[Insight-users] Image index limits
Luis Ibanez
luis.ibanez at kitware.com
Mon Dec 21 19:07:41 EST 2009
Hi Alex,
Did you changed to "float" the pixel type of
ImageReadRegionOfInterestWrite.cxx ?
by default the pixel type is "signed short".
and your image is of pixel type "float".
ITK will perform silent C-Style casting
at the moment of reading the image.
Please let us know,
Thanks,
Luis
----------------------------------------------
On Mon, Dec 14, 2009 at 1:20 PM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
> Hi Luis,
>
> I followed the procedure 1) through 8) that you suggested.
> All four tests have successfully passed and the results are below.
> According to the results, the parameter 70,000L provides the image size
> "Trying to allocate an image of size 9346 Mb " which is what I actually
> need.
> From these tests it looks like it should work.
>
> However, I just created and image using a Matlab code below.
>
> ***** Star Matlab code ******
>
> % Create single square 1340x1300x720
> clc;
> clear all;
> close all;
>
>
> matrix = zeros(1340, 1300, 720);
> matrix(600:809, 600:809, :) = 1000;
>
> % imshow(matrix);
>
> fid = fopen('Bar_3Dsquare_I1000_1340x1300x720.bin', 'wb');
> fwrite(fid, matrix, 'float');
> status = fclose(fid);
>
> ******* Stop Matlab code ************
>
> This code exactly creates an 4.7 GB image with white square extruded along
> the Z-derection.
> Now I use the ITK program ImageReadRegionOfInterestWrite to sequentially
> extract series of 100 slices as below.
>
> dzyubak at helium: /Square$ ./ImageReadRegionOfInterestWrite
> Bar_3Dsquare_I1000_1340x1300x720_float.hdr
> Bar_3Dsquare_I1000_1340x1300x720_float_s1_s100.hdr 0 0 0 1340 1300 100
>
> and
>
> dzyubak at helium: /Square$ ./ImageReadRegionOfInterestWrite
> Bar_3Dsquare_I1000_1340x1300x720_float.hdr
> Bar_3Dsquare_I1000_1340x1300x720_float_s100_s200.hdr 0 0 100 1340 1300 100
>
> I checked the Bar_3Dsquare_I1000_1340x1300x720_float.hdr image and it is OK,
> the square goes all the way through.
> The first set is also OK and the "white square" shows up but the second set
> is empty. Any ideas what could cause this problem?
>
> Thanks,
>
> Alex
>
>
>
> ******** Start *******
>
>
> root at helium: /BUILD# ctest -R LargeImageWrite -V
>
> Test command: /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/bin/itkIOTests
> itkLargeImageWriteReadTest
> /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/Testing/Temporary/LargeImage01.mhd
> 30000L
> Test timeout computed to be: 1500
> Trying to allocate an image of size 1716 Mb
> Initializing pixel values
> Trying to write the image to disk
> Trying to read the image back from disk
> Comparing the pixel values.. :
> Probe Tag Starts Stops Time (s)
> Allocate 1 1 3.19481e-05
> Compare 1 1 4.85127
> Initializing 1 1 8.84029
> Read 1 1 2.71803
> Write 1 1 4.17017
>
> Test PASSED !
> -- Process completed
> Passed
> 863/1701 Testing itkLargeImageWriteReadTest2
> Test command: /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/bin/itkIOTests
> itkLargeImageWriteReadTest
> /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/Testing/Temporary/LargeImage02.mhd
> 40000L
> Test timeout computed to be: 1500
> Trying to allocate an image of size 3051 Mb
> Initializing pixel values
> Trying to write the image to disk
> Trying to read the image back from disk
> Comparing the pixel values.. :
> Probe Tag Starts Stops Time (s)
> Allocate 1 1 3.00407e-05
> Compare 1 1 7.89822
> Initializing 1 1 12.6574
> Read 1 1 4.8622
> Write 1 1 12.6875
>
> Test PASSED !
> -- Process completed
> Passed
> 864/1701 Testing itkLargeImageWriteConvertReadT
> Test command: /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/bin/itkIOTests
> itkLargeImageWriteConvertReadTest
> /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/Testing/Temporary/LargeImageConvert.nrrd
> 50000L
> Test timeout computed to be: 1500
> Initializing pixel values
> Trying to write the image to disk
> Trying to read the image back from disk
> Probe Tag Starts Stops Time (s)
> Allocate 1 1 3.69549e-05
> Initializing 1 1 11.7354
> Read 1 1 15.7987
> Write 1 1 10.5514
>
> Test PASSED !
>
> 865/1701 Testing itkLargeImageWriteReadTest3
> Test command: /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/bin/itkIOTests
> itkLargeImageWriteReadTest
> /mnt/helium/Root_BUILDs/ITK_3_16/BUILD/Testing/Temporary/LargeImage03.mhd
> 70000L
> Test timeout computed to be: 1500
> Trying to allocate an image of size 9346 Mb
> Initializing pixel values
> Trying to write the image to disk
> Trying to read the image back from disk
> Comparing the pixel values.. :
> Probe Tag Starts Stops Time (s)
> Allocate 1 1 3.19481e-05
> Compare 1 1 24.2805
> Initializing 1 1 40.3377
> Read 1 1 14.4607
> Write 1 1 32.6605
>
> Test PASSED !
>
> The following tests passed:
> itkLargeImageWriteReadTest1
> itkLargeImageWriteReadTest2
> itkLargeImageWriteConvertReadTest
> itkLargeImageWriteReadTest3
>
> 100% tests passed, 0 tests failed out of 4
>
>
> ********* End ********
>
>
>
> On Fri, Dec 11, 2009 at 6:50 PM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Oleksandr,
>>
>>
>> The components of the itk::Index are of type "long",
>> while the components of the itk::Size are of type
>> "unsigned long".
>>
>> Therefore, On Linux 64 bits, you can manage
>> images up to the size of your memory.
>>
>> With your small machine of 16 CPUs and
>> only 128 Gb of RAM you should do fine.
>>
>> ... and yes, I'm saying that with envy :-)
>>
>>
>> On Windows 64 bits, on the other hand
>> we are working on fixing a problem with
>> the integer representation used in Windows.
>>
>>
>> Back to your report on Linux:
>>
>> In the directory Insight/Testing/Code/IO
>> we have a test for large memory that
>> will attempt to create, write and read back
>> and image of large size (above 2 Gb).
>> Let's try running it in your computer.
>>
>> Please do the following:
>>
>> 1) go to the binary directory where you
>> built ITK and do
>>
>> make edit_cache
>>
>>
>> 2) Turn BUILD_TESTING ON
>>
>>
>> 3) Go to the Advanced mode,
>> search for
>>
>> ITK_COMPUTER_MEMORY_SIZE
>>
>> and set it to 128
>>
>> (yes, the units are in Gb).
>>
>>
>>
>> 4) Do, "c" for configure
>>
>> 5) Do, "g" to generate
>>
>>
>> 6) make -j32
>>
>> (that shouldn't take long) :-)
>>
>>
>> 7) Run the LargeImage test with
>> the command:
>>
>> ctest -R LargeImageWrite -V
>>
>> and see if they pass.
>>
>> 8) Now you can take it further,
>> by looking at the command
>> that is used to run the tests,
>> The last numeric argument is
>> the number of pixels along each
>> dimension, of the image that is
>> created by the test.
>>
>> You could force this number
>> until the total size of this 2D
>> image is comparable to your 3D
>> image.
>>
>> For example, by 70,000 the
>> image will be of size 1,2 Gb.
>>
>>
>>
>> Please let us know what you find
>> after running these tests.
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> --------------------------------------------------------------
>> On Fri, Dec 11, 2009 at 4:37 PM, Oleksandr Dzyubak <adzyubak at gmail.com>
>> wrote:
>> >
>> > Dear users,
>> >
>> > I tried to process the 1340x1300x720 pixel image and after the slice
>> > #104 I
>> > am getting all zeros.
>> > I checked the original image and it's good. It's full of info.
>> > So I first decided to split that file using the
>> > itkRegionOfInterestImageFilter class.
>> > What I found is that all the chunks after the slice #104 are zeros
>> > thus it's not the image processing filter that causes the problem.
>> >
>> > Here is my question.
>> > Is there any limitation on an image index range?
>> > Or in other words, what is the largest pixel volume that ITK still can
>> > handle?
>> >
>> > Thanks,
>> >
>> > Alex
>> >
>> > PS.
>> > I am using 64 bit Debian Linux.
>> > 16 CPUs and 128 GB.
>> >
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>> >
>> >
>
>
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