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Implement P10 cine file capability for cine reader #469

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97d66cf
Add linlut file for use in translating P10 compressed cine files.
Tlhbobby Feb 6, 2026
3c1c169
Implement linlut function for P10 images and interpolate the intensit…
Tlhbobby Feb 6, 2026
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5 changes: 5 additions & 0 deletions pims/cine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from pims.frame import Frame
from pims.base_frames import FramesSequence, index_attr
from pims.utils.misc import FileLocker
from pims.utils.linlut import apply_linLUT
import time
import struct
import numpy as np
Expand Down Expand Up @@ -648,6 +649,10 @@ def _get_frame(self, number):
# un-pack packed data
if (actual_bits == 10):
frame = _ten2sixteen(frame)
# apply linLUT as specified in documentation for converting 10P -> 12 bit linear
frame = apply_linLUT(frame)
# Normalize black and white levels to full 12-bit range. Black level is 64 because of gamma function
frame = np.interp(frame, [64,4064], [0,(2**12)-1]).astype(np.uint16)
elif (actual_bits == 12):
frame = _twelve2sixteen(frame)
elif (actual_bits % 8):
Expand Down
88 changes: 88 additions & 0 deletions pims/utils/linlut.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
import numpy as np

linLUT = np.array([
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
])

def apply_linLUT(image):
"""Apply linearization lookup table to a 10P compressed cine image.

Parameters
----------
image : ndarray
Input image with pixel values in the range [0, 1023].

Returns
-------
ndarray
Linearized image with pixel values adjusted according to the linLUT.
"""
if not np.issubdtype(image.dtype, np.integer):
raise ValueError("Input image must have integer pixel values.")
if np.any(image < 0) or np.any(image > 1023):
raise ValueError("Input image pixel values must be in the range [0, 1023].")

return linLUT[image].astype(np.uint16)