fix imports in GUI components

src/tomography_python_programs/_qt/components/checkable_tilt_image_list.py

@@ -16,6 +16,7 @@ def __init__(self, tilt_image_file: Path):
 
 class TiltImageListWidget(QListWidget):
     """QListWidget of QTiltImageItem"""
+
     def __init__(self):
         super().__init__()
         self.images = []
@@ -64,5 +65,3 @@ def select_all(self):
     def deselect_all(self):
         for i in range(self.count()):
             self.item(i).setCheckState(Qt.CheckState.Unchecked)
-
-

src/tomography_python_programs/_qt/components/tilt_series_browser.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List, Tuple, Dict, Optional, Iterable
+from typing import List, Dict, Iterable
 
 import mrcfile
 import napari
@@ -30,12 +30,12 @@ class TiltSeriesBrowserWidget(QWidget):
     tilt_series_changed: Signal = Signal()
 
     def __init__(
-            self,
-            viewer: napari.Viewer,
-            tilt_series: GuiTiltSeriesSet,
-            cache_size: int,
-            *args,
-            **kwargs
+        self,
+        viewer: napari.Viewer,
+        tilt_series: GuiTiltSeriesSet,
+        cache_size: int,
+        *args,
+        **kwargs
     ):
         super().__init__(*args, **kwargs)
         self.viewer = viewer
@@ -103,7 +103,8 @@ def on_tilt_series_change(self):
             self._disconnect_worker_safe(worker)
 
         if self.selected_tilt_series.name not in self._cache:
-            self.load_tilt_series_async(self.selected_tilt_series.name, update_viewer=True)
+            self.load_tilt_series_async(self.selected_tilt_series.name,
+                                        update_viewer=True)
         else:
             self.load_tilt_series_from_cache(self.selected_tilt_series.name)
         self._remove_workers_for_uncached_tilt_series()
@@ -165,11 +166,13 @@ def _create_thread_worker(self, tilt_series_id: str) -> GeneratorWorker:
         worker = _read_tilt_series(tilt_series_id, list(tilt_images))
         return worker
 
-    def _connect_events_for_background_loading(self, worker: GeneratorWorker) -> GeneratorWorker:
+    def _connect_events_for_background_loading(self,
+                                               worker: GeneratorWorker) -> GeneratorWorker:
         worker.yielded.connect(self._cache_tilt_series)
         return worker
 
-    def _connect_events_for_gui_updates(self, worker: GeneratorWorker) -> GeneratorWorker:
+    def _connect_events_for_gui_updates(self,
+                                        worker: GeneratorWorker) -> GeneratorWorker:
         worker.yielded.connect(self._update_tilt_series_in_viewer)
         worker.finished.connect(self.tilt_series_changed.emit)
         worker.finished.connect(self.preload_next_tilt_series)
@@ -214,7 +217,8 @@ def next_tilt_series(self, event=None):
     @property
     def background_workers(self) -> Iterable[GeneratorWorker]:
         background_worker_keys = self._workers.keys() - {self.selected_tilt_series.name}
-        return (self._workers[tilt_series_id] for tilt_series_id in background_worker_keys)
+        return (self._workers[tilt_series_id] for tilt_series_id in
+                background_worker_keys)
 
     def _update_list_from_combobox(self):
         idx = self.tilt_series_combo_box.currentIndex()
@@ -227,14 +231,16 @@ def _update_combobox_from_list(self):
         self.tilt_series_combo_box.blockSignals(False)
 
 
-def _create_empty_tilt_series_data(tilt_image_files: List[Path], dtype=np.float32) -> np.ndarray:
+def _create_empty_tilt_series_data(tilt_image_files: List[Path],
+                                   dtype=np.float32) -> np.ndarray:
     with mrcfile.open(tilt_image_files[0], header_only=True) as mrc:
         tilt_series_shape = (len(tilt_image_files), mrc.header.ny, mrc.header.nx)
     return np.zeros(shape=tilt_series_shape, dtype=dtype)
 
 
 @thread_worker(progress={'total': 40}, start_thread=False)
-def _read_tilt_series(tilt_series_id: str, tilt_image_files: List[Path]) -> LazyTiltSeriesData:
+def _read_tilt_series(tilt_series_id: str,
+                      tilt_image_files: List[Path]) -> LazyTiltSeriesData:
     tilt_series = _create_empty_tilt_series_data(tilt_image_files, dtype=np.float16)
     lazy_tilt_series_data = LazyTiltSeriesData(
         name=tilt_series_id, data=tilt_series, last_loaded_index=None, n_images_loaded=0

src/tomography_python_programs/_qt/components/tomogram_browser.py

@@ -1,26 +1,29 @@
-import mrcfile
 import napari
+import mrcfile
 import numpy as np
 from psygnal import Signal
 from qtpy.QtWidgets import QWidget, QVBoxLayout, QLabel, QSizePolicy
 from lru import LRU
 
-from ..._metadata_models.gui.tilt_series_set import GuiTiltSeriesSet as GuiTiltSeriesSet
+from ..._metadata_models.gui.tilt_series_set import GuiTiltSeriesSet
 from ..._metadata_models.gui.tilt_series import GuiTiltSeries
 from .tilt_series_list import TiltSeriesListWidget
 
+IMAGE_LAYER_NAME = 'tomogram'
+
 
 class TomogramBrowserWidget(QWidget):
     changing_tomogram: Signal = Signal()
     tomogram_changed: Signal = Signal()
+    image_layer: napari.layers.Image
 
     def __init__(
-            self,
-            viewer: napari.Viewer,
-            tilt_series: GuiTiltSeriesSet,
-            cache_size: int,
-            *args,
-            **kwargs
+        self,
+        viewer: napari.Viewer,
+        tilt_series: GuiTiltSeriesSet,
+        cache_size: int,
+        *args,
+        **kwargs
     ):
         super().__init__(*args, **kwargs)
         self.viewer = viewer
@@ -48,6 +51,10 @@ def __init__(
         self.next_tilt_series = self.viewer.bind_key(']', self.next_tilt_series)
         self._on_tomogram_selection_change()
 
+    @property
+    def image_layer(self) -> napari.layers.Image:
+        return self.viewer.layers[IMAGE_LAYER_NAME]
+
     @property
     def selected_tilt_series(self) -> GuiTiltSeries:
         return self._selected_tilt_series
@@ -64,11 +71,11 @@ def _on_tomogram_selection_change(self):
 
     def _update_tomogram_in_viewer(self, tomogram: np.ndarray):
         if 'tomogram' in self.viewer.layers:
-            self.viewer.layers['tomogram'].data = tomogram
+            self.viewer.layers[IMAGE_LAYER_NAME].data = tomogram
         else:
             self.viewer.add_image(
                 data=tomogram,
-                name='tomogram',
+                name=IMAGE_LAYER_NAME,
                 depiction='plane',
                 plane={'thickness': 1},
                 rendering='minip',
@@ -87,15 +94,13 @@ def _load_tomogram(self, tilt_series_id: str, add_to_viewer: bool) -> None:
         self._cache[tilt_series_id] = tomogram
         if add_to_viewer:
             self._update_tomogram_in_viewer(tomogram)
-            self.tomogram_changed.emit()
 
     def _load_tomogram_from_cache(self, tilt_series_id: str, add_to_viewer: bool):
         if add_to_viewer is True:
             self._update_tomogram_in_viewer(self._cache[tilt_series_id])
-            self._on_tomogram_loaded()
 
     def _on_tomogram_loaded(self):
-        layer = self.viewer.layers['tomogram']
+        layer = self.viewer.layers[IMAGE_LAYER_NAME]
         layer.depiction = 'plane'
         layer.plane.position = np.array(layer.data.shape) / 2
         layer.plane.normal = (1, 0, 0)
@@ -118,4 +123,3 @@ def previous_tilt_series(self, event=None):
 
     def next_tilt_series(self, event=None):
         self.tilt_series_list_widget.next()
-