Quantification3d

# [DocSampleImports]
import os
import sys, getopt
import PyIPSDK
import PyIPSDK.IPSDKIPLFiltering as filter
import PyIPSDK.IPSDKIPLBinarization as bin
import PyIPSDK.IPSDKIPLAdvancedMorphology as advmorpho
import PyIPSDK.IPSDKIPLShapeAnalysis as shapeanalysis
# [DocSampleImports]

def readCmdArguments(argv):
    
    # Default parameters values
    imagesSamplePath = PyIPSDK.getIPSDKDirectory(PyIPSDK.eInternalDirectory.eID_Images)
    inputImgPath = os.path.join(imagesSamplePath,  "blobs3d_483x348x31_UInt8.tif")
    tmpPath = PyIPSDK.getIPSDKDefaultDirectory(PyIPSDK.eDefaultExternalDirectory.eDED_Tmp)
    outputReportPath = os.path.join(tmpPath, "quantification3d.csv")
    inHalfKnlSize = 3
    inSpaceSigma = 8
    inDilateFactor = 5
    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:o:k:s:f:",["inputImg3dFilePath=","outputReportPath=", "inHalfKnlSize=", "inSpaceSigma=", "inDilateFactor="])
    except getopt.GetoptError:
        print('<application_script_filename> [--inputImg3dFilePath <input_3d_image_file_path>] [--outputReportPath <output_report_file_path>] [--inHalfKnlSize <half_kernel_size>] [--inSpaceSigma <space_sigma_value>] [--inDilateFactor <dilate_factor>]')
        sys.exit(2)
    
    # Parse the program options
    for opt, arg in opts:
        if opt == '-h':
            print('<application_script_filename> [--inputImg3dFilePath <input_3d_image_file_path>] [--outputReportPath <output_report_file_path>] [--inHalfKnlSize <half_kernel_size>] [--inSpaceSigma <space_sigma_value>] [--inDilateFactor <dilate_factor>]')
            sys.exit(0)
        elif opt in ("-i", "--inputImg3dFilePath"):
            inputImgPath = arg
        elif opt in ("-k", "--inHalfKnlSize"):
            inHalfKnlSize = int(arg)
        elif opt in ("-s", "--inSpaceSigma"):
            inSpaceSigma = float(arg)
        elif opt in ("-f", "--inDilateFactor"):
            inDilateFactor = int(arg)
    
    return inputImgPath, outputReportPath, inHalfKnlSize, inSpaceSigma, inDilateFactor
    
def main(argv):
    tmpPath = PyIPSDK.getIPSDKDefaultDirectory(PyIPSDK.eDefaultExternalDirectory.eDED_Tmp)

# [DocSampleDefineArguments]
    # retrieve program parameters
    inputImgPath, outputReportPath, inHalfKnlSize, inSpaceSigma, inDilateFactor = readCmdArguments(argv)
# [DocSampleDefineArguments]

# [DocSampleLoadImage]
    # opening of input image
    greyImg = PyIPSDK.loadTiffImageFile(inputImgPath, PyIPSDK.eTiffDirectoryMode.eTDM_Volume)
# [DocSampleLoadImage]

# [DocSampleFilteringStep]
    # filtering of input image to smooth defaults
    greyFilteredImg = filter.separatedBilateral3dImg(greyImg, 3, 8)
# [DocSampleFilteringStep]

# [DocSampleBinarizationStep]
    # auto threshold on filtered image
    binImg,  threshold = bin.otsuThresholdImg(greyFilteredImg)
    PyIPSDK.saveTiffImageFile(os.path.join(tmpPath, "binImg.tif"), binImg)
# [DocSampleBinarizationStep]

# [DocSampleSeparationStep]
    # automatic separation of binary shapes
    binSepImg = advmorpho.watershedBinarySeparation3dImg(binImg, 5, PyIPSDK.eWatershedSeparationMode.eWSM_Split)
    PyIPSDK.saveTiffImageFile(os.path.join(tmpPath, "binSepImg.tif"), binSepImg)
# [DocSampleSeparationStep]

# [DocSampleConnectedComponentsStep]
    # connected components analysis of separated binary image
    labelImg = advmorpho.connectedComponent3dImg(binSepImg)
    PyIPSDK.saveTiffImageFile(os.path.join(tmpPath, "labelImg.tif"), labelImg)
# [DocSampleConnectedComponentsStep]

# [DocSampleDefineMeasureSet]
    # definition of a geometric calibration (if available)
    geometricCalibration = PyIPSDK.createGeometricCalibration3d(0.01, 0.02, 0.05, "mm");

    # definition of measure set on shapes
    measureInfoSet3d = PyIPSDK.createMeasureInfoSet3d(geometricCalibration);
    PyIPSDK.createMeasureInfo(measureInfoSet3d, "Area3dMsr");
    PyIPSDK.createMeasureInfo(measureInfoSet3d, "EquivalentRayMsr");
    PyIPSDK.createMeasureInfo(measureInfoSet3d, "MaxFeretDiameterMsr",  shapeanalysis.createMaxFeretDiameterMsrParams(180));
    PyIPSDK.createMeasureInfo(measureInfoSet3d, "MeanMsr");
# [DocSampleDefineMeasureSet]

# [DocSampleShapeAnalysis]
    # shape analysis computation
    measureSet = shapeanalysis.labelAnalysis3d(greyImg, labelImg, measureInfoSet3d)
# [DocSampleShapeAnalysis]

# [DocSampleSaveReport]
    # save report in csv format
    print("Saving measure report in file " + outputReportPath)
    PyIPSDK.saveCsvMeasureFile(outputReportPath, measureSet)
# [DocSampleSaveReport]

# [DocSampleAccessData]
    # retrieve area measure results
    areaMsrResults = measureSet.getMeasure("Area3dMsr").getMeasureResult()

    # extract associated results collection
    areaValues = areaMsrResults.getColl(0)
    print("First label area equals " + str(areaValues[1]))
# [DocSampleAccessData]

    try:  
    # [DocPlotResults]
        # retrieve histogram from measure results
        areaHistogram = areaMsrResults.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:])