Open laopenti opened 3 years ago
@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:
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
Hello Biafra,
Glad to receive your reply so soon. The actual situation that available facilities of my own just as below:
===================== 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!
@laopenti Thanks for the additional information.
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.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? Hello, Biafra
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'
@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
).
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