├── .gitignore ├── LICENSE.txt ├── README.md ├── TextureAnalysis ├── GLCM.py ├── GLCM_3D.py ├── GLHA.py ├── GLSZM.py ├── GLSZM_3D.py ├── NGTDM.py ├── NGTDM_3D.py ├── Utils.py ├── __init__.py └── suvs.npy ├── Utils.py ├── VoiExtractionManager.py ├── data └── PA0 │ └── ST0 │ ├── SE0 │ ├── IM-0002-0001.dcm │ ├── IM-0002-0002.dcm │ ├── IM-0002-0003.dcm │ ├── IM-0002-0004.dcm │ ├── IM-0002-0005.dcm │ ├── IM-0002-0006.dcm │ ├── IM-0002-0007.dcm │ ├── IM-0002-0008.dcm │ ├── IM-0002-0009.dcm │ ├── IM-0002-0010.dcm │ ├── IM-0002-0011.dcm │ ├── IM-0002-0012.dcm │ ├── IM-0002-0013.dcm │ ├── IM-0002-0014.dcm │ ├── IM-0002-0015.dcm │ ├── IM-0002-0016.dcm │ ├── IM-0002-0017.dcm │ ├── IM-0002-0018.dcm │ ├── IM-0002-0019.dcm │ ├── IM-0002-0020.dcm │ ├── IM-0002-0021.dcm │ ├── IM-0002-0022.dcm │ ├── IM-0002-0023.dcm │ ├── IM-0002-0024.dcm │ ├── IM-0002-0025.dcm │ ├── IM-0002-0026.dcm │ ├── IM-0002-0027.dcm │ ├── IM-0002-0028.dcm │ ├── IM-0002-0029.dcm │ ├── IM-0002-0030.dcm │ ├── IM-0002-0031.dcm │ ├── IM-0002-0032.dcm │ ├── IM-0002-0033.dcm │ ├── IM-0002-0034.dcm │ ├── IM-0002-0035.dcm │ ├── IM-0002-0036.dcm │ ├── IM-0002-0037.dcm │ ├── IM-0002-0038.dcm │ ├── IM-0002-0039.dcm │ ├── IM-0002-0040.dcm │ ├── IM-0002-0041.dcm │ ├── IM-0002-0042.dcm │ ├── IM-0002-0043.dcm │ ├── IM-0002-0044.dcm │ ├── IM-0002-0045.dcm │ ├── IM-0002-0046.dcm │ ├── IM-0002-0047.dcm │ ├── IM-0002-0048.dcm │ ├── IM-0002-0049.dcm │ ├── IM-0002-0050.dcm │ ├── IM-0002-0051.dcm │ ├── IM-0002-0052.dcm │ ├── IM-0002-0053.dcm │ ├── IM-0002-0054.dcm │ ├── IM-0002-0055.dcm │ ├── IM-0002-0056.dcm │ ├── IM-0002-0057.dcm │ ├── IM-0002-0058.dcm │ ├── IM-0002-0059.dcm │ ├── IM-0002-0060.dcm │ ├── IM-0002-0061.dcm │ ├── IM-0002-0062.dcm │ ├── IM-0002-0063.dcm │ ├── IM-0002-0064.dcm │ ├── IM-0002-0065.dcm │ ├── IM-0002-0066.dcm │ ├── IM-0002-0067.dcm │ ├── IM-0002-0068.dcm │ ├── IM-0002-0069.dcm │ ├── IM-0002-0070.dcm │ ├── IM-0002-0071.dcm │ ├── IM-0002-0072.dcm │ ├── IM-0002-0073.dcm │ ├── IM-0002-0074.dcm │ ├── IM-0002-0075.dcm │ ├── IM-0002-0076.dcm │ ├── IM-0002-0077.dcm │ ├── IM-0002-0078.dcm │ ├── IM-0002-0079.dcm │ ├── IM-0002-0080.dcm │ ├── IM-0002-0081.dcm │ ├── IM-0002-0082.dcm │ ├── IM-0002-0083.dcm │ ├── IM-0002-0084.dcm │ ├── IM-0002-0085.dcm │ ├── IM-0002-0086.dcm │ ├── IM-0002-0087.dcm │ ├── IM-0002-0088.dcm │ ├── IM-0002-0089.dcm │ ├── IM-0002-0090.dcm │ ├── IM-0002-0091.dcm │ ├── IM-0002-0092.dcm │ ├── IM-0002-0093.dcm │ ├── IM-0002-0094.dcm │ ├── IM-0002-0095.dcm │ ├── IM-0002-0096.dcm │ ├── IM-0002-0097.dcm │ ├── IM-0002-0098.dcm │ ├── IM-0002-0099.dcm │ ├── IM-0002-0100.dcm │ ├── IM-0002-0101.dcm │ ├── IM-0002-0102.dcm │ ├── IM-0002-0103.dcm │ ├── IM-0002-0104.dcm │ ├── IM-0002-0105.dcm │ ├── IM-0002-0106.dcm │ ├── IM-0002-0107.dcm │ ├── IM-0002-0108.dcm │ ├── IM-0002-0109.dcm │ ├── IM-0002-0110.dcm │ ├── IM-0002-0111.dcm │ ├── IM-0002-0112.dcm │ ├── IM-0002-0113.dcm │ ├── IM-0002-0114.dcm │ ├── IM-0002-0115.dcm │ ├── IM-0002-0116.dcm │ ├── IM-0002-0117.dcm │ ├── IM-0002-0118.dcm │ ├── IM-0002-0119.dcm │ ├── IM-0002-0120.dcm │ ├── IM-0002-0121.dcm │ ├── IM-0002-0122.dcm │ ├── IM-0002-0123.dcm │ ├── IM-0002-0124.dcm │ ├── IM-0002-0125.dcm │ ├── IM-0002-0126.dcm │ ├── IM-0002-0127.dcm │ ├── IM-0002-0128.dcm │ ├── IM-0002-0129.dcm │ ├── IM-0002-0130.dcm │ ├── IM-0002-0131.dcm │ ├── IM-0002-0132.dcm │ ├── IM-0002-0133.dcm │ ├── IM-0002-0134.dcm │ ├── IM-0002-0135.dcm │ ├── IM-0002-0136.dcm │ ├── IM-0002-0137.dcm │ ├── IM-0002-0138.dcm │ ├── IM-0002-0139.dcm │ ├── IM-0002-0140.dcm │ ├── IM-0002-0141.dcm │ ├── IM-0002-0142.dcm │ ├── IM-0002-0143.dcm │ ├── IM-0002-0144.dcm │ ├── IM-0002-0145.dcm │ ├── IM-0002-0146.dcm │ ├── IM-0002-0147.dcm │ ├── IM-0002-0148.dcm │ ├── IM-0002-0149.dcm │ ├── IM-0002-0150.dcm │ ├── IM-0002-0151.dcm │ ├── IM-0002-0152.dcm │ ├── IM-0002-0153.dcm │ ├── IM-0002-0154.dcm │ ├── IM-0002-0155.dcm │ ├── IM-0002-0156.dcm │ ├── IM-0002-0157.dcm │ ├── IM-0002-0158.dcm │ ├── IM-0002-0159.dcm │ ├── IM-0002-0160.dcm │ ├── IM-0002-0161.dcm │ ├── IM-0002-0162.dcm │ ├── IM-0002-0163.dcm │ ├── IM-0002-0164.dcm │ ├── IM-0002-0165.dcm │ ├── IM-0002-0166.dcm │ ├── IM-0002-0167.dcm │ ├── IM-0002-0168.dcm │ ├── IM-0002-0169.dcm │ ├── IM-0002-0170.dcm │ ├── IM-0002-0171.dcm │ ├── IM-0002-0172.dcm │ ├── IM-0002-0173.dcm │ ├── IM-0002-0174.dcm │ ├── IM-0002-0175.dcm │ ├── IM-0002-0176.dcm │ ├── IM-0002-0177.dcm │ ├── IM-0002-0178.dcm │ ├── IM-0002-0179.dcm │ ├── IM-0002-0180.dcm │ ├── IM-0002-0181.dcm │ ├── IM-0002-0182.dcm │ ├── IM-0002-0183.dcm │ ├── IM-0002-0184.dcm │ ├── IM-0002-0185.dcm │ ├── IM-0002-0186.dcm │ ├── IM-0002-0187.dcm │ ├── IM-0002-0188.dcm │ ├── IM-0002-0189.dcm │ ├── IM-0002-0190.dcm │ ├── IM-0002-0191.dcm │ ├── IM-0002-0192.dcm │ ├── IM-0002-0193.dcm │ ├── IM-0002-0194.dcm │ ├── IM-0002-0195.dcm │ ├── IM-0002-0196.dcm │ ├── IM-0002-0197.dcm │ ├── IM-0002-0198.dcm │ ├── IM-0002-0199.dcm │ ├── IM-0002-0200.dcm │ ├── IM-0002-0201.dcm │ ├── IM-0002-0202.dcm │ ├── IM-0002-0203.dcm │ ├── IM-0002-0204.dcm │ ├── IM-0002-0205.dcm │ ├── IM-0002-0206.dcm │ ├── IM-0002-0207.dcm │ ├── IM-0002-0208.dcm │ ├── IM-0002-0209.dcm │ ├── IM-0002-0210.dcm │ ├── IM-0002-0211.dcm │ ├── IM-0002-0212.dcm │ ├── IM-0002-0213.dcm │ ├── IM-0002-0214.dcm │ ├── IM-0002-0215.dcm │ ├── IM-0002-0216.dcm │ ├── IM-0002-0217.dcm │ ├── IM-0002-0218.dcm │ ├── IM-0002-0219.dcm │ ├── IM-0002-0220.dcm │ ├── IM-0002-0221.dcm │ ├── IM-0002-0222.dcm │ ├── IM-0002-0223.dcm │ ├── IM-0002-0224.dcm │ ├── IM-0002-0225.dcm │ ├── IM-0002-0226.dcm │ ├── IM-0002-0227.dcm │ ├── IM-0002-0228.dcm │ ├── IM-0002-0229.dcm │ ├── IM-0002-0230.dcm │ ├── IM-0002-0231.dcm │ ├── IM-0002-0232.dcm │ ├── IM-0002-0233.dcm │ ├── IM-0002-0234.dcm │ ├── IM-0002-0235.dcm │ ├── IM-0002-0236.dcm │ ├── IM-0002-0237.dcm │ ├── IM-0002-0238.dcm │ ├── IM-0002-0239.dcm │ ├── IM-0002-0240.dcm │ ├── IM-0002-0241.dcm │ ├── IM-0002-0242.dcm │ ├── IM-0002-0243.dcm │ ├── IM-0002-0244.dcm │ ├── IM-0002-0245.dcm │ ├── IM-0002-0246.dcm │ ├── IM-0002-0247.dcm │ ├── IM-0002-0248.dcm │ ├── IM-0002-0249.dcm │ ├── IM-0002-0250.dcm │ ├── IM-0002-0251.dcm │ ├── IM-0002-0252.dcm │ ├── IM-0002-0253.dcm │ ├── IM-0002-0254.dcm │ ├── IM-0002-0255.dcm │ ├── IM-0002-0256.dcm │ ├── IM-0002-0257.dcm │ ├── IM-0002-0258.dcm │ ├── IM-0002-0259.dcm │ ├── IM-0002-0260.dcm │ ├── IM-0002-0261.dcm │ ├── IM-0002-0262.dcm │ ├── IM-0002-0263.dcm │ ├── IM-0002-0264.dcm │ ├── IM-0002-0265.dcm │ ├── IM-0002-0266.dcm │ ├── IM-0002-0267.dcm │ ├── IM-0002-0268.dcm │ ├── IM-0002-0269.dcm │ ├── IM-0002-0270.dcm │ ├── IM-0002-0271.dcm │ ├── IM-0002-0272.dcm │ ├── IM-0002-0273.dcm │ ├── IM-0002-0274.dcm │ ├── IM-0002-0275.dcm │ ├── IM-0002-0276.dcm │ ├── IM-0002-0277.dcm │ ├── IM-0002-0278.dcm │ ├── IM-0002-0279.dcm │ ├── IM-0002-0280.dcm │ ├── IM-0002-0281.dcm │ ├── IM-0002-0282.dcm │ ├── IM-0002-0283.dcm │ ├── IM-0002-0284.dcm │ ├── IM-0002-0285.dcm │ ├── IM-0002-0286.dcm │ ├── IM-0002-0287.dcm │ ├── IM-0002-0288.dcm │ ├── IM-0002-0289.dcm │ ├── IM-0002-0290.dcm │ ├── IM-0002-0291.dcm │ ├── IM-0002-0292.dcm │ ├── IM-0002-0293.dcm │ ├── IM-0002-0294.dcm │ ├── IM-0002-0295.dcm │ ├── IM-0002-0296.dcm │ ├── IM-0002-0297.dcm │ ├── IM-0002-0298.dcm │ ├── IM-0002-0299.dcm │ ├── IM-0002-0300.dcm │ ├── IM-0002-0301.dcm │ ├── IM-0002-0302.dcm │ ├── IM-0002-0303.dcm │ ├── IM-0002-0304.dcm │ ├── IM-0002-0305.dcm │ ├── IM-0002-0306.dcm │ ├── IM-0002-0307.dcm │ ├── IM-0002-0308.dcm │ ├── IM-0002-0309.dcm │ ├── IM-0002-0310.dcm │ ├── IM-0002-0311.dcm │ ├── IM-0002-0312.dcm │ ├── IM-0002-0313.dcm │ ├── IM-0002-0314.dcm │ ├── IM-0002-0315.dcm │ ├── IM-0002-0316.dcm │ ├── IM-0002-0317.dcm │ ├── IM-0002-0318.dcm │ ├── IM-0002-0319.dcm │ ├── IM-0002-0320.dcm │ ├── IM-0002-0321.dcm │ ├── IM-0002-0322.dcm │ ├── IM-0002-0323.dcm │ ├── IM-0002-0324.dcm │ ├── IM-0002-0325.dcm │ ├── IM-0002-0326.dcm │ ├── IM-0002-0327.dcm │ ├── IM-0002-0328.dcm │ ├── IM-0002-0329.dcm │ ├── IM-0002-0330.dcm │ ├── IM-0002-0331.dcm │ ├── IM-0002-0332.dcm │ ├── IM-0002-0333.dcm │ ├── IM-0002-0334.dcm │ └── IM-0002-0335.dcm │ ├── SE1 │ ├── IM-0001-0001.dcm │ ├── IM-0001-0002.dcm │ ├── IM-0001-0003.dcm │ ├── IM-0001-0004.dcm │ ├── IM-0001-0005.dcm │ ├── IM-0001-0006.dcm │ ├── IM-0001-0007.dcm │ ├── IM-0001-0008.dcm │ ├── IM-0001-0009.dcm │ ├── IM-0001-0010.dcm │ ├── IM-0001-0011.dcm │ ├── IM-0001-0012.dcm │ ├── IM-0001-0013.dcm │ ├── IM-0001-0014.dcm │ ├── IM-0001-0015.dcm │ ├── IM-0001-0016.dcm │ ├── IM-0001-0017.dcm │ ├── IM-0001-0018.dcm │ ├── IM-0001-0019.dcm │ ├── IM-0001-0020.dcm │ ├── IM-0001-0021.dcm │ ├── IM-0001-0022.dcm │ ├── IM-0001-0023.dcm │ ├── IM-0001-0024.dcm │ ├── IM-0001-0025.dcm │ ├── IM-0001-0026.dcm │ ├── IM-0001-0027.dcm │ ├── IM-0001-0028.dcm │ ├── IM-0001-0029.dcm │ ├── IM-0001-0030.dcm │ ├── IM-0001-0031.dcm │ ├── IM-0001-0032.dcm │ ├── IM-0001-0033.dcm │ ├── IM-0001-0034.dcm │ ├── IM-0001-0035.dcm │ ├── IM-0001-0036.dcm │ ├── IM-0001-0037.dcm │ ├── IM-0001-0038.dcm │ ├── IM-0001-0039.dcm │ ├── IM-0001-0040.dcm │ ├── IM-0001-0041.dcm │ ├── IM-0001-0042.dcm │ ├── IM-0001-0043.dcm │ ├── IM-0001-0044.dcm │ ├── IM-0001-0045.dcm │ ├── IM-0001-0046.dcm │ ├── IM-0001-0047.dcm │ ├── IM-0001-0048.dcm │ ├── IM-0001-0049.dcm │ ├── IM-0001-0050.dcm │ ├── IM-0001-0051.dcm │ ├── IM-0001-0052.dcm │ ├── IM-0001-0053.dcm │ ├── IM-0001-0054.dcm │ ├── IM-0001-0055.dcm │ ├── IM-0001-0056.dcm │ ├── IM-0001-0057.dcm │ ├── IM-0001-0058.dcm │ ├── IM-0001-0059.dcm │ ├── IM-0001-0060.dcm │ ├── IM-0001-0061.dcm │ ├── IM-0001-0062.dcm │ ├── IM-0001-0063.dcm │ ├── IM-0001-0064.dcm │ ├── IM-0001-0065.dcm │ ├── IM-0001-0066.dcm │ ├── IM-0001-0067.dcm │ ├── IM-0001-0068.dcm │ ├── IM-0001-0069.dcm │ ├── IM-0001-0070.dcm │ ├── IM-0001-0071.dcm │ ├── IM-0001-0072.dcm │ ├── IM-0001-0073.dcm │ ├── IM-0001-0074.dcm │ ├── IM-0001-0075.dcm │ ├── IM-0001-0076.dcm │ ├── IM-0001-0077.dcm │ ├── IM-0001-0078.dcm │ ├── IM-0001-0079.dcm │ ├── IM-0001-0080.dcm │ ├── IM-0001-0081.dcm │ ├── IM-0001-0082.dcm │ ├── IM-0001-0083.dcm │ ├── IM-0001-0084.dcm │ ├── IM-0001-0085.dcm │ ├── IM-0001-0086.dcm │ ├── IM-0001-0087.dcm │ ├── IM-0001-0088.dcm │ ├── IM-0001-0089.dcm │ ├── IM-0001-0090.dcm │ ├── IM-0001-0091.dcm │ ├── IM-0001-0092.dcm │ ├── IM-0001-0093.dcm │ ├── IM-0001-0094.dcm │ ├── IM-0001-0095.dcm │ ├── IM-0001-0096.dcm │ ├── IM-0001-0097.dcm │ ├── IM-0001-0098.dcm │ ├── IM-0001-0099.dcm │ ├── IM-0001-0100.dcm │ ├── IM-0001-0101.dcm │ ├── IM-0001-0102.dcm │ ├── IM-0001-0103.dcm │ ├── IM-0001-0104.dcm │ ├── IM-0001-0105.dcm │ ├── IM-0001-0106.dcm │ ├── IM-0001-0107.dcm │ ├── IM-0001-0108.dcm │ ├── IM-0001-0109.dcm │ ├── IM-0001-0110.dcm │ ├── IM-0001-0111.dcm │ ├── IM-0001-0112.dcm │ ├── IM-0001-0113.dcm │ ├── IM-0001-0114.dcm │ ├── IM-0001-0115.dcm │ ├── IM-0001-0116.dcm │ ├── IM-0001-0117.dcm │ ├── IM-0001-0118.dcm │ ├── IM-0001-0119.dcm │ ├── IM-0001-0120.dcm │ ├── IM-0001-0121.dcm │ ├── IM-0001-0122.dcm │ ├── IM-0001-0123.dcm │ ├── IM-0001-0124.dcm │ ├── IM-0001-0125.dcm │ ├── IM-0001-0126.dcm │ ├── IM-0001-0127.dcm │ ├── IM-0001-0128.dcm │ ├── IM-0001-0129.dcm │ ├── IM-0001-0130.dcm │ ├── IM-0001-0131.dcm │ ├── IM-0001-0132.dcm │ ├── IM-0001-0133.dcm │ ├── IM-0001-0134.dcm │ ├── IM-0001-0135.dcm │ ├── IM-0001-0136.dcm │ ├── IM-0001-0137.dcm │ ├── IM-0001-0138.dcm │ ├── IM-0001-0139.dcm │ ├── IM-0001-0140.dcm │ ├── IM-0001-0141.dcm │ ├── IM-0001-0142.dcm │ ├── IM-0001-0143.dcm │ ├── IM-0001-0144.dcm │ ├── IM-0001-0145.dcm │ ├── IM-0001-0146.dcm │ ├── IM-0001-0147.dcm │ ├── IM-0001-0148.dcm │ ├── IM-0001-0149.dcm │ ├── IM-0001-0150.dcm │ ├── IM-0001-0151.dcm │ ├── IM-0001-0152.dcm │ ├── IM-0001-0153.dcm │ ├── IM-0001-0154.dcm │ ├── IM-0001-0155.dcm │ ├── IM-0001-0156.dcm │ ├── IM-0001-0157.dcm │ ├── IM-0001-0158.dcm │ ├── IM-0001-0159.dcm │ ├── IM-0001-0160.dcm │ ├── IM-0001-0161.dcm │ ├── IM-0001-0162.dcm │ ├── IM-0001-0163.dcm │ ├── IM-0001-0164.dcm │ ├── IM-0001-0165.dcm │ ├── IM-0001-0166.dcm │ ├── IM-0001-0167.dcm │ ├── IM-0001-0168.dcm │ ├── IM-0001-0169.dcm │ ├── IM-0001-0170.dcm │ ├── IM-0001-0171.dcm │ ├── IM-0001-0172.dcm │ ├── IM-0001-0173.dcm │ ├── IM-0001-0174.dcm │ ├── IM-0001-0175.dcm │ ├── IM-0001-0176.dcm │ ├── IM-0001-0177.dcm │ ├── IM-0001-0178.dcm │ ├── IM-0001-0179.dcm │ ├── IM-0001-0180.dcm │ ├── IM-0001-0181.dcm │ ├── IM-0001-0182.dcm │ ├── IM-0001-0183.dcm │ ├── IM-0001-0184.dcm │ ├── IM-0001-0185.dcm │ ├── IM-0001-0186.dcm │ ├── IM-0001-0187.dcm │ ├── IM-0001-0188.dcm │ ├── IM-0001-0189.dcm │ ├── IM-0001-0190.dcm │ ├── IM-0001-0191.dcm │ ├── IM-0001-0192.dcm │ ├── IM-0001-0193.dcm │ ├── IM-0001-0194.dcm │ ├── IM-0001-0195.dcm │ ├── IM-0001-0196.dcm │ ├── IM-0001-0197.dcm │ ├── IM-0001-0198.dcm │ ├── IM-0001-0199.dcm │ ├── IM-0001-0200.dcm │ ├── IM-0001-0201.dcm │ ├── IM-0001-0202.dcm │ ├── IM-0001-0203.dcm │ ├── IM-0001-0204.dcm │ ├── IM-0001-0205.dcm │ ├── IM-0001-0206.dcm │ ├── IM-0001-0207.dcm │ ├── IM-0001-0208.dcm │ ├── IM-0001-0209.dcm │ ├── IM-0001-0210.dcm │ ├── IM-0001-0211.dcm │ ├── IM-0001-0212.dcm │ ├── IM-0001-0213.dcm │ ├── IM-0001-0214.dcm │ ├── IM-0001-0215.dcm │ ├── IM-0001-0216.dcm │ ├── IM-0001-0217.dcm │ ├── IM-0001-0218.dcm │ ├── IM-0001-0219.dcm │ ├── IM-0001-0220.dcm │ ├── IM-0001-0221.dcm │ ├── IM-0001-0222.dcm │ ├── IM-0001-0223.dcm │ ├── IM-0001-0224.dcm │ ├── IM-0001-0225.dcm │ ├── IM-0001-0226.dcm │ ├── IM-0001-0227.dcm │ ├── IM-0001-0228.dcm │ ├── IM-0001-0229.dcm │ ├── IM-0001-0230.dcm │ ├── IM-0001-0231.dcm │ ├── IM-0001-0232.dcm │ ├── IM-0001-0233.dcm │ ├── IM-0001-0234.dcm │ ├── IM-0001-0235.dcm │ ├── IM-0001-0236.dcm │ ├── IM-0001-0237.dcm │ ├── IM-0001-0238.dcm │ ├── IM-0001-0239.dcm │ ├── IM-0001-0240.dcm │ ├── IM-0001-0241.dcm │ ├── IM-0001-0242.dcm │ ├── IM-0001-0243.dcm │ ├── IM-0001-0244.dcm │ ├── IM-0001-0245.dcm │ ├── IM-0001-0246.dcm │ ├── IM-0001-0247.dcm │ ├── IM-0001-0248.dcm │ ├── IM-0001-0249.dcm │ ├── IM-0001-0250.dcm │ ├── IM-0001-0251.dcm │ ├── IM-0001-0252.dcm │ ├── IM-0001-0253.dcm │ ├── IM-0001-0254.dcm │ ├── IM-0001-0255.dcm │ ├── IM-0001-0256.dcm │ ├── IM-0001-0257.dcm │ ├── IM-0001-0258.dcm │ ├── IM-0001-0259.dcm │ ├── IM-0001-0260.dcm │ ├── IM-0001-0261.dcm │ ├── IM-0001-0262.dcm │ ├── IM-0001-0263.dcm │ ├── IM-0001-0264.dcm │ ├── IM-0001-0265.dcm │ ├── IM-0001-0266.dcm │ ├── IM-0001-0267.dcm │ ├── IM-0001-0268.dcm │ ├── IM-0001-0269.dcm │ ├── IM-0001-0270.dcm │ ├── IM-0001-0271.dcm │ ├── IM-0001-0272.dcm │ ├── IM-0001-0273.dcm │ ├── IM-0001-0274.dcm │ ├── IM-0001-0275.dcm │ ├── IM-0001-0276.dcm │ ├── IM-0001-0277.dcm │ ├── IM-0001-0278.dcm │ ├── IM-0001-0279.dcm │ ├── IM-0001-0280.dcm │ ├── IM-0001-0281.dcm │ ├── IM-0001-0282.dcm │ ├── IM-0001-0283.dcm │ ├── IM-0001-0284.dcm │ ├── IM-0001-0285.dcm │ ├── IM-0001-0286.dcm │ ├── IM-0001-0287.dcm │ ├── IM-0001-0288.dcm │ ├── IM-0001-0289.dcm │ ├── IM-0001-0290.dcm │ ├── IM-0001-0291.dcm │ ├── IM-0001-0292.dcm │ ├── IM-0001-0293.dcm │ ├── IM-0001-0294.dcm │ ├── IM-0001-0295.dcm │ ├── IM-0001-0296.dcm │ ├── IM-0001-0297.dcm │ ├── IM-0001-0298.dcm │ ├── IM-0001-0299.dcm │ ├── IM-0001-0300.dcm │ ├── IM-0001-0301.dcm │ ├── IM-0001-0302.dcm │ ├── IM-0001-0303.dcm │ ├── IM-0001-0304.dcm │ ├── IM-0001-0305.dcm │ ├── IM-0001-0306.dcm │ ├── IM-0001-0307.dcm │ ├── IM-0001-0308.dcm │ ├── IM-0001-0309.dcm │ ├── IM-0001-0310.dcm │ ├── IM-0001-0311.dcm │ ├── IM-0001-0312.dcm │ ├── IM-0001-0313.dcm │ ├── IM-0001-0314.dcm │ ├── IM-0001-0315.dcm │ ├── IM-0001-0316.dcm │ ├── IM-0001-0317.dcm │ ├── IM-0001-0318.dcm │ ├── IM-0001-0319.dcm │ ├── IM-0001-0320.dcm │ ├── IM-0001-0321.dcm │ ├── IM-0001-0322.dcm │ ├── IM-0001-0323.dcm │ ├── IM-0001-0324.dcm │ ├── IM-0001-0325.dcm │ ├── IM-0001-0326.dcm │ ├── IM-0001-0327.dcm │ ├── IM-0001-0328.dcm │ ├── IM-0001-0329.dcm │ ├── IM-0001-0330.dcm │ ├── IM-0001-0331.dcm │ ├── IM-0001-0332.dcm │ ├── IM-0001-0333.dcm │ ├── IM-0001-0334.dcm │ └── IM-0001-0335.dcm │ └── SE2 │ └── IM0 ├── doc ├── Gallery.md ├── TextureAnalysis.ipynb └── imgs │ ├── GLCM.png │ ├── GLSZM.png │ ├── NGTDM.png │ ├── example_img.png │ ├── glcm_example.png │ ├── glha_example.png │ ├── glszm_example.png │ └── ngtdm_example.png ├── main.py └── tests ├── __init__.py ├── context.py └── test_core.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | .idea/ 3 | __pycache__/ 4 | *.png 5 | *.xlsx 6 | data/PA0/ST0/*.npy 7 | data/PA0/ST0/*.json 8 | data/PA0/ST0/*.png 9 | doc/.ipynb_checkpoints -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2016 Testuya Shinaji 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | 23 | 24 | The VoiEextactionManager.py is build with the routine for performing the 25 | "point in polygon" inclusion which major design was performed by softSurfer. 26 | The softSurfer's code was translated to Python by Maciej Kalisiak. 27 | Here is the original copyright notice. 28 | 29 | Copyright 2001, softSurfer (www.softsurfer.com) 30 | This code may be freely used and modified for any purpose 31 | providing that this copyright notice is included with it. 32 | SoftSurfer makes no warranty for this code, and cannot be held 33 | liable for any real or imagined damage resulting from its use. 34 | Users of this code must verify correctness for their application. 35 | 36 | translated to Python by Maciej Kalisiak 37 | 38 | http://www.dgp.toronto.edu/~mac/e-stuff/point_in_polygon.py 39 | -------------------------------------------------------------------------------- /TextureAnalysis/GLCM.py: -------------------------------------------------------------------------------- 1 | #-*- coding:utf-8 -*- 2 | """ 3 | GLCM 4 | 5 | Copyright (c) 2016 Tetsuya Shinaji 6 | 7 | This software is released under the MIT License. 8 | 9 | http://opensource.org/licenses/mit-license.php 10 | 11 | Date: 2016/01/29 12 | 13 | """ 14 | 15 | import numpy as np 16 | from matplotlib import pyplot as plt 17 | from TextureAnalysis.Utils import normalize 18 | 19 | 20 | class GLCM: 21 | """ 22 | Gray-Level Co-occurrence Matrix 23 | """ 24 | def __init__(self, img, theta=[0, 1], level_min=1, level_max=256, threshold=None): 25 | """ 26 | initialize 27 | 28 | :param img: normalized image 29 | :param theta: definition of neighbor 30 | :param level_min: min intensity of normalized image 31 | :param level_max: max intensity of normalized image 32 | :param threshold: threshold of the minimal value 33 | """ 34 | 35 | assert len(img.shape) == 2, 'image must be 2D' 36 | self.img, self.slope, self.intercept = \ 37 | normalize(img, level_min, level_max, threshold) 38 | self.n_level = (level_max - level_min) + 1 39 | self.level_min = level_min 40 | self.level_max = level_max 41 | self.theta = theta 42 | self.matrix = self._construct_matrix() 43 | self.features = self._calc_features() 44 | 45 | def _calc_features(self): 46 | """ 47 | calculate feature values 48 | 49 | :return: feature values 50 | """ 51 | 52 | I, J = np.ogrid[self.level_min:self.level_max+1, 53 | self.level_min:self.level_max+1] 54 | mat = np.array(self.matrix) 55 | features = {} 56 | features['uniformity'] = (mat**2).sum() 57 | features['entropy'] = -(mat[mat>0]*np.log(mat[mat>0])).sum() 58 | features['dissimilarity'] = (mat*np.abs(I-J)).sum() 59 | features['contrast'] = (mat*((I-J)**2)).sum() 60 | features['homogeneity'] = (mat/(1+np.abs(I-J))).sum() 61 | features['inverse difference moment'] = (mat/(1+(I-J)**2)).sum() 62 | features['maximum probability'] = mat.max()*100 63 | return features 64 | 65 | 66 | def _construct_matrix(self): 67 | """ 68 | construct GLC-Matrix 69 | 70 | :return: GLC-Matrix 71 | """ 72 | 73 | mat = np.zeros((self.n_level, self.n_level)).astype(np.float) 74 | unique = np.unique(self.img) 75 | width = self.img.shape[1] 76 | height = self.img.shape[0] 77 | print(self.img.max()) 78 | print(self.img.min()) 79 | for uni in unique: 80 | if uni < self.level_min: 81 | continue 82 | indices = np.argwhere(self.img == uni) 83 | for idx in indices: 84 | pos = np.array(idx + self.theta, dtype=np.int32) 85 | if 0 <= pos[0] < height and 0 <= pos[1] < width: 86 | neighbor_value = self.img[pos[0], pos[1]] 87 | if neighbor_value >= self.level_min: 88 | mat[self.img[idx[0], idx[1]]-self.level_min, 89 | self.img[pos[0], pos[1]]-self.level_min] += 1 90 | pos = idx + (self.theta*-1) 91 | if 0 <= pos[0] < height and 0 <= pos[1] < width: 92 | neighbor_value = self.img[pos[0], pos[1]] 93 | if neighbor_value >= self.level_min: 94 | mat[self.img[idx[0], idx[1]]-self.level_min, 95 | self.img[pos[0], pos[1]]-self.level_min] += 1 96 | return mat 97 | 98 | 99 | if __name__ == '__main__': 100 | 101 | suvs = np.load("suvs.npy") 102 | mats = [] 103 | for i in range(suvs.shape[0]): 104 | glcm = GLCM(suvs[i], theta=np.array([0, 1]), 105 | level_min=1, level_max=32, 106 | threshold=suvs.max()*0.5) 107 | mats.append(glcm.matrix) 108 | mats = np.array(mats) 109 | print(mats) 110 | print(mats.shape) -------------------------------------------------------------------------------- /TextureAnalysis/GLHA.py: -------------------------------------------------------------------------------- 1 | #-*- coding:utf-8 -*- 2 | """ 3 | GLHA 4 | 5 | Copyright (c) 2016 Tetsuya Shinaji 6 | 7 | This software is released under the MIT License. 8 | 9 | http://opensource.org/licenses/mit-license.php 10 | 11 | Date: 2016/01/29 12 | 13 | """ 14 | 15 | import numpy as np 16 | from matplotlib import pyplot as plt 17 | from TextureAnalysis.Utils import normalize 18 | 19 | class GLHA: 20 | """ 21 | Gray Level Histogram Analysis 22 | """ 23 | def __init__(self, img, level_min=1, level_max=256, threshold=None): 24 | """ 25 | initialize 26 | 27 | :param img: normalized image 28 | :param level_min: min intensity of normalized image 29 | :param level_max: max intensity of normalized image 30 | :param threshold: threshold of the minimal value 31 | """ 32 | 33 | self.img, self.slope, self.intercept = \ 34 | normalize(img, level_min, level_max, threshold) 35 | self.n_level = (level_max - level_min) + 1 36 | self.level_min = level_min 37 | self.level_max = level_max 38 | 39 | hist, bin_edges = np.histogram(self.img.flatten(), 40 | bins=self.n_level, 41 | range=[level_min, level_max], 42 | density=False) 43 | self.hist = np.array(hist) 44 | hist, bin_edges = np.histogram(self.img.flatten(), 45 | bins=self.n_level, 46 | range=[level_min, level_max], 47 | density=True) 48 | self.bin_centers = (bin_edges[:-1] + bin_edges[1:]) / 2 49 | 50 | self.p_glha = np.array(hist) 51 | self.features = self._calc_features() 52 | 53 | def _calc_features(self): 54 | """ 55 | calculate feature values 56 | 57 | :return: feature values 58 | """ 59 | 60 | features = {} 61 | x = np.arange(self.level_min, self.level_max+1) 62 | features['mean'] = (self.p_glha*x).sum() 63 | features['sd'] = np.sqrt((self.p_glha*(x-features['mean'])**2).sum()) 64 | features['skewness'] = \ 65 | (self.p_glha*(x-features['mean'])**3).sum() / features['sd']**3 66 | features['kurtosis'] = \ 67 | (self.p_glha*(x-features['mean'])**4).sum() / features['sd']**4 68 | 69 | return features 70 | 71 | def print_features(self, show_figure=False): 72 | """ 73 | print features 74 | 75 | :param show_figure: if True, show figure 76 | """ 77 | 78 | print("----GLHA-----") 79 | feature_labels = [] 80 | feature_values = [] 81 | for key in sorted(self.features.keys()): 82 | print("{}: {}".format(key, self.features[key])) 83 | feature_labels.append(key) 84 | feature_values.append(self.features[key]) 85 | 86 | if show_figure: 87 | plt.plot(self.bin_centers, self.p_glha, 'o-b', label='Dencity') 88 | plt.plot([self.features['mean'], self.features['mean']], 89 | [0, self.p_glha.max()*1.2], '-r', label='mean') 90 | plt.plot([self.features['mean']-self.features['sd'], 91 | self.features['mean']-self.features['sd']], 92 | [0, self.p_glha.max()*1.2], '-.r', label='sd lower') 93 | plt.plot([self.features['mean']+self.features['sd'], 94 | self.features['mean']+self.features['sd']], 95 | [0, self.p_glha.max()*1.2], '-.r', label='sd upper') 96 | plt.legend(loc=0, numpoints=1) 97 | plt.ylim(0, self.p_glha.max()*1.2) 98 | plt.show() 99 | 100 | return feature_labels, feature_values 101 | 102 | if __name__ == '__main__': 103 | pass -------------------------------------------------------------------------------- /TextureAnalysis/Utils.py: -------------------------------------------------------------------------------- 1 | #-*- coding:utf-8 -*- 2 | """ 3 | Utills 4 | 5 | Copyright (c) 2016 Tetsuya Shinaji 6 | 7 | This software is released under the MIT License. 8 | 9 | http://opensource.org/licenses/mit-license.php 10 | 11 | Date: 2016/01/29 12 | 13 | """ 14 | 15 | import numpy as np 16 | from matplotlib import pyplot as plt 17 | 18 | 19 | def normalize(img, level_min=1, level_max=256, threshold=None): 20 | """ 21 | normalize the given image 22 | 23 | :param img: image array 24 | :param level_min: min intensity of normalized image 25 | :param level_max: max intensity of normalized image 26 | :param threshold: threshold of the minimal value 27 | 28 | :return: normalized image array, slope, intercept 29 | """ 30 | 31 | tmp_img = np.array(img) 32 | if threshold is None: 33 | threshold = tmp_img.min() 34 | tmp_img[tmp_img 26 | 27 | http://www.dgp.toronto.edu/~mac/e-stuff/point_in_polygon.py 28 | 29 | """ 30 | import numpy as np 31 | 32 | 33 | def is_inside(z0, z1, pet_img): 34 | """ 35 | check if z0 is within z1 polygon 36 | :param z0: point 37 | :param z1: vertex positions of roi polygon 38 | :param pet_img: pet image 39 | :return: 40 | """ 41 | tmp = np.ones_like(pet_img) * -1 42 | for i in range(len(z0)): 43 | if __get_wn(z0[i], z1): 44 | tmp[z0[i][1], z0[i][0]] = pet_img[z0[i][1], z0[i][0]] 45 | return tmp 46 | 47 | 48 | def __is_left(P0, P1, P2): 49 | """ 50 | check if P2 is left of the vector P0->P1 51 | :param P0: vertex position of polygon 52 | :param P1: vertex position of polygon next to p1 53 | :param P2: target position for this check process 54 | """ 55 | return (P1[0] - P0[0]) * (P2[1] - P0[1]) - (P2[0] - P0[0]) * (P1[1] - P0[1]) 56 | 57 | 58 | def __get_wn(z0, z1): 59 | """ 60 | retrun wn value of the Winding Number Algorithm 61 | :param z0: target position for this check process 62 | :param z1: vertex positions of polygon 63 | :return: wn 64 | """ 65 | 66 | wn = 0 67 | for i in range(z1.shape[0] - 1): 68 | 69 | v1 = z1[i + 1] - z1[i] 70 | v2 = z1[i + 1] - z0 71 | lv1 = np.linalg.norm(v1) 72 | lv2 = np.linalg.norm(v2) 73 | if lv2 == 0: 74 | return 1 75 | if (np.abs(np.dot(v1 / lv1, v2 / lv2) - 1) <= 1e-5) and ( 76 | lv1 >= lv2) and (lv1 > np.linalg.norm(v1 + v2)): 77 | return 1 78 | 79 | if z1[i, 1] <= z0[1]: # start y <= P[1] 80 | if z1[i + 1, 1] > z0[1]: # an upward crossing 81 | if __is_left(z1[i], z1[i + 1], z0) > 0: # P left of edge 82 | wn += 1 # have a valid up intersect 83 | else: # start y > P[1] (no test needed) 84 | if z1[i + 1, 1] <= z0[1]: # a downward crossing 85 | if __is_left(z1[i], z1[i + 1], z0) < 0: # P right of edge 86 | wn -= 1 # have a valid down intersect 87 | return wn 88 | -------------------------------------------------------------------------------- /data/PA0/ST0/SE0/IM-0002-0001.dcm: -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/shinaji/texture_analysis/1beb4c887d20eb011f0e8b5c98c223fa33d22a9c/data/PA0/ST0/SE1/IM-0001-0335.dcm -------------------------------------------------------------------------------- /data/PA0/ST0/SE2/IM0: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shinaji/texture_analysis/1beb4c887d20eb011f0e8b5c98c223fa33d22a9c/data/PA0/ST0/SE2/IM0 -------------------------------------------------------------------------------- /doc/Gallery.md: -------------------------------------------------------------------------------- 1 | # Gallery 2 | 3 | The following images were generated by [TextureAnalysis.ipynb](https://github.com/shinaji/texture_analysis/blob/master/doc/TextureAnalysis.ipynb) 4 | 5 | ## GLCM 6 | ![image](./imgs/glcm_example.png) 7 | 8 | ## GLSZM 9 | ![image](./imgs/glszm_example.png) 10 | 11 | ## NGTDM 12 | ![image](./imgs/ngtdm_example.png) 13 | 14 | ## GLHA 15 | ![image](./imgs/glha_example.png) -------------------------------------------------------------------------------- /doc/imgs/GLCM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shinaji/texture_analysis/1beb4c887d20eb011f0e8b5c98c223fa33d22a9c/doc/imgs/GLCM.png -------------------------------------------------------------------------------- /doc/imgs/GLSZM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shinaji/texture_analysis/1beb4c887d20eb011f0e8b5c98c223fa33d22a9c/doc/imgs/GLSZM.png -------------------------------------------------------------------------------- /doc/imgs/NGTDM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shinaji/texture_analysis/1beb4c887d20eb011f0e8b5c98c223fa33d22a9c/doc/imgs/NGTDM.png 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-------------------------------------------------------------------------------- /tests/context.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | import sys 4 | import os 5 | sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) 6 | 7 | import TextureAnalysis -------------------------------------------------------------------------------- /tests/test_core.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | from nose.tools import with_setup, raises, ok_, timed 4 | import os 5 | import copy 6 | import numpy as np 7 | from .context import TextureAnalysis 8 | 9 | 10 | class TestCore: 11 | 12 | simple_test_data = np.zeros((4, 4, 4), dtype=np.float64) 13 | simple_test_data[0] = -1 14 | simple_test_data[1] = 1 15 | simple_test_data[2] = 2 16 | simple_test_data[3] = 3 17 | 18 | glcm = TextureAnalysis.GLCM_3D(simple_test_data, d=1, 19 | level_min=0, level_max=2, threshold=1) 20 | glha = TextureAnalysis.GLHA(simple_test_data, 21 | level_min=0, level_max=2, threshold=1) 22 | glszm = TextureAnalysis.GLSZM_3D(simple_test_data, 23 | level_min=1, level_max=3, threshold=1) 24 | ngtdm = TextureAnalysis.NGTDM_3D(simple_test_data, d=1, 25 | level_min=1, level_max=3, threshold=1) 26 | 27 | @classmethod 28 | def setup_class(clazz): 29 | print('Test start!') 30 | 31 | @classmethod 32 | def teardown_class(clazz): 33 | print('Done!') 34 | 35 | def setup(self): 36 | pass 37 | 38 | def teardown(self): 39 | pass 40 | 41 | def test_glcm(self): 42 | assert np.all(self.glcm.matrix_non_norm == 43 | np.array([[84, 100, 0], 44 | [100, 84, 100], 45 | [0, 100, 84]])), \ 46 | 'Constructed matrix is not correct.' 47 | --------------------------------------------------------------------------------