def shp2pol(shpfile,outdir):
"""
Converts a polygon shape file to a *.pol file
Uses the first polygon in the file and the filename as the polygon name
"""
XY, name = readShpPoly(shpfile)
xy = XY[0]
numverts = xy.shape[0]
polynameext = os.path.basename(shpfile)
polyname,ext = os.path.splitext(polynameext)
outfile = '%s/%s.pol'%(outdir,polyname)
print 'Writing polygon to: %s...'%outfile
f = open(outfile,'w')
f.write('POLYGON_NAME\n')
f.write('%s\n'%polyname)
f.write('NUMBER_OF_VERTICES\n')
f.write('%d\n'%numverts)
for ii in range(numverts):
f.write('%6.10f %6.10f\n'%(xy[ii,0],xy[ii,1]))
f.close()
print 'Done.'
def shp2pol(shpfile, outdir):
"""
Converts a polygon shape file to a *.pol file
Uses the first polygon in the file and the filename as the polygon name
"""
XY, name = readShpPoly(shpfile)
xy = XY[0]
numverts = xy.shape[0]
polynameext = os.path.basename(shpfile)
polyname, ext = os.path.splitext(polynameext)
outfile = '%s/%s.pol' % (outdir, polyname)
print('Writing polygon to: %s...' % outfile)
f = open(outfile, 'w')
f.write('POLYGON_NAME\n')
f.write('%s\n' % polyname)
f.write('NUMBER_OF_VERTICES\n')
f.write('%d\n' % numverts)
for ii in range(numverts):
f.write('%6.10f %6.10f\n' % (xy[ii, 0], xy[ii, 1]))
f.close()
print('Done.')
def setAgeSource(self,shpfile):
"""
Sets the age source term using a polygon shapefile
"""
# Read the shapefile
XY,tmp = readShpPoly(shpfile,FIELDNAME=None)
if len(XY)<1:
raise Exception, ' could not find any polygons in shapefile: %s'%shpfile
for xpoly in XY:
xycells = np.asarray([self.xv,self.yv])
#ind1 = nxutils.points_inside_poly(xycells.T,xpoly)
ind1 = inpolygon(xycells.T,xpoly)
# Sets all vertical layers for now...
self.agesource[:,ind1] = 1.
def calc_agebin(binfile, ncfile, polyfile, ntout):
"""
Calculate the from a binary file and save to netcdf
"""
# Load the polygon from a shapefile
xypoly, field = readShpPoly(polyfile)
# Load the binary file object
PTM = PtmBin(binfile)
# Count the number of particles from the first time step
time, pdata = PTM.read_timestep()
N = pdata.shape[0]
tsec = othertime.SecondsSince(PTM.time)
dt = tsec[1] - tsec[0]
# Initialize the age particle object
Age = ParticleAge(xypoly[0], N)
# Loop through
outctr = ntout
ncctr = 0
for tt in range(PTM.nt - 1):
# Read the current time step
time, pdata = PTM.read_timestep(ts=tt)
# Update the age variable
Age.update_age(pdata['x'][:, 0], pdata['x'][:, 1], pdata['x'][:, 2],
dt)
# Write to netcdf
if outctr == ntout:
Age.write_nc(time, ncctr, ncfile=ncfile)
ncctr += 1
outctr = 0
outctr += 1
print('Done.')
def calc_agebin(binfile,ncfile,polyfile,ntout):
"""
Calculate the from a binary file and save to netcdf
"""
# Load the polygon from a shapefile
xypoly,field = readShpPoly(polyfile)
# Load the binary file object
PTM = PtmBin(binfile)
# Count the number of particles from the first time step
time,pdata = PTM.read_timestep()
N = pdata.shape[0]
tsec = othertime.SecondsSince(PTM.time)
dt = tsec[1] - tsec[0]
# Initialize the age particle object
Age = ParticleAge(xypoly[0],N)
# Loop through
outctr = ntout
ncctr=0
for tt in range(PTM.nt-1):
# Read the current time step
time,pdata = PTM.read_timestep(ts=tt)
# Update the age variable
Age.update_age(pdata['x'][:,0],pdata['x'][:,1],pdata['x'][:,2],dt)
# Write to netcdf
if outctr==ntout:
Age.write_nc(time,ncctr,ncfile=ncfile)
ncctr+=1
outctr=0
outctr+=1
print 'Done.'
def modifyBCmarker(suntanspath, bcfile, saveplot=False):
"""
Modifies SUNTANS boundary markers with a shapefile
The shapefile must contain polygons with the integer-type field "marker"
"""
print '#######################################################'
print ' Modifying the boundary markers for grid in folder:'
print ' %s'%suntanspath
# Load the grid into an object
grd = sunpy.Grid(suntanspath)
# Find the edge points
xe = np.mean(grd.xp[grd.edges],axis=1)
ye = np.mean(grd.yp[grd.edges],axis=1)
# Read the shapefile
if not bcfile==None:
XY,newmarker = readShpPoly(bcfile,FIELDNAME='marker')
if len(XY)<1:
print 'Error - could not find any polygons with the field name "marker" in shapefile: %s'%bcfile
return
XY,edge_id = readShpPoly(bcfile,FIELDNAME='edge_id')
if len(XY)<1:
print 'Error - could not find any polygons with the field name "edge_id" in shapefile: %s'%bcfile
return
else:
XY=[]
newmarker=[]
edge_id=[]
# Plot before updates
#plt.figure()
#grd.plotBC()
#plt.plot(XY[0][:,0],XY[0][:,1],'m',linewidth=2)
#plt.show()
# Reset all markers to one (closed)
ind0 = grd.mark>0
grd.mark[ind0]=1
# Find the points inside each of the polygon and assign new bc
grd.edge_id = grd.mark*0 # Flag to identify linked edges/segments (marker=4 only)
for xpoly, bctype,segmentID in zip(XY,newmarker,edge_id):
ind0 = grd.mark>0
edges = np.asarray([xe[ind0],ye[ind0]])
mark = grd.mark[ind0]
#ind1 = nxutils.points_inside_poly(edges.T,xpoly)
ind1 = inpolygon(edges.T,xpoly)
if bctype==4:
eflag = grd.edge_id[ind0]
eflag[ind1]=segmentID
grd.edge_id[ind0]=eflag
bctype=2
mark[ind1]=bctype
grd.mark[ind0]=mark
# Save the new markers to edges.dat
edgefile = suntanspath+'/edges.dat'
grd.saveEdges(edgefile)
print 'Updated markers written to: %s'%(edgefile)
# Plot the markers
if saveplot:
plt.figure()
grd.plotBC()
if len(XY)>0:
plt.plot(XY[0][:,0],XY[0][:,1],'m',linewidth=2)
figfile = suntanspath+'/BoundaryMarkerTypes.pdf'
plt.savefig(figfile)
print 'Marker plot saved to: %s'%(figfile)
print 'Done.'
print '#######################################################'
def create_gmsh_geo(shpfile, scalefile, geofile,
startpoly=0, ndmin=8, scalefac=1.0,\
r=1.08, lcmax=2000.0, sigmoid=0,\
linetype='BSpline'):
"""
Generate a gmsh *.geo file using a boundary from a shpfile
Inputs:
---
- shpfile : a polygon shapefile with the domain boundaries. Make sure
that the first polygon is the outer ring. If not change 'startpoly' parameter.
- scalefile : a line shapefile with field 'scale' specifying the target grid
resolution for that region.
- geofile: output geo ascii file.
*Optional*
- startpoly [default=0] - the index of the outer polygon in the shapefile.
- ndmin [default=8] - the minimum range of the scale = ndmin*scale
- r : expansion factor
- lcmax [default=2000] - the maximum grid cell size.
- sigmoid [default=0]
- linetype - 'BSpline' or 'Line'
"""
# Load the polygon shape file
xy, field = readShpPoly(shpfile, FIELDNAME='FID')
# Load the scale shape file
xyscale, scale = readShpPointLine(scalefile, FIELDNAME='scale')
# Load the 'embed' flag to see if the scale layer should be embedded
#try:
# exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
#except:
# print 'Warning - could not find "embed" field in shapefile. Setting embed = 0.'
# embed = [ss*0 for ss in scale]
exyscale, embed = readShpPointLine(scalefile, FIELDNAME='embed')
if embed == []:
embed = [ss * 0 for ss in scale]
## output geo and svg file
fgeo = open(geofile, 'w')
fgeo.write("""IP = newp;
IL = newl;
IS = news;
IF = newf;
""")
ip = 0 # Point counter
il = 0 # Line counter
rp = 0
lines = []
for loop in xy:
firstp = ip
for p in range(loop.shape[0]):
rp = rp + 1
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" %
(ip, loop[p, 0], loop[p, 1], 0., rp - 1))
ip = ip + 1
if linetype == 'Line' and ip > 1:
fgeo.write("Line(IL + %i) = {IP + %i , IP + %i};\n" % \
(il, ip-2, ip-1))
il = il + 1
lines.append(il - 1)
if linetype == 'BSpline':
fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i, IP + %i};\n" % \
(il, firstp, ip - 1, firstp))
il = il + 1
lines.append(il - 1)
# Create the surface polygon
fgeo.write('\n//%s\n//Surface Polygon Definition\n//%s\n\n' %
(72 * '#', 72 * '#'))
surfstart = il
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il, startpoly))
il += 1
for ll in lines:
if ll != startpoly:
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il, ll))
il += 1
surfend = il - 1
fgeo.write("Plane Surface(IL + %i) = {IL + %i : IL + %i};\n" %
(il, surfstart, surfend))
fgeo.write('Physical Surface("Ocean") = {IL + %i};\n' % il)
surface_id = il # Keep this to embed lines into
il += 1
# Create the grid scale lines and fields
fgeo.write('\n//%s\n//Grid Scale Definition\n//%s\n\n' %
(72 * '#', 72 * '#'))
slines = [] # Reference to scale lines
for loop, ss, ee in zip(xyscale, scale, embed):
firstp = ip
ss *= scalefac # Applies scale factor
for p in range(loop.shape[0]):
rp = rp + 1
#fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
fgeo.write(
"Point(IP + %i) = {%.16e, %.16e, %.16e,%.16e}; // %i\n" %
(ip, loop[p, 0], loop[p, 1], 0., rp - 1, float(ss)))
ip = ip + 1
if ee:
#fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i};\n" % (il, firstp, ip - 1))
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" %
(linetpye, il, firstp, ip - 1))
# Embed this line in the main surface so that cells are aligned
fgeo.write("Line{IL + %i} In Surface{IL + %i};\n" %
(il, surface_id))
else:
# Don't embed (can set as BSpline)
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" %
(linetype, il, firstp, ip - 1))
slines.append(il)
il = il + 1
ifield = 0 # Field counter
fids = []
ii = 0
for ss, line in zip(scale, slines):
fgeo.write("Field[IF + %i] = Attractor;\n" % ifield)
fgeo.write("Field[IF + %i].EdgesList = {IL + %i};\n" % (ifield, line))
nodesperedge = get_nnodes_from_line(xyscale[ii], 2.0 * float(ss))
fgeo.write("Field[IF + %i].NNodesByEdge = %i;\n" %
(ifield, nodesperedge))
ifield += 1
fgeo.write("Field[IF + %i] = Threshold;\n" % ifield)
# Find the maximum distance
Nk = np.log(lcmax / ss) / np.log(r)
print(ss, Nk)
lmin = float(ndmin) * float(ss)
lmax = lmin + Nk * ss
fgeo.write("Field[IF + %i].DistMax = %6.2f;\n" % (ifield, lmax))
fgeo.write("Field[IF + %i].DistMin = %6.2f;\n" % (ifield, lmin))
fgeo.write("Field[IF + %i].IField = IF + %i;\n" % (ifield, ifield - 1))
fgeo.write("Field[IF + %i].LcMax = %6.2f;\n" % (ifield, lcmax))
fgeo.write("Field[IF + %i].LcMin = %6.2f;\n" % (ifield, float(ss)))
fgeo.write("Field[IF + %i].Sigmoid = %d;\n" % (ifield, sigmoid))
fids.append(ifield)
ifield += 1
ii += 1
fieldlist = '{'
for ff in fids:
fieldlist += 'IF + %d, ' % ff
fieldlist = fieldlist[:-2] + '}'
fgeo.write("Field[IF + %i] = Min;\n" % ifield)
fgeo.write("Field[IF + %i].FieldsList = %s;\n" % (ifield, fieldlist))
fgeo.write("Background Field = IF + %i;\n" % ifield)
# Set Quad options by default
fgeo.write("Mesh.CharacteristicLengthMax=%.16e;//Max cell size\n" % lcmax)
fgeo.write("Mesh.RecombineAll=0;//recombine all defined surfaces\n")
fgeo.write("Mesh.Algorithm=6;//front\n")
fgeo.write("Mesh.Smoothing=10;//10 smoothing steps\n")
fgeo.write("Mesh.Remove4Triangles = 1;\n")
fgeo.close()
print('Complete. GMSH geo file written to:\n\t %s' % geofile)
def create_gmsh_geo(shpfile, scalefile, geofile,
startpoly=0, ndmin=8, scalefac=1.0,\
r=1.08, lcmax=2000.0, sigmoid=0,\
linetype='BSpline'):
"""
Generate a gmsh *.geo file using a boundary from a shpfile
Inputs:
---
- shpfile : a polygon shapefile with the domain boundaries. Make sure
that the first polygon is the outer ring. If not change 'startpoly' parameter.
- scalefile : a line shapefile with field 'scale' specifying the target grid
resolution for that region.
- geofile: output geo ascii file.
*Optional*
- startpoly [default=0] - the index of the outer polygon in the shapefile.
- ndmin [default=8] - the minimum range of the scale = ndmin*scale
- r : expansion factor
- lcmax [default=2000] - the maximum grid cell size.
- sigmoid [default=0]
- linetype - 'BSpline' or 'Line'
"""
# Load the polygon shape file
xy,field = readShpPoly(shpfile,FIELDNAME='FID')
# Load the scale shape file
xyscale,scale = readShpPointLine(scalefile,FIELDNAME='scale')
# Load the 'embed' flag to see if the scale layer should be embedded
#try:
# exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
#except:
# print 'Warning - could not find "embed" field in shapefile. Setting embed = 0.'
# embed = [ss*0 for ss in scale]
exyscale,embed = readShpPointLine(scalefile,FIELDNAME='embed')
if embed == []:
embed = [ss*0 for ss in scale]
## output geo and svg file
fgeo = open(geofile,'w')
fgeo.write("""IP = newp;
IL = newl;
IS = news;
IF = newf;
""" )
ip = 0 # Point counter
il = 0 # Line counter
rp = 0
lines=[]
for loop in xy:
firstp = ip
for p in range(loop.shape[0]):
rp = rp + 1
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
ip = ip + 1
if linetype == 'Line' and ip > 1:
fgeo.write("Line(IL + %i) = {IP + %i , IP + %i};\n" % \
(il, ip-2, ip-1))
il = il + 1
lines.append(il-1)
if linetype =='BSpline':
fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i, IP + %i};\n" % \
(il, firstp, ip - 1, firstp))
il = il + 1
lines.append(il-1)
# Create the surface polygon
fgeo.write('\n//%s\n//Surface Polygon Definition\n//%s\n\n'%(72*'#',72*'#'))
surfstart=il
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il,startpoly) )
il += 1
for ll in lines:
if ll != startpoly:
fgeo.write("Line Loop(IL + %i) = {IL + %s};\n" % (il,ll) )
il += 1
surfend = il - 1
fgeo.write("Plane Surface(IL + %i) = {IL + %i : IL + %i};\n"%(il,surfstart,surfend))
fgeo.write('Physical Surface("Ocean") = {IL + %i};\n'%il)
surface_id = il # Keep this to embed lines into
il += 1
# Create the grid scale lines and fields
fgeo.write('\n//%s\n//Grid Scale Definition\n//%s\n\n'%(72*'#',72*'#'))
slines=[] # Reference to scale lines
for loop,ss,ee in zip(xyscale,scale,embed):
firstp = ip
ss *= scalefac # Applies scale factor
for p in range(loop.shape[0]):
rp = rp + 1
#fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1))
fgeo.write("Point(IP + %i) = {%.16e, %.16e, %.16e,%.16e}; // %i\n" % (ip, loop[p,0], loop[p,1], 0., rp -1,float(ss)))
ip = ip + 1
if ee:
#fgeo.write("BSpline(IL + %i) = {IP + %i : IP + %i};\n" % (il, firstp, ip - 1))
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" % (linetpye,il, firstp, ip - 1))
# Embed this line in the main surface so that cells are aligned
fgeo.write("Line{IL + %i} In Surface{IL + %i};\n"%(il,surface_id))
else:
# Don't embed (can set as BSpline)
fgeo.write("%s(IL + %i) = {IP + %i : IP + %i};\n" % (linetype,il, firstp, ip - 1))
slines.append(il)
il = il + 1
ifield = 0 # Field counter
fids = []
ii=0
for ss,line in zip(scale,slines):
fgeo.write("Field[IF + %i] = Attractor;\n"%ifield)
fgeo.write("Field[IF + %i].EdgesList = {IL + %i};\n"%(ifield,line))
nodesperedge = get_nnodes_from_line(xyscale[ii],2.0*float(ss))
fgeo.write("Field[IF + %i].NNodesByEdge = %i;\n"%(ifield,nodesperedge))
ifield+=1
fgeo.write("Field[IF + %i] = Threshold;\n"%ifield)
# Find the maximum distance
Nk = np.log(lcmax/ss)/np.log(r)
print ss,Nk
lmin = float(ndmin)*float(ss)
lmax = lmin + Nk * ss
fgeo.write("Field[IF + %i].DistMax = %6.2f;\n"%(ifield,lmax))
fgeo.write("Field[IF + %i].DistMin = %6.2f;\n"%(ifield,lmin))
fgeo.write("Field[IF + %i].IField = IF + %i;\n"%(ifield,ifield-1))
fgeo.write("Field[IF + %i].LcMax = %6.2f;\n"%(ifield,lcmax))
fgeo.write("Field[IF + %i].LcMin = %6.2f;\n"%(ifield,float(ss)))
fgeo.write("Field[IF + %i].Sigmoid = %d;\n"%(ifield,sigmoid))
fids.append(ifield)
ifield+=1
ii+=1
fieldlist = '{'
for ff in fids:
fieldlist += 'IF + %d, '%ff
fieldlist = fieldlist[:-2]+'}'
fgeo.write("Field[IF + %i] = Min;\n"%ifield)
fgeo.write("Field[IF + %i].FieldsList = %s;\n"%(ifield,fieldlist))
fgeo.write("Background Field = IF + %i;\n"%ifield)
# Set Quad options by default
fgeo.write("Mesh.CharacteristicLengthMax=%.16e;//Max cell size\n"%lcmax)
fgeo.write("Mesh.RecombineAll=0;//recombine all defined surfaces\n")
fgeo.write("Mesh.Algorithm=6;//front\n")
fgeo.write("Mesh.Smoothing=10;//10 smoothing steps\n")
fgeo.write("Mesh.Remove4Triangles = 1;\n")
fgeo.close()
print 'Complete. GMSH geo file written to:\n\t %s'%geofile