Segmentation fault in some .pv files about trex

[mooch443]

Hey, thanks for your report.
I am wondering if this might be something that'll be fixed with the next update, but it is impossible to figure this out merely based on the logs you've provided. If you cannot provide a clip that reproducibly causes this crash to happen, I recommend to try and clone the repository and compile manually (or using conda build as per docs https://trex.run/docs/install.html#local-conda-channel), or to wait until I can release the new version next month.

Otherwise - from what I gather it seems this is reproducible for specific files? So that it happens every time with these specific files?

[srsbh]

Thank you for the reply. I have attached one instance where it crashes and throws out a seg fault. This is the error message and the zip file has the raw and pv file. https://drive.google.com/file/d/1T8QU1WB6tg2sKQyOIjL2WyrQdx4ZTwyt/view?usp=sharing

subha@subha-lab6:~/Videos/test$ trex -i /home/subha/Videos/out.pv 
[12:02:43] ------------------------
[12:02:43] LOADING DEFAULT SETTINGS
[12:02:43] ------------------------
[12:02:43] Found ffmpeg in '/home/subha/anaconda3/envs/tracking/bin/ffmpeg'
[12:02:43] Property<path>('ffmpeg_path') = "/home/subha/anaconda3/envs/tracking/bin/ffmpeg"
[12:02:43] Property<string>('build') = "2375994fff55a5446ba2615aa00da334dada0938"
[12:02:43] Property<string>('cmd_line') = " trex -i /home/subha/Videos/out.pv"
[12:02:43] -------------------
[12:02:43] LOADING COMMANDLINE
[12:02:43] -------------------
[12:02:43] Property<path>('wd') = "/home/subha/anaconda3/envs/tracking/bin"
[12:02:43] -------------------------------
[12:02:43] LOADING FROM 'default.settings'
[12:02:43] -------------------------------
[12:02:43] -------------------------
[12:02:43] LOADED 'default.settings'
[12:02:43] -------------------------
[12:02:43] Property<path>('filename') = "/home/subha/Videos/out"
[12:02:43] ------------
[12:02:43] LOADING FILE
[12:02:43] ------------
[12:02:43] Property<string>('meta_species') = ""
[12:02:43] Property<int>('meta_age_days') = -1
[12:02:43] Property<string>('meta_conditions') = ""
[12:02:43] Property<string>('meta_misc') = ""
[12:02:43] Property<int>('cam_limit_exposure') = 5500
[12:02:43] Property<float>('meta_real_width') = 30
[12:02:43] Property<path>('meta_source_path') = "/home/subha/Videos/test/out.mp4"
[12:02:43] Property<string>('meta_cmd') = " tgrabs -i /home/subha/Videos/test/out.mp4 -average_samples 500 -blob_size_range [0.005,5] -dilation_size 2 -color_channel 1 -threshold 30 -crop_window false"
[12:02:43] Property<string>('meta_build') = "2375994fff55a5446ba2615aa00da334dada0938"
[12:02:43] Property<string>('meta_conversion_time') = "15-10-2021 11:59:30"
[12:02:43] Property<int>('frame_rate') = 29
[12:02:43] Property<array<float>>('cam_undistort_vector') = [-0.257663,-0.192336,0.002455,0.003988,0.35924]
[12:02:43] Property<array<float>>('cam_matrix') = [2945.0896,0,617.255432,0,2942.825195,682.473633,0,0,1]
[12:02:43] Property<size>('video_size') = [484,1184]
[12:02:43] Property<bool>('video_mask') = false
[12:02:43] Property<ulong>('video_length') = 35965
[12:02:43] Property<string>('video_info') = "pv::File<V7, 235.24MB, '/home/subha/Videos/out', [484 x 1184], 35965 frames, no mask>

crop_offsets: [0,0,0,0]
Time of recording: 'Fri Oct 15 12:00:03 2021'
Length of recording: '00d:00h:20m:40s'
Framerate: 28fps (34.483ms)

Metadata: {\"meta_species\": \"\", \"meta_age_days\": -1, \"meta_conditions\": \"\", \"meta_misc\": \"\", \"cam_limit_exposure\": 5500, \"meta_real_width\": 30, \"meta_source_path\": \"/home/subha/Videos/test/out.mp4\", \"meta_cmd\": \" tgrabs -i /home/subha/Videos/test/out.mp4 -average_samples 500 -blob_size_range [0.005,5] -dilation_size 2 -color_channel 1 -threshold 30 -crop_window false\", \"meta_build\": \"2375994fff55a5446ba2615aa00da334dada0938\", \"meta_conversion_time\": \"15-10-2021 11:59:30\", \"frame_rate\": 29, \"cam_undistort_vector\": [-0.257663,-0.192336,0.002455,0.003988,0.35924], \"cam_matrix\": [2945.0896,0,617.255432,0,2942.825195,682.473633,0,0,1]}"
[12:02:43] Property<path>('settings_file') = ""
[WARNING 12:02:43 main.cpp:701] Settings file '/home/subha/Videos/out.settings' does not exist.
[12:02:43] Property<float>('cm_per_pixel') = 0.061983
[12:02:43] Initialized with 8 threads.
[12:02:43] Setting home to '/home/subha/anaconda3/envs/tracking'
[WARNING 12:02:43 Recognition.cpp:165] Does not exist in working dir: './trex_check_python'
[WARNING 12:02:43 main.cpp:990] No settings file can be loaded, so the program will try to automatically determine individual sizes and numbers.
[12:02:43] Property<bool>('auto_number_individuals') = true
[12:02:43] Property<bool>('auto_minmax_size') = true
[12:02:43] Determining blob size in 35965 frames...
[12:02:44] Property<BlobSizeRange>('blob_size_ranges') = [[0.057929,1.020278]]
[WARNING 12:02:44 Tracker.cpp:4209] The set (0) number of individuals differs from the detected number of individuals / frame (45).
[12:02:44] Setting number of individuals as 45.
[12:02:44] Property<uint>('track_max_individuals') = 45
[12:02:44] Property<set<Idx_t>>('manual_identities') = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44]
[12:02:44] Property<array<pair<string,array<string>>>>('output_graphs') = [["X",["RAW","WCENTROID"]],["Y",["RAW","WCENTROID"]],["X",["RAW","HEAD"]],["Y",["RAW","HEAD"]],["VX",["RAW","HEAD"]],["VY",["RAW","HEAD"]],["AX",["RAW","HEAD"]],["AY",["RAW","HEAD"]],["ANGLE",["RAW"]],["ANGULAR_V",["RAW"]],["ANGULAR_A",["RAW"]],["MIDLINE_OFFSET",["RAW"]],["normalized_midline",["RAW"]],["midline_length",["RAW"]],["midline_x",["RAW"]],["midline_y",["RAW"]],["segment_length",["RAW"]],["SPEED",["RAW","WCENTROID"]],["SPEED",["SMOOTH","WCENTROID"]],["SPEED",["RAW","PCENTROID"]],["SPEED",["RAW","HEAD"]],["BORDER_DISTANCE",["PCENTROID"]],["time",[]],["timestamp",[]],["frame",[]],["missing",[]],["num_pixels",[]],["ACCELERATION",["RAW","PCENTROID"]],["ACCELERATION",["RAW","WCENTROID"]]]
[12:02:44] ----------------
[12:02:44] STARTING PROGRAM
[12:02:44] ----------------
[12:02:44] 20 Individual:800 Blob:232 Physical:32 Vec2Prop:48 Image::Ptr:16 std::shared_ptr<std::vector<HorizontalLine>>:16 Bounds:16 bool:1 cmn::Blob::properties:32
[12:02:44] localcache:120 identity:48 std::map<long_t, Vec2>:48
[12:02:44] BasicStuff:80 pv::Blob:232 Compressed:40
[12:02:44] Midline:64 MinimalOutline:32
[12:02:44] Initialized 2 stages
[12:02:44] Property<ulong>('app_last_update_check') = 1634275645569918
[12:02:44] Property<app_update_check_t>('app_check_for_updates') = automatically
[12:02:44] Property<string>('app_last_update_version') = "\"1.1.3\""
[ERROR 12:02:44 main.cpp:1318] Settings file '/home/subha/Videos/out.settings' cannot be found.
[12:02:44] blob_split_max_shrink = 0.200000
[12:02:44] blob_split_global_shrink_limit = 0.200000
[12:02:44] sqrcm = 0.003842
[12:02:44] blob_size_ranges = [[0.057929,1.020278]]
[12:02:44] track_posture_threshold = 15
[12:02:44] blob_size_ranges = [[0.057929,1.020278]]
[12:02:44] Property<array<string>>('gui_foi_types') = ["lost >=2 fish"]
[12:02:44] Property<array<string>>('gui_foi_types') = ["lost >=2 fish","lost >=1 fish"]
[12:02:44] Property<array<string>>('gui_foi_types') = ["lost >=2 fish","lost >=1 fish","weird angle"]
[12:02:44] Property<array<string>>('gui_foi_types') = ["lost >=2 fish","lost >=1 fish","weird angle","segment end"]
[12:02:44] Property<array<string>>('gui_foi_types') = ["lost >=2 fish","lost >=1 fish","weird angle","segment end","correcting"]
[12:02:44] Using OpenGL3.2 (seems supported, 4.6.0 NVIDIA 460.91.03).
[12:02:44] Property<bool>('terminate') = false
[12:02:44] Property<bool>('gui_show_blobs') = true
[12:02:44] Property<bool>('gui_show_paths') = true
[12:02:44] Property<bool>('gui_show_texts') = true
[12:02:44] Property<bool>('gui_show_selections') = true
[12:02:44] Property<bool>('gui_show_inactive_individuals') = true
[12:02:44] Property<bool>('gui_show_outline') = true
[12:02:44] Property<bool>('gui_show_midline') = true
[12:02:44] Property<bool>('gui_show_posture') = true
[12:02:44] Property<bool>('gui_show_recognition_bounds') = true
[12:02:44] Property<bool>('gui_auto_scale_focus_one') = true
trex[0x867586]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f4766f58980]
trex(_ZN3cmn11CPULabeling8run_fastEPNS0_6DLListE+0x5a4)[0xed5014]
trex(_ZN3cmn11CPULabeling3runERKSt6vectorINS_14HorizontalLineESaIS2_EERKS1_IhSaIhEE+0x5cc)[0xed5ebc]
trex[0xeb0aaa]
trex(_ZN5pixel26threshold_get_biggest_blobESt10shared_ptrIN2pv4BlobEEiPKN3cmn10BackgroundEhh+0x62)[0xeb0dc2]
trex(_ZN5track7Posture17calculate_postureEiSt10shared_ptrIN2pv4BlobEE+0x1a1)[0x91bf31]
trex(_ZN5track10Individual12save_postureESt10shared_ptrINS0_10BasicStuffEEi+0x7d)[0x8e325d]
trex[0x979b5d]
trex(_ZNSt17_Function_handlerIFSt10unique_ptrINSt13__future_base12_Result_baseENS2_8_DeleterEEvENS1_12_Task_setterIS0_INS1_7_ResultIvEES3_EZNS1_11_Task_stateISt5_BindIFPFviRKSt6vectorISt5tupleIJPN5track10IndividualESt10shared_ptrINSF_10BasicStuffEEEESaISK_EEEiSM_EESaIiEFvvEE6_M_runEvEUlvE_vEEE9_M_invokeERKSt9_Any_data+0x31)[0x967a71]
trex[0x83f8b9]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf907)[0x7f4766f55907]
trex(_ZNSt13__future_base11_Task_stateISt5_BindIFPFviRKSt6vectorISt5tupleIJPN5track10IndividualESt10shared_ptrINS5_10BasicStuffEEEESaISA_EEEiSC_EESaIiEFvvEE6_M_runEv+0x107)[0x969367]
trex[0xebb5f1]
/home/subha/anaconda3/envs/tracking/bin/../lib/libstdc++.so.6(+0xc9039)[0x7f4764689039]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76db)[0x7f4766f4d6db]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f47642f071f]
FATAL: Segmentation Fault. Logged StackTrace
double free or corruption (fasttop)
Aborted (core dumped)

[mooch443]

Thank you. As suspected, this relates to an issue that I had encountered before. Updating to 1.1.4 seems to fix it!