Only reindex after deleting all the ROIs in multiple removal

Author: chenyenchung

cellpose/gui/delete_utils.py

@@ -0,0 +1,56 @@
+"""
+Utilities for deleting and relabeling GUI masks.
+"""
+
+import numpy as np
+
+
+def normalize_remove_ids(remove_ids, ncells):
+    """Return unique valid label IDs in descending order."""
+    remove_ids = np.asarray(remove_ids, dtype=np.int64).reshape(-1)
+    if remove_ids.size == 0 or ncells <= 0:
+        return np.zeros(0, dtype=np.int64)
+    valid = (remove_ids > 0) & (remove_ids <= int(ncells))
+    if not np.any(valid):
+        return np.zeros(0, dtype=np.int64)
+    remove_ids = np.unique(remove_ids[valid])
+    return np.sort(remove_ids)[::-1]
+
+
+def batch_delete_reindex(cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids):
+    """Delete labels and reindex all state in one pass.
+
+    Returns updated `(cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids, remove_mask)`.
+    """
+    if cellpix.shape != outpix.shape:
+        raise ValueError("cellpix and outpix must have the same shape")
+
+    ncells = int(len(cellcolors) - 1)
+    remove_ids = normalize_remove_ids(remove_ids, ncells)
+    if remove_ids.size == 0:
+        remove_mask = np.zeros(ncells + 1, dtype=bool)
+        return (
+            cellpix,
+            outpix,
+            ismanual,
+            cellcolors,
+            list(zdraw),
+            remove_ids,
+            remove_mask,
+        )
+
+    remove_mask = np.zeros(ncells + 1, dtype=bool)
+    remove_mask[remove_ids] = True
+    keep_mask = ~remove_mask
+
+    lut_dtype = cellpix.dtype if np.issubdtype(cellpix.dtype, np.integer) else np.int64
+    relabel_map = np.cumsum(keep_mask, dtype=lut_dtype) - 1
+    relabel_map[remove_mask] = 0
+
+    cellpix = relabel_map[cellpix]
+    outpix = relabel_map[outpix]
+    ismanual = ismanual[keep_mask[1:]]
+    cellcolors = cellcolors[keep_mask]
+    zdraw = [z for z, keep in zip(zdraw, keep_mask[1:]) if keep]
+
+    return cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids, remove_mask