Read c3d-files into Matlab

I have two directories of data: 'data_stair_rise' and 'data_sts'. Each directory contains 5 subfolders: 'pp1', 'pp2', 'pp3', 'pp4' en 'pp5'. Each subfolder contains some '.c3d-files'. (see attachment).

We need to read these files into Matlab. The teacher gave us a function who can read these c3d-files, but we need to create 5x5 struct (5 subjects x 5 measurements). (see attachment).

I don't have ANY idea how to start... Please help.

[Suad Abu Shaar]

Can you share the command used to read the c3d file please

[Image Analyst]

@Suad Abu Shaar, @Sam had a function he called "read_c3d_file" but he never attached it. And since it's 9 years later, I doubt he ever will.

Answer 1

[Image Analyst]

I don't know what's in the file. In a single .c3d file, how many subjects, and how many measurements are in it?

When you use your teacher's function, what kind of variable does the file get read in to? A single structure? An array of structures? We have no idea, but you should since you and your teacher have the code.

[Sam]

In the single .c3d-file are 6 things: VideoSignals (datapoints), VideoSignal_header, AnalogSignals, AnalogSignals_headers, VideoFramerate, Analogframerate. Each subject has (at least) 4 .c3d-files. So 1 .c3d-file represent 1 single measurement.

We need to create a 5x5struct, so that each cell is a struct which contains the '6 things' of the .c3d-file.

I think we need to start off with creating a path and using command like 'dir' and 'sprintf'... I'm trying to, but I think this is to difficult at the moment. All help is welcome!

[Image Analyst]

If you have questions still after reading the FAQ, come back and ask. http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

[Sam]

This is what I already have:

aantal_proefpersonen = length(dir('data_stair_rise'))-2 %for 5 subjects
for welke_pp=1:aantal_proefpersonen
  myFolder =sprintf('data_stair_rise/pp%c',num2str(welke_pp)); %define folder
  filePattern = fullfile(myFolder,'*.c3d');
c3dFiles = dir(filePattern); %list c3dfiles
for i_files=1:length(c3dFiles); %for all cd3files in the folder
   baseFileName = c3dFiles(i_files).name;
   fullFileName = fullfile(myFolder, baseFileName);
   [VideoSignals,VideoSignals_headers,AnalogSignals,AnalogSignals_headers,AnalogFrameRate,VideoFrameRate] = read_c3d_file(fullFileName) %function the teacher gave us
end
end

The problem is that the program overwrites everything when going through the for-loops. It also stores everything seperately (see attachment), but I want to stores each c3dfile into a 5x5 struct (as said above, also see attachment above). I hope you understand what I mean and that you can help me. Thanks!

[Image Analyst]

I'm not sure how a 5x5 struct array holds 6 things. But you can just dynamically create indexes and fields, like

for col = 1 : 5
  for row = 1 : 5
    sa(row, col).field1 = thing1; % Whatever this is.
    sa(row, col).field2 = thing2; % Whatever this is.
    sa(row, col).field3 = thing3; % Whatever this is.
    sa(row, col).field4 = thing4; % Whatever this is.
    sa(row, col).field5 = thing5; % Whatever this is.
    sa(row, col).field6 = thing6; % Whatever this is.
  end
end

You can call the fields whatever you want and somehow read the 6 "things" from your data file before assigning them to the structure array, sa. I don't really know what rows and columns represent but I guess you will. Add a third index to sa if you need to, to represent the four cd3 files for each subject.

[Sam]

Indeed, this creates the 5x5struct that I want (a 5x5 struct and each cell is also a struct containing the 6 datafiles). But the problem is now that each cell (=1x1struct) of the 5x5struct (=sa) is the same...

This is my code:

aantal_proefpersonen = length(dir('data_stair_rise'))-2
for welke_pp=1:aantal_proefpersonen
  myFolder =sprintf('data_stair_rise/pp%c',num2str(welke_pp));
      filePattern = fullfile(myFolder,'*.c3d');
c3dFiles = dir(filePattern);
for i_files=1:length(c3dFiles);
   baseFileName = c3dFiles(i_files).name;
   fullFileName = fullfile(myFolder, baseFileName);
   [VideoSignals,VideoSignals_headers,AnalogSignals,AnalogSignals_headers,AnalogFrameRate,VideoFrameRate] = read_c3d_file(fullFileName)
for col = 1:length(c3dFiles)
for row = 1:aantal_proefpersonen
  sa(row, col).VideoSignals = VideoSignals; % Whatever this is.
  sa(row, col).VideoSignals_headers = VideoSignals_headers; % Whatever this is.
  sa(row, col).AnalogSignals = AnalogSignals; % Whatever this is.
  sa(row, col).AnalogSignals_headers = AnalogSignals_headers; % Whatever this is.
  sa(row, col).AnalogFrameRate = AnalogFrameRate; % Whatever this is.
  sa(row, col).VideoFrameRate = VideoFrameRate; % Whatever this is.
end
end
end
end

What should I do so that each cell is not the same?

[Image Analyst]

First of all, let's not call it a cell since it's not. That's an entirely different animal One element of a structure array is a structure, not a cell.

In your loop, the values like VideoSignals are not changing. Why not? Well it's because they're always the same since there were assigned before the loop. If you want different ones, then you have to call read_c3d_file() INSIDE THE LOOP, not prior to it. Don't you understand that if you call read_c3d_file() before then those values will be the same no matter how many times you iterate a loop? Why should they change? They won't , unless you update them with a call to read_c3d_file().

[Sam]

Thanks, I understand that. But where exactly should I place 'reac_c3d_file()' to solve the problem? I tried different things, I replaced 'read_c3d_file()' but I still don't get the result I want...

[Sam]

How can I jump back to the first for-loop?

Answer 2

[Walter Roberson]

see https://www.mathworks.com/matlabcentral/fileexchange/69372-ezc3d

and tools listed at https://www.c3d.org/c3dapps.html