[vtkusers] vtkStructuredPointsWriter writes a blank file

Matheus Viana vianamp at gmail.com
Fri Jun 20 08:58:46 EDT 2014


Sorry, there was a typo. Actually the correct size is:

TIFFReader -> SetDataExtent(0,653,0,934,0,3959);

still a big dataset though!!

As I told in my first message, both TIFFReader and TIFFWriter work fine for
small dataset.

I just tested the upper limit that I can go. I found that when a try to
read SetDataExtent(0,653,0,934,0,3500) it works and the writer writes a
file of 2.14Gb. When I try SetDataExtent(0,653,0,934,0,3600), the writes
write a blank file of 122kb instead.

It seems that there is a size limit for files that I can write. Does it
make sense? Would it be a limit of VTK or OS X?

I have no idea of what's going on.. A quick search on google I saw that
photoshop, for instance, limits the size of tiff files you can write to 2Gb
and you can manually increase this limit. Is there any reason to believe
that there is something similar in VTK?

*Matheus Viana*
*Postdoctoral Research Employee*
*Developmental and Cell Biology*
*University of California Irvine*




2014-06-20 9:19 GMT-03:00 Bill Lorensen <bill.lorensen at gmail.com>:

> 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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