MeanSmoothing3d

# [DocSampleImports]
import os
import sys, getopt
import PyIPSDK
import PyIPSDK.IPSDKIPLFiltering as filter
# [DocSampleImports]

def readCmdArguments(argv):
    
    # Default parameters values
    imagesSamplePath = PyIPSDK.getIPSDKDirectory(PyIPSDK.eInternalDirectory.eID_Images)
    inputImgPath = os.path.join(imagesSamplePath,  "Rope3d.tif")
    tmpPath = PyIPSDK.getIPSDKDefaultDirectory(PyIPSDK.eDefaultExternalDirectory.eDED_Tmp)
    outputImgPath = os.path.join(tmpPath, "meanSmoothing3d.tif")
    inHalfKnlSizeX = inHalfKnlSizeY = inHalfKnlSizeZ = 3
    
    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:x:y:z:",["inputImgFilePath=","outputImgFilePath=","inHalfKnlSizeX=","inHalfKnlSizeY=","inHalfKnlSizeZ="])
    except getopt.GetoptError:
        print('<application_script_filename> [--inputImgFilePath <input_image_file_path>] [--outputImgFilePath <output_image_file_path>] [--inHalfKnlSizeX <half_kernel_size_along_x>] [--inHalfKnlSizeY <half_kernel_size_along_y>] [--inHalfKnlSizeZ <half_kernel_size_along_z>]')
        sys.exit(2)
    
    # Parse the program options
    for opt, arg in opts:
        if opt == '-h':
            print('<application_script_filename> [--inputImgFilePath <input_image_file_path>] [--outputImgFilePath <output_image_file_path>] [--inHalfKnlSizeX <half_kernel_size_along_x>] [--inHalfKnlSizeY <half_kernel_size_along_y>] [--inHalfKnlSizeZ <half_kernel_size_along_z>]')
            sys.exit(0)
        elif opt in ("-i", "--inputImgFilePath"):
            inputImgPath = arg
        elif opt in ("-o", "--outputImgFilePath"):
            outputImgPath = arg
        elif opt in ("-x", "--inHalfKnlSizeX"):
            inHalfKnlSizeX = int(arg)
        elif opt in ("-y", "--inHalfKnlSizeY"):
            inHalfKnlSizeY = int(arg)
        elif opt in ("-z", "--inHalfKnlSizeZ"):
            inHalfKnlSizeZ = int(arg)
    
    return inputImgPath, outputImgPath, inHalfKnlSizeX, inHalfKnlSizeY, inHalfKnlSizeZ

def main(argv):
# [DocSampleDefineArguments]
    # retrieve program parameters
    inputImgPath, outputImgPath, inHalfKnlSizeX, inHalfKnlSizeY, inHalfKnlSizeZ = readCmdArguments(argv)
# [DocSampleDefineArguments]

# [DocSampleLoadImage]
    # opening of 3D input image
    # specifying argument PyIPSDK.eTiffDirectoryMode.eTDM_Volume, input image plans are interpreted as a 3d stack
    inImg = PyIPSDK.loadTiffImageFile(inputImgPath, PyIPSDK.eTiffDirectoryMode.eTDM_Volume)
# [DocSampleLoadImage]

# [DocSampleApplyOp]
    # mean smoothing computation
    outImg = filter.meanSmoothing3dImg(inImg, inHalfKnlSizeX, inHalfKnlSizeY, inHalfKnlSizeZ);
# [DocSampleApplyOp]

# [DocSampleSaveImage]
    # save generated image
    print("Writing result in file : " + outputImgPath)
    PyIPSDK.saveTiffImageFile(outputImgPath, outImg)
# [DocSampleSaveImage]
    
if __name__ == "__main__":
   main(sys.argv[1:])