Fix on GetExtinctions (8441320a) · Commits · github_fork / Homer3

FuncRegistry/UserFunctions/GetExtinctions.m

+287 −127

Original line number	Diff line number	Diff line
		@@ -121,7 +121,7 @@ num_lambda = length(lambda);


		if ~exist('WhichSpectrum')
		WhichSpectrum=1;
		WhichSpectrum=0;
		end


		@@ -132,6 +132,166 @@ switch(WhichSpectrum)
		%**************************************************************************
		%**************************************************************************

		case 0
		Citation=sprintf('%s\n%s','Wray, S., Cope, M., Delpy, D., Wyatt, J., Reynolds, E. (1988). Characterization of the near infrared absorption spectra of cytochrome aa3 and haemoglobin for the non-invasive monitoring of cerebral oxygenation Biochimica et Biophysica Acta (BBA) - Bioenergetics 933(1), 184-192. https://dx.doi.org/10.1016/0005-2728(88)90069-2');

		% These values for the molar extinction coefficient e in
		% [cm-1/(moles/liter)] come from
		%
		% Wray, S., Cope, M., Delpy, D., Wyatt, J., Reynolds, E. (1988).
		% Characterization of the near infrared absorption spectra of cytochrome aa3 and
		% haemoglobin for the non-invasive monitoring of cerebral oxygenation Biochimica et Biophysica Acta (BBA) -
		% Bioenergetics 933(1), 184-192. https://dx.doi.org/10.1016/0005-2728(88)90069-2
		%
		% To convert this data to absorbance A, multiply by the molar concentration and the pathlength. For example, if x is the number of grams per liter and a 1 cm cuvette is being used, then the absorbance is given by
		%
		% (e) [(1/cm)/(moles/liter)] (x) [g/liter] (1) [cm]
		% A = ---------------------------------------------------
		% 66,500 [g/mole]
		%
		% using 66,500 as the gram molecular weight of hemoglobin.
		% To convert this data to absorption coefficient in (cm-1), multiply by the molar concentration and 2.303,
		%
		% µa = (2.303) e (x g/liter)/(66,500 g Hb/mole)
		% where x is the number of grams per liter. A typical value of x for whole blood is x=150 g Hb/liter.

		vLambdaHbOHb = [
		650.0 506.0 3743.0;
		652.0 488.0 3677.0;
		654.0 474.0 3612.0;
		656.0 464.0 3548.0;
		658.0 454.3 3491.3;
		660.0 445.0 3442.0;
		662.0 438.3 3364.7;
		664.0 433.8 3292.8;
		666.0 431.3 3226.3;
		668.0 429.0 3133.0;
		670.0 427.0 3013.0;
		672.0 426.5 2946.0;
		674.0 426.0 2879.0;
		676.0 424.0 2821.7;
		678.0 423.0 2732.3;
		680.0 423.0 2610.8;
		682.0 422.0 2497.3;
		684.0 420.0 2392.0;
		686.0 418.0 2292.7;
		688.0 416.5 2209.3;
		690.0 415.5 2141.8;
		692.0 415.0 2068.7;
		694.0 415.0 1990.0;
		696.0 415.5 1938.5;
		698.0 416.0 1887.0;
		700.0 419.3 1827.7;
		702.0 422.5 1778.5;
		704.0 425.5 1739.5;
		706.0 429.7 1695.7;
		708.0 435.0 1647.0;
		710.0 441.0 1601.7;
		712.0 446.5 1562.5;
		714.0 451.5 1529.5;
		716.0 458.0 1492.0;
		718.0 466.0 1450.0;
		720.0 472.7 1411.3;
		722.0 479.5 1380.0;
		724.0 486.5 1356.0;
		726.0 494.3 1331.7;
		728.0 503.0 1307.0;
		730.0 510.0 1296.5;
		732.0 517.0 1286.0;
		734.0 521.0 1286.0;
		736.0 530.7 1293.0;
		738.0 546.0 1307.0;
		740.0 553.5 1328.0;
		742.0 561.0 1349.0;
		744.0 571.0 1384.3;
		746.0 581.3 1431.3;
		748.0 592.0 1490.0;
		750.0 600.0 1532.0;
		752.0 608.0 1574.0;
		754.0 618.7 1620.7;
		756.0 629.7 1655.3;
		758.0 641.0 1678.0;
		760.0 645.5 1669.0;
		762.0 650.0 1660.0;
		764.0 666.7 1613.3;
		766.0 681.0 1555.0;
		768.0 693.0 1485.0;
		770.0 701.5 1425.0;
		772.0 710.0 1365.0;
		774.0 722.0 1288.3;
		776.0 733.7 1216.3;
		778.0 745.0 1149.0;
		780.0 754.0 1107.5;
		782.0 763.0 1066.0;
		784.0 775.0 1021.3;
		786.0 787.0 972.0;
		788.0 799.0 918.0;
		790.0 808.0 913.0;
		792.0 817.0 908.0;
		794.0 829.0 887.3;
		796.0 840.7 868.7;
		798.0 852.0 852.0;
		800.0 863.3 838.7;
		802.0 873.3 828.0;
		804.0 881.8 820.0;
		806.0 891.7 812.0;
		808.0 903.0 804.0;
		810.0 914.3 798.7;
		812.0 924.7 793.7;
		814.0 934.0 789.0;
		816.0 943.0 787.0;
		818.0 952.0 785.0;
		820.0 962.7 783.0;
		822.0 973.0 781.0;
		824.0 983.0 779.0;
		826.0 990.5 778.5;
		828.0 998.0 778.0;
		830.0 1008.0 778.0;
		832.0 1018.0 777.7;
		834.0 1028.0 777.0;
		836.0 1038.0 777.0;
		838.0 1047.7 777.0;
		840.0 1057.0 777.0;
		842.0 1063.5 777.5;
		844.0 1070.0 778.0;
		846.0 1079.3 779.3;
		848.0 1088.3 780.3;
		850.0 1097.0 781.0;
		852.0 1105.7 783.0;
		854.0 1113.0 785.0;
		856.0 1119.0 787.0;
		858.0 1126.0 789.3;
		860.0 1134.0 792.0;
		862.0 1142.0 795.3;
		864.0 1149.7 799.0;
		866.0 1157.0 803.0;
		868.0 1163.7 807.7;
		870.0 1170.3 812.3;
		872.0 1177.0 817.0;
		874.0 1182.0 820.5;
		876.0 1187.0 824.0;
		878.0 1193.0 830.0;
		880.0 1198.7 835.7;
		882.0 1204.0 841.0;
		884.0 1209.3 847.0;
		886.0 1214.3 852.7;
		888.0 1219.0 858.0;
		890.0 1223.7 863.3;
		892.0 1227.5 867.8;
		894.0 1230.5 871.3;
		896.0 1234.0 875.3;
		898.0 1238.0 880.0;
		900.0 1241.3 883.3 ];


		vLambdaHbOHb(:,2) = vLambdaHbOHb(:,2) * 2.303;
		vLambdaHbOHb(:,3) = vLambdaHbOHb(:,3) * 2.303;

		%**************************************************************************
		%**************************************************************************
		%**************************************************************************
		%**************************************************************************

		case 1
		Citation=sprintf('%s\n%s','W. B. Gratzer, Med. Res. Council Labs, Holly Hill,London',...
		'N. Kollias, Wellman Laboratories, Harvard Medical School, Boston');
		@@ -353,132 +513,132 @@ switch(WhichSpectrum)
		644 405.2 4088.4;
		646 390.4 3965.08;
		648 379.2 3857.6;
		650.0 506.0 3743.0;
		652.0 488.0 3677.0;
		654.0 474.0 3612.0;
		656.0 464.0 3548.0;
		658.0 454.3 3491.3;
		660.0 445.0 3442.0;
		662.0 438.3 3364.7;
		664.0 433.8 3292.8;
		666.0 431.3 3226.3;
		668.0 429.0 3133.0;
		670.0 427.0 3013.0;
		672.0 426.5 2946.0;
		674.0 426.0 2879.0;
		676.0 424.0 2821.7;
		678.0 423.0 2732.3;
		680.0 423.0 2610.8;
		682.0 422.0 2497.3;
		684.0 420.0 2392.0;
		686.0 418.0 2292.7;
		688.0 416.5 2209.3;
		690.0 415.5 2141.8;
		692.0 415.0 2068.7;
		694.0 415.0 1990.0;
		696.0 415.5 1938.5;
		698.0 416.0 1887.0;
		700.0 419.3 1827.7;
		702.0 422.5 1778.5;
		704.0 425.5 1739.5;
		706.0 429.7 1695.7;
		708.0 435.0 1647.0;
		710.0 441.0 1601.7;
		712.0 446.5 1562.5;
		714.0 451.5 1529.5;
		716.0 458.0 1492.0;
		718.0 466.0 1450.0;
		720.0 472.7 1411.3;
		722.0 479.5 1380.0;
		724.0 486.5 1356.0;
		726.0 494.3 1331.7;
		728.0 503.0 1307.0;
		730.0 510.0 1296.5;
		732.0 517.0 1286.0;
		734.0 521.0 1286.0;
		736.0 530.7 1293.0;
		738.0 546.0 1307.0;
		740.0 553.5 1328.0;
		742.0 561.0 1349.0;
		744.0 571.0 1384.3;
		746.0 581.3 1431.3;
		748.0 592.0 1490.0;
		750.0 600.0 1532.0;
		752.0 608.0 1574.0;
		754.0 618.7 1620.7;
		756.0 629.7 1655.3;
		758.0 641.0 1678.0;
		760.0 645.5 1669.0;
		762.0 650.0 1660.0;
		764.0 666.7 1613.3;
		766.0 681.0 1555.0;
		768.0 693.0 1485.0;
		770.0 701.5 1425.0;
		772.0 710.0 1365.0;
		774.0 722.0 1288.3;
		776.0 733.7 1216.3;
		778.0 745.0 1149.0;
		780.0 754.0 1107.5;
		782.0 763.0 1066.0;
		784.0 775.0 1021.3;
		786.0 787.0 972.0;
		788.0 799.0 918.0;
		790.0 808.0 913.0;
		792.0 817.0 908.0;
		794.0 829.0 887.3;
		796.0 840.7 868.7;
		798.0 852.0 852.0;
		800.0 863.3 838.7;
		802.0 873.3 828.0;
		804.0 881.8 820.0;
		806.0 891.7 812.0;
		808.0 903.0 804.0;
		810.0 914.3 798.7;
		812.0 924.7 793.7;
		814.0 934.0 789.0;
		816.0 943.0 787.0;
		818.0 952.0 785.0;
		820.0 962.7 783.0;
		822.0 973.0 781.0;
		824.0 983.0 779.0;
		826.0 990.5 778.5;
		828.0 998.0 778.0;
		830.0 1008.0 778.0;
		832.0 1018.0 777.7;
		834.0 1028.0 777.0;
		836.0 1038.0 777.0;
		838.0 1047.7 777.0;
		840.0 1057.0 777.0;
		842.0 1063.5 777.5;
		844.0 1070.0 778.0;
		846.0 1079.3 779.3;
		848.0 1088.3 780.3;
		850.0 1097.0 781.0;
		852.0 1105.7 783.0;
		854.0 1113.0 785.0;
		856.0 1119.0 787.0;
		858.0 1126.0 789.3;
		860.0 1134.0 792.0;
		862.0 1142.0 795.3;
		864.0 1149.7 799.0;
		866.0 1157.0 803.0;
		868.0 1163.7 807.7;
		870.0 1170.3 812.3;
		872.0 1177.0 817.0;
		874.0 1182.0 820.5;
		876.0 1187.0 824.0;
		878.0 1193.0 830.0;
		880.0 1198.7 835.7;
		882.0 1204.0 841.0;
		884.0 1209.3 847.0;
		886.0 1214.3 852.7;
		888.0 1219.0 858.0;
		890.0 1223.7 863.3;
		892.0 1227.5 867.8;
		894.0 1230.5 871.3;
		896.0 1234.0 875.3;
		898.0 1238.0 880.0;
		900.0 1241.3 883.3;
		650 368 3750.12;
		652 356.8 3642.64;
		654 345.6 3535.16;
		656 335.2 3427.68;
		658 325.6 3320.2;
		660 319.6 3226.56;
		662 314 3140.28;
		664 308.4 3053.96;
		666 302.8 2967.68;
		668 298 2881.4;
		670 294 2795.12;
		672 290 2708.84;
		674 285.6 2627.64;
		676 282 2554.4;
		678 279.2 2481.16;
		680 277.6 2407.92;
		682 276 2334.68;
		684 274.4 2261.48;
		686 272.8 2188.24;
		688 274.4 2115;
		690 276 2051.96;
		692 277.6 2000.48;
		694 279.2 1949.04;
		696 282 1897.56;
		698 286 1846.08;
		700 290 1794.28;
		702 294 1741;
		704 298 1687.76;
		706 302.8 1634.48;
		708 308.4 1583.52;
		710 314 1540.48;
		712 319.6 1497.4;
		714 325.2 1454.36;
		716 332 1411.32;
		718 340 1368.28;
		720 348 1325.88;
		722 356 1285.16;
		724 364 1244.44;
		726 372.4 1203.68;
		728 381.2 1152.8;
		730 390 1102.2;
		732 398.8 1102.2;
		734 407.6 1102.2;
		736 418.8 1101.76;
		738 432.4 1100.48;
		740 446 1115.88;
		742 459.6 1161.64;
		744 473.2 1207.4;
		746 487.6 1266.04;
		748 502.8 1333.24;
		750 518 1405.24;
		752 533.2 1515.32;
		754 548.4 1541.76;
		756 562 1560.48;
		758 574 1560.48;
		760 586 1548.52;
		762 598 1508.44;
		764 610 1459.56;
		766 622.8 1410.52;
		768 636.4 1361.32;
		770 650 1311.88;
		772 663.6 1262.44;
		774 677.2 1213;
		776 689.2 1163.56;
		778 699.6 1114.8;
		780 710 1075.44;
		782 720.4 1036.08;
		784 730.8 996.72;
		786 740 957.36;
		788 748 921.8;
		790 756 890.8;
		792 764 859.8;
		794 772 828.8;
		796 786.4 802.96;
		798 807.2 782.36;
		800 816 761.72;
		802 828 743.84;
		804 836 737.08;
		806 844 730.28;
		808 856 723.52;
		810 864 717.08;
		812 872 711.84;
		814 880 706.6;
		816 887.2 701.32;
		818 901.6 696.08;
		820 916 693.76;
		822 930.4 693.6;
		824 944.8 693.48;
		826 956.4 693.32;
		828 965.2 693.2;
		830 974 693.04;
		832 982.8 692.92;
		834 991.6 692.76;
		836 1001.2 692.64;
		838 1011.6 692.48;
		840 1022 692.36;
		842 1032.4 692.2;
		844 1042.8 691.96;
		846 1050 691.76;
		848 1054 691.52;
		850 1058 691.32;
		852 1062 691.08;
		854 1066 690.88;
		856 1072.8 690.64;
		858 1082.4 692.44;
		860 1092 694.32;
		862 1101.6 696.2;
		864 1111.2 698.04;
		866 1118.4 699.92;
		868 1123.2 701.8;
		870 1128 705.84;
		872 1132.8 709.96;
		874 1137.6 714.08;
		876 1142.8 718.2;
		878 1148.4 722.32;
		880 1154 726.44;
		882 1159.6 729.84;
		884 1165.2 733.2;
		886 1170 736.6;
		888 1174 739.96;
		890 1178 743.6;
		892 1182 747.24;
		894 1186 750.88;
		896 1190 754.52;
		898 1194 758.16;
		900 1198 761.84;
		902 1202 765.04;
		904 1206 767.44;
		906 1209.2 769.8;

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