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