Merged in fix_output (pull request #6)

fix: reset eurobench pi format and update reference pis

Eurobench_format_code/Dockerfile

@@ -9,7 +9,11 @@ RUN apt-get update \
 RUN wget -O signal-1.4.1.tar.gz https://octave.sourceforge.io/download.php?package=signal-1.4.1.tar.gz \
     && wget -O control-3.2.0.tar.gz https://octave.sourceforge.io/download.php?package=control-3.2.0.tar.gz \
     && wget -O io-2.4.12.tar.gz https://octave.sourceforge.io/download.php?package=io-2.4.12.tar.gz \
-    && wget -O statistics-1.4.1.tar.gz https://octave.sourceforge.io/download.php?package=statistics-1.4.1.tar.gz
+    && wget -O statistics-1.4.1.tar.gz https://octave.sourceforge.io/download.php?package=statistics-1.4.1.tar.gz \
+    && wget -O mapping-1.4.1.tar.gz https://octave.sourceforge.io/download.php?package=mapping-1.4.1.tar.gz \
+    && wget -O matgeom-1.2.2.tar.gz https://octave.sourceforge.io/download.php?package=matgeom-1.2.2.tar.gz \
+    && wget -O geometry-4.0.0.tar.gz https://octave.sourceforge.io/download.php?package=geometry-4.0.0.tar.gz
+
 
 ADD Eurobench_format_code/package_install.m package_install.m
 RUN pwd; ls

Eurobench_format_code/package_install.m

@@ -4,3 +4,6 @@
 pkg install io-2.4.12.tar.gz;
 pkg install statistics-1.4.1.tar.gz;
 pkg install signal-1.4.1.tar.gz;
+pkg install matgeom-1.2.2.tar.gz
+pkg install geometry-4.0.0.tar.gz;
+pkg install mapping-1.4.1.tar.gz;

Eurobench_format_code/run_bench_5sts_pi

@@ -19,8 +19,8 @@ is_ok = 0;
 
 try
   computePI_5sts(arg_list{1}, arg_list{2}, arg_list{3});
-catch err
-  warning(err.identifier, err.message);
+catch
+  printf("Error: %s\n", lasterr);
   is_ok = 1;
 end_try_catch
 

Eurobench_format_code/src/computePI_30sts.m

@@ -55,41 +55,40 @@
 
     protocol = false;
 
-
+    disp("so far so good")
 
     %computes the PIs
 
     sts_metrics = calculate_sts_metrics(data, kinematics, fsamp, protocol);
 
+    sts_metrics
     types = {"scalar\n", "array of scalars\n", "vector\n"};
 
-    labels = strcat("",'\n');  
     filename = strcat(result_dir, "/", "30sSTS_repetitions", ".yaml")
-    store_vector(filename, sts_metrics{1}, labels, types{1});
+    store_scalar(filename, sts_metrics{1});
 
-    labels = strcat("{Flexion Momentum, Momentum Transfer, Extension}",'\n');
+    labels = "[Flexion Momentum, Momentum Transfer, Extension]"
     filename = strcat(result_dir, "/", "subphases_duration", ".yaml")
-    store_vector(filename, sts_metrics{2}, labels, types{2});
+    store_vector(filename, sts_metrics{2}, labels);
 
-    labels = strcat("",'\n');
+    labels = "";
     filename = strcat(result_dir, "/", "CoP_stability", ".yaml")
-    store_vector(filename, sts_metrics{3}, labels, types{1});
+    reshape(sts_metrics{3}, 1, 2)
+    store_vector(filename, reshape(sts_metrics{3}, 1, 2), labels);
 
-    labels = strcat("",'\n');
     filename = strcat(result_dir, "/", "ult_time", ".yaml")
-    store_vector(filename, sts_metrics{4}, labels, types{1});
+    store_scalar(filename, sts_metrics{4});
 
-    labels = strcat("{antero-posterior, medio-lateral}",'\n');
+    labels = "[antero-posterior, medio-lateral]";
     filename = strcat(result_dir, "/", "ult_overshoot", ".yaml")
-    store_vector(filename, sts_metrics{5}, labels, types{2});
+    store_vector(filename, sts_metrics{5}, labels);
 
-    labels = strcat("{Ankle, Knee, Hip, Trunk}",'\n');
+    labels = "[Ankle, Knee, Hip, Trunk]";
     filename = strcat(result_dir, "/", "kinematic_repeatability", ".yaml")
-    store_vector(filename, sts_metrics{6}, labels, types{2});
+    store_vector(filename, sts_metrics{6}, labels);
 
-    labels = strcat("",'\n');
     filename = strcat(result_dir, "/", "CoM_work", ".yaml")
-    store_vector(filename, sts_metrics{7}, labels, types{1});
+    store_scalar(filename, sts_metrics{7});
 
 
     PI = sts_metrics;

Eurobench_format_code/src/computePI_5sts.m

@@ -22,7 +22,6 @@
     else
         disp('Using Matlab')
     end
-
     % get the csv data and calculate kinematics
 
     calib = csv2cell(csv_calib_file);
@@ -55,40 +54,39 @@
 
     protocol = true;
 
-
-    %computes the PIs
-
     sts_metrics = calculate_sts_metrics(data, kinematics, fsamp, protocol);
-
+    sts_metrics
+    typeinfo(sts_metrics)
     types = {"scalar\n", "array of scalars\n", "vector\n"};
 
-    labels = strcat("",'\n');
     filename = strcat(result_dir, "/", "5STS_duration", ".yaml")
-    store_vector(filename, sts_metrics{1}, labels, types{1});
+    store_scalar(filename, sts_metrics{1});
 
-    labels = strcat("{Flexion Momentum, Momentum Transfer, Extension}",'\n');
+    labels = "[Flexion Momentum, Momentum Transfer, Extension]";
     filename = strcat(result_dir, "/", "subphases_duration", ".yaml")
-    store_vector(filename, sts_metrics{2}, labels, types{2});
+    typeinfo(sts_metrics{2})
+    store_vector(filename, sts_metrics{2}, labels);
 
-    labels = strcat("",'\n');
+    labels = ""
     filename = strcat(result_dir, "/", "CoP_stability", ".yaml")
-    store_vector(filename, sts_metrics{3}, labels, types{1});
+    typeinfo(sts_metrics{3})
+    sts_metrics{3}
+    reshape(sts_metrics{3}, 1, 2)
+    store_vector(filename, reshape(sts_metrics{3}, 1, 2), labels);
 
-    labels = strcat("",'\n');
     filename = strcat(result_dir, "/", "ult_time", ".yaml")
-    store_vector(filename, sts_metrics{4}, labels, types{1});
+    store_scalar(filename, sts_metrics{4}, labels);
 
-    labels = strcat("{antero-posterior, medio-lateral}",'\n');
+    labels = "[antero-posterior, medio-lateral]";
     filename = strcat(result_dir, "/", "ult_overshoot", ".yaml")
-    store_vector(filename, sts_metrics{5}, labels, types{2});
+    store_vector(filename, sts_metrics{5}, labels);
 
-    labels = strcat("{Ankle, Knee, Hip, Trunk}",'\n');
+    labels = "[Ankle, Knee, Hip, Trunk]";
     filename = strcat(result_dir, "/", "kinematic_repeatability", ".yaml")
-    store_vector(filename, sts_metrics{6}, labels, types{2});
-
-    labels = strcat("",'\n');
+    store_vector(filename, sts_metrics{6}, labels);
+
     filename = strcat(result_dir, "/", "CoM_work", ".yaml")
-    store_vector(filename, sts_metrics{7}, labels, types{1});
+    store_scalar(filename, sts_metrics{7});
 
 
     PI = sts_metrics;

Eurobench_format_code/src/store_scalar.m

@@ -0,0 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% store_scalar.m
+%
+% Store a scalar into yaml file
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function is_ok = store_scalar(filename, data)
+
+    file_id = fopen(filename, "w");
+
+    fprintf(file_id, "type: \'scalar\'\n");
+
+    value_str = sprintf("value: %.5f\n", data);
+
+    fprintf(file_id, value_str);
+    fclose(file_id);
+    is_ok = true;
+end

Eurobench_format_code/src/store_vector.m

@@ -1,18 +1,21 @@
-function is_ok = store_vector(filename, data, labels, type)
+function is_ok = store_vector(filename, data, labels)
 
 %taken from https://github.com/eurobench/pi_octave_csic/blob/master/src/store_vector.m
 
     file_id = fopen(filename, "w");
-    fprintf(file_id, type);
-    fprintf(file_id, labels);
-    value_str = "value: ";
+    fprintf(file_id, "type: \'vector\'\n");
+
+    if size(labels) != 0
+        fprintf(file_id, "label: %s\n", labels);
+    endif
+    value_str = "value: [";
     for i = 1:size(data)(2)
         value_str = sprintf("%s%.5f", value_str, data(i));
         if (i != size(data)(2))
             value_str = sprintf("%s, ", value_str);
         endif
     endfor
-    value_str = sprintf("%s\n", value_str);
+    value_str = sprintf("%s]\n", value_str);
     fprintf(file_id, value_str);
     fclose(file_id);
     is_ok = true;

Eurobench_format_code/test/output/subject_01_30sts/CoM_work.yaml

@@ -1,2 +1,2 @@
-type: 'vector'
-value: [24.11805, 58.74444]
+type: 'scalar'
+value: 678.03756

Eurobench_format_code/test/output/subject_01_30sts/CoP_stability.yaml

@@ -1,2 +1,2 @@
-type: 'scalar'
-value: 0.11515
+type: 'vector'
+value: [0.37768, 0.04183]

Eurobench_format_code/test/output/subject_01_30sts/kinematic_repeatability.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [Ankle, Knee, Hip, Trunk]
-value: [0.78648, 0.99112, 0.98944, 0.94391]
+value: [0.78648, 0.99112, 0.98944, 0.94836]

Eurobench_format_code/test/output/subject_01_30sts/subphases_duration.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [Flexion Momentum, Momentum Transfer, Extension]
-value: [0.21656, 0.19256, 0.62234]
+value: [0.19089, 0.21824, 0.62234]

Eurobench_format_code/test/output/subject_01_30sts/ult_overshoot.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [antero-posterior, medio-lateral]
-value: [0.01238, 0.01215]
+value: [0.04233, 0.00340]

Eurobench_format_code/test/output/subject_01_30sts/ult_time.yaml

@@ -1,2 +1,2 @@
 type: 'scalar'
-value: 0.80038
+value: 0.75294

Eurobench_format_code/test/output/subject_01_5sts/CoM_work.yaml

@@ -1,2 +1,2 @@
-type: 'vector'
-value: [9.84384, 12.28107]
+type: 'scalar'
+value: 221.31481

Eurobench_format_code/test/output/subject_01_5sts/CoP_stability.yaml

@@ -1,2 +1,2 @@
-type: 'scalar'
-value: 0.11301
+type: 'vector'
+value: [0.40186, 0.04002]

Eurobench_format_code/test/output/subject_01_5sts/subphases_duration.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [Flexion Momentum, Momentum Transfer, Extension]
-value: [0.20790, 0.22040, 0.60494]
+value: [0.18289, 0.24541, 0.60494]

Eurobench_format_code/test/output/subject_01_5sts/ult_overshoot.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [antero-posterior, medio-lateral]
-value: [0.01413, 0.01007]
+value: [0.04413, 0.00419]

Eurobench_format_code/test/output/subject_01_5sts/ult_time.yaml

@@ -1,2 +1,2 @@
 type: 'scalar'
-value: 0.95196
+value: 0.88161

Eurobench_format_code/test/output/subject_02_5sts/CoM_work.yaml

@@ -1,2 +1,2 @@
-type: 'vector'
-value: [3.40741, 343.27661]
+type: 'scalar'
+value: -1862.09669

Eurobench_format_code/test/output/subject_02_5sts/CoP_stability.yaml

@@ -1,2 +1,2 @@
-type: 'scalar'
-value: 0.12424
+type: 'vector'
+value: [0.41141, 0.02398]

Eurobench_format_code/test/output/subject_02_5sts/subphases_duration.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [Flexion Momentum, Momentum Transfer, Extension]
-value: [0.18292, 0.16103, 0.47527]
+value: [0.16415, 0.17979, 0.47527]

Eurobench_format_code/test/output/subject_02_5sts/ult_overshoot.yaml

@@ -1,3 +1,3 @@
 type: 'vector'
 label: [antero-posterior, medio-lateral]
-value: [0.01333, 0.01131]
+value: [0.06211, 0.00319]

Eurobench_format_code/test/output/subject_02_5sts/ult_time.yaml

@@ -1,2 +1,2 @@
 type: 'scalar'
-value: 0.67225
+value: 0.47839