add hdf5 preprocessing script and update readme instructions

README.md

@@ -87,7 +87,8 @@ mv mimicplay_release_dataset your_installation_path/mimicplay/datasets
 - Transform raw data to image dataset
 ```	
 cd MimicPlay-dev/mimicplay
-python scripts/dataset_states_to_obs.py --dataset 'datasets/playdata/demo.hdf5' --done_mode 0 --camera_names agentview robot0_eye_in_hand --camera_height 84 --camera_width 84 --output_name image_demo_local.hdf5 --exclude-next-obs
+python scripts/preprocess_hdf5.py -i ./datasets/playdata/demo.hdf5 -o ./datasets/playdata/demo_modified.hdf5
+python scripts/dataset_states_to_obs.py --dataset 'datasets/playdata/demo_modified.hdf5' --done_mode 0 --camera_names agentview robot0_eye_in_hand --camera_height 84 --camera_width 84 --output_name image_demo_local.hdf5 --exclude-next-obs
 ```
 - Extract end-effector trajectory for the training of high-level planner
 ```

mimicplay/scripts/preprocess_hdf5.py

@@ -0,0 +1,91 @@
+"""
+Date: Oct 16, 2023
+
+This script addresses relative file path issue by replacing all relative
+file path in given hdf5 file with absolute file. This step is necessary 
+because Libero library will override relative file path inconsistent with
+our project setting.
+
+Example usage:
+(recommended): python ./scripts/preprocess_hdf5.py -i ./datasets/playdata/demo.hdf5 -o ./datasets/playdata/demo_modified.hdf5
+(if want to update hdf5 file inplace): python ./scripts/preprocess_hdf5.py -i ./datasets/playdata/demo.hdf5 --override
+"""
+
+import argparse
+import h5py
+import os
+
+import xml.etree.ElementTree as ET
+
+
+def replace_relative_path(xml_string):
+    """
+    Replacing all relative path in of mesh and texture with absolute path
+
+    @param xml_string, input xml string from model_file fields of hdf5 file
+    @return updated xml string with absolute path
+    """
+    tree = ET.fromstring(xml_string)
+    root = tree
+    asset = root.find("asset")
+    meshes = asset.findall("mesh")
+    textures = asset.findall("texture")
+    all_elements = meshes + textures
+
+    for elem in all_elements:
+        old_path = elem.get("file")
+        if old_path is None:
+            continue
+        new_path = os.path.abspath(old_path)
+        elem.set("file", new_path)
+
+    return ET.tostring(root, encoding="utf8").decode("utf8")
+
+
+def process_file(input_path, output_path=None):
+    """
+    Preprocess given hdf5 file by replacing relative file path with absolute path
+
+    @param input_path, input hdf5 file path
+    @param output_path, output path of updated hdf5 file. If no output_path is specified,
+                        the function will override input file path inplace
+    """
+
+    # if no output_path, set output_path to input_path, this is equivelent to write inplace
+    if not output_path:
+        output_path = input_path
+    # otherwise, make a full copy of input file, then modify in place
+    else:
+        os.system(f"cp {input_path} {output_path}")
+
+    with h5py.File(output_path, "r+") as f:
+        for demo_name in f["data"].keys():
+            f["data"][demo_name].attrs["model_file"] = replace_relative_path(f["data"][demo_name].attrs["model_file"])
+
+def main():
+    parser = argparse.ArgumentParser(description="Process XML file to replace relative paths.")
+    parser.add_argument("-i", "--input", 
+                        type=str, 
+                        default="./datasets/playdata/demo.hdf5",
+                        help="Path to the input XML file")
+    parser.add_argument("--override", 
+                        action="store_true", 
+                        help="Override the input file with changes")
+    parser.add_argument("-o", "--output", 
+                        type=str, 
+                        default=None, 
+                        help="Path to the output file (only if not overriding original hdf5 file)")
+
+    args = parser.parse_args()
+
+    if args.override:
+        process_file(args.input)
+    else:
+        if not args.output:
+            raise ValueError("You must specify an output file path if not overriding the input file.")
+        if os.path.abspath(args.input) == os.path.abspath(args.output):
+            raise ValueError("Input and output file paths are the same. Use --override or specify a different output path.")
+        process_file(args.input, args.output)
+
+if __name__ == "__main__":
+    main()