This notebook is to show how to read a LiPD file and generate ensemble of age-depth models by python packages LiPD (https://github.com/nickmckay/LiPD-utilities) and Pyleoclim (https://github.com/LinkedEarth/Pyleoclim_util)
In [17]:
%matplotlib inline
import numpy as np
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
In [12]:
import lipd
In [13]:
lipd_file = lipd.readLipd('Crystal.McCabe-Glynn.2013.lpd')
Disclaimer: LiPD files may be updated and modified to adhere to standards
reading: Crystal.McCabe-Glynn.2013.lpd
Finished read: 1 record
In [1]:
import pyleoclim as pyleo
In [2]:
lipds = pyleo.openLipd("Crystal.McCabe-Glynn.2013.lpd")
Disclaimer: LiPD files may be updated and modified to adhere to standards
reading: Crystal.McCabe-Glynn.2013.lpd
Finished read: 1 record
In [3]:
ts_list = pyleo.fetchTs(lipds)
extracting paleoData...
extracting: Crystal.McCabe-Glynn.2013
Created time series: 3 entries
In [4]:
fig = pyleo.mapLipd()
0 : Crystal.McCabe-Glynn.2013 : depth
1 : Crystal.McCabe-Glynn.2013 : age_ad
2 : Crystal.McCabe-Glynn.2013 : d18o_vpdb
Enter the number of the variable you wish to use: 2
In [7]:
# get d18o time series
d18o=ts_list[2]['paleoData_values']
In [14]:
# Run age model BChron
depth, chron, positions, ageDist, fig = pyleo.Bchron(lipd_file, calCurves = ["normal"],reservoirAgeCorr=[0,0],saveLipd=False)
No previous model available. Creating model...
Looking for age data...
No match found on exact search, running partial match
No match found.
Here are the available variables:
0 : sample
1 : depth
2 : 238u
3 : 238u_uncertainty
4 : 232th
5 : 232th_uncertainty
6 : 230th/232th
7 : 230th/232th_uncertainty
8 : d234u
9 : d234u_undertainty
10 : 230th/238u
11 : 230th/238u_uncertainty
12 : 230th age
13 : 230th age_uncertainty
14 : 230th age-1
15 : 230th age_uncertaity
16 : d234uinitial
17 : d234uinitial_uncertainty
18 : 230th age-2
19 : 230th age_uncertainty-1
Please select the variable you'd like to use or enter to continue: 18
Age data found.
Looking for a depth/position column...
Depth information found.
Looking for age uncertainty...
More than one series match your search criteria
0 : d234uinitial_uncertainty
1 : 230th age_uncertainty-1
2 : 230th age_uncertainty
3 : 230th/238u_uncertainty
4 : 230th/232th_uncertainty
5 : 238u_uncertainty
6 : 232th_uncertainty
Enter the number for the variable: 1
Uncertainty data found.
Checking that list contains valid calibration curves ...
Verification complete!
Calibration curves found.
Running Bchron. This could take a few minutes...
Checking that list contains valid calibration curves ...
Verification complete!
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Placing all the tables in the LiPD object...
Plotting...
In [15]:
#chron is the array of the ensemble of age model, the first dimension is number of depth_sample
# the second dimension is Monte-Carlo numbers (here is 1000)
chron.shape
Out[15]:
(1054, 1000)
In [18]:
# plot one of possible realization of d18O time series
plt.plot(chron[:,0],d18o)
Out[18]:
[<matplotlib.lines.Line2D at 0x1d2bb45588>]
In [ ]:
Content source: ClimateTools/Correlation_EPSL
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