Your welcome, I had recently written code to write and read the "Analyze"
format which I needed to get data into a medical image registration
software. Might be good to polish this up (also your vtk code) and get this
into a package. Not entirely sure if this should stand on its own or be
integrated into Images.jl.
Cheers
Tobi
Am Sonntag, 15. März 2015 16:10:56 UTC+1 schrieb Christian Dengler:
>
> "bswap()" worked perfectly! Everything is working now, finally :) For
> those interested, the appended file contains a working vtk export function.
> Thanks for the help Tobias!
>
> Am Sonntag, 15. März 2015 13:28:58 UTC+1 schrieb Tobias Knopp:
>>
>> for l=1:length(x)
>> x[l] = bswap(x[l])
>> y[l] = bswap(y[l])
>> z[l] = bswap(z[l])
>> end
>>
>>
>> Am Sonntag, 15. März 2015 11:17:53 UTC+1 schrieb Christian Dengler:
>>>
>>> Hello again,
>>>
>>> No that did not do the trick, but i managed to compare the julia output
>>> to a working .vtk file, using a binary reader. The problem with the julia
>>> output, is that it is written LittleEndian, while paraview needs BigEndian.
>>> Also the structure must be write(fid, hcat(x[:]', y[:]', z[:]') ), but
>>> written with BigEndians, which i haven't figured out how to do yet. I tried
>>> the hton() function, as well as NetworkByteOrder from the docs, but i
>>> guess i'm applying it wrong. I tried
>>>
>>> write(fid, hcat(x[:]', y[:]', z[:]') , NetworkByteOrder) ->
>>> NetworkByteOrder
>>> not defined
>>> write(fid, hcat(x[:]', y[:]', z[:]') , "NetworkByteOrder") -> writes
>>> the string to the file, instead of changing endianness
>>> write(fid, hton(hcat(x[:]', y[:]', z[:]'))) -> ERROR: `bswap` has no
>>> method matching bswap(::Array{Float64,2})
>>>
>>> Any suggestions how to write big endian?
>>>
>>>
>>> Am Samstag, 14. März 2015 20:05:50 UTC+1 schrieb Tobias Knopp:
>>>>
>>>> not familiar with the vtk format but are you sure the the x,y,z
>>>> coordinates lay not directly after each other?
>>>> Could try:
>>>>
>>>> write(fid, vcat(x[:]', y[:]', z[:]') )
>>>>
>>>> Am Samstag, 14. März 2015 18:54:59 UTC+1 schrieb Christian Dengler:
>>>>>
>>>>> Ty for your answers. I'm not familiar with vtk export on python, and
>>>>> i'm confident that finding my mistake will be easier than trying to
>>>>> understand what you did there with pycall.
>>>>> As for the nrrd code, it seems to be doing exactly what i did. I found
>>>>> one mistake i did previously though, telling paraview to load float
>>>>> instead
>>>>> of double values. Now with the function below, paraview loads the files
>>>>> withoud error message, yet doesnt display anything reasonable, seems that
>>>>> there is another mistake somewhere, i still assume it to be the "write"
>>>>> function, where i'm not sure if it does what i want it to.
>>>>> I'll keep you up to date, should i find my mistake
>>>>>
>>>>> function exportVTK(DataMat, NameMat ,filename, dh, Nxyz)
>>>>>
>>>>> nx = dh[1]*(Nxyz[1]-1);
>>>>> ny = dh[2]*(Nxyz[2]-1);
>>>>> nz = dh[3]*(Nxyz[3]-1);
>>>>>
>>>>> x, y, z = ndgrid(0:dh[1]:nx, 0:dh[2]:ny, 0:dh[3]:nz );
>>>>>
>>>>> nr_of_elements = length(x);
>>>>> fid = open(filename, "w");
>>>>>
>>>>> #ASCII file header
>>>>> println(fid, "# vtk DataFile Version 3.0");
>>>>> println(fid, "VTK from Julia");
>>>>> println(fid, "BINARY\n");
>>>>> println(fid, "DATASET STRUCTURED_GRID");
>>>>> println(fid, "DIMENSIONS $(size(x,1)) $(size(x,2)) $(size(x,3)) ");
>>>>> println(fid, "POINTS $(nr_of_elements) double");
>>>>> write(fid, [x[:] y[:] z[:]] )
>>>>>
>>>>> #append data
>>>>> print(fid, "\nPOINT_DATA $(nr_of_elements) \n");
>>>>>
>>>>> for i = 1:length(DataMat)
>>>>>
>>>>> if size(DataMat[i], 2) == 3
>>>>> #append a vector
>>>>> println(fid, "\nVECTORS $(NameMat[i]) double");
>>>>> elseif size(DataMat[i], 2) == 1
>>>>> #append a scalar
>>>>> println(fid, "\nSCALARS $(NameMat[i]) double");
>>>>> println(fid, "LOOKUP_TABLE default");
>>>>> else
>>>>> error("DataMat $i is not a vector or scalar, or not shaped
>>>>> the way it should be")
>>>>> end
>>>>>
>>>>> write(fid, DataMat[i]);
>>>>>
>>>>> end
>>>>>
>>>>> close(fid);
>>>>>
>>>>> end
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Am Samstag, 14. März 2015 17:49:50 UTC+1 schrieb Kristoffer Carlsson:
>>>>>>
>>>>>> One method that I have used to export VTK from Julia is simply using
>>>>>> the VTK-library from python and calling it with PyCall.
>>>>>>
>>>>>> Something like this:
>>>>>> https://gist.github.com/KristofferC/9a989a2c0518bb70009c
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Saturday, March 14, 2015 at 1:41:04 PM UTC+1, Christian Dengler
>>>>>> wrote:
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I'm trying to save my data as .vtk files, and ran into a problem
>>>>>>> with the "print" and "write" function.
>>>>>>>
>>>>>>> Resumee of what would solve my problems:
>>>>>>> - Using print(filestream, data), but omitting the square brackets,
>>>>>>> and
>>>>>>> - using print(filestream, vector), and actually writes the vector,
>>>>>>> one element per line
>>>>>>>
>>>>>>> Does anyone know how this is done?
>>>>>>>
>>>>>>> Another way of creating .vtk files using binary data, using the
>>>>>>> write function, didn't lead to any success, but i cant really say whats
>>>>>>> wrong, because the files are unreadable. Could it be, that write also
>>>>>>> somehow includes brackets?
>>>>>>>
>>>>>>>
>>>>>>> For those who want to see my problem in code, i attached a script,
>>>>>>> creating and saving a simple veocity field as .vtk (ASCII) file.
>>>>>>> After manually deleting the brackets, atleast the velocity can be
>>>>>>> imported into paraview.
>>>>>>> In order to create the binary .vtk file (thats not working at all),
>>>>>>> i used to replace "ASCII" by "BINARY", and "print" in line 22 and 41
>>>>>>> by
>>>>>>> "write".
>>>>>>>
>>>>>>> Greetings,
>>>>>>> Christian
>>>>>>>
>>>>>>
