Merge pull request #1187 from MouseLand/tilebug

bug with tile norm

Author: carsen-stringer

cellpose/models.py

@@ -299,7 +299,7 @@ def eval(self, x, batch_size=8, resample=None, channels=None, channel_axis=None,
             x = transforms.normalize_img(x, **normalize_params)
             do_normalization = False # do not normalize again
         else:
-            if normalize_params["norm3D"] and nimg > 1:
+            if normalize_params["norm3D"] and nimg > 1 and do_normalization:
                 models_logger.warning(
                     "normalize_params['norm3D'] is True but do_3D is False and stitch_threshold=0, so setting to False"
                 )

cellpose/transforms.py

@@ -730,6 +730,7 @@ def normalize_img(img, normalize=True, norm3D=True, invert=False, lowhigh=None,
                 smooth3D=tile_norm_smooth3D,
                 norm3D=norm3D,
             )
+            cgood[:] = True
         elif normalize:
             if img_norm.ndim == 3 or norm3D:  # i.e. if YXC, or ZYXC with norm3D=True
                 for c in range(nchan):
@@ -774,7 +775,7 @@ def normalize_img(img, normalize=True, norm3D=True, invert=False, lowhigh=None,
             if img_norm.ndim == 3:
                 img_norm[:, :, i] = 0
             if img_norm.ndim == 4:
-                img_norm[0, :, :, i] = 0
+                img_norm[:, :, :, i] = 0
 
     return img_norm