Small changes for napari 0.4.17 (#133)

README.md

@@ -37,3 +37,7 @@ napari -w blik -- /path/to.star /path/to/mrc/files/*
 The `-w blik` is important for proper initialization of all the layers. Keep the main widget open to ensure nothing goes wrong!
 
 *`blik` is just `napari`*. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly other [napari plugins](https://napari-hub.org/).
+
+## Widget
+
+The main widget has a few functions:

blik/_tests/test_widget.py

@@ -8,13 +8,12 @@
 
 
 def test_main_widget(make_napari_viewer):
-    viewer = make_napari_viewer()
+    wdg = MainBlikWidget()
+    assert 'test' not in wdg[0].experiment_id.choices
 
+    viewer = make_napari_viewer()
     with napari.layers._source.layer_source(reader_plugin='blik'):
         viewer.add_points(metadata={'experiment_id': 'test'})
-
-    wdg = MainBlikWidget()
-    assert 'test' not in wdg[0].experiment_id.choices
     viewer.window.add_dock_widget(wdg)
     assert 'test' in wdg[0].experiment_id.choices
 

blik/napari.yaml

@@ -56,5 +56,3 @@ contributions:
       display_name: bandpass filter
     - command: blik.gaussian_filter
       display_name: gaussian filter
-    - command: blik.filament_picker
-      display_name: filament picker

blik/reader.py

@@ -42,7 +42,7 @@ def read_particles(particles):
                 edge_width=0,
                 scale=scale,
                 shading='spherical',
-                # antialiasing=0,
+                antialiasing=0,
                 metadata={'experiment_id': exp_id, 'p_id': p_id},
                 out_of_slice_display=True,
             ),
@@ -80,8 +80,8 @@ def read_image(image):
             name=f'{image.experiment_id} - image',
             scale=[px_size] * image.data.ndim,
             metadata={'experiment_id': image.experiment_id, 'stack': image.stack},
-            interpolation='spline36',
-            # interpolation3d='linear',
+            interpolation2d='spline36',
+            interpolation3d='linear',
             rendering='average',
             depiction='plane',
             blending='translucent',

blik/widgets/main_widget.py

@@ -33,6 +33,9 @@ def _get_choices(wdg):
 
 
 def _connect_points_to_vectors(p, v):
+    """
+    connect a particle points layer to a vectors layer to keep them in sync.
+    """
     def _update_vectors():
         vec_data, vec_color = generate_vectors(p.data, p.features[PSDL.ORIENTATION])
         v.data = vec_data
@@ -52,44 +55,42 @@ def _update_points_from_features():
     p.events.features.connect(_update_vectors)
 
 
-def _on_init(wdg):
+def _attach_callbacks_to_viewer(wdg):
     """
-    hook up widget to update choices wheneven things change in the layerlist
-
-    also sets up a few things on the viewer
+    attach all callbacks to the napari viewer and enable scale bar
     """
-    @wdg.parent_changed.connect
-    def _look_for_viewer():
-        viewer = find_viewer_ancestor(wdg.native)
-        if viewer:
-            viewer.layers.events.inserted.connect(wdg.experiment_id.reset_choices)
-            viewer.layers.events.removed.connect(wdg.experiment_id.reset_choices)
-            viewer.layers.events.inserted.connect(lambda e: _connect_layers(viewer, e))
-            _connect_layers(viewer, None)
+    viewer = find_viewer_ancestor(wdg.native)
+    if viewer:
+        viewer.layers.events.inserted.connect(lambda e: _connect_layers(viewer, e))
+        _connect_layers(viewer, None)
 
-            viewer.scale_bar.unit = '0.1nm'  # pixels are 1 Angstrom
-            viewer.scale_bar.visible = True
+        viewer.scale_bar.unit = '0.1nm'  # pixels are 1 Angstrom
+        viewer.scale_bar.visible = True
 
-    def _connect_layers(viewer, e):
-        points = {}
-        vectors = {}
-        for lay in viewer.layers:
-            p_id = lay.metadata.get('p_id', None)
-            if p_id is not None:
-                if isinstance(lay, Points):
-                    points[p_id] = lay
-                elif isinstance(lay, Vectors):
-                    vectors[p_id] = lay
-        for p_id, p in points.items():
-            v = vectors.get(p_id, None)
-            if v is not None:
-                _connect_points_to_vectors(p, v)
+
+def _connect_layers(viewer, e):
+    """
+    connect all points and vectors layers with the necessary callbacks
+    """
+    points = {}
+    vectors = {}
+    for lay in viewer.layers:
+        p_id = lay.metadata.get('p_id', None)
+        if p_id is not None:
+            if isinstance(lay, Points):
+                points[p_id] = lay
+            elif isinstance(lay, Vectors):
+                vectors[p_id] = lay
+    for p_id, p in points.items():
+        v = vectors.get(p_id, None)
+        if v is not None:
+            _connect_points_to_vectors(p, v)
 
 
 @magic_factory(
     auto_call=True,
     call_button=False,
-    widget_init=_on_init,
+    labels=False,
     experiment_id=dict(widget_type='ComboBox', choices=_get_choices, nullable=True),
 )
 def experiment(viewer: 'napari.Viewer', experiment_id):
@@ -136,8 +137,8 @@ def new(l_type) -> 'napari.types.LayerDataTuple':
     """
     create a new layer to add to this experiment
     """
+    layers = getattr(new._main_widget['experiment'], 'current_layers', [])
     if l_type == 'segmentation':
-        layers = getattr(new._main_widget['experiment'], 'current_layers', [])
         for lay in layers:
             if isinstance(lay, Image):
                 exp_id = lay.metadata['experiment_id']
@@ -154,12 +155,21 @@ def new(l_type) -> 'napari.types.LayerDataTuple':
 
 
 class MainBlikWidget(Container):
+    """
+    Main widget for blik controls.
+
+    Allows to select which layers to view based on the experiment id, to add
+    existing layer to a certain experiment id, and to create new analysis layers
+    within.
+    """
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.append(experiment(labels=False))
 
+        exp = experiment()
+        self.parent_changed.connect(lambda _: _attach_callbacks_to_viewer(exp))
+        self.append(exp)
         self.append(new)
-
         self.append(add_layer)
 
     def append(self, item):

setup.cfg

@@ -57,12 +57,12 @@ install_requires =
 
 [options.extras_require]
 all =
-    napari[all]>=0.4.16
+    napari[all]>=0.4.17
     napari-properties-plotter
     napari-properties-viewer
     napari-label-interpolator
 testing =
-    napari[all]>=0.4.16
+    napari[all]>=0.4.17
     tox
     pytest
     pytest-qt