ahof1704 / vocalmat Goto Github PK

HI,
I know that VocalMat recommends Fmax=125kHz, but in trying to apply it to monkey's calls, errors reported when VocalMat Identifier computing the spectrogram:

`Error using stretchlim
Expected input number 1, I or RGB, to be nonempty.

Error in stretchlim>ParseInputs (line 84)
validateattributes(img, {'uint8', 'uint16', 'double', 'int16', 'single'}, {'real', ...

Error in stretchlim (line 41)
[img,tol] = ParseInputs(varargin{:});

Error in imadjust>parseInputs (line 228)
lowhigh_in = stretchlim(img);

Error in imadjust (line 105)
parseInputs(varargin{:});

Error in vocalmat_identifier (line 153)
B = imadjust(imcomplement(abs(A)./max(abs(A(:)))));

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Error in VocalMat (line 98)
cd(fullfile(root_path, 'audios')); run('vocalmat_identifier.m')`

Hello.
Thank you for sharing your code :)
After running it with the example audio, I get the error:

Unable to perform assignment because the indices on the left side are not compatible with the size of the right side.

Error in diffusion_maps (line 35)
eval(['maps_' vfilename '= maps;'])

Error in run (line 91)
evalin('caller', strcat(script, ';'));

I understand it is because the char 'vfilename' and the array 'maps' do not have the same size, but I do not know how to solve this issue. How should I resolve this?

I still get some of the output files, the 2 excel files and the folder named "All" with all the pictures inside it.

Thanks in advance :)

One of the audios (1795 - 2nd stage) is not running in the VocalMat due to the followed issue (See attached).

Hello,

is there a plan in the future to release a standalone version of VocalMat (i.e. which is not dependent on MATLAB)?

Thank you
Giorgio

Attempting to detect rat USVs using VocalMat. Is it possible to widen the window of USV detection from 220 ms to a longer value (>500 ms)? As well as lowering any frequency threshold to below 20 Hz?

Hi, I'd like to make figures of Pairwise distance matrices and their comparison in Fig 5B and Fig 5C in the eLife paper, at p10. I have identified variables needed. How can I make those figures?

Hello, I installed the program and ran on several files but for some reason the "all_axes" folder is missing from the outputs. Everything else seems to be working fine. Do you have any suggestions?

Audio file 2409 from October 29th wasn't working when classifier was running. Audio was uploaded at Box (Marcelo-Antonio) in the folder called "Errors".

We are not able to use different extension files (.WAV or .wav) to run the Vocal mat. Antonio has changed the mult_jobs code and also the identifier. Please, see below the screenshots with these changes.

Hello,
Thanks for developing this great tool.
I'm getting couple of errors in the end of the analysis and wants to check if there are any reasons to be concerned about it.
This this the errors I get:

plotting for sigma= 0.5...
Error using diffusion_maps
Invalid expression. Check for missing multiplication operator, missing or unbalanced delimiters, or other
syntax error. To construct matrices, use brackets instead of parentheses.

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Error in VocalMat (line 110)
cd(analysis_path); run('diffusion_maps.m')

I will appreciate your help.

Hello,

Firstly I needed to replace Mdl_categorical_DL.mat as suggested in #9 because the file on git is corrupt (also the example audio file is corrupt). Maybe you could add to the Readme where to obtain the proper files? Edit: it is already there …

After that the classification analysis ran successfully. During plotting I then experienced following error:

[vocalmat]: starting VocalMat Analsyis...
plotting for sigma= 0.5...
Dot indexing is not supported for variables of this type.

Error in alternateGetframe

Error in getframe (line 138)
x = alternateGetframe(parentFig, offsetRect, scaledOffsetRect,
includeDecorations);

Error in diffusion_maps (line 91)
        F(int) = getframe(gcf) ;

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Error in VocalMat (line 110)
cd(analysis_path); run('diffusion_maps.m')

I used a fresh install of Matlab 2019b on Linux 5.10.167-1-MANJARO.

Hello,

When I run the VocalMat with my own audio files I received the following errors even though I didn't touched the code:

Error using load
Unable to read MAT-file C:\Users\ambst\Desktop\VocalMat-master\vocalmat_classifier\Mdl_categorical_DL.mat. Not a binary MAT-file. Try load -ASCII to read as text.

Error in vocalmat_classifier (line 26)
model_class_DL = load('Mdl_categorical_DL.mat');

Error in run (line 91)
evalin('caller', strcat(script, ';'));

Error in VocalMat (line 102)
cd(classifier_path); run('vocalmat_classifier.m')

I'm using the lastest version which is R2021a

Could you help me please?

Thank you in advance for your help.

Hi,

First of all, very nice work!

I am currently trying your VocalMat pipeline and I realized something that I found quite surprising.
I was comparing the VocalMat detections in one of my 4min recordings with a DeepSqueak detection that I had corrected (so it was my "ground truth") and I realized that at somepoint in the frames from VocalMet there was a jump from 89sec to 92sec, with various and very obvious spectrograms not being detected at all. It didn't make sense because VocalMat was able to detect spectrograms with similar caracteristics in the previous frames and the signal for these USV's is quite good. I was wondering if you have any idea of why this problem may occur. I tried changing the overlaping of the samplings (set to 5sec originally) and the time (set to 1min originally) but the problem remained.
FYI: I tried Matlab 2019a and 2023b

Thank you very much for your help.

Hello! I hope this message finds you well. I'm wondering if you're able to provide some more information on the example audio file on this website? Is the audio example a recording of a mouse / rodent and its vocalizations? A recording of a various, known rodent USVs? Either way, under what conditions was the 10 minute recording run? We are using the audio example file as a baseline for our vocal analysis - it helps us to shape our understanding of what the kind / frequency of speech that should be expecting from our mice - and it would be helpful to know the experimental conditions for that file. Thank you!

Error in VocalMat_Classifier_v10_MZ (line 135)
vocal_classified{k}.harmonic = [vocal_classified{k}.harmonic;
start_harmonic];

Hello! I ran a file today on an empty restraint device (no mouse in it), but oddly VocalMat picked up what looked to be like 10-15 total USVs (which, of course, there weren’t - or at least shouldn't have been - any). This is nearly five times the number that we’ve been seeing in analysis of recordings of our actual mice, so we are curious whether this is a result of background noise in the absence of any actual USVs. I would really appreciate hearing any thoughts that you may have regarding this issue and how we may troubleshoot - is there a way to calibrate for the background noise? Is it simply just the result of picking up any noise when there are no vocalizations? Thank you for this awesome tool and any help you can provide!

Hi,
Not so much an issue but I was wondering if it would be possible to train VocalMat on a rodent dataset. I am currently organizing images categorized by each subtype, similar to the OSF repo, to be used.
Thanks

Hi Antonio, de output matlabs with frequency etc are very heavy. Is it possible, to have these results copied into the vocal classified matlab?