Added mocap.py for loading in motion capture data.

GPy/util/mocap.py

@@ -0,0 +1,78 @@
+import os
+import numpy as np
+
+def load_text_data(dataset, directory, centre=True):
+    """Load in a data set of marker points from the Ohio State University C3D motion capture files (http://accad.osu.edu/research/mocap/mocap_data.htm)."""
+
+    points, point_names = parse_text(os.path.join(directory, dataset + '.txt'))[0:2]
+    # Remove markers where there is a NaN
+    present_index = [i for i in range(points[0].shape[1]) if not (np.any(np.isnan(points[0][:, i])) or np.any(np.isnan(points[0][:, i])) or np.any(np.isnan(points[0][:, i])))]
+
+    # Concatanate the X, Y and Z markers together
+    Y = np.concatenate((points[0][:, present_index], points[1][:, present_index], points[2][:, present_index]), axis=1)
+    if centre:
+        Y = Y - Y.mean(axis=0)
+    Y = Y/400.
+    return Y
+
+def parse_text(file_name):
+    """Parse data from Ohio State University text mocap files (http://accad.osu.edu/research/mocap/mocap_data.htm)."""
+
+    # Read the header
+    fid = open(file_name, 'r')
+    point_names = np.array(fid.readline().split())[2:-1:3]
+    fid.close()
+    for i in range(len(point_names)):
+        point_names[i] = point_names[i][0:-3]
+
+    # Read the matrix data
+    S = np.loadtxt(file_name, skiprows=1)
+    field = np.uint(S[:, 0])
+    times = S[:, 1]
+    S = S[:, 2:]
+
+    # Set the -9999.99 markers to be not present
+    S[S==-9999.99] = np.NaN
+
+    # Store x, y and z in different arrays
+    points = []
+    points.append(S[:, 0:-1:3])
+    points.append(S[:, 1:-1:3])
+    points.append(S[:, 2:-1:3])
+
+    return points, point_names, times
+
+#def read_connections():
+
+
+#     fid = fopen(fileName);
+#     i = 1;
+#     rem = fgets(fid);	
+#     while(rem ~= -1)		
+#         [token, rem] = strtok(rem, ',');
+#         connections{i, 1} = fliplr(deblank(fliplr(deblank(token))));
+#         [token, rem] = strtok(rem, ',');
+#         connections{i, 2} = fliplr(deblank(fliplr(deblank(token))));
+#         i = i + 1;
+#         rem = fgets(fid);	
+#     end
+
+#     connect = zeros(length(pointNames));
+#     fclose(fid);
+#     for i = 1:size(connections, 1);
+#         for j = 1:length(pointNames)
+#             if strcmp(pointNames{j}, connections{i, 1}) | ...
+#                 strcmp(pointNames{j}, connections{i, 2})
+#       for k = 1:length(pointNames)
+#         if k == j
+#           break
+#         end
+#         if strcmp(pointNames{k}, connections{i, 1}) | ...
+#               strcmp(pointNames{k}, connections{i, 2})
+#           connect(j, k) = 1;
+#         end
+#       end
+#     end
+#   end
+# end
+# connect = sparse(connect);