update?

[mooch443]

update?

[mooch443]

Hey,
it seems like your conda environment is a bit broken. Do you have an M1 MacBook Pro, or do you have an Intel processor?
Additionally, it would likely be helpful if you could provide the entire terminal log. E.g. you could select/copy everything, or use some terminal specific mechanism to stream outputs to a file.
Thank you for your report!

[naroberto]

Hi,
Thanks so much for your quick response!

Here are my Macbook specs:
MacBook Pro (Retina, 15-inch, Mid 2015)
Processor: 2.5 GHz Quad-Core Intel Core i7
Memory: 16 GB 1600 MHz DDR3 $
Graphics: AMD Radeon R9 M370X 2 GB, Intel Iris Pro 1536 MB
SN: C02PV8Z0G8WP

currently the conversion to .pv worked and also the trex GUI seems to be functional to some degree.

• I sometimes get this warning:
  [WARNING 17:06:51 gui.cpp:4767] Python is not available. Check your configuration.
• on the bottom right it is often displayed ("python not available" - not sure this is an issue)

• not really sure if all functionalities are there (outlines of objects are not displayed for instance):

Thanks so much for you help!!!

(here is the entire log):
(tracking) rob@staff-net-hix-1032 ~ % trex
Using conda prefix '/Users/rob/opt/anaconda3/envs/tracking/bin/'.
Calling '/Users/rob/opt/anaconda3/envs/tracking/bin/TRex.app/Contents/MacOS/TRex'...
[16:49:57] ------------------------
[16:49:57] LOADING DEFAULT SETTINGS
[16:49:57] ------------------------
[16:49:57] Found ffmpeg in '/Users/rob/opt/anaconda3/envs/tracking/bin/ffmpeg'
[16:49:57] Property('ffmpeg_path') = "/Users/rob/opt/anaconda3/envs/tracking/bin/ffmpeg"
[16:49:57] Property('build') = "2375994fff55a5446ba2615aa00da334dada0938"
[16:49:57] Property('cmd_line') = " /Users/rob/opt/anaconda3/envs/tracking/bin/TRex.app/Contents/MacOS/TRex"
[16:49:57] -------------------
[16:49:57] LOADING COMMANDLINE
[16:49:57] -------------------
[16:49:57] Property('wd') = "/Users/rob/opt/anaconda3/envs/tracking/bin/TRex.app/Contents/MacOS"
[16:49:57] Changed directory to '../Resources/'.
[16:49:57] -------------------------------
[16:49:57] LOADING FROM 'default.settings'
[16:49:57] -------------------------------
[16:49:57] -------------------------
[16:49:57] LOADED 'default.settings'
[16:49:57] -------------------------
[16:49:57] Property('settings_file') = ""
[16:49:57] Property<array>('cam_undistort_vector') = [-0.257663,-0.192336,0.002455,0.003988,0.35924]
[16:49:57] Property<array>('cam_matrix') = [2945.0896,0,617.255432,0,2942.825195,682.473633,0,0,1]
[16:49:57] Property('cam_scale') = 1
[16:49:57] Property('app_name') = "TGrabs"
[16:49:57] Property('version') = "v1.1.3"
[16:49:57] Property('color_channel') = 1
[16:49:57] Property('system_memory_limit') = 0
[16:49:57] Property('frame_rate') = -1
[16:49:57] Property('blob_size_range') = [0.01,500000]
[16:49:57] Property('crop_offsets') = [0,0,0,0]
[16:49:57] Property('crop_window') = false
[16:49:57] Property('approximate_length_minutes') = 0
[16:49:57] Property('stop_after_minutes') = 0
[16:49:57] Property('threshold') = 9
[16:49:57] Property('threshold_maximum') = 255
[16:49:57] Property('web_quality') = 75
[16:49:57] Property('save_raw_movie') = false
[16:49:57] Property<pair<int,int>>('video_conversion_range') = [-1,-1]
[16:49:57] Property('output_dir') = "/Users/rob/Videos"
[16:49:57] Property('output_prefix') = ""
[16:49:57] Property('video_source') = "basler"
[16:49:57] Property('test_image') = "checkerboard"
[16:49:57] Property('filename') = ""
[16:49:57] Property('settings_file') = ""
[16:49:57] Property('recording') = true
[16:49:57] Property('terminate') = false
[16:49:57] Property('terminate_error') = false
[16:49:57] Property('web_time_threshold') = 0.125
[16:49:57] Property('grabber_use_threads') = true
[16:49:57] Property('adaptive_threshold_scale') = 2
[16:49:57] Property('use_adaptive_threshold') = false
[16:49:57] Property('dilation_size') = 0
[16:49:57] Property('use_closing') = false
[16:49:57] Property('closing_size') = 3
[16:49:57] Property('image_adjust') = false
[16:49:57] Property('image_square_brightness') = false
[16:49:57] Property('image_contrast_increase') = 3
[16:49:57] Property('image_brightness_increase') = 0
[16:49:57] Property('enable_difference') = true
[16:49:57] Property('enable_absolute_difference') = true
[16:49:57] Property('correct_luminance') = false
[16:49:57] Property('equalize_histogram') = false
[16:49:57] Property('quit_after_average') = false
[16:49:57] Property<averaging_method_t>('averaging_method') = mean
[16:49:57] Property('average_samples') = 100
[16:49:57] Property('reset_average') = false
[16:49:57] Property('video_size') = [-1,-1]
[16:49:57] Property<size>('cam_resolution') = [2048,2048]
[16:49:57] Property('cam_framerate') = 30
[16:49:57] Property('cam_limit_exposure') = 5500
[16:49:57] Property('cam_circle_mask') = false
[16:49:57] Property('cam_undistort') = false
[16:49:57] Property('image_invert') = false
[16:49:57] Property('gui_interface_scale') = 1.25
[16:49:57] Property('meta_species') = ""
[16:49:57] Property('meta_age_days') = -1
[16:49:57] Property('meta_conditions') = ""
[16:49:57] Property('meta_misc') = ""
[16:49:57] Property('meta_real_width') = 30
[16:49:57] Property('meta_source_path') = ""
[16:49:57] Property('meta_cmd') = ""
[16:49:57] Property('meta_build') = ""
[16:49:57] Property('meta_conversion_time') = ""
[16:49:57] Property('mask_path') = ""
[16:49:57] Property('log_file') = ""
[16:49:57] Property<array>('meta_write_these') = ["meta_species","meta_age_days","meta_conditions","meta_misc","cam_limit_exposure","meta_real_width","meta_source_path","meta_cmd","meta_build","meta_conversion_time","frame_rate","cam_undistort_vector","cam_matrix"]
[16:49:57] Property('nowindow') = false
[16:49:57] Property('enable_closed_loop') = false
[16:49:57] Property('enable_live_tracking') = false
[16:49:57] Property('grabber_force_settings') = false
[16:49:57] Property('output_name') = "video"
[16:49:57] Property('cmd_parameters') = "-reset_average"
[16:50:07] Selected 'output_prefix' =
[16:50:07] ------------
[16:50:07] LOADING FILE
[16:50:07] ------------
[16:50:07] Property('meta_species') = ""
[16:50:07] Property('meta_age_days') = -1
[16:50:07] Property('meta_conditions') = ""
[16:50:07] Property('meta_misc') = ""
[16:50:07] Property('cam_limit_exposure') = 5500
[16:50:07] Property('meta_real_width') = 200
[16:50:07] Property('meta_source_path') = "/Users/rob/Videos/acclim_side_green.mp4"
[16:50:07] Property('meta_cmd') = " /Users/rob/opt/anaconda3/envs/tracking/bin/TRex.app/Contents/MacOS/../../../TGrabs.app/Contents/MacOS/TGrabs -i /Users/rob/Videos/acclim_side_green.mp4 -o acclim_side_green -threshold 34 -average_samples 100 -averaging_method mean -meta_real_width 200 -reset_average"
[16:50:07] Property('meta_build') = "2375994fff55a5446ba2615aa00da334dada0938"
[16:50:07] Property('meta_conversion_time') = "12-10-2021 15:15:16"
[16:50:07] Property('frame_rate') = 24
[16:50:07] Property<array>('cam_undistort_vector') = [-0.257663,-0.192336,0.002455,0.003988,0.35924]
[16:50:07] Property<array>('cam_matrix') = [2945.0896,0,617.255432,0,2942.825195,682.473633,0,0,1]
[16:50:07] Property('video_size') = [1840,276]
[16:50:07] Property('video_mask') = false
[16:50:07] Property('video_length') = 21600
[16:50:07] Property('video_info') = "pv::File<V7, 17.44MB, '/Users/rob/Videos/acclim_side_green', [1840 x 276], 21600 frames, no mask>

crop_offsets: [0,0,0,0]
Time of recording: 'Tue Oct 12 15:15:18 2021'
Length of recording: '00d:00h:14m:59s'
Framerate: 23fps (41.667ms)

Metadata: {"meta_species": "", "meta_age_days": -1, "meta_conditions": "", "meta_misc": "", "cam_limit_exposure": 5500, "meta_real_width": 200, "meta_source_path": "/Users/rob/Videos/acclim_side_green.mp4", "meta_cmd": " /Users/rob/opt/anaconda3/envs/tracking/bin/TRex.app/Contents/MacOS/../../../TGrabs.app/Contents/MacOS/TGrabs -i /Users/rob/Videos/acclim_side_green.mp4 -o acclim_side_green -threshold 34 -average_samples 100 -averaging_method mean -meta_real_width 200 -reset_average", "meta_build": "2375994fff55a5446ba2615aa00da334dada0938", "meta_conversion_time": "12-10-2021 15:15:16", "frame_rate": 24, "cam_undistort_vector": [-0.257663,-0.192336,0.002455,0.003988,0.35924], "cam_matrix": [2945.0896,0,617.25543 (shortened)...
[16:50:07] ------------------------------------------------------
[16:50:07] LOADING '/Users/rob/Videos/acclim_side_green.settings'
[16:50:07] ------------------------------------------------------
[16:50:07] Property('blob_size_ranges') = [[0.1,7]]
[16:50:07] Property('calculate_posture') = false
[16:50:07] Property('frame_rate') = 24
[16:50:07] Property('gui_foi_name') = "global segment"
[16:50:07] Property('gui_show_detailed_probabilities') = true
[16:50:07] Property('gui_show_number_individuals') = true
[16:50:07] Property('gui_show_selections') = false
[16:50:07] Property('recognition_enable') = false
[16:50:07] Property('track_max_individuals') = 4
[16:50:07] Property('track_speed_decay') = 0.2
[16:50:07] -----------------------------------------------------
[16:50:07] LOADED '/Users/rob/Videos/acclim_side_green.settings'
[16:50:07] -----------------------------------------------------
[16:50:07] Property('cm_per_pixel') = 0.108696
[16:50:07] Initialized with 8 threads.
[16:50:07] Property<set<Idx_t>>('manual_identities') = [0,1,2,3]
[16:50:07] Property<array<pair<string,array>>>('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"]]]
[16:50:07] ----------------
[16:50:07] STARTING PROGRAM
[16:50:07] ----------------
[16:50:07] 20 Individual:512 Blob:232 Physical:32 Vec2Prop:48 Image::Ptr:16 std::shared_ptr<std::vector>:16 Bounds:16 bool:1 cmn::Blob::properties:32
[16:50:07] localcache:104 identity:40 std::map<long_t, Vec2>:24
[16:50:07] BasicStuff:80 pv::Blob:232 Compressed:40
[16:50:07] Midline:64 MinimalOutline:32
[16:50:07] Initialized 2 stages
[16:50:07] Property('app_last_update_check') = 0
[16:50:07] Property<app_update_check_t>('app_check_for_updates') = automatically
[16:50:07] Property('app_last_update_version') = """"
[16:50:07] Property<array>('gui_foi_types') = ["segment end"]
[16:50:07] Property<array>('gui_foi_types') = ["segment end","lost >=1 fish"]
[16:50:07] Property<array>('gui_foi_types') = ["segment end","lost >=1 fish","correcting"]
[16:50:07] Property<array>('gui_foi_types') = ["segment end","lost >=1 fish","correcting","global segment"]
[16:50:07] Property<array>('gui_foi_types') = ["segment end","lost >=1 fish","correcting","global segment","weird angle"]
[16:50:07] Property<array>('gui_foi_types') = ["segment end","lost >=1 fish","correcting","global segment","weird angle","lost >=2 fish"]
[16:50:07] Property('terminate') = false
[16:50:07] Property('gui_show_blobs') = true
[16:50:07] Property('gui_show_paths') = true
[16:50:07] Property('gui_show_texts') = true
[16:50:07] Property('gui_show_inactive_individuals') = true
[16:50:07] Property('gui_show_outline') = true
[16:50:07] Property('gui_show_midline') = true
[16:50:07] Property('gui_show_posture') = true
[16:50:07] Property('gui_show_number_individuals') = true
[16:50:07] Property('gui_show_recognition_bounds') = true
[16:50:07] Property('gui_auto_scale_focus_one') = true
[16:50:07] blob_split_max_shrink = 0.200000
[16:50:07] blob_split_global_shrink_limit = 0.200000
[16:50:07] sqrcm = 0.011815
[16:50:07] blob_size_ranges = [[0.1,7]]
[16:50:07] track_posture_threshold = 15
[16:50:07] blob_size_ranges = [[0.1,7]]
[16:50:08] Took 0.724331s to calculate percentiles in 18230 frames.
[=============== ] 28.24% frame 6100/21599 (4.[============================ ] 55.95% frame 12085/21599 (4[========================================= ] 81.25% frame 17551/21599 (4[16:50:11] Property('analysis_paused') = true
[16:50:14] [CHECK_UPDATES] It has been a week. Let us check for updates...
[16:50:14] Property('app_last_update_check') = 1634050214242701
[WARNING 16:50:14 GPURecognition.cpp:739] Python not yet initialized. Waiting...
[EXCEPTION 16:50:14 GPURecognition.cpp:1008] ModuleNotFoundError: No module named 'requests'

At:
(2):

[ERROR 16:50:14 CheckUpdates.cpp:302] Failed to retrieve github status to determine what the current version is. Assuming current version is the most up-to-date one.
[EXCEPTION 16:50:14 CheckUpdates.cpp:223] Status suggested the check failed.
[ERROR 16:50:14 CheckUpdates.cpp:227] There was an error checking for the newest version:

ModuleNotFoundError: No module named 'requests'
see terminal for full stack...
<string>(2): <module>

Please check your internet connection and try again. This also happens if you are checking for versions too often, or if GitHub changed their API (in which case you should probably update).
[16:55:07] Writing backup of settings...
[16:55:07] Saved '/Users/rob/Videos/acclim_side_green.settings.backup'.
[17:00:07] Writing backup of settings...
[17:00:07] Saved '/Users/rob/Videos/acclim_side_green.settings.backup'.
[17:02:21] Adding to queue...
[17:02:21] Added.
[17:02:21] Property('analysis_paused') = false
[17:02:21] Removing frames after and including 302
[17:02:21] Last remaining 15
[17:02:21] 297-301
[17:02:21] Erased 18989 FOIs of type 'segment end' from Tracker.
[17:02:21] Erased 337 FOIs of type 'lost >=1 fish' from Tracker.
[17:02:21] Erased 337 FOIs of type 'correcting' from Tracker.
[17:02:21] Erased 289 FOIs of type 'global segment' from Tracker.
[17:02:21] Erased 3570 FOIs of type 'weird angle' from Tracker.
[17:02:21] Erased 14 FOIs of type 'lost >=2 fish' from Tracker.
[17:02:21] Inactive individuals: []
[17:02:21] Active individuals: [(Individual*)fish3,(Individual*)fish2,(Individual*)fish0,(Individual*)fish1]
[17:02:21] After removing frames: 0
[17:02:21] posture: 0
[17:02:21] physical props: 0
[17:02:21] all blobs: 0
[17:02:21] Range: 0-301
[17:02:21] Clearing from 25.727116 to 1840.000000
[17:02:21] thread 'GUI::_work_thread' held the lock for 205ms with purpose 'reanalyse_from'
[17:02:21] Property('analysis_paused') = false
[17:02:21] ConnectedTasks[2] -> 0.108338ms -> 0.175369ms (total: 0.283706ms)
[17:02:21] Paused.
[17:02:21] 1.40% frame 302/21599 (0.00MB/s @ 5.54fps eta 5s)rame 302/21599 (0.00MB/s @ 5.54fps eta 5s)
[17:02:24] Property('analysis_paused') = true] 70.67% frame 15266/21599 (5.47MB/s @ 7509.62fps eta 1s)
[17:02:54] Property('gui_show_recognition_bounds') = false
[17:03:00] Property('gui_show_recognition_bounds') = true
[17:03:01] Property('gui_show_posture') = false
[17:03:02] Property('gui_show_posture') = true
[17:03:05] Property('gui_show_blobs') = false
[17:03:05] Property('gui_show_blobs') = true
[17:03:06] Property('gui_show_blobs') = false
[17:03:10] Property('gui_auto_scale_focus_one') = false
[17:03:12] Property<array>('heatmap_ids') = [0]
[17:03:14] Property<array>('heatmap_ids') = []
[17:03:14] Property<array>('heatmap_ids') = [0]
[17:03:26] Property('gui_show_heatmap') = true
[17:03:26] Creating a grid of size 2048x2048 (for image of size 1840x276)
[17:05:07] Writing backup of settings...
[17:05:07] Saved '/Users/rob/Videos/acclim_side_green.settings.backup'.
[WARNING 17:06:15 gui.cpp:4767] Python is not available. Check your configuration.
[17:06:46] Property('gui_show_number_individuals') = false
[WARNING 17:06:51 gui.cpp:4767] Python is not available. Check your configuration.
[WARNING 17:06:56 gui.cpp:4734] Overwriting file '/Users/rob/Videos/acclim_side_green.settings'.
[17:07:07] Property('gui_show_number_individuals') = true
[17:07:15] Property('gui_show_outline') = false
[17:07:16] Property('gui_show_inactive_individuals') = false
[17:07:17] Property('gui_show_inactive_individuals') = true
[17:07:18] Property('gui_show_outline') = true
[17:07:18] Property('gui_show_selections') = true
[17:07:21] Property('gui_show_heatmap') = false
[17:07:23] Property('gui_show_number_individuals') = false
[17:07:24] Property('gui_show_number_individuals') = true
[17:07:28] Property('gui_show_texts') = false
[17:07:29] Property('gui_show_texts') = true
[17:07:36] Property('gui_show_export_options') = true
[WARNING 17:07:48 gui.cpp:4320] No identity network loaded and training internally is disabled. Restart with -use_network true

[mooch443]

It seems that your calculate_posture is set to false in your settings file - which would disable posture.
It also seems that your Python environment is broken. How did you install the software exactly?
Sorry for the late response!