I am using Ethoscope velocity data to distinguish between genotype. I don't have a license for the econometrics toolbox so I get a few errors about that. Additionally I get errors about functions not being supported. Are these issue with my installation or is it because the data is not amenable to that particular analysis?

Execution of script nn_prepare as a function is not supported:
/home/luca/Toolboxes/OpenTSTOOL/tstoolbox/mex/nn_prepare.m

Some operations output results that depend on the random seed, and thus running the same operation on the same time series can produce different results if run multiple times. A solution to this is required, and could be done by allowing a random seed input to each non-deterministic function, to allow reproducible results. If none is provided, a default could be rng('default') at the start of each function. I should implement this as a priority going forward.

Hi Ben,

I get this error when trying to GetIds of a part of name from the Operations.Name table.

When I leave the 'Name' flag out it searches the keywords field and it works fine.

>> OperationIDs = TS_GetIDs('mystring', myFile, 'ops', 'Name');
Loading data from....mat... Done.
Brace indexing is not supported for variables of this type.

Error in TS_GetIDs (line 114)
            cmatch = find(contains(theDataTable.Name,theMatchString{i}));

However it works when I use 'contains' below (partially copying the method used in keywords). I'm not sure the reason for the loop in Name using cmatch?

    case {'name','Name'}
        % The cell of comma-delimited keyword strings:
        theKeywordCell = theDataTable.Name;

        % Find objects with a keyword that matches the input string:
        matches = find(contains(theKeywordCell, theMatchString));

        % Return the IDs of the matches:
        IDs = theDataTable.ID(matches);

        % Check for empty:
        if isempty(IDs)
            warning('No matches to ''%s'' found in %s',theMatchString,theDataFile)
        end

On a side note, I think there is unlikely but possible danger of having temporary fn colisions when running on parallel (it happened to me already once). We probably should create those in the system temporary dir and make sure they are unique.

Hello,

Thank you for such an amazing tool. I'm wondering about how to approach multivariate time series using hctsa. Is there a special way of assigning the keywords before using TS_LabelGroups?

Thank you in advance, Konstantin

mysql_dbopen.m throws error even after including the appropriate connector via

javaaddpath('/home/philip/work/CompEngineMatlab/Database/mysql-connector-java-5.1.34-bin.jar')

% -- Error -- 
Error using mysql_dbopen (line 24)
Error with java database connector: Java exception occurred:
java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)

Hi,

I am trying to extract the temporal features from a large number of BOLD resting state fMRI signals using hctsa toolbox. Therefore, I have written a script which loads keyword matrices, labels, and timeseries in a loop and inputs them sequentially to TS_Init for creation of HCTSA.mat files. But, for each loop the algorithm requires a user input "y" to confirm the time series. I could not find the corresponding line of the code in "TS_Init.m" file of the toolbox to modify it and skip this step, and I was wondering if you could please guide me towards solving this issue.

Thank you for the great toolbox. Regards, Ali

Hi Ben,

I have been using your HCTSA toolbox for sometime and had a question. HCTSA is an outstanding job. When I get start with "hctsa_phenotypingWorm-master" and "hctsa_phenotypingFly-master" project. Here was the question that plotconfusion(realLabels,predictLabels); plotconfusion (line 111) update_args = standard_args(args{:}); plotconfusion>standard_args (line 255) Value is not a matrix or cell array. I did not understand how to solve this problem. Can you give me some suggestions?

Dear Ben, first of all thank you for all the work and effort you put into the hctsa package. It has been really helpful so far!

In the beginning I was dealing with a single sensor to monitor a pressure ts. The classification is mostly a 2-class but can also be a multiple class problem. Now, I have multiple sensors available that monitor one and the same process. I would like to include possible relations and dependencies between the sampled variables into my analsis. Therefore, I like to ask if you have made any experience yet on how to implement a multivariate ts analysis in a smart way, still using all the beautiful functions within this package.

Thank you in advance and best regards, Alex

Hi,

I'm generating features for a forecasting application. I require "causal" features, i.e. features that at any point in time do not use future information. I noted that there is a subset of features with the keyword 'forecasting.' Are these all causal? Are any features in other subsets also causal? Is there a simple way to extract only those sorts of features?

Thanks for any help on this matter, Gavin.

Hi Ben, added the legend into the time series plot. The code may seem a little clunky so feel free to edit/make it a bit nicer :)

Also went through and added further options to TS_classify so classification rates are returned, and there is the option to suppress the confusion matrix.

Nic

When I try to compile the install.m file I get this error:

Error using compile_mex An error occurred while compiling ML_Fastdfa_core C code. It appears that mex is not set up to work on this system (cf. 'doc mex' and 'mex -setup'). Get 'mex ML_fastdfa_core.c' to work, and then re-run compile_mex.m

In the code warns you of this but I do not know how to configure it 'Please make sure that mex is set up with the right compilers for this system.'

Hi Ben,

I have encountered an error when compiling MEX as part of the installation process. When compiling the OpenTSTOOL, I get a series of warnings followed by an error. This is generated from the range_search.cpp file line 116 (see screenshot below):

I suspect that the error arises as the code is trying to compare a range to an integer, which is an invalid operation? When justifying that part of the code, the MEX is compiled successfully (see screenshot below):

I just wanted to share this and I would be grateful for any suggestions. FYI - I am using macOS Catalina v10.15.7 and Matlab R2021a.

Many thanks! Irene

Hi Ben

I'm just trying to save the classifier produced by TS_Classify, and I'm getting an error saying both Unrecognized function or variable 'foldLosses', and Unrecognized function or variable 'whatLoss'. It looks like these variables are no longer produced by TS_Classify (when I use the find function to look for the variables within TS_Classify, they are not produced as outputs on any line). When I comment out the lines that require these variables, the function works.

It looks like the aspect of the TS_Classify function that utilizes these variables might have been removed at some stage, because I've noticed the following in the output description (I was also interested in the doPCs option, but couldn't work out how to perform it):

%---OUTPUTS: % Text output on classification rate using all features, and if doPCs = true, also % shows how this varies as a function of reduced PCs (text and as an output plot) % foldLosses, the performance metric across repeats of cross-validation % nullStats, the performance metric across randomizations of the data labels % jointClassifier, details of the saved all-features classifier

Kind regards,

Neil

Given public open source projects have free support for cloud ci services, consider leveraging one of them here. 🎉

https://blogs.mathworks.com/developer/2020/12/15/cloud-ci-services/

Analysis methods, like TS_TopFeatures, assume that there are no errors in the data matrix (i.e., that all bad values have been filtered out of the dataset, using TS_normalize). There should be better checks on this, to avoid the zeros in TS_DataMat being treated as actual zeros (rather than error symbols in TS_Quality. Best solution would be to use data in TS_Quality to restrict the computation to good values (where meaningful analysis is possible), e.g., in the case of TS_TopFeatures.

Perhaps it's time to update the terminology, since Feature is more common usage than Operation. Could consider changing the name of the Operations data object to Features...