Merge pull request #4 from elnazazmi/main

add an upper level to the code dir

config.toml

@@ -1,7 +1,7 @@
 # NOTE: this config is provided as a TEMPLATE, it should be changed by the user before using it.
 [simulation]
     name = "syria_new" # name of the simulation.
-    experiment_path = "cases/" # path where experiment folder should be placed
+    experiment_path = "WITOIL_iMagine/cases/" # path where experiment folder should be placed
     start_datetime = 2021-08-22T03:43:00 # start date of the simulation
     sim_length = 24.0 # length of the simulation in HOURS
     spill_lat = [35.25] # lat of oil spill (deg N)
@@ -10,11 +10,11 @@
     spill_rate = [27.78] # spill rate TONS/HOUR
     slick_age = [0.0] # age of oil slick in HOURS
     oil = [28] # either oil api (number) or name (string), e.g. ["Ragusa"]. Please, consider that name must be exact.
-    area_spill = true
+    area_spill = false
     area_vertex = false # comprehends thre levels of lists. 1st: all slicks. 2nd: individual slick. 3rd: Coordinates of each vertex in each individual slick
     multiple_slick = false
     advanced_parameters = false # if = true, user must provide parameters.toml file
-    advanced_parameters_path = "src/parameters.toml" # this path shuld be provided only if "advanced_parameters" is = true
+    advanced_parameters_path = "WITOIL_iMagine/src/parameters.toml" # this path shuld be provided only if "advanced_parameters" is = true
 [download]
     download_data = true # = true if data are not provided by the user
     download_curr = true # = true : OCE data are downloaded from Copernicus Marine Service
@@ -29,8 +29,8 @@
     delta = [0.75] # default domain length in degrees (applied to both lon/lat), to download or crop data
     # note: delta is used only if set_domain = false
     [input_files.dtm]
-        bathymetry_path = "data/gebco/GEBCO_2023.nc" # GEBCO 2023 bathymetry file
-        coastline_path = "data/gshhs/f/GSHHS_f_L1.shp" # coastline shapefile gshhg
+        bathymetry_path = "WITOIL_iMagine/data/gebco/GEBCO_2023.nc" # GEBCO 2023 bathymetry file
+        coastline_path = "WITOIL_iMagine/data/gshhs/f/GSHHS_f_L1.shp" # coastline shapefile gshhg
     [input_files.metoce]
         oce_data_path = false # to provide if dowload_curr = false
         met_data_path = false # to provide if dowload_wind = false

src/download/download_copernicus_parser.py

@@ -7,7 +7,7 @@
 import xarray as xr
 
 # Functions outside this script
-from src.utils.utils import *
+from WITOIL_iMagine.src.utils.utils import *
 
 
 def download_copernicus(

src/download/download_era5_parser.py

@@ -8,7 +8,7 @@
 import time
 
 # Functions outside this script
-from src.utils.utils import *
+from WITOIL_iMagine.src.utils.utils import *
 
 def write_cds(token):
     """
@@ -73,13 +73,13 @@ def get_era5(xmin,xmax,ymin,ymax,start_date,end_date,output_path,output_name):
 
 def process_era5(output_path,output_name):
 
-    met = xr.open_mfdataset('data/ERA5/temp*.nc')
+    met = xr.open_mfdataset('WITOIL_iMagine/data/ERA5/temp*.nc')
     met = Utils.rename_netcdf_variables_mdk3(met)
 
     met.to_netcdf(output_name)
 
     #remove the temporary files
-    subprocess.run([f'rm -rf {output_path}/temp*.nc'],shell=True)  
+    subprocess.run([f'rm -rf {output_path}/temp*.nc'],shell=True)
 
 
 if __name__ == '__main__':

src/plot/plot_mdk3.py

@@ -192,7 +192,7 @@ def plot_pyngl(
         """
         config = self.config
         current_folder = os.path.dirname(os.path.abspath(__file__))
-        path_to_plotspill = 'src/plot/plotngl.py'
+        path_to_plotspill = 'WITOIL_iMagine/src/plot/plotngl.py'
         root_directory = self.root_directory
         spill_lon = config["simulation"]["spill_lon"][0]
         spill_lat = config["simulation"]["spill_lat"][0]

src/preprocessing/preprocessing_mdk3.py

@@ -9,8 +9,8 @@
 from numpy.typing import NDArray
 from datetime import datetime, timedelta, date
 
-from src.utils.utils import Utils
-from src.utils.config import Config
+from WITOIL_iMagine.src.utils.utils import Utils
+from WITOIL_iMagine.src.utils.config import Config
 
 import logging
 
@@ -56,9 +56,8 @@ def process_currents(self, oce_path: str = None):
         logger.info("Pre processing currents")
         lon_min, lon_max, lat_min, lat_max = self.domain
         # opening all files in the directory and concatenating them automatically through open_mfdataset
-        if oce_path is None:
-            oce_path = f"{self.exp_folder}/oce_files/"
-        oce_path = os.path.join(oce_path, "*.nc")
+        oce_path = f"{self.exp_folder}/oce_files/*.nc"
+
         if glob(oce_path) == []:
             oce_path = f"{self.exp_folder}/oce_files/*.nc"
         concat = xr.open_mfdataset(oce_path, combine="nested", engine="netcdf4")
@@ -77,9 +76,8 @@ def process_winds(self, met_path: str = None):
         logger.info("Pre processing winds")
         lon_min, lon_max, lat_min, lat_max = self.domain
         # opening all files in the directory and concatenating them automatically through open_mfdataset
-        if met_path is None:
-            met_path = f"{self.exp_folder}/met_files/*.nc"
-        met_path = os.path.join(met_path, "*.nc")
+        met_path = f"{self.exp_folder}/met_files/*.nc"
+
         if glob(met_path) == []:
             met_path = f"{self.exp_folder}/met_files/*.nc"
         concat = xr.open_mfdataset(met_path, combine="nested", engine="netcdf4")
@@ -221,14 +219,14 @@ def process_medslik_memmory_array(self):
 
         med_for = f'{self.exp_folder}/xp_files/medslik_II.for'
 
-        subprocess.run([f'cp src/templates/medslik_II_template.for {med_for}'],shell=True)
+        subprocess.run([f'cp WITOIL_iMagine/src/templates/medslik_II_template.for {med_for}'],shell=True)
 
         # Replacing NMAX in medslik fortran with a python function
         Utils.search_and_replace(med_for, 'NMAX', str(nmax))
 
     def configuration_parameters(self):
 
-        subprocess.run([f'cp src/templates/config2.txt {self.exp_folder}/xp_files/config2.txt'],shell=True)
+        subprocess.run([f'cp WITOIL_iMagine/src/templates/config2.txt {self.exp_folder}/xp_files/config2.txt'],shell=True)
 
     def common_grid(self):
 
@@ -270,11 +268,11 @@ def write_config_files(self,
         print("...config1.txt...")
         # Iterating through slicks or doing for single simulation
         if separate_slicks == False:
-            config_file = f"cases/{simname}/xp_files/config1.txt"
+            config_file = f"WITOIL_iMagine/cases/{simname}/xp_files/config1.txt"
         else:
-            config_file = f"cases/{simname}/xp_files/slick{s_num+1}/config1.txt"
+            config_file = f"WITOIL_iMagine/cases/{simname}/xp_files/slick{s_num+1}/config1.txt"
         subprocess.run(
-            [f"cp src/templates/config1_template_0.txt {config_file}"], shell=True
+            [f"cp WITOIL_iMagine/src/templates/config1_template_0.txt {config_file}"], shell=True
         )
         # adding spill Name - Add slick number if separate slicks
         if separate_slicks == False: