Unrecognized field name "GroupHierarchy" + other errors when running modelExtractSignalsFromMovie with EXTRACT algorithm

[RandallJEllis]

Any help is appreciated. Matlab R2022b, CIAtah v4.5.9. All toolboxes installed. Full traceback: `1

!!!!!!!!!!!!!!!!!!!!! Running: obj.modelExtractSignalsFromMovie

options =

struct with fields:

 signalExtractionRootPath: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\_external_programs'
            saveNwbOutput: 0
            nwbSaveFolder: 'nwbFiles'
           settingsFolder: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\+ciapkg\+settings'
settingsPrivateSaveFolder: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\private\settings\signal_extraction'
               nwbYmlPath: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\_external_programs\nwbpkg\+nwbpkg\ExampleMetadata.yml'

Did not find: extractor.m Adding folders: C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\debug_utils;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\debug_utils\brewermap;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\helper_functions;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\solvers; Found: extractor.m Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead.

In inputdlg (line 265) In ciatah/modelExtractSignalsFromMovie (line 121) In ciatah/runPipeline (line 209) In ciatah/display (line 6) Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead. In inputdlgcol (line 316) In ciatah/modelExtractSignalsFromMovie/getAlgorithmOptions (line 1000) In ciatah/modelExtractSignalsFromMovie (line 167) In ciatah/runPipeline (line 209) In ciatah/display (line 6)

Subject: m000

Getting movie info for 1\1: C:\Users\rellis01\projects\juanita_calcium_analysis_feb2023\5minTL.2023-02-14-15-56-28\dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5 Warning: HDF5 dataset name not found in hinfo.Datasets.Name. Trying another method to load HDF5 dataset. In ciapkg.io.loadMovieList/getHdf5Info (line 1081) In ciapkg.io.loadMovieList (line 373) In ciapkg.api.loadMovieList (line 9) In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044) In ciatah/modelExtractSignalsFromMovie (line 202) In ciatah/runPipeline (line 209) In ciatah/display (line 6) Warning: Could not find /1 in C:\Users\rellis01\projects\juanita_calcium_analysis_feb2023\5minTL.2023-02-14-15-56-28\dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5. In ciapkg.io.loadMovieList/getHdf5Info (line 1096) In ciapkg.io.loadMovieList (line 373) In ciapkg.api.loadMovieList (line 9) In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044) In ciatah/modelExtractSignalsFromMovie (line 202) In ciatah/runPipeline (line 209) In ciatah/display (line 6) Warning: HDF5 hinfo.GroupHierarchy.Groups.Datasets contains no dataset . In ciapkg.io.loadMovieList/getHdf5Info (line 1111) In ciapkg.io.loadMovieList (line 373) In ciapkg.api.loadMovieList (line 9) In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044) In ciatah/modelExtractSignalsFromMovie (line 202) In ciatah/runPipeline (line 209) In ciatah/display (line 6) @@@@@@@ Unrecognized field name "GroupHierarchy".

Error in ciapkg.io.loadMovieList/getHdf5Info (line 1115) nGroups = length(hinfo.GroupHierarchy.Groups);

Error in ciapkg.io.loadMovieList (line 373) [hReadInfo, thisDatasetName, datasetDims] = getHdf5Info();

Error in ciapkg.api.loadMovieList (line 9) [outputMovie, movieDims, nPixels, nFrames] = ciapkg.io.loadMovieList(movieList, 'passArgs', varargin);

Error in ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044) DFOFList.(thisSubjectStr) = loadMovieList(movieList,'convertToDouble',0,'frameList',[1:500],'inputDatasetName',obj.inputDatasetName,'treatMoviesAsContinuous',1);

Error in ciatah/modelExtractSignalsFromMovie (line 202) [gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209) obj.(thisFxn{1});

Error in ciatah/display (line 6) obj.runPipeline; @@@@@@@

Subject: m000 @@@@@@@ Unrecognized function or variable 'DFOFList'.

Error in ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2066) DFOF = DFOFList.(thisSubjectStr);

Error in ciatah/modelExtractSignalsFromMovie (line 202) [gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209) obj.(thisFxn{1});

Error in ciatah/display (line 6) obj.runPipeline; @@@@@@@ @@@@@@@ Output argument "gridWidth" (and possibly others) not assigned a value in the execution with "ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing" function.

Error in ciatah/modelExtractSignalsFromMovie (line 202) [gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209) obj.(thisFxn{1});

Error in ciatah/display (line 6) obj.runPipeline; @@@@@@@ Removing unneeded directory from "to add" path list: extractor.m. Removing unneeded directory from "to add" path list: patchwarp.m. Adding to JAVA path: C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\bfmatlab_readers\SlideBook6Reader.jar Folders still need to be removed. Removing unneeded directory from path: extractor.m. Removing unneeded directory from path: patchwarp.m. ImageJ already loaded! Skipping loading of Miji.

Run processing pipeline by typing below (or clicking link) into command window (no semi-colon!): obj`

[bahanonu]

Can you get back with the output of the below command on your HDF5 file? Want to see if I can see why it is not being loaded, or if you can send me a link to the file I can check.

h5disp('C:\Users\rellis01\projects\juanita_calcium_analysis_feb2023\5minTL.2023-02-14-15-56-28\dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5')

As a heads up: looks like ciatah found EXTRACT, modelExtractSignalsFromMovie will load it if it is not found. Because EXTRACT is not yet a package, EXTRACT is not added to the path to reduce naming conflicts.

[RandallJEllis]

Thanks for the fast reply. The output is below. Also I saw that EXTRACT was loaded and changed the title of the Issue to mention the error related to GroupHierarchy not being found.

HDF5 dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5 
Group '/' 
Dataset 'dfof' 
        Size:  384x512x6023
        MaxSize:  384x512x6023
        Datatype:   H5T_IEEE_F64LE (double)
        ChunkSize:  []
        Filters:  none
        FillValue:  0.000000

[bahanonu]

Thanks, looks like it is likely because the default HDF5 dataset name /1 is being specified instead of /dfof for your data. You can let ciatah know to look for /dfof a couple ways, see below. I'll see about updating the code to make this clearer for users when it occurs in that module.

CIAtah main GUI

Within modelExtractSignalsFromMovie

[RandallJEllis]

That did it :) thanks!

[bahanonu]

Glad to hear!