; pc2vdf, program to create vdf files
; vdf is the format required by vapor for 3d visualization
; last modified 14/07/2010: Guerrero
pro pc2vdf,tinit=tinit,tend=tend,rhof=rhof,sph=sph,variables=variables,beq=beq
; KEYWORD TINIT: INITIAL VARFILE
; KEYWORD TEND: FINAL VARFILE
; KEYWORD RHOF: COMPUTES DENSITY PERTURBATIONS INSTEAD OF DENSITY
; KEYWORD SPH: READ PC VARFILES IN SPHERICAL COORDS.
; KEYWORD BEQ: DEFINES A NORMALIZATION VALUE FOR THE MAGNETIC FIELD
;e.g.:pc2vdf,tinit=2,tend=2,variebles=['uu','bb','lnrho'],/rhof,beq=0.26
default, tinit, '0'
default, tend, '1'
default,variables,['uu','lnrho']
default,beq,1.
k = strmatch(variables,'bb')
mag = where(k EQ 1)
if (mag GE 0) then begin
if (keyword_set(sph)) then begin
varnames=['rho_sph','vr','vt','vp','br','bt','bp','Eb_sph']
endif else begin
varnames=['rho','vx','vy','vz','bx','by','bz','Eb']
endelse
endif else begin
if (keyword_set(sph)) then begin
varnames=['rho_sph','vr','vt','vp']
endif else begin
varnames=['rho','vx','vy','vz']
endelse
endelse
;
cd, current=c
readpath=c
spawn,'mkdir VAPOR'
writepath=c+'/VAPOR'
cd, writepath
if (tinit EQ 0) then begin
varfile1 = 'var.dat'
endif else begin
varfile1 = 'VAR'+strtrim(tinit,2)
endelse
;
cd, readpath
;
OPENR,1, readpath+'data/proc0/'+varfile1, ERROR = err
close,1
pc_read_grid,o=g,/trimxyz,/quiet
;
cd, writepath
; $Id: WriteVDF.pro,v 1.6 2008/09/03 20:51:55 clynejp Exp $
;
; This example shows how to create a data set containing
; a single variable and at a single time step
;
;
; Dimensions of the data volumes - all volumes in a data set must be
; of the same dimension
;
cd, writepath
nx = (size(g.x))[1] ; (size(test.uu))[1]-6
ny = (size(g.y))[1] ; (size(test.uu))[2]-6
nz = (size(g.z))[1] ; (size(test.uu))[3]-6
if (keyword_set(sph)) then dim = [nz,ny,nx] else dim = [nx,ny,nz]
if (keyword_set(rhof)) then rho_f = fltarr(nx,ny,nz)
;
;
; The number of coarsened approximations to create. A value of 0
; indicates that the data should not be transformed, i.e. the
; data will only exist at it's native resolution. A value of 1
; indicates that a single coarsening should be applied, and so on.
;
num_levels = 1
; Create a new VDF metadata object of the indicated dimension and
; transform
; level. vdf_create() returns a handle for future operations on
; the metadata object.
;
mfd = vdf_create(dim,num_levels)
; Set the maximum number of timesteps in the data set. Note, valid data
; set may contain less than the maximum number of time steps,
; but not more
;
timesteps = tend-tinit+1
vdf_setnumtimesteps, mfd,timesteps
;
; Set the names of the variables the data set will contain. In this case,
;
numvar = size(varnames)
numvar = numvar(1)
print,'number of variables to write =', numvar
;
vdf_setvarnames, mfd, varnames
;
; Set the extents of the volume in user-defined
; physical coordinates. Note, as the aspect ratio of
; the user-defined coordinates do not match that of
; the volume resolution (512x512x512), the volume
; will be stretched when rendered. I.e. the spacing
; between the Z coordinate samples is defined to
; be twice that of X or Y.
;
if (keyword_set(sph)) then begin
vdf_setcoordtype,mfd,'spherical'
; order for spherical coordinates phi(z),theta(y),r(x)
extents = [-180+(180.*g.z[0]/!pi), -90+(180.*g.y[0]/!pi), g.x[0], $
-180+(180.*g.z[nz-1]/!pi),-90+(180.*g.y[ny-1]/!pi), g.x[nx-1]]
print,extents
;new variables
rho_sph = fltarr(nz,ny,nx)
vr = fltarr(nz,ny,nx)
vt = fltarr(nz,ny,nx)
vp = fltarr(nz,ny,nx)
print,'size of v = ', size(vr)
br = fltarr(nz,ny,nx)
bt = fltarr(nz,ny,nx)
bp = fltarr(nz,ny,nx)
Eb_sph = fltarr(nz,ny,nx)
last_dim = nx-1
endif else begin
extents = [g.x[0], g.y[0], g.z[0], g.x[nx-1], g.y[ny-1], g.z[nz-1]]
last_dim = nz-1
endelse
;
vdf_setextents, mfd, extents
;
; Store the metadata object in a file for subsequent use
;
vdffile = 'work.vdf'
vdf_write, mfd, vdffile
;
; Destroy the metadata object. We're done with it.
;
vdf_destroy, mfd
;
; At this point we've defined all of the metadata associated with
; the test data set. Now we're ready to begin populating the data
; set with actual data.
;
;
; Create a "buffered write" data transformation object. The data
; transformation object will permit us to write (transform) raw
; data into the data set. The metadata for the data volumes is
; obtained from the metadata file we created previously. I.e.
; 'vdffile' must contain the path to a previously created .vdf
; file. The 'vdc_bufwritecreate' returns a handle, 'dfd', for
; subsequent ; operations.
; Prepare the data set for writing. We need to identify the time step
; and the name of the variable that we wish to store
;
;
itt = 0
for it = tinit,tend do begin
vars = variables
fac=1
varfile = 'VAR'+strtrim(string(format="(i2)",it),1)
OPENR,1, readpath+'data/proc0/'+varfile, ERROR = err
close,1
cd, readpath
print,'Reading: ',varfile
print,'vars = ',vars
pc_read_var,varfile=varfile,obj=test,/trimall,variables=vars,/magic,/quiet
rho=exp(test.lnrho)
;
if (keyword_set(rhof)) then begin
rhoy = total(rho[*,*,*],2)/ny
rhoxy = total(rhoy[*,*],1)/nx
for k = 0,nz-1 do rho_f[*,*,k] = rho[*,*,k] - rhoxy[k]
rho = rho_f
endif
;
ss=[0,ny/2,0]
rho = shift(rho,ss)
v1 =shift(test.uu[*,*,*,0],ss)
v2 =shift(test.uu[*,*,*,1],ss)
v3 =shift(test.uu[*,*,*,2],ss)
if (mag GT 0) then begin
b1 = shift(test.bb[*,*,*,0],ss)/beq
b2 = shift(test.bb[*,*,*,1],ss)/beq
b3 = shift(test.bb[*,*,*,2],ss)/beq
Eb = alog(b1^2 + b2^2 + b2^2)
endif
; reordering
if (keyword_set(sph)) then begin
for l = 0, nx-1 do begin
for m =0, ny-1 do begin
for n =0, nz-1 do begin
rho_sph(n,m,l) = rho(l,m,n)
vr(n,m,l) = v1(l,m,n)
vt(n,m,l) = v2(l,m,n)
vp(n,m,l) = v3(l,m,n)
if (mag GT 0) then begin
br(n,m,l) = b1(l,m,n)
bt(n,m,l) = b2(l,m,n)
bp(n,m,l) = b3(l,m,n)
Eb_sph(n,m,l) = Eb(l,m,n)
endif
endfor
endfor
endfor
endif
;
print,'changing to previous directory'
cd, writepath
cd, current=c
print,c
for nvar = 0, numvar-1 do begin
dfd = vdc_bufwritecreate(vdffile)
vdc_openvarwrite, dfd, itt, varnames(nvar), -1
; Write (transform) the volume to the data set one slice at a time
if (keyword_set(sph)) then begin
case nvar of
0: tmp_var = rho_sph
1: tmp_var = vr
2: tmp_var = vt
3: tmp_var = vp
4: tmp_var = br
5: tmp_var = bt
6: tmp_var = bp
7: tmp_var = Eb_sph
endcase
endif else begin
case nvar of
0: tmp_var = rho
1: tmp_var = v1
2: tmp_var = v2
3: tmp_var = v3
4: tmp_var = b1
5: tmp_var = b2
6: tmp_var = b3
7: tmp_var = Eb
endcase
endelse
for z = 0, last_dim do begin
vdc_bufwriteslice, dfd, float(tmp_var[*,*,z])
endfor
; Close the currently opened variable/time-step. We're done writing
; to it
vdc_closevar, dfd
endfor
itt++
endfor
; Destroy the "buffered write" data transformation object.
; We're done with it.
cd, readpath
vdc_bufwritedestroy,dfd
end