[vtkusers] vtkImageReader much faster than vtkImageReader2??

[Marco Sambin]

Hi David,

Thanks for your feedback, tomorrow I will do the tests that you suggested,
and will report back.
Best regards,

Marco Sambin

> Il 12/giu/2014 20:06 "David Gobbi" <david.gobbi at gmail.com> ha scritto:
>
>> I made a major typo in my last email.  I meant to say "try
>> repeating the tests with SetDataByteOrderToLittleEndian()"
>>
>> On Thu, Jun 12, 2014 at 11:55 AM, David Gobbi <david.gobbi at gmail.com>
wrote:
>> > Hi Marco,
>> >
>> > Try repeating the tests with SetDataByteOrderToBigEndian().  If the
>> > byte reordering is really the most CPU-intensive part of the read, as
>> > I suspect, then this should reduce both times but perhaps one more
>> > than the other.
>> >
>> > Other than that, I don't have any guesses.  In vtkImageReader.cxx, I
>> > notice that it reads into a buffer where it performs the byte swap,
>> > whereas vtkImageReader2.cxx doesn't use a buffer.  If this makes any
>> > difference at all, though, it should be in favor of vtkImageReader2
>> > (unless CPU cache misses are involved).
>> >
>> > The only way to be sure is to run the tests in a C++ profiler, on OS X
>> > I use "Instruments" but I've never done profiling on Windows.  On a
>> > related note, one thing that I did find via profiling is that fread()
>> > was 4x faster than doing read() on a C++ fstream.  But this was only
>> > meaningful when reading from disk cache.  When the reads were hitting
>> > the actual disk, the difference was negligible.
>> >
>> >   David
>> >
>> >
>> >
>> > On Thu, Jun 12, 2014 at 11:37 AM, Marco Sambin <m.sambin at gmail.com>
wrote:
>> >> Hi David,
>> >>
>> >> first of all, thank you for your reply.
>> >> No, the difference is not related to disk caching issues. Here are
two test
>> >> methods that I've written:
>> >>
>> >>
>> >> public static void testVTKImageReader()
>> >>   {
>> >>     long startTime = System.currentTimeMillis();
>> >>
>> >>     vtkImageReader testReaderVTK =  new vtkImageReader();
>> >>     testReaderVTK.FileLowerLeftOn();
>> >>     testReaderVTK.SetFileDimensionality(3);
>> >>     testReaderVTK.SetFileName("C:\\Test\\SeriesVolume.raw");
>> >>
>> >>     testReaderVTK.SetDataExtent(0, 511,
>> >>                           0, 511,
>> >>                           0, 520);
>> >>     testReaderVTK.SetDataSpacing(1.0, 1.0, 1.0);
>> >>     testReaderVTK.SetDataOrigin(0.0, 0.0, 0.0);
>> >>     testReaderVTK.SetDataScalarTypeToUnsignedShort();
>> >>     testReaderVTK.SetDataByteOrderToBigEndian();
>> >>     testReaderVTK.UpdateWholeExtent();
>> >>
>> >>     long endTime = System.currentTimeMillis();
>> >>
>> >>     System.out.println("Volume read by vtkImageReader. Total time
millis = "
>> >> + (endTime - startTime));
>> >>   }
>> >>
>> >>   public static void testVTKImageReader2()
>> >>   {
>> >>     long startTime = System.currentTimeMillis();
>> >>
>> >>     vtkImageReader2 testReaderVTK =  new vtkImageReader2();
>> >>     testReaderVTK.FileLowerLeftOn();
>> >>     testReaderVTK.SetFileDimensionality(3);
>> >>     testReaderVTK.SetFileName("C:\\Test\\SeriesVolume.raw");
>> >>
>> >>     testReaderVTK.SetDataExtent(0, 511,
>> >>                           0, 511,
>> >>                           0, 520);
>> >>     testReaderVTK.SetDataSpacing(1.0, 1.0, 1.0);
>> >>     testReaderVTK.SetDataOrigin(0.0, 0.0, 0.0);
>> >>     testReaderVTK.SetDataScalarTypeToUnsignedShort();
>> >>     testReaderVTK.SetDataByteOrderToBigEndian();
>> >>     testReaderVTK.UpdateWholeExtent();
>> >>
>> >>     long endTime = System.currentTimeMillis();
>> >>
>> >>     System.out.println("Volume read by vtkImageReader2. Total time
millis =
>> >> " + (endTime - startTime));
>> >>   }
>> >>
>> >> After doing a couple of "cold starts" in order to "warm up" disk
caches, on
>> >> my test PC method "testVTKImageReader()" executes in around 2
seconds, while
>> >> method "testVTKImageReader2()" executes in around 10 seconds.
>> >> I've tried executing testVTKImageReader() before and
testVTKImageReader2()
>> >> after or viceversa during the same execution session, but the result
doesn't
>> >> change: testVTKImageReader() is always around 5 times faster than
>> >> testVTKImageReader2().
>> >>
>> >> Can you guess why?
>> >> Thanks and best regards,
>> >>
>> >> Marco Sambin
>> >>
>> >>
>> >>
>> >> On Thu, Jun 12, 2014 at 7:12 PM, David Gobbi <david.gobbi at gmail.com>
wrote:
>> >>>
>> >>> Hi Marco,
>> >>>
>> >>> When used the way they are in your example code, vtkImageReader and
>> >>> vtkImageReader2 should be exactly the same speed.
>> >>>
>> >>> Can you explain your testing methodology in more detail?  I suspect
that
>> >>> when you tested vtkImageReader2, it was reading from disk, and when
>> >>> testing vtkImageReader, it was reading from disk cache.  The only
part
>> >>> of the "read" operation that actually requires any CPU time is the
byte
>> >>> swapping, but that should be identical for the two readers.
>> >>>
>> >>>  - David
>> >>>
>> >>>
>> >>> On Thu, Jun 12, 2014 at 11:00 AM, Marco Sambin <m.sambin at gmail.com>
wrote:
>> >>> > Hi all.
>> >>> > I am reading a volume made up of a set of "slices" stored in a
single
>> >>> > large
>> >>> > raw file, containing just the raw pixels of each slice (unsigned
short
>> >>> > values), one slice after the other. I know in advance image size,
>> >>> > position,
>> >>> > orientation and spacing information related to each slice.
>> >>> > I used to read my input raw volume through the vtkImageReader2
class, as
>> >>> > documentation of vtkImageReader states:
>> >>> >
>> >>> > "vtkImageReader provides methods needed to read a region from a
file. It
>> >>> > supports both transforms and masks on the input data, but as a
result is
>> >>> > more complicated and slower than its parent class vtkImageReader2."
>> >>> >
>> >>> > so I always assumed vtkImageReader2 to be faster than
vtkImageReader to
>> >>> > read
>> >>> > a simple volume made up of a set of raw slices.
>> >>> > This until today, when I tried replacing my instance of
vtkImageReader2
>> >>> > with
>> >>> > an instance of vtkImageReader. Guess what? My volume reading code
now
>> >>> > executes around 10 times faster!
>> >>> >
>> >>> > Is this expected? Can you guess what may be the reason for such a
>> >>> > significant difference in performance between vtkImageReader2 and
>> >>> > vtkImageReader, the latter being much faster in my scenario
(despite
>> >>> > what
>> >>> > the documentation states)?
>> >>> >
>> >>> > For completeness, I am using VTK 6.1 64-bit from Java 7 64-bit,
under
>> >>> > Windows 7 Professional 64-bit. Here is a code fragment showing how
I
>> >>> > configure my reader:
>> >>> >
>> >>> > [...]
>> >>> > imageReaderVTK =  new vtkImageReader(); // much slower if I use
>> >>> > "vtkImageReader2" here
>> >>> > imageReaderVTK.FileLowerLeftOn();
>> >>> > imageReaderVTK.SetFileDimensionality(3);
>> >>> > imageReaderVTK.SetFileName(curRawVolFile.getAbsolutePath());
>> >>> > imageReaderVTK.SetDataExtent(0, sliceCols - 1,
>> >>> >                       0, sliceRows - 1,
>> >>> >                       0, numOfUsedImages - 1);
>> >>> > imageReaderVTK.SetDataSpacing(xSpacing, ySpacing, zSpacing);
>> >>> > imageReaderVTK.SetDataOrigin(0.0, 0.0, 0.0);
>> >>> > imageReaderVTK.SetDataScalarTypeToUnsignedShort();
>> >>> > imageReaderVTK.SetDataByteOrderToBigEndian();
>> >>> > imageReaderVTK.UpdateWholeExtent();
>> >>> > [...]
>> >>> >
>> >>> > My typical input raw volume is made up of around 500 slices, each
one
>> >>> > 512x512 pixels large.
>> >>> >
>> >>> > Thanks in advance for your feedback.
>> >>> > Best regards,
>> >>> >
>> >>> > Marco Sambin
>> >>
>> >>
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