added test script folder and added output data folder to git ignore

.gitignore

@@ -24,6 +24,7 @@ wheels/
 .installed.cfg
 *.egg
 MANIFEST
+outputs
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

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

pynemo/tests/bdy_coords.py

+'''
+###
+## 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

test_scripts/bdy_coords_plot.py

+#!/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