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#principal python codes for a) NARCLIM interrogation on CCRC STORM servers (Linux) where we go from netcdf to a csv file for single locations. and b)

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b) code for creating some variability shift plots from the CSV files
which is done locally
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tinoheimhuber 7 years ago
commit 4bd8d40c6d
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121
Analysis/Code/P1_NARCliM_NC_to_CSV_CCRC_SS.py
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# -*- coding: utf-8 -*-
from netCDF4 import *
import numpy as np
import os
import pandas as pd
import glob
import matplotlib
import matplotlib.pyplot as plt
from datetime import datetime
from datetime import timedelta
import argparse
import time
#
# Set working direcotry (where postprocessed NARClIM data is located)
os.chdir('/srv/ccrc/data30/z3393020/NARCliM/postprocess/')
#
#User input for location and variable type - from command line
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--lat", help="first number")
parser.add_argument("--lon", help="second number")
parser.add_argument("--varName", help="operation")
parser.add_argument("--timestep", help="operation")
parser.add_argument("--domain", help="operation")
args = parser.parse_args()
print(args.lat)
print(args.lon)
print(args.varName)
mylat= float(args.lat)
mylon= float(args.lon)
Clim_var_type = args.varName
NC_Domain = args.domain
Timestep = args.timestep
print("Extracting all NARCLIM time series for variable: ", Clim_var_type, " for lat lon: ", mylat, mylon, "domain", NC_Domain, "timestep ", Timestep)
#set directory path for output files
output_directory = '/srv/ccrc/data02/z5025317/NARCliM_out'
#output_directory = 'J:\Project wrl2016032\NARCLIM_Raw_Data\Extracted'
if not os.path.exists(output_directory):
os.makedirs(output_directory)
print("output directory folder didn't exist and was generated here:")
print(output_directory)
#
time.sleep(10)
#manual input via script
#mylat= -33.9608578
#mylon= 151.1339882
#Clim_var_type = 'pr1Hmaxtstep'
#NC_Domain = 'd02'
#
#set up the loop variables for interrogating the entire NARCLIM raw data
NC_Periods = ('1950-2009','2020-2039','2060-2079')
#
#Define empty pandas data frames
Full_df = pd.DataFrame()
GCM_df = pd.DataFrame()
R13_df = pd.DataFrame()
MultiNC_df = pd.DataFrame()
#
#Loop through models and construct CSV per site
for NC_Period in NC_Periods:
Period_short = NC_Period[:4]
GCMs = os.listdir('./'+ NC_Period)
for GCM in GCMs:
Warf_runs = os.listdir('./' + NC_Period + '/' + GCM + '/')
for Warf_run in Warf_runs:
Current_input_dir = './' + NC_Period + '/' + GCM + '/' + Warf_run + '/' + NC_Domain + '/'
print Current_input_dir
Climvar_ptrn = '*' + Timestep + '_*' + Clim_var_type + '.nc'
Climvar_NCs = glob.glob(Current_input_dir + Climvar_ptrn)
#Climvar_NCs = Climvar_NCs[0:2]
#print(Climvar_NCs)
for netcdf in Climvar_NCs:
f=Dataset(netcdf)
# Based on the desired inputs, this finds the nearest grid centerpoint index (x,y) in the *.nc file
dist_x=np.abs(f.variables['lon'][:,:]-float(mylon))
dist_y=np.abs(f.variables['lat'][:,:]-float(mylat))
dist=dist_x + dist_y
latindex=np.where(dist_y==np.min(dist_y))
lonindex=np.where(dist_x==np.min(dist_x))
index=np.where(dist==np.min(dist))
print '---------------------------------------------------------'
print netcdf
print 'Information on the nearest point'
print 'Your desired lat,lon = ',mylat,mylon
print 'The nearest lat,lon = ', f.variables['lat'][latindex[0],latindex[1]], f.variables['lon'][lonindex[0],lonindex[1]]
print 'The index of the nearest lat,lon (x,y) = ',index[0], index[1]
#Here we constract a pandas data frame, having the "time"/day as an index and a numer of variables (i.e. Clim_var_type, pracc, as columns)
d={}
#d["time"] = f.variables['time'][:]
d[ GCM +'_'+ Warf_run +'_'+ Period_short] = f.variables[Clim_var_type][:, int(index[0]), int(index[1])]
#if GCM == 'NNRP' and Warf_run == 'R1':
# d['Period']= NC_Period
timestamp = f.variables['time'][:]
timestamp_dates = pd.to_datetime(timestamp, unit='h', origin=pd.Timestamp('1949-12-01'))
df1=pd.DataFrame(d, index=timestamp_dates)
f.close()
print 'closing '+ os.path.basename(os.path.normpath(netcdf)) + ' moving to next netcdf file'
print '---------------------------------------------------------'
#append in time direction each new time series to the data frame
MultiNC_df = MultiNC_df.append(df1)
#append in columns direction individual GCM-RCM-123 run time series (along x axis)
MultiNC_df = MultiNC_df.sort_index(axis=0, ascending=True)
R13_df = pd.concat([R13_df, MultiNC_df], axis=1)
MultiNC_df =pd.DataFrame()
#append blocks of R1 R2 and R3 in x axis direction
R13_df = R13_df.sort_index(axis=0, ascending=True)
GCM_df = pd.concat([GCM_df, R13_df], axis=1)
R13_df = pd.DataFrame()
#append time periods in x axis direction (change axis=1 to =0 if periods for same model should be added to same model R123 column)
GCM_df = GCM_df.sort_index(axis=0, ascending=True)
Full_df = pd.concat([Full_df, GCM_df], axis=1)
GCM_df = pd.DataFrame()
Full_df = Full_df.sort_index(axis=0, ascending=True)
#adding a column with the NARCLIM decade
Full_df.loc[(Full_df.index > '1990-01-01') & (Full_df.index < '2009-01-01'), 'period']= '1990-2009'
Full_df.loc[(Full_df.index > '2020-01-01') & (Full_df.index < '2039-01-01'), 'period']= '2020-2039'
Full_df.loc[(Full_df.index > '2060-01-01') & (Full_df.index < '2079-01-01'), 'period']= '2060-2079'
#export the pandas data frame as a CSV file within the output directory
out_file_name = Clim_var_type + '_' + str(abs(round(mylat,3))) + '_' + str(round(mylon, 3)) + '_NARCliM_summary.csv'
out_path = output_directory +'/' + out_file_name
Full_df.to_csv(out_path)

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Analysis/Code/P1_NARCliM_plots_Windows.py
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# -*- coding: utf-8 -*-
#####################################----------------------------------
#Last Updated - March 2018
#@author: z5025317 Valentin Heimhuber
#code for creating climate prioritization plots for NARCLIM variables.
#Inputs: Uses CSV files that contain all 12 NARCLIM model runs time series for 1 grid cell created with: P1_NARCliM_NC_to_CSV_CCRC_SS.py
#####################################----------------------------------
#Load packages
#####################################----------------------------------
import numpy as np
import os
import pandas as pd
import glob
import matplotlib
import matplotlib.pyplot as plt
from datetime import datetime
from datetime import timedelta
from matplotlib.backends.backend_pdf import PdfPages
matplotlib.style.use('ggplot')
#
# Set working direcotry (where postprocessed NARClIM data is located)
os.chdir('C:/Users/z5025317/WRL_Postdoc/Projects/Paper#1/NARCLIM/')
#
#
#####################################----------------------------------
#set input parameters
Base_period_start = '1990-01-01'
Base_period_end = '2080-01-01' #use last day that's not included in period as < is used for subsetting
#Clim_var_type = 'tasmean' will create pdf for all variables in folder
#####################################----------------------------------
#set directory path for output files
output_directory = 'Output'
#output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
if not os.path.exists(output_directory):
os.makedirs(output_directory)
print("output directory folder didn't exist and was generated")
Clim_Var_CSVs = glob.glob('./Site_CSVs/*')
#Clim_Var_CSV = glob.glob('./Site_CSVs/' + Clim_var_type + '*' )
#read CSV file
for clim_var_csv_path in Clim_Var_CSVs:
Filename = os.path.basename(os.path.normpath(clim_var_csv_path))
Clim_var_type = Filename.split('_', 1)[0]
print(clim_var_csv_path)
Full_df = pd.read_csv(clim_var_csv_path, index_col=0, parse_dates = True)
#pandas datestamp index to period (we don't need the 12 pm info in the index (daily periods are enough))
Full_df.index = Full_df.index.to_period('D')
#check data types of columns
#Full_df.dtypes
#substract a constant from all values (temp)
if Clim_var_type == 'tasmean':
Full_df = Full_df.iloc[:,0:26]-273.15
#index the narclim periods if needed
#Full_df.loc[(Full_df.index >= '1990-01-01') & (Full_df.index < '2010-01-01'), 'period']= '1990-2009'
#Full_df.loc[(Full_df.index >= '2020-01-01') & (Full_df.index < '2040-01-01'), 'period']= '2020-2039'
#Full_df.loc[(Full_df.index >= '2060-01-01') & (Full_df.index < '2080-01-01'), 'period']= '2060-2079'
#Subset the data to the minimum base period and above (used to set the lenght of the present day climate period)
Fdf_1900_2080 = Full_df.loc[(Full_df.index >= Base_period_start) & (Full_df.index < Base_period_end)]
#Aggregate daily df to annual time series
if (Clim_var_type == 'pracc' or Clim_var_type == 'evspsblmean' or Clim_var_type == 'potevpmean'
or Clim_var_type == 'pr1Hmaxtstep' or Clim_var_type == 'wss1Hmaxtstep'):
Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').sum()
Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
Fdf_1900_2080_monthly = Fdf_1900_2080.resample('M').sum()
Fdf_1900_2080_monthly = Fdf_1900_2080_monthly.replace(0, np.nan)
Fdf_1900_2080_weekly = Fdf_1900_2080.resample('W').sum()
Fdf_1900_2080_weekly = Fdf_1900_2080_weekly.replace(0, np.nan)
Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').sum() #seasonal means
Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
else:
Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').mean()
Fdf_1900_2080_monthly = Fdf_1900_2080.resample('M').mean()
Fdf_1900_2080_weekly = Fdf_1900_2080.resample('W').mean()
Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').mean() #seasonal means
#plot the mean of all model runs
print('-------------------------------------------')
print('mean of all models for climate variable: ' + Clim_var_type)
Fdf_1900_2080_means = Fdf_1900_2080.mean()
Fdf_1900_2080_means.plot(kind='bar', ylim=(16,22)).figure
print('-------------------------------------------')
#time series plots:
#ranks = Fdf_1900_2080_means[3:].rank(axis=0)
df3 = Fdf_1900_2080_annual
Fdf_annual_sorted = df3.reindex_axis(df3.mean().sort_values().index, axis=1)
Fdf_annual_sorted_subset = Fdf_annual_sorted.iloc[:,[0,1,2,3,5,7,13,15,18, 22, 24,25]]
#write the key plots to a single pdf document
pdf_out_file_name = Clim_var_type + '_start_' + Base_period_start + '_NARCliM_summary4.pdf'
pdf_out_path = output_directory +'/' + pdf_out_file_name
#open pdf and add the plots
#developement
#I want to create a simple density plot for all values in present day, near future and far future
#this should be an easy indicator of change
#subset present day simulations
Full_current_df = Fdf_1900_2080.iloc[:,[0,1,2]]
Full_current_df = Full_current_df.stack()
#nearfuture
Full_nearfuture_df = Fdf_1900_2080.iloc[:,range(3,15)]
Full_nearfuture_df = Full_nearfuture_df.stack()
#farfuture
Full_farfuture_df = Fdf_1900_2080.iloc[:,range(15,27)]
Full_farfuture_df = Full_farfuture_df.stack()
Summarized_df = pd.concat([Full_current_df, Full_nearfuture_df], axis=1, ignore_index=True)
Summarized_df = pd.concat([Summarized_df, Full_farfuture_df], axis=1, ignore_index=True)
Summarized_df.columns = ['presentday', 'nearfuture', 'farfuture']
#end of developement
with PdfPages(pdf_out_path) as pdf:
#barplot of model means
plt.title(Clim_var_type + ' - model means - full period')
ymin = min(Fdf_1900_2080_means)
ymax = max(Fdf_1900_2080_means)
Fdf_1900_2080_means.plot(kind='bar', ylim=(ymin,ymax))
Fdf_1900_2080_means.plot(kind='bar')
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#full period density comparison
plt.title(Clim_var_type + ' - density comparison - full period')
Summarized_df.plot.kde()
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#annual box
plt.title(Clim_var_type + ' - Annual means')
Fdf_1900_2080_annual.boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#monthly box
plt.title(Clim_var_type + ' - Monthly means')
Fdf_1900_2080_monthly.boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#weekly box
plt.title(Clim_var_type + ' - Weekly means')
Fdf_1900_2080_weekly.boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#daily box
plt.title(Clim_var_type + ' - Daily means')
Fdf_1900_2080.boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
# time series plot annual ALL models
plt.title(Clim_var_type + ' - Time series - all models')
Fdf_1900_2080_annual.plot(legend=False)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#
plt.title(Clim_var_type + ' - Time series - representative models')
Fdf_annual_sorted_subset.plot(legend=False)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
# seasonal mean boxplots
ymin = min(Fdf_Seas_means[Fdf_Seas_means.index.quarter==1].mean())
ymax = max(Fdf_Seas_means[Fdf_Seas_means.index.quarter==1].mean())
plt.title(Clim_var_type + ' - DJF Summer means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==1].mean().plot(kind='bar', ylim=(ymin,ymax))
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
plt.title(Clim_var_type + ' - DJF Summer means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==1].boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
ymin = min(Fdf_Seas_means[Fdf_Seas_means.index.quarter==2].mean())
ymax = max(Fdf_Seas_means[Fdf_Seas_means.index.quarter==2].mean())
plt.title(Clim_var_type + ' - MAM Autumn means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==2].mean().plot(kind='bar', ylim=(ymin,ymax))
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
plt.title(Clim_var_type + ' - MAM Autumn means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==2].boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
ymin = min(Fdf_Seas_means[Fdf_Seas_means.index.quarter==3].mean())
ymax = max(Fdf_Seas_means[Fdf_Seas_means.index.quarter==3].mean())
plt.title(Clim_var_type + ' - JJA Winter means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==3].mean().plot(kind='bar', ylim=(ymin,ymax))
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
plt.title(Clim_var_type + ' - JJA Winter means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==3].boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
ymin = min(Fdf_Seas_means[Fdf_Seas_means.index.quarter==4].mean())
ymax = max(Fdf_Seas_means[Fdf_Seas_means.index.quarter==4].mean())
plt.title(Clim_var_type + ' - SON Spring means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==4].mean().plot(kind='bar', ylim=(ymin,ymax))
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
plt.title(Clim_var_type + ' - SON Spring means')
Fdf_Seas_means[Fdf_Seas_means.index.quarter==4].boxplot(rot=90)
pdf.savefig(bbox_inches='tight', pad_inches=0.4)
plt.close()
#plots not used
#Fdf_annual_sorted_subset.plot(legend=False, subplots=True)
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