diff preprocessing.py @ 0:252fd085940d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557
author bgruening
date Fri, 13 Jun 2025 11:23:35 +0000
parents
children 97bc82ee2a61
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocessing.py	Fri Jun 13 11:23:35 2025 +0000
@@ -0,0 +1,68 @@
+import argparse
+import os
+import shutil
+
+from sklearn.model_selection import train_test_split
+
+
+def get_basename(f):
+    return os.path.splitext(os.path.basename(f))[0]
+
+
+def pair_files(images_dir, labels_dir):
+
+    img_files = [f for f in os.listdir(images_dir)]
+    lbl_files = [f for f in os.listdir(labels_dir)]
+
+    image_dict = {get_basename(f): f for f in img_files}
+    label_dict = {get_basename(f): f for f in lbl_files}
+
+    keys = sorted(set(image_dict) & set(label_dict))
+
+    return [(image_dict[k], label_dict[k]) for k in keys]
+
+
+def copy_pairs(pairs, image_src, label_src, image_dst, label_dst):
+    os.makedirs(image_dst, exist_ok=True)
+    os.makedirs(label_dst, exist_ok=True)
+    for img, lbl in pairs:
+        shutil.copy(os.path.join(image_src, img), os.path.join(image_dst, img))
+        shutil.copy(os.path.join(label_src, lbl), os.path.join(label_dst, lbl))
+
+
+def write_yolo_yaml(output_dir):
+
+    yolo_yaml_path = os.path.join(output_dir, "yolo.yml")
+    with open(yolo_yaml_path, 'w') as f:
+        f.write(f"path: {output_dir}\n")
+        f.write("train: train\n")
+        f.write("val: valid\n")
+        f.write("test: test\n")
+        f.write("\n")
+        f.write("names: ['dataset']\n")
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--images", required=True)
+    parser.add_argument("-y", "--labels", required=True)
+    parser.add_argument("-o", "--output", required=True)
+    parser.add_argument("-p", "--train_percent", type=int, default=70)
+    args = parser.parse_args()
+
+    all_pairs = pair_files(args.images, args.labels)
+    train_size = args.train_percent / 100.0
+    val_test_size = 1.0 - train_size
+
+    train_pairs, val_test_pairs = train_test_split(all_pairs, test_size=val_test_size, random_state=42)
+    val_pairs, test_pairs = train_test_split(val_test_pairs, test_size=0.5, random_state=42)
+
+    copy_pairs(train_pairs, args.images, args.labels, os.path.join(args.output, "train/images"), os.path.join(args.output, "train/labels"))
+    copy_pairs(val_pairs, args.images, args.labels, os.path.join(args.output, "valid/images"), os.path.join(args.output, "valid/labels"))
+    copy_pairs(test_pairs, args.images, args.labels, os.path.join(args.output, "test/images"), os.path.join(args.output, "test/labels"))
+
+    write_yolo_yaml(args.output)
+
+
+if __name__ == "__main__":
+    main()