Resample fix

cellpose/dynamics.py

@@ -2,6 +2,8 @@
 Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer , Michael Rariden and Marius Pachitariu.
 """
 import os
+import cv2
+from cellpose import transforms
 from scipy.ndimage import find_objects, center_of_mass, mean
 import torch
 import numpy as np
@@ -614,7 +616,22 @@ def resize_and_compute_masks(dP, cellprob, niter=200, cellprob_threshold=0.0,
                             device=device)
 
     if resize is not None:
-        dynamics_logger.warning("Resizing is deprecated in v4.0.1+")
+        if len(resize) == 2:
+            mask = transforms.resize_image(mask, resize[0], resize[1], no_channels=True,
+                                           interpolation=cv2.INTER_NEAREST)
+        else:
+            Lz, Ly, Lx = resize
+            if mask.shape[0] != Lz or mask.shape[1] != Ly:
+                dynamics_logger.info("resizing 3D masks to original image size")
+                if mask.shape[1] != Ly:
+                    mask = transforms.resize_image(mask, Ly=Ly, Lx=Lx,
+                                                no_channels=True, 
+                                                interpolation=cv2.INTER_NEAREST)
+                if mask.shape[0] != Lz:
+                    mask = transforms.resize_image(mask.transpose(1,0,2),
+                                                    Ly=Lz, Lx=Lx,
+                                                    no_channels=True, 
+                                                    interpolation=cv2.INTER_NEAREST).transpose(1,0,2)
 
     mask = utils.fill_holes_and_remove_small_masks(mask, min_size=min_size)
 

cellpose/models.py

@@ -212,12 +212,6 @@ def eval(self, x, batch_size=8, resample=True, channels=None, channel_axis=None,
             styles (list of 1D arrays of length 256 or single 1D array): Style vector containing only zeros. Retained for compaibility with CP3. 
 
         """
-
-        if rescale is not None:
-            models_logger.warning("rescaling deprecated in v4.0.1+") 
-        if channels is not None:
-            models_logger.warning("channels deprecated in v4.0.1+. If data contain more than 3 channels, only the first 3 channels will be used")
-
         if isinstance(x, list) or x.squeeze().ndim == 5:
             self.timing = []
             masks, styles, flows = [], [], []

tests/test_shape.py

@@ -9,6 +9,12 @@ def test_shape_2D_grayscale(cellposemodel_fixture_24layer):
     assert masks.shape == (224, 224)
 
 
+def test_shape_2D_grayscale_resample(cellposemodel_fixture_2layer):
+    img = np.zeros((224, 224))
+    masks, _, _ = cellposemodel_fixture_2layer.eval(img, diameter=20, resample=False)
+    assert masks.shape == (224, 224)
+
+
 def test_shape_2D_chan_first_diam_resize(cellposemodel_fixture_24layer):
     img = np.zeros((1, 224, 224))
     masks, flows, _ = cellposemodel_fixture_24layer.eval(img, diameter=50)