ImageDev

Custom Analysis

This example shows how to set the attributes of a measurement and how to create a new measurement from a user defined formula.
Several native measurements of ImageDev can be customized by setting some parameters. For instance, the orientation of the Feret diameters to be computed can be user-defined. By default, the Feret diameter measurement contains 10 orientations with a pitch of 18 degrees.

This example shows first how to reduce these orientations to 0 and 90 degrees by selecting two diameters and resampling the distribution between 0 and 180 degrees. The setOrientation method can also be used for this purpose, especially if the expected distribution is not uniform.

Then, this example shows how to create a new measurement from a user-defined formula corresponding to a circularity factor. The validity of the formula is checked, and the new measurement is selected in the analysis. 

#include <ImageDev/ImageDev.h>
#include <ioformat/IOFormat.h>
#include <string.h>

using namespace imagedev;
using namespace ioformat;
using namespace iolink;

int
main( int argc, char* argv[] )
{
    int status = 0;

    try
    {
        // ImageDev library initialization if not done
        if ( isInitialized() == false )
            imagedev::init();

        // Open a grayscale image from a tif file
        auto imageInput = readImage( std::string( IMAGEDEVDATA_IMAGES_FOLDER ) + "objects.tif" );

        // Threshold and label the binary input
        auto imageBin = thresholdingByCriterion( imageInput,
                                                 ThresholdingByCriterion::ComparisonCriterion::GREATER_THAN_OR_EQUAL_TO,
                                                 40 );
        auto imageLab = labeling2d( imageBin, Labeling2d::LABEL_8_BIT, Labeling2d::CONNECTIVITY_8 );

        // Change the number of Feret diameter to 2 (0 and 90 degrees)
        MeasurementAttributes::feret2d()->setOrientationCount( 2 );
        MeasurementAttributes::feret2d()->resample();
        std::cout << "FeretDiameter[0] = " + std::to_string( MeasurementAttributes::feret2d()->orientation( 0 ) )
                  << std::endl;
        std::cout << "FeretDiameter[1] = " + std::to_string( MeasurementAttributes::feret2d()->orientation( 1 ) )
                  << std::endl;

        // Create a circularity factor between 0 and 1
        std::string myFormula( "4*Pi*" + NativeMeasurements::area2d->name() + "/" +
                               NativeMeasurements::polygonePerimeter2d->name() + "**2" );
        if ( !checkMeasurementFormula( myFormula ) )
            // Raise an exception if the formula is not valid
            throw imagedev::Exception( "Invalid formula: " + myFormula );

        const auto* myCircularity = AnalysisMsr::registerCustomMeasurement( "MyCircularity",
                                                                            myFormula,
                                                                            "A circularity factor between 0 and 1." );

        // Define the analysis features to be computed
        AnalysisMsr::Ptr analysis = std::make_shared< AnalysisMsr >();
        analysis->select( NativeMeasurements::feretDiameter2d );
        analysis->select( myCircularity );

        // Launch the feature extraction on the segmented image
        labelAnalysis( imageLab, imageInput, analysis );

        // Export the analysis in a dataframe and save it in a csv file
        auto dataframe = analysis->toDataFrame();
        writeView( dataframe, "T04_04_analysis.csv" );

        std::cout << "This example ran successfully." << std::endl;
    }
    catch ( const imagedev::Exception& error )
    {
        // Print potential exception in the standard output
        std::cerr << "T04_05_CustomAnalysis exception: " << error.what() << std::endl;
        status = -1;
    }

    // ImageDev library finalization
    imagedev::finish();

    // Check if we must ask for an enter key to close the program
    if ( !( ( argc == 2 ) && strcmp( argv[1], "--no-stop-at-end" ) == 0 ) )
        std::cout << "Press Enter key to close this window." << std::endl, getchar();

    return status;
}


See also