Thank you so much. I'll start working on a python reader, if I could create it, I will share it with the community.
Best regards, Samer Eric E. Monson wrote: > Hey Samer, > > Part of my point was that I had trouble loading data into ParaView, so I was > creating it within PV to see how it handled bit data. > > It looks like you are right that the legacy VTK format supports bit > attributes, so that may be your best bet for trying to get your data into PV. > There are various warnings around, though, that you _must_ write your binary > data in *BigEndian* format. I was able to create a data set in PV and then > save it in legacy VTK and load it back in okay. I'll attach both binary and > ascii version of this so you can compare the two to see how the binary is > constructed. It looks like you just need a newline after the header part, and > then your binary data written out as 8 bit characters, and then a newline at > the end. > > I don't think that the VTK file formats can refer to data in another file, so > if I understand you correctly it won't work as a markup language like .xmf > files with HDF5. So, if you really need to stick with bit images you'll > probably have to write the legacy VTK as a separate, single file. > > Good luck, > -Eric > > > ------------------------------------------------------------------------ > > > > On Jul 1, 2010, at 6:27 PM, sa...@icp.uni-stuttgart.de wrote: > > >> Hello Eric, >> >> Thanks again that you're the one answering my questions. Well >> unfortunately I haven't ever worked on python before, so it would be a >> good idea to avoid it in the beginning till I find it the only solution to >> my problem. Could you please tell me how you managed to open the bit >> images with Paraview and/or VTK? even if it gives some errors, it's OK, >> because I'm not asking for so much in the output, I just want to see some >> simple 3D visualisation for my images. >> >> Actually I'm surprised, that in VTK I read in the manual that it's >> supposed to accept the bit format, but it did not open on paraview when I >> tried converting my binary images to VTK format by adding the appropriate >> header. So did I miss something in that conversion? The header I added is >> the following: >> >> # vtk DataFile Version 3.0 >> blablabla >> BINARY >> DATASET STRUCTURED_POINTS >> DIMENSIONS 1024 1024 512 >> ORIGIN 0 0 0 >> SPACING 1 1 1 >> POINT_DATA 536870912 >> SCALARS OutArray bit 1 >> LOOKUP_TABLE default >> >> >> Actually this discussion tempts me to ask the question, can I use VTK as a >> markup language to open my data files? or should I install this header >> into my data file so that both the data and the header are in one file? >> >> Thank you for your time. >> >> Best regards, >> Samer >> >> >> >> >>> Hello Samer, >>> >>> Well, hopefully someone more knowledgeable will speak up if I'm wrong, but >>> after playing around for a while I don't think you're going to be happy >>> with ParaView's support (and probably VTK underneath) for image data with >>> bit attributes. (For example, I couldn't get volume rendering to work, and >>> I got some errors like: vtkOpenGLScalarsToColorsPainter (0x12a099f70): >>> Cannot color by bit array, even though it _would_ actually color it.) >>> >>> I don't know of a reader offhand that will support single bit data >>> attributes (I tried the old VTK and newer XML-based VTK formats and it >>> didn't work well, and I'm not sure what other readers would work -- the >>> .raw reader in ParaView also seems to have a limit of char at the small >>> end). I have a feeling you could create a custom reader with the Python >>> Programmable Source. You can look at some examples here: >>> >>> http://www.paraview.org/Wiki/Python_Programmable_Filter >>> http://www.paraview.org/Wiki/Here_are_some_more_examples_of_simple_ParaView_3_python_filters. >>> >>> You can create a sample of this type of data directly in ParaView to see >>> what is supported and not with single bit attributes: >>> >>> 1. Create a Wavelet Source >>> 2. Apply a Python Programmable Filter >>> Use this as the Script: >>> >>> # --------------- >>> from paraview.vtk import vtkBitArray >>> import random >>> >>> pdi = self.GetInputDataObject(0,0) >>> pdo = self.GetOutputDataObject(0) >>> pdo.ShallowCopy(pdi) >>> >>> ba = vtkBitArray() >>> ba.SetNumberOfComponents(1) >>> ba.SetNumberOfTuples(pdi.GetNumberOfPoints()) >>> ba.SetName('bits') >>> for ii in range(ba.GetNumberOfTuples()): >>> ba.SetTuple1(ii,round(random.random())) >>> >>> pdo.GetPointData().AddArray(ba) >>> pdo.GetPointData().SetActiveScalars('bits') >>> # --------------- >>> >>> You can see in the Information tab that a bit array is created, and you >>> can try coloring by that array, but only Slice representation seems to >>> work well. Contour filter seems to deal with it okay, though, so maybe >>> this will still be useful to you. >>> >>> Talk to you later, >>> -Eric >>> >>> ------------------------------------------------------ >>> Eric E Monson >>> Duke Visualization Technology Group >>> >>> >>> On Jun 30, 2010, at 6:16 PM, sa...@icp.uni-stuttgart.de wrote: >>> >>> >>>> Hello guys, >>>> >>>> I have a binary image that consists of bits, every bit indicates to a >>>> pixel (or voxel) in my 3D image. The file is nothing special, it's >>>> simply >>>> a contiguous file format I write as an output in a C++ program, I mean >>>> it's not HDF or something common. >>>> Is it possible to view this image in Paraview without being converted to >>>> byte for every pixel? I mean is there a way that I could write an XML or >>>> XDMF script that tells paraview how to view it? >>>> I succeeded in viewing the image, but after converting every bit to a >>>> byte, which means that the image is now 8 times bigger in size! this is >>>> not effective at all I guess. >>>> >>>> I would appreciate an example very much. >>>> >>>> Thank you >>>> >>>> Regards, >>>> Samer >>>> >>>> _______________________________________________ >>>> 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
