put passive viewers in one program

pyproject.toml

@@ -64,12 +64,7 @@ dev = [
     "pytest",
     "rich",
 ]
-gui = [
-    "napari",
-    "qtpy",
-    "psygnal"
-]
-gui-pyqt = [
+vis = [
     "napari",
     "qtpy",
     "psygnal",
@@ -84,11 +79,10 @@ repository = "https://github.com/3dem/relion"
 # same as console_scripts entry point
 [project.scripts]
 relion_tomo_import = "tomography_python_programs.import_tilt_series:cli"
-relion_tomo_view_tilt_series = "tomography_python_programs.view_tilt_series:cli"
-relion_tomo_view_tomograms = "tomography_python_programs.view_tomograms:cli"
 relion_tomo_exclude_tilt_images = "tomography_python_programs.exclude_tilt_images:cli"
-relion_tomo_pick = "tomography_python_programs.pick:cli"
 relion_tomo_align_tilt_series = "tomography_python_programs.align_tilt_series:cli"
+relion_tomo_view = "tomography_python_programs.view:cli"
+relion_tomo_pick = "tomography_python_programs.pick:cli"
 relion_tomo_denoise = "tomography_python_programs.denoise:cli"
 
 

src/gui_mainwindow.cpp

@@ -1470,7 +1470,7 @@ void GuiMainWindow::cb_display_io_node_i()
     else if (pipeline.nodeList[mynode].type.find(LABEL_TOMO_TILTSERIES) != std::string::npos )
     {
 
-        command = "relion_tomo_view_tilt_series --tilt-series-star-file " + pipeline.nodeList[mynode].name;
+        command = "relion_tomo_view tilt-series --tilt-series-star-file " + pipeline.nodeList[mynode].name;
 
         // Read cache-size from gui_tomo_exclude_tilt_imagesjob.star if that file exists
 		RelionJob excludetiltseriesjob;
@@ -1489,7 +1489,7 @@ void GuiMainWindow::cb_display_io_node_i()
     else if (pipeline.nodeList[mynode].type.find(LABEL_TOMO_TOMOGRAMS) != std::string::npos )
     {
 
-        command = "relion_tomo_view_tomograms --tilt-series-star-file " + pipeline.nodeList[mynode].name;
+        command = "relion_tomo_view tomograms --tilt-series-star-file " + pipeline.nodeList[mynode].name;
 
         // Read cache-size from gui_tomo_exclude_tilt_imagesjob.star if that file exists
         RelionJob excludetiltseriesjob;

src/tomography_python_programs/view/__init__.py

@@ -0,0 +1,6 @@
+"""Passive visualisation tools for browsing RELION cryo-ET data."""
+
+from .tilt_series import view_tilt_series
+from .tomograms import view_tomograms
+
+from ._cli import cli

src/tomography_python_programs/view/_cli.py

@@ -0,0 +1,4 @@
+import typer
+
+CLI_NAME = 'relion_tomo_view'
+cli = typer.Typer(name=CLI_NAME, add_completion=False, no_args_is_help=True)

src/tomography_python_programs/view/tilt_series.py

@@ -0,0 +1,33 @@
+from pathlib import Path
+
+import typer
+
+from .._qt.components.tilt_series_browser import TiltSeriesBrowserWidget
+from .._metadata_models.relion.tilt_series_set import RlnTiltSeriesSet
+from ..view._cli import cli
+
+COMMAND_NAME = 'tilt-series'
+
+
+@cli.command(name=COMMAND_NAME, no_args_is_help=True)
+def view_tilt_series(
+    tilt_series_star_file: Path = typer.Option(...),
+    cache_size: int = typer.Option(5, help='number of cached tilt-series')
+):
+    import napari  # local to speedup CLI
+    viewer = napari.Viewer(ndisplay=3)
+    relion_metadata = RlnTiltSeriesSet.from_star_file(tilt_series_star_file)
+    for tilt_series in relion_metadata.tilt_series:
+        tilt_series.data = tilt_series.data.sort_values(
+            by='rlnTomoNominalStageTiltAngle')
+    gui_model = relion_metadata.as_gui_model()
+    dock_widget = TiltSeriesBrowserWidget(viewer, gui_model, cache_size=cache_size)
+    viewer.window.add_dock_widget(
+        dock_widget, name='RELION tilt-series viewer', area='left'
+    )
+    viewer.text_overlay.text = """
+    keyboard shortcuts
+    - '[' and ']' for previous/next tilt-series
+    """
+    viewer.text_overlay.visible = True
+    napari.run()

src/tomography_python_programs/view/tomograms.py

@@ -0,0 +1,37 @@
+from pathlib import Path
+import typer
+
+from .._qt.components.tomogram_browser import TomogramBrowserWidget
+from .._metadata_models.relion.tilt_series_set import RlnTiltSeriesSet
+from ..view._cli import cli
+
+COMMAND_NAME = 'tomograms'
+
+
+@cli.command(name=COMMAND_NAME, no_args_is_help=True)
+def view_tomograms(
+    tilt_series_star_file: Path = typer.Option(...),
+    cache_size: int = typer.Option(3, help='number of cached tomograms')
+):
+    import napari  # local to speed up CLI
+    viewer = napari.Viewer(ndisplay=3)
+    relion_metadata = RlnTiltSeriesSet.from_star_file(tilt_series_star_file)
+    gui_model = relion_metadata.as_gui_model()
+    dock_widget = TomogramBrowserWidget(viewer, gui_model, cache_size=cache_size)
+    viewer.window.add_dock_widget(
+        dock_widget, name='RELION tomogram viewer', area='left'
+    )
+    viewer.axes.visible = True
+    viewer.axes.labels = False
+    viewer.camera.angles = (-15, 30, 150)
+    viewer.camera.zoom *= 0.7
+    viewer.text_overlay.text = """
+    keyboard shortcuts
+    - '[' and ']' for previous/next tomogram
+    - 'x'/'y'/'z'/'o' to reorient the plane (around the cursor)
+    
+    mouse controls
+    - 'Shift' + click + drag to move the plane along its normal
+    """
+    viewer.text_overlay.visible = True
+    napari.run()