<div dir="ltr">Sorry, there was a typo. Actually the correct size is:<div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif"><br></span></div><div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">TIFFReader -> SetDataExtent(0,653,0,934,0,3959</span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">);</span><br>
</div><div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif"><br></span></div><div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">still a big dataset though!!</span></div>
<div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif"><br></span></div><div><font color="#000000" face="Verdana, Geneva, Helvetica, Arial, sans-serif">As I told in my first message, both </font><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:12.727272033691406px">TIFFReader and </span><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:12.727272033691406px">TIFFWriter work fine for small dataset.</span></div>
<div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:12.727272033691406px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:12.727272033691406px">I just tested the upper limit that I can go. I found that when a try to read </span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">SetDataExtent(0,653,0,934,0,3500</span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">) it works and the writer writes a file of 2.14Gb. When I try </span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">SetDataExtent(0,653,0,934,0,3600</span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">), the writes write a blank file of 122kb instead.</span></div>
<div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif"><br></span></div><div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">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?</span></div>
<div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif"><br></span></div><div><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">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?</span></div>
</div><div class="gmail_extra"><br clear="all"><div><div><div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>Matheus Viana</b></span></font></div><div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>Postdoctoral Research Employee</b></span></font></div>
<div><b><span style="color:rgb(85,85,85);line-height:16px;font-family:Helvetica,Arial,sans-serif;font-size:13px">Developmental and Cell Biology</span></b></div><div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>University of California Irvine</b></span></font></div>
<div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b><br></b></span></font><b><i><br></i></b></div></div></div>
<br><br><div class="gmail_quote">2014-06-20 9:19 GMT-03:00 Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><p dir="ltr">These are very large files. Try reading just 2 or 3</p><p dir="ltr"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">TIFFReader -> SetDataExtent(0,653,0,3959,0,2</span><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">); </span><br>
</p><div><div class="h5">
<div class="gmail_quote">On Jun 19, 2014 7:06 PM, "Matheus Viana" <<a href="mailto:vianamp@gmail.com" target="_blank">vianamp@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">Hi Bill, this is the code. </span><span style="font-size:13px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">I also tried to comments the lines related to </span><span style="font-size:12.727272033691406px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">SetDataByteOrderToBigEndian and </span><span style="font-size:12.727272033691406px;color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif">SetDataScalarTypeToUnsignedShort, but they don't make any difference.</span></div>
<div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"><br></span></div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">int main() { </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> vtkTIFFReader *TIFFReader = vtkTIFFReader::New(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> SetDataByteOrderToBigEndian(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> SetDataExtent(0,653,0,3959,0,3959); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> SetFilePrefix("/Users/matheusviana/Desktop/images/im"); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> SetFilePattern("%s%04d.tif"); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> SetDataScalarTypeToUnsignedShort(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> TIFFReader -> Update(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> vtkStructuredPointsWriter *ImageDataWriter = vtkStructuredPointsWriter::New(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> ImageDataWriter -> SetFileType(VTK_BINARY); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> ImageDataWriter -> SetInput(TIFFReader -> GetOutput()); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> ImageDataWriter -> SetFileName("Result.vtk"); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> ImageDataWriter -> Write(); </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px"> return 1; </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">
<span style="color:rgb(0,0,0);font-family:Verdana,Geneva,Helvetica,Arial,sans-serif;font-size:13px">}</span><br></div><div class="gmail_extra"><br clear="all"><div><div><div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>Matheus Viana</b></span></font></div>
<div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>Postdoctoral Research Employee</b></span></font></div><div><b><span style="color:rgb(85,85,85);line-height:16px;font-family:Helvetica,Arial,sans-serif;font-size:13px">Developmental and Cell Biology</span></b></div>
<div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b>University of California Irvine</b></span></font></div><div><font color="#555555" face="Helvetica, Arial, sans-serif"><span style="line-height:16px"><b><br>
</b></span></font><b><i><br></i></b></div></div></div>
<br><br><div class="gmail_quote">2014-06-19 18:46 GMT-03:00 Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Please post your updated code.<br>
<div><div><br>
<br>
On Thu, Jun 19, 2014 at 4:56 PM, Matheus Viana <<a href="mailto:vianamp@gmail.com" target="_blank">vianamp@gmail.com</a>> wrote:<br>
> I got the same result, blank file.<br>
><br>
> Matheus Viana<br>
> Postdoctoral Research Employee<br>
> Developmental and Cell Biology<br>
> University of California Irvine<br>
><br>
><br>
><br>
><br>
> 2014-06-19 17:35 GMT-03:00 Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>>:<br>
><br>
>> So, lets say each image is 512 x 512, and you have 3960 images,<br>
>> TIFFReader -> SetDataExtent(0,511,0,511,0,3959);<br>
>><br>
>> On Thu, Jun 19, 2014 at 3:29 PM, Matheus Viana <<a href="mailto:vianamp@gmail.com" target="_blank">vianamp@gmail.com</a>> wrote:<br>
>> > They are in separate files.<br>
>> ><br>
>> > Matheus Viana<br>
>> > Postdoctoral Research Employee<br>
>> > Developmental and Cell Biology<br>
>> > University of California Irvine<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > 2014-06-19 16:21 GMT-03:00 Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>>:<br>
>> ><br>
>> >> Are the images all in one file? Or separate files for each image?<br>
>> >><br>
>> >><br>
>> >> On Thu, Jun 19, 2014 at 1:56 PM, Matheus Viana <<a href="mailto:vianamp@gmail.com" target="_blank">vianamp@gmail.com</a>><br>
>> >> wrote:<br>
>> >> > Dear David,<br>
>> >> ><br>
>> >> > I tried to use XMLImageDataWriter and it seems to be working.<br>
>> >> > However,<br>
>> >> > the<br>
>> >> > original VTK file that has 2Gb is then saved as a vti file that has<br>
>> >> > only<br>
>> >> > 10Mb. I think this is fine because my data is very sparse with a lot<br>
>> >> > of<br>
>> >> > zeros. I can make sure that it is working well because Paraview<br>
>> >> > crashes<br>
>> >> > when<br>
>> >> > I tried to load the file. I'll check it again later on. Anyway, do<br>
>> >> > you<br>
>> >> > think<br>
>> >> > the bug is in the StructuredPointsWriter?<br>
>> >> ><br>
>> >> > Bill, I tried to not specify the data extent, but in this case the<br>
>> >> > reader<br>
>> >> > reads only the first image of the sequence. Is there anything else I<br>
>> >> > have to<br>
>> >> > set up?<br>
>> >> ><br>
>> >> > Matheus Viana<br>
>> >> > Postdoctoral Research Employee<br>
>> >> > Developmental and Cell Biology<br>
>> >> > University of California Irvine<br>
>> >> ><br>
>> >> ><br>
>> >> ><br>
>> >> ><br>
>> >> > 2014-06-19 14:20 GMT-03:00 Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>>:<br>
>> >> ><br>
>> >> >> The data extents you specified will produce a zero length structured<br>
>> >> >> points.<br>
>> >> >><br>
>> >> >> For the tiff reader, you need not specify the extents if you want<br>
>> >> >> all<br>
>> >> >> of the data. And I'm not sure what the other methods will do in the<br>
>> >> >> tiff reader.<br>
>> >> >> vtkTIFFReader *TIFFReader = vtkTIFFReader::New();<br>
>> >> >> TIFFReader -><br>
>> >> >> SetFilePrefix("/Users/matheusviana/Desktop/images/im");<br>
>> >> >> TIFFReader -> SetFilePattern("%s%04d.tif");<br>
>> >> >> TIFFReader -> Update();<br>
>> >> >><br>
>> >> >> On Thu, Jun 19, 2014 at 8:14 AM, matheus_viana <<a href="mailto:vianamp@gmail.com" target="_blank">vianamp@gmail.com</a>><br>
>> >> >> wrote:<br>
>> >> >> > Guys, I'd like to know if there is any error in this code below.<br>
>> >> >> > The<br>
>> >> >> > code<br>
>> >> >> > works fine for small size dataset, but it writes a blank file when<br>
>> >> >> > the<br>
>> >> >> > dataset has more than 2Gb. I'm working on 64bit OSX.<br>
>> >> >> ><br>
>> >> >> > Thanks a lot.<br>
>> >> >> ><br>
>> >> >> > int main() {<br>
>> >> >> > vtkTIFFReader *TIFFReader = vtkTIFFReader::New();<br>
>> >> >> > TIFFReader -> SetDataByteOrderToBigEndian();<br>
>> >> >> > TIFFReader -> SetDataExtent(0,0,0,0,0,3959);<br>
>> >> >> > TIFFReader -><br>
>> >> >> > SetFilePrefix("/Users/matheusviana/Desktop/images/im");<br>
>> >> >> > TIFFReader -> SetFilePattern("%s%04d.tif");<br>
>> >> >> > TIFFReader -> SetDataScalarTypeToUnsignedShort();<br>
>> >> >> > TIFFReader -> Update();<br>
>> >> >> ><br>
>> >> >> > vtkStructuredPointsWriter *ImageDataWriter =<br>
>> >> >> > vtkStructuredPointsWriter::New();<br>
>> >> >> > ImageDataWriter -> SetFileType(VTK_BINARY);<br>
>> >> >> > ImageDataWriter -> SetInput(TIFFReader -> GetOutput());<br>
>> >> >> > ImageDataWriter -> SetFileName("Result.vtk");<br>
>> >> >> > ImageDataWriter -> Write();<br>
>> >> >> ><br>
>> >> >> > return 1;<br>
>> >> >> > }<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > --<br>
>> >> >> > View this message in context:<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > <a href="http://vtk.1045678.n5.nabble.com/vtkStructuredPointsWriter-writes-a-blank-file-tp5727536.html" target="_blank">http://vtk.1045678.n5.nabble.com/vtkStructuredPointsWriter-writes-a-blank-file-tp5727536.html</a><br>
>> >> >> > Sent from the VTK - Users mailing list archive at Nabble.com.<br>
>> >> >> > _______________________________________________<br>
>> >> >> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>> >> >> ><br>
>> >> >> > Visit other Kitware open-source projects at<br>
>> >> >> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >> >> ><br>
>> >> >> > Please keep messages on-topic and check the VTK FAQ at:<br>
>> >> >> > <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">http://www.vtk.org/Wiki/VTK_FAQ</a><br>
>> >> >> ><br>
>> >> >> > Follow this link to subscribe/unsubscribe:<br>
>> >> >> > <a href="http://public.kitware.com/mailman/listinfo/vtkusers" target="_blank">http://public.kitware.com/mailman/listinfo/vtkusers</a><br>
>> >> >><br>
>> >> >><br>
>> >> >><br>
>> >> >> --<br>
>> >> >> Unpaid intern in BillsBasement at noware dot com<br>
>> >> ><br>
>> >> ><br>
>> >><br>
>> >><br>
>> >><br>
>> >> --<br>
>> >> Unpaid intern in BillsBasement at noware dot com<br>
>> ><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Unpaid intern in BillsBasement at noware dot com<br>
><br>
><br>
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Unpaid intern in BillsBasement at noware dot com<br>
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