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removing lat/lon #383

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Apr 12, 2023
Merged

removing lat/lon #383

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6 changes: 0 additions & 6 deletions example_data/metadata.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,8 +87,6 @@ AACO2:
value_name: '$CO_2$'
value_unit: 'ppm'
archiveType: 'Glacier Ice'
lat: -75.1011
lon: 123.3478
importedFrom: 'https://www.ncei.noaa.gov/pub/data/paleo/icecore/antarctica/antarctica2015co2composite.txt'
time_column: Age [kyr BP]
value_column: $CO_2$ [ppm]
Expand All @@ -105,8 +103,6 @@ EDC-dD:
value_name: '$\delta \mathrm{D}$'
value_unit: '‰'
archiveType: 'Glacier Ice'
lat: -75.1011
lon: 123.3478
importedFrom: 'https://www.ncei.noaa.gov/pub/data/paleo/icecore/antarctica/epica_domec/edc3deuttemp2007.txt'
time_column: Age
value_column: Deuterium
Expand All @@ -122,8 +118,6 @@ GISP2:
value_unit: '‰'
value_name: '$\delta^{18} \mathrm{O}$'
label: 'GISP2'
lat: 72.6
lon: -38.5
archiveType: 'Glacier Ice'
importedFrom: 'https://www.ncei.noaa.gov/access/paleo-search/study/17796'
time_column: Age [yr BP]
Expand Down
208 changes: 1 addition & 207 deletions pyleoclim/core/series.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,12 +100,6 @@ class Series:

keep_log : bool
Whether to keep a log of applied transformations. False by default

lat : float
latitude N in decimal degrees.

lon : float
longitude East in decimal degrees. Negative values will be converted to an angle in [0 , 360)

importedFrom : string
source of the dataset. If it came from a LiPD file, this could be the datasetID property
Expand Down Expand Up @@ -139,7 +133,7 @@ class Series:
'''

def __init__(self, time, value, time_unit=None, time_name=None,
value_name=None, value_unit=None, label=None, lat=None, lon=None,
value_name=None, value_unit=None, label=None,
importedFrom=None, archiveType = None, log=None, keep_log=False,
sort_ts = 'ascending', dropna = True, verbose=True, clean_ts=False):

Expand Down Expand Up @@ -229,28 +223,6 @@ def __init__(self, time, value, time_unit=None, time_name=None,
self.dropna = dropna
self.sort_ts = sort_ts
self.clean_ts = clean_ts
# assign latitude
if lat is not None:
lat = float(lat)
if -90 <= lat <= 90:
self.lat = lat
else:
ValueError('Latitude must be a number in [-90; 90]')
else:
self.lat = None # assign a default value to prevent bugs ?

# assign longitude
if lon is not None:
lon = float(lon)
if 0 <= lon < 360:
self.lon = lon
elif -180 <= lon < 0:
self.lon = 360 - lon
else:
ValueError('Longitude must be a number in [-180,360]')
else:
self.lon = None # assign a default value to prevent bugs ?

self.importedFrom = importedFrom
self.archiveType = archiveType #TODO: implement a check on allowable values (take from LipdVerse + 'model' + 'instrumental')

Expand Down Expand Up @@ -313,8 +285,6 @@ def metadata(self):
value_unit = self.value_unit,
value_name = self.value_name,
label = self.label,
lat = self.lat,
lon = self.lon,
archiveType = self.archiveType,
importedFrom = self.importedFrom,
log = self.log,
Expand Down Expand Up @@ -4168,182 +4138,6 @@ def bin(self, keep_log = False, **kwargs):
new.log += ({len(new.log):'bin', 'args': kwargs},)
return new

def map(self, projection='Orthographic', proj_default=True,
background=True, borders=False, rivers=False, lakes=False,
figsize=None, ax=None, marker=None, color=None,
markersize=None, scatter_kwargs=None,
legend=True, lgd_kwargs=None, savefig_settings=None):
'''Map the location of the record

Parameters
----------
projection : str, optional

The projection to use. The default is 'Robinson'.

proj_default : bool; {True, False}, optional

Whether to use the Pyleoclim defaults for each projection type. The default is True.

background : bool; {True, False}, optional

Whether to use a background. The default is True.

borders : bool; {True, False}, optional

Draw borders. The default is False.

rivers : bool; {True, False}, optional

Draw rivers. The default is False.

lakes : bool; {True, False}, optional

Draw lakes. The default is False.

figsize : list or tuple, optional

The size of the figure. The default is None.

ax : matplotlib.ax, optional

The matplotlib axis onto which to return the map. The default is None.

marker : str, optional

The marker type for each archive. The default is None. Uses plot_default

color : str, optional

Color for each archive. The default is None. Uses plot_default

markersize : float, optional

Size of the marker. The default is None.

scatter_kwargs : dict, optional

Parameters for the scatter plot. The default is None.

legend : bool; {True, False}, optional

Whether to plot the legend. The default is True.

lgd_kwargs : dict, optional

Arguments for the legend. The default is None.

savefig_settings : dict, optional

the dictionary of arguments for plt.savefig(); some notes below:
- "path" must be specified; it can be any existed or non-existed path,
with or without a suffix; if the suffix is not given in "path", it will follow "format"
- "format" can be one of {"pdf", "eps", "png", "ps"}. The default is None.

Returns
-------

res : fig,ax

See also
--------

pyleoclim.utils.mapping.map : Underlying mapping function for Pyleoclim

Examples
--------

.. ipython:: python
:okwarning:
:okexcept:

import pyleoclim as pyleo
url = 'http://wiki.linked.earth/wiki/index.php/Special:WTLiPD?op=export&lipdid=MD982176.Stott.2004'
data = pyleo.Lipd(usr_path = url)
ts = data.to_LipdSeries(number=5)
@savefig mapone.png
fig, ax = ts.map()
pyleo.closefig(fig)

'''
scatter_kwargs = {} if scatter_kwargs is None else scatter_kwargs.copy()
# get the information from the timeseries

if self.lat is None or self.lon is None:
raise ValueError('Latitude and longitude should be provided for mapping')
else:
lat = [self.lat]
lon = [self.lon]

if self.archiveType is None:
archiveType = 'other'
else:
archiveType = lipdutils.LipdToOntology(self.archiveType).lower().replace(" ", "")

if markersize is not None:
scatter_kwargs.update({'s': markersize})

plot_default = plotting.set_archive_color(archiveType)

if marker == None:
marker = plot_default[1]

if color == None:
color = plot_default[0]

if proj_default == True:
proj1 = {'central_latitude': lat[0],
'central_longitude': lon[0]}
proj2 = {'central_latitude': lat[0]}
proj3 = {'central_longitude': lon[0]}

archiveType = [archiveType] # list so it will work with map
marker = [marker]
color = [color]

if proj_default == True:

try:
res = mapping.map(lat=lat, lon=lon, criteria=archiveType,
marker=marker, color=color,
projection=projection, proj_default=proj1,
background=background, borders=borders,
rivers=rivers, lakes=lakes,
figsize=figsize, ax=ax,
scatter_kwargs=scatter_kwargs, legend=legend,
lgd_kwargs=lgd_kwargs, savefig_settings=savefig_settings, )

except:
try:
res = mapping.map(lat=lat, lon=lon, criteria=archiveType,
marker=marker, color=color,
projection=projection, proj_default=proj3,
background=background, borders=borders,
rivers=rivers, lakes=lakes,
figsize=figsize, ax=ax,
scatter_kwargs=scatter_kwargs, legend=legend,
lgd_kwargs=lgd_kwargs, savefig_settings=savefig_settings)
except:
res = mapping.map(lat=lat, lon=lon, criteria=archiveType,
marker=marker, color=color,
projection=projection, proj_default=proj2,
background=background, borders=borders,
rivers=rivers, lakes=lakes,
figsize=figsize, ax=ax,
scatter_kwargs=scatter_kwargs, legend=legend,
lgd_kwargs=lgd_kwargs, savefig_settings=savefig_settings)

else:
res = mapping.map(lat=lat, lon=lon, criteria=archiveType,
marker=marker, color=color,
projection=projection, proj_default=proj_default,
background=background, borders=borders,
rivers=rivers, lakes=lakes,
figsize=figsize, ax=ax,
scatter_kwargs=scatter_kwargs, legend=legend,
lgd_kwargs=lgd_kwargs, savefig_settings=savefig_settings)
return res

def resample(self, rule, keep_log = False, **kwargs):
"""
Run analogue to pandas.Series.resample.
Expand Down
2 changes: 0 additions & 2 deletions pyleoclim/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,6 @@ def metadata():
'value_unit': 'mb',
'value_name': 'SOI',
'label': 'Southern Oscillation Index',
'lat': None,
'lon': None,
'archiveType': 'Instrumental',
'importedFrom': None,
'log': (
Expand Down
4 changes: 0 additions & 4 deletions pyleoclim/tests/test_core_Series.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1169,8 +1169,6 @@ def test_resample_simple(self, rule, dataframe_dt, metadata):
'value_unit': 'mb',
'value_name': 'SOI',
'label': f'Southern Oscillation Index ({rule} resampling)',
'lat': None,
'lon': None,
'archiveType': 'Instrumental',
'importedFrom': None,
'log': (
Expand Down Expand Up @@ -1213,8 +1211,6 @@ def test_resample_long_periods(self, rule, expected_idx, expected_values, metada
'value_unit': 'mb',
'value_name': 'SOI',
'label': f'Southern Oscillation Index ({rule} resampling)',
'lat': None,
'lon': None,
'archiveType': 'Instrumental',
'importedFrom': None,
'log': (
Expand Down