Dot indexing is not supported for variables of this type

[laopenti]

Hello Biafra,

First of all, I would like to thank you for the fantastic job in the Algorithms-based Neuroscience Analysis, it helps me a lot while studying calcium imaging analysis. Although I know nothing about codes, algorithms, Matlab, etc. before Jan. 2021, still I believe I could accomplish more results meaningfully following your amazing Matlab protocols, as its name CIAtah.

However, lately, I got some confusing outputs as below every time when I run obj2 relative commands. Frankly, it has been checked whether it procedurally or manually inappropriate compared with Quick start (command-line) and CIAtah main GUI notes. Sadly, I didnt
find any reasons for them. would you please help me to handle all these errors?

Sincerely appreciate your time!
Benson Kin

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Dot indexing is not supported for variables of this type.
Error in calciumImagingAnalysis/viewMovie/getProperFrameList (line 738)
nMovieFrames = sum(movieDims.z);
Error in calciumImagingAnalysis/viewMovie (line 287)
[frameListTmp] = getProperFrameList('primary');
Error in calciumImagingAnalysis/runPipeline (line 202)
obj.(thisFxn{1});
Error in calciumImagingAnalysis/display (line 817)
obj.runPipeline;
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[bahanonu]

@laopenti

Glad to hear! Let me know if anything needs clarifying in the CIAtah user guides.

To help debug this issue, could you let me know the following:

• What type of movies (e.g. HDF5, TIF, AVI) are in the folder you are trying to analyze? What is the source of the data (e.g. miniscope, 2p microscope, etc.)?
• Which OS and Matlab version are you using?
• If you run modelAddNewFolders and select Add CIAtah example folders then run viewMovie on the default folders, are you able to load the example movies properly (after running obj.setup so they are downloaded)?

cheers!
-Biafra

[laopenti]

Hello Biafra,

Glad to receive your reply so soon. The actual situation that available facilities of my own just as below:

• All my raw data using Two-Photon Microscopy recorded by a TIF movie.
• All analyzing experiments and codes management was on Matlab-R2020b in Windows10.
• As the steps tips hinted I run your abovementioned works one by one, intrestingly, the example movies could run smoothly via Fiji expect one of them which named 2014_04_01_p203_m19_check01 . The error information meanwhile jumpped out like this:

=====================
PRE-LOADING MOVIES
=====================
1/1: m19 check01
data\2014_04_01_p203_m19_check01\concat_recording_20140401_180333.h5
movie 1/1: data\2014_04_01_p203_m19_check01\concat_recording_20140401_180333.h5
Getting movie info for 1\1: data\2014_04_01_p203_m19_check01\concat_recording_20140401_180333.h5
@@@@@@@
Error using h5infoc
The filename specified was either not found on the MATLAB path or it contains unsupported characters.
Error in h5info (line 125)
hinfo = h5infoc(filename,location, useUtf8);
Error in loadMovieList (line 246)
hinfo = h5info(thisMoviePath);
Error in calciumImagingAnalysis/viewMovie/getProperFrameList (line 732)
movieDims = loadMovieList(movieListTmp2,'convertToDouble',0,'frameList',[],'inputDatasetName',obj.inputDatasetName,'getMovieDims',1,'treatMoviesAsContinuous',treatMoviesAsContinuous);
Error in calciumImagingAnalysis/viewMovie (line 287)
[frameListTmp] = getProperFrameList('primary');
Error in calciumImagingAnalysis/runPipeline (line 202)
obj.(thisFxn{1});
Error in calciumImagingAnalysis/display (line 817)
obj.runPipeline;
@@@@@@@
ImageJ instance ended cleanly

Again, thank you for your patient and advise!

[bahanonu]

@laopenti
Thanks for the additional information.

• Could you send me the output before Dot indexing is not supported for variables of this type. from your first message (or just link a text file with the full command window output)? Trying to determine what exactly ciatah was reading before the error.
• If possible, you can send a Box or Dropbox link with one of the TIFF movies, then I can quickly debug this.
• For the 2014_04_01_p203_m19_check01 error, what is the current directory of Matlab (e.g. if you type pwd what is the output) when the error occurs?

[laopenti]

Hello, Biafra

• Actually, I have done some checks some days before, such as whether the loadDependencies files are good. Would there be any chance that one of these files was broken or missing for some unpredictable reason?
  Just now, I run the CIAtah-calciumImagingAnalysis. After running the obj.loadDependencies the error info I got, as it always showed everytime, are below:

@@@@@@@
Error using run (line 68)
RUN cannot execute the file '_external_programs\cvx_rd\cvx_setup.m'. RUN requires a valid MATLAB script
Error in downloadCnmfGithubRepositories (line 53)
run(mfileToRun);
Error in calciumImagingAnalysis/loadDependencies (line 55)
[success] = downloadCnmfGithubRepositories('forceUpdate',forceUpdate);
Error in calciumImagingAnalysis/runPipeline (line 202)
obj.(thisFxn{1});
Error in calciumImagingAnalysis/display (line 817)
obj.runPipeline;
@@@@@@@

• Unfortunately, my Win10 couldn't download and set up the Dropbox.exe, apologize for that situation. If it's convenient for you to access google drive, I would like to send the raw and relative file I used via e-mail. According to the web information you have posted at https://github.com/bahanonu/calciumImagingAnalysis, an e-mail will be sent to your university-mail-address if that is okay. (entitled with GitHub Issues @laopenti Benson Kin )

• The current directory of Matlab when the error occurred was :

pwd
ans =
'D:\New Files\MATLAB\calciumImagingAnalysis-master'

[bahanonu]

@laopenti
Just checked on Win 10 with Matlab 2020b with a fresh download of the ciatah master branch and was able to download movies, view them, and run the setup fine. Do you have admin privileges on the computer you are using? For the CVX setup script and at other instances, will likely need elevated privileges to allow Matlab to run those files and properly create directories.

Emailing a google drive link works, I'll keep an eye out for your email.

What is the size of the file at data\2014_04_01_p203_m19_check01\concat_recording_20140401_180333.h5? The error you're getting happens if a file is corrupt (e.g. not downloaded completely) or the extension does not match the file contents (e.g. if a TIF file ended in .h5).