Example #1
0
    def get_shoreline_mask(self):
        """Get the shoreline mask"""
        # We already have it
        if self._shoreline_mask is not None:
            return self._shoreline_mask
        # We skip
        if self._shoreline_arg is None: return

        # We compute it
        lon = self.get_lon()
        lat = self.get_lat()
        xres, yres = self.get_res()
        clip = [lon.getValue().min()-self._shoreline_margin*xres,
            lat.getValue().min()-self._shoreline_margin*yres,
            lon.getValue().max()+self._shoreline_margin*xres,
            lat.getValue().max()+self._shoreline_margin*yres]
        if not isinstance(self._shoreline_arg, ShoreLine):
            shoreline = get_shoreline(self._shoreline_arg, clip=clip)
            if shoreline is None: return
        else:
            shoreline = shoreline.clip(clip)

        # Get the polygons
        polys = shoreline.get_shapes()

        # Create the mask
        self._shoreline_mask = polygon_mask(self.get_grid(), polys)
        del polys
        return self._shoreline_mask
Example #2
0
"""
Masquages évolués

Modules: :mod:`vacumm.misc.grid.masking`
"""

from vcmq import *
from vacumm.misc.grid.masking import polygon_mask, erode_coast, get_coastal_indices, \
    get_coastal_indices, envelop, polygons, polygon_select, get_dist_to_coast, \
    convex_hull


# Creation d'un masque via un trait de cote
grid = create_grid((-6., -4., 0.1), (47.5, 49.1, 0.1))  # grille de l'iroise
resolution = 'h'                                        # resolution gshhs : testez 'i'
mask = polygon_mask(grid, resolution, thresholds=0.5)   # testez threshold = 0.1
mvmask = MV2.array(mask)
set_grid(mvmask, grid)
map2(mvmask, fillcontinents=False, drawcoastlines_color='r', drawcoastlines_zorder=100,
    res=resolution, proj='merc', fill='pcolor', drawcoastlines_linewidth=2,
    cmap=cmap_rs(['1', '0.6']), contour=False, colorbar=False,
    savefig ='courses_masking_0.png', show=True)


# Cote via mask
indices = get_coastal_indices(mask)
dist = get_dist_to_coast(grid, mask)


# Erosion de la cote
f = cdms2.open(data_sample('mars3d.xy.nc'))
Example #3
0
	def run(self):
	
		if self.netcdf3: io.netcdf3()
		else: io.netcdf4(level=self.netcdf4level)
		cdms2.setAutoBounds(0)

		self.notice('Masking %s to %s', self.inpfile, self.outfile)
		inpfile = cdms2.open(self.inpfile)
		if os.path.isfile(self.outfile):
			if os.path.samefile(self.inpfile, self.outfile):
				raise Exception('Cannot use same input and output file')
			if self.overwrite:
				os.remove(self.outfile)
			else:
				raise Exception('Output file already exists and overwriting is not requested')
		outfile = cdms2.open(self.outfile, 'w')

		# Copy global attributes
		for a,v in inpfile.attributes.items():
			setattr(outfile, a, v)

		# Keep grid masks in memory to improve performances (TODO: use a file cache as for basemaps ?)
		mask_cache = dict()
		stats = True # self.is_verbose()

		# Iterate over input variables
		for varid,filevar in inpfile.variables.items():
			
			# Process only gridded/specified variables
			grid = filevar.getGrid()
			maskit = grid is not None
			if maskit and self.included_variables and varid not in self.included_variables: maskit = False
			if maskit and self.excluded_variables and varid in self.excluded_variables: maskit = False
			if not maskit and self.masked_only:
				self.verbose('Ignoring %s: variable has no grid and masked_only was specified')
				continue
			
			self.logger.info(bases.psinfo())
			self.notice('Processing variable: %s, grid: %s', varid, grid.shape if grid else None)
			# NOTE: With scalar variables, memvar could be numpy.<type> instead of cdms2.tvariable.TransientVariable
			memvar = filevar()
			self.info(bases.describe(memvar, stats=stats))
			self.logger.info(bases.psinfo())
			
			if maskit:
				# Build the mask, check if it is already cached ?
				cache_id = id(grid)
				self.info('Get mask for grid %s', cache_id)
				mask = mask_cache.get(cache_id, None)
				if mask is None:
					self.notice('Loading mask: %s', dict(resolution=self.resolution, mode=self.mode, thresholds=self.thresholds, reverse=self.reverse))
					mask = masking.polygon_mask(grid, self.resolution, mode=self.mode, thresholds=self.thresholds)
					if self.reverse: mask = ~mask
					mask_cache[cache_id] = mask
					self.info(bases.describe(mask, stats=stats))
					self.logger.info(bases.psinfo())
				
				# Mask variable
				# TODO: check/handle dimensions count and order
				self.notice('Masking variable: %s, mask: %s', memvar.shape, mask.shape)
				mask = MV2.resize(mask, filevar.shape)
				memvar[:] = MV2.masked_where(mask, memvar)
				self.info(bases.describe(memvar, stats=stats))
			
			# Special scalar case which could fail if directly written (because fill_value is None)
			if not filevar.shape:
				fill_value = filevar.getMissing()
				if fill_value is None:
					fill_value = -memvar
				memvar = cdms2.createVariable(
					memvar, id=filevar.id, shape=(), typecode=filevar.typecode(),
					fill_value=fill_value, attributes=filevar.attributes)
			
			# Write masked variable to output file
			self.notice('Writing variable to file')
			outfile.write(memvar)

		self.logger.info(bases.psinfo())
		outfile.close()
		inpfile.close()
Example #4
0
# Plot params
import pylab as P
import vacumm.misc.color as C
P.figure(figsize=(6, 5))
P.subplots_adjust(top=.92, left=.03, bottom=.03, wspace=.05, hspace=.2)
kwplot = dict(colorbar=False,cmap=C.cmap_linear([(.6, .8, 1), C.land]), \
    contour=False,show=False,fillcontinents=False,fill='pcolor',
    drawmeridians=False, drawparallels=False, res='h', key=True, xymasked=False)

# Mask using shoreline
from vacumm.misc.grid.masking import polygon_mask
from vacumm.misc.plot import map2
import MV2 as MV
# - mask if central point sur terre (mode = 0 = 'inside')
lon2, lat2 = N.meshgrid(lon, lat)
mask0 = polygon_mask((lon2, lat2), 'h', mode=0, ocean=False)
mask0 = MV.array(mask0, axes=[lat, lon])
mask0.long_name = "'inside'"
map2(mask0, subplot=221, **kwplot)
# - mask if cell more than 50% of land (mode = 1 = 'intersect')
thresholds = .5
mask1 = polygon_mask((lon2, lat2),
                     'h',
                     mode=1,
                     thresholds=thresholds,
                     ocean=False)
mask1 = MV.array(mask1, axes=[lat, lon])
mask1.long_name = "'intersect': threshold=%g" % thresholds
map2(mask1, subplot=222, **kwplot)
# - mask if cell if more than 30% of land
thresholds = .3
Example #5
0
# -*- coding: utf-8 -*-
"""
Masquages évolués

Modules: :mod:`vacumm.misc.grid.masking`
"""

from vcmq import *
from vacumm.misc.grid.masking import polygon_mask, erode_coast, get_coastal_indices, \
    get_coastal_indices, envelop, polygons, polygon_select, get_dist_to_coast, \
    convex_hull

# Creation d'un masque via un trait de cote
grid = create_grid((-6., -4., 0.1), (47.5, 49.1, 0.1))  # grille de l'iroise
resolution = 'h'  # resolution gshhs : testez 'i'
mask = polygon_mask(grid, resolution, thresholds=0.5)  # testez threshold = 0.1
mvmask = MV2.array(mask)
set_grid(mvmask, grid)
map2(mvmask,
     fillcontinents=False,
     drawcoastlines_color='r',
     drawcoastlines_zorder=100,
     res=resolution,
     proj='merc',
     fill='pcolor',
     drawcoastlines_linewidth=2,
     cmap=cmap_rs(['1', '0.6']),
     contour=False,
     colorbar=False,
     savefig='courses_masking_0.png',
     show=True)
# Plot params
import pylab as P
import vacumm.misc.color as C
P.figure(figsize=(6, 5))
P.subplots_adjust(top=.92,left=.03,bottom=.03,wspace=.05,hspace=.2)
kwplot = dict(colorbar=False,cmap=C.cmap_linear([(.6, .8, 1), C.land]), \
    contour=False,show=False,fillcontinents=False,fill='pcolor',
    drawmeridians=False, drawparallels=False, res='h', key=True, xymasked=False)

# Mask using shoreline
from vacumm.misc.grid.masking import polygon_mask
from vacumm.misc.plot import map2
import MV2 as MV
# - mask if central point sur terre (mode = 0 = 'inside')
lon2,lat2 = N.meshgrid(lon,lat)
mask0 = polygon_mask((lon2, lat2), 'h', mode=0, ocean=False)
mask0 = MV.array(mask0, axes=[lat, lon])
mask0.long_name = "'inside'"
map2(mask0, subplot=221, **kwplot)
# - mask if cell more than 50% of land (mode = 1 = 'intersect')
thresholds = .5
mask1 = polygon_mask((lon2, lat2), 'h', mode=1, thresholds=thresholds, ocean=False)
mask1 = MV.array(mask1, axes=[lat, lon])
mask1.long_name = "'intersect': threshold=%g" %thresholds
map2(mask1, subplot=222, **kwplot)
# - mask if cell if more than 30% of land
thresholds = .3
mask1 = polygon_mask((lon2, lat2), 'h', mode=1, thresholds=thresholds, ocean=False)
mask1 = MV.array(mask1, axes=[lat, lon])
mask1.long_name = "'intersect': threshold=%g" %thresholds
map2(mask1, subplot=223, **kwplot)