#a new srcipt for silo and backup for the other paper#1 codes

Analysis/Code/NARCLIM_Download/R_Preparing_BASH_script_for_NARCLIM_batch_download.R

@@ -15,9 +15,9 @@
 # 'wss1Hmaxtstep'		Max. 1-hour time-window moving averaged surface wind speed units: m s-1 maximum 1-hour time-window moving averaged values from point values 60.0 second
 # 'wssmax' 		Surface wind speed standard_name: air_velocity units: m s-1 height: 10 m
 # 'wssmean'		Surface wind speed standard_name: air_velocity units: m s-1
+# 'sstmean'   Sea surface temperatuer daily mean
 
-
-Clim_Var <- 'wssmax'
+Clim_Var <- 'sstmean'
 Datatype <- 'T_GCMS'  #T_GCMS for GCM forcing, T_NNRP for reanalysis (only 1950-2009)
 Biasboolean <- 'False' #use bias corrected data?
 
@@ -43,6 +43,10 @@ for (i in 1:(length(Location.df$Name))){
   # }
   latitude=round(as.numeric(Location.df$Lat[i]),3)
   longitude=round(as.numeric(Location.df$Long[i]),3)
+  if (Clim_Var == 'sstmean'){
+    latitude=round(as.numeric(Location.df$Ocean_Lat[i]),3)
+    longitude=round(as.numeric(Location.df$Ocean_Long[i]),3)
+    }
   text <- c(paste("latitude=",latitude,"", sep=""), paste("longitude=",longitude,"", sep=""),
 paste("name='",name,"'", sep=""),
 "python /srv/ccrc/data02/z5025317/Code_execution/\\

Analysis/Code/P1_NARCliM_NC_to_CSV_CCRC_SS.py

@@ -169,7 +169,8 @@ if Bias_Correction_BOOL == 'True':
                 Period_short = NC_Period[:4]
                 Current_input_dir = './' + GCM + '/' + Warf_run + '/' + NC_Period + '/' + NC_Domain + '/'
                 print Current_input_dir
-                Climvar_ptrn = '*' + Timestep + '_*' + Clim_var_type + '_bc.nc'
+                Clim_var_type = Clim_var_type + '_bc.nc'
+                Climvar_ptrn = '*' + Timestep + '_*' + Clim_var_type 
                 Climvar_NCs = glob.glob(Current_input_dir + Climvar_ptrn)
                 print Climvar_NCs[1]
                 print Climvar_NCs[2]
@@ -178,14 +179,14 @@ if Bias_Correction_BOOL == 'True':
                     #print netcdf
                     f=Dataset(netcdf)
                     # This section print on the screen information contained in the headings of the file
-#                    print '---------------------------------------------------------'
-#                    print f.ncattrs()
-#                    print f.title
-#                    print f.variables
-#                    print
-#                    for varname in f.variables:
-#                    	print varname,' -> ',np.shape(f.variables[varname])
-#                    print '---------------------------------------------------------'
+                    print '---------------------------------------------------------'
+                    print f.ncattrs()
+                    print f.title
+                    print f.variables
+                    print
+                    for varname in f.variables:
+                    	print varname,' -> ',np.shape(f.variables[varname])
+                    print '---------------------------------------------------------'
                     # 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))

Analysis/Code/P1_NARCliM_plots_Windows.py

@@ -24,6 +24,9 @@ matplotlib.style.use('ggplot')
 # Set working direcotry (where postprocessed NARClIM data is located)
 os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Analysis/Code')
 import climdata_fcts as fct
+import silo as sil
+
+
 
 #==========================================================#
 # Set working direcotry (where postprocessed NARClIM data is located)
@@ -34,18 +37,19 @@ os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdo
 #==========================================================#
 #set input parameters
 Base_period_start = '1990-01-01'
+Case_Study_Name = 'CASESTUDY2'
 Base_period_end = '2080-01-01' #use last day that's not included in period as < is used for subsetting
 Estuary = 'HUNTER' # 'Belongil'
-Clim_var_type  = "pracc"   #  '*' will create pdf for all variables in folder  "pracc*|tasmax*"        
+Clim_var_type  = "sstmean"   #  '*' will create pdf for all variables in folder  "pracc*|tasmax*"        
 plot_pdf = 'yes'
 delta_csv = 'yes'
-Stats = 'dailymax'
+Stats = 'maxdaily'
 Version = 'V4'
 #==========================================================#
 
 #==========================================================#
 #set directory path for output files
-output_directory = 'Output/Case_Study_1/'+ Estuary
+output_directory = 'Output/' + Case_Study_Name + '/' + Estuary
 #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
 if not os.path.exists(output_directory):
     os.makedirs(output_directory)
@@ -55,7 +59,7 @@ if not os.path.exists(output_directory):
 #==========================================================#    
 
 #==========================================================#
-Estuary_Folder = glob.glob('./Data/NARCLIM_Site_CSVs/' + Estuary + '*' )
+Estuary_Folder = glob.glob('./Data/NARCLIM_Site_CSVs/'+ Case_Study_Name + '/' + Estuary + '*' )
 Clim_Var_CSVs = glob.glob(Estuary_Folder[0] + '/' + Clim_var_type + '*')
 #==========================================================#
 
@@ -77,7 +81,7 @@ Ncols_df = len(Full_df)
 
 #==========================================================#
 #substract a constant from all values to convert from kelvin to celcius (temp)
-if Clim_var_type == 'tasmean' or Clim_var_type == 'tasmax':
+if Clim_var_type == 'tasmean' or Clim_var_type == 'tasmax' or Clim_var_type == 'sstmean':
     Full_df = Full_df.iloc[:,0:(Ncols_df-1)]-273.15
 if Clim_var_type == 'evspsblmean' or Clim_var_type == 'potevpmean':
     Full_df = Full_df.iloc[:,0:(Ncols_df-1)]*60*60*24
@@ -135,53 +139,7 @@ dfall_annual = dfa1.append(dfa2).append(dfa3)
 #==========================================================#
 #Create Deltas of average change for annual and seasonal basis
 #==========================================================#
-times = ['annual', 'DJF', 'MAM', 'JJA','SON']
-delta_all_df = pd.DataFrame()
-for temp in times:
-    if temp == 'annual':
-        Mean_df = Fdf_1900_2080_annual.mean()
-        Column_names = ['near', 'far']
-    if temp == 'DJF':
-        Mean_df = Fdf_Seas_means[Fdf_Seas_means.index.quarter==1].mean()
-        Column_names = ['DJF_near', 'DJF_far']
-    if temp == 'MAM':
-        Mean_df = Fdf_Seas_means[Fdf_Seas_means.index.quarter==2].mean()
-        Column_names = ['MAM_near', 'MAM_far']
-    if temp == 'JJA':
-        Mean_df = Fdf_Seas_means[Fdf_Seas_means.index.quarter==3].mean()
-        Column_names = ['JJA_near', 'JJA_far']
-    if temp == 'SON':
-        Mean_df = Fdf_Seas_means[Fdf_Seas_means.index.quarter==4].mean()
-        Column_names = ['SON_near', 'SON_far']
-    models = list(Fdf_1900_2080_means.index)
-    newmodel = []
-    type(newmodel)
-    for each in models:
-        newmodel.append(each[:-5])
-    unique_models = set(newmodel)
-    # calculate diff for each unique model
-    delta_NF_ensemble = []
-    delta_FF_ensemble = []
-    for unique_model in unique_models:
-        dfdiff = Mean_df.filter(regex= unique_model)
-        type(dfdiff)
-        delta_NF = dfdiff[1] - dfdiff[0]
-        delta_NF_ensemble.append(delta_NF)
-        delta_FF = dfdiff[2] - dfdiff[1]
-        delta_FF_ensemble.append(delta_FF)
-
-    delta_df1=pd.DataFrame(delta_NF_ensemble, index=unique_models)
-    delta_df2=pd.DataFrame(delta_FF_ensemble, index=unique_models)
-    delta_df= pd.concat([delta_df1, delta_df2], axis=1)
-    
-    #rename columns
-    delta_df.columns = Column_names
-    #add a row with medians and 10 and 90th percentiles
-    delta_df.loc['10th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 10), Column_names[1]:np.percentile(delta_df[Column_names[1]], 10)})
-    delta_df.loc['median'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 50), Column_names[1]:np.percentile(delta_df[Column_names[1]], 50)})
-    delta_df.loc['90th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 90), Column_names[1]:np.percentile(delta_df[Column_names[1]], 90)})
-    #append df to overall df
-    delta_all_df = pd.concat([delta_all_df, delta_df], axis=1)
+delta_all_df = fct.calculate_deltas_NF_FF2(Fdf_1900_2080_annual, Fdf_Seas_means)
 
 
 #==========================================================#

Analysis/Code/P1_SILO_Batch_Download.py

@@ -0,0 +1,115 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jun 20 18:03:25 2018
+
+@author: z5025317
+"""
+
+#==========================================================#
+#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
+from ggplot import *
+matplotlib.style.use('ggplot')
+import csv
+from datetime import datetime
+
+# import own modules
+# Set working direcotry (where postprocessed NARClIM data is located)
+os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Analysis/Code')
+import climdata_fcts as fct
+import silo as sil
+
+
+#==========================================================#
+# Set working direcotry (where postprocessed NARClIM data is located)
+os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/')
+#==========================================================#
+
+         
+#==========================================================#
+#set input parameters
+Case_Study_Name = 'CASESTUDY2' 
+Casestudy2_csv_path =  "Data/NARCLIM_Site_CSVs/CASESTUDY2/CASESTDUY2_NARCLIM_Point_Sites.csv"
+Silo_variables = ['daily_rain', "max_temp", "min_temp", 'et_short_crop']      
+#==========================================================#
+
+#==========================================================#
+#set directory path for output files
+output_directory = 'Data/SILO/' + Case_Study_Name + '/'
+#output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
+if not os.path.exists(output_directory):
+    os.makedirs(output_directory)
+    print('-------------------------------------------')
+    print("output directory folder didn't exist and was generated")
+    print('-------------------------------------------')
+#==========================================================#  
+    
+
+#read the CSV to extract the lat long and case stuy sites
+with open(Casestudy2_csv_path, mode='r') as infile:
+    reader = csv.reader(infile)
+    next(reader, None) 
+    with open('coors_new.csv', mode='w') as outfile:
+        writer = csv.writer(outfile)
+        mydict = dict((rows[0],[rows[1],rows[2]]) for rows in reader)
+        
+for Estuary in mydict:
+    print Estuary
+    print str(mydict[Estuary][0])
+    
+    #==========================================================#
+    #set directory path for output files
+    output_directory_internal = output_directory  + Estuary + '/'
+    #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
+    if not os.path.exists(output_directory_internal):
+        os.makedirs(output_directory_internal)
+        print('-------------------------------------------')
+        print("output directory folder didn't exist and was generated")
+        print('-------------------------------------------')
+    #==========================================================#
+    
+    output_csv = output_directory_internal + 'SILO_climdata_' + Estuary +'_' + mydict[Estuary][0] + '_' +  mydict[Estuary][1] + '.csv'
+    silo_df = sil.pointdata(Silo_variables, 'Okl9EDxgS2uzjLWtVNIBM5YqwvVcCxOmpd3nCzJh','19900101','20100101',
+                            None, mydict[Estuary][0], mydict[Estuary][1], True, output_csv)
+
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Analysis/Code/climdata_fcts.py

@@ -40,6 +40,8 @@ def datenum2datetime(datenum):
     return time
 
 
+
+
 def select_min_med_max_dif_model(NARCLIM_df):
     #Select the 3 most representative models (min med and max difference betwen far future and present)
     Fdf_1900_2080_sorted = NARCLIM_df.reindex_axis(sorted(NARCLIM_df.columns), axis=1)
@@ -69,3 +71,56 @@ def select_min_med_max_dif_model(NARCLIM_df):
     dfmax = NARCLIM_df.filter(regex= Max_dif_mod_name[:-5])
     dfmed = NARCLIM_df.filter(regex= Max_dif_mod_name[:-5])
     return dfall , dfmin, dfmed, dfmax, Min_dif_mod_name,Med_dif_mod_name, Max_dif_mod_name
+
+
+def calculate_deltas_NF_FF2(Annual_df, Seasonal_df):
+    """calculates the "deltas" between nearfuture and present day for annual or seasonal climate data in pandas TS format"""
+
+    times = ['annual', 'DJF', 'MAM', 'JJA','SON']
+    delta_all_df = pd.DataFrame()
+    for temp in times:
+        if temp == 'annual':
+            Mean_df = Annual_df.mean()
+            Column_names = ['near', 'far']
+        if temp == 'DJF':
+            Mean_df = Seasonal_df[Seasonal_df.index.quarter==1].mean()
+            Column_names = ['DJF_near', 'DJF_far']
+        if temp == 'MAM':
+            Mean_df = Seasonal_df[Seasonal_df.index.quarter==2].mean()
+            Column_names = ['MAM_near', 'MAM_far']
+        if temp == 'JJA':
+            Mean_df = Seasonal_df[Seasonal_df.index.quarter==3].mean()
+            Column_names = ['JJA_near', 'JJA_far']
+        if temp == 'SON':
+            Mean_df = Seasonal_df[Seasonal_df.index.quarter==4].mean()
+            Column_names = ['SON_near', 'SON_far']
+        models = list(Seasonal_df.mean().index)
+        newmodel = []
+        type(newmodel)
+        for each in models:
+            newmodel.append(each[:-5])
+        unique_models = set(newmodel)
+        # calculate diff for each unique model
+        delta_NF_ensemble = []
+        delta_FF_ensemble = []
+        for unique_model in unique_models:
+            dfdiff = Mean_df.filter(regex= unique_model)
+            type(dfdiff)
+            delta_NF = dfdiff[1] - dfdiff[0]
+            delta_NF_ensemble.append(delta_NF)
+            delta_FF = dfdiff[2] - dfdiff[1]
+            delta_FF_ensemble.append(delta_FF)
+    
+        delta_df1=pd.DataFrame(delta_NF_ensemble, index=unique_models)
+        delta_df2=pd.DataFrame(delta_FF_ensemble, index=unique_models)
+        delta_df= pd.concat([delta_df1, delta_df2], axis=1)
+    
+        #rename columns
+        delta_df.columns = Column_names
+        #add a row with medians and 10 and 90th percentiles
+        delta_df.loc['10th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 10), Column_names[1]:np.percentile(delta_df[Column_names[1]], 10)})
+        delta_df.loc['median'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 50), Column_names[1]:np.percentile(delta_df[Column_names[1]], 50)})
+        delta_df.loc['90th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 90), Column_names[1]:np.percentile(delta_df[Column_names[1]], 90)})
+        #append df to overall df
+        delta_all_df = pd.concat([delta_all_df, delta_df], axis=1)
+        return delta_all_df