
if i == 3:
out.append("UV occult.")
if i == 4:
out.append("Vis. occult.")
if i == 5:
out.append("Offpoint")
if i == 6:
out.append("SAA")
if i == 7:
out.append("Auroral zone")
if i == 8:
out.append("Moon in LYRA")
if i == 9:
out.append("Moon in SWAP")
if i == 10:
out.append("Venus in LYRA")
if i == 11:
out.append("Venus in SWAP")
return out
# TODO: Change this function to only need the amount of channels to be passed in.
@add_common_docstring(**_variables_for_parse_time_docstring())
def _prep_columns(time, channels=None, filecolumns=None):
"""
Checks and prepares data to be written out to a file.
Parameters
----------
time: {parse_time_types}
A list or array of times.
channels: `list`, optional
A list of the channels found within the data.
filecolumns: `list`, optional
A list of strings that are the column names for the file.
Defaults to `None`, which means that a filenames list is generated
equal to ``["time", "channel0", "channel1",..., "channelN"]``
where ``N`` is the number of arrays in the ``channels`` list (if provided).
Returns
-------
`numpy.ndarray`, `list`
The time strings in an array and a list of string headers for each column of data.
"""
time = parse_time(time)
time.precision = 9
string_time = np.array(time.isot)
if filecolumns:
if all(isinstance(column, str) for column in filecolumns) is False:
raise TypeError("All elements in filecolumns must by strings.")
# ...and that there are the same number of elements as there
# are arrays in channels, plus 1 for a time array. Otherwise
# raise a ValueError.
if channels:
ncol = 1 + len(channels)
else:
ncol = 1
if len(filecolumns) != ncol:
raise ValueError(
"Number of elements in filecolumns must be "
"equal to the number of input data arrays, "
"i.e. time + elements in channels."
)
# If filenames not given, create a list of columns names of the
# form: ["time", "channel0", "channel1",...,"channelN"] where N
# is the number of arrays in channels (assuming 0-indexed counting).
else:
if channels:
filecolumns = [f"channel{fluxnum}" for fluxnum in range(len(channels))]
filecolumns.insert(0, "time")
else:
filecolumns = ["time"]
return string_time, filecolumns
