output file

[alfonsotecnalia]

Only one output file is generated. That file contains the result of several PIs. We are suggesting to generate one output file per PI. The name of the files should contain the name of the pi the result inside belongs to. In your case:

xxx_muscle_synergy_number.yaml
xxx_emg_reco_quality.yaml
xxx_pattern_fwhm.yaml
xxx_pattern_coa.yaml
...

The content of these files would be two keys (type and value) with their respective values. Example for xxx_muscle_synergy_number.yaml:

type: vector
value: [5, 5, 5]

[aremazeilles]

Why xxx? Shouldn't it be always pi_muscle_synergy_number.yaml?

[alfonsotecnalia]

It does not matter. The algorithm looks for a file containing the name of the PI.

[dzhvansky]

In the last commits, we solved this issue. Now the output files are in this format (for each PI): subject_N_run_R_muscle_synergy_number.yaml

[alfonsotecnalia]

I am testing octave_version branch and getting the following output:

current directory: /home/pepato
body side: left
NMF stop criteria: BLF
database name: db_healthy_adults_8m
file list: [s2_emg.csv, s2_gaitEvents.yaml, s4_emg.csv, s4_gaitEvents.yaml, s6_emg.csv, s6_gaitEvents.yaml, ]
result dir: /out
error: 'trials' undefined near line 37 column 24
error: called from
    check_filenames at line 37 column 5
    pipeline at line 44 column 45
    ./run_pepato at line 33 column 1

[dzhvansky]

Sorry, I did not specify the parameters in detail (for brevity). It should be: docker run --rm -v $PWD/test_data:/in -v $PWD/output:/out pi_pepato ./run_pepato left BLF db_healthy_adults_8m ./test_data/subject_0005_run_001_speed2kmh_emg.csv ./test_data/subject_0005_run_001_speed2kmh_gaitEvents.yaml ./test_data/subject_0005_run_001_speed4kmh_emg.csv ./test_data/subject_0005_run_001_speed4kmh_gaitEvents.yaml ./test_data/subject_0005_run_001_speed6kmh_emg.csv ./test_data/subject_0005_run_001_speed6kmh_gaitEvents.yaml ./test_data The last argument is the output folder, which should already be created. So here I specify ./test_data.

[dzhvansky]

Currently, the input is configured only for standard file names such as:

subject_N_run_R_speedVkmh_emg.csv
subject_N_run_R_speedVkmh_gaitEvents.yaml

Any other filenames will fail the name check.

[alfonsotecnalia]

Following command should be specified in the docker part:

docker run --rm -v $PWD/test_data:/in -v $PWD/output:/out pi_pepato ./run_pepato left BLF db_healthy_adults_8m /in/subject_0005_run_001_speed2kmh_emg.csv /in/subject_0005_run_001_speed2kmh_gaitEvents.yaml /in/subject_0005_run_001_speed4kmh_emg.csv /in/subject_0005_run_001_speed4kmh_gaitEvents.yaml /in/subject_0005_run_001_speed6kmh_emg.csv /in/subject_0005_run_001_speed6kmh_gaitEvents.yaml /out

Please, correct it in the README.md. Thanks!

[dzhvansky]

Done!

[alfonsotecnalia]

Thanks! I will close the issue