ShapeAnalysis2d

# [DocSampleImports]
import os
import sys, getopt
import PyIPSDK
import PyIPSDK.IPSDKIPLAdvancedMorphology as advmorpho
import PyIPSDK.IPSDKIPLShapeSegmentation as shapesegmentation
import PyIPSDK.IPSDKIPLShapeAnalysis as shapeanalysis
# [DocSampleImports]

def readCmdArguments(argv):
    
    # Default parameters values
    imagesSamplePath = PyIPSDK.getIPSDKDirectory(PyIPSDK.eInternalDirectory.eID_Images)
    inputImgPath = os.path.join(imagesSamplePath,  "blobs_483x348_UInt8.tif")
    inputBinImgPath = os.path.join(imagesSamplePath,  "blobs_483x348_Binary.tif")
    tmpPath = PyIPSDK.getIPSDKDefaultDirectory(PyIPSDK.eDefaultExternalDirectory.eDED_Tmp)
    outputXmlResultPath = os.path.join(tmpPath, "shapeAnalysis2d.xml")
    
    try:
        # Read the command line, the second argument is a string with all the possible options (short version)
        # with a ':' if the option requires an argument and the third argument is the set of trings corresponding
        # to the long versions of the program options
        opts, args = getopt.getopt(argv,"hi:b:o:",["inputGreyImgPath=","inputBinImgPath=","outputXmlResultPath="])
    except getopt.GetoptError:
        print('<application_script_filename> [--inputGreyImgPath <input_grey_image_file_path>] [--inputBinImgPath <input_binary_image_file_path>] [--outputXmlResultPath <output xml result path>]')
        sys.exit(2)
    
    # Parse the program options
    for opt, arg in opts:
        if opt == '-h':
            print('<application_script_filename> [--inputGreyImgPath <input_grey_image_file_path>] [--inputBinImgPath <input_binary_image_file_path>] [--outputXmlResultPath <output xml result path>]')
            sys.exit(0)
        elif opt in ("-i", "--inputGreyImgPath"):
            inputImgPath = arg
        elif opt in ("-b", "--inputBinImgPath"):
            inputBinImgPath = arg
        elif opt in ("-o", "--outputXmlResultPath"):
            outputXmlResultPath = arg
    
    return inputImgPath, inputBinImgPath, outputXmlResultPath

def main(argv):
    tmpPath = PyIPSDK.getIPSDKDefaultDirectory(PyIPSDK.eDefaultExternalDirectory.eDED_Tmp)

# [DocSampleDefineArguments]
    # retrieve program parameters
    inputImgPath, inputBinImgPath, outputXmlResultPath = readCmdArguments(argv)
# [DocSampleDefineArguments]

# [DocSampleLoadImage]
    # opening of input image
    inImg = PyIPSDK.loadTiffImageFile(inputImgPath)
    inBinImg = PyIPSDK.loadTiffImageFile(inputBinImgPath)
# [DocSampleLoadImage]

# [DocSampleProcess]
    # connected components analysis of separated binary image
    labelImg = advmorpho.connectedComponent2dImg(inBinImg)
    PyIPSDK.saveTiffImageFile(os.path.join(tmpPath, "labelImg.tif"), labelImg)

    # extraction of contours from connected components image
    shape2dColl = shapesegmentation.labelShapeExtraction2d(labelImg)
    
    # definition of a geometric calibration (if available)
    geometricCalibration = PyIPSDK.createGeometricCalibration2d(0.01, 0.02, "mm");

    # definition of measure set on shapes
    measureInfoSet2d = PyIPSDK.createMeasureInfoSet2d(geometricCalibration)
    PyIPSDK.createMeasureInfo(measureInfoSet2d, "AreaMinusHoles", "Area2dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(True))
    PyIPSDK.createMeasureInfo(measureInfoSet2d, "AreaWithHoles", "Area2dMsr", shapeanalysis.createHolesBasicPolicyMsrParams(False))
    PyIPSDK.createMeasureInfo(measureInfoSet2d, "EquivalentRay", "EquivalentRayMsr")
    PyIPSDK.createMeasureInfo(measureInfoSet2d, "SumMsr")

    # shape analysis computation
    measureSet = shapeanalysis.shapeAnalysis2d(inImg,  shape2dColl,  measureInfoSet2d)
# [DocSampleProcess]

# [DocSampleExtractResults]
    # retrieve area 2d results for 'minus holes' parametrization for example
    # (note that in case of default input image, shapes are not associated to holes
    # so both area measures have same values)
    areaMinusHolesOutMsr = measureSet.getMeasure("AreaMinusHoles")
    areaMinusHolesRes = areaMinusHolesOutMsr.getMeasureResult()
    print("First area minus holes = " + str(areaMinusHolesRes.getColl(0)[1]))
# [DocSampleExtractResults]

# [DocSampleSaveResults]
    PyIPSDK.writeToXmlFile(outputXmlResultPath, measureSet)
# [DocSampleSaveResults]

    try:  
    # [DocPlotResults]
        # retrieve histogram from measure results
        areaHistogram = areaMinusHolesRes.extractHistogram(15, 0)
                
        # plot histogram results
        import matplotlib.pyplot as plt
        fig, ax = plt.subplots()
        ax.bar(areaHistogram.getBinMidValues(), areaHistogram.getFrequencies(), areaHistogram.getBinWidth(), color='r')
        plt.title("Area histogram")
        plt.xlabel('Bin mean')
        plt.ylabel('Frequencies')
        plt.grid(True)
        plt.show()
    # [DocPlotResults]
    except:
        print("This part of sample requires matplotlib to be executed.")
    
if __name__ == "__main__":
   main(sys.argv[1:])