[Insight-users] Re: compare speed of dilate and erode in itk, vtk and matlab
Luis Ibanez
luis.ibanez@kitware.com
Thu, 01 May 2003 11:33:41 -0400
Hi Chen,
The address of the insight users list was misspelled in
your message. (pulbic instead of public). I'm forwarding
your original message to the list.
Regards,
Luis
---------------------------------------------------------
Chen Fu wrote:
> Hi Lius,
> Yes, i build ITK and my demo in both "Release" option
> and "Debug" option in vc6, but not directly select in
> CMake.
> To my understand, they are the same. BTW, vc6 report a
> internal error(should call MS support according to the
> error info) when compile release option on
> itkDanielssonDistanceMapImageFilter.txx Line 286, i
> have to seperate it into two lines to get pass, but in
> debug option it is not a problem.
> OutputImageType::PixelType p = static_cast<typename
> OutputImageType::PixelType>(sqrt( distance ));
> dt.Set( p );
> I don't know the reason, any idea?
>
> You are right. The "release" is much quicker than
> "debug" option. But compare to matlab, it is still
> slower.
>
> My code list below, it takes itk release option 56
> seconds to finish, debug option takes 608 seconds,
> while vtk(written in tcl script) cost 20 seconds,
> matlab code cost only 1.6 seconds.
>
> I carefully exam the code and at last find out the
> speed of matlab is benefit from computing on really
> blackwhite image format which means 8 pixels in one
> byte. If i replace "BW = im2bw(Ic, graythresh(Ic));"
> with "BW = Ic", matlab will compute in a gray image
> mode, that will take 19 seconds to finished.
>
>>From these tests, i think the morphology operators in
> itk deserve more efforts to enhance their performance.
> Maybe the pure iterator system is expensive for visit
> every pixel. But i am not familiar enough with source
> code yet, so can not give any really constructive
> suggestion, sorry. These tests are just my exercises
> to use itk and vtk.
>
> matlab code:
> ========================================
> t0 = clock;
> I = imread('d:\nova\pearbig.tif');
> Ic = imcomplement(I);
> BW = im2bw(Ic, graythresh(Ic));
> se = strel('disk', 6);
> BWc = imclose(BW, se);
> BWco = imopen(BWc, se);
> mask = BW & BWco;
> etime(clock, t0)
> =======================================
>
> my itk code:
> =======================================
> // itkTester2.cpp : Defines the entry point for the
> console application.
> //
>
> #include "stdafx.h"
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkBinaryThresholdImageFilter.h"
> #include <itkBinaryDilateImageFilter.h>
> #include <itkBinaryErodeImageFilter.h>
> #include <itkBinaryBallStructuringElement.h>
> #include <time.h>
>
> void itkBinaryThresholdImageFilterTest()
> {
>
> // Use a random image source as input
> typedef unsigned char PixelType;
> typedef itk::Image< PixelType, 2 > ImageType;
> typedef itk::ImageFileReader< ImageType >
> ReaderType;
> ReaderType::Pointer source = ReaderType::New();
> source->SetFileName("d:\\pearbig.png");
>
> // Declare the type for the binary threshold
> binaryThreshold
> typedef itk::BinaryThresholdImageFilter< ImageType,
> ImageType > FilterType;
>
>
> // Create a binaryThreshold
>
> FilterType::Pointer binaryThreshold =
> FilterType::New();
>
> // Setup ivars
> PixelType lower = 180;
> PixelType upper = 255;
> binaryThreshold->SetUpperThreshold( upper );
> binaryThreshold->SetLowerThreshold( lower );
>
> PixelType inside = 0;
> PixelType outside = 255;
> binaryThreshold->SetInsideValue( inside );
> binaryThreshold->SetOutsideValue( outside );
>
> // Connect the input images
> binaryThreshold->SetInput( source->GetOutput() );
>
> // Declare the type for the structuring element
> typedef itk::BinaryBallStructuringElement<unsigned
> char, 2>
> KernelType;
> // Create the structuring element
> KernelType ball;
> KernelType::SizeType ballSize;
> ballSize[0] = 5;
> ballSize[1] = 5;
> ball.SetRadius(ballSize);
> ball.CreateStructuringElement();
>
> // Declare the type for the morphology Filter
> typedef itk::BinaryDilateImageFilter<ImageType,
> ImageType, KernelType>
> BinaryDilateType;
> typedef itk::BinaryErodeImageFilter<ImageType,
> ImageType, KernelType>
> BinaryErodeType;
>
> //Close = Erode then Dilate
> BinaryErodeType::Pointer binaryErode =
> BinaryErodeType::New();
> binaryErode->SetInput(binaryThreshold->GetOutput() );
> binaryErode->SetKernel( ball );
> binaryErode->SetErodeValue( 255 );
>
> BinaryDilateType::Pointer binaryDilate =
> BinaryDilateType::New();
> binaryDilate->SetInput(binaryErode->GetOutput() );
> binaryDilate->SetKernel( ball );
> binaryDilate->SetDilateValue( 255 );
>
> //Open = Dilate then Erode
> BinaryDilateType::Pointer binaryDilate2 =
> BinaryDilateType::New();
> binaryDilate2->SetInput(binaryDilate->GetOutput() );
> binaryDilate2->SetKernel( ball );
> binaryDilate2->SetDilateValue( 255 );
>
> BinaryErodeType::Pointer binaryErode2 =
> BinaryErodeType::New();
> binaryErode2->SetInput(binaryDilate2->GetOutput() );
> binaryErode2->SetKernel( ball );
> binaryErode2->SetErodeValue( 255 );
>
> typedef itk::ImageFileWriter< ImageType >
> WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName("d:\\pearlite2.png");
> writer->SetInput (binaryErode2->GetOutput() );
> writer->Update();
> }
>
>
> void main(int argc, char* argv[])
> {
> clock_t a = clock();
> itkBinaryThresholdImageFilterTest();
> clock_t b = clock();
> printf("time %lf\n", 1.0*(b-a)/CLOCKS_PER_SEC);
> }
>
> ======================================
>
> vtk tcl script
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> package require vtk
>
> vtkPNGReader reader1
> reader1 SetFileName d:/pearbig.png
>
> vtkImageCast cast
> cast SetOutputScalarTypeToFloat
> cast SetInput [reader1 GetOutput]
>
> vtkImageThreshold thresh
> thresh SetInput [cast GetOutput]
> thresh ThresholdByUpper 180
> thresh SetInValue 0.0000
> thresh SetOutValue 255.0000
> thresh ReleaseDataFlagOff
>
> vtkImageOpenClose3D my_close
> my_close SetInput [thresh GetOutput]
> my_close SetOpenValue 0.0000
> my_close SetCloseValue 255.0000
> my_close SetKernelSize 11 11 1
> my_close ReleaseDataFlagOff
>
> vtkImageOpenClose3D my_open
> my_open SetInput [my_close GetOutput]
> my_open SetOpenValue 255.0000
> my_open SetCloseValue 0.0000
> my_open SetKernelSize 11 11 1
> my_open ReleaseDataFlagOff
>
> vtkImageToImageStencil imageToStencil
> imageToStencil SetInput [my_open GetOutput]
> imageToStencil ThresholdBetween 0 127
> # silly stuff to increase coverage
> #imageToStencil SetUpperThreshold [imageToStencil
> GetUpperThreshold]
> #imageToStencil SetLowerThreshold [imageToStencil
> GetLowerThreshold]
>
> vtkImageStencil stencil
> stencil SetInput [reader1 GetOutput]
> stencil SetBackgroundValue 120
> stencil ReverseStencilOn
> stencil SetStencil [imageToStencil GetOutput]
>
> vtkPNGWriter writer
> writer SetInput [ stencil GetOutput ]
> writer SetFileName d:/pearbig2.png
> writer Write
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> --- Luis Ibanez <luis.ibanez@kitware.com> 的正文：>
>
>>Hi Chen,
>>
>>The ITK implementation of morphology operations
>>also decompose the processing of the boundary
>>regions. This is done by the SmartNeighborhood
>>iterator.
>>
>>So, the difference in preformance is not due to
>>boundary processing.
>>
>>
>>
>>About your speed comparison:
>>
>>1) In what platform are you compiling ITK ?
>>
>>2) Did you enable the "Release" option in
>> CMake when configuring ITK ?
>>
>> Enabling "Release" will add the flags for
>> code optimization, given that most of ITK
>> is templated code, there is a dramatic speed
>> difference between code compiled for debug
>> and code compiled for release.
>>
>>
>>
>>Regards,
>>
>>
>> Luis
>>
>>
>>-----------------------
>>
>>Chen Fu wrote:
>>
>>>Hi!
>>>I recently compare the morphology operation in
>>
>>vtk,
>>
>>>itk and matlab. To my surprise, vtk and itk is
>>
>>much
>>
>>>slower than matlab.
>>>I believe the problem is the boundary processing.
>>
>>In
>>
>>>vtk and itk code, every pixel must take 8 compares
>>
>>to
>>
>>>confirm whether it is inside the image boundary.
>>
>>But
>>
>>>in matlab, the boundary is preprocessed by
>>
>>extending
>>
>>>the size of image, so get rid of such compares. I
>>
>>will
>>
>>>try to do some modify of itk code to enhance its
>>>performance, but i am not very clearly how to do
>>>extend the image in itk's pipeline architecture.
>>>Maybe somebody can give me some hints?
>>>
>>>
>>>=====
>>>Remote Scensing Satellite Ground Station
>>>Chinese Academy of Science
>>>
>>
>>
>
>
> =====
> Remote Scensing Satellite Ground Station
> Chinese Academy of Science
>
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