FragmentationIndex

Computes an index of relative convexity or concavity of the surface of objects from a binary image.

Access to parameter description

For an introduction:

section Image Analysis
section Morphometry

This algorithm computes an indicator of connectivity. It calculates an index of relative convexity or concavity of the surface.
This index can be interpreted in mater of connectivity taken into account that concavity indicates connectivity, and that convexity indicates isolated disconnected structures.

The fragmentation index is calculated by comparing:

Area $Ar$ and perimeter $P$ for a 2D image
Volume $V$ and surface $S$ for a 3D image

The fragmentation $FI$ is computed on a binarized image before and after an image dilation.

In 2D, it defined as: $$ FI = \frac{P_d-P}{Ar_d-Ar} $$
In 3D, it defined as: $$ FI = \frac{S_d-S}{V_d-V} $$

where

$P$ and $Ar$ are respectively the object perimeter and area.
$S$ and $V$ are respectively the object surface and volume.
The subscript $d$ means 'after dilation'.

Dilation of an highly connected area narrows spaces and then produces a smaller perimeter. On the other hand, it expands the perimeter of open ends or nodes. Consequently, a low fragmentation index signifies better connected area while a high fragmentation index means a more disconnected structure. In some cases, a high ratio of enclosed cavities and concave surfaces can result in a negative fragmentation index.

See also

Function Syntax

This function returns outputMeasurement.

// Function prototype
FragmentationMsr::Ptr
fragmentationIndex( std::shared_ptr< iolink::ImageView > inputBinaryImage,
                    int32_t kernelRadius,
                    FragmentationMsr::Ptr outputMeasurement = nullptr );

This function returns outputMeasurement.

// Function prototype.
fragmentation_index(input_binary_image: idt.ImageType,
                    kernel_radius: int = 3,
                    output_measurement: Union[Any, None] = None) -> FragmentationMsr

This function returns outputMeasurement.

// Function prototype.
public static FragmentationMsr
FragmentationIndex( IOLink.ImageView inputBinaryImage,
                    Int32 kernelRadius = 3,
                    FragmentationMsr outputMeasurement = null );

Class Syntax

// Command constructor.
FragmentationIndex();

/// Gets the inputBinaryImage parameter.
/// The binary input image.
std::shared_ptr< iolink::ImageView > inputBinaryImage() const;
/// Sets the inputBinaryImage parameter.
/// The binary input image.
void setInputBinaryImage( std::shared_ptr< iolink::ImageView > inputBinaryImage );

/// Gets the kernelRadius parameter.
/// The number of iterations of the dilation (that is, the half side size of the cubic structuring element in voxels). A cube structuring element always has an odd side length (3x3x3, 5x5x5, etc.) which is defined by twice the kernel radius + 1.
int32_t kernelRadius() const;
/// Sets the kernelRadius parameter.
/// The number of iterations of the dilation (that is, the half side size of the cubic structuring element in voxels). A cube structuring element always has an odd side length (3x3x3, 5x5x5, etc.) which is defined by twice the kernel radius + 1.
void setKernelRadius( const int32_t& kernelRadius );

/// Gets the outputMeasurement parameter.
/// The output measurement result.
FragmentationMsr::Ptr outputMeasurement() const;


// Method to launch the command.
void execute();

# Property of the inputBinaryImage parameter.
FragmentationIndex.input_binary_image
# Property of the kernelRadius parameter.
FragmentationIndex.kernel_radius
# Property of the outputMeasurement parameter.
FragmentationIndex.output_measurement

// Method to launch the command.
execute()

// Command constructor.
FragmentationIndex()

// Property of the inputBinaryImage parameter.
FragmentationIndex.inputBinaryImage
// Property of the kernelRadius parameter.
FragmentationIndex.kernelRadius
// Property of the outputMeasurement parameter.
FragmentationIndex.outputMeasurement

// Method to launch the command.
Execute()

Parameters

	Description	Type	Supported Values	Default Value
inputBinaryImage	The binary input image.	Image	Binary	nullptr
kernelRadius	The number of iterations of the dilation (that is, the half side size of the cubic structuring element in voxels). A cube structuring element always has an odd side length (3x3x3, 5x5x5, etc.) which is defined by twice the kernel radius + 1.	Int32	>=1	3
outputMeasurement	The output measurement result.	FragmentationMsr		nullptr

	Description	Type	Supported Values	Default Value
input_binary_image	The binary input image.	image	Binary	None
kernel_radius	The number of iterations of the dilation (that is, the half side size of the cubic structuring element in voxels). A cube structuring element always has an odd side length (3x3x3, 5x5x5, etc.) which is defined by twice the kernel radius + 1.	int32	>=1	3
output_measurement	The output measurement result.	FragmentationMsr		None

	Description	Type	Supported Values	Default Value
inputBinaryImage	The binary input image.	Image	Binary	null
kernelRadius	The number of iterations of the dilation (that is, the half side size of the cubic structuring element in voxels). A cube structuring element always has an odd side length (3x3x3, 5x5x5, etc.) which is defined by twice the kernel radius + 1.	Int32	>=1	3
outputMeasurement	The output measurement result.	FragmentationMsr		null

Object Examples

auto polystyrene_sep = readVipImage( std::string( IMAGEDEVDATA_IMAGES_FOLDER ) + "polystyrene_sep.vip" );

FragmentationIndex fragmentationIndexAlgo;
fragmentationIndexAlgo.setInputBinaryImage( polystyrene_sep );
fragmentationIndexAlgo.setKernelRadius( 3 );
fragmentationIndexAlgo.execute();

std::cout << "index: " << fragmentationIndexAlgo.outputMeasurement()->index( 0 ) ;

polystyrene_sep = imagedev.read_vip_image(imagedev_data.get_image_path("polystyrene_sep.vip"))

fragmentation_index_algo = imagedev.FragmentationIndex()
fragmentation_index_algo.input_binary_image = polystyrene_sep
fragmentation_index_algo.kernel_radius = 3
fragmentation_index_algo.execute()

print("index: ", str(fragmentation_index_algo.output_measurement.index(0)))

ImageView polystyrene_sep = Data.ReadVipImage( @"Data/images/polystyrene_sep.vip" );

FragmentationIndex fragmentationIndexAlgo = new FragmentationIndex
{
    inputBinaryImage = polystyrene_sep,
    kernelRadius = 3
};
fragmentationIndexAlgo.Execute();

Console.WriteLine( "index: " + fragmentationIndexAlgo.outputMeasurement.index( 0 ) );

Function Examples

auto polystyrene_sep = readVipImage( std::string( IMAGEDEVDATA_IMAGES_FOLDER ) + "polystyrene_sep.vip" );

auto result = fragmentationIndex( polystyrene_sep, 3 );

std::cout << "index: " << result->index( 0 ) ;

polystyrene_sep = imagedev.read_vip_image(imagedev_data.get_image_path("polystyrene_sep.vip"))

result = imagedev.fragmentation_index(polystyrene_sep, 3)

print("index: ", str(result.index(0)))

ImageView polystyrene_sep = Data.ReadVipImage( @"Data/images/polystyrene_sep.vip" );

FragmentationMsr result = Processing.FragmentationIndex( polystyrene_sep, 3 );

Console.WriteLine(  "index: " + result.index( 0 )  );

FragmentationIndex

- Function Syntax

+ Class Syntax

Parameters

Object Examples

Function Examples

Function Syntax

Class Syntax