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Re-structuring package layout
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Craig Warren
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## Tissue properties
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## Non-dispersive properties (900MHz) from http://niremf.ifac.cnr.it/tissprop/htmlclie/htmlclie.php
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#material: 1 0 1 0 Air
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#material: 44.77 0.6961 1 0 Aorta
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#material: 18.94 0.3831 1 0 Bladder
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#material: 61.36 1.538 1 0 Blood
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#material: 44.77 0.6961 1 0 BloodVessel
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#material: 68.9 1.636 1 0 BodyFluid
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#material: 20.79 0.34 1 0 BoneCancellous
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#material: 12.45 0.1433 1 0 BoneCortical
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#material: 5.504 0.04021 1 0 BoneMarrow
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#material: 52.73 0.9423 1 0 BrainGreyMatter
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#material: 38.89 0.5908 1 0 BrainWhiteMatter
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#material: 5.424 0.04896 1 0 BreastFat
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#material: 42.65 0.7824 1 0 Cartilage
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#material: 49.44 1.263 1 0 Cerebellum
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#material: 68.64 2.413 1 0 CerebroSpinalFluid
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#material: 49.78 0.9591 1 0 Cervix
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#material: 57.94 1.08 1 0 Colon
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#material: 55.23 1.394 1 0 Cornea
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#material: 65.06 1.187 1 0 Duodenum
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#material: 44.43 0.9611 1 0 Dura
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#material: 55.27 1.167 1 0 EyeSclera
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#material: 5.462 0.05104 1 0 Fat
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#material: 59.14 1.257 1 0 GallBladder
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#material: 70.19 1.838 1 0 GallBladderBile
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#material: 59.68 1.038 1 0 Gland
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#material: 59.89 1.23 1 0 Heart
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#material: 58.67 1.392 1 0 Kidney
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#material: 46.57 0.7934 1 0 Lens
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#material: 46.83 0.855 1 0 Liver
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#material: 51.42 0.858 1 0 LungDeflated
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#material: 22 0.4567 1 0 LungInflated
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#material: 59.68 1.038 1 0 Lymph
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#material: 46.08 0.8447 1 0 MucousMembrane
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#material: 55.03 0.9429 1 0 Muscle
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#material: 12.45 0.1433 1 0 Nail
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#material: 32.53 0.5737 1 0 Nerve
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#material: 65.06 1.187 1 0 Oesophagus
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#material: 50.47 1.29 1 0 Ovary
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#material: 59.68 1.038 1 0 Pancreas
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#material: 60.55 1.21 1 0 Prostate
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#material: 55.27 1.167 1 0 Retina
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#material: 41.41 0.8667 1 0 SkinDry
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#material: 46.08 0.8447 1 0 SkinWet
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#material: 59.49 2.165 1 0 SmallIntestine
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#material: 32.53 0.5737 1 0 SpinalCord
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#material: 57.18 1.273 1 0 Spleen
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#material: 65.06 1.187 1 0 Stomach
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#material: 45.83 0.7184 1 0 Tendon
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#material: 60.55 1.21 1 0 Testis
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#material: 59.68 1.038 1 0 Thymus
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#material: 59.68 1.038 1 0 Thyroid
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#material: 55.27 0.9363 1 0 Tongue
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#material: 12.45 0.1433 1 0 Tooth
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#material: 42.01 0.7711 1 0 Trachea
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#material: 61.12 1.27 1 0 Uterus
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#material: 68.9 1.636 1 0 VitreousHumor
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## Tissue properties
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## 3-Pole Debye model (1MHz-100GHz) from http://dx.doi.org/10.1109/LMWC.2011.2180371
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## Non-dispersive properties (900MHz) from http://niremf.ifac.cnr.it/tissprop/htmlclie/htmlclie.php
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#material: 1 0 1 0 Air
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#material: 44.77 0.6961 1 0 Aorta
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#material: 3.4969 0.2261 1 0 Bladder
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#add_dispersion_debye: 3 370.48 9.1145e-8 21.866 4.6778e-10 15.38 0.94981e-11 Bladder
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#material: 7.5425 0.73265 1 0 Blood
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#add_dispersion_debye: 3 3529.4 8.8589e-8 110.21 5.4229e-9 53.637 0.89892 Blood
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#material: 44.77 0.6961 1 0 BloodVessel
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#material: 68.9 1.636 1 0 BodyFluid
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## Avg. Bone used for BoneCancellous & BoneMarrow
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#material: 3.8518 0.095687 1 0 BoneCancellous
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#add_dispersion_debye: 3 125.82 3.2802e-8 18.125 2.4901e-9 11.748 1.379e-11 BoneCancellous
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#material: 3.4498 0.022411 1 0 BoneCortical
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#add_dispersion_debye: 3 118.19 4.6747e-8 9.5114 2.2822e-9 8.807 1.3731e-11 BoneCortical
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## Avg. Bone used for BoneCancellous & BoneMarrow
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#material: 3.8518 0.095687 1 0 BoneMarrow
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#add_dispersion_debye: 3 125.82 3.2802e-8 18.125 2.4901e-9 11.748 1.379e-11 BoneMarrow
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## Avg. Brain used for BrainGreyMatter & BrainWhiteMatter
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#material: 6.9992 0.17911 1 0 BrainGreyMatter
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#add_dispersion_debye: 3 787.41 2.2589e-8 142.26 2.5012e-9 40.264 0.91939e-11 BrainGreyMatter
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#material: 6.9992 0.17911 1 0 BrainWhiteMatter
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#add_dispersion_debye: 3 787.41 2.2589e-8 142.26 2.5012e-9 40.264 0.91939e-11 BrainWhiteMatter
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#material: 5.424 0.04896 1 0 BreastFat
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#material: 42.65 0.7824 1 0 Cartilage
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#material: 6.9992 0.17911 1 0 Cerebellum
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#add_dispersion_debye: 3 787.41 2.2589e-8 142.26 2.5012e-9 40.264 0.91939e-11 Cerebellum
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#material: 5.7772 2.0002 1 0 CerebroSpinalFluid
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#add_dispersion_debye: 3 40.84 0.15293e-8 27.951 0.014519e-9 34.334 0.50631e-11 CerebroSpinalFluid
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#material: 49.78 0.9591 1 0 Cervix
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#material: 57.94 1.08 1 0 Colon
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#material: 55.23 1.394 1 0 Cornea
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#material: 7.8582 0.55004 1 0 Duodenum
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#add_dispersion_debye: 3 1674.5 6.273e-8 74.699 4.4123e-9 56.797 0.85287e-11 Duodenum
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#material: 44.43 0.9611 1 0 Dura
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#material: 55.27 1.167 1 0 EyeSclera
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#material: 3.261 0.043999 1 0 Fat
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#add_dispersion_debye: 3 34.522 1.3971e-8 2.2452 0.04806e-9 6.2928 0.60675e-11 Fat
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#material: 4.7563 0.90026 1 0 GallBladder
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#add_dispersion_debye: 3 40.681 0.1583e-8 20.066 0.01249e-9 33.876 0.57641e-11 GallBladder
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#material: 70.19 1.838 1 0 GallBladderBile
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#material: 59.68 1.038 1 0 Gland
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#material: 7.8989 0.27449 1 0 Heart
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#add_dispersion_debye: 3 1935.3 7.9786e-8 138.97 3.2768e-9 50.762 0.93944e-11 Heart
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#material: 7.8691 0.23004 1 0 Kidney
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#add_dispersion_debye: 3 2025 6.5466e-8 167.3 3.0341e-9 48.945 0.96655e-11 Kidney
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## Avg. Lens
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#material: 5.8421 0.27596 1 0 Lens
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#add_dispersion_debye: 3 630.99 5.9556e-8 62.733 3.6647e-9 30.811 0.89718e-11 Lens
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#material: 6.809 0.14243 1 0 Liver
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#add_dispersion_debye: 3 1529.8 8.4314e-8 112.04 3.7562e-9 39.593 1.0293e-11 Liver
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## Avg. Lung used for LungDeflated & LungInflated
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#material: 5.5014 0.21296 1 0 LungDeflated
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#add_dispersion_debye: 3 899.49 6.9396e-8 62.733 3.6647e-9 30.811 0.89718e-11 LungDeflated
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#material: 5.5014 0.21296 1 0 LungInflated
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#add_dispersion_debye: 3 899.49 6.9396e-8 62.733 3.6647e-9 30.811 0.89718e-11 LungInflated
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#material: 59.68 1.038 1 0 Lymph
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#material: 46.08 0.8447 1 0 MucousMembrane
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## Avg. Muscle
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#material: 7.5933 0.42066 1 0 Muscle
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#add_dispersion_debye: 3 2646.6 13.044e-8 87.588 6.1808e-9 47.546 0.79767e-11 Muscle
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#material: 12.45 0.1433 1 0 Nail
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#material: 32.53 0.5737 1 0 Nerve
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#material: 65.06 1.187 1 0 Oesophagus
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#material: 50.47 1.29 1 0 Ovary
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#material: 59.68 1.038 1 0 Pancreas
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#material: 60.55 1.21 1 0 Prostate
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#material: 55.27 1.167 1 0 Retina
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## Avg. Skin used from SkinDry & SkinWet
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#material: 5.8661 0.092415 1 0 SkinDry
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#add_dispersion_debye: 3 1123 5.4817e-8 144.69 4.0078e-9 37.434 0.88726e-11 SkinDry
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#material: 5.8661 0.092415 1 0 SkinWet
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#add_dispersion_debye: 3 1123 5.4817e-8 144.69 4.0078e-9 37.434 0.88726e-11 SkinWet
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#material: 7.7811 0.6884 1 0 SmallIntestine
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#add_dispersion_debye: 3 6590.7 9.123e-8 211.31 4.2003e-9 50.6 0.92249e-11 SmallIntestine
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#material: 32.53 0.5737 1 0 SpinalCord
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#material: 57.18 1.273 1 0 Spleen
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#material: 7.8582 0.55004 1 0 Stomach
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#add_dispersion_debye: 3 1674.5 6.273e-8 74.699 4.4123e-9 56.797 0.85287e-11 Stomach
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#material: 45.83 0.7184 1 0 Tendon
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#material: 60.55 1.21 1 0 Testis
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#material: 59.68 1.038 1 0 Thymus
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#material: 59.68 1.038 1 0 Thyroid
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#material: 55.27 0.9363 1 0 Tongue
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#material: 12.45 0.1433 1 0 Tooth
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#material: 42.01 0.7711 1 0 Trachea
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#material: 61.12 1.27 1 0 Uterus
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#material: 4.0041 1.5001 1 0 VitreousHumor
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#add_dispersion_debye: 3 21.766 12.46e-8 1.364 15.742e-9 65.024 0.72371e-11 VitreousHumor
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User libraries is a sub-package where useful Python modules contributed by users are stored.
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*********************
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AustinMan/AustinWoman
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*********************
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Information
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===========
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**Authors**: Jackson W. Massey, Cemil S. Geyik, Jungwook Choi, Hyun-Jae Lee, Natcha Techachainiran, Che-Lun Hsu, Robin Q. Nguyen, Trevor Latson, Madison Ball, and Ali E. Yılmaz
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**Contact**: Ali E. Yılmaz (ayilmaz@mail.utexas.edu), The University of Texas at Austin
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**License**: `Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License <http://creativecommons.org/licenses/by-nc-nd/3.0/>`_
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**Attribution/cite**: Please follow the instructions at http://web.corral.tacc.utexas.edu/AustinManEMVoxels/AustinMan/citing_the_model/index.html
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`AustinMan and AustinWoman <http://bit.ly/AustinMan>`_ are open source electromagnetic voxel models of the human body, which are developed by the `Computational Electromagnetics Group <http://www.ece.utexas.edu/research/areas/electromagnetics-acoustics>`_ at `The University of Texas at Austin <http://www.utexas.edu>`_. The models are based on data from the `National Library of Medicine’s Visible Human Project <https://www.nlm.nih.gov/research/visible/visible_human.html>`_.
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.. figure:: ../../images_shared/AustinMan_head.png
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:width: 600 px
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FDTD geometry mesh showing the head of the AustinMan model (2x2x2mm :math:`^3`).
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The following whole body models are available.
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=========== ========================== ==================
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Model Resolution (mm :math:`^3`) Dimensions (cells)
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=========== ========================== ==================
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AustinMan 8x8x8 86 x 47 x 235
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AustinMan 4x4x4 171 x 94 x 470
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AustinMan 2x2x2 342 x 187 x 939
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AustinMan 1x1x1 683 x 374 x 1877
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AustinWoman 8x8x8 86 x 47 x 217
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AustinWoman 4x4x4 171 x 94 x 433
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AustinWoman 2x2x2 342 x 187 x 865
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AustinWoman 1x1x1 683 x 374 x 1730
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=========== ========================== ==================
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Package contents
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================
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.. code-block:: none
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AustinManWoman_materials.txt
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AustinManWoman_materials_dispersive.txt
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head_only_h5.py
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* ``AustinManWoman_materials.txt`` is a text file containing `non-dispersive material properties at 900 MHz <http://niremf.ifac.cnr.it/tissprop/>`_.
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* ``AustinManWoman_materials_dispersive.txt`` is a text file containing `dispersive material properties using a 3-pole Debye model <http://dx.doi.org/10.1109/LMWC.2011.2180371>`_.
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.. note::
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* The main body tissues are described using a 3-pole Debye model, but not all materials have a dispersive description.
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* The dispersive material properties can only be used with the 1x1x1mm or 2x2x2mm AustinMan/Woman models. This is because the time step of the model must always be less than any of the relaxation times of the poles of the Debye models used for the dispersive material properties.
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* ``head_only_h5.py`` is a script to assist with creating a model of only the head from a full body AustinMan/Woman model.
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How to use the package
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======================
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The AustinMan and AustinWoman models themselves are not included in the user libraries sub-package.
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* `Download a HDF5 file (.h5) of AustinMan or AustinWoman <http://bit.ly/AustinMan>`_ at the resolution you wish to use
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To insert either AustinMan or AustinWoman models into a simulation use the ``#geometry_objects_read``.
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Example
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-------
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To insert a 2x2x2mm :math:`^3` AustinMan with the lower left corner 40mm from the origin of the domain, using disperive material properties, and with no dielectric smoothing, use the command:
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.. code-block:: none
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#geometry_objects_read: 0.04 0.04 0.04 ../user_libs/AustinManWoman/AustinMan_v2.3_2x2x2.h5 ../user_libs/AustinManWoman/AustinManWoman_materials_dispersive.txt
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For further information on the ``#geometry_objects_read`` see the section on object contruction commands in the :ref:`Input commands section <commands>`.
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.. figure:: ../../images_shared/AustinMan.png
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:width: 300 px
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FDTD geometry mesh showing the AustinMan body model (2x2x2mm :math:`^3`).
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import argparse
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import logging
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import os
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import h5py
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logger = logging.getLogger(__name__)
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# Parse command line arguments
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parser = argparse.ArgumentParser(description='Writes a HDF5 file of AustinMan or AustinWoman head only.', usage='python head_only_hdf5 filename')
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parser.add_argument('filename', help='name and path to (HDF5) file containing AustinMan or AustinWoman model')
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args = parser.parse_args()
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# Read full body HDF5 file
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f = h5py.File(args.filename, 'r')
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dx_dy_dz = f.attrs['dx_dy_dz']
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data = f['/data'][:, :, :]
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# Define head as last 1/8 of total body height
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nzhead = 7 * int(data.shape[2] / 8)
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logger.info(f'Dimensions of head model: {data.shape[0]:g} x {data.shape[1]:g} x {data.shape[2] - nzhead:g} cells')
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# Write HDF5 file
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headfile = os.path.splitext(args.filename)[0] + '_head.h5'
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f = h5py.File(headfile, 'w')
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f.attrs['dx_dy_dz'] = dx_dy_dz
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f['/data'] = data[:, :, nzhead:data.shape[2]]
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