denardolab / behaviordepot Goto Github PK

Hi!

I’m running BehaviorDEPOT on MATLAB_R2020a on Mac.
I’m struggling with this error message that comes up when I try to run the program. I’ve uploaded a .csv file that was generated from training DLC and the video that I want to analyse, but once I’ve selected the OFT boundaries it comes up with this error:

Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
Unrecognized function or variable 'part_names'.

Error in importDLCTracking (line 66)
Params.part_names = part_names;

Error in importTracking (line 25)
[data, Params] = importDLCTracking(Params);

Error in BehDEPOT_mainscript (line 128)
[data, Params] = importTracking(Params);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 382)
Error while evaluating Button PrivateButtonPushedFcn.

If you know a solution it would be great if you could help me out! :)

Sorry to bug you again. I am getting an error in Matlab. I created a .csv tracking file, but I am unclear if there are specific body parts I need to label for my file to work with your program? The error I got is:

Argument to dynamic structure reference must evaluate to a valid
field name.

Error in genTracking_custom (line 20)
Tracking.Raw.(this_part) = data(i3-1:i3+1,:);

Error in BehDEPOT_mainscript (line 109)
Tracking = genTracking_custom(data, Params);

Error in BehaviorDEPOT_GUI_v1_2/StartButtonPushed (line 386)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Thanks so much for your help/patience.

Hello,
matlab prompts me to upload a tracking file before uploading the video file. What file is it referring to ?

I have a h5 file exported from SLEAP and the associated video file. I can't seem to get past the first step, please see below. I have checked that my h5 file is complete and no tracks are missing. Unfortunately Github does not allow me to upload the file to this post.

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
Error using h5readc
The HDF5 library encountered an error and produced the following stack trace information:

H5G_traverse_real    component not found
H5G_traverse         internal path traversal failed
H5G_loc_find         can't find object
H5Dopen2             not found

Error in h5read (line 93)
[data,var_class] = h5readc(Filename,Dataset,start,count,stride);

Error in importDLCTracking (line 49)
dataAdd = h5read(Params.tracking_file, '/df_with_missing/table');

Error in importTracking (line 25)
[data, Params] = importDLCTracking(Params);

Error in BehDEPOT_mainscript (line 128)
[data, Params] = importTracking(Params);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Hi,
I am running BehaviorDepot 1.3 on Matlab 2020b on Windows11
Although I am able to run classifiers such as calculate moving or calculate freezing jitter, some other classifiers won't work.
Rearing, escape, open field problems seem related with message "Reference to non-existent field"
exploration seems to relate to another problem "brace indexing is not supported for variables of this type"
Thank you
Matthieu

rearing : "Reference esto non-existent field 'windowWidth'."

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Reference esto non-existent field 'windowWidth'.

Error in calculateRearing (line 11)
in_arena = convolveFrames(in_arena, Params.Rearing.windowWidth, Params.Rearing.countThreshold);

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

escape "Reference to non-existent field 'RearBack'."

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Reference to non-existent field 'RearBack'.

Error in calculateEscape (line 15)
body_velocity = nanmean([Metrics.Velocity.Head; Metrics.Velocity.RearBack]);

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Open Field Unrecognized function or variable 'beh_check'.

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Unrecognized function or variable 'beh_check'.

Error in plotTrajectoryMap (line 23)
beh_name = beh_name(logical(beh_check));

Error in BehDEPOT_mainscript (line 172)
plotTrajectoryMap(Metrics, frame1, Params, Behavior, analyzed_folder_name);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Exploration : Brace indexing is not supported for variables of this type.

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Brace indexing is not supported for variables of this type.

Error in calculateExploration (line 16)
obj_roi = Params.roi{1,1};

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Hello,

I'm getting an error when I attempt to run batch analysis on some data.

Here is what the error message looks like:

It seems to be an issue with reuse_roi_names, which I tried to comment out in the makeParamsStruct.m code, but any changes are not preserved when I run the application.

Is there any way to resolve this?

Using:
MATLAB R2021b
Windows 10

I get the following error:

Undefined function 'smooth' for input arguments of type 'double'.

Error in smoothTracking_custom (line 23)
x = smooth(ux, smoothSpan, smoothMethod);

Error in BehDEPOT_mainscript (line 137)
Tracking = smoothTracking_custom(Tracking, Params);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Hi!
I’m working on detecting freezing in several conditions and luckily found your software. Thanks for making BehaviorDepot open source :)

I am running BehaviorDepot v1.3c on Matlab 2022a on Windows10.

I’m struggling with the part of the analysis that smoothes and corrects keypoint tracking data. It is giving me poor pose-estimation data. To see if I am using the tool correctly, I have a few questions:

1. In general, do you recommend using the default parameters (except for distance calibration, which needs to be calculated) – i.e. tracking cutoff threshold 0.1, smoothing span 14, Hampel span 7- or modifying them depending on the data?
2. Is it normal that data with a likelihood >0.9 (even 1) change so much after smoothing?
3. What does BehaviourDepot do when a body part is hidden in DLC (with an associated likelihood close to 0)? E.g. This is very frequent for the nose in mice, but in my case, BehaviourDepot is estimating a position which doesn’t match reality or DLC estimation.

Thanks a lot!

Hello I'm getting an error at the time of calibration is saying duplicate file and it doesn't proceed.

Hello. I am a first-time user of behaviorDEPOT with very limited coding experience.
I encountered an issue while using BehaviorDEPOT and would like to inquire about it. Specifically, I have questions regarding the alignment problem of body parts when inputting tracking files and video files.
As a result of my analysis, I noticed that multiple points are detected for each body part, leading to outcomes that differ from my expectations. I am curious about the root cause of this discrepancy and seek guidance on how to address it.

Dear team,

after downloading the repository and running the .mlappinstall file I get the following error when trying to launch BehaviorDEPOT from App window in Matlab (version 2020a):

Unrecognized property 'WordWrap' for class 'matlab.ui.control.CheckBox'.
Error in BehaviorDEPOT_GUI_v1_5/createComponents (line 765)
app.ApplyHampelCorrectionCheckBox.WordWrap = 'on';
Error in BehaviorDEPOT_GUI_v1_5 (line 1041)
createComponents(app)
Error in BehaviorDEPOTv151App/startApp (line 86)
obj.AppHandle = eval('BehaviorDEPOT_GUI_v1_5');
Error in BehaviorDEPOTv151App (line 48)
startApp(obj)
Error in appinstall.internal.runapp>execute (line 116)
out = evalin('caller', [script ';']);
Error in appinstall.internal.runapp>runapp13a (line 95)
outobj = execute(fullfile(appinstalldir, [wrapperfile 'App.m']));
Error in appinstall.internal.runapp>preamble18b (line 60)
appobj = runapp13a(appinstalldir);
Error in appinstall.internal.runapp (line 13)
out = preamble18b(appinstalldir);
Error in matlab.apputil.run (line 45)
appinstall.internal.runapp(appName, appLocation);

Any suggestions or ideas why this might be happening?
Thank you!
Natalia

I indicated more than 1 ROI in the GUI. However, there is an error when selecting more than 1 ROI. I can outline the 1st ROI fine, but there is an error afterward with no option to select another ROI. Here is the output from matplot:

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Select ROI # 1
Select ROI # 2
Unrecognized field name "roi_limits".

Error in drawROIs (line 23)
plot(polyshape(P.roi_limits{nroi}),
'FaceAlpha', 0.25)

Error in BD_dataPrep (line 14)
P = drawROIs(Frame, P);

Error in BehDEPOT_mainscript (line 29)
[Params, Tracking, Metrics, P] = BD_dataPrep(P, j);

Error in BehaviorDEPOT_GUI_v1_5/StartButtonPushed (line 422)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 410)
Error while evaluating Button PrivateButtonPushedFcn.

Thank you for helping!

First off, this program looks amazing. However, when I try to it on my data, I am getting an the error:

'Undefined function 'smooth' for input arguments of type 'double'.

Error in smoothTracking_custom (line 23)
x = smooth(ux, smoothSpan, smoothMethod);

Error in BehDepo_mainscript_single (line 54)
Tracking = smoothTracking_custom(Tracking, Params);

Error in BehDep_GUI_v051/StartButtonPushed (line 131)
BehDepo_mainscript_single(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 410)
Error while evaluating Button PrivateButtonPushedFcn.`

Any recommendations on how to avoid this error?

Thanks in advance!

Hi,
I am running BehaviorDepot 1.3 on Matlab 2020b on Windows11
Although I am able to run classifiers such as calculate moving or calculate freezing jitter, some other classifiers won't work.
Rearing, escape, open field problems seem related with message "Reference to non-existent field"
exploration seems to relate to another problem "brace indexing is not supported for variables of this type"
Thank you
Matthieu

rearing : "Reference esto non-existent field 'windowWidth'."

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Reference esto non-existent field 'windowWidth'.

Error in calculateRearing (line 11)
in_arena = convolveFrames(in_arena, Params.Rearing.windowWidth, Params.Rearing.countThreshold);

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

escape "Reference to non-existent field 'RearBack'."

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Reference to non-existent field 'RearBack'.

Error in calculateEscape (line 15)
body_velocity = nanmean([Metrics.Velocity.Head; Metrics.Velocity.RearBack]);

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Open Field Unrecognized function or variable 'beh_check'.

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Unrecognized function or variable 'beh_check'.

Error in plotTrajectoryMap (line 23)
beh_name = beh_name(logical(beh_check));

Error in BehDEPOT_mainscript (line 172)
plotTrajectoryMap(Metrics, frame1, Params, Behavior, analyzed_folder_name);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Exploration : Brace indexing is not supported for variables of this type.

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Data smoothed using lowess method and stored in Tracking.Smooth
Select corresponding body part for tracked point labels. Select "Other" if part is not listed
Tracked point dynamics calculated.
Brace indexing is not supported for variables of this type.

Error in calculateExploration (line 16)
obj_roi = Params.roi{1,1};

Error in BehDEPOT_mainscript (line 143)
Behavior.(beh_names{i}) = this_classifier(Params, Tracking, Metrics);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)

Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback (line 386)
Error while evaluating Button PrivateButtonPushedFcn.

Hi,
Congrats and thanks for making BehaviorDepot available. I am running BehaviorDepot v1.2 GUI on windows 10 with MATLAB 2022a (and dependency toolboxes) installed. When selecting a csv tracking file (from DLC), Matlab outputs the following error message. Do you have any idea what it could be related to ?
Matthieu

Select tracking file
Select video file
Loading video. May take some time depending on size of video.
Video Loaded
Reading tracking file
CSV Loaded
Tracking Structure Assembled
Hampel Correction Applied
Tracked 16 points
Unrecognized field name "Raw".

Error in smoothTracking_custom (line 20)
        time = (1:size(Tracking.Raw.(i_part), 2))';

Error in BehDEPOT_mainscript (line 113)
    Tracking = smoothTracking_custom(Tracking, Params);

Error in BehaviorDEPOT_GUI_v1_2/StartButtonPushed (line 386)
            BehDEPOT_mainscript(app.P)

Error in appdesigner.internal.service.AppManagementService/executeCallback (line 138)
                callback(appOrUserComponent, event);

Error in matlab.apps.AppBase>@(source,event)executeCallback(appdesigner.internal.service.AppManagementService.instance(),app,callback,requiresEventData,event) (line 63)
            newCallback = @(source, event)executeCallback(appdesigner.internal.service.AppManagementService.instance(), ...
 
Error using matlab.ui.control.internal.controller.ComponentController/executeUserCallback
Error while evaluating Button PrivateButtonPushedFcn.

Using:
MATLAB R2019a
BehavioralDepot v1.3a

when I press start to upload the tracking file and video file I get the following error:

Unrecognized method, property, or field 'NumFrames' for class 'VideoReader'.

Error in videoInterface (line 12)
P.Video.totalFrames = vid.NumFrames;

Error in BehDEPOT_mainscript (line 21)
[frame, frame1, frame_idx, P] = videoInterface([pv fv], P);

Error in BehaviorDEPOT_GUI_v1_3/StartButtonPushed (line 385)
BehDEPOT_mainscript(app.P)