CylindricalIntensityProfile3d

Computes a radial intensity profile on a 3D image by performing a projection along an axis.

Access to parameter description

This algorithm computes an intensity profile that consists in the average intensity at a distance r from a given center. It is computed on a 2D projection of the input volume performed by averaging intensity values along a user-defined axis.
The output is a 2-column spreadsheet indicating, for each radius, the corresponding average intensity value.

Figure 1. Cylindrical intensity profile along a given axis

See also

Function Syntax

This function returns outputMeasurement.

// Function prototype
CylindricalIntensityProfileMsr::Ptr
cylindricalIntensityProfile3d( std::shared_ptr< iolink::ImageView > inputImage,
                               CylindricalIntensityProfile3d::AxisDirection axisDirection,
                               CylindricalIntensityProfile3d::CenterMode centerMode,
                               iolink::Vector3u32 center,
                               uint32_t maximumRadius,
                               CylindricalIntensityProfileMsr::Ptr outputMeasurement = NULL );

This function returns outputMeasurement.

// Function prototype.
cylindrical_intensity_profile_3d( input_image,
                                  axis_direction = CylindricalIntensityProfile3d.AxisDirection.Z_AXIS,
                                  center_mode = CylindricalIntensityProfile3d.CenterMode.IMAGE_CENTER,
                                  center = [0, 0, 0],
                                  maximum_radius = 0,
                                  output_measurement = None )

This function returns outputMeasurement.

// Function prototype.
public static CylindricalIntensityProfileMsr
CylindricalIntensityProfile3d( IOLink.ImageView inputImage,
                               CylindricalIntensityProfile3d.AxisDirection axisDirection = ImageDev.CylindricalIntensityProfile3d.AxisDirection.Z_AXIS,
                               CylindricalIntensityProfile3d.CenterMode centerMode = ImageDev.CylindricalIntensityProfile3d.CenterMode.IMAGE_CENTER,
                               uint[] center = null,
                               UInt32 maximumRadius = 0,
                               CylindricalIntensityProfileMsr outputMeasurement = null );

Class Syntax

// Command constructor.
CylindricalIntensityProfile3d();

/// Gets the inputImage parameter.
/// The input image. Any type of image is accepted.
std::shared_ptr< iolink::ImageView > inputImage() const;
/// Sets the inputImage parameter.
/// The input image. Any type of image is accepted.
void setInputImage( std::shared_ptr< iolink::ImageView > inputImage );

/// Gets the axisDirection parameter.
/// The axis along which slices are projected.
CylindricalIntensityProfile3d::AxisDirection axisDirection() const;
/// Sets the axisDirection parameter.
/// The axis along which slices are projected.
void setAxisDirection( const CylindricalIntensityProfile3d::AxisDirection& axisDirection );

/// Gets the centerMode parameter.
/// The way to define the origin of the radii.
CylindricalIntensityProfile3d::CenterMode centerMode() const;
/// Sets the centerMode parameter.
/// The way to define the origin of the radii.
void setCenterMode( const CylindricalIntensityProfile3d::CenterMode& centerMode );

/// Gets the center parameter.
/// The origin of the radii in pixel coordinates. It is only used in OTHER mode.
iolink::Vector3u32 center() const;
/// Sets the center parameter.
/// The origin of the radii in pixel coordinates. It is only used in OTHER mode.
void setCenter( const iolink::Vector3u32& center );

/// Gets the maximumRadius parameter.
/// The radius in voxels up to which intensities are included in the profile.
uint32_t maximumRadius() const;
/// Sets the maximumRadius parameter.
/// The radius in voxels up to which intensities are included in the profile.
void setMaximumRadius( const uint32_t& maximumRadius );

/// Gets the outputMeasurement parameter.
/// The output object containing the computed radii and averaged intensities.
CylindricalIntensityProfileMsr::Ptr outputMeasurement() const;


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

# Property of the inputImage parameter.
CylindricalIntensityProfile3d.input_image
# Property of the axisDirection parameter.
CylindricalIntensityProfile3d.axis_direction
# Property of the centerMode parameter.
CylindricalIntensityProfile3d.center_mode
# Property of the center parameter.
CylindricalIntensityProfile3d.center
# Property of the maximumRadius parameter.
CylindricalIntensityProfile3d.maximum_radius
# Property of the outputMeasurement parameter.
CylindricalIntensityProfile3d.output_measurement

// Method to launch the command.
execute()

// Command constructor.
CylindricalIntensityProfile3d()

// Property of the inputImage parameter.
CylindricalIntensityProfile3d.inputImage
// Property of the axisDirection parameter.
CylindricalIntensityProfile3d.axisDirection
// Property of the centerMode parameter.
CylindricalIntensityProfile3d.centerMode
// Property of the center parameter.
CylindricalIntensityProfile3d.center
// Property of the maximumRadius parameter.
CylindricalIntensityProfile3d.maximumRadius
// Property of the outputMeasurement parameter.
CylindricalIntensityProfile3d.outputMeasurement

// Method to launch the command.
Execute()

Parameters

Parameter Name

Description

Type

Supported Values

Default Value

inputImage

The input image. Any type of image is accepted.

Image

Grayscale or Multispectral

nullptr

centerMode

The way to define the origin of the radii.

IMAGE_CENTER	The origin of the radii is the center of the input image.
OTHER	The origin of the radii is user defined.

Enumeration

IMAGE_CENTER

axisDirection

The axis along which slices are projected.
If axis direction is set to X, YZ slices are projected.

X_AXIS	The YZ slices are projected.
Y_AXIS	The XZ slices are projected.
Z_AXIS	The XY slices are projected.

Enumeration

Z_AXIS

center

The origin of the radii in pixel coordinates. It is only used in OTHER mode.

Vector3u32

Any value

{0, 0, 0}

maximumRadius

The radius in voxels up to which intensities are included in the profile.

UInt32

Any value

outputMeasurement

The output object containing the computed radii and averaged intensities.

CylindricalIntensityProfileMsr

nullptr

Object Examples

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

CylindricalIntensityProfile3d cylindricalIntensityProfile3dAlgo;
cylindricalIntensityProfile3dAlgo.setInputImage( foam );
cylindricalIntensityProfile3dAlgo.setAxisDirection( CylindricalIntensityProfile3d::AxisDirection::Z_AXIS );
cylindricalIntensityProfile3dAlgo.setCenterMode( CylindricalIntensityProfile3d::CenterMode::IMAGE_CENTER );
cylindricalIntensityProfile3dAlgo.setCenter( {0, 0, 0} );
cylindricalIntensityProfile3dAlgo.setMaximumRadius( 255 );
cylindricalIntensityProfile3dAlgo.execute();

std::cout << "mean: " << cylindricalIntensityProfile3dAlgo.outputMeasurement()->mean( 0 , 0 , 0 ) ;

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

cylindrical_intensity_profile_3d_algo = imagedev.CylindricalIntensityProfile3d()
cylindrical_intensity_profile_3d_algo.input_image = foam
cylindrical_intensity_profile_3d_algo.axis_direction = imagedev.CylindricalIntensityProfile3d.Z_AXIS
cylindrical_intensity_profile_3d_algo.center_mode = imagedev.CylindricalIntensityProfile3d.IMAGE_CENTER
cylindrical_intensity_profile_3d_algo.center = [0, 0, 0]
cylindrical_intensity_profile_3d_algo.maximum_radius = 255
cylindrical_intensity_profile_3d_algo.execute()

print( "mean: ", str( cylindrical_intensity_profile_3d_algo.output_measurement.mean( 0 , 0 , 0 ) ) )

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

CylindricalIntensityProfile3d cylindricalIntensityProfile3dAlgo = new CylindricalIntensityProfile3d
{
    inputImage = foam,
    axisDirection = CylindricalIntensityProfile3d.AxisDirection.Z_AXIS,
    centerMode = CylindricalIntensityProfile3d.CenterMode.IMAGE_CENTER,
    center = new uint[]{0, 0, 0},
    maximumRadius = 255
};
cylindricalIntensityProfile3dAlgo.Execute();

Console.WriteLine( "mean: " + cylindricalIntensityProfile3dAlgo.outputMeasurement.mean( 0 , 0 , 0 ) );

Function Examples

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

auto result = cylindricalIntensityProfile3d( foam, CylindricalIntensityProfile3d::AxisDirection::Z_AXIS, CylindricalIntensityProfile3d::CenterMode::IMAGE_CENTER, {0, 0, 0}, 255 );

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

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

result = imagedev.cylindrical_intensity_profile_3d( foam, imagedev.CylindricalIntensityProfile3d.Z_AXIS, imagedev.CylindricalIntensityProfile3d.IMAGE_CENTER, [0, 0, 0], 255 )

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

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

CylindricalIntensityProfileMsr result = Processing.CylindricalIntensityProfile3d( foam, CylindricalIntensityProfile3d.AxisDirection.Z_AXIS, CylindricalIntensityProfile3d.CenterMode.IMAGE_CENTER, new uint[]{0, 0, 0}, 255 );

Console.WriteLine(  "mean: " + result.mean( 0 , 0 , 0 )  );

CylindricalIntensityProfile3d

- Function Syntax

+ Class Syntax

Parameters

Object Examples

Function Examples

Function Syntax

Class Syntax