Index: /trunk/src/get_file_info.m =================================================================== --- /trunk/src/get_file_info.m (revision 978) +++ /trunk/src/get_file_info.m (revision 979) @@ -59,4 +59,11 @@ FileInfo.CivStage=6; % A MODIFIER end + case '.cine' + [FileInfo,BitmapInfoHeader, CameraSetup]=readCineHeader(fileinput); + FileInfo.FileType='cine_phantom'; + FileInfo.NumberOfFrames=FileInfo.ImageCount; + FileInfo.FrameRate=CameraSetup.FrameRate; + FileInfo.Height=BitmapInfoHeader.biHeight; + FileInfo.Width=BitmapInfoHeader.biWidth; otherwise if ~isempty(FileExt)% exclude empty extension Index: /trunk/src/readCineHeader.m =================================================================== --- /trunk/src/readCineHeader.m (revision 979) +++ /trunk/src/readCineHeader.m (revision 979) @@ -0,0 +1,72 @@ +function [CineFileHeader, BitmapInfoHeader, CameraSetup, imageLocations, annotationSize] = readCineHeader(filePath) + +fid = fopen(filePath); + +CineFileHeader.Type = fread(fid, 1, 'uint16'); +CineFileHeader.Headersize = fread(fid, 1, 'uint16'); +CineFileHeader.Compression = fread(fid, 1, 'uint16'); +CineFileHeader.Version = fread(fid, 1, 'uint16'); +CineFileHeader.FirstMovieImage = fread(fid, 1, 'int32'); +CineFileHeader.TotalImageCount = fread(fid, 1, 'uint32'); +CineFileHeader.FirstImageNo = fread(fid, 1, 'int32'); +CineFileHeader.ImageCount = fread(fid, 1, 'uint32'); +CineFileHeader.OffImageHeader = fread(fid, 1, 'uint32'); +CineFileHeader.OffSetup = fread(fid, 1, 'uint32'); +CineFileHeader.OffImageOffsets = fread(fid, 1, 'uint32'); +CineFileHeader.TriggerTime = fread(fid, 1, 'uint64')/2^32; % Epoch time (secs since jan 1, 1970) +%CineFileHeader.TriggerTime2 = fread(fid, 1, 'uint32'); + +BitmapInfoHeader.biSize = fread(fid, 1, 'int32'); +BitmapInfoHeader.biWidth = fread(fid, 1, 'int32'); +BitmapInfoHeader.biHeight = fread(fid, 1, 'int32'); +BitmapInfoHeader.biPlanes = fread(fid, 1, 'uint16'); +BitmapInfoHeader.biBitCount = fread(fid, 1, 'uint16'); +BitmapInfoHeader.biCompression = fread(fid, 1, 'uint32'); +BitmapInfoHeader.biSizeImage = fread(fid, 1, 'uint32'); +BitmapInfoHeader.biXPelsPerMeter= fread(fid, 1, 'uint32'); +BitmapInfoHeader.biYPelsPerMeter= fread(fid, 1, 'int32'); +BitmapInfoHeader.biClrUsed = fread(fid, 1, 'uint32'); +BitmapInfoHeader.biClrImportant = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('0354'), 'bof'); +CameraSetup.FrameRate = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('0360'), 'bof'); +CameraSetup.PostTrigger = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('03D4'), 'bof'); +CameraSetup.RealBPP = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('16B8'), 'bof'); +CameraSetup.BlackLevel = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('16BC'), 'bof'); +CameraSetup.WhiteLevel = fread(fid, 1, 'uint32'); + +fseek(fid, hex2dec('1B48'), 'bof'); +CameraSetup.fGain16_8 = fread(fid, 1, 'float32'); + +fseek(fid, hex2dec('17CC'), 'bof'); +CameraSetup.fOffset = fread(fid, 1, 'float32'); + +fseek(fid, hex2dec('17D0'), 'bof'); +CameraSetup.fGain = fread(fid, 1, 'float32'); + +fseek(fid, hex2dec('17DC'), 'bof'); +CameraSetup.fGamma = fread(fid, 1, 'float32'); + +fseek(fid, hex2dec('27D4'), 'bof'); +CameraSetup.RecBPP = fread(fid, 1, 'uint32'); + + +fseek(fid, CineFileHeader.OffImageOffsets, 'bof'); +imageBlockLocations = fread(fid, CineFileHeader.ImageCount, 'int64'); + + +fseek(fid, imageBlockLocations(1), 'bof'); +annotationSize = fread(fid, 1, 'uint32'); + + +imageLocations = imageBlockLocations + annotationSize; + +fclose(fid); Index: /trunk/src/read_cine_phantom.m =================================================================== --- /trunk/src/read_cine_phantom.m (revision 979) +++ /trunk/src/read_cine_phantom.m (revision 979) @@ -0,0 +1,115 @@ +function [imMat,CineFileHeader] = read_cine_phantom( cineFilePath, frames ) +tic; + + +[CineFileHeader, BitmapInfoHeader, CameraSetup, 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'); + 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 +disp( ['Reading time = ' num2str(toc) ] ) +fclose(fid); +end + +function lookupTable = lookupTablePackedFun() + +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 Index: /trunk/src/read_image.m =================================================================== --- /trunk/src/read_image.m (revision 978) +++ /trunk/src/read_image.m (revision 979) @@ -46,21 +46,23 @@ ObjectOut=VideoObject;%default switch FileType - case 'video' - if strcmp(class(VideoObject),'VideoReader') - A=read(VideoObject,num); - else - ObjectOut=VideoReader(FileName); - A=read(ObjectOut,num); - end - case 'mmreader' - if strcmp(class(VideoObject),'mmreader') - A=read(VideoObject,num); - else - ObjectOut=mmreader(FileName); - A=read(ObjectOut,num); - end + case 'video' + if strcmp(class(VideoObject),'VideoReader') + A=read(VideoObject,num); + else + ObjectOut=VideoReader(FileName); + A=read(ObjectOut,num); + end + case 'mmreader' + if strcmp(class(VideoObject),'mmreader') + A=read(VideoObject,num); + else + ObjectOut=mmreader(FileName); + A=read(ObjectOut,num); + end + case 'cine_phantom' + A = read_cine_phantom(FileName,num ); case 'multimage' A=imread(FileName,num); - case 'image' + case 'image' A=imread(FileName); end Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 978) +++ /trunk/src/series.m (revision 979) @@ -1822,7 +1822,7 @@ case {'PCWIN','PCWIN64'} %Windows system filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters - system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system + system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);% TODO: adapt to DOS system case {'GLNX86','GLNXA64','MACI64'}%Linux system - system([ActionFullName ' ' RunTime ' ' filexml]); + system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); end end Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 978) +++ /trunk/src/series/civ_input.m (revision 979) @@ -111,5 +111,5 @@ iview_image=1;%line # for the input images switch FileType - case {'image','multimage','video','mmreader','netcdf'} + case {'image','multimage','video','mmreader','cine_phantom','netcdf'} % NomTypeImaA=NomTypeInput; % iview_image=1;%line # for the input images Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 978) +++ /trunk/src/series/extract_rdvision.m (revision 979) @@ -283,5 +283,5 @@ return end - difftime=XmlData.Time(2:end,2:end)-(reshape(timestamp,nbfield2,[]))'; + difftime=XmlData.Time(2:end,2:end)-(reshape(timestamp(1:end-1),nbfield2,[]))'; disp(['time from xml and timestamp differ by ' num2str(max(max(abs(difftime))))]) if max(abs(difftime))>0.01