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annotate segment_text_yolo.py @ 0:28b4dc80d58b draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
author bgruening
date Fri, 13 Jun 2025 14:54:15 +0000
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28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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1 """
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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2 Segment text using DocLayout Yolo model
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3 """
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5 import argparse
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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6 import json
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7 import os
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8
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9 import cv2
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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10 from doclayout_yolo import YOLOv10
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11 from geojson import Feature, FeatureCollection
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12 from shapely.geometry import box, mapping
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15 def load_model_and_predict(
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16 model_path, input_image_path, input_confidence, image_size, output_image_path
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17 ):
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19 model = YOLOv10(model=model_path)
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21 det_res = model.predict(
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22 input_image_path, imgsz=int(image_size), conf=float(input_confidence)
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23 )
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24 annotated_frame = det_res[0].plot(pil=True, line_width=5, font_size=20)
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25 cv2.imwrite(output_image_path, annotated_frame)
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26 return det_res[0]
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29 def extract_bb_crop(results, output_segmentation_coordiates):
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30 bounding_boxes = []
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31 features = []
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32 for bx in results.boxes.xyxy.cpu().numpy():
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33 x1, y1, x2, y2 = bx
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34 bounding_boxes.append((x1, y1, x2, y2))
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36 for i, (x1, y1, x2, y2) in enumerate(bounding_boxes):
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37 poly = box(x1, y1, x2, y2)
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38 feature = Feature(geometry=mapping(poly), properties={"id": i})
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39 features.append(feature)
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41 geojson_obj = FeatureCollection(features)
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43 with open(output_segmentation_coordiates, "w") as f:
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44 json.dump(geojson_obj, f)
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47 if __name__ == "__main__":
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48 arg_parser = argparse.ArgumentParser()
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49 arg_parser.add_argument(
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50 "-im", "--yolo_model", required=True, help="Input Yolo model"
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51 )
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52 arg_parser.add_argument(
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53 "-ii", "--input_image", required=True, help="Input image file"
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54 )
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55 arg_parser.add_argument(
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56 "-ie", "--input_image_ext", required=True, help="Input image file extension"
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57 )
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58 arg_parser.add_argument(
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59 "-ic", "--input_confidence", required=True, help="Input confidence"
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60 )
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61 arg_parser.add_argument(
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62 "-is", "--input_image_size", required=True, help="Input image size"
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63 )
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64 arg_parser.add_argument("-oi", "--output_image", required=True, help="Output image")
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65 arg_parser.add_argument(
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66 "-ogj", "--output_geojson", required=True, help="Output segmented coordinates"
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67 )
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68 args = vars(arg_parser.parse_args())
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69 model_path = args["yolo_model"]
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70 input_image_path = args["input_image"]
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71 input_ext = args["input_image_ext"]
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72 confidence = args["input_confidence"]
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73 image_size = args["input_image_size"]
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74 output_image_path = args["output_image"]
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75 output_segmentation_coordiates = args["output_geojson"]
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76
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77 model_link = "yolo_model.pt"
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78 input_image = f"input_image.{input_ext}"
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79 output_image = f"output_image.{input_ext}"
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81 os.symlink(model_path, model_link)
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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82 os.symlink(input_image_path, input_image)
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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83 os.symlink(output_image_path, output_image)
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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84
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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85 segmented_image = load_model_and_predict(
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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86 model_link, input_image, confidence, image_size, output_image
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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87 )
28b4dc80d58b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo-utils/doclayoutyolo commit 80167f52fb9bd60b57e4df9d68152876171228d6
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88 extract_bb_crop(segmented_image, output_segmentation_coordiates)