added folder input argument for cookie cutter

cookie-cutter/nc_cookie_cutter.py

@@ -1,6 +1,7 @@
 import argparse
 import os
 import sys
+import glob
 
 import xarray as xr
 import numpy as np
@@ -14,15 +15,23 @@ def main():
     parser.add_argument("-m", "--mask", help='mask file (cookie-cutter), .map if pcraster, .nc if netcdf', required=True)
     parser.add_argument("-l", "--list",
                         help='list of files to be cut, in a text file, one file per line, '
-                             'main variable i.e. pr/e0/tx/tavg must be last variable in the input file', required=True)
+                             'main variable i.e. pr/e0/tx/tavg must be last variable in the input file', required=False)
+    parser.add_argument("-f", "--folder", help='Directory with netCDF files to be cut', required=False)
     parser.add_argument("-o", "--outpath", help='path where to save cut files', required=True)
     args = parser.parse_args()
 
     filelist = args.list
     mask = args.mask
     pathout = args.outpath
+    input_folder = args.folder
+    print('File list{} Mask: {} Output: {} Input: {}'.format(filelist, mask, pathout, input_folder))
+    if filelist:
+        list_to_cut = open(filelist).readlines()
+    elif input_folder:
+        list_to_cut = glob.glob(os.path.join(input_folder, '*.nc'))
+    else:
+        raise ValueError('You must issue either list or folder input arguments.')
 
-    list_to_cut = open(filelist).readlines()
     maskname, ext = os.path.splitext(mask)
 
     if ext == '.map':
@@ -46,11 +55,11 @@ def main():
     x_max = np.max(mask_filter[0])
     y_min = np.min(mask_filter[1])
     y_max = np.max(mask_filter[1])
-
+    print('{} {} {} {}'.format(x_min, x_max, y_min, y_max))
     # walk through list_to_cut
     for f in list_to_cut:
-        fileout = os.path.join(pathout, f)
-        if os.path.isfile(fileout):
+        fileout = os.path.join(pathout, os.path.basename(f))
+        if os.path.isfile(fileout) and os.path.exists(fileout):
             print(fileout, 'Alreay existing, are you sure you are not swiping original file with cut version? this file will not be overwrote ')
             continue
         filename, ext = os.path.splitext(f)
@@ -62,12 +71,18 @@ def main():
         except:  # file has no time component
             nc = xr.open_dataset(f)
 
-        var = nc.variables.items()[-1][0]
+        var = list(nc.variables.items())[-1][0]
+        if 'lat' in nc.variables:
+            nc.variables[var].attrs['esri_pe_string'] ='GEOGCS[\"GCS_WGS_1984\",DATUM[\"D_WGS_1984\",SPHEROID[\"WGS_1984\",6378137,298.257223563]],PRIMEM[\"Greenwich\",0],UNIT[\"Degree\",0.0174532925199433]]"'
+        else:
+            nc.variables[var].attrs['esri_pe_string'] ='PROJCS["ETRS_1989_LAEA",GEOGCS["GCS_ETRS_1989",DATUM["D_ETRS_1989",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Lambert_Azimuthal_Equal_Area"],PARAMETER["False_Easting",4321000.0],PARAMETER["False_Northing",3210000.0],PARAMETER["Central_Meridian",10.0],PARAMETER["Latitude_Of_Origin",52.0],UNIT["Meter",1.0]]'
+            nc.variables[var].attrs['proj4_params'] = "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs"
         if 'time' in nc.variables:
             sliced_var = nc[var][:, x_min:x_max+1, y_min:y_max+1]
         else:
             sliced_var = nc[var][x_min:x_max+1, y_min:y_max+1]
 
+        print('Creating ', fileout)
         sliced_var.to_netcdf(fileout)
         nc.close()
 

cookie-cutter/requirements.txt

@@ -1,3 +1,5 @@
 dask
 xarray
 pandas
+numpy
+netCDF4

gfit/gfit2.r

@@ -1,3 +1,16 @@
+## Copyright 2019 European Union
+##
+## Licensed under the EUPL, Version 1.2 or as soon they will be approved by the European Commission  subsequent versions of the EUPL (the "Licence");
+##
+## You may not use this work except in compliance with the Licence.
+## You may obtain a copy of the Licence at:
+##
+## https://joinup.ec.europa.eu/sites/default/files/inline-files/EUPL%20v1_2%20EN(1).txt
+##
+## Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the Licence for the specific language governing permissions and limitations under the Licence.
+
 
 ##purpose: estimating return levels from a Gumbel extreme value distribution functions fit to annual maxima 
 ##Created: Zuzanna, August 2015; 

pcr2nc/pcr2nc/main.py

@@ -1,4 +1,17 @@
 """
+Copyright 2019 European Union
+
+Licensed under the EUPL, Version 1.2 or as soon they will be approved by the European Commission  subsequent versions of the EUPL (the "Licence");
+
+You may not use this work except in compliance with the Licence.
+You may obtain a copy of the Licence at:
+
+https://joinup.ec.europa.eu/sites/default/files/inline-files/EUPL%20v1_2%20EN(1).txt
+
+Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the Licence for the specific language governing permissions and limitations under the Licence.
+
 pcr2nc
 A tool that convert PCRaster maps to a netCDF4 mapstack CF-1.7
 """

pcr2nc/pcr2nc/reader.py

@@ -1,4 +1,17 @@
 """
+Copyright 2019 European Union
+
+Licensed under the EUPL, Version 1.2 or as soon they will be approved by the European Commission  subsequent versions of the EUPL (the "Licence");
+
+You may not use this work except in compliance with the Licence.
+You may obtain a copy of the Licence at:
+
+https://joinup.ec.europa.eu/sites/default/files/inline-files/EUPL%20v1_2%20EN(1).txt
+
+Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the Licence for the specific language governing permissions and limitations under the Licence.
+
 PCRaster related code. It contains classes representing a PCRaster map and the reader.
 """
 

pcr2nc/pcr2nc/writer.py

@@ -1,6 +1,20 @@
 """
+Copyright 2019 European Union
+
+Licensed under the EUPL, Version 1.2 or as soon they will be approved by the European Commission  subsequent versions of the EUPL (the "Licence");
+
+You may not use this work except in compliance with the Licence.
+You may obtain a copy of the Licence at:
+
+https://joinup.ec.europa.eu/sites/default/files/inline-files/EUPL%20v1_2%20EN(1).txt
+
+Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the Licence for the specific language governing permissions and limitations under the Licence.
+
 Module containing the code for the NetCDFWriter class
 """
+
 import datetime
 import time