non-existent field 'GroupHierarchy'

[Yancy81]

Hi,Biafra
I'm following the steps of your video in youtube to run ciatah,but i have a error.
When viewMovieRegistrationTest is running,the following error occurs.

I don't know how to handle it. Would you help me find the problem? Looking forward to your reply.

Yancy

[bahanonu]

Hi Yancy, thanks for reaching out. A couple things so I can help:

• What type of file is your movie saved as (e.g. HDF5, TIFF, etc.)?
• Which version of Matlab and CIAtah (Can run ciapkg.version() in command window) you are using?
• Copy and paste here the entire Command Window output up until the error.

[Yancy81]

Hi,Biafra
Thanks for your prompt response.

1. My movie saved as avi. and HDF5.
   
   2.The version of Matlab is 2016.The result of running ciapkg.version() is as follows.
   ciapkg.version()
   verStr =
   v3.26.2
   20210325200706
   ans =
   v3.26.2
   3.Entire Command is pasted below.

!!!!!!!!!!!!!!!!!!!!!
Running: obj.viewMovieRegistrationTest
Warning: The DrawMode property will be removed in a future release. Use the
SortMethod property instead. 
> In inputdlg (line 237)
  In ciatah/viewMovieRegistrationTest (line 48)
  In ciatah/runPipeline (line 202)
  In ciatah/display (line 6) 
Miji located in: C:\Users\DELL\Documents\MATLAB\ciatah-master\_external_programs\fiji-win64-20151222\Fiji.app\scripts\Miji.m
ans =
double
1/1: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging
ans =
result
movieList =
  1×4 cell array
  Columns 1 through 2
    'C:\Users\DELL\Doc…'    'C:\Users\DELL\Doc…'
  Columns 3 through 4
    'C:\Users\DELL\Doc…'    'C:\Users\DELL\Doc…'
###
Getting movie info for 1\1: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.avi
checking movies: 100|
-------
-------
loading 1/1: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.avi
loading avi: 100|
movie class: uint8
movie size: 512  512
x-dims: 512
y-dims: 512
z-dims: 1
movie size: 0.25Mb | 512  512 | uint8
Elapsed time is 0.114513 seconds.
###
Warning: Error updating Text.

 Character vector must have valid interpreter syntax:
1\1:
C:/Users/DELL/Documents/MATLAB/ciatah-master/imaging
 
> In defaulterrorcallback (line 12)
  In uiwait (line 81)
  In manageInteractivePlacement (line 95)
  In imrect>imrectAPI (line 275)
  In imrect (line 82)
  In ciatah/viewMovieRegistrationTest>subfxnCropSelection (line 490)
  In ciatah/viewMovieRegistrationTest (line 108)
  In ciatah/runPipeline (line 202)
  In ciatah/display (line 6) 
=====================
1/1 (1/1): m000 NULL000
C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging
###
removing unsupported file from list: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.raw
removing unsupported file from list: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.txt
Getting movie info for 1\2: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.avi
checking movies: 50|Getting movie info for 2\2: C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.h5
Warning: HDF5 dataset name not found in hinfo.Datasets.Name. Trying
another method to load HDF5 dataset. 
> In loadMovieList/getHdf5Info (line 777)
  In loadMovieList (line 252)
  In ciatah/viewMovieRegistrationTest (line 144)
  In ciatah/runPipeline (line 202)
  In ciatah/display (line 6) 
Warning: Could not find /1 in
C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.h5. 
> In loadMovieList/getHdf5Info (line 792)
  In loadMovieList (line 252)
  In ciatah/viewMovieRegistrationTest (line 144)
  In ciatah/runPipeline (line 202)
  In ciatah/display (line 6) 
@@@@@@@
Reference to non-existent field 'GroupHierarchy'.
Error in loadMovieList/getHdf5Info (line 811)
 						nGroups = length(hinfo.GroupHierarchy.Groups);
Error in loadMovieList (line 252)
 				[hReadInfo, thisDatasetName, datasetDims] = getHdf5Info();
Error in ciatah/viewMovieRegistrationTest (line 144)
 					movieDims = loadMovieList(movieList,'convertToDouble',0,'frameList',[],'inputDatasetName',inputDatasetName,'getMovieDims',1,'treatMoviesAsContinuous',treatMoviesAsContinuousSwitch);
Error in ciatah/runPipeline (line 202)
 				obj.(thisFxn{1});
Error in ciatah/display (line 6)
 	obj.runPipeline;
@@@@@@@

[bahanonu]

What is the output of h5disp(C:\Users\DELL\Documents\MATLAB\ciatah-master\imaging\result.h5)? That will help determine the HDF5 dataset name that CIAtah needs to read in your movie from that file type.

Is the .avi and .HDF5 movies the same movie? If so you can make CIAtah only look for one of the movies for processing, e.g.
AVI only

HDF5 only

And looks like you are using an old (3.0) version of CIAtah, you can try updating to CIAtah 4.0 as there are a number of improvements.

[Yancy81]

Hi,Biafra
Thanks for your solution. I make CIAtah only look for avi and update CIAtah. This problem did not occur.Thanks again for your help!! Have a nice day! !
Yancy

[bahanonu]

Great to hear! Let me know if any other questions arise.