Mercurial > repos > imgteam > points2labelimage
diff points2label.py @ 3:2ae122d5d85a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
author | imgteam |
---|---|
date | Wed, 23 Apr 2025 14:37:31 +0000 |
parents | 714a57d6f3a1 |
children | 64c155acb864 |
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--- a/points2label.py Fri Sep 27 17:41:06 2024 +0000 +++ b/points2label.py Wed Apr 23 14:37:31 2025 +0000 @@ -33,6 +33,17 @@ radius_list = [0] * len(pos_x_list) try: + width_column = giatools.pandas.find_column(df, ['width', 'WIDTH']) + height_column = giatools.pandas.find_column(df, ['height', 'HEIGHT']) + width_list = df[width_column] + height_list = df[height_column] + assert len(pos_x_list) == len(width_list) + assert len(pos_x_list) == len(height_list) + except KeyError: + width_list = [0] * len(pos_x_list) + height_list = [0] * len(pos_x_list) + + try: label_column = giatools.pandas.find_column(df, ['label', 'LABEL']) label_list = df[label_column] assert len(pos_x_list) == len(label_list) @@ -45,7 +56,7 @@ pos_x_list = df[0].round().astype(int) pos_y_list = df[1].round().astype(int) assert len(pos_x_list) == len(pos_y_list) - radius_list = [0] * len(pos_x_list) + radius_list, width_list, height_list = [[0] * len(pos_x_list)] * 3 label_list = list(range(1, len(pos_x_list) + 1)) # Optionally swap the coordinates @@ -53,7 +64,9 @@ pos_x_list, pos_y_list = pos_y_list, pos_x_list # Perform the rasterization - for y, x, radius, label in zip(pos_y_list, pos_x_list, radius_list, label_list): + for y, x, radius, width, height, label in zip( + pos_y_list, pos_x_list, radius_list, width_list, height_list, label_list, + ): if fg_value is not None: label = fg_value @@ -61,10 +74,23 @@ raise IndexError(f'The point x={x}, y={y} exceeds the bounds of the image (width: {shape[1]}, height: {shape[0]})') # Rasterize circle and distribute overlapping image area - if radius > 0: - mask = np.ones(shape, dtype=bool) - mask[y, x] = False - mask = (ndi.distance_transform_edt(mask) <= radius) + # Rasterize primitive geometry + if radius > 0 or (width > 0 and height > 0): + + # Rasterize circle + if radius > 0: + mask = np.ones(shape, dtype=bool) + mask[y, x] = False + mask = (ndi.distance_transform_edt(mask) <= radius) + else: + mask = np.zeros(shape, dtype=bool) + + # Rasterize rectangle + if width > 0 and height > 0: + mask[ + y:min(shape[0], y + width), + x:min(shape[1], x + height) + ] = True # Compute the overlap (pretend there is none if the rasterization is binary) if fg_value is None: