run spinner when saving targets

src/napari_tomotwin/common.py

@@ -0,0 +1,15 @@
+import napari
+from pyqtspinner import WaitingSpinner
+from qtpy.QtCore import Qt
+from qtpy.QtGui import QColor  # pylint: disable=E0611
+
+
+def make_spinner():
+    return WaitingSpinner(napari.current_viewer().window._qt_window,
+                             True,
+                             True, Qt.ApplicationModal,
+                             color=QColor(255, 255, 255),
+                             fade=60,
+                             line_width=5,
+                             line_length=15,
+                             )

src/napari_tomotwin/load_umap.py

@@ -10,6 +10,7 @@
 from qtpy.QtGui import QGuiApplication, QColor # pylint: disable=E0611
 from typing import List
 from pyqtspinner import WaitingSpinner
+from napari.qt.threading import thread_worker
 
 plotter_widget: PlotterWidget = None
 circles: List[Circle] = []
@@ -46,7 +47,6 @@ def _draw_circle(data_coordinates, label_layer, umap):
     plotter_widget.graphics_widget.axes.add_patch(circle)
     plotter_widget.graphics_widget.draw_idle()
 
-from napari.qt.threading import thread_worker
 
 @thread_worker()
 def run_clusters_plotter(plotter_widget,
@@ -115,15 +115,7 @@ def get_event(viewer, event):
         data_coordinates = label_layer.world_to_data(event.position)
         _draw_circle(data_coordinates,label_layer,umap)
 
-def make_spinner():
-    return WaitingSpinner(napari.current_viewer().window._qt_window,
-                             True,
-                             True, Qt.ApplicationModal,
-                             color=QColor(255, 255, 255),
-                             fade=60,
-                             line_width=5,
-                             line_length=15,
-                             )
+
 def stop_spinner():
     spinner.stop()
 
@@ -133,7 +125,7 @@ def load_umap(label_layer: "napari.layers.Labels",
     global plotter_widget
     global spinner
 
-
+    from napari_tomotwin.common import make_spinner
     spinner = make_spinner()
     spinner.start()  # starts spinning
 

src/napari_tomotwin/make_targets.py

@@ -1,13 +1,15 @@
 import os
 import pathlib
-import sys
 from typing import List, Tuple, Literal, Callable
 
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
 from magicgui import magic_factory
 from scipy.spatial.distance import cdist
+from napari.qt.threading import thread_worker
+
+global spinner
 
 def get_non_numeric_column_titles(df: pd.DataFrame):
 
@@ -33,7 +35,6 @@ def _get_avg_embedding(embeddings: pd.DataFrame) -> Tuple[pd.DataFrame, npt.Arra
     target = only_emb.mean(axis=0)
     return target, np.array([])
 
-
 def _make_targets(embeddings: pd.DataFrame, clusters: pd.DataFrame, avg_func: Callable[[pd.DataFrame], npt.ArrayLike]) -> Tuple[pd.DataFrame, List[pd.DataFrame], dict]:
     targets = []
     sub_embeddings = []
@@ -62,6 +63,7 @@ def _make_targets(embeddings: pd.DataFrame, clusters: pd.DataFrame, avg_func: Ca
     return targets, sub_embeddings, target_locations
 
 
+
 def _run(clusters,
                   embeddings: pd.DataFrame,
                   output_folder: pathlib.Path,
@@ -73,9 +75,12 @@ def _run(clusters,
     if average_method_name == "Average":
         avg_method = _get_avg_embedding
 
+
+
     print("Make targets")
     #embeddings = embeddings.reset_index()
     embeddings = embeddings.drop(columns=["level_0","index"], errors="ignore")
+
     targets, sub_embeddings, target_locations = _make_targets(embeddings, clusters, avg_func=avg_method)
 
     print("Write targets")
@@ -98,6 +103,20 @@ def _run(clusters,
 
     print("Done")
 
+
+@thread_worker
+def _run_worker(embeddings_filepath, label_layer, output_folder: str, average_method_name: str):
+    print("Read clusters")
+    clusters = label_layer.features['MANUAL_CLUSTER_ID']
+
+    print("Read embeddings")
+    embeddings = pd.read_pickle(embeddings_filepath)
+    _run(clusters, embeddings, output_folder, average_method_name)
+
+def stop_spinner():
+    global spinner
+    spinner.stop()
+
 @magic_factory(
     call_button="Save",
     label_layer={'label': 'TomoTwin Label Mask:'},
@@ -115,11 +134,11 @@ def make_targets(
         output_folder: pathlib.Path,
         average_method_name: Literal["Average", "Medoid"] = "Medoid",
 ):
+    global spinner
+    from napari_tomotwin.common import make_spinner
+    spinner = make_spinner()
+    spinner.start()  # starts spinning
+    worker = _run_worker(embeddings_filepath, label_layer, output_folder, average_method_name) # create "worker" object
+    worker.returned.connect(stop_spinner)
+    worker.start()
 
-    print("Read clusters")
-    clusters = label_layer.features['MANUAL_CLUSTER_ID']
-
-    print("Read embeddings")
-    embeddings = pd.read_pickle(embeddings_filepath)
-
-    _run(clusters, embeddings, output_folder, average_method_name)