Error when run "preprocess_dannce(filename_in,filename_out,species_name,'')"

[yuan0821]

Hi. I try to run the demo scrip preprocess_dannce, the error occur as below. i think it is better to modify the original code that can deal with the issue of infinite values. many thanks for your effort @spoonsso @jessedmarshall ################################################################ median filtering getting velocities Error using filtfilt Expected input to be finite.

Error in filtfilt>efiltfilt (line 114) validateattributes(x,{'double'},{'finite','nonempty'},'filtfilt');

Error in filtfilt (line 89) y=efiltfilt(b,a,x);

Error in compute_preprocessed_mocapstruct (line 44) abs_velocity_antialiased(ll,:) = filtfilt(f1,f2, marker_velocity(ll,:,4));

Error in preprocess_ratception_struct_demo (line 43) ratception_struct_temppreproc = compute_preprocessed_mocapstruct(ratception_struct_temp,preprocessing_parameters);

Error in preprocess_dannce (line 105) ratception_struct = preprocess_ratception_struct_demo(datahere,preprocessing_parameters,params);

[spoonsso]

Can you please describe in more detail what exactly you are trying to run (i.e. the exact command) and with what data? and what version of Matlab are you using?

[yuan0821]

Hi, thank you very much for your reply!! i just try to run the script of preprocess_dannce.mat as the demo page shows:

filename_in = 'predictions.mat'; filename_out = 'predictions_preprocessed.mat'; species_name = 'mouse' preprocess_dannce(filename_in,filename_out,species_name, ' ')

the error is reported as below:

Error using filtfilt Expected input to be finite.

Error in filtfilt>efiltfilt (line 114) validateattributes(x,{'double'},{'finite','nonempty'},'filtfilt');

Error in filtfilt (line 89) y=efiltfilt(b,a,x);

Error in compute_preprocessed_mocapstruct (line 44) abs_velocity_antialiased(ll,:) = filtfilt(f1,f2, marker_velocity(ll,:,4));

Error in preprocess_ratception_struct_demo (line 43) ratception_struct_temppreproc = compute_preprocessed_mocapstruct(ratception_struct_temp,preprocessing_parameters);

Error in preprocess_dannce (line 107) ratception_struct = preprocess_ratception_struct_demo(datahere,preprocessing_parameters,params); ############################################################################################ i think it is cased by the calculation of abs_velocity_antialiased value as it has infinite values. So i wonder whether it is possible to ask how to fix the issue of infinite values? or is there any suggestions? thank you so so much for all!!! @spoonsso

[jessedmarshall]

Hi Yuan,

You are right that the filtfilt was the problem. I added a simple masking in that section of the code (in the CAPTURE repo) to address this. I pushed the change to the capture demo and included the fix below. Did this work?

frames_to_mask = union(find(isnan(marker_velocity(ll,:,4))),find(isinf(marker_velocity(ll,:,4)))); marker_velocity(ll,frames_to_mask,4) = 0; abs_velocity_antialiased(ll,:) = filtfilt(f1,f2, marker_velocity(ll,:,4)); marker_velocity(ll,frames_to_mask,4) = nan; abs_velocity_antialiased(ll,frames_to_mask) = nan;

[yuan0821]

Hi Jesse, thank you so so much for your update. yes!! it works smoothly !!! thanks a lot!

[spoonsso]

cool! Let us know if you need any other help.