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Matlab crashes when using ezc3dWrite() #125

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MelaroJ opened this issue Jun 2, 2020 · 11 comments
Closed

Matlab crashes when using ezc3dWrite() #125

MelaroJ opened this issue Jun 2, 2020 · 11 comments

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@MelaroJ
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MelaroJ commented Jun 2, 2020

Hello there,

I'm trying to append virtual markers to the c3d file through Matlab and when I execute the ezc3dWrite() function while inputting the new c3d structure Matlab crashes.

C3D_Import_Add_Virtual_Markers.txt
matlab_crash_dump.txt
@pariterre
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Hello!

What you wrote seems right, so I'll have a look why you get a core dump! I'll reach ASAP!

@pariterre
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Based on the code you provided, I was unable to reproduce a core krash. However, I spotted a mistake that may explain your bug. The line 78 should read: currentVirtualMarker = virtualMarkerLabels{k}; (with curly brackets) because otherwise it stores the cells containing the names, instead of the names themselves. In any case, that does not produce a segmentation fault here (but it does raise an error).

Can you confirm that the following simplified code from yours (using the c3d files Vicon.c3d from https://github.com/pyomeca/ezc3d-testFiles) actually works? If if does not, that is probably an OS dependent issue, so I would need to know which OS you are using and which commit you compiled from.

% Housecleaning
close all 
clear
clc

c3d = ezc3dRead('Vicon.c3d');
frameToPlot = 1;


% Virtual Marker Label list %
virtualMarkerLabels = {'midAC'}';

% Append virtual marker labels to c3d label list %
for k = 1:length(virtualMarkerLabels)
    c3d.parameters.POINT.LABELS.DATA{end+1} = virtualMarkerLabels(k);
end

% Marker Labels and positions to be used for virtual marker position
% calculation
markerLabels = {'Daphnee:SCAP_CP' 'Daphnee:SCAP_RS'}';
idx_markerLabels = zeros(1,length(markerLabels))';
markerCoordinates = zeros(3,length(markerLabels));
for i = 1:length(markerLabels)
    idx_markerLabels(i) = find(strcmp(c3d.parameters.POINT.LABELS.DATA,markerLabels(i)));
    markerCoordinates(:,i) = c3d.data.points(:,idx_markerLabels(i),frameToPlot);
end
virtualMarkerCoordinates = zeros(3,length(virtualMarkerLabels));

% midAC coordinates from acromion processes
virtualMarkerCoordinates(:,1) = mean(markerCoordinates(:,1:2),2);

% Append virtual marker coordinates to c3d structure and save as new c3d
% Append virtual marker coordinates to the c3d coordinates data
frame1 = horzcat(c3d.data.points(:,:,1),virtualMarkerCoordinates);
frame2 = horzcat(c3d.data.points(:,:,2),zeros(size(virtualMarkerCoordinates)));
c3d.data.points = cat(3,frame1,frame2);

% Correct dimensions of... everything...
% data residuals
c3d.data.meta_points.residuals = horzcat(c3d.data.meta_points.residuals(:,:,1),zeros(1,size(virtualMarkerCoordinates,2)));
c3d.data.meta_points.residuals = cat(3,c3d.data.meta_points.residuals,c3d.data.meta_points.residuals);

% camera masks
c3d.data.meta_points.camera_masks = horzcat(c3d.data.meta_points.camera_masks(:,:,1),zeros(7,size(virtualMarkerCoordinates,2)));
c3d.data.meta_points.camera_masks = cat(3,c3d.data.meta_points.camera_masks,c3d.data.meta_points.camera_masks);

% Write new c3d file
ezc3dWrite('test.c3d',c3d);

c3d_2 = ezc3dRead('test.c3d');

Thanks!

@MelaroJ
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MelaroJ commented Jun 2, 2020 via email

@MelaroJ
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MelaroJ commented Jun 2, 2020 via email

@pariterre
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That seems to be OS related then, I'll test on a windows computer as soon as I have access to one (I have colleagues that I can ask), I'll come back to you afterwards!

The compilation question is more related on how did you install ezc3d?

@MelaroJ
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MelaroJ commented Jun 2, 2020

I followed the youtube video you posted in response to another issue, i.e., downloaded CMake and VisualStudio

@pariterre
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Okay! I'll have a look very soon :)

@pariterre
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pariterre commented Jun 3, 2020 •
edited
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Ok my bad... I actually made the same mistake as you! I wanted to test if it was the actual problem, so I changed the curly brackets for round brackets, but when I copied the code to send it here, I forgot to put back the curly brackets...

% Housecleaning
close all 
clear
clc

c3d = ezc3dRead('Vicon.c3d');
frameToPlot = 1;


% Virtual Marker Label list %
virtualMarkerLabels = {'midAC'}';

% Append virtual marker labels to c3d label list %
for k = 1:length(virtualMarkerLabels)
    c3d.parameters.POINT.LABELS.DATA{end+1} = virtualMarkerLabels{k};
end

% Marker Labels and positions to be used for virtual marker position
% calculation
markerLabels = {'Daphnee:SCAP_CP' 'Daphnee:SCAP_RS'}';
idx_markerLabels = zeros(1,length(markerLabels))';
markerCoordinates = zeros(3,length(markerLabels));
for i = 1:length(markerLabels)
    idx_markerLabels(i) = find(strcmp(c3d.parameters.POINT.LABELS.DATA,markerLabels(i)));
    markerCoordinates(:,i) = c3d.data.points(:,idx_markerLabels(i),frameToPlot);
end
virtualMarkerCoordinates = zeros(3,length(virtualMarkerLabels));

% midAC coordinates from acromion processes
virtualMarkerCoordinates(:,1) = mean(markerCoordinates(:,1:2),2);

% Append virtual marker coordinates to c3d structure and save as new c3d
% Append virtual marker coordinates to the c3d coordinates data
frame1 = horzcat(c3d.data.points(:,:,1),virtualMarkerCoordinates);
frame2 = horzcat(c3d.data.points(:,:,2),zeros(size(virtualMarkerCoordinates)));
c3d.data.points = cat(3,frame1,frame2);

% Correct dimensions of... everything...
% data residuals
c3d.data.meta_points.residuals = horzcat(c3d.data.meta_points.residuals(:,:,1),zeros(1,size(virtualMarkerCoordinates,2)));
c3d.data.meta_points.residuals = cat(3,c3d.data.meta_points.residuals,c3d.data.meta_points.residuals);

% camera masks
c3d.data.meta_points.camera_masks = horzcat(c3d.data.meta_points.camera_masks(:,:,1),zeros(7,size(virtualMarkerCoordinates,2)));
c3d.data.meta_points.camera_masks = cat(3,c3d.data.meta_points.camera_masks,c3d.data.meta_points.camera_masks);

% Write new c3d file
ezc3dWrite('test.c3d',c3d);

c3d_2 = ezc3dRead('test.c3d');

This should actually works!

@MelaroJ
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MelaroJ commented Jun 3, 2020

Worked like a charm!

Thanks a ton!

JM

@pariterre
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pariterre commented Jun 3, 2020 •
edited
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Just as a reminder for me, I will leave this issue open so I can produce a proper error message when non strings are casted as string.
Thanks for finding the bug!

@pariterre pariterre mentioned this issue Jun 26, 2020
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@pariterre
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Thanks again for reporting!

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@pariterre @MelaroJ