Update README.md

README.md

@@ -30,6 +30,67 @@ configs:
     path: data/train-*
 ---
 
+# Converting script
+
+```py
+
+DATA_DIR = Path("/path/to/cached/hugging_face/datasets/for/MLDS-NUS/Experimental_Images")
+# should end with something like "snapshots/fd299418e9435f8fd98956a3f0a7344d208cc142"
+
+
+def calc_left_right(data: np.ndarray):
+    left_rights = []
+    for im in data:
+        nonzero_columns = (im != 0).any(axis=-2)
+        left = nonzero_columns.argmax() if nonzero_columns.any() else -1
+        # Find the rightmost non-zero column
+        right = len(nonzero_columns) - 1 - nonzero_columns[::-1].argmax() if nonzero_columns.any() else -1
+        left_right = np.array([left, right])
+        left_rights.append(left_right)
+    left_rights = np.stack(left_rights, axis=0)  # shape: (seq_len, 2)
+    return left_rights
+
+
+def calc_barycenter(data: np.ndarray) -> np.ndarray:
+    """
+    Calculate the barycenter of the polymer from the snapshot.
+    Assumes snapshot shape is (100, 500).
+    """
+    xx = np.arange(data.shape[-2]).reshape(-1, 1)
+    bary_x = (data * xx).sum(axis=(-2, -1)) / data.sum(axis=(-2, -1))
+    yy = np.arange(data.shape[-1]).reshape(1, -1)
+    bary_y = (data * yy).sum(axis=(-2, -1)) / data.sum(axis=(-2, -1))
+    barycenter = np.stack([bary_x, bary_y], axis=-1)  # (seq_len, 2)
+    return barycenter
+
+
+def gen():
+    for folder in ["30V_Jan24", "60V_Dec24"]:
+
+        with open(DATA_DIR / f"{folder}.pkl", "rb") as f:
+            data = pickle.load(f)
+    
+        for k, v in data.items():
+            frame = np.clip(v, 0, 255).astype(np.uint8) # save memory
+            left_rights = calc_left_right(255 - frame)
+            barycenters = calc_barycenter(255 - frame)
+    
+            yield {
+                "config": folder,
+                "traj_id": k,
+                "shape": list(frame.shape),
+                "data": frame,
+                "left_right": left_rights,
+                "barycenter": barycenters,
+            }
+
+
+ds = Dataset.from_generator(gen)
+ds = ds.with_format("numpy")
+
+ds.push_to_hub("MLDS-NUS/polymer_re-upload")
+```
+
 # How to use
 
 ```py