Merge pull request #34 from MPI-Dortmund/fixes-for-latest-cluster-plo…

…tter

fixes for the latest cluster plotter

.github/workflows/test_and_deploy.yml

@@ -32,11 +32,10 @@ jobs:
       run:
         shell: bash -el {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.2.0
     - name: Set up conda ${{ matrix.python-version }}
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3.0.4
       with:
-        mamba-version: "*"
         activate-environment: napari-tomotwin
         channel-priority: true
         python-version: ${{ matrix.python-version }}

conda_env.yml

@@ -22,4 +22,4 @@ dependencies:
   - pip
   - pip:
       - napari-boxmanager # Install napari-boxmanager via pip because otherwise scripts in setup.cfg are ignored
-      - git+https://github.com/BiAPoL/napari-clusters-plotter.git@b9b08f3500c9b0831d2cd1b4d9a757c688f76005 #until 0.7.4 is released
+      - napari-clusters-plotter

src/napari_tomotwin/_tests/test_load_umap.py

@@ -46,6 +46,7 @@ def test_something(self):
             widget, _ = viewer.window.add_plugin_dock_widget('napari-tomotwin', widget_name='TomoTwin clustering workflow')
             lyr = tool.load_umap(filename=f"{tmpdirname}/umap.tumap")
             viewer.add_layer(lyr)
+            viewer.close()
 
             assert True # just make sure that now exception is raised
 

src/napari_tomotwin/cluster_widget.py

@@ -303,6 +303,7 @@ def after_draw_event(self):
                     self._recalc_umap.setEnabled(True)
                 self._add_candidate.setEnabled(True)
                 self._show_targets.setEnabled(True)
+            self.plotter_widget.layer_select.value.opacity = 0 # hot fix until line 108 in load_umap works (PR must be accepted)
 
         except Exception as e:
             print(e)
@@ -557,7 +558,8 @@ def update_items_cluster_dropdown(
 
         dropdown.clear()
         for c in np.unique(cluster_ids):
-            if c == 0:
+
+            if c <= 0:
                 continue
             rgba = self.index_to_rgba(c)
             dropdown.addItem("")

src/napari_tomotwin/load_umap.py

@@ -94,18 +94,18 @@ def show_umap(self, label_layer):
 
         self.update_progress_bar("Visualize umap")
         self.viewer.add_layer(label_layer)
-
-        label_layer.opacity = 0
-        label_layer.visible = True
         self.created_layers.append(label_layer)
 
         try:
             # napari-clusters-plotter > 0.7.4
+            label_layer.opacity = 0
+            label_layer.visible = True
             self.plotter_widget.layer_select.value = label_layer
         except:
+            print("ERROR!!")
             # napari-clusters-plotter < 0.7.4
             pass
-
+        #self.plotter_widget.manual_label_opacity = 0
         self.plotter_widget.plot_x_axis.setCurrentIndex(3)
         self.plotter_widget.plot_y_axis.setCurrentIndex(4)
         self.plotter_widget.bin_auto.setChecked(True)