fixed an error where .git files were parsed as input in the data example

run.py

@@ -33,12 +33,14 @@ def parse_params(path):
 
 def load_contours(path):
     contour_dir = os.path.join(path, 'domain_contours')
-    file_fnames = os.listdir(contour_dir)
+    file_fnames = [fname for fname in os.listdir(contour_dir) if fname.lower().startswith('z_')]
     z_values = [float(file_fname[2:-4]) for file_fname in file_fnames]
     z_values, file_fnames = zip(*sorted(zip(z_values, file_fnames)))
     contours = []
 
     for file_fname, z in zip(file_fnames, z_values):
+        if '.git' in file_fname:
+            continue
         X = np.loadtxt(os.path.join(contour_dir, file_fname))
         Xp = np.pad(X, ((0,1), (0,0)), mode='wrap')
         contours.append((z, X))      
@@ -52,7 +54,7 @@ def load_points(path):
 
     points = defaultdict(list)
     for point_dir, marker_name in zip(point_dirs, marker_names):
-        file_fnames = os.listdir(point_dir)
+        file_fnames = [fname for fname in os.listdir(point_dir) if '.git' not in fname]
         z_values = [float(file_fname[2:-4]) for file_fname in file_fnames]
         z_values, file_fnames = zip(*sorted(zip(z_values, file_fnames)))
         for file_fname, z in zip(file_fnames, z_values):
@@ -86,9 +88,13 @@ def run(base_dir, output_dir):
     os.makedirs(output_dir, exist_ok=True)
 
     for experiment in tqdm(os.listdir(base_dir), desc='experiment'):
+        if '.git' in experiment:
+            continue
         for reading in os.listdir(os.path.join(base_dir, experiment)):
 
             data_dir = os.path.join(base_dir, experiment, reading)
+            if '.git' in data_dir:
+                continue
             origin, thickness = parse_params(data_dir)
             
             contours = sorted(load_contours(data_dir))