added an option to allow jumping beads to considered as part of the granular media surface

-> grasslooper v1.1

fixes #1

grassloper/main.py

@@ -9,7 +9,8 @@ import argparse
 from improtools.imageprocessing import ImageProcessDebugger, IMovieProcessListener, NullMovieProcessListener, MovieProcessDebugger
 from typing import Dict, Tuple
 
-GRASSLOPER_VERSION = '1.0'
+GRASSLOPER_VERSION = '1.1'
+
 
 def create_slope_image(image_width: int, image_height: int, p1_angle: float, p1_radius: float, bg_color: float = 0.0, fg_color: float = 1.0):
     """
@@ -91,8 +92,9 @@ def hdf5_to_trac_data(hdf5_file_path: Path):
 
 class SlopeFinder():
 
-    def __init__(self, beads_radius: float):
+    def __init__(self, beads_radius: float, exclude_jumping_beads: bool):
         self.beads_radius = beads_radius
+        self.exclude_jumping_beads = exclude_jumping_beads
 
     def find_slope(self, trac_data: TracData, frame_index: int, mo_pro_listener: IMovieProcessListener = NullMovieProcessListener()):
         isbead_image = SlopeFinder.create_isbead_image(trac_data, frame_index, self.beads_radius)
@@ -116,9 +118,13 @@ class SlopeFinder():
         mo_pro_listener.onImage(labels_image, 'labels')
         is_non_jumping_bead_image = np.zeros(shape=labels_image.shape, dtype=np.uint8)
         bead_area = math.pi * self.beads_radius * self.beads_radius
+        min_area = bead_area * 1.1 if self.exclude_jumping_beads else 0.0
+        # print(f'self.exclude_jumping_beads = {self.exclude_jumping_beads}')
+        # print(f'min_area = {min_area}')
         for label in range(1, num_labels):  # ignore the first label, as it's the background
             area = stats[label][4]
-            if area > bead_area * 1.1:
+            # print(f'area = {area}')
+            if area > min_area:
                 is_non_jumping_bead_image[labels_image == label] = 255
         mo_pro_listener.onImage(is_non_jumping_bead_image, 'non_jumping_beads')
 
@@ -127,7 +133,7 @@ class SlopeFinder():
         surface_y.fill(is_non_jumping_bead_image.shape[0])
         contours, hierarchy = cv2.findContours(is_non_jumping_bead_image, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
         # print('num contours: ', len(contours))
-        assert(len(contours) == 1)
+        assert len(contours) >= 1
         contour = contours[0]
         for point in contour:
             x, y = point[0]
@@ -180,8 +186,8 @@ def save_results(results_file_path: Path, fitted_lines: Dict[int, scipy.stats._s
             stderr_array[frame_index] = fitted_line.stderr
             intercept_stderr_array[frame_index] = fitted_line.intercept_stderr
 
-    f = h5py.File(results_file_path,'w')
+    f = h5py.File(results_file_path, 'w')
-    f.attrs['version']='HDF5 file made with grassloper v %s' % GRASSLOPER_VERSION
+    f.attrs['version'] = 'HDF5 file made with grassloper v %s' % GRASSLOPER_VERSION
     f.attrs['date'] = time.strftime("%d/%m/%Y")
     f.attrs['input_file'] = str(input_file_path)
     f.attrs['num_frames'] = num_frames
@@ -194,12 +200,24 @@ def save_results(results_file_path: Path, fitted_lines: Dict[int, scipy.stats._s
     f.close()
 
 
+def str2bool(v):
+    if isinstance(v, bool):
+        return v
+    if v.lower() in ('yes', 'true', 't', 'y', '1'):
+        return True
+    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
+        return False
+    else:
+        raise argparse.ArgumentTypeError('Boolean value expected.')
+
+
 def main():
-    parser = argparse.ArgumentParser('grassloper', description='estimates the slope of granular surface', epilog='example: \n\tgrassloper --part-pos-file=./grassloper.git/samples/TracTrac/sample002_track.hdf5 --particle-radius=11.0 --debug-dir=\'./improdebug\' --results-file ./grassloper.git/samples/TracTrac/sample002_track_slopes.hdf5')
+    parser = argparse.ArgumentParser('grassloper', description='estimates the slope of granular surface', epilog='example: \n\tgrassloper --part-pos-file=./grassloper.git/samples/TracTrac/sample002_track.hdf5 --particle-radius=11.0 --exclude-jumping-beads=true --debug-dir=\'./improdebug\' --results-file ./grassloper.git/samples/TracTrac/sample002_track_slopes.hdf5')
     parser.add_argument('--part-pos-file', type=Path, default=None, required=True, help='the input file containing the particle positions')
     parser.add_argument('--results-file', type=Path, default=None, required=True, help='the output file containing for each frame one line fitting the granular surface (hdf5 file format)')
     parser.add_argument('--part-pos-file-format', type=str, choices=['tractrac-hdf5'], default='tractrac-hdf5', help='the file format of the input file that contains particle positions')
     parser.add_argument('--particle-radius', type=float, required=True, help='the radius of the particles in pixels (make sure that the radius is big enough to unsure that neighbouring particles touch each other)', default=11)
+    parser.add_argument('--exclude-jumping-beads', type=str2bool, default=True, required=True, help='if true, the isolated beads (supposedly because they are jumping) are not considered as being part of the granular media surface')
     parser.add_argument('--debug-dir', type=Path, default=None, help='where to store image processing debug files')
     args = parser.parse_args()
     # python3 ./tractrac.git/Python/tractrac.py -f ./grassloper.git/samples/sample002.avi --output 1 -a --saveplot
@@ -208,13 +226,13 @@ def main():
     else:
         mo_pro_listener = NullMovieProcessListener()
     trac_data = hdf5_to_trac_data(args.part_pos_file)
-    slope_finder = SlopeFinder(beads_radius=args.particle_radius)
+    slope_finder = SlopeFinder(beads_radius=args.particle_radius, exclude_jumping_beads=args.exclude_jumping_beads)
-    print(trac_data.num_frames)
+    print(f'number of frames: {trac_data.num_frames}')
     fitted_lines = {}
     for frame_index in range(1, trac_data.num_frames + 1):
         mo_pro_listener.onImageProcessingStart()
         line = slope_finder.find_slope(trac_data, frame_index=frame_index, mo_pro_listener=mo_pro_listener)
-        print('frame %d: %s' % (frame_index, str(line)))
+        print(f'frame {frame_index}: {str(line)}')
         fitted_lines[frame_index] = line
         mo_pro_listener.onImageProcessingEnd()
 

setup.py

@@ -1,8 +1,11 @@
-import setuptools
+from setuptools import setup
 
-setuptools.setup(
+setup(
     name="grassloper",
-    version="1.0",
+    description="a tool to estimate the slope of a granular surface",
+    version="1.1",
+    author='Guillaume Raffy',
+    author_email='guillaume.raffy@univ-rennes.fr',
     packages=['grassloper'],
     install_requires=['improtools(>=1.0)', 'numpy', 'opencv-python', 'scipy', 'h5py'],
     entry_points={