diff --git a/sed_cores/options.py b/sed_cores/options.py
index 239c8156b2caa30f2543a9cc9395f776a4f93a6f..92bbef055ed1481ffe99bf5c02d01cf3748e3781 100644
--- a/sed_cores/options.py
+++ b/sed_cores/options.py
@@ -1,5 +1,5 @@
extract_adists_data = True
-adists_bin_data_dir = "./adists_res"
+adists_bin_data_dir = "."
adists_extracted_data_dir = "./adists_out"
adists_exe = "adists"
output_accumulation_to_csv = True
diff --git a/sed_cores/sediment_cores.py b/sed_cores/sediment_cores.py
index 5a5dfdbd87eed08f5de6d838eccee2127b5e45ef..07e6bc73e97631273c7b0a56a09934a158f236b8 100644
--- a/sed_cores/sediment_cores.py
+++ b/sed_cores/sediment_cores.py
@@ -5,9 +5,9 @@ except:
print("Error: sys not found")
exit()
try:
- import importlib as imp
+ import imp
except:
- print("Error: importlib not found")
+ print("Error: imp not found")
exit()
try:
import getopt
@@ -120,9 +120,12 @@ if not os.path.isfile(options_path):
else:
option_file = options_path
-imp.machinery.SourceFileLoader("options", option_file)
+print("we are in",os.getcwd())
+print("option file is ",option_file)
+imp.load_source("options", option_file)
from options import extract_adists_data
-from options import adists_data_dir
+from options import adists_bin_data_dir
+from options import adists_extracted_data_dir
from options import adists_exe
from options import output_accumulation_to_csv
from options import output_accumulation_to_png
@@ -142,6 +145,8 @@ values = dict()
nb_pk = len(list_pk)
nb_files = len(list_files)
nb_sediments = len(list_sediments)
+cwd = os.getcwd()
+print("we are in",os.getcwd())
#===========#
# read data #
@@ -161,19 +166,20 @@ if extract_adists_data:
if extract_adists_data:
if (not os.path.isdir(adists_extracted_data_dir)):
- print("Error: "+adists_extracted_data_dir+" folder not found")
- exit()
+ os.mkdir(adists_extracted_data_dir)
os.chdir(adists_extracted_data_dir)
print("Extracting data from Adis-TS to CSV files...")
+ print("we are in",os.getcwd())
output = ""
if not verbose: output = " > /dev/null"
for bed in list_beds:
for file in list_files:
for i,pk in enumerate(list_pk):
+ print("Extracting data from "+adists_bin_data_dir+"/"+file+".bin")
os.system( adists+" -b "+adists_bin_data_dir+"/"+file+".bin "+bed+"dt "+str(pk)+" "+file+"_"+bed+str(i)+output)
- os.chdir("..")
+ os.chdir(cwd)
print("Reading CSV files...")
@@ -212,7 +218,7 @@ for bed in list_beds:
for t,row in enumerate(csv_reader):
values.get(bed)[j][i][t] = float(row[1])
f.close()
-os.chdir("..")
+os.chdir(cwd)
if verbose: print(" Reading done")
#========================#
@@ -247,13 +253,13 @@ for bed in list_beds:
val_acc[pk][0] = val[0][pk][0]
val_acc_tot[pk][0] = val[0][pk][0]
for t in range(nb_timesteps-1):
+ val_acc[pk][t+1] = val[0][pk][t+1] - val[0][pk][t]
if val[0][pk][t+1]>val[0][pk][t]:
- val_acc[pk][t+1] = val[0][pk][t+1] - val[0][pk][t]
layers[pk] += 1
+ val_acc_tot[pk][t+1] = val_acc_tot[pk][t] + val_acc[pk][t+1]
else:
- val_acc[pk][t+1] = 0
- val_acc_tot[pk][t+1] = val_acc_tot[pk][t] + val_acc[pk][t+1]
-os.chdir("..")
+ val_acc_tot[pk][t+1] = val_acc_tot[pk][t]
+os.chdir(cwd)
if verbose: print(" Computing accumulation done")
if output_accumulation_to_csv:
@@ -265,9 +271,9 @@ if output_accumulation_to_csv:
os.chdir("./accumulation")
if def_numpy:
- row_data=np.zeros((nb_timesteps,3),float)
+ row_data=np.zeros((nb_timesteps,4),float)
else:
- row_data = create_float_list([nb_timesteps,3])
+ row_data = create_float_list([nb_timesteps,4])
for i in range(nb_timesteps):
row_data[i][0]=list_timesteps[i]
@@ -280,16 +286,17 @@ if output_accumulation_to_csv:
for t in range(nb_timesteps):
row_data[t][1]=val_acc[pk][t]
row_data[t][2]=val_acc_tot[pk][t]
+ row_data[t][3]=val[0][pk][t]
if layers[pk]>0:
if verbose: print(" Writing values_accumulated_"+list_pk[pk]+"_"+bed+".csv")
with open("values_accumulated_"+list_pk[pk]+"_"+bed+".csv", "w") as f:
writer = csv.writer(f)
- writer.writerow(["timestep","val_acc_instant","val_acc_tot"])
+ writer.writerow(["timestep","instant_accumulation","positive accumulation","total_accumulation"])
for t in range(nb_timesteps):
writer.writerow(row_data[t][:])
f.close()
if verbose: print(" Writing accumulation done")
- os.chdir("..")
+ os.chdir(cwd)
if def_matplotlib and output_accumulation_to_png:
@@ -301,6 +308,7 @@ if def_matplotlib and output_accumulation_to_png:
val_acc = values_accumulated.get(bed)
val_acc_tot = values_accumulated_tot.get(bed)
layers = nb_layers.get(bed)
+ val = values.get(bed)
for pk in range(nb_pk):
if layers[pk]>0:
if verbose: print(" Plotting values_accumulated_"+list_pk[pk]+"_"+bed+".png")
@@ -309,15 +317,16 @@ if def_matplotlib and output_accumulation_to_png:
ax.set_xlabel("time")
ax.set_ylabel("height")
#ax.set_title("Sediment accumulated at pk"+list_pk[pk]+" in bed "+bed)
- plt.plot(list_timesteps[:],val_acc[pk][:],label="instant accumulated")
- plt.plot(list_timesteps[:],val_acc_tot[pk][:],label="total accumulated")
+ plt.plot(list_timesteps[:],val_acc[pk][:],label="instant accumulation")
+ plt.plot(list_timesteps[:],val_acc_tot[pk][:],label="positive accumulation")
+ plt.plot(list_timesteps[:],val[0][pk][:],label="total accumulation")
plt.legend()
plt.title(label="Sediment accumulated at pk"+list_pk[pk]+" in bed "+bed+"\n", fontsize = 20)
fig.savefig("values_accumulated_"+list_pk[pk]+"_"+bed+".png")
plt.close(fig)
if verbose: print(" Plotting accumulation done")
- os.chdir("..")
+ os.chdir(cwd)
####################
# % of sed classes #
@@ -361,7 +370,7 @@ for bed in list_beds:
val_temp1[s] = sum(val[s+j][pk][t] for j in range(1,nb_files,nb_sediments))
if val_temp2>0.0 and val_temp1[s]>0.0 :
layers[bed][pk][l-1][s+2] = val_temp1[s]/val_temp2
-os.chdir("..")
+os.chdir(cwd)
if verbose: print("Computing sediment cores done")
if output_cores_to_csv:
@@ -383,7 +392,7 @@ if output_cores_to_csv:
writer.writerow(layers[bed][pk][i][:])
f.close()
if verbose: print(" Writing sediment cores done")
- os.chdir("..")
+ os.chdir(cwd)
if def_matplotlib and output_cores_to_png:
print("Output sediment cores as png...")
@@ -422,7 +431,7 @@ if def_matplotlib and output_cores_to_png:
fig.savefig("sed_core_"+list_pk[pk]+"_"+bed+".png")
plt.close(fig)
if verbose: print(" Plotting sediment cores done")
- os.chdir("..")
+ os.chdir(cwd)
print("Done !")