[Paraview] Writing binary files: C/Fortran interface to VTK
XMLfiles.
Randall Hand
randall.hand at gmail.com
Tue Jan 31 15:13:43 EST 2006
It's got a bit of a learning curve, but have you thought about trying to
integrate HDF5 into your code? It supports a whole heck of alot of
datatypes, and has built-in compression. Couple it with Xdmf from ARL
(Write an HDF5 file & a simple ascii Metadata file) or Xmdf from ERDC (Just
write the HDF5 stuff into specially named fields) and it's pretty nice to
work with.
On 1/31/06, Dominik Szczerba <domi at vision.ee.ethz.ch> wrote:
>
> I see the point. And yes, I want to stay far away from ASCII. So what
> format would you recommend to STORE my results in a COMPRESSED way
> maintaining readability with Paraview? Any binary legacy file I produce
> takes gigabytes - crunched with gzip a fraction of it, but paraview
> won't read it. ASCII is simply prohibitive, base64'ed with
> zlibcompressor not much better. At the moment I store my results in my
> own gzipped format, and convert them to VTK format on demand - but that
> is pretty annoying.
> regards,
> --dsz
>
> Berk Geveci wrote:
> > Base64 encoding is only necessary if you want your XML file to be
> > ASCII. This is necessary if you want the file to conform to XML so
> > that the file can be opened in XML viewers (like a browser). Also,
> > some people prefer transferring ASCII files instead of binary files.
> > If you are not interested in either of these, there is no need to have
> > base64 encoding. I would recommend not using it in fact. One of these
> > days I will change the default in paraview so that it does not write
> > base64 encoded files.
> >
> >
> > On 1/31/06, Dominik Szczerba <domi at vision.ee.ethz.ch> wrote:
> >
> > Sorry to interupt your discussion but nobody ever explained me this: why
> > use base64 encoding at all? Isint it a step back to huge ASCII files??
> > E.g. I see no significant compression with the VTK's zlib compressor
> > when using XML data files because the compressed stream is converted to
> > ASCII. Will someone kindly explain me this paradox?
> > Thanks
> > Dominik
> >
> > Thierry Dubuis wrote:
> >
> >>There are lot of encoding Base 64 program on the web but only in C, Java
> >>or Visual Basic.
> >
> >>If you can use C/C++ compiler, I thing the best way for you is to use
> >>the Brad King's fortran code example (see my last email).
> >>To convert a data array to a string in C we use the memory copy in
> >>fortran I don't know.
> >>Could you use pointer? 2 pointer on the same memory adress
> >>1. the fist with the real*8 type
> >>2. the second with a character type
> >
> >>Try in this way.
> >
> >>Best regards,
> >>Thierry Dubuis
> >
> >>Stéphane Montésino wrote:
> >
> >
> >>>Thanks for all tese answers, but I 'm still like an an homosexual with
> >>>a wonderfull girl. I don't know how to use it (sorry her).
> >
> >>>In fact, I would like to directly write this type of file that I can
> >>>obtain when I save my data with Paraview:
> >
> >>><?xml version="1.0"?>
> >>><VTKFile type="RectilinearGrid" version="0.1"
> >>>byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
> >>> <RectilinearGrid WholeExtent="1 8 1 4 1 16">
> >>> <Piece Extent="1 8 1 4 1 16">
> >>> <PointData>
> >>> <DataArray type="Float32" Name="pressure" format="appended"
> >>>offset="0" />
> >>> </PointData>
> >>> <CellData>
> >>> </CellData>
> >>> <Coordinates>
> >>> <DataArray type="Float32" Name="X_COORDINATES"
> >>>format="appended" offset="956" />
> >>> <DataArray type="Float32" Name="Y_COORDINATES"
> >>>format="appended" offset="1036" />
> >>> <DataArray type="Float32" Name="Z_COORDINATES"
> >>>format="appended" offset="1092" />
> >>> </Coordinates>
> >>> </Piece>
> >>> </RectilinearGrid>
> >>> <AppendedData encoding="base64">
> >>> _AQAAAACAAAAACAAAuQIAAA==eJwVy8fvoFMUx+HDdIkyWOiG/0Bvmzfm etc.....
> >>> </AppendedData>
> >>></VTKFile>
> >
> >>>My knowledge are only reduces to Fluid mechanics.
> >
> >
> >>>>>>>>>>>>>>>>Encode in Base 64 ? More details please...How to ?
> >
> >>><<<<<<<<<<<<<<<<<<<<<<
> >
> >>>Link properly to vtkIO ? More details please.
> >
> >>>>>>>>>>>>>>>>>Does it mean that VTK IO library should be installed on
> >
> >>>the Computer where my CFD code run ?.
> >>>I don't run my code on my own computer. It runs in Computing center
> >>>where I can't install what I want.
> >
> >>>>>>>>>>>So I would like to obtain some fortran routine I could link
> >
> >>>myself to my CFD code <<<<<<<<<<<<<<<<
> >
> >>>When I try to write binary data in a formatted file:
> >>>run-time error F6204: WRITE(pressure.vtr)
> >>>- unformatted I/O not consistent with OPEN options
> >
> >>>When I try to write formatted string in an unformatted file:
> >>>run-time error F6200: WRITE(pressure.vtr)
> >>>- formatted I/O not consistent with OPEN options
> >
> >
> >>>>>>>>>>>>>>>>>>>How to convert my data to a string ?
> >
> >>><<<<<<<<<<<<<<<<<<<<<
> >
> >
> >>>The format for raw appended binary data should be
> >
> >>><AppendedData encoding="raw">
> >>> _NNNN...........................
> >>></AppendedData>
> >
> >>>Where the underscore is literal (as you already have) and the NNNN is a
> >>>four-byte block containing an unsigned 32-bit count of the number of
> >>>"words" in the array. A word is one value of the type of the array, so
> >>>in your case the NNNN would have the number of float values. Then the
> >>>number of bytes of binary data to follow should be NNNN*sizeof(float).
> >
> >>>If you have another appended data array in the same file then start it
> >>>immediately after the end of the first array (with no newline or any
> >>>other character. Then specify in the offset="..." attribute for the
> >>>corresponding DataArray the number of bytes beyond the underscore where
> >>>the second array begins.
> >
> >>>-Brad
> >
> >
> >
> >
> >>>Thierry Dubuis wrote:
> >
> >
> >>>>Hello Stéphane,
> >>>>
> >>>>perhaps this email can help you ?
> >>>>
> >>>>Else if you want code directly your program in fortran :
> >>>>1. You must encode all you data in Base64
> >>>>2. And write them like a string.
> >>>>3. don't forget to add the size of your data block (integer*4)
> >>>>encoded in base64 before you block.
> >>>>
> >>>>Best regards,
> >>>>Thierry Dubuis
> >>>>
> >>>>-------- Original Message --------
> >>>>Subject: Re: [Paraview] Writing binary files: C/Fortran interface
> >>>>to VTK XML files.
> >>>>Date: Tue, 07 Jun 2005 10:06:51 -0400
> >>>>From: Brad King <brad.king at kitware.com>
> >>>>To: SamuelKey <samuelkey at comcast.net>
> >>>>CC: paraview <paraview at paraview.org>, "Wylie, Brian"
> >>>><bnwylie at sandia.gov>
> >>>>References:
> >>>><200506030152.j531quWp005650 at rrcs-mta-04.hrndva.rr.com>
> >>>><42A05837.3010206 at kitware.com> <000a01c5684c$1d1a6740$6e01a8c0 at last>
> >>>>
> >>>>
> >>>>
> >>>>SamuelKey wrote:
> >>>>
> >>>>
> >>>>>Needing to have a C-compiler is not a problem for me; I have one.
> >>>>>
> >>>>>Let me try to work with what you commit next week and see if I have
> >>>>>any ideas. I will be gone all next week, so you won't hear from me
> >>>>>until week after next. With luck you may hear from someone else
> >>>>>that will help keep you busy, though I suspect "busy" is not a
> >>>>>problem for you.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>Okay, the C/Fortran interface is now available. A C program can do
> >>>>
> >>>>#include "vtkXMLWriterC.h"
> >>>>
> >>>>and link to vtkIO. A Fortran program can use the interface (see the
> >>>>example code below) but will need to compile one extra .c file to
> >>>>link properly to vtkIO. See VTK/IO/vtkXMLWriterF.h for instructions.
> >>>>
> >>>>-Brad
> >>>>
> >>>> PROGRAM Hello
> >>>> INTEGER writer
> >>>> INTEGER success
> >>>> INTEGER*8 numpoints/8/
> >>>> INTEGER*8 numcells/1/
> >>>> INTEGER*8 cellsSize/9/
> >>>> REAL*4 pdata(8)/0,0,0,0,1,1,1,1/
> >>>> REAL*4 points(24)/0,0,0, 1,0,0, 1,1,0, 0,1,0,
> >>>> _ 0,0,1, 1,0,1, 1,1,1, 0,1,1/
> >>>> INTEGER*8 cells(9)/8,0,1,2,3,4,5,6,7/
> >>>> call vtkXMLWriterF_New(writer)
> >>>> call vtkXMLWriterF_SetDataObjectType(writer, 4)
> >>>> call vtkXMLWriterF_SetFileName(writer, 'test1.vtu')
> >>>> call vtkXMLWriterF_SetPoints(writer, 10, points, numpoints)
> >>>> call vtkXMLWriterF_SetCellsWithType(writer, 12, numcells, cells,
> >>>> _ cellsSize)
> >>>> call vtkXMLWriterF_SetPointData(writer, 'example data', 10,
> pdata,
> >>>> _ numpoints, 1, 'SCALARS')
> >>>> call vtkXMLWriterF_Write(writer, success)
> >>>> call vtkXMLWriterF_Delete(writer)
> >>>> PRINT *, 'success =', success
> >>>> END PROGRAM Hello
> >>>>_______________________________________________
> >>>>ParaView mailing list
> >>>>ParaView at paraview.org
> >>>>http://www.paraview.org/mailman/listinfo/paraview
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>Stéphane Montésino wrote:
> >>>>
> >>>>
> >>>>>With Asci, all is OK except the size of my file.
> >>>>>So how to write my data array in binary with my fortran code.
> >>>>>Does anyone have some details ?
> >>>>>
> >>>>>!
>
> >>>>>******************************************************************************
> >>>>>
> >>>>>! **** subrout
> >>>>>paraview_scalar ****
> >>>>>!
>
> >>>>>******************************************************************************
> >>>>>
> >>>>>! Export 3D scalar data upon a Non uniform rectilinear Grid
> >>>>>!
> >>>>>! n1m,n2m,n3m: size of the data and the grid
> >>>>>! y1,y2,y3: coordinates
> >>>>>! scal_data: data to write
> >>>>>! name: name of the data
> >>>>>!
> >>>>> subroutine
> paraview_3d_scalar(n1m,n2m,n3m,y1,y2,y3,scal_data,name)
> >>>>>!
> >>>>> implicit none
> >>>>>!
> >>>>> INTEGER ,INTENT(IN)::n1m,n2m,n3m
> >>>>> REAL*8,DIMENSION(n1m) ,INTENT(IN)::y1
> >>>>> REAL*8,DIMENSION(n2m) ,INTENT(IN)::y2
> >>>>> REAL*8,DIMENSION(n3m) ,INTENT(IN)::y3
> >>>>> REAL*8,DIMENSION(n1m,n2m,n3m),INTENT(IN)::scal_data
> >>>>> CHARACTER(LEN=10) ,INTENT(IN)::name
> >>>>>!
> >>>>> integer::i,j,k,nfil
> >>>>>!
> >>>>> nfil=41
> >>>>> open(nfil,file=trim(name)//'.vtr')
> >>>>> write(nfil,*)'<VTKFile type="RectilinearGrid" version="0.1"',
> >>>>> & ' byte_order="LittleEndian">'
> >>>>> write(nfil,*)' <RectilinearGrid WholeExtent=',
> >>>>> & '"1 ',n1m,' 1 ',n2m,' 1 ',n3m,'">'
> >>>>> write(nfil,*)' <Piece Extent=',
> >>>>> & '"1 ',n1m,' 1 ',n2m,' 1 ',n3m,'">'
> >>>>> write(nfil,*)' <Coordinates>'
> >>>>> write(nfil,*)' <DataArray type="Float32"',
> >>>>> & ' Name="X_COORDINATES"',
> >>>>> & ' NumberOfComponents="1">'
> >>>>> write(nfil,*) (y1(i),i=1,n1m)
> >>>>> write(nfil,*)' </DataArray>'
> >>>>> write(nfil,*)' <DataArray type="Float32"',
> >>>>> & ' Name="Y_COORDINATES"',
> >>>>> & ' NumberOfComponents="1">'
> >>>>> write(nfil,*) (y2(j),j=1,n2m)
> >>>>> write(nfil,*)' </DataArray>'
> >>>>> write(nfil,*)' <DataArray type="Float32"',
> >>>>> & ' Name="Z_COORDINATES"',
> >>>>> & ' NumberOfComponents="1">'
> >>>>> write(nfil,*) (y3(k),k=1,n3m)
> >>>>> write(nfil,*)' </DataArray>'
> >>>>> write(nfil,*)' </Coordinates>'
> >>>>> write(nfil,*)' <PointData Scalars="scalar">'
> >>>>> write(nfil,*)' <DataArray Name="'//trim(name)//'"',
> >>>>> & ' type="Float32"',
> >>>>> & ' NumberOfComponents="1"',
> >>>>> & ' format="ascii">'
> >>>>> write(nfil,*) (((scal_data(i,j,k),i=1,n1m),j=1,n2m),k=1,n3m)
> >>>>> write(nfil,*)' </DataArray>'
> >>>>> write(nfil,*)' </PointData>'
> >>>>> write(nfil,*)' </Piece>'
> >>>>> write(nfil,*)' </RectilinearGrid>'
> >>>>> write(nfil,*)'</VTKFile>'
> >>>>> close(nfil)
> >>>>>!
> >>>>> return
> >>>>> end
> >>>>>
> >>>>>_______________________________________________
> >>>>>ParaView mailing list
> >>>>>ParaView at paraview.org
> >>>>>http://www.paraview.org/mailman/listinfo/paraview
> >>>>>
> >>>>>
> >>>>
> >
> >
> > --
> > Dominik Szczerba, Dr.
> > Computer Vision Lab CH-8092 Zurich
> > http://www.vision.ee.ethz.ch/~domi
> _______________________________________________
> ParaView mailing list
> ParaView at paraview.org
> http://www.paraview.org/mailman/listinfo/paraview
>
> --
> Dominik Szczerba, Dr.
> Computer Vision Lab CH-8092 Zurich
> http://www.vision.ee.ethz.ch/~domi
> _______________________________________________
> ParaView mailing list
> ParaView at paraview.org
> http://www.paraview.org/mailman/listinfo/paraview
>
--
Randall Hand
Visualization Scientist,
ERDC-MSRC Vicksburg, MS
Homepage: http://www.yeraze.com
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