Only reindex after deleting all the ROIs in multiple removal

chenyenchung · chenyenchung · commit 4ccfa5faef23 · 2026-03-27T16:32:08.000-04:00
diff --git a/cellpose/gui/delete_utils.py b/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
diff --git a/cellpose/gui/gui.py b/cellpose/gui/gui.py
@@ -15,7 +15,7 @@
 from scipy.stats import mode
 import cv2
 
-from . import guiparts, menus, io
+from . import guiparts, menus, io, delete_utils
 from .. import models, core, dynamics, version, train
 from ..utils import download_url_to_file, masks_to_outlines, diameters
 from ..io import get_image_files, imsave, imread
@@ -1090,12 +1090,60 @@ def unselect_cell_multi(self, idx):
     def remove_cell(self, idx):
         if isinstance(idx, (int, np.integer)):
             idx = [idx]
-        # because the function remove_single_cell updates the state of the cellpix and outpix arrays
-        # by reindexing cells to avoid gaps in the indices, we need to remove the cells in reverse order
-        # so that the indices are correct
-        idx.sort(reverse=True)
-        for i in idx:
-            self.remove_single_cell(i)
+        idx = delete_utils.normalize_remove_ids(idx, self.ncells.get())
+        if idx.size == 0:
+            return
+
+        if idx.size == 1:
+            self.remove_single_cell(int(idx[0]))
+        else:
+            self.selected = 0
+            remove_mask = np.zeros(self.ncells.get() + 1, dtype=bool)
+            remove_mask[idx] = True
+
+            if self.currentZ < self.cellpix.shape[0]:
+                self.layerz[remove_mask[self.cellpix[self.currentZ]]] = np.array([0, 0, 0,
+                                                                                  0])
+
+            if self.NZ == 1:
+                last_idx = int(idx[-1])
+                cp_last = self.cellpix[0] == last_idx
+                op_last = self.outpix[0] == last_idx
+                self.removed_cell = [
+                    self.ismanual[last_idx - 1], self.cellcolors[last_idx],
+                    np.nonzero(cp_last),
+                    np.nonzero(op_last)
+                ]
+                self.redo.setEnabled(True)
+
+                ar_all, ac_all = np.nonzero(remove_mask[self.cellpix[0]])
+                coord_map = {}
+                if ar_all.size > 0:
+                    labels = self.cellpix[0, ar_all, ac_all]
+                    order = np.argsort(labels, kind="mergesort")
+                    labels = labels[order]
+                    ar_all = ar_all[order]
+                    ac_all = ac_all[order]
+                    unique_labels, first_inds = np.unique(labels, return_index=True)
+                    last_inds = np.append(first_inds[1:], labels.size)
+                    for label, i0, i1 in zip(unique_labels, first_inds, last_inds):
+                        coord_map[int(label)] = (ar_all[i0:i1], ac_all[i0:i1])
+
+                for i in idx:
+                    ar, ac = coord_map.get(
+                        int(i), (np.zeros(0, np.int64), np.zeros(0, np.int64)))
+                    d = datetime.datetime.now()
+                    self.track_changes.append(
+                        [d.strftime("%m/%d/%Y, %H:%M:%S"), "removed mask", [ar, ac]])
+                    print("GUI_INFO: removed cell %d" % (i - 1))
+            else:
+                for i in idx:
+                    print("GUI_INFO: removed cell %d" % (i - 1))
+
+            (self.cellpix, self.outpix, self.ismanual, self.cellcolors, self.zdraw, _,
+             _) = delete_utils.batch_delete_reindex(self.cellpix, self.outpix,
+                                                    self.ismanual, self.cellcolors,
+                                                    self.zdraw, idx)
         self.ncells -= len(idx)  # _save_sets uses ncells
         self.update_layer()
 
diff --git a/tests/test_gui_delete_utils.py b/tests/test_gui_delete_utils.py
@@ -0,0 +1,148 @@
+import numpy as np
+import importlib.util
+from pathlib import Path
+
+
+_DELETE_UTILS_PATH = (
+    Path(__file__).resolve().parents[1] / "cellpose/gui/delete_utils.py"
+)
+_DELETE_UTILS_SPEC = importlib.util.spec_from_file_location(
+    "cellpose_gui_delete_utils", _DELETE_UTILS_PATH
+)
+delete_utils = importlib.util.module_from_spec(_DELETE_UTILS_SPEC)
+_DELETE_UTILS_SPEC.loader.exec_module(delete_utils)
+
+
+def _legacy_remove_state(cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids):
+    cellpix = cellpix.copy()
+    outpix = outpix.copy()
+    ismanual = ismanual.copy()
+    cellcolors = cellcolors.copy()
+    zdraw = list(zdraw)
+
+    for idx in remove_ids:
+        cp = cellpix == idx
+        op = outpix == idx
+        cellpix[cp] = 0
+        outpix[op] = 0
+        cellpix[cellpix > idx] -= 1
+        outpix[outpix > idx] -= 1
+        ismanual = np.delete(ismanual, idx - 1)
+        cellcolors = np.delete(cellcolors, [idx], axis=0)
+        del zdraw[idx - 1]
+
+    return cellpix, outpix, ismanual, cellcolors, zdraw
+
+
+def _random_state(seed, nz=1, ly=64, lx=64, ncells=40):
+    rng = np.random.default_rng(seed)
+    dtype = np.uint16 if ncells < 2**16 - 1 else np.uint32
+
+    cellpix = rng.integers(0, ncells + 1, size=(nz, ly, lx), dtype=dtype)
+    force_idx = rng.choice(cellpix.size, size=ncells, replace=False)
+    cellpix.flat[force_idx] = np.arange(1, ncells + 1, dtype=dtype)
+
+    outline_mask = rng.random(cellpix.shape) < 0.2
+    outpix = np.where(outline_mask, cellpix, 0).astype(dtype, copy=False)
+
+    ismanual = rng.integers(0, 2, size=ncells, dtype=np.uint8).astype(bool)
+    cellcolors = rng.integers(0, 256, size=(ncells + 1, 3), dtype=np.uint8)
+    cellcolors[0] = np.array([255, 255, 255], dtype=np.uint8)
+
+    zdraw = []
+    for _ in range(ncells):
+        nplanes = int(rng.integers(1, max(2, nz + 1)))
+        zdraw.append(list(rng.integers(0, max(1, nz), size=nplanes)))
+
+    return cellpix, outpix, ismanual, cellcolors, zdraw
+
+
+def _assert_state_equal(expected, actual):
+    exp_cellpix, exp_outpix, exp_ismanual, exp_cellcolors, exp_zdraw = expected
+    got_cellpix, got_outpix, got_ismanual, got_cellcolors, got_zdraw = actual
+
+    assert np.array_equal(exp_cellpix, got_cellpix)
+    assert np.array_equal(exp_outpix, got_outpix)
+    assert np.array_equal(exp_ismanual, got_ismanual)
+    assert np.array_equal(exp_cellcolors, got_cellcolors)
+    assert len(exp_zdraw) == len(got_zdraw)
+    for z0, z1 in zip(exp_zdraw, got_zdraw):
+        assert np.array_equal(np.asarray(z0), np.asarray(z1))
+
+
+def test_batch_delete_reindex_matches_legacy_small_example():
+    cellpix = np.array(
+        [[[1, 1, 2, 2], [1, 3, 3, 2], [4, 4, 5, 5], [4, 0, 5, 5]]], dtype=np.uint16
+    )
+    outpix = np.array(
+        [[[1, 0, 2, 0], [0, 3, 0, 2], [4, 0, 5, 0], [0, 0, 0, 5]]], dtype=np.uint16
+    )
+    ismanual = np.array([True, False, True, False, True])
+    cellcolors = np.array(
+        [[255, 255, 255], [10, 0, 0], [20, 0, 0], [30, 0, 0], [40, 0, 0], [50, 0, 0]],
+        dtype=np.uint8,
+    )
+    zdraw = [[0], [0], [0], [0], [0]]
+
+    remove_ids = np.array([5, 3, 2], dtype=np.int64)
+
+    expected = _legacy_remove_state(
+        cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+    )
+    got = delete_utils.batch_delete_reindex(
+        cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+    )[:5]
+    _assert_state_equal(expected, got)
+
+
+def test_batch_delete_reindex_matches_legacy_random_2d():
+    for seed in range(20):
+        cellpix, outpix, ismanual, cellcolors, zdraw = _random_state(seed, nz=1)
+        rng = np.random.default_rng(seed + 1000)
+        ncells = len(cellcolors) - 1
+        remove_n = int(rng.integers(1, ncells + 1))
+        remove_ids = rng.choice(np.arange(1, ncells + 1), size=remove_n, replace=False)
+        remove_ids = delete_utils.normalize_remove_ids(remove_ids, ncells)
+
+        expected = _legacy_remove_state(
+            cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+        )
+        got = delete_utils.batch_delete_reindex(
+            cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+        )[:5]
+        _assert_state_equal(expected, got)
+
+
+def test_batch_delete_reindex_matches_legacy_random_3d():
+    for seed in range(12):
+        cellpix, outpix, ismanual, cellcolors, zdraw = _random_state(seed + 100, nz=4)
+        rng = np.random.default_rng(seed + 2000)
+        ncells = len(cellcolors) - 1
+        remove_n = int(rng.integers(1, ncells + 1))
+        remove_ids = rng.choice(np.arange(1, ncells + 1), size=remove_n, replace=False)
+        remove_ids = delete_utils.normalize_remove_ids(remove_ids, ncells)
+
+        expected = _legacy_remove_state(
+            cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+        )
+        got = delete_utils.batch_delete_reindex(
+            cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+        )[:5]
+        _assert_state_equal(expected, got)
+
+
+def test_batch_delete_reindex_noop_invalid_ids():
+    cellpix, outpix, ismanual, cellcolors, zdraw = _random_state(999, nz=1)
+    ncells = len(cellcolors) - 1
+    remove_ids = np.array([0, -1, ncells + 10], dtype=np.int64)
+
+    got = delete_utils.batch_delete_reindex(
+        cellpix, outpix, ismanual, cellcolors, zdraw, remove_ids
+    )
+    got_state = got[:5]
+    out_ids = got[5]
+    remove_mask = got[6]
+
+    _assert_state_equal((cellpix, outpix, ismanual, cellcolors, zdraw), got_state)
+    assert out_ids.size == 0
+    assert not remove_mask.any()
