[vtkusers] vtkStructuredPointsWriter writes a blank file

[Bill Lorensen]

These are very large files. Try reading just 2 or 3

TIFFReader -> SetDataExtent(0,653,0,3959,0,2);
On Jun 19, 2014 7:06 PM, "Matheus Viana" <vianamp at gmail.com> wrote:

> Hi Bill, this is the code. I also tried to comments the lines related to SetDataByteOrderToBigEndian
> and SetDataScalarTypeToUnsignedShort, but they don't make any difference.
>
> int main() {
>     vtkTIFFReader *TIFFReader = vtkTIFFReader::New();
>     TIFFReader -> SetDataByteOrderToBigEndian();
>     TIFFReader -> SetDataExtent(0,653,0,3959,0,3959);
>     TIFFReader -> SetFilePrefix("/Users/matheusviana/Desktop/images/im");
>     TIFFReader -> SetFilePattern("%s%04d.tif");
>     TIFFReader -> SetDataScalarTypeToUnsignedShort();
>     TIFFReader -> Update();
>
>     vtkStructuredPointsWriter *ImageDataWriter =
> vtkStructuredPointsWriter::New();
>     ImageDataWriter -> SetFileType(VTK_BINARY);
>     ImageDataWriter -> SetInput(TIFFReader -> GetOutput());
>     ImageDataWriter -> SetFileName("Result.vtk");
>     ImageDataWriter -> Write();
>
>     return 1;
> }
>
> *Matheus Viana*
> *Postdoctoral Research Employee*
> *Developmental and Cell Biology*
> *University of California Irvine*
>
>
>
>
> 2014-06-19 18:46 GMT-03:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
>> Please post your updated code.
>>
>>
>> On Thu, Jun 19, 2014 at 4:56 PM, Matheus Viana <vianamp at gmail.com> wrote:
>> > I got the same result, blank file.
>> >
>> > Matheus Viana
>> > Postdoctoral Research Employee
>> > Developmental and Cell Biology
>> > University of California Irvine
>> >
>> >
>> >
>> >
>> > 2014-06-19 17:35 GMT-03:00 Bill Lorensen <bill.lorensen at gmail.com>:
>> >
>> >> So, lets say each image is 512 x 512, and you have 3960 images,
>> >> TIFFReader -> SetDataExtent(0,511,0,511,0,3959);
>> >>
>> >> On Thu, Jun 19, 2014 at 3:29 PM, Matheus Viana <vianamp at gmail.com>
>> wrote:
>> >> > They are in separate files.
>> >> >
>> >> > Matheus Viana
>> >> > Postdoctoral Research Employee
>> >> > Developmental and Cell Biology
>> >> > University of California Irvine
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > 2014-06-19 16:21 GMT-03:00 Bill Lorensen <bill.lorensen at gmail.com>:
>> >> >
>> >> >> Are the images all in one file? Or separate files for each image?
>> >> >>
>> >> >>
>> >> >> On Thu, Jun 19, 2014 at 1:56 PM, Matheus Viana <vianamp at gmail.com>
>> >> >> wrote:
>> >> >> > Dear David,
>> >> >> >
>> >> >> > I tried to use XMLImageDataWriter and it seems to be working.
>> >> >> > However,
>> >> >> > the
>> >> >> > original VTK file that has 2Gb is then saved as a vti file that
>> has
>> >> >> > only
>> >> >> > 10Mb. I think this is fine because my data is very sparse with a
>> lot
>> >> >> > of
>> >> >> > zeros. I can make sure that it is working well because Paraview
>> >> >> > crashes
>> >> >> > when
>> >> >> > I tried to load the file. I'll check it again later on. Anyway, do
>> >> >> > you
>> >> >> > think
>> >> >> > the bug is in the StructuredPointsWriter?
>> >> >> >
>> >> >> > Bill, I tried to not specify the data extent, but in this case the
>> >> >> > reader
>> >> >> > reads only the first image of the sequence. Is there anything
>> else I
>> >> >> > have to
>> >> >> > set up?
>> >> >> >
>> >> >> > Matheus Viana
>> >> >> > Postdoctoral Research Employee
>> >> >> > Developmental and Cell Biology
>> >> >> > University of California Irvine
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > 2014-06-19 14:20 GMT-03:00 Bill Lorensen <bill.lorensen at gmail.com
>> >:
>> >> >> >
>> >> >> >> The data extents you specified will produce a zero length
>> structured
>> >> >> >> points.
>> >> >> >>
>> >> >> >> For the tiff reader, you need not specify the extents if you want
>> >> >> >> all
>> >> >> >> of the data. And I'm not sure what the other methods will do in
>> the
>> >> >> >> tiff reader.
>> >> >> >> vtkTIFFReader *TIFFReader = vtkTIFFReader::New();
>> >> >> >>     TIFFReader ->
>> >> >> >> SetFilePrefix("/Users/matheusviana/Desktop/images/im");
>> >> >> >>     TIFFReader -> SetFilePattern("%s%04d.tif");
>> >> >> >>     TIFFReader -> Update();
>> >> >> >>
>> >> >> >> On Thu, Jun 19, 2014 at 8:14 AM, matheus_viana <
>> vianamp at gmail.com>
>> >> >> >> wrote:
>> >> >> >> > Guys, I'd like to know if there is any error in this code
>> below.
>> >> >> >> > The
>> >> >> >> > code
>> >> >> >> > works fine for small size dataset, but it writes a blank file
>> when
>> >> >> >> > the
>> >> >> >> > dataset has more than 2Gb. I'm working on 64bit OSX.
>> >> >> >> >
>> >> >> >> > Thanks a lot.
>> >> >> >> >
>> >> >> >> > int main() {
>> >> >> >> >     vtkTIFFReader *TIFFReader = vtkTIFFReader::New();
>> >> >> >> >     TIFFReader -> SetDataByteOrderToBigEndian();
>> >> >> >> >     TIFFReader -> SetDataExtent(0,0,0,0,0,3959);
>> >> >> >> >     TIFFReader ->
>> >> >> >> > SetFilePrefix("/Users/matheusviana/Desktop/images/im");
>> >> >> >> >     TIFFReader -> SetFilePattern("%s%04d.tif");
>> >> >> >> >     TIFFReader -> SetDataScalarTypeToUnsignedShort();
>> >> >> >> >     TIFFReader -> Update();
>> >> >> >> >
>> >> >> >> >     vtkStructuredPointsWriter *ImageDataWriter =
>> >> >> >> > vtkStructuredPointsWriter::New();
>> >> >> >> >     ImageDataWriter -> SetFileType(VTK_BINARY);
>> >> >> >> >     ImageDataWriter -> SetInput(TIFFReader -> GetOutput());
>> >> >> >> >     ImageDataWriter -> SetFileName("Result.vtk");
>> >> >> >> >     ImageDataWriter -> Write();
>> >> >> >> >
>> >> >> >> >     return 1;
>> >> >> >> > }
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > View this message in context:
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> http://vtk.1045678.n5.nabble.com/vtkStructuredPointsWriter-writes-a-blank-file-tp5727536.html
>> >> >> >> > Sent from the VTK - Users mailing list archive at Nabble.com.
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