HI Alexey,
I'm using Metashape 1.5.5 build 9097. Save keypoints is enabled. I attached a screenshot of the chunk info dialog, and included relevant logfile output from (scipted) generic selection filtering below
2019-10-29 21:52:09 Finished processing in 9549.9 sec (exit code 1)
2019-10-29 21:54:49 59160567 points selected
2019-10-29 21:54:49 RU threshold 10.0 selected 59160567 / 172014583 ( 34.3928 %) of points. Adjusting
2019-10-29 21:57:29 RU threshold 11.0 selected 54139925 / 172014583 ( 31.474 %) of points. Adjusting
2019-10-29 22:00:08 RU threshold 12.0 selected 44628315 / 172014583 ( 25.9445 %) of points. Adjusting
2019-10-29 22:02:46 RU threshold 13.0 is 18.9606 % of total points. Ready to delete
2019-10-29 22:02:49 RU 13.0 deleted 32615010 points
2019-10-29 22:02:49 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-29 22:02:50 Optimizing camera locations...
2019-10-29 22:07:24 removed 2 cameras: 29296, 41560
2019-10-29 22:07:24 removed 2 stations
2019-10-29 22:08:45 adjusting: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.117036 -> 0.115838
2019-10-30 01:23:12 coordinates applied in 0 sec
2019-10-30 01:23:30 Finished processing in 12041.3 sec (exit code 1)
2019-10-30 01:23:30 completed optimization # 1
2019-10-30 01:23:31 initializing with RU = 10.0
2019-10-30 01:23:31 Analyzing point cloud...
2019-10-30 03:24:49 Finished processing in 7277.72 sec (exit code 1)
2019-10-30 03:26:57 26545093 points selected
2019-10-30 03:26:57 RU threshold 10.0 is 19.0424 % of total points. Ready to delete
2019-10-30 03:26:59 RU 10.0 deleted 26545093 points
2019-10-30 03:26:59 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 03:27:00 Optimizing camera locations...
2019-10-30 03:31:45 removed 8 cameras: 27741, 28752, 29297, 35695, 35722, 36602, 39689, 39691
2019-10-30 03:31:45 removed 8 stations
2019-10-30 03:31:45 removed 1 points
2019-10-30 03:33:00 adjusting: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.116194 -> 0.116075
2019-10-30 06:54:56 coordinates applied in 0 sec
2019-10-30 06:55:11 Finished processing in 12491.8 sec (exit code 1)
2019-10-30 06:55:11 completed optimization # 2
2019-10-30 06:55:12 initializing with RU = 10.0
2019-10-30 06:55:12 Analyzing point cloud...
2019-10-30 08:32:50 Finished processing in 5858.23 sec (exit code 1)
2019-10-30 08:34:33 163 points selected
2019-10-30 08:34:33 RU threshold 10.0 is 0.0001 % of total points. Ready to delete
2019-10-30 08:34:35 RU 10.0 deleted 163 points
2019-10-30 08:34:35 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 08:34:35 Optimizing camera locations...
2019-10-30 08:39:11 removed 2 cameras: 31292, 31294
2019-10-30 08:39:11 removed 2 stations
2019-10-30 08:39:11 removed 1 points
2019-10-30 08:40:24 adjusting: !xxxxxxxxxxxx!xx!x!x!x!x!x!x!x!!xx!x!x!x!x!x!!x!x! 0.116274 -> 0.115059
2019-10-30 11:07:04 LM singular S
2019-10-30 11:07:16 coordinates applied in 0 sec
2019-10-30 11:07:32 Finished processing in 9177.12 sec (exit code 1)
2019-10-30 11:07:32 completed optimization # 3
2019-10-30 11:07:32 initializing with RU = 10.0
2019-10-30 11:07:32 Analyzing point cloud...
2019-10-30 12:45:45 Finished processing in 5892.99 sec (exit code 1)
2019-10-30 12:47:28 805 points selected
2019-10-30 12:47:28 RU threshold 10.0 is 0.0007 % of total points. Ready to delete
2019-10-30 12:47:29 RU 10.0 deleted 805 points
2019-10-30 12:47:29 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 12:47:30 Optimizing camera locations...
2019-10-30 12:53:13 adjusting: !xxxxxxxxxxxx!xx!!xx!x!!xx!x!!xx!x!x!x!!xx!x!x!x!x 0.116108 -> 0.115059
2019-10-30 15:25:53 LM singular S
2019-10-30 15:26:07 coordinates applied in 0 sec
2019-10-30 15:26:21 Finished processing in 9531.87 sec (exit code 1)
2019-10-30 15:26:21 completed optimization # 4
2019-10-30 15:26:22 initializing with RU = 10.0
2019-10-30 15:26:22 Analyzing point cloud...
2019-10-30 17:03:45 Finished processing in 5843.01 sec (exit code 1)
2019-10-30 17:05:27 3 points selected
2019-10-30 17:05:27 RU threshold 10.0 is 0.0 % of total points. Ready to delete
2019-10-30 17:05:28 RU 10.0 deleted 3 points
2019-10-30 17:05:28 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 17:05:28 Optimizing camera locations...
2019-10-30 17:11:11 adjusting: !xxxxxxxxxxxxxx!!x!!xx!x!x!x!x!!xx!x!x!x!x!x!x!x!x 0.116108 -> 0.115059
2019-10-30 19:43:02 LM singular S
2019-10-30 19:43:15 coordinates applied in 0 sec
2019-10-30 19:43:30 Finished processing in 9482.14 sec (exit code 1)
2019-10-30 19:43:30 completed optimization # 5
2019-10-30 19:43:31 initializing with RU = 10.0
2019-10-30 19:43:31 Analyzing point cloud...
2019-10-30 21:21:37 Finished processing in 5885.84 sec (exit code 1)
2019-10-30 21:23:20 0 points selected
2019-10-30 21:25:03 Reconstruction Uncertainty optimization completed.
2019-10-30 21:25:03 59161074 of 172014583 removed in 5 optimizations on chunk "Chunk 1_RU10.0".
2019-10-30 21:25:03
2019-10-30 21:25:03 SaveProject: path = SfM:/Dorian/All_Dorian_4D_finalPositions.psx
2019-10-30 21:25:03 Saving project...
2019-10-30 21:30:33 saved project in 329.8 sec
2019-10-30 21:30:33 Finished processing in 329.8 sec (exit code 1)
2019-10-30 21:30:33 DuplicateChunk: items = (keypoints, depth maps, dense cloud, model, DEM, orthomosaic, tiled model)
2019-10-30 21:30:33 Duplicating chunk...
2019-10-30 22:31:23 Finished processing in 3625.46 sec (exit code 1)
2019-10-30 22:31:23 Copied chunk Chunk 1_RU10.0 to chunk Chunk 1_RU10.0_PA3.0
2019-10-30 22:31:23 Running Projection Accuracy optimization
2019-10-30 22:33:18 initializing with PA = 3.0
2019-10-30 22:33:22 Analyzing point cloud...
2019-10-31 00:08:59 Finished processing in 5740.74 sec (exit code 1)
2019-10-31 00:10:46 55240979 points selected
2019-10-31 00:10:46 PA threshold 3.0 is 48.9493 % of total points. Ready to delete
2019-10-31 00:10:49 PA 3.0 deleted 55240979 points
2019-10-31 00:10:49 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-31 00:10:49 Optimizing camera locations...
2019-10-31 00:15:28 removed 167 cameras: 499, 500, 501, 502, 598, 599, 621, 622, 623, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 2272, 2273, 2274, 2275, 2276, 2277, 2278, 2279, 2280, 2281, 2282, 2283, 2284, 2285, 2287, 2288, 2289, 2935, 2936, 2937, 2938, 2939, 2940, 2941, 2942, 2943, 2944, 2945, 2946, 4184, 4185, 4186, 4187, 4188, 4879, 4884, 4885, 4886, 4887, 4888, 4889, 4890, 4891, 4892, 4893, 4894, 4895, 4896, 5366, 5367, 5371, 5386, 5387, 6137, 6138, 6139, 6141, 6143, 6144, 6169, 6171, 6172, 6173, 6174, 6215, 6220, 6221, 6222, 6603, 6632, 8493, 8494, 10593, 27745, 27746, 27747, 27750, 27752, 27753, 28753, 28754, 28755, 28756, 28757, 28759, 28761, 28763, 28764, 29298, 29306, 29307, 29439, 31291, 31293, 31305, 31318, 31326, 31327, 31328, 31332, 31343, 31349, 31350, 31851, 32437, 32881, 32882, 35694, 35721, 36279, 36549, 36550, 36551, 36603, 36604, 39682, 39687, 39692, 40154, 40155, 40882, 41541, 41542, 41561, 41562, 41702, 41703, 42287, 44476, 44937, 44954, 44979, 2286, 2947, 27748, 28758, 28762, 29304, 29305, 39690, 28760, 29303
2019-10-31 00:15:28 removed 167 stations
2019-10-31 00:15:28 removed 78 points
2019-10-31 00:16:13 adjusting: !xxxxxxxxxxxx!xx!x!x!x!x!x!!x!xx!x!!xx!x!x!x!x!x!x 0.133599 -> 0.131582
2019-10-31 01:40:02 LM singular S
2019-10-31 01:40:10 coordinates applied in 0 sec
2019-10-31 01:40:19 Finished processing in 5369.24 sec (exit code 1)
2019-10-31 01:40:19 completed optimization # 1
2019-10-31 01:40:20 initializing with PA = 3.0
2019-10-31 01:40:20 Analyzing point cloud...
2019-10-31 02:29:29 Finished processing in 2948.8 sec (exit code 1)
2019-10-31 02:30:22 0 points selected
2019-10-31 02:31:13 Projection Accuracy optimization completed.
2019-10-31 02:31:13 55240979 of 112853507 removed in 1 optimizations on chunk "Chunk 1_RU10.0_PA3.0".
2019-10-31 02:31:13
2019-10-31 02:31:13 SaveProject: path = SfM:/Dorian/All_Dorian_4D_finalPositions.psx
2019-10-31 02:31:13 Saving project...
2019-10-31 02:36:24 saved project in 310.708 sec
2019-10-31 02:36:24 Finished processing in 310.708 sec (exit code 1)