diff --git a/.gitignore b/.gitignore
index 78f64563e5784a02a66632b07f387220c7a9c16d..6c5fd0777cd0321f61523b5e77e2fb55c3fecff8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,6 +24,7 @@ wheels/
.installed.cfg
*.egg
MANIFEST
+outputs
# PyInstaller
# Usually these files are written by a python script from a template
diff --git a/inputs/namelist_remote.bdy b/inputs/namelist_remote.bdy
index ef6bf5d76feac030beb46e965938f45f416800d7..72b58c848840f7985bcd296a2fc4f6b475442701 100644
--- a/inputs/namelist_remote.bdy
+++ b/inputs/namelist_remote.bdy
@@ -40,8 +40,8 @@
!------------------------------------------------------------------------------
! I/O
!------------------------------------------------------------------------------
- sn_src_dir = './PyNEMO/inputs/src_data_remote.ncml' ! src_files/'
- sn_dst_dir = './outputs'
+ sn_src_dir = '/Users/thopri/Projects/PyNEMO/inputs/src_data_remote.ncml' ! src_files/'
+ sn_dst_dir = '/Users/thopri/Projects/PyNEMO/outputs'
sn_fn = 'NNA_R12' ! prefix for output files
nn_fv = -1e20 ! set fill value for output files
nn_src_time_adj = 0 ! src time adjustment
diff --git a/pynemo/tests/bdy_coords.py b/pynemo/tests/bdy_coords.py
new file mode 100755
index 0000000000000000000000000000000000000000..5f801fffa9bbd0b20850bc610c951db156828237
--- /dev/null
+++ b/pynemo/tests/bdy_coords.py
@@ -0,0 +1,157 @@
+'''
+###
+## This is a subset of pynemo for Robinson. It should be able to read a mask
+## file and produce a coordinates.bdy.nc file (jdha@noc.ac.uk)
+###
+'''
+
+# pylint: disable=E1103
+# pylint: disable=no-name-in-module
+
+#External imports
+from time import clock
+import numpy as np
+import logging
+
+#local imports
+from pynemo import nemo_bdy_setup as setup
+from pynemo import nemo_bdy_gen_c as gen_grid
+from pynemo import nemo_coord_gen_pop as coord
+
+from pynemo import nemo_bdy_source_coord as source_coord
+from pynemo import nemo_bdy_dst_coord as dst_coord
+from pynemo import nemo_bdy_ice
+from pynemo import pynemo_settings_editor
+from pynemo.utils import Constants
+
+from pynemo.gui.nemo_bdy_mask import Mask as Mask_File
+from PyQt4.QtGui import QMessageBox
+#import pickle
+
+
+logger = logging.getLogger(__name__)
+def process_bdy(setup_filepath=0, mask_gui=False):
+ """ Main entry to the processing of the bdy
+ Keyword arguments:
+ setup_filepath -- file path to bdy file
+ mask_gui -- whether gui to select the mask file needs to be poped up
+ """
+ #Logger
+ logger.info('START')
+ start = clock()
+ SourceCoord = source_coord.SourceCoord()
+ DstCoord = dst_coord.DstCoord()
+
+ logger.info(clock() - start)
+ start = clock()
+ Setup = setup.Setup(setup_filepath) # default settings file
+ settings = Setup.settings
+
+ logger.info(clock() - start)
+ ice = settings['ice']
+ logger.info('ice = %s', ice)
+
+ logger.info('Done Setup')
+ # default file, region settingas
+
+ start = clock()
+ bdy_msk = _get_mask(Setup, mask_gui)
+ logger.info(clock() - start)
+ logger.info('Done Mask')
+
+ DstCoord.bdy_msk = bdy_msk == 1
+ reload(gen_grid)
+ start = clock()
+ logger.info('start bdy_t')
+ grid_t = gen_grid.Boundary(bdy_msk, settings, 't')
+
+ logger.info(clock() - start)
+ start = clock()
+ logger.info('start bdy_u')
+ grid_u = gen_grid.Boundary(bdy_msk, settings, 'u')
+ logger.info('start bdy_v')
+
+ logger.info(clock() - start)
+ start = clock()
+ grid_v = gen_grid.Boundary(bdy_msk, settings, 'v')
+ logger.info('start bdy_f')
+
+ logger.info(clock() - start)
+ start = clock()
+
+ grid_f = gen_grid.Boundary(bdy_msk, settings, 'f')
+ logger.info('done bdy t,u,v,f')
+
+ logger.info(clock() - start)
+ start = clock()
+ if ice:
+ grid_ice = nemo_bdy_ice.BoundaryIce()
+ grid_ice.grid_type = 't'
+ grid_ice.bdy_r = grid_t.bdy_r
+
+ bdy_ind = {'t': grid_t, 'u': grid_u, 'v': grid_v, 'f': grid_f}
+
+ for k in bdy_ind.keys():
+ logger.info('bdy_ind %s %s %s', k, bdy_ind[k].bdy_i.shape, bdy_ind[k].bdy_r.shape)
+
+ start = clock()
+ co_set = coord.Coord(settings['dst_dir']+'/coordinates.bdy.nc', bdy_ind)
+ logger.info('done coord gen')
+ logger.info(clock() - start)
+ start = clock()
+ logger.info(settings['dst_hgr'])
+ co_set.populate(settings['dst_hgr'])
+ logger.info('done coord pop')
+
+ logger.info(clock() - start)
+
+ # may need to rethink grid info
+ # tracer 3d frs over rw
+ # tracer 2d frs over rw (i.e. ice)
+ # dyn 2d over 1st rim of T grid (i.e. ssh)
+ # dyn 2d over 1st rim
+ # dyn 2d frs over rw
+ # dyn 3d over 1st rim
+ # dyn 3d frs over rw
+
+def _get_mask(Setup, mask_gui):
+ """ This method reads the mask information from the netcdf file or opens a gui
+ to create a mask depending on the mask_gui input. return the mask data. The default mask
+ data is using bathymetry and applying a 1px halo
+ Keyword arguments:
+ Setup -- settings for bdy
+ mask_gui -- boolean to open mask gui.
+ """
+ bdy_msk = None
+ if mask_gui:
+ #Open the gui to create a mask
+ _, mask = pynemo_settings_editor.open_settings_dialog(Setup)
+ bdy_msk = mask.data
+ Setup.refresh()
+ else:
+ try:
+ #mask filename and mask file flag is set
+ if Setup.bool_settings['mask_file'] and Setup.settings['mask_file'] is not None:
+ mask = Mask_File(mask_file=Setup.settings['mask_file'])
+ bdy_msk = mask.data
+ elif Setup.bool_settings['mask_file']:
+ logger.error("Mask file is not given")
+ return
+ else: #no mask file specified then use default 1px halo mask
+ logger.warning("Using default mask with bathymetry!!!!")
+ mask = Mask_File(Setup.settings['bathy'])
+ mask.apply_border_mask(Constants.DEFAULT_MASK_PIXELS)
+ bdy_msk = mask.data
+ except ValueError: # why is this except here? as there is an else: statement TODO
+ print 'something wrong?'
+ return
+ if np.amin(bdy_msk) == 0:
+ # Mask is not set throw a warning message and set border to 1px.
+ logger.warning("Setting the mask to 1px border")
+ QMessageBox.warning(None,"pyNEMO", "Mask is not set, setting a 1 pixel border mask")
+ if bdy_msk is not None and 1 < bdy_msk.shape[0] and 1 < bdy_msk.shape[1]:
+ tmp = np.ones(bdy_msk.shape, dtype=bool)
+ tmp[1:-1, 1:-1] = False
+ bdy_msk[tmp] = -1
+
+ return bdy_msk
diff --git a/test_scripts/bdy_coords_plot.py b/test_scripts/bdy_coords_plot.py
new file mode 100755
index 0000000000000000000000000000000000000000..09bbf7c42b5408902b368c6955a4e068dbc4739e
--- /dev/null
+++ b/test_scripts/bdy_coords_plot.py
@@ -0,0 +1,61 @@
+#!/usr/bin/env python2
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Oct 24 11:28:04 2019
+
+@author: thopri
+"""
+
+# Must be run from the PyNEMO main folder. Otherwise permission errors abound
+
+import matplotlib.pyplot as plt
+from netCDF4 import Dataset
+import numpy as np
+from mpl_toolkits.basemap import Basemap
+
+from pynemo.tests import bdy_coords as bdc
+
+bdc.process_bdy('/Users/thopri/Projects/PyNEMO/inputs/namelist_remote.bdy',False)
+
+rootgrp = Dataset('/Users/thopri/Projects/PyNEMO/outputs/NNA_R12_bdyT_y1979m11.nc', "r", format="NETCDF4")
+bdy_msk = np.squeeze(rootgrp.variables['bdy_msk'][:]) - 1
+bdy_lon = np.squeeze(rootgrp.variables['nav_lon'][:])
+bdy_lat = np.squeeze(rootgrp.variables['nav_lat'][:])
+rootgrp.close()
+
+rootgrp = Dataset('/Users/thopri/Projects/PyNEMO/outputs/coordinates.bdy.nc', "r", format="NETCDF4")
+bdy_it = np.squeeze(rootgrp.variables['nbit'][:])
+bdy_jt = np.squeeze(rootgrp.variables['nbjt'][:])
+bdy_rt = np.squeeze(rootgrp.variables['nbrt'][:])
+rootgrp.close()
+
+bdy_msk = np.ma.masked_where(bdy_msk < 0, bdy_msk)
+for f in range(len(bdy_it)):
+ bdy_msk[bdy_jt[f,],bdy_it[f,]] = bdy_rt[f,]
+
+# Plot to check output
+fig=plt.figure(figsize=(12,12))
+ax=fig.add_subplot(111)
+
+map = Basemap(llcrnrlat=41.,urcrnrlat=65.,\
+ llcrnrlon=-22.,urcrnrlon=25.,\
+ rsphere=(6378137.00,6356752.3142),\
+ resolution='l',projection='lcc',\
+ lat_1=57.,lon_0=-12.5)
+map.drawcoastlines()
+map.drawcountries()
+map.fillcontinents(color='grey')
+map.drawmeridians(np.arange(-25.,25.,2),labels=[0,0,0,1])
+map.drawparallels(np.arange(40.,66.,2),labels=[1,0,0,0])
+
+cmap = plt.cm.get_cmap('jet',10)
+cmaplist = [cmap(i) for i in range(cmap.N)]
+cmaplist[0] = (.7,.7,.7,1.0)
+cmap = cmap.from_list('Custom cmap', cmaplist, cmap.N)
+
+x1,y1 = map(bdy_lon[:,:],bdy_lat[:,:])
+im = map.pcolormesh(x1, y1, bdy_msk, cmap=cmap, vmin=-0.5, vmax=9.5)
+cb = plt.colorbar(orientation='vertical', shrink=0.75, aspect=30, fraction=0.1,pad=0.05)
+cb.set_label('RimWidth Number')
+cb.set_ticks(np.arange(10))
+th=plt.title(('BDY Points'),fontweight='bold')
\ No newline at end of file