--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create-config.py	Wed Jun 26 08:03:08 2024 +0000
@@ -0,0 +1,58 @@
+import argparse
+import json
+
+import yaml
+
+
+# This script genereates the config file required by PlantSeg.
+# For an overview of the config fields, see:
+# https://github.com/kreshuklab/plant-seg/blob/master/examples/config.yaml
+
+
+def listify(d, k, sep=',', dtype=float):
+    if k not in d:
+        return
+    d[k] = [dtype(token.strip()) for token in str(d[k]).split(sep)]
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--inputs', type=str, help='Path to the inputs file', required=True)
+    parser.add_argument('--config', type=str, help='Path to the config file', required=True)
+    parser.add_argument('--img_in', type=str, help='Path to the input image', required=True)
+    parser.add_argument('--workers', type=int, default=1)
+    args = parser.parse_args()
+
+    with open(args.inputs, 'r') as fp:
+        inputs = json.load(fp)
+
+    # Set configuration options from the tool wrapper
+    cfg = dict(path=args.img_in)
+    for section_name in (
+        'preprocessing',
+        'cnn_prediction',
+        'cnn_postprocessing',
+        'segmentation',
+        'segmentation_postprocessing',
+    ):
+        cfg[section_name] = inputs[section_name]
+
+    # Set additional required configuration options
+    cfg['preprocessing']['save_directory'] = 'PreProcessing'
+    cfg['preprocessing']['crop_volume'] = '[:,:,:]'
+    cfg['preprocessing']['filter'] = dict(state=False, type='gaussian', filter_param=1.0)
+
+    cfg['cnn_prediction']['device'] = 'cuda'
+    cfg['cnn_prediction']['num_workers'] = args.workers
+    cfg['cnn_prediction']['model_update'] = False
+
+    cfg['segmentation']['name'] = 'MultiCut'
+    cfg['segmentation']['save_directory'] = 'MultiCut'
+
+    # Parse lists of values encoded as strings as actual lists of values
+    listify(cfg['preprocessing'], 'factor')
+    listify(cfg['cnn_prediction'], 'patch')
+
+    with open(args.config, 'w') as fp:
+        fp.write(yaml.dump(cfg))