Hello Eric, Man... I'm really unable to express my gratitude for your help! you just gave me what I exactly needed, the first step into XDMF. I'm really grateful! now I can learn more by manipulating that file :-) .
Thank you again, and wish you the best. Sincerest regards, Samer > Hey Samer, > > You had the right idea, looking at the HDF5 file with hdfview, but since > the file doesn't contain any coordinate information, you will want to use > one of the regular grid meshes where you set the origin and spacing of the > mesh in each direction and then the positions of the nodes are implicitly > defined. I can't tell if the grid spacing is buried somewhere in the > metadata for your file, but there's a lot of into there, so it might be. > > Besides the model and format page > (http://xdmf.org/index.php/XDMF_Model_and_Format), if you download the > Xdmf source code there are a lot of examples of .xmf files in > [xdmf_src]/Examples/Data. > > Following is a .xmf file that works for me and a screenshot from ParaView. > > Talk to you later, > -Eric > > > <Xdmf> > <Domain Name="TEST"> > <Grid Name="Pressure_Grid" GridType="Uniform"> > <Topology TopologyType="3DCoRectMesh" Dimensions="320 > 304 304"> > </Topology> > <Geometry GeometryType="Origin_DxDyDz"> > <DataItem Name="Origin" DataType="Float" > Dimensions="3" Format="XML"> > 0.000 0.000 0.000 > </DataItem> > <DataItem Name="Spacing" DataType="Float" > Dimensions="3" Format="XML"> > 1.000 1.000 1.000 > </DataItem> > </Geometry> > <Attribute AttributeType="Scalar" Center="Node" > Name="Pressure"> > <DataItem NumberType="Float" Precision="8" > Dimensions="320 304 304" > Format="HDF"> > data.h5:OutArray > </DataItem> > </Attribute> > </Grid> > </Domain> > </Xdmf> > > > > On Jun 30, 2010, at 5:53 AM, sa...@icp.uni-stuttgart.de wrote: > >> Hello Eric, >> >> Thank you for your answer. Actually what I mean with not pleasing, is >> that >> the program is crashing a lot, giving this message in the terminal. >> >> XDMF Error in >> /build/buildd/paraview-3.4.0/Utilities/Xdmf2/libsrc/XdmfValuesHDF.cxx >> line >> 77 (Can't Open Dataset data.h5:/X) >> XDMF Error in >> /build/buildd/paraview-3.4.0/Utilities/Xdmf2/libsrc/XdmfDataItem.cxx >> line >> 498 (Reading Values Failed) >> XDMF Error in >> /build/buildd/paraview-3.4.0/Utilities/Xdmf2/libsrc/XdmfGrid.cxx line >> 607 >> (Error in Update() of Geometry) >> Segmentation fault >> >> I'm aware that my data does not contain XYZ information, it only >> contains >> pressure data, but when I remove the XYZ information from my XDMF I get >> a >> null shape in paraview (of course, because there won't be a geometry >> then), and the "volume" preview is wouldn't be available, only surface >> and >> some other useless choices, and they all give empty views. Therefore I'm >> not sure how I can tell the program that those pressures correspond to a >> grid. >> >> Starting from the very beginning, I got this file "data.h5" from someone >> telling me that it's the output of some analysis for pressure. I need to >> visualise this file to understand the type before I do the analysis on >> my >> sample. I used the program hdfview to view its contents, and I found >> that >> it's a 3D matrix of 8-byte doubles, every double contains a pressure, >> and >> the dimensions of this matrix is 320x304x304, and this is the only >> information I have. >> >> The size of the file is 225 MB, which is equal to: 8*304*304*320 bytes. >> In >> other words the data file does not contain any other information about >> the >> coordinates. >> >> I wrote this XDMF file while I don't really understand what I'm doing, >> it's just the first step, so I don't know anything like different >> mesh(s) >> and so on. >> >> I expected to get a 3D view for my samples with different colours per >> pressure, isn't this what I should get? >> >> Now the question, does it suffice to state only the pressure information >> in the XDMF file without coordinates? and what should paraview show me >> for >> such data? is it colour per voxel as I expected? is what I'm doing the >> right way to visualise this data? >> >> For convenience, I uploaded the data file to Megaupload, please find it >> at >> >> http://www.megaupload.com/?d=F8M6XU4D >> >> Thank you, I really appreciate the time you're using for this. >> >> Best regards, >> Samer >> >> >> >>> Hello Samer, >>> >>> You may need to explain a bit more what you mean by "the final result I >>> got was not pleasing". >>> >>> It looks like there may be a problem in that you are defining >>> 320x304x304 >>> points for your grid, but you also are stating that the same number of >>> Pressure attributes exist, centered on the cells. If you really have >>> that >>> many pressure values, you should probably put them as Center="Node", >>> otherwise there should be one less value in each direction, as the >>> cells >>> will be implicitly defined between the points. >>> >>> (Also, you probably already know this, but if your grid has a constant >>> spacing in each direction you can either use 3DRectMesh or 3DCoRectMesh >>> topology and not have to specify the XYZ positions of the points.) >>> >>> If changing cell centered to point centered doesn't help, just explain >>> a >>> little more about what's not working and we'll try to help more. There >>> is >>> also an Xdmf mailing list, but this is an okay place to post for now if >>> you're trying to load your data into ParaView. >>> >>> Talk to you later, >>> -Eric >>> >>> ------------------------------------------------------ >>> Eric E Monson >>> Duke Visualization Technology Group >>> >>> >>> On Jun 29, 2010, at 11:19 AM, Samer Afach wrote: >>> >>>> Hello programmers, >>>> >>>> I'm new to this list, I'm not sure I'm asking in the right place, but >>>> I'll try to ask and I hope I'll get the answer I'm looking for :) . >>>> >>>> I have an HDF5 file which is an array of 8-bit double 3D array of >>>> pressure values for a sample I have, the size of this array is >>>> 320x304x304. I'm trying to read this file to (visualise it in) >>>> Paraview, >>>> and I heard that I have to write an XDMF file for that. So I started >>>> reading about it, but the final result I got was not pleasing. I >>>> attached with this e-mail the XDMF file I wrote for this purpose >>>> (reading my data.h5 file). >>>> >>>> Could someone please tell me what's wrong in my XDMF? >>>> >>>> Thank you, any efforts are highly appreciated. >>>> >>>> Regards, >>>> Samer Afach >>>> Institute for Computational physics, University of Stuttgart >>>> <?xml version="1.0" ?> >>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []> >>>> <Xdmf Version="2.0"> >>>> <domain> >>>> <Grid Name="mesh1" GridType="Uniform"> >>>> <Topology TopologyType="3DSMesh" NumberOfElements="304 304 320"/> >>>> <Geometry GeometryType="X_Y_Z"> >>>> <DataItem Dimensions="304 304 320" NumberType="Float" >>>> Precision="8" Format="HDF"> >>>> data.h5:/X >>>> </DataItem> >>>> <DataItem Dimensions="304 304 320" NumberType="Float" >>>> Precision="8" Format="HDF"> >>>> data.h5:/Y >>>> </DataItem> >>>> <DataItem Dimensions="304 304 320" NumberType="Float" >>>> Precision="8" Format="HDF"> >>>> data.h5:/Z >>>> </DataItem> >>>> </Geometry> >>>> <Attribute Name="Pressure" AttributeType="Scalar" Center="Cell"> >>>> <DataItem Dimensions="304 304 320" NumberType="Float" >>>> Precision="8" Format="HDF"> >>>> data.h5:/Pressure >>>> </DataItem> >>>> </Attribute> >>>> </Grid> >>>> </domain> >>>> </Xdmf> >>>> _______________________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Please keep messages on-topic and check the ParaView Wiki at: >>>> http://paraview.org/Wiki/ParaView >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.paraview.org/mailman/listinfo/paraview >>> >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview > > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview