Update test config and fix minor issues

Author: constantinpape

.github/workflows/test.yaml

@@ -20,7 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.11", "3.12"]
+        # 3.12 currently not supported due to issues with nifty.
+        # python-version: ["3.11", "3.12"]
+        python-version: ["3.11"]
 
     steps:
       - name: Checkout

environment_cpu.yaml

@@ -4,8 +4,8 @@ channels:
     - conda-forge
 dependencies:
     - cpuonly
-      # - nifty =1.2.1=*_4
-    - nifty
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
     - imagecodecs
     - magicgui
     - napari

environment_gpu.yaml

@@ -5,6 +5,7 @@ channels:
     - conda-forge
 dependencies:
     - imagecodecs
+    # This pin is necessary because later nifty versions have import errors on windows.
     - nifty =1.2.1=*_4
     - magicgui
     - napari

micro_sam/multi_dimensional_segmentation.py

@@ -325,7 +325,7 @@ def merge_instance_segmentation_3d(
     uv_ids = np.array([[edge["source"], edge["target"]] for edge in edges])
     overlaps = np.array([edge["score"] for edge in edges])
 
-    n_nodes = int(slice_segmentation[-1].max() + 1)
+    n_nodes = int(slice_segmentation.max() + 1)
     graph = nifty.graph.undirectedGraph(n_nodes)
     graph.insertEdges(uv_ids)
 

micro_sam/sam_annotator/_widgets.py

@@ -174,7 +174,7 @@ def _add_path_param(self, name, value, select_type, title=None, placeholder=None
         layout.addWidget(label)
 
         path_textbox = QtWidgets.QLineEdit()
-        path_textbox.setText(value)
+        path_textbox.setText(str(value))
         if placeholder is not None:
             path_textbox.setPlaceholderText(placeholder)
         path_textbox.textChanged.connect(lambda val: setattr(self, name, val))
@@ -210,7 +210,7 @@ def _get_directory_path(self, name, textbox, tooltip=None):
         if tooltip:
             directory.setToolTip(tooltip)
         if directory and Path(directory).is_dir():
-            textbox.setText(directory)
+            textbox.setText(str(directory))
         else:
             # Handle the case where the selected path is not a directory
             print("Invalid directory selected. Please try again.")
@@ -222,7 +222,7 @@ def _get_file_path(self, name, textbox, tooltip=None):
         if tooltip:
             file_path.setToolTip(tooltip)
         if file_path and Path(file_path).is_file():
-            textbox.setText(file_path)
+            textbox.setText(str(file_path))
         else:
             # Handle the case where the selected path is not a file
             print("Invalid file selected. Please try again.")

micro_sam/sam_annotator/util.py

@@ -684,10 +684,10 @@ def _sync_embedding_widget(widget, model_type, save_path, checkpoint_path, devic
         widget.model_dropdown.setCurrentIndex(index)
 
     if save_path is not None:
-        widget.embeddings_save_path_param.setText(save_path)
+        widget.embeddings_save_path_param.setText(str(save_path))
 
     if checkpoint_path is not None:
-        widget.custom_weights_param.setText(checkpoint_path)
+        widget.custom_weights_param.setText(str(checkpoint_path))
 
     if device is not None:
         widget.device = device