source: trunk/src/read_cine_phantom.m @ 1160

function [imMat,CineFileHeader] = read_cine_phantom( cineFilePath, frames )
tic;


% [CineFileHeader, BitmapInfoHeader, CameraSetup, imageLocations] = readCineHeader(cineFilePath);       % old
[CineFileHeader, BitmapInfoHeader, CameraSetup, TimeOnlyBlock, ExposureOnlyBlock, TimeCodeBlock, imageLocations] = readCineHeader(cineFilePath);
fid = fopen(cineFilePath);
lookupTable = lookupTablePackedFun;
%imMat = zeros(800,1280, framerange(2) - framerange(1) + 1 );
imMat = zeros(BitmapInfoHeader.biHeight,BitmapInfoHeader.biWidth, numel(frames));
%tt=1:CineFileHeader.ImageCount;

% tmin=max([framerange(1) min(tt)]);
% tmax=min([framerange(2) max(tt)]);
% frames = tt( (tt>=tmin) & (tt<=tmax) );
% 
% Nf=tmax-tmin+1; % frame count
Nf=numel(frames);
for ii=1:Nf
    
    %% Read image from Cine file
    
    fseek(fid, imageLocations( frames(ii) ), 'bof');
    if ~BitmapInfoHeader.biCompression
        imTemp = fread(fid, [BitmapInfoHeader.biWidth BitmapInfoHeader.biHeight],'uint16');
        imMat(:,:,ii) = imTemp';
    else
    imTemp = fread(fid, [BitmapInfoHeader.biWidth BitmapInfoHeader.biHeight], 'ubit10','b');
    im = imTemp';
    im( im < 1 ) = 1;
    im =reshape( interp1( 1:1024, lookupTable, im(:) ), BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth);
    im( im < CameraSetup.BlackLevel ) = CameraSetup.BlackLevel;
    im( im > 4064 )=4064;
    imMat(:,:,ii) = reshape(interp1( CameraSetup.BlackLevel:4064, linspace(0,4095,4064 - CameraSetup.BlackLevel+1), im(:)),...
        BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth); 
    
    if mod( round(0.01*Nf), ii)
       if ~exist('dispStr', 'var')
           dispStr = ' ';
           disp( dispStr )
       end
       
     lenDispStr = length( dispStr );
     dispStr = ['Reading is ' num2str( round( 100*ii/Nf ) ) '% complete'];
     disp( [char(8)*ones(1,lenDispStr+1) dispStr] )
    end
    end
end
disp( ['Reading time = ' num2str(toc) ] )
fclose(fid);
end

function lookupTable = lookupTablePackedFun() 
% function to transform the compressed 10 bit images back, close to the 12 bit camera images
lookupTable = [ 2,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15,  16,  17,  17,  18,...
19,  20,  21,  22, 23,  24,  25,  26,  27,  28,  29,  30,  31,  32,  33,  33,...
34,  35,  36,  37,  38,  39,  40,  41,  42,  43,  44,  45,  46,  47,  48,  48,...
49,  50,  51,  52,  53,  54,  55,  56,  57,  58,  59,  60,  61,  62,  63,  63,...
64,  65,  66,  67,  68,  69,  70,  71,  72,  73,  74,  75,  76,  77,  78,  79,...
79,  80,  81,  82,  83,  84,  85,  86,  87,  88,  89,  90,  91,  92,  93,  94,...
94,  95,  96,  97,  98,  99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,...
110, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,...
125, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 137, 138,...
139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,...
156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 167, 168, 169, 170, 171, 172,...
173, 175, 176, 177, 178, 179, 181, 182, 183, 184, 186, 187, 188, 189, 191, 192,...
193, 194, 196, 197, 198, 200, 201, 202, 204, 205, 206, 208, 209, 210, 212, 213,...
215, 216, 217, 219, 220, 222, 223, 225, 226, 227, 229, 230, 232, 233, 235, 236,...
238, 239, 241, 242, 244, 245, 247, 249, 250, 252, 253, 255, 257, 258, 260, 261,...
263, 265, 266, 268, 270, 271, 273, 275, 276, 278, 280, 281, 283, 285, 287, 288,...
290, 292, 294, 295, 297, 299, 301, 302, 304, 306, 308, 310, 312, 313, 315, 317,...
319, 321, 323, 325, 327, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348,...
350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 377, 379, 381,...
383, 385, 387, 389, 391, 394, 396, 398, 400, 402, 404, 407, 409, 411, 413, 416,...
418, 420, 422, 425, 427, 429, 431, 434, 436, 438, 441, 443, 445, 448, 450, 452,...
455, 457, 459, 462, 464, 467, 469, 472, 474, 476, 479, 481, 484, 486, 489, 491,...
494, 496, 499, 501, 504, 506, 509, 511, 514, 517, 519, 522, 524, 527, 529, 532,...
535, 537, 540, 543, 545, 548, 551, 553, 556, 559, 561, 564, 567, 570, 572, 575,...
578, 581, 583, 586, 589, 592, 594, 597, 600, 603, 606, 609, 611, 614, 617, 620,...
623, 626, 629, 632, 635, 637, 640, 643, 646, 649, 652, 655, 658, 661, 664, 667,...
670, 673, 676, 679, 682, 685, 688, 691, 694, 698, 701, 704, 707, 710, 713, 716,...
719, 722, 726, 729, 732, 735, 738, 742, 745, 748, 751, 754, 758, 761, 764, 767,...
771, 774, 777, 781, 784, 787, 790, 794, 797, 800, 804, 807, 811, 814, 817, 821,...
824, 828, 831, 834, 838, 841, 845, 848, 852, 855, 859, 862, 866, 869, 873, 876,...
880, 883, 887, 890, 894, 898, 901, 905, 908, 912, 916, 919, 923, 927, 930, 934,...
938, 941, 945, 949, 952, 956, 960, 964, 967, 971, 975, 979, 982, 986, 990, 994,...
998,1001,1005,1009,1013,1017,1021,1025,1028,1032,1036,1040,1044,1048,1052,1056,...
1060,1064,1068,1072,1076,1080,1084,1088,1092,1096,1100,1104,1108,1112,1116,1120,...
1124,1128,1132,1137,1141,1145,1149,1153,1157,1162,1166,1170,1174,1178,1183,1187,...
1191,1195,1200,1204,1208,1212,1217,1221,1225,1230,1234,1238,1243,1247,1251,1256,...
1260,1264,1269,1273,1278,1282,1287,1291,1295,1300,1304,1309,1313,1318,1322,1327,...
1331,1336,1340,1345,1350,1354,1359,1363,1368,1372,1377,1382,1386,1391,1396,1400,...
1405,1410,1414,1419,1424,1428,1433,1438,1443,1447,1452,1457,1462,1466,1471,1476,...
1481,1486,1490,1495,1500,1505,1510,1515,1520,1524,1529,1534,1539,1544,1549,1554,...
1559,1564,1569,1574,1579,1584,1589,1594,1599,1604,1609,1614,1619,1624,1629,1634,...
1639,1644,1649,1655,1660,1665,1670,1675,1680,1685,1691,1696,1701,1706,1711,1717,...
1722,1727,1732,1738,1743,1748,1753,1759,1764,1769,1775,1780,1785,1791,1796,1801,...
1807,1812,1818,1823,1828,1834,1839,1845,1850,1856,1861,1867,1872,1878,1883,1889,...
1894,1900,1905,1911,1916,1922,1927,1933,1939,1944,1950,1956,1961,1967,1972,1978,...
1984,1989,1995,2001,2007,2012,2018,2024,2030,2035,2041,2047,2053,2058,2064,2070,...
2076,2082,2087,2093,2099,2105,2111,2117,2123,2129,2135,2140,2146,2152,2158,2164,...
2170,2176,2182,2188,2194,2200,2206,2212,2218,2224,2231,2237,2243,2249,2255,2261,...
2267,2273,2279,2286,2292,2298,2304,2310,2317,2323,2329,2335,2341,2348,2354,2360,...
2366,2373,2379,2385,2392,2398,2404,2411,2417,2423,2430,2436,2443,2449,2455,2462,...
2468,2475,2481,2488,2494,2501,2507,2514,2520,2527,2533,2540,2546,2553,2559,2566,...
2572,2579,2586,2592,2599,2605,2612,2619,2625,2632,2639,2645,2652,2659,2666,2672,...
2679,2686,2693,2699,2706,2713,2720,2726,2733,2740,2747,2754,2761,2767,2774,2781,...
2788,2795,2802,2809,2816,2823,2830,2837,2844,2850,2857,2864,2871,2878,2885,2893,...
2900,2907,2914,2921,2928,2935,2942,2949,2956,2963,2970,2978,2985,2992,2999,3006,...
3013,3021,3028,3035,3042,3049,3057,3064,3071,3078,3086,3093,3100,3108,3115,3122,...
3130,3137,3144,3152,3159,3166,3174,3181,3189,3196,3204,3211,3218,3226,3233,3241,...
3248,3256,3263,3271,3278,3286,3294,3301,3309,3316,3324,3331,3339,3347,3354,3362,...
3370,3377,3385,3393,3400,3408,3416,3423,3431,3439,3447,3454,3462,3470,3478,3486,...
3493,3501,3509,3517,3525,3533,3540,3548,3556,3564,3572,3580,3588,3596,3604,3612,...
3620,3628,3636,3644,3652,3660,3668,3676,3684,3692,3700,3708,3716,3724,3732,3740,...
3749,3757,3765,3773,3781,3789,3798,3806,3814,3822,3830,3839,3847,3855,3863,3872,...
3880,3888,3897,3905,3913,3922,3930,3938,3947,3955,3963,3972,3980,3989,3997,4006,...
4014,4022,4031,4039,4048,4056,4064,4095,4095,4095,4095,4095,4095,4095,4095,4095];

end