Skip to content

Commit ff92cc6

Browse files
labdalalabdala
authored
ENH: Add example derivativeImage (#380)
* ENH: Add example derivativeImage * ENH: Add baseline check to verify against previous data
1 parent 5d3a1ab commit ff92cc6

File tree

10 files changed

+282
-0
lines changed

10 files changed

+282
-0
lines changed

‎src/Filtering/ImageFeature/CMakeLists.txt

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -33,3 +33,6 @@ add_example(FindZeroCrossingsInSignedImage)
3333
#===================================
3434

3535
add_example(AdditiveGaussianNoiseImageFilter)
36+
37+
add_example(DerivativeImage)
38+
compare_to_baseline(EXAMPLE_NAME DerivativeImage BASELINE_PREFIX Output)

‎src/Filtering/ImageFeature/DerivativeImage/BrainProtonDensitySlice.png.sha512

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
86cbe2a809e90d72fb464868449477fe6d83809ddd0493cfca92033d7d3dd4bc3e0b831b17735926ed990735234a4eb8034aeaca70a3f5ba18fffe8f3c8e7eaa

‎src/Filtering/ImageFeature/DerivativeImage/CMakeLists.txt

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
cmake_minimum_required(VERSION 3.16.3)
2+
3+
project( DerivativeImage )
4+
5+
find_package( ITK REQUIRED )
6+
include( ${ITK_USE_FILE} )
7+
8+
add_executable( DerivativeImage Code.cxx )
9+
target_link_libraries( DerivativeImage ${ITK_LIBRARIES} )
10+
11+
install( TARGETS DerivativeImage
12+
DESTINATION bin/ITKSphinxExamples/Filtering/ImageFeature
13+
COMPONENT Runtime
14+
)
15+
16+
install( FILES Code.cxx CMakeLists.txt
17+
DESTINATION share/ITKSphinxExamples/Code/Filtering/ImageFeature/DerivativeImage
18+
COMPONENT Code
19+
)
20+
21+
enable_testing()
22+
add_test( NAME DerivativeImageTest
23+
COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/DerivativeImage
24+
${CMAKE_CURRENT_BINARY_DIR}/BrainProtonDensitySlice.png
25+
Output.mha Output_normalized.mha 1 1
26+
)
27+
28+
#if( ITK_WRAP_PYTHON )
29+
# add_test( NAME DerivativeImageTestPython
30+
# COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
31+
# ${CMAKE_CURRENT_BINARY_DIR}/BrainProtonDensitySlice.png
32+
# OutputPython.png
33+
# )
34+
#endif()

‎src/Filtering/ImageFeature/DerivativeImage/Code.cxx

Lines changed: 190 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,190 @@
1+
/*=========================================================================
2+
*
3+
* Copyright NumFOCUS
4+
*
5+
* Licensed under the Apache License, Version 2.0 (the "License");
6+
* you may not use this file except in compliance with the License.
7+
* You may obtain a copy of the License at
8+
*
9+
* https://www.apache.org/licenses/LICENSE-2.0.txt
10+
*
11+
* Unless required by applicable law or agreed to in writing, software
12+
* distributed under the License is distributed on an "AS IS" BASIS,
13+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14+
* See the License for the specific language governing permissions and
15+
* limitations under the License.
16+
*
17+
*=========================================================================*/
18+
19+
// Software Guide : BeginCommandLineArgs
20+
// INPUTS: {BrainProtonDensitySlice.png}
21+
// ARGUMENTS: {DerivativeImageFilterFloatOutput.mhd}
22+
// OUTPUTS: {DerivativeImageFilterOutput.png}
23+
// ARGUMENTS: 1 0
24+
// Software Guide : EndCommandLineArgs
25+
26+
// Software Guide : BeginLatex
27+
//
28+
// The \doxygen{DerivativeImageFilter} is used for computing the partial
29+
// derivative of an image, the derivative of an image along a particular
30+
// axial direction.
31+
//
32+
// \index{itk::DerivativeImageFilter}
33+
//
34+
// Software Guide : EndLatex
35+
36+
37+
#include "itkImage.h"
38+
#include "itkImageFileReader.h"
39+
#include "itkImageFileWriter.h"
40+
#include "itkRescaleIntensityImageFilter.h"
41+
42+
// Software Guide : BeginLatex
43+
//
44+
// The header file corresponding to this filter should be included first.
45+
//
46+
// \index{itk::DerivativeImageFilter!header}
47+
//
48+
// Software Guide : EndLatex
49+
50+
51+
// Software Guide : BeginCodeSnippet
52+
#include "itkDerivativeImageFilter.h"
53+
// Software Guide : EndCodeSnippet
54+
55+
56+
int
57+
main(int argc, char * argv[])
58+
{
59+
if (argc < 6)
60+
{
61+
std::cerr << "Usage: " << std::endl;
62+
std::cerr << argv[0] << " inputImageFile outputImageFile normalizedOutputImageFile ";
63+
std::cerr << " derivativeOrder direction" << std::endl;
64+
return EXIT_FAILURE;
65+
}
66+
67+
68+
// Software Guide : BeginLatex
69+
//
70+
// Next, the pixel types for the input and output images must be defined
71+
// and, with them, the image types can be instantiated. Note that it is
72+
// important to select a signed type for the image, since the values of the
73+
// derivatives will be positive as well as negative.
74+
//
75+
// Software Guide : EndLatex
76+
77+
// Software Guide : BeginCodeSnippet
78+
using InputPixelType = float;
79+
using OutputPixelType = float;
80+
81+
constexpr unsigned int Dimension = 2;
82+
83+
using InputImageType = itk::Image<InputPixelType, Dimension>;
84+
using OutputImageType = itk::Image<OutputPixelType, Dimension>;
85+
// Software Guide : EndCodeSnippet
86+
87+
88+
using ReaderType = itk::ImageFileReader<InputImageType>;
89+
using WriterType = itk::ImageFileWriter<OutputImageType>;
90+
91+
auto reader = ReaderType::New();
92+
auto writer = WriterType::New();
93+
94+
reader->SetFileName(argv[1]);
95+
writer->SetFileName(argv[2]);
96+
97+
// Software Guide : BeginLatex
98+
//
99+
// Using the image types, it is now possible to define the filter type
100+
// and create the filter object.
101+
//
102+
// \index{itk::DerivativeImageFilter!instantiation}
103+
// \index{itk::DerivativeImageFilter!New()}
104+
// \index{itk::DerivativeImageFilter!Pointer}
105+
//
106+
// Software Guide : EndLatex
107+
108+
// Software Guide : BeginCodeSnippet
109+
using FilterType = itk::DerivativeImageFilter<InputImageType, OutputImageType>;
110+
111+
auto filter = FilterType::New();
112+
// Software Guide : EndCodeSnippet
113+
114+
115+
// Software Guide : BeginLatex
116+
//
117+
// The order of the derivative is selected with the \code{SetOrder()}
118+
// method. The direction along which the derivative will be computed is
119+
// selected with the \code{SetDirection()} method.
120+
//
121+
// \index{itk::DerivativeImageFilter!SetOrder()}
122+
// \index{itk::DerivativeImageFilter!SetDirection()}
123+
//
124+
// Software Guide : EndLatex
125+
126+
// Software Guide : BeginCodeSnippet
127+
filter->SetOrder(std::stoi(argv[4]));
128+
filter->SetDirection(std::stoi(argv[5]));
129+
// Software Guide : EndCodeSnippet
130+
131+
132+
// Software Guide : BeginLatex
133+
//
134+
// The input to the filter can be taken from any other filter, for example
135+
// a reader. The output can be passed down the pipeline to other filters,
136+
// for example, a writer. An \code{Update()} call on any downstream filter
137+
// will trigger the execution of the derivative filter.
138+
//
139+
// \index{itk::DerivativeImageFilter!SetInput()}
140+
// \index{itk::DerivativeImageFilter!GetOutput()}
141+
//
142+
// Software Guide : EndLatex
143+
144+
145+
// Software Guide : BeginCodeSnippet
146+
filter->SetInput(reader->GetOutput());
147+
writer->SetInput(filter->GetOutput());
148+
writer->Update();
149+
// Software Guide : EndCodeSnippet
150+
151+
152+
// Software Guide : BeginLatex
153+
//
154+
// \begin{figure}
155+
// \center
156+
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
157+
// \includegraphics[width=0.44\textwidth]{DerivativeImageFilterOutput}
158+
// \itkcaption[Effect of the Derivative filter.]{Effect of the Derivative
159+
// filter on a slice from a MRI proton density brain image.}
160+
// \label{fig:DerivativeImageFilterOutput}
161+
// \end{figure}
162+
//
163+
// Figure \ref{fig:DerivativeImageFilterOutput} illustrates the effect of
164+
// the DerivativeImageFilter on a slice of MRI brain image. The derivative
165+
// is taken along the $x$ direction. The sensitivity to noise in the image
166+
// is evident from this result.
167+
//
168+
// Software Guide : EndLatex
169+
170+
171+
using WriteImageType = itk::Image<unsigned char, Dimension>;
172+
173+
using NormalizeFilterType = itk::RescaleIntensityImageFilter<OutputImageType, WriteImageType>;
174+
175+
using NormalizedWriterType = itk::ImageFileWriter<WriteImageType>;
176+
177+
auto normalizer = NormalizeFilterType::New();
178+
auto normalizedWriter = NormalizedWriterType::New();
179+
180+
normalizer->SetInput(filter->GetOutput());
181+
normalizedWriter->SetInput(normalizer->GetOutput());
182+
183+
normalizer->SetOutputMinimum(0);
184+
normalizer->SetOutputMaximum(255);
185+
186+
normalizedWriter->SetFileName(argv[3]);
187+
normalizedWriter->Update();
188+
189+
return EXIT_SUCCESS;
190+
}

‎src/Filtering/ImageFeature/DerivativeImage/Documentation.rst

Lines changed: 49 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,49 @@
1+
:name: DerivativeImage
2+
3+
Compute Derivative
4+
===================
5+
6+
.. index::
7+
single: DerivativeImageFilter
8+
9+
Synopsis
10+
--------
11+
12+
This filter computes a n-th Derivative of a scalar-valued image in a specified direction.
13+
14+
15+
Results
16+
-------
17+
18+
.. figure:: BrainProtonDensitySlice.png
19+
:scale: 50%
20+
:alt: Input image
21+
22+
Input image
23+
24+
.. figure:: Output.png
25+
:scale: 50%
26+
:alt: Output image
27+
28+
Output image
29+
30+
31+
.. figure:: Output_normalized.png
32+
:scale: 50%
33+
:alt: Output normalized image
34+
35+
Output normalized image
36+
37+
Code
38+
----
39+
40+
C++
41+
...
42+
43+
.. literalinclude:: Code.cxx
44+
:lines: 18-
45+
46+
Classes demonstrated
47+
--------------------
48+
49+
.. breathelink:: itk::DerivativeImageFilter

‎src/Filtering/ImageFeature/DerivativeImage/Output.mha.sha512

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
1bba1d72a84bf2d171c85834a9e9e7e485b26ef60a05fb0fe93c1103ff920071fc5ccc14b7c27348abf5dcd537825838bdefd7a8b27336c8115677ceb80af227

‎src/Filtering/ImageFeature/DerivativeImage/Output.png.sha512

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
29e67a22a4218b780ca75af045544178e193aefce7ceff7923fcd858068918efab6d41c37ea3020fe3747abb35172a67be33ff85c9595ff3a19fffdc37d6a2d1

‎src/Filtering/ImageFeature/DerivativeImage/Output_normalized.mha.sha512

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
346c92583d339826d3ebf9cede566d1d215e50b3cd431fe63e693e97f03f0b9f48c2f461a4dd73218f0e5852f5a12e9d90e8360c522fb8e5752aadc86e6d3362

‎src/Filtering/ImageFeature/DerivativeImage/Output_normalized.png.sha512

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
1cf70adf30331a9c1a084e64f13dc7c263d212ebcad0880048413af3490ee81f5e1f77caf5cd98b52a0181a66ad2ced1c02392dd8c8e2d46f615e93d205df6c4

‎src/Filtering/ImageFeature/index.rst

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@ ImageFeature
1010
BilateralFilterAnImage/Documentation.rst
1111
ComputeLaplacian/Documentation.rst
1212
DetectEdgesWithCannyEdgeDetectionFilter/Documentation.rst
13+
DerivativeImage/Documentation.rst
1314
ExtractContoursFromImage/Documentation.rst
1415
FindZeroCrossingsInSignedImage/Documentation.rst
1516
LaplacianRecursiveGaussianImageFilter/Documentation.rst

0 commit comments

Comments
 (0)