forked from EPCCed/pmpic
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display_parcels.py
executable file
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display_parcels.py
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#!/usr/bin/env python
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import sys
import math
import os
file="parcels_000_0100.dat"
gwidth=4
root="vort"
def read_file(fname):
print("File: %s:"%fname)
f=open(fname,"rb")
t=np.fromfile(f,dtype=np.float64,count=1)
t=t[0]
xrange=np.fromfile(f,dtype=np.float64,count=2)
yrange=np.fromfile(f,dtype=np.float64,count=2)
zrange=np.fromfile(f,dtype=np.float64,count=2)
n=np.fromfile(f,dtype=np.int64,count=1)
n=n[0]
x=np.fromfile(f,dtype=np.float64,count=n)
y=np.fromfile(f,dtype=np.float64,count=n)
z=np.fromfile(f,dtype=np.float64,count=n)
p=np.fromfile(f,dtype=np.float64,count=n)
q=np.fromfile(f,dtype=np.float64,count=n)
r=np.fromfile(f,dtype=np.float64,count=n)
dxdt=np.fromfile(f,dtype=np.float64,count=n)
dydt=np.fromfile(f,dtype=np.float64,count=n)
dzdt=np.fromfile(f,dtype=np.float64,count=n)
dpdt=np.fromfile(f,dtype=np.float64,count=n)
dqdt=np.fromfile(f,dtype=np.float64,count=n)
drdt=np.fromfile(f,dtype=np.float64,count=n)
h=np.fromfile(f,dtype=np.float64,count=n)
b=np.fromfile(f,dtype=np.float64,count=n)
vol=np.fromfile(f,dtype=np.float64,count=n)
stretch=np.fromfile(f,dtype=np.float64,count=n)
tag=np.fromfile(f,dtype=np.int32,count=n)
# print("time= %f"%t)
# print("xrange= %f to %f"%(xrange[0],xrange[1]))
# print("yrange= %f to %f"%(yrange[0],yrange[1]))
# print("zrange= %f to %f"%(zrange[0],zrange[1]))
print("Num parcels= %d"%n)
f.close()
# f = np.sqrt(p**2 + q**2 + r**2)
# hliq=np.zeros(n)
# for i in range(len(hliq)):
# hliq[i] = max(0.,h[i] - np.exp(-z[i]))
#
# render_slice(x,y,z,b, vol,xrange,yrange,zrange,"x",(xrange[1]-xrange[0])/2,200,kernel="gaussian",number=number,root="buoyancy",time=t)
# render_slice(x,y,z,hliq, vol,xrange,yrange,zrange,"x",(xrange[1]-xrange[0])/2,200,kernel="gaussian",number=number,root="hgliq",time=t)
# render_slice(x,y,z,f, vol,xrange,yrange,zrange,"x",(xrange[1]-xrange[0])/2,200,kernel="gaussian",number=number,root="vort",time=t)
return x,y,z,p,q,r,dxdt,dydt,dzdt,dpdt,dqdt,drdt,h,b,vol,stretch,tag
def render_slice(x,y,z,var,vol,xrange,yrange,zrange,plane,loc,resolution,kernel="gaussian",number=0, root=root, time=0.):
dx = (xrange[1]-xrange[0])/(resolution)
dy = (yrange[1]-yrange[0])/(resolution)
dz = (zrange[1]-zrange[0])/(resolution)
print('rendering %s slice at %s=%f using %s kernel'%(root,plane,loc,kernel))
#create new xp, yp coordinates corresponding to x, y of image, and a z for depth.
xp=[]
yp=[]
zp=[]
volp=[]
varp=[]
if plane == "x":
if kernel == "gaussian":
xmin = loc-gwidth*dx
xmax = loc+gwidth*dx
else:
xmin = loc-dx
xmax = loc+dx
dxp=dy
dyp=dz
dzp=dx
for i in range(len(x)):
if x[i] > xmin and x[i] < xmax:
xp.append(y[i])
yp.append(z[i])
zp.append(x[i])
volp.append(vol[i])
varp.append(var[i])
xg=np.arange(yrange[0],yrange[1]+dy,dy)
yg=np.arange(zrange[0],zrange[1]+dz,dz)
elif plane == "y":
if kernel == "gaussian":
ymin = loc-gwidth*dy
ymax = loc+gwidth*dy
else:
ymin = loc-dy
ymax = loc+dy
dxp=dx
dyp=dz
dzp=dy
for i in range(len(y)):
if y[i] > ymin and y[i] < ymax:
xp.append(x[i])
yp.append(z[i])
zp.append(y[i])
volp.append(vol[i])
varp.append(var[i])
xg=np.arange(xrange[0],xrange[1]+dx,dx)
yg=np.arange(zrange[0],zrange[1]+dz,dz)
elif plane == "z":
if kernel == "gaussian":
zmin = loc-gwidth*dz
zmax = loc+gwidth*dz
else:
zmin = loc-dz
zmax = loc+dz
dxp=dx
dyp=dy
dzp=dz
for i in range(len(z)):
if z[i] > zmin and z[i] < zmax:
xp.append(x[i])
yp.append(y[i])
zp.append(z[i])
volp.append(vol[i])
varp.append(var[i])
xg=np.arange(xrange[0],xrange[1]+dx,dx)
yg=np.arange(yrange[0],yrange[1]+dy,dy)
else:
print("Invalid plane. Aborting")
print(plane)
sys.exit()
print("Identified %d parcels in plane"%len(xp))
img=np.zeros((resolution+1,resolution+1))
wgt=np.zeros((resolution+1,resolution+1))
for num in range(len(xp)):
#identify the cell we're in (index of lower left corner)
i=int(math.floor(xp[num]/dxp))
j=int(math.floor(yp[num]/dyp))
if kernel == "linear":
for ii in range(i,i+2):
for jj in range(j,j+2):
w = (1.-np.abs(xp[num]-xg[ii])/dxp)*(1.-np.abs(yp[num]-yg[jj])/dyp)*(1-np.abs(zp[num]-loc)/dzp)*volp[num]
img[ii,jj] += varp[num]*w
wgt[ii,jj] += w
elif kernel == "gaussian":
for ii in range(i-gwidth,i+gwidth):
if ii >= 0 and ii <= resolution:
for jj in range(j-gwidth,j+gwidth):
if jj >= 0 and jj <= resolution:
w = np.exp( -(xp[num] - xg[ii])**2/dxp**2 - (yp[num] - yg[jj])**2/dyp**2 -(zp[num] - loc)**2/dzp**2) * volp[num]
img[ii,jj] += varp[num]*w
wgt[ii,jj] += w
else:
print("Error, invalid kernel '%s'. Aborting."%kernel)
print(sys.abort())
#Remove any zero weights
counter=0
for i in range(resolution+1):
for j in range(resolution+1):
if wgt[i,j] == 0.:
wgt[i,j]=1.
counter+=1
print("Removed %d zeroed pixels"%counter)
img=img/wgt
img=img.T
if root == "vort":
plt.imshow(img,origin='lower',extent=[0,1,0,1],vmin=0.,vmax=max(10.,np.amax(img)))
elif root == "hgliq":
plt.imshow(img,origin='lower',extent=[0,1,0,1],vmin=0.,vmax=0.08)
else:
plt.imshow(img,origin='lower',extent=[0,1,0,1])
plt.colorbar()
plt.title("Time = %f"%time)
#plt.savefig("%s_%04d.png"%(root,number))
#plt.clf()
plt.show()
if __name__ == "__main__":
if len(sys.argv) < 2 or len(sys.argv) > 3:
print("Usage: 'display_parcels.py [framenumber] [optional: number of files]'")
sys.exit()
filenum = int(sys.argv[1])
if len(sys.argv) == 3:
numfiles=int(sys.argv[2])
else:
numfiles=1
#first check that the files exist
fail=False
for i in range(numfiles):
fname = "parcels_%05d_%05d.dat"%(i,filenum)
if not os.path.isfile(fname):
print("Error: cannot find '%s'"%fname)
fail=True
else:
print("Found '%s'"%fname)
if fail:
print("Aborting")
sys.exit()
xrange=[]
yrange=[]
zrange=[]
#now get the global x/y/z ranges
for i in range(numfiles):
fname = "parcels_%05d_%05d.dat"%(i,filenum)
f=open(fname,"rb")
t=np.fromfile(f,dtype=np.float64,count=1)
t=t[0]
xmin=float(np.fromfile(f,dtype=np.float64,count=1))
xmax=float(np.fromfile(f,dtype=np.float64,count=1))
ymin=float(np.fromfile(f,dtype=np.float64,count=1))
ymax=float(np.fromfile(f,dtype=np.float64,count=1))
zmin=float(np.fromfile(f,dtype=np.float64,count=1))
zmax=float(np.fromfile(f,dtype=np.float64,count=1))
if i==0:
xrange.append(xmin)
xrange.append(xmax)
yrange.append(ymin)
yrange.append(ymax)
zrange.append(zmin)
zrange.append(zmax)
else:
if xmin<xrange[0]: xrange[0]=xmin
if xmax>xrange[1]: xrange[1]=xmax
if ymin<yrange[0]: yrange[0]=ymin
if ymax>yrange[1]: yrange[1]=ymax
if zmin<zrange[0]: zrange[0]=zmin
if zmax>zrange[1]: zrange[1]=zmax
f.close()
print("xrange=",xrange)
print("yrange=",yrange)
print("zrange=",zrange)
#now read in the files
x=np.zeros(0)
y=np.zeros(0)
z=np.zeros(0)
p=np.zeros(0)
q=np.zeros(0)
r=np.zeros(0)
dxdt=np.zeros(0)
dydt=np.zeros(0)
dzdt=np.zeros(0)
dpdt=np.zeros(0)
dqdt=np.zeros(0)
drdt=np.zeros(0)
h=np.zeros(0)
b=np.zeros(0)
vol=np.zeros(0)
stretch=np.zeros(0)
tag=np.zeros(0)
for i in range(numfiles):
fname = "parcels_%05d_%05d.dat"%(i,filenum)
xp,yp,zp,pp,qp,rp,dxdtp,dydtp,dzdtp,dpdtp,dqdtp,drdtp,hp,bp,volp,sp,tp = read_file(fname)
x=np.append(x,xp)
y=np.append(y,yp)
z=np.append(z,zp)
p=np.append(p,pp)
q=np.append(q,qp)
r=np.append(r,rp)
dxdt=np.append(dxdt,dxdtp)
dydt=np.append(dydt,dydtp)
dzdt=np.append(dzdt,dzdtp)
dpdt=np.append(dpdt,dpdtp)
dqdt=np.append(dqdt,dqdtp)
drdt=np.append(drdt,drdtp)
h=np.append(h,hp)
b=np.append(b,bp)
vol=np.append(vol,volp)
stretch=np.append(stretch,sp)
tag=np.append(tag,tp)
print(len(x))
print("read everything properly")
render_slice(x,y,z,b, vol,xrange,yrange,zrange,"x",np.pi,200,kernel="gaussian",number=filenum,root="buoyancy",time=t)