rename plugin

src/napari_segment/__init__.py

@@ -6,7 +6,7 @@ except ImportError:
 
 from ._reader import napari_get_reader
 from ._sample_data import make_sample_data
-from ._widget import ExampleQWidget, example_magic_widget
+from ._widget import SegmentStack, example_magic_widget
 from ._writer import write_multiple, write_single_image
 
 __ALL__ = [
@@ -14,6 +14,6 @@ __ALL__ = [
     write_multiple,
     write_single_image,
     make_sample_data,
-    ExampleQWidget,
+    SegmentStack,
     example_magic_widget,
 ]

src/napari_segment/_sample_data.py

@@ -12,4 +12,4 @@ import numpy
 
 def make_sample_data():
     """Generates an image"""
-    return numpy.random.rand(512, 512)
+    return [(numpy.random.rand(512, 512),)]

src/napari_segment/_widget.py

@@ -57,7 +57,7 @@ ff.setFormatter(formatter)
 logger.addHandler(ff)
 
 
-class ExampleQWidget(q.QWidget):
+class SegmentStack(q.QWidget):
     # your QWidget.__init__ can optionally request the napari viewer instance
     # in one of two ways:
     # 1. use a parameter called `napari_viewer`, as done here
@@ -327,13 +327,15 @@ class ExampleQWidget(q.QWidget):
                 opacity=0.3,
                 **{"name": name, "scale": self.scale},
             )
-            self.viewer.layers[name].contour = 8 // self.binning
 
         else:
             logger.debug(f'Updating Detections layer with {self.labels}')
             self.viewer.layers[name].data = self.labels
             self.viewer.layers[name].scale = self.scale
         
+        self.viewer.layers[name].contour = 8 // self.binning
+        
+        
         logger.debug(f'Thresholding succesful. \
             Sending labels {self.labels} to filtering')
         self.update_out()

src/napari_segment/napari.yaml

@@ -15,14 +15,14 @@ contributions:
       python_name: napari_segment._sample_data:make_sample_data
       title: Load sample data from Segment organoid
     - id: napari-segment.make_qwidget
-      python_name: napari_segment._widget:ExampleQWidget
-      title: Make example QWidget
-    - id: napari-segment.make_magic_widget
-      python_name: napari_segment._widget:example_magic_widget
-      title: Make example magic widget
-    - id: napari-segment.segment_organoid
-      python_name: napari_segment._widget:segment_organoid
-      title: Segment organoid
+      python_name: napari_segment._widget:SegmentStack
+      title: Segment nd2 stack with multiple positions
+    # - id: napari-segment.make_magic_widget
+    #   python_name: napari_segment._widget:example_magic_widget
+    #   title: Make example magic widget
+    # - id: napari-segment.segment_organoid
+    #   python_name: napari_segment._widget:segment_organoid
+    #   title: Segment organoid
   readers:
     - command: napari-segment.get_reader
       accepts_directories: True
@@ -40,9 +40,9 @@ contributions:
       key: unique_id.1
   widgets:
     - command: napari-segment.make_qwidget
-      display_name: Example QWidget
-    - command: napari-segment.make_magic_widget
-      display_name: Example Magic Widget
-    - command: napari-segment.segment_organoid
-      # autogenerate: true
-      display_name: Segment organoid
+      display_name: Segment multipos
+    # - command: napari-segment.make_magic_widget
+    #   display_name: Example Magic Widget
+    # - command: napari-segment.segment_organoid
+    #   # autogenerate: true
+    #   display_name: Segment organoid