195 lines
6.4 KiB
Python
195 lines
6.4 KiB
Python
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import optparse
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import shutil, distutils.dir_util, os, sys, glob
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import numpy
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import math
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import matplotlib.pyplot as plt
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from pylagrit import PyLaGriT
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#
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# Create parser and options
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#
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p = optparse.OptionParser()
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p.add_option('--dem-file', help='DEM data file name including path', type='string', dest='dem_filename' )
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p.add_option('--exo-file', help='Exodus II mesh output including path', type='string', dest='exo_filename')
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p.add_option('--dry-run', help='Show commands and diagnostics but no execution', default=False, dest='dry_run', action='store_true')
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p.add_option('--plot', help='Show commands and diagnostics but no execution', default=False, dest='plot', action='store_true')
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#
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(opts,args) = p.parse_args()
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print(opts.dem_filename)
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print(opts.dry_run)
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# Input: DEM data
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dem_file_fullname=opts.dem_filename
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dem_file_noext, dem_file_ext=os.path.splitext(opts.dem_filename)
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dem_file_base=os.path.basename(opts.dem_filename).rstrip(dem_file_ext)
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dem_file_path=os.path.dirname(opts.dem_filename)
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# Output: Exodus II mesh
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exo_file_fullname=opts.exo_filename
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exo_file_noext, exo_file_ext=os.path.splitext(opts.exo_filename)
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exo_file_base=os.path.basename(opts.exo_filename).rstrip(exo_file_ext)
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exo_file_path=os.path.dirname(opts.exo_filename)
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# Output: XML region specifications for the new mesh
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xml_file_fullname=exo_file_path+exo_file_base+'.xml'
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# DEM parsing
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#
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with open(dem_file_fullname) as dem_header:
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for line in dem_header:
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if ("ncols" in line):
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nx=int(line.split()[1])
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elif ("nrows" in line):
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ny=int(line.split()[1])
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elif ("xllcorner" in line):
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xll_corner=float(line.split()[1])
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elif ("yllcorner" in line):
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yll_corner=float(line.split()[1])
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elif ("cellsize" in line):
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dx=float(line.split()[1])
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dy=dx
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elif ("NODATA_value" in line):
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no_data_value=int(line.split()[1])
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break
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print(nx, ny, xll_corner, yll_corner, dx, dy, no_data_value)
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dem_header.close()
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d = numpy.flipud(numpy.genfromtxt(dem_file_fullname,skip_header=6))
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#plt.matshow(d)
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# Create mesh based on ncols and nrows in file, could automatically read
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x = numpy.linspace(xll_corner,dx*(nx-1),nx)
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y = numpy.linspace(yll_corner,dy*(ny-1),ny)
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x=numpy.arange(xll_corner,dx*nx,dx)
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y=numpy.arange(yll_corner,dy*ny,dy)
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xx, yy = numpy.meshgrid(x,y)
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# Write avs file
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fh = open(dem_file_base+'.avs','w')
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# Find number of data values and write avs header
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N = numpy.where(numpy.isnan(d)==False)[0].shape[0]
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fh.write(str(N)+' 0 0 0 0\n')
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# Collect data into avs format
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# JDM: Not sure if this should be nx*ny?
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davs = numpy.zeros([nx*ny,4])
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ind = 0
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for i,row in enumerate(d):
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for j,v in enumerate(row):
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davs[ind,:] = [ind + 1, xx[i,j], yy[i,j], v]
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ind += 1
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# Write data to avs file
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numpy.savetxt(fh,davs,fmt=['%4d','%.1lf','%.1lf','%.8lf'])
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fh.close()
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# Crank up pylagrit
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lg = PyLaGriT()
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# Read in elevations in avs fromat
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m = lg.read(dem_file_base+'.avs')
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# Take a look, change paraview exe
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# Will need to use glyph filter to view points
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#m.paraview(exe='paraview')
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# Copy z values over to attribute
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m.addatt('z_save',vtype='vdouble',rank='scalar')
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m.copyatt('zic','z_save')
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# Not sure why this has to be done, but not data elements don't get removed otherwise
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m.setatt('zic',0.)
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# Create connected quad mesh surface
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m2 = lg.create()
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#m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1],connect=True)
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m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
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# Create temporary z value attribute
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m2.addatt('z_save',vtype='vdouble',rank='scalar')
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# Interpolate elevations to z_save
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m2.interpolate_voronoi('z_save',m,'z_save')
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# Find nodes associated with nodata
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pdel = m2.pset_attribute('z_save',-9999)
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# Create element set from these nodes and remove elements
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edel = pdel.eltset()
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m2.rmpoint_eltset(edel)
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# Copy temp z values over to actual a values
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#m2.copyatt('z_save','zic')
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# Take a look to make sure everything is ok
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#m2.paraview(exe='paraview')
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m3 = m2.copypts(elem_type='triplane')
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m3.connect()
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# To lazy to add to pylagrit now, and don't know how to make it intuitive
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# Creates edge_max element attribute containing max edge length
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m3.sendline('quality/edge_max/y')
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# Query created attribute
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#m3.printatt('edgemax')
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m3.minmax('edgemax')
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# Figure out max desired edge length
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max_edge = numpy.sqrt(dx**2+dy**2)
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# Identify elements with longer edges
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edel = m3.eltset_attribute('edgemax',max_edge*2.05,'gt')
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m3.rmpoint_eltset(edel)
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#m3 = m2.grid2grid_quadtotri2()
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#m3=m2
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# Create temporary z value attribute
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m3.addatt('z_save',vtype='vdouble',rank='scalar')
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# Interpolate elevations to z_save
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m3.interpolate_voronoi('z_save',m,'z_save')
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# Find nodes associated with nodata
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pdel = m3.pset_attribute('z_save',-9999)
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# Create element set from these nodes and remove elements
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edel = pdel.eltset()
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m3.rmpoint_eltset(edel)
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# Copy temp z values over to actual a values
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m3.copyatt('z_save','zic')
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# Take a look to make sure everything is ok
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#m2.paraview(exe='paraview')
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# Create top surface avs
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m3.dump('top.inp')
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## Subtract 1 from z values of top and dump into bottom surface avs
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m3.math('sub',1,'zic',cmosrc=m3)
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m3.dump('mid.inp')
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m3.setatt('zic',0.0)
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m3.dump('bot.inp')
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# Stack the layers in a new mesh object
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stack = lg.create()
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stack.stack_layers('avs',['bot.inp 1','mid.inp 1,3','top.inp 1,0'],flip_opt=True)
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stack_hex = stack.stack_fill()
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# Automatically create face sets based on normal vectors and layer id
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#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True)
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#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=False)
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# Diagnostic
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#stack_hex.sendline('quality volume itetclr')
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# Write exo file with boundary facesets
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#stack_hex.dump_exo(exo_file_fullname,facesets=fs.values())
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stack_hex.dump_exo(exo_file_fullname)
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# Write region and faceset identifier file for ats_xml
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matnames = {10000:'computational domain peat'}
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facenames = {1:'bottom face',
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2:'surface',
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3:'front',
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4:'right',
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5:'back',
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6:'left'}
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# Dump ats style xml for mesh, can provide options for other schemas easily also
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#stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
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stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
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# Take a look
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if opts.plot:
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stack_hex.paraview(exe='/Applications/paraview.app/Contents/MacOS/paraview')
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