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anTraX: high throughput tracking of color-tagged insects

Home Page: https://antrax.readthedocs.io/

License: GNU General Public License v3.0

Python 26.84% MATLAB 73.04% M 0.02% Objective-C 0.02% Shell 0.08%

video-tracking behavioral-tracking collective-behavior social-behavior social-insects ants machine-vision machine-learning tensorflow

antrax's Introduction

anTraX: high throughput tracking of color-tagged insects

anTraX is a software for video tracking of ants and other small animals tagged with a unique pattern of color dots. It was designed for behavioral experiment using the Clonal Raider Ant Ooceraea biroi, but can be used for any other model system. anTraX is a brute force type tracking algorithm, which was designed to handle high throuput long duration experiments (many colonies over many days). Therefore, it will require considerable computational resources.

The software was designed and written by Jonathan Saragosti and Asaf Gal of the Laboratory of Social Evolution and Behavior in the Rockefeller University, and is distributed under the GPLv3 licence.

Requirements

anTraX works natively on machines running Linux or OSX operating system. It benefits significantly from a multicore system. It is recommended to have at least 2GB of RAM per used core, and a similar sized swap. Computational GPU will speedup the classification phase considerabley.

Installation and usage

See online documentation at https://antrax.readthedocs.io/. An example dataset to be used in the tutorial can be found here. All datasets used to benchmark anTraX are available from the Zenodeo repository.

References

The anTraX paper is now available on eLife.

antrax's People

Contributors

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Watchers

Forkers

asafgal janamach yijint

antrax's Issues

Many small non-ant objects still tracked and classified

Hi,
I have many videos in which small particles of food or trashed are tracked, increasing enormously the size of the trajectories tracked (15000+ for 10 minutes videos), and slowing down the classification and trainset-extraction steps. These objects are smaller than the min area single ant threshold, and are marked with a pink outline. Would it be possible to include an option that tells the software to discard automatically all pink blobs below the min area threshold?

MATLAB:badsubscript error crashes solve step

An Error similar to #17 (comment) but happens during the solving step, and it causes the job to crash and no output to be exported. The full error message is:


10:49:18 -I- Reading video information from file
10:49:53 -I- Loading trgraph from antrax/graphs/C6/graph_9_9.mat
10:50:09 -I- Finished loading trgraph with 2025 tracklets
10:50:09 -I- Loading ids
10:50:11 -I- Finding single ant nodes
10:50:11 -I- Some preperations
10:50:12 -I- Looking for bottleneck pairs
10:50:12 -I- done distance mat
Index in position 2 exceeds array bounds.
Error in trgraph/get_bottleneck_pairs (line 523)

Error in trgraph/solve (line 28)

Error in solve_single_movie (line 54)

Error in antrax_mcr_interface (line 30)
MATLAB:badsubscript

Thanks!

Exception handler for "Reference to non-existent field" in antrax validate?

Hi!

This is not really an issue, more of a suggestion (or a question?). The problem is antrax quits with an error when labels.csv contains an undetected label and proceeds further once the label is removed (in my case until it runs into the next unused label). So I kept removing the "extra" labels from the csv file, the output in the terminal looked like this:

(antrax) jana@unicorn:~/ants$ antrax validate CN0307/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/03/21 20:27:42 -D- running matlab mcr 
08/03/21 20:27:42 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking CN0307/
20:27:58 -D- initializing expreader object
20:27:58 -I- Reading video information from file
Reference to non-existent field 'G-GY'.
Error in validate_tracking/set_experiment (line 275)

Error in validate_tracking/startupFcn (line 429)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in validate_tracking (line 640)

Error in antrax_mcr_interface (line 20)
MATLAB:nonExistentField
08/03/21 20:28:08 -D- matlab app exited with code 249
(antrax) jana@unicorn:~/ants$ antrax validate CN0307/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/03/21 20:28:23 -D- running matlab mcr 
08/03/21 20:28:23 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking CN0307/
20:28:38 -D- initializing expreader object
20:28:38 -I- Reading video information from file
Reference to non-existent field 'GBB'.
Error in validate_tracking/set_experiment (line 275)

Error in validate_tracking/startupFcn (line 429)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in validate_tracking (line 640)

Error in antrax_mcr_interface (line 20)
MATLAB:nonExistentField
08/03/21 20:28:48 -D- matlab app exited with code 249
(antrax) jana@unicorn:~/ants$ antrax validate CN0307/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/03/21 20:29:05 -D- running matlab mcr 
08/03/21 20:29:05 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking CN0307/
20:29:20 -D- initializing expreader object
20:29:20 -I- Reading video information from file
Reference to non-existent field 'GBG'.
Error in validate_tracking/set_experiment (line 275)

Error in validate_tracking/startupFcn (line 429)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in validate_tracking (line 640)

Error in antrax_mcr_interface (line 20)
MATLAB:nonExistentField
08/03/21 20:29:30 -D- matlab app exited with code 249
(antrax) jana@unicorn:~/ants$ antrax validate CN0307/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/03/21 20:29:54 -D- running matlab mcr 
08/03/21 20:29:54 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking CN0307/
20:30:09 -D- initializing expreader object
20:30:09 -I- Reading video information from file
Reference to non-existent field 'GBR'.
Error in validate_tracking/set_experiment (line 275)

Error in validate_tracking/startupFcn (line 429)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in validate_tracking (line 640)

Error in antrax_mcr_interface (line 20)
MATLAB:nonExistentField
08/03/21 20:30:19 -D- matlab app exited with code 249

In this particular case I was trying out antrax on a set of short videos and due to the open boundary condition not all ants could be in the frame throughout that time (hence the error). Provided that labels.csv contains undetected labels, would antrax validate load if an exception handler for the Reference to non-existent field error was added or would it cause further problems?

MATLAB:nonLogicalConditional during export

Hello, I ran into a problem while attempting to export antdata results. Launching the 3rd step of the solve function, both tracklets_tables and xy.mat files are created, but not xy.csv files. The error in the log is the following:

23:10:50 -I- Reading video information from file
23:10:54 -I- Loading trgraph from antrax_HD32_camtag6/graphs/C5/graph_1_1.mat
23:10:57 -I- Finished loading trgraph with 1291 tracklets
23:10:57 -I- Loading tracklet data for movie 1
Operands to the || and && operators must be convertible to logical scalar values.
Error in trgraph/export_xy (line 163)

Error in export_single_movie (line 60)

Error in antrax_mcr_interface (line 42)
MATLAB:nonLogicalConditional

Any idea why this is happening? thanks!

Giacomo

Error in extracting CTF file

Hello,
I'm running antrax on two different HPC environments and suddenly one of them stopped working properly, while the other one still works fine. I tried both "master" and "debug-giacomo" branches.
When I run the function solve, I get the following message in both the matlab_solve.log and matlab_export.log files:

Error in extracting CTF file to '/users/tkay/.mcrCache9.6/antrax1'. Details: 'Could not create file: /users/tkay/.mcrCache9.6/antrax1/toolbox/shared/spcuilib/unifiedscopes/@uiservices/@DialogBase/closedlg.m'
Could not access the MATLAB Runtime component cache. Details: Some error has occurred in the file: core/mclCtfFileExtractor.cpp, at line: 64.
 The error message is: 
Error in extracting CTF file to '/users/tkay/.mcrCache9.6/antrax1'. Details: 'Could not create file: /users/tkay/.mcrCache9.6/antrax1/toolbox/shared/spcuilib/unifiedscopes/@uiservices/@DialogBase/closedlg.m'
; component cache root:/users/tkay/.mcrCache9.6; componentname: antrax_glnxa64_mcr_interface

I haven't changed the runtime version that was working before, nor the path to the matlab version, any idea what might cause this problem?

antrax graph-explore refuses to work with MCR

Long story short, antrax graph-explorer does not work for me on Ubuntu 20.04. I tried with both MCR and MATLAB installation, the end result is the same (the GUI doesn't load), but they behave differently.

With MCR, it exits nicely without attempting to load the GUI:

(antrax-debug-jan21) jana@str09:~/src/anTraX-data$ antrax graph-explorer JS16/


==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

02/02/21 17:21:37 -D- running matlab mcr 
02/02/21 17:21:37 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface graph_explorer_app JS16/ m 0
02/02/21 17:21:44 -D- matlab app exited with code 0
(antrax-debug-jan21) jana@str09:~/src/anTraX-data$

With MATLAB (ran remotely, see in issue #5 why) it does load a GUI, but it looks like this:

All other GUIs seem to load fine. Any ideas what could be the issue?

`Dot indexing is not supported for variables of this type` error when running `validate`

Running validate is behaving strangely:

With matlab on either master or debug-jana branch:

$ antrax validate H1CN0304/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

11:12:48 -I- Reading video information from file
Dot indexing is not supported for variables of this type.

Error in generate_assignment_rate_report (line 27)
        Tid = T(strcmp(T.id,id) |  strcmp(T.id,'all'),:);

Error in validate_tracking/set_experiment (line 332)
            app.assigment_rate = generate_assignment_rate_report(app.Trck, app.XY);

Error in validate_tracking/startupFcn (line 441)
            set_experiment(app, Trck, p.Results.session)

Error in validate_tracking (line 659)
            runStartupFcn(app, @(app)startupFcn(app, varargin{:}))

Traceback (most recent call last):
  File "/home/jana/anaconda3/envs/antrax/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/cli.py", line 651, in main
    """)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/cli.py", line 149, in validate
    launch_matlab_app('validate_tracking', args, mcr=mcr)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/matlab.py", line 204, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: 
  File /home/jana/src/anTraX/matlab/misc/generate_assignment_rate_report.m, line 27, in generate_assignment_rate_report

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 332, in validate_tracking.set_experiment

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 441, in validate_tracking.startupFcn

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 659, in validate_tracking.validate_tracking
Dot indexing is not supported for variables of this type.

With MCR on debug-jana branch:

$ antrax validate H1CN0304/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/04/21 11:14:49 -D- running matlab mcr 
08/04/21 11:14:49 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking H1CN0304/
11:15:00 -D- initializing expreader object
11:15:00 -I- Reading video information from file
Dot indexing is not supported for variables of this type.
Error in generate_assignment_rate_report (line 27)

Error in validate_tracking/set_experiment (line 332)

Error in validate_tracking/startupFcn (line 441)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in validate_tracking (line 659)

Error in antrax_mcr_interface (line 20)
MATLAB:structRefFromNonStruct
08/04/21 11:15:30 -D- matlab app exited with code 249

But it loads with MCR on the master branch:

$ antrax validate H1CN0304/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

08/04/21 11:16:02 -D- running matlab mcr 
08/04/21 11:16:02 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface validate_tracking H1CN0304/
11:16:13 -D- initializing expreader object
11:16:13 -I- Reading video information from file
11:16:42 -I- opening video file H1CN0304/videos//01_12/H1CN0304_10.mp4
11:16:42 -D- Running ffprobe #1 for file H1CN0304/videos//01_12/H1CN0304_10.mp4

mov,mp4,m4a,3gp,3g2,mj2
900382322

11:16:42 -D- Running ffprobe #2 for file H1CN0304/videos//01_12/H1CN0304_10.mp4

1640
1232
yuv420p
25/1
0.000000
3600.000000
90000

This does not seem to be dataset-specific, as I get the same error when I try to run validate on your test dataset:

$ antrax validate JS16/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

11:36:34 -D- initializing expreader object
11:36:34 -I- Reading video information from file
Dot indexing is not supported for variables of this type.

Error in generate_assignment_rate_report (line 27)
        Tid = T(strcmp(T.id,id) |  strcmp(T.id,'all'),:);

Error in validate_tracking/set_experiment (line 332)
            app.assigment_rate = generate_assignment_rate_report(app.Trck, app.XY);

Error in validate_tracking/startupFcn (line 441)
            set_experiment(app, Trck, p.Results.session)

Error in validate_tracking (line 659)
            runStartupFcn(app, @(app)startupFcn(app, varargin{:}))

Traceback (most recent call last):
  File "/home/jana/anaconda3/envs/antrax/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/cli.py", line 651, in main
    """)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/cli.py", line 149, in validate
    launch_matlab_app('validate_tracking', args, mcr=mcr)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/antrax/matlab.py", line 204, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: 
  File /home/jana/src/anTraX/matlab/misc/generate_assignment_rate_report.m, line 27, in generate_assignment_rate_report

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 332, in validate_tracking.set_experiment

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 441, in validate_tracking.startupFcn

  File /home/jana/src/anTraX/matlab/apps/validate_tracking.mlapp, line 659, in validate_tracking.validate_tracking
Dot indexing is not supported for variables of this type.

But it loads properly with MCR and master branch.

Error in configure step

Hi,

Thanks for developing the tool!
I'm getting an issue in the configure step while running on the JS16 dataset

14:51:48 -I- Reading video information from file
14:52:02 -I- opening video file JS16/videos//1_6/JS16_1.mp4
Index exceeds the number of array elements (1).
Error in ffinfo (line 30)

Error in ffreader/collectInfo (line 176)

Error in ffreader (line 59)

Error in expreader/open_vid (line 393)

Error in expreader/fetch_frame (line 338)

Error in expreader/read_frame (line 263)

Error in trhandles/read_frame (line 415)

Error in antrax/set_Trck (line 410)

Error in antrax/set_experiment (line 344)

Error in antrax/startupFcn (line 1184)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 336)

Error in matlab.apps.AppBase/runStartupFcn (line 41)

Error in antrax (line 3563)

Error in antrax_mcr_interface (line 8)
MATLAB:badsubscript

Could you please help me with this?

"ValueError: invalid literal for int() with base 10: 'images' " during classification step

Hello, I recently ran into this error while launching the classification step and I'm not sure where it is coming from.
What I have tried:

Run the classification on the same cluster profile and with the same conda environment on another dataset, it worked
Repeat the tracking, in case the images files were corrupted. Same error pops up
the error is the same for all videos in the camera

I am at a loss because it seems like it's an incompatibility between this specific experimental folder and a code which works well with other folders.

Here is the error message:

WARNING:tensorflow:From /cluster/home/yulrich/miniconda3/envs/antrax2/lib/python3.6/site-packages/tensorflow_core/python/ops/init_ops.py:97: calling GlorotUniform.__init__ (from tensorflow.python
.ops.init_ops) with dtype is deprecated and will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
WARNING:tensorflow:From /cluster/home/yulrich/miniconda3/envs/antrax2/lib/python3.6/site-packages/tensorflow_core/python/ops/init_ops.py:97: calling Zeros.__init__ (from tensorflow.python.ops.ini
t_ops) with dtype is deprecated and will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
WARNING:tensorflow:From /cluster/home/yulrich/miniconda3/envs/antrax2/lib/python3.6/site-packages/tensorflow_core/python/ops/resource_variable_ops.py:1630: calling BaseResourceVariable.__init__ (
from tensorflow.python.ops.resource_variable_ops) with constraint is deprecated and will be removed in a future version.
Instructions for updating:
If using Keras pass *_constraint arguments to layers.
WARNING:tensorflow:From /cluster/home/yulrich/miniconda3/envs/antrax2/lib/python3.6/site-packages/tensorflow_core/python/ops/init_ops.py:97: calling Ones.__init__ (from tensorflow.python.ops.init
_ops) with dtype is deprecated and will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
WARNING:tensorflow:OMP_NUM_THREADS is no longer used by the default Keras config. To configure the number of threads, use tf.config.threading APIs.
2021-10-04 14:00:46.890561: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcuda.so.1
2021-10-04 14:00:47.113362: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2021-10-04 14:00:47.113438: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (eu-g1-021-2): /proc/driver/nvidia/version does not exist
2021-10-04 14:00:47.114343: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-10-04 14:00:47.126270: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2249985000 Hz
2021-10-04 14:00:47.126717: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x558b01973730 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-10-04 14:00:47.126733: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version
Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

Traceback (most recent call last):
  File "/cluster/home/user/miniconda3/envs/antrax2/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/antrax/cli.py", line 659, in main
    """)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/antrax/cli.py", line 482, in classify
    c.predict_experiment(e, movlist=movlist, report=True)
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/antrax/classifier.py", line 369, in predict_experiment
    movieindex = [int(x.rstrip('.mat').split('_')[1]) for x in self.imagefiles]
  File "/cluster/home/user/miniconda3/envs/antrax2/lib/python3.6/site-packages/antrax/classifier.py", line 369, in <listcomp>
    movieindex = [int(x.rstrip('.mat').split('_')[1]) for x in self.imagefiles]
ValueError: invalid literal for int() with base 10: 'images'
Sender: LSF System <lsfadmin@eu-g1-042-4>
Subject: Job 186880930[38]: <Class_3a_v[1-56]> in cluster <euler> Exited

Job <Class_3a_v[1-56]> was submitted from host <eu-login-38> by user <user> in cluster <euler> at Mon Oct  4 14:00:09 2021
Job was executed on host(s) <4*eu-g1-042-4>, in queue <normal.24h>, as user <user> in cluster <euler> at Mon Oct  4 14:00:38 2021
</cluster/home/user> was used as the home directory.
</cluster/scratch/user/Age> was used as the working directory.
Started at Mon Oct  4 14:00:38 2021
Terminated at Mon Oct  4 14:00:49 2021
Results reported at Mon Oct  4 14:00:49 2021

Problems with using command train

Hi
I am currently setting up Antrax on an Ubuntu 21.10. I am using conda as a virtual environment and have installed the Matlab python engine that came with Matlab R2019a. The issue I currently am having is that when using the command antrax train I am seeing an error of:

Traceback (most recent call last):
  File "/home/sean/anaconda3/envs/test/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/antrax/cli.py", line 659, in main
    """)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/antrax/cli.py", line 447, in train
    c.train(examplesdir, ne=ne, aug_options=aug_options)
  File "/home/sean/anaconda3/envs/test/lib/python3.7/site-packages/antrax/classifier.py", line 513, in train
    cw = class_weight.compute_class_weight('balanced', np.unique(FL.classes), FL.classes)
TypeError: compute_class_weight() takes 1 positional argument but 3 were given

It seems to be an error regarding the Matlab python engine version however I am using Matlab R2019a and pip list shows I have matlabengineforpython R2018a installed.
Any help fixing this would be appreciated.

problems with setting up the ffmpeg

Hello anTraX team.
I'm trying to run your example but I find difficulties with the ffmpeg.
I download it. installed it, and added to the PATH. I also checked, and ffmpeg is working.
But I get this error:

Error using ffinfo (line 17)
Could not locate ffprobe

Thank you very much!

and here is the full transcript:

Z:\Dor_Gabay\ThesisProject\scripts\anTraX>antrax configure Z:/Dor_Gabay/ThesisProject/scripts/anTraX-data/JS16
2023-11-21 20:32:50.682240: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library cudart64_100.dll

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

20:33:00 -I- Reading video information from file
Warning: Escaped character '\J' is not valid. See 'doc sprintf' for supported special characters.
> In report (line 86)
In expreader/open_vid (line 389)
In expreader/fetch_frame (line 338)
In expreader/read_frame (line 263)
In trhandles/read_frame (line 415)
In antrax/set_Trck (line 410)
In antrax/set_experiment (line 344)
In antrax/startupFcn (line 1184)
In antrax>@(app)startupFcn(app,varargin{:}) (line 3567)
In appdesigner.internal.service/AppManagementService/tryCallback (line 380)
In appdesigner.internal.service/AppManagementService/runStartupFcn (line 153)
In matlab.apps/AppBase/runStartupFcn (line 43)
In antrax (line 3567)
20:33:03 -I- opening video file Z:/Dor_Gabay/ThesisProject/scripts/anTraX-data/JS16♂ideos\1_620:33:03 -E- Could not locate ffprobe
Error using ffinfo (line 17)
Could not locate ffprobe

Error in ffreader/collectInfo (line 176)
            self.info = ffinfo(self.file);

Error in ffreader (line 59)
            obj.collectInfo;

Error in expreader/open_vid (line 393)
            er.vr = er.VideoReader(er.cur_mov_name);

Error in expreader/fetch_frame (line 338)
                er.open_vid(m);

Error in expreader/read_frame (line 263)
            er.fetch_frame(t);

Error in trhandles/read_frame (line 415)
            [Trck.currfrm.CData,Trck.currfrm.dat] = Trck.er.read_frame(f);

Error in antrax/set_Trck (line 410)
            app.himage = imshow(app.Trck.read_frame(1),'Parent',app.ax);

Error in antrax/set_experiment (line 344)
            app.set_Trck();

Error in antrax/startupFcn (line 1184)
            set_experiment(app, Trck, p.Results.session)

Traceback (most recent call last):
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\dorg\AppData\Local\Programs\Python\Python37\Scripts\antrax.exe\__main__.py", line 9, in <module>
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\antrax\cli.py", line 659, in main
    """)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\sigtools\modifiers.py", line 161, in __call__
    return self.func(*args, **kwargs)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\clize\runner.py", line 404, in run
    ret = cli(*args)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\clize\runner.py", line 271, in __call__
    return func(*posargs, **kwargs)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\clize\runner.py", line 313, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\clize\runner.py", line 271, in __call__
    return func(*posargs, **kwargs)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\antrax\cli.py", line 118, in configure
    launch_matlab_app('antrax', args, mcr=mcr)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\antrax\matlab.py", line 208, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\matlab\engine\matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\matlab\engine\futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "c:\users\dorg\appdata\local\programs\python\python37\lib\site-packages\matlab\engine\fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError:
  File C:\Program Files\MATLAB\R2021a\toolbox\matlab\appdesigner\appdesigner\runtime\+appdesigner\+internal\+service\AppManagementService.m, line 424, in AppManagementService.tryCallback

  File C:\Program Files\MATLAB\R2021a\toolbox\matlab\appdesigner\appdesigner\runtime\+appdesigner\+internal\+service\AppManagementService.m, line 153, in AppManagementService.runStartupFcn

  File C:\Program Files\MATLAB\R2021a\toolbox\matlab\appdesigner\appdesigner\runtime\+matlab\+apps\AppBase.m, line 43, in AppBase.runStartupFcn

  File Z:\Dor_Gabay\ThesisProject\scripts\anTraX\matlab\apps\antrax.mlapp, line 3567, in antrax.antrax
Could not locate ffprobe

Commit b3def69: GUIs works with MCR, but MATLAB giving new errors

While looking into the #5 issue, new errors occurred with MATLAB after installing the updated software. The exact same installation works with MCR, but not with MATLAB it gives new errors:

(matlab2019a) jana@str09:~/src/anTraX-data$ antrax configure JS16/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

03/02/21 11:52:24 -D- antrax cli entry point
11:52:38 -D- starting antrax configure app
11:52:40 -D- set_experiment function
11:52:40 -D- initializing expreader object
11:52:40 -I- Reading video information from file
Error using matlab.ui.Figure/getId
Invalid or deleted object.

Error in matlab.ui.internal.dialog.DialogHelper.getFigureID (line 8)
            out = f.getId();

Error in matlab.ui.internal.dialog.DialogHelper.validateUIfigure (line 21)
            id = matlab.ui.internal.dialog.DialogHelper.getFigureID(h);

Error in matlab.ui.dialog.ProgressDialog (line 45)
            obj.FigureID = matlab.ui.internal.dialog.DialogHelper.validateUIfigure(f);

Error in uiprogressdlg (line 33)
progressDialog = matlab.ui.dialog.ProgressDialog(hUIFigure, varargin{:});

Error in antrax/set_experiment (line 315)
            d = uiprogressdlg(app.UIFigure,'Title','Loading experiment','Indeterminate','on');

Error in antrax/startupFcn (line 1184)
            set_experiment(app, Trck, p.Results.session)

Error in antrax (line 3563)
            runStartupFcn(app, @(app)startupFcn(app, varargin{:}))

Traceback (most recent call last):
  File "/home/jana/anaconda3/envs/matlab2019a/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/cli.py", line 651, in main
    """)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/cli.py", line 104, in configure
    launch_matlab_app('antrax', args, mcr=mcr)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/matlab.py", line 198, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: 
  File /usr/local/MATLAB/R2019a/toolbox/matlab/uitools/uicomponents/components/+matlab/+ui/+internal/+dialog/DialogHelper.m, line 8, in DialogHelper.getFigureID

  File /usr/local/MATLAB/R2019a/toolbox/matlab/uitools/uicomponents/components/+matlab/+ui/+internal/+dialog/DialogHelper.m, line 21, in DialogHelper.validateUIfigure

  File /usr/local/MATLAB/R2019a/toolbox/matlab/uitools/uicomponents/components/+matlab/+ui/+dialog/ProgressDialog.m, line 45, in ProgressDialog.ProgressDialog

  File /usr/local/MATLAB/R2019a/toolbox/matlab/uitools/uicomponents/components/uiprogressdlg.m, line 33, in uiprogressdlg

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 315, in antrax.set_experiment

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 1184, in antrax.startupFcn

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 3563, in antrax.antrax
Invalid or deleted object.

and

(matlab2019a) jana@str09:~/src/anTraX-data$ antrax graph-explorer JS16/

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

Undefined function or variable 'graph_explorer'.

Traceback (most recent call last):
  File "/home/jana/anaconda3/envs/matlab2019a/bin/antrax", line 8, in <module>
    sys.exit(main())
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/cli.py", line 651, in main
    """)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/cli.py", line 142, in graph_explorer
    launch_matlab_app('graph_explorer', args, mcr=mcr)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/antrax/matlab.py", line 198, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "/home/jana/anaconda3/envs/matlab2019a/lib/python3.6/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: Undefined function 'graph_explorer' for input arguments of type 'int64'.

Classifying issues

Hi,

I have installed anTrax and run antrax configure <expdir> to display the application window, but the "Classification" tab does not exist. Is this a problem?

Additionally, when I run antrax extract-trainset <expdir>, the Classifier application window only appears momentarily (the app exits immediately). There is no error massage on command line.
The same symptoms appear when I set the “JS16” demo file as . Since I’m using the same as when I ran antrax configure, it is unlikely that the file path is incorrect.
I would be very happy to receive any information that would solve the above problem!

'antrax configure' crashes on Debian 10

Hi there,

I am very excited to try out your software. I was following your instructions for Linux and I think I got everything right. I do not have a full MATLAB installation at the moment, so I went with the MATLAB Runtime option instead.

Problem: when running

$ antrax configure anTraX-data/JS16/

I see a window appear (see screenshot) and then it disappears with no warning. There is no error message in the terminal too.

Any thoughts why this may be happening? Is there a traceback/verbose mode available?

solve step 1 produce error contains `MATLAB:UndefinedFunction`

Hi :) I am running the solve step 1 on a SLURM cluster with command antrax solve EXPDIR --step 1 --clist 1 --hpc --hpc-options cpus=3,mem-per-cpu=3000,time=72:00:00, and encountered two types of error in some of the .log files (see below). I have 334 videos, each includes 6 colonies, and 211 of them has at least 1 colony failed in the solve step 1. logs of track step does not show error.

$ cat matlab_solve_m_263_c_1.log
02:57:52 -I- Reading video information from file
02:58:02 -I- Loading trgraph from antrax_20220112/graphs/C1/graph_263_263.mat
02:58:03 -I- Finished loading trgraph with 10 tracklets
02:58:04 -I- Loading ids
02:58:04 -I- Finding single ant nodes
02:58:04 -I- Some preperations
02:58:04 -I- Looking for bottleneck pairs
02:58:04 -I- done distance mat
Undefined function or variable 'pairs'.
Error in trgraph/get_bottleneck_pairs (line 515)

Error in trgraph/solve (line 28)

Error in solve_single_movie (line 54)

Error in antrax_mcr_interface (line 30)
MATLAB:UndefinedFunction

$ cat matlab_solve_m_303_c_1.log
03:01:16 -I- Reading video information from file
03:01:28 -I- Loading trgraph from antrax_20220112/graphs/C1/graph_303_303.mat
Warning: Variable 'trjs' not found.
> In trgraph.load (line 875)
  In trhandles/loaddata (line 609)
  In solve_single_movie (line 52)
  In antrax_mcr_interface (line 30)
Undefined function or variable 'trjs'.
Error in trgraph.load (line 876)

Error in trhandles/loaddata (line 609)

Error in solve_single_movie (line 52)

Error in antrax_mcr_interface (line 30)
MATLAB:UndefinedFunction

Solve step 2 Non-binary MAT file

Hi! I am running antrax solve step 2 and encountering the problem that some graphs cannot be load.
I have 6 colonies in each movie. The previous steps: track and classification were all normal.

My command for step 2:

bsub -n 4 -W 4:00 -J "s2_c5s[1-238:1]" -R "rusage[mem=6144]" 'antrax solve /cluster/scratch/galciatore/Nema_3/cam5 --movlist $LSB_JOBINDEX --step 2'

The graph did exists and the size of the graph seems normal, however after solve step 2 the file turns empty.
Graph file before solve step 2 (I duplicated it and saved it in another folder)

(anTraX) [galciatore@eu-login-02 cam5_before_solve]$ ls -l graphs/C5/graph_5_5.mat
-rw-r----- 1 galciatore galciatore-group 41229 Mar 22 12:06 graphs/C5/graph_5_5.mat

Not all colonies failed in the solve step 2, for example colony 1 were finished.

(anTraX) [galciatore@eu-login-02 logs]$ grep -rHnoL "Done" matlab_*.log
matlab_link_across_movies.log
matlab_solve_g_1_c_3.log
matlab_solve_g_1_c_4.log
matlab_solve_g_1_c_5.log
matlab_solve_g_1_c_6.log
matlab_solve_g_2_c_2.log
matlab_solve_g_2_c_4.log
matlab_solve_g_2_c_5.log
matlab_solve_g_2_c_6.log

The error message in matlab_solve_g_1_c_3.log

18:12:09 -I- Loading trgraph from antrax/graphs/C3/graph_26_26.mat
18:12:11 -I- Loading trgraph from antrax/graphs/C3/graph_27_27.mat
18:12:13 -I- Loading trgraph from antrax/graphs/C3/graph_28_28.mat
18:12:17 -I- Loading trgraph from antrax/graphs/C3/graph_29_29.mat
18:12:20 -I- Loading trgraph from antrax/graphs/C3/graph_30_30.mat
18:12:21 -I- Loading trgraph from antrax/graphs/C3/graph_31_31.mat
18:12:22 -I- Loading trgraph from antrax/graphs/C3/graph_32_32.mat
18:12:25 -I- Loading trgraph from antrax/graphs/C3/graph_33_33.mat
18:12:29 -I- Loading trgraph from antrax/graphs/C3/graph_34_34.mat
Error using load
Cannot read file /cluster/scratch/galciatore/Nema_3/cam5/antrax/graphs/C3/graph_34_34.mat.
Error in trgraph.load (line 880)

Error in trhandles/loaddata (line 609)

Error in solve_across_movies (line 70)

Error in antrax_mcr_interface (line 53)
MATLAB:load:cantReadFile

Running antrax on HPC / `MATLAB:badsubscript` and related errors during solve

Hi :-)

The HPC server I am using has certain limits per user (100 schedules jobs, 3 days max per job). The solve step in my case generated more than 100 jobs, causing some of the jobs getting cancelled. Since the solve step is a three step process, I figured I can start each step manually, e.g.:
$ sbatch path/to/hpc_solve1.sh
Is this a reasonable way to do it? Is there a different way to go around the max job per user thing?

Installation issue on m1 Mac

Hi Asaf,
Thanks for publishing your neat code!

I want to use anTraX for tracking ants. However, I run into a problem when trying to open the app.
I followed the installation guide on my m1-chipped Mac (OS Big Sur), but upon launching either "antrax configure" or "antrax track" I get the following message in terminal:

zsh: illegal hardware instruction antrax configure

or:

zsh: illegal hardware instruction antrax track

A google search raised a suspicion that it has to do with the m1 chip. Did you encounter this issue before? any ideas?
Thanks!!

Error while running validate

I'm trying to run antrx on demo data. I'm getting errors in the 'validate' step.
When I run this command there's some error.

USR@COMPUTER:~/Documents/anTraX-data$ antrax validate JS16
16:34:45 -I- Reading video information from file
Unrecognized method, property, or field 'cla' for class 'matlab.ui.control.UIAxes'.

Error in validate_tracking/show_next (line 83)
app.ImageAxes.cla;

Error in validate_tracking/set_experiment (line 351)
show_next(app);

Error in validate_tracking/startupFcn (line 429)
set_experiment(app, Trck, p.Results.session)

Error using matlab.apps.internal.GraphicsCallbackProxy/runCallbackFunction (line 23)
Error while evaluating GraphicsCallbackProxy CallbackFcn.
Please help.

[enhancement] Printing details of validation session

Hello,
Would it be possible to export information from the current "validation" session in a file?

I'm thinking about a table with the assigned ID of ants, if it's correct or not, the colony name, frame number and xy coordinates of the blob. This way it would be easier to extract detailed information about tag, colony and time biases. Also, it would be possible to merge information coming from different validation runs and have a better picture of the whole experiment.

Thanks!
Giacomo

Opening anTrax issue

Hi,
thank you for the app!
I tried opening the app but kept getting the below error: (I am on Mac OS)

First, I downloaded tensorflow version 1.15 in the conda env tf15 and successfully installed anTrax:

(base) markthomas@Marks-Air anTrax % conda activate tf15

Next, I tried running the code as per the instructions:

(tf15) markthomas@Marks-Air anTrax % antrax configure /Users/markthomas/Desktop/Home/MRes/Other_chapters/Ants/anTraX/anTraX-data/JS16

But got this error:

Traceback (most recent call last):
File "/Users/markthomas/miniconda3/envs/tf15/bin/antrax", line 5, in
from antrax.cli import main
File "/Users/markthomas/miniconda3/envs/tf15/lib/python3.7/site-packages/antrax/cli.py", line 5, in
from .matlab import *
File "/Users/markthomas/miniconda3/envs/tf15/lib/python3.7/site-packages/antrax/matlab.py", line 22, in
ANTRAX_BIN_PATH = ANTRAX_PATH + '/bin/'
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

Any help is greatly appreciated!

Installation help needed

Hi!
I would like to use your nice tool to track some crickets.
I am having trouble installing anTraX on my macbook pro with macOS Big Sur v11.1. After I changed the bash profile and ran "antrax configure" I get the message "-bash: antrax: command not found". I tried both with full matlab installation and MCR, both didn't work. Did I get the paths wrong? Or does this have to do with the bash to zsh transition (https://support.apple.com/en-us/HT208050)?
Thanks !

export ANTRAX_MCR=/Applications/MATLAB/MATLAB_Runtime/v96
export ANTRAX_PATH=/Users/lavn0007/anTraX
export ANTRAX_USE_MCR=True

Two different errors when exploring `antrax configure`

Hi again!

This time I was going through the user guide and while exploring different functions of antrax configure, I ran into different errors.

When clicking Scale > Circle > Draw, nothing happens. when I click the X to close the GUI, I see the following output in the bash terminal:

app closing..
Error using Ellipse
Expected Center to be of size 1x2, but it is of size 2x1.
Error in images.roi.Ellipse/set.Center

Error in images.roi.internal.ROI/parseInputs

Error in images.roi.Ellipse

Error in drawellipse (line 196)

Error in antrax/ScaleDrawButtonPushed (line 1309)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 333)

Error in matlab.apps.AppBase>@(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event)
Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 335)
Error while evaluating Button PrivateButtonPushedFcn.

15/02/21 17:06:24 -D- matlab app exited with code 0

In ROI, adding a shape works, but clicking Remove does not do anything. As above, the error appears when I click X to close the GUI:

app closing..
Invalid or deleted object.
Error in antrax/ROIAddRemoveButtonPushed (line 1485)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 333)

Error in matlab.apps.AppBase>@(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event)
Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 335)
Error while evaluating DestroyedObject PrivateButtonPushedFcn.

Invalid or deleted object.
Error in antrax/ROIAddRemoveButtonPushed (line 1485)

Error in appdesigner.internal.service.AppManagementService/tryCallback (line 333)

Error in matlab.apps.AppBase>@(source,event)tryCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event)
Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 335)
Error while evaluating DestroyedObject PrivateButtonPushedFcn.

15/02/21 17:17:31 -D- matlab app exited with code 0

Same thing happens when adding Open Boundary and then clicking Remove or Reset.

Running Debian 10 with MCR.

Potential graph corruption at solve 2 resulting three types of error messages in matlab_export_*.log

Hi! I wonder if anyone could help me fix a problem when running antrax on hpc. This is a problem that I encountered when running a big continuous experiment (~288 videos, each contains 6000 frames) on a cluster managed by SLURM.

Although all the previous steps may not produce any errors, three types of error pop up for some videos at the last step of propagation and some seems to be related to graph corruption at solve step 2 since the problematic graphs before step 2 seems to be fine after opened from Matlab on my local machine.

Note that the problem is not present in all videos, only in a subset. After rerunning all the previous steps (track, classification, etc) on the problematic videos, sometimes the problem can be solved by itself. However, I should run all the steps twice (sometimes even more) which is quite time-consuming.

Here are the three types of error messages that I get:

Variable 'trjs' not found

17:25:39 -I- Loading trgraph from antrax/graphs/C4/graph_10_10.mat
Warning: Variable 'trjs' not found.
> In trgraph.load (line 887)
  In trhandles/loaddata (line 609)
  In export_single_movie (line 59)
  In antrax_mcr_interface (line 42)
Undefined function or variable 'trjs'.
Error in trgraph.load (line 888)
Error in trhandles/loaddata (line 609)
Error in export_single_movie (line 59)
Error in antrax_mcr_interface (line 42)
MATLAB:UndefinedFunction

Warning: Variable 'G' not found

14:32:26 -I- Loading trgraph from antrax/graphs/C1/graph_1_1.mat
Warning: Variable 'G' not found.
> In trgraph.load (line 880)
  In trhandles/loaddata (line 609)
  In export_single_movie (line 59)
  In antrax_mcr_interface (line 42)
Reference to non-existent field 'trjs'.
Error in trgraph.load (line 886)
Error in trhandles/loaddata (line 609)
Error in export_single_movie (line 59)
Error in antrax_mcr_interface (line 42)

MATLAB:nonExistentField

File might be corrupt.

14:59:40 -I- Loading trgraph from antrax/graphs/C2/graph_101_101.mat
Error using load
Unable to read MAT-file /scratch1/users/zimai.li/idol/idol_cam2/antrax/graphs/C2/graph_101_101.mat. File might be corrupt.
Error in trgraph.load (line 880)
Error in trhandles/loaddata (line 609)
Error in export_single_movie (line 59)
Error in antrax_mcr_interface (line 42)
MATLAB:load:unableToReadMatFile

Thanks a lot in advance!

Extract Trainset Responding Slow

Hi! I encounter the slow response issue when I am using the graphic tool of anTrax: Extract Trainset.

When I try to change between images in antrax, the software start to respond really slow (> 30s) after the 50th image.
When I try to switch between movies via the "Tracklets" option in the top bar menu, the process of "Preparaing validation datset, loading images..." takes around 5-10 mins.

The first issue was also observed in a different higher memory machine. However, I don't know if the second issue is due to the low memory on my machine.

Thanks a lot!

Information of my machine:
MacBook Pro 2017,
Processor 2.3 GHZ Dual Core Intel Core i5
Memory 8 GB 2133 MHz LPDDR3
MacOS Catalina 10.15.7
Matlab 2020a
Python 3.7.10

The multi-colony masks do not get generated when using MATLAB full installation

This might be a my-system-specific-bug, but I will report it here in case someone else experiences a similar problem.

When using MATLAB full installation and trying to use the multi-colony option, "geometry_multi_colony": gets set to true in prmtrs.json, but no mask png is generated and I get the following errors on master and other branches:

$ antrax configure 25C

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

20/09/22 11:18:05 -D- antrax cli entry point
11:18:14 -D- starting antrax configure app
11:18:15 -D- set_experiment function
11:18:15 -D- initializing expreader object
11:18:15 -I- Reading video information from file
Error using imread>get_full_filename (line 566)
File "25C/antrax/parameters/masks/colony_index_mask.png" does not exist.

Error in imread (line 375)
    fullname = get_full_filename(filename);

Error in trhandles/load_masks (line 272)
                Trck.Masks.colony_index_mask = imread([mskdir,'colony_index_mask.png']);

Error in trhandles.load (line 1026)
            Trck.load_masks;

Error in antrax/set_experiment (line 291)
                    app.Trck = trhandles.load(app.expdir);

Error in antrax/startupFcn (line 1184)
            set_experiment(app, Trck, p.Results.session)

Error in antrax (line 3567)
            runStartupFcn(app, @(app)startupFcn(app, varargin{:}))

Traceback (most recent call last):
  File "/home/jana/anaconda3/envs/antrax/bin/antrax", line 33, in <module>
    sys.exit(load_entry_point('antrax', 'console_scripts', 'antrax')())
  File "/home/jana/src/anTraX/antrax/cli.py", line 644, in main
    """)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/sigtools/modifiers.py", line 158, in __call__
    return self.func(*args, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 363, in run
    ret = cli(*args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 262, in _cli
    return func('{0} {1}'.format(name, command), *args)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/clize/runner.py", line 220, in __call__
    return func(*posargs, **kwargs)
  File "/home/jana/src/anTraX/antrax/cli.py", line 104, in configure
    launch_matlab_app('antrax', args, mcr=mcr)
  File "/home/jana/src/anTraX/antrax/matlab.py", line 208, in launch_matlab_app
    app = eval('eng.' + appname + '(' + ','.join([str(a) for a in args]) + ')')
  File "<string>", line 1, in <module>
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/matlabengine.py", line 71, in __call__
    _stderr, feval=True).result()
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/futureresult.py", line 67, in result
    return self.__future.result(timeout)
  File "/home/jana/anaconda3/envs/antrax/lib/python3.6/site-packages/matlab/engine/fevalfuture.py", line 82, in result
    self._result = pythonengine.getFEvalResult(self._future,self._nargout, None, out=self._out, err=self._err)
matlab.engine.MatlabExecutionError: 
  File /usr/local/MATLAB/R2019a/toolbox/matlab/imagesci/imread.p, line 566, in get_full_filename

  File /usr/local/MATLAB/R2019a/toolbox/matlab/imagesci/imread.p, line 375, in imread

  File /home/jana/src/anTraX/matlab/@trhandles/trhandles.m, line 272, in trhandles.load_masks

  File /home/jana/src/anTraX/matlab/@trhandles/trhandles.m, line 1026, in trhandles.load

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 291, in antrax.set_experiment

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 1184, in antrax.startupFcn

  File /home/jana/src/anTraX/matlab/apps/antrax.mlapp, line 3567, in antrax.antrax
File "25C/antrax/parameters/masks/colony_index_mask.png" does not exist.

However, when I use MCR (instead of the full MATLAB installation), the mask gets properly generated and multi-colony tracking works as described.

MATLAB:badsubscript occasionally shows up in track logs

Hi,

I was wondering if this is something to be concerned about: for some of the videos I track I get a MATLAB:badsubscript error in logs at the point where the word Done! is usually printed out. The files in tracklets/ and images/ seem to be properly generated. Re-tracking the same video seems to result in the same error, while other videos from the same experiment do not seem to have this problem. There is also an error in matlab_link_across_movies.log.

How bad is this?

$ cat CN0307/antrax/logs/matlab_track_m_110.log 
10:15:07 -I- Reading video information from file
10:15:09 -I- Linking method is link_blobs
10:15:10 -I- Starting the frame loop
10:15:10 -I- opening video file CN0307/videos//1_144/CN0307_110.mp4
10:20:58 -I- Finished tracking frame #818500 (1000/7500)
10:26:34 -I- Finished tracking frame #819500 (2000/7500)
10:31:51 -I- Finished tracking frame #820500 (3000/7500)
10:36:52 -I- Finished tracking frame #821500 (4000/7500)
10:40:44 -I- Finished tracking frame #822500 (5000/7500)
10:45:44 -I- Finished tracking frame #823500 (6000/7500)
10:51:06 -I- Finished tracking frame #824500 (7000/7500)
10:53:53 -I- Finished frame loop, cleaning up
10:53:56 -I- Closed tracklet graph object
10:53:56 -I- ... movies 110
10:53:56 -I- ... 339 tracklets
10:53:58 -I- Looking for bottleneck pairs
10:53:58 -I- done distance mat
Index in position 2 exceeds array bounds.
Error in trgraph/get_bottleneck_pairs (line 523)

Error in track_single_movie (line 169)

Error in antrax_mcr_interface (line 36)
MATLAB:badsubscript

$ cat CN0307/antrax/logs/matlab_link_across_movies.log 
Undefined function or variable 'link_across_moives'.
Error in antrax_mcr_interface (line 47)
MATLAB:UndefinedFunction

anTraX with MATLAB 2019a freezes on Ubuntu 20.04 unless ran remotely

I have a very strange issue on my Ubuntu 20.04 computer: anTraX does not load GUI's unless I run it remotely (from another computer with ssh -X). I thought this might be a graphics problem, so I purged all nvidia software from the computer. That didn't help.

Here is how it looks locally:

And remotely:

The content for the matlab-antrax.sh file (the first two lines are unnecessary, it loads without them through ssh as well):

alias matlab="LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 matlab"
LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6
export ANTRAX_PATH=/home/jana/src/anTraX
export ANTRAX_USE_MCR=False
export ANTRAX_DEBUG_MODE=True

The GUIs (at least most of them) load fine with MCR, so this issue is not critical for me. I thought I should document this peculiarity here in case somebody else runs into this weird problem.

What causes "Segmentation violation" during the tracking stage?

I ran into an error while running tracking on multiple files on HPC and I was able to reproduce the same error by starting the job with an identical command, which was:

antrax track H1CN0304/ --movlist 1-5,13,14,21-39,43,45,49-59 --hpc --hpc-options partition=single,[email protected],cpus=10,mem-per-cpu=5000,time=09:00:00

All instances failed with a similar error (see below) twice. However, with a slightly different command all movies were tracked successfully:

antrax track H1CN0304/ --movlist 1-5,13,14,21-39,43,45,49-59 --hpc --hpc-options partition=fat,[email protected],cpus=8,mem-per-cpu=5000,time=11:00:00

The difference between the two commands was the partition used (single vs fat) and the number of cpus (10 vs 8). The partition called single is usually less busy and by default I can run many more tasks in parallel. I was wondering if there was an explanation for the error with the first command? Am I overdoing it with the number of CPUs? Still trying to get a feeling for this :-)

(base) [fr_jm1121@uc2n994 ~]$ cat ants/H1CN0304/antrax/logs2/matlab_track_m_1.log 
07:18:55 -I- Reading video information from file
07:19:02 -I- Linking method is link_blobs
07:19:03 -I- Starting the frame loop
07:19:03 -I- opening video file H1CN0304/videos//01_12/H1CN0304_01.mp4
07:23:01 -I- Finished tracking frame #1000 (1000/90000)
07:26:58 -I- Finished tracking frame #2000 (2000/90000)
07:30:46 -I- Finished tracking frame #3000 (3000/90000)
07:34:38 -I- Finished tracking frame #4000 (4000/90000)
07:37:55 -I- Finished tracking frame #5000 (5000/90000)
07:41:23 -I- Finished tracking frame #6000 (6000/90000)
07:45:00 -I- Finished tracking frame #7000 (7000/90000)
07:48:56 -I- Finished tracking frame #8000 (8000/90000)
07:53:02 -I- Finished tracking frame #9000 (9000/90000)
07:56:45 -I- Finished tracking frame #10000 (10000/90000)
08:00:17 -I- Finished tracking frame #11000 (11000/90000)
08:03:32 -I- Finished tracking frame #12000 (12000/90000)
08:06:59 -I- Finished tracking frame #13000 (13000/90000)
08:10:45 -I- Finished tracking frame #14000 (14000/90000)
08:14:49 -I- Finished tracking frame #15000 (15000/90000)
08:18:59 -I- Finished tracking frame #16000 (16000/90000)
08:23:09 -I- Finished tracking frame #17000 (17000/90000)
08:27:27 -I- Finished tracking frame #18000 (18000/90000)
08:31:56 -I- Finished tracking frame #19000 (19000/90000)
08:35:45 -I- Finished tracking frame #20000 (20000/90000)
08:39:40 -I- Finished tracking frame #21000 (21000/90000)
08:44:15 -I- Finished tracking frame #22000 (22000/90000)
08:48:02 -I- Finished tracking frame #23000 (23000/90000)
08:51:45 -I- Finished tracking frame #24000 (24000/90000)
08:55:47 -I- Finished tracking frame #25000 (25000/90000)
09:00:07 -I- Finished tracking frame #26000 (26000/90000)
09:04:35 -I- Finished tracking frame #27000 (27000/90000)
09:08:14 -I- Finished tracking frame #28000 (28000/90000)
09:12:14 -I- Finished tracking frame #29000 (29000/90000)
09:16:03 -I- Finished tracking frame #30000 (30000/90000)
09:20:33 -I- Finished tracking frame #31000 (31000/90000)
09:25:10 -I- Finished tracking frame #32000 (32000/90000)
09:28:56 -I- Finished tracking frame #33000 (33000/90000)
09:32:44 -I- Finished tracking frame #34000 (34000/90000)

--------------------------------------------------------------------------------
       Segmentation violation detected at Fri Mar 26 09:36:04 2021 +0100
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Deployed                 : true
  GNU C Library            : 2.28 stable
  Graphics Driver          : Unknown hardware 
  Graphics card 1          : 0x102b ( 0x102b ) 0x538 Version 0.0.0.0 (0-0-0)
  Java Version             : Java 1.8.0_181-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
  MATLAB Architecture      : glnxa64
  MATLAB Entitlement ID    : Unknown
  MATLAB Root              : /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96
  MATLAB Version           : 9.6.0.1472908 (R2019a) Update 9
  OpenGL                   : hardware
  Operating System         : "Red Hat Enterprise Linux release 8.2 (Ootpa)"
  Process ID               : 1450793
  Processor ID             : x86 Family 6 Model 85 Stepping 7, GenuineIntel
  Session Key              : 9ae81582-ff3f-4ec2-a5e5-5e2a1ecbd7d3
  Static TLS mitigation    : Enabled: Full
  Window System            : The X.Org Foundation (12004000), display 10.0.3.226:14.0

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 00000000000000c0  RBX = 0000148f4e8d1000
  RCX = 00000000dc40bce8  RDX = 000000008d000500
  RSP = 0000148eafffbc60  RBP = 000000000000000a
  RSI = 0000000000000062  RDI = 00000000dc40bce8

   R8 = 0000000000000467   R9 = 0000148f527fc710
  R10 = 000000000000000b  R11 = 0000000000000202
  R12 = 0000000000000000  R13 = 0000000000000000
  R14 = 0000148f527fd6b8  R15 = 0000148e30e620b0

  RIP = 0000148f531c20b6  EFL = 0000000000010202

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x0000148f531c20b6                        /lib64/ld-linux-x86-64.so.2+00041142
[  1] 0x0000148f531c2c31                        /lib64/ld-linux-x86-64.so.2+00044081
[  2] 0x0000148f52571ddc                                   /lib64/libc.so.6+01277404
[  3] 0x0000148f52fb5328                                  /lib64/libdl.so.2+00004904
[  4] 0x0000148f52572414                                   /lib64/libc.so.6+01278996 _dl_catch_exception+00000132
[  5] 0x0000148f525724d3                                   /lib64/libc.so.6+01279187 _dl_catch_error+00000051
[  6] 0x0000148f52fb5939                                  /lib64/libdl.so.2+00006457
[  7] 0x0000148f52fb5393                                  /lib64/libdl.so.2+00005011 dlsym+00000099
[  8] 0x0000148f4b2b6054 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libut.so+00376916 utFindSymbolInLibrary+00000308
[  9] 0x0000148e54097bf5 /pfs/data5/home/fr/fr_fr/fr_jm1121/.mcrCache9.6/antrax0/toolbox/images/images/private/../../../../bin/glnxa64/libmwhalideBinder.so+00011253 _ZN12HalideBinder16getMethodPointerEPKcS1_+00000613
[ 10] 0x0000148e5409c982 /pfs/data5/home/fr/fr_fr/fr_jm1121/.mcrCache9.6/antrax0/toolbox/images/images/private/morphmex_halide.mexa64+00006530 mexFunction+00000978
[ 11] 0x0000148f488f7d60 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmex.so+00544096
[ 12] 0x0000148f488f8d73 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmex.so+00548211
[ 13] 0x0000148f488e471c /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmex.so+00464668
[ 14] 0x0000148f482d457f /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_dispatcher.so+01082751 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000207
[ 15] 0x0000148f482d607e /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_dispatcher.so+01089662
[ 16] 0x0000148f482d65c1 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_dispatcher.so+01091009 _ZN8Mfh_file8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 17] 0x0000148f467a09ea /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+13859306
[ 18] 0x0000148f467a637f /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+13882239
[ 19] 0x0000148f4689e971 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+14899569
[ 20] 0x0000148f4680b044 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+14295108
[ 21] 0x0000148f46831a3d /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+14453309
[ 22] 0x0000148f46112700 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+06985472
[ 23] 0x0000148f460fca92 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+06896274
[ 24] 0x0000148f46100f73 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+06913907
[ 25] 0x0000148f46660571 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+12547441
[ 26] 0x0000148f4678ef97 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+13787031
[ 27] 0x0000148f4678f3d5 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+13788117
[ 28] 0x0000148f482d457f /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_dispatcher.so+01082751 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000207
[ 29] 0x0000148f482d6713 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_dispatcher.so+01091347 _ZN8Mfh_file19dispatch_with_reuseEiPP11mxArray_tagiS2_+00000323
[ 30] 0x0000148f468cdf2e /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+15093550
[ 31] 0x0000148f4660c8d6 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+12204246
[ 32] 0x0000148f4660ca4c /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+12204620
[ 33] 0x0000148f466ace48 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+12861000
[ 34] 0x0000148f466ade78 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_lxe.so+12865144
[ 35] 0x0000148f4989ac60 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwm_interpreter.so+01289312 _Z44inCallFcnWithTrapInDesiredWSAndPublishEventsiPP11mxArray_tagiS1_PKcbP15inWorkSpace_tag+00000080
[ 36] 0x0000148f48a4ee7d /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwiqm.so+00712317 _ZN3iqm15BaseFEvalPlugin7executeEP15inWorkSpace_tag+00000525
[ 37] 0x0000148f4a2ef749 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwmcr.so+00943945
[ 38] 0x0000148f48a43f2d /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwiqm.so+00667437
[ 39] 0x0000148f48a26eba /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwiqm.so+00548538
[ 40] 0x0000148f48a27b2f /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwiqm.so+00551727
[ 41] 0x0000148f4a2d2e8e /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwmcr.so+00827022
[ 42] 0x0000148f4a2d3648 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwmcr.so+00829000
[ 43] 0x0000148f4a2ccd92 /pfs/data5/home/fr/fr_fr/fr_jm1121/MATLAB/v96/bin/glnxa64/libmwmcr.so+00802194
[ 44] 0x0000148f52d9c2de                             /lib64/libpthread.so.0+00033502
[ 45] 0x0000148f52535e83                                   /lib64/libc.so.6+01031811 clone+00000067
[ 46] 0x0000000000000000                                   <unknown-module>+00000000


This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.
** This crash report has been saved to disk as /home/fr/fr_fr/fr_jm1121/matlab_crash_dump.1450793-1 **



MATLAB is exiting because of fatal error

MCR Interface scaling on high resolution displays

Hi!

Not sure if this is an anTraX problem per se, but the menu text is awfully small on a 4K display. MATLAB full installation seems to have a solution for this (e.g., here), but I didn't find anything for MCR.

With MCR it looks like this on 4K:

The text on the left is "normal" size. MCR seems to ignore the system-wide scaling settings. Do you happen to have a quick solution for this?

graph-explorer app crashes on open (OSX, MCR mode)

anTraX on HPC and writing to /scratch issue

Hi!

I am not sure if you will be able to help with this one, but maybe you've seen something like this before. I got access to a remote HPC cluster (first time for me, I've only used local computers and servers up until now). When running pip install . I get a permission denied error because pip tries to write into the /scratch directory. Generally, the output looks like this:

With virtualenv or anaconda:

Processing /pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX
ERROR: Could not install packages due to an OSError: [('/pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack', '/scratch/pip-req-build-5g6wd_w5/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack', "[Errno 13] Permission denied: '/scratch/pip-req-build-5g6wd_w5/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack'"), ('/pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx', '/scratch/pip-req-build-5g6wd_w5/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx', "[Errno 13] Permission denied: '/scratch/pip-req-build-5g6wd_w5/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx'")]

With global pip and --user flag:

[fr_jm1121@uc2n997 anTraX]$ pip3.6 install . --user
Processing /pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX
Exception:
Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/lib/python3.6/site-packages/pip/commands/install.py", line 346, in run
    requirement_set.prepare_files(finder)
  File "/usr/lib/python3.6/site-packages/pip/req/req_set.py", line 381, in prepare_files
    ignore_dependencies=self.ignore_dependencies))
  File "/usr/lib/python3.6/site-packages/pip/req/req_set.py", line 623, in _prepare_file
    session=self.session, hashes=hashes)
  File "/usr/lib/python3.6/site-packages/pip/download.py", line 809, in unpack_url
    unpack_file_url(link, location, download_dir, hashes=hashes)
  File "/usr/lib/python3.6/site-packages/pip/download.py", line 686, in unpack_file_url
    shutil.copytree(link_path, location, symlinks=True)
  File "/usr/lib64/python3.6/shutil.py", line 365, in copytree
    raise Error(errors)
shutil.Error: [('/pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack', '/scratch/pip-hppf66nt-build/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack', "[Errno 13] Permission denied: '/scratch/pip-hppf66nt-build/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.pack'"), ('/pfs/data5/home/fr/fr_fr/fr_jm1121/src/anTraX/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx', '/scratch/pip-hppf66nt-build/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx', "[Errno 13] Permission denied: '/scratch/pip-hppf66nt-build/.git/objects/pack/pack-d30091f4eb8139eba7e89868113a6ebdca569f82.idx'")]

I was able to install other packages using pip (e.g., pip install pandas), so this issue seems to be more specific.

A Google search didn't help much and I already contacted the HPC technical support for that. I thought I should ask here too in case you've seen this before :-)

Problems with compiling mex file

Hi I'm trying to install the software for a project and ran into this issue when compiling the mex file.
I am not a coding person so have no idea what any of this means, but would appreciate any help!

sean@sean-VirtualBox:~/Downloads/anTraX/matlab/external/popenmatlab$ mex popenr.c
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=mex)
restricted \write18 enabled.
entering extended mode
(./popenr.c
This is MeX Version 1.05 18 XII 1993 (B. Jackowski & M. Ry'cko)

Overfull \hbox (166.50084pt too wide) in paragraph at lines 1--14
\tenrm EOF, re-turn ma-trix si-zed ac-cor-ding to what was ac-tu-ally read * *
$\teni Header \tenrm : \teni =homes=drspeech=src=matlabpopen=RCS=popenr:c; v\te
nrm 1\teni :\tenrm 22007\teni =\tenrm 01\teni =\tenrm 1404 :|
! You can't use `macro parameter character #' in vertical mode.
l.15 #
include <stdio.h>
? ^C! Interruption.

i
l.15 #i
nclude <stdio.h>
?

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