Minor fixes

qim3d/gui/layers2d.py

@@ -25,7 +25,8 @@ import numpy as np
 from .interface import BaseInterface
 
 # from qim3d.processing import layers2d as l2d
-from qim3d.processing import overlay_rgb_images, segment_layers, get_lines
+from qim3d.processing import segment_layers, get_lines
+from qim3d.operations import overlay_rgb_images
 from qim3d.io import load
 from qim3d.viz._layers2d import image_with_lines
 from typing import Dict, Any

qim3d/io/_loading.py

@@ -239,7 +239,7 @@ class DataLoader:
 
         return vol
 
-    def load_txrm(self, path: str|os.PathLike) -> tuple[dask.array|np.ndarray, Optional[Dict]]:
+    def load_txrm(self, path: str|os.PathLike) -> tuple[dask.array.core.Array|np.ndarray, Optional[Dict]]:
         """Load a TXRM/XRM/TXM file from the specified path.
 
         Args:

qim3d/io/_ome_zarr.py

@@ -52,7 +52,7 @@ class OMEScaler(
         self.max_layer = max_layer
         self.method = method
 
-    def scaleZYX(self, base: dask.array):
+    def scaleZYX(self, base: da.core.Array):
         """Downsample using :func:`scipy.ndimage.zoom`."""
         rv = [base]
         log.info(f"- Scale 0: {rv[-1].shape}")
@@ -63,7 +63,7 @@ class OMEScaler(
 
         return list(rv)
 
-    def scaleZYXdask(self, base: dask.array):
+    def scaleZYXdask(self, base: da.core.Array):
         """
         Downsample a 3D volume using Dask and scipy.ndimage.zoom.
 
@@ -82,7 +82,7 @@ class OMEScaler(
 
 
         """
-        def resize_zoom(vol: dask.array, scale_factors, order, scaled_shape):
+        def resize_zoom(vol: da.core.Array, scale_factors, order, scaled_shape):
 
             # Get the chunksize needed so that all the blocks match the new shape
             # This snippet comes from the original OME-Zarr-python library
@@ -182,7 +182,7 @@ class OMEScaler(
 
 def export_ome_zarr(
     path: str|os.PathLike,
-    data: np.ndarray|dask.array,
+    data: np.ndarray|da.core.Array,
     chunk_size: int = 256,
     downsample_rate: int = 2,
     order: int = 1,

qim3d/io/_saving.py

@@ -255,7 +255,7 @@ class DataSaver:
 
         ds.save_as(path)
 
-    def save_to_zarr(self, path: str|os.PathLike, data: np.ndarray):
+    def save_to_zarr(self, path: str|os.PathLike, data: da.core.Array):
         """Saves a Dask array to a Zarr array on disk.
 
         Args:

qim3d/viz/_cc.py

@@ -2,7 +2,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import qim3d
 from qim3d.utils._logger import log
-from segmentation._connected_components import CC
+from qim3d.segmentation._connected_components import CC
 
 def plot_cc(
     connected_components: CC,