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Commit 9bd8195c authored by Hunsinger, Heather Elizabeth's avatar Hunsinger, Heather Elizabeth
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Change methods to return local dictionaries/lists

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geomagio/JSON/JSONFactory.py
+ 0
− 19
View file @ 9bd8195c
......@@ -26,25 +26,6 @@ class JSONFactory(TimeseriesFactory):
def __init__(self, **kwargs):
TimeseriesFactory.__init__(self, **kwargs)
# TODO: Write parser method
def parse_string(self, data, observatory=None, interval='minute',
**kwargs):
"""Parse the contents of a string in the format of an json file.
Parameters
----------
jsonString : str
string containing IAGA2002 content.
observatory : str
observatory in case headers are unavailable.
parses observatory from headers when available.
Returns
-------
obspy.core.Stream
parsed data.
"""
pass
def write_file(self, fh, timeseries, channels):
"""writes timeseries data to the given file object.
......
geomagio/JSON/JSONWriter.py
+ 56
− 60
View file @ 9bd8195c
......@@ -5,21 +5,17 @@ from io import BytesIO
from collections import OrderedDict
from datetime import datetime
import json
import numpy
import numpy as np
import textwrap
from .. import ChannelConverter, TimeseriesUtility
from ..edge import EdgeFactory
from ..TimeseriesFactoryException import TimeseriesFactoryException
from ..Util import create_empty_trace
class JSONWriter(object):
"""JSON writer.
"""
def __init__(self):
self.dictionary = OrderedDict()
def write(self, out, timeseries, channels, **kwargs):
"""write timeseries to json file
......@@ -32,6 +28,7 @@ class JSONWriter(object):
channels: array_like
channels to be written from timeseries object
"""
dictionary = OrderedDict()
request = kwargs.get('request')
for channel in channels:
if timeseries.select(channel=channel).count() == 0:
......@@ -39,14 +36,13 @@ class JSONWriter(object):
'Missing channel "%s" for output, available channels %s' %
(channel, str(TimeseriesUtility.get_channels(timeseries))))
stats = timeseries[0].stats
if len(channels) != 4:
channels = self._pad_to_four_channels(timeseries, channels)
self._format_metadata(stats, channels)
dictionary['type'] = 'Timeseries'
dictionary['metadata'] = self._format_metadata(stats, channels)
if request:
self.dictionary['metadata']['url'] = 'http://geomag.usgs.gov/ws/edge/?' + request
self._format_times(timeseries, channels)
self._format_data(timeseries, channels, stats)
out.write(json.dumps(self.dictionary, ensure_ascii=True).encode(
dictionary['metadata']['url'] = 'http://geomag.usgs.gov/ws/edge/?' + request
dictionary['times'] = self._format_times(timeseries, channels)
dictionary['values'] = self._format_data(timeseries, channels, stats)
out.write(json.dumps(dictionary, ensure_ascii=True).encode(
'utf8'))
def _format_metadata(self, stats, channels):
......@@ -58,15 +54,18 @@ class JSONWriter(object):
holds the observatory metadata
channels: array_like
channels to be reported.
Returns
-------
dictionary
a dictionary containing metadata.
"""
dict = self.dictionary.copy()
dict['type'] = 'Timeseries'
dict['metadata'] = OrderedDict()
dict['metadata']['intermagnet'] = OrderedDict()
dict['metadata']['intermagnet']['imo'] = OrderedDict()
dict['metadata']['intermagnet']['imo']['iaga_code'] = stats.station
metadata_dict = OrderedDict()
intermag = OrderedDict()
imo = OrderedDict()
imo['iaga_code'] = stats.station
if 'station_name' in stats:
dict['metadata']['intermagnet']['imo']['name'] = stats.station_name
imo['name'] = stats.station_name
coords = [None] * 3
if 'geodetic_longitude' in stats:
coords[0] = str(stats.geodetic_longitude)
......@@ -74,12 +73,13 @@ class JSONWriter(object):
coords[1] = str(stats.geodetic_latitude)
if 'elevation' in stats:
coords[2] = str(stats.elevation)
dict['metadata']['intermagnet']['imo']['coordinates'] = coords
dict['metadata']['intermagnet']['reported_orientation'] = ''.join(channels)
imo['coordinates'] = coords
intermag['imo'] = imo
intermag['reported_orientation'] = ''.join(channels)
if 'sensor_orientation' in stats:
dict['metadata']['intermagnet']['sensor_orientation'] = stats.sensor_orientation
intermag['sensor_orientation'] = stats.sensor_orientation
if 'data_type' in stats:
dict['metadata']['intermagnet']['data_type'] = stats.data_type
intermag['data_type'] = stats.data_type
if 'sampling_rate' in stats:
if stats.sampling_rate == 1. / 60.:
rate = 60
......@@ -89,22 +89,28 @@ class JSONWriter(object):
rate = 86400
else:
rate = 1
dict['metadata']['intermagnet']['sampling_period'] = str(rate)
intermag['sampling_period'] = str(rate)
if 'sensor_sampling_rate' in stats:
dict['metadata']['intermagnet']['digital_sampling_rate'] = str(1 / stats.sensor_sampling_rate)
dict['metadata']['status'] = 200
dict['metadata']['generated'] = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
self.dictionary = dict
intermag['digital_sampling_rate'] = str(1 / stats.sensor_sampling_rate)
metadata_dict['intermagnet'] = intermag
metadata_dict['status'] = 200
metadata_dict['generated'] = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
return metadata_dict
def _format_times(self, timeseries, channels):
"""format times for json file and update dictionary
Parameters
----------
timeseries: obspy.core.stream
timeseries object with data to be written
stats: obspy.core.trace.stats
holds the observatory metadata
channels: array_like
channels to be reported.
Returns
-------
array_like
an array containing formatted strings of time data.
"""
times = []
traces = [timeseries.select(channel=c)[0] for c in channels]
......@@ -113,7 +119,7 @@ class JSONWriter(object):
for i in range(len(traces[0].data)):
times.append(self._format_time_string(
datetime.utcfromtimestamp(starttime + i * delta)))
self.dictionary['times'] = times
return times
def _format_time_string(self, time):
"""format one time.
......@@ -144,8 +150,12 @@ class JSONWriter(object):
list and order of channel values to output.
stats: obspy.core.trace.stats
holds the observatory metadata
Returns
-------
array_like
an array containing dictionaries of data.
"""
self.dictionary['values'] = []
if timeseries.select(channel='D'):
d = timeseries.select(channel='D')
d[0].data = ChannelConverter.get_minutes_from_radians(d[0].data)
......@@ -155,38 +165,24 @@ class JSONWriter(object):
value_dict = OrderedDict()
trace = timeseries.select(channel=c)[0]
value_dict['id'] = c
value_dict['metadata'] = OrderedDict()
value_dict['metadata']['element'] = c
value_dict = OrderedDict()
value_dict['element'] = c
if 'network' in stats:
value_dict['metadata']['network'] = stats.network
value_dict['metadata']['station'] = stats.station
edge_channel = self.edge._get_edge_channel(stats.station,
c,
stats.data_type,
stats.data_interval)
value_dict['metadata']['channel'] = edge_channel
value_dict['network'] = stats.network
value_dict['station'] = stats.station
if 'channel' in stats:
edge_channel = trace.stats.channel
else:
edge_channel = c
value_dict['channel'] = edge_channel
if 'location' in stats:
value_dict['metadata']['location'] = stats.location
value_dict['location'] = stats.location
# TODO: Add flag metadata
values += [value_dict]
data = []
for i in range(len(trace.data)):
if numpy.isnan(trace.data[i]):
data += ['null']
else:
data += [str(trace.data[i])]
value_dict['values'] = data
self.dictionary['values'] += values
def _pad_to_four_channels(self, timeseries, channels):
padded = channels[:]
for x in range(len(channels), 4):
channel = 'NUL'
padded.append(channel)
timeseries += create_empty_trace(timeseries[0], channel)
return padded
data = np.copy(trace.data)
data[np.isnan(data)] = None
value_dict['values'] = data.tolist()
return values
@classmethod
def format(self, timeseries, channels, **kwargs):
......
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