# breakout group 1 - RMR solver

Let's code some matlab...

code repo:

https://github.com/ComputationalBiomechanicsLab/rmr-solver

preprint:

https://www.biorxiv.org/content/10.1101/2023.07.11.548542v1

FIgures to reproduce

figure 3 - code?

figure 4 - left panels

figure 5

table 1 - numbers should be reproducible.

table 2 - code present, but takes long run time, so perhaps skip for now.

figure 6 - code takes >> 1 hour to run, so probably not reproducible for now.

ideally, like to see a "manifest", which is what code generates each figure.

Figure 6 and Table 2 have a source of randomness.

# getting dependencies

Needed a free account to get opensim 4.3.

Downloaded opensim (this is a matlab toolbox)

spm1d -- make sure to set up path correctly.

github repository downloaded - rmrsolver

## getting extra data

needed the opensim account.

Question: is it easier to download the other repository, or copy just the data required? Pros and cons to both approaches.

Copy the data to the github folder in the right place!

cp /Users/stephen/Downloads/ThoracoscapularShoulderPaperMaterials/ExperimentalData/EMG/* /Users/stephen/live2/rmr-solver/ExperimentalData/EMG
cp /Users/stephen/Downloads/ThoracoscapularShoulderPaperMaterials/ExperimentalData/Markers/* /Users/stephen/live2/rmr-solver/ExperimentalData/Markers

# running the code

## Figure 3 and Table 1

Code\Image Generation\PlotResults.m

Error:

Error using cd
Unable to change current folder to '/Users/stephen/live2/rmr-solver/Code/Image
Generation/..\..\' (Name is nonexistent or not a folder).

Error in PlotResults (line 13)
cd '..\..\'
 
>> 

code asks for parameters:

flx 2kg
100hz
100hz

next error

onsidering CMC results
Error using textscan
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in PlotResults (line 294)
        CMCflx21=textscan(fileID,format_CMC,'headerlines',7);
 
>> file(10,:)

ans =

    '/Users/stephen/live2/rmr-solver/Results/CMC analysis/flx21/ThoracoscapularShoulderCMC_states.sto  '

>> 

Where are the spaces at the end of the file coming from?

Italo: matlab 2021b on windows

SJE: 2023b

Solution: change to cell array

Next error:

butter requires one of the following:
  DSP System Toolbox
  Signal Processing Toolbox

Error in EMG_CMC_RMR_plot (line 38)
[b_h,a_h]=butter(4,fc/(fs/2),'high');

Error in PlotResults (line 334)
        [MAE_flx2kg_CMC, MAE_flx2kg_RMR_GH, MAE_flx2kg_RMR_noGH, corr_flx2kg_CMC, corr_flx2kg_RMR_GH, corr_flx2kg_RMR_noGH]=EMG_CMC_RMR_plot(CMCflx21,CMCflx22,CMCflx23,EMGflx21,EMGflx22,EMGflx23,indsflx21,indendflx21,indmaxflx21,indsflx22,indendflx22,indmaxflx22,indsflx23,indendflx23,indmaxflx23,muscle_CMC(i),muscle_EMG(i),MVC(i),muscle_Name(i), path_RMR_GH, path_RMR_noGH, muscle_RMR(i), task);
 

next error:

Warning: Integer operands are required for colon operator when used as index.
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)

Error using load
Unable to find file or directory 'Results\timings_matrix_experiments.mat'.

Error in evaluate_mean_std_RMR (line 22)
load('Results\timings_matrix_experiments.mat')

Error in EMG_CMC_RMR_plot (line 93)
[RMR_GH_average,RMR_GH_stdup,RMR_GH_stdlow, target_RMR_GH] = evaluate_mean_std_RMR(path_RMR_GH, muscle_RMR, task, 0);

Error in PlotResults (line 334)
[MAE_flx2kg_CMC, MAE_flx2kg_RMR_GH, MAE_flx2kg_RMR_noGH, corr_flx2kg_CMC, corr_flx2kg_RMR_GH, corr_flx2kg_RMR_noGH]=EMG_CMC_RMR_plot(CMCflx21,CMCflx22,CMCflx23,EMGflx21,EMGflx22,EMGflx23,indsflx21,indendflx21,indmaxflx21,indsflx22,indendflx22,indmaxflx22,indsflx23,indendflx23,indmaxflx23,muscle_CMC(i),muscle_EMG(i),MVC(i),muscle_Name(i), path_RMR_GH, path_RMR_noGH, muscle_RMR(i), task);

### Success!

(Captured to desktop -- too big to upload!)

Screenshot 2023-09-18 art 13.57.17.png

### Table 1 (partial)

output from command line matches what is put into the table 1

Task considered: FLX_2kg
Considering RMR results at 100 Hz (with GH constraint)
Considering RMR results at 100 Hz (without GH constraint)
Considering CMC results
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Trapezius, scapula middle'}

CMC:          0.03 [MAE] ,0.97 [xcorr]
RMR (GH):     0.04 [MAE] ,0.94 [xcorr]
RMR (no GH):  0.04 [MAE] ,0.94 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Trapezius, scapula superior'}

CMC:          0.06 [MAE] ,0.94 [xcorr]
RMR (GH):     0.08 [MAE] ,0.92 [xcorr]
RMR (no GH):  0.08 [MAE] ,0.92 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Trapezius, scapula inferior'}

CMC:          0.02 [MAE] ,0.94 [xcorr]
RMR (GH):     0.02 [MAE] ,0.9 [xcorr]
RMR (no GH):  0.02 [MAE] ,0.9 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Deltoid anterior'}

CMC:          0.05 [MAE] ,0.96 [xcorr]
RMR (GH):     0.05 [MAE] ,0.94 [xcorr]
RMR (no GH):  0.04 [MAE] ,0.95 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Deltoid posterior'}

CMC:          0.06 [MAE] ,0.44 [xcorr]
RMR (GH):     0.07 [MAE] ,0.14 [xcorr]
RMR (no GH):  0.07 [MAE] ,0.16 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Deltoid middle'}

CMC:          0.06 [MAE] ,0.94 [xcorr]
RMR (GH):     0.04 [MAE] ,0.97 [xcorr]
RMR (no GH):  0.05 [MAE] ,0.95 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Pectoralis major clavical'}

CMC:          0.04 [MAE] ,0.94 [xcorr]
RMR (GH):     0.04 [MAE] ,0.88 [xcorr]
RMR (no GH):  0.02 [MAE] ,0.91 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Serratus anterior'}

CMC:          0.06 [MAE] ,0.93 [xcorr]
RMR (GH):     0.06 [MAE] ,0.92 [xcorr]
RMR (no GH):  0.06 [MAE] ,0.92 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Infraspinatus (Superior)'}

CMC:          0.02 [MAE] ,0.93 [xcorr]
RMR (GH):     0.02 [MAE] ,0.73 [xcorr]
RMR (no GH):  0.04 [MAE] ,0.56 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Latissimus Dorsi (Medialis)'}

CMC:          0.15 [MAE] ,0.84 [xcorr]
RMR (GH):     0.16 [MAE] ,0.52 [xcorr]
RMR (no GH):  0.16 [MAE] ,0.55 [xcorr]

 
Warning: Integer operands are required for colon operator when used as index. 
> In EMG_CMC_RMR_plot (line 55)
In PlotResults (line 334)
 
MAE_flx2kg
    {'Teres major'}

CMC:          0.09 [MAE] ,0.4 [xcorr]
RMR (GH):     0.11 [MAE] ,0.06 [xcorr]
RMR (no GH):  0.1 [MAE] ,0.05 [xcorr]

 
>>