PR3: napari widget button for plate overview

src/pyphenix/_widget.py

@@ -1,3 +1,5 @@
+import subprocess
+import sys
 import napari
 from napari.utils import notifications
 import numpy as np
@@ -13,6 +15,7 @@
 
 from ._reader import OperaPhenixReader
 from ._colormaps import channel_color
+from ._overview import generate_plate_overview
 
 def _normalise_well_str(well: str) -> str:
     """
@@ -786,6 +789,28 @@ def _build_ui(self):
         save_group.setContentLayout(save_layout)
         layout.addWidget(save_group)
 
+        # ── Plate overview ────────────────────────────────────────────
+        overview_group = CollapsibleSection("Plate Overview")
+        overview_layout = QVBoxLayout()
+
+        self.plate_overview_btn = QPushButton("Generate plate overview")
+        self.plate_overview_btn.setToolTip(
+            "Render a grid of every well as PNGs (one per channel combo) "
+            "into a directory of your choice.\n"
+            "Uses plate-wide contrast limits so wells are visually "
+            "comparable."
+        )
+        self.plate_overview_btn.clicked.connect(self._generate_plate_overview)
+        self.plate_overview_btn.setEnabled(False)
+        overview_layout.addWidget(self.plate_overview_btn)
+
+        self.plate_overview_status_label = QLabel("")
+        self.plate_overview_status_label.setWordWrap(True)
+        overview_layout.addWidget(self.plate_overview_status_label)
+
+        overview_group.setContentLayout(overview_layout)
+        layout.addWidget(overview_group)
+
         # Add stretch to push everything to the top
         layout.addStretch()
 
@@ -1074,6 +1099,7 @@ def _set_controls_enabled(self, enabled: bool):
         self.channel_clear_all_btn.setEnabled(enabled)
         self.z_select_all_btn.setEnabled(enabled)
         self.z_clear_all_btn.setEnabled(enabled)
+        self.plate_overview_btn.setEnabled(enabled)
 
         if enabled and self.reader and self.reader.ffc_profiles:
             self.ffc_checkbox.setEnabled(True)
@@ -1305,6 +1331,69 @@ def _save_data(self):
             import traceback
             traceback.print_exc()
 
+    # ------------------------------------------------------------------
+    # Plate overview
+    # ------------------------------------------------------------------
+
+    def _generate_plate_overview(self):
+        """Render plate-wide overview PNGs into a user-chosen directory."""
+        if self.reader is None:
+            notifications.show_warning("Please load an experiment first")
+            return
+
+        exp_path = self.path_input.text()
+
+        output_dir = QFileDialog.getExistingDirectory(
+            self,
+            "Select output directory for plate overview",
+            exp_path,
+        )
+        if not output_dir:
+            return
+
+        self.plate_overview_status_label.setText(
+            "Generating plate overview… (see terminal for progress)"
+        )
+        notifications.show_info(
+            "Generating plate overview — this may take a while."
+        )
+
+        try:
+            generate_plate_overview(exp_path, output_dir)
+        except Exception as e:
+            self.plate_overview_status_label.setText(
+                f"<b>Error:</b> {e}"
+            )
+            notifications.show_error(
+                f"Error generating plate overview: {str(e)}"
+            )
+            import traceback
+            traceback.print_exc()
+            return
+
+        self.plate_overview_status_label.setText(
+            f"<b>Done:</b> wrote PNGs to {output_dir}"
+        )
+        notifications.show_info(f"Plate overview written to {output_dir}")
+
+        self._open_in_file_viewer(output_dir)
+
+    def _open_in_file_viewer(self, path: str):
+        """Open ``path`` in the host OS's native file viewer."""
+        if sys.platform == "darwin":
+            cmd = ["open", path]
+        elif sys.platform == "win32":
+            cmd = ["explorer", path]
+        else:
+            cmd = ["xdg-open", path]
+
+        try:
+            subprocess.run(cmd, check=False)
+        except Exception as e:
+            notifications.show_warning(
+                f"Could not open {path} in file viewer: {e}"
+            )
+
     # ------------------------------------------------------------------
     # Build a human-readable label for the current selection
     # ------------------------------------------------------------------

tests/test_widget.py

@@ -319,19 +319,89 @@ def test_add_layers_creates_image_layers(widget_with_viewer):
 def test_set_controls_enabled(widget_with_viewer):
     """Test _set_controls_enabled method."""
     widget, _ = widget_with_viewer
-    
+
     # Enable all controls
     widget._set_controls_enabled(True)
-    
+
     assert widget.well_combo.isEnabled()
     assert widget.field_combo.isEnabled()
     assert widget.time_list.isEnabled()
     assert widget.channel_list.isEnabled()
-
+    assert widget.plate_overview_btn.isEnabled()
+
     # Disable all controls
     widget._set_controls_enabled(False)
-    
+
     assert not widget.well_combo.isEnabled()
     assert not widget.field_combo.isEnabled()
     assert not widget.time_list.isEnabled()
     assert not widget.channel_list.isEnabled()
+    assert not widget.plate_overview_btn.isEnabled()
+
+
+def test_plate_overview_button_disabled_initially(widget_with_viewer):
+    """Plate overview button starts disabled until an experiment is loaded."""
+    widget, _ = widget_with_viewer
+    assert not widget.plate_overview_btn.isEnabled()
+
+
+def test_plate_overview_warns_without_experiment(widget_with_viewer):
+    """Clicking with no reader loaded shows a warning, not a crash."""
+    widget, _ = widget_with_viewer
+    assert widget.reader is None
+
+    with patch('pyphenix._widget.notifications.show_warning') as mock_warn:
+        widget._generate_plate_overview()
+        mock_warn.assert_called_once()
+
+
+def test_plate_overview_button_wiring(widget_with_viewer, tmp_path,
+                                      monkeypatch):
+    """Mock QFileDialog and the OS-open call, verify wiring to
+    generate_plate_overview()."""
+    widget, _ = widget_with_viewer
+
+    # Pretend an experiment is loaded.
+    widget.reader = Mock()
+    widget.path_input.setText("/some/experiment")
+
+    chosen_dir = str(tmp_path)
+    dialog_mock = Mock(return_value=chosen_dir)
+    monkeypatch.setattr(
+        'pyphenix._widget.QFileDialog.getExistingDirectory', dialog_mock
+    )
+
+    with patch('pyphenix._widget.generate_plate_overview') as mock_gen, \
+         patch('pyphenix._widget.subprocess.run') as mock_run:
+        widget._generate_plate_overview()
+
+        # Dialog was opened defaulting to the experiment directory.
+        args, _kwargs = dialog_mock.call_args
+        assert "/some/experiment" in args
+
+        # generate_plate_overview called with (experiment_path, output_dir).
+        mock_gen.assert_called_once_with("/some/experiment", chosen_dir)
+
+        # OS file viewer was invoked with the chosen directory.
+        mock_run.assert_called_once()
+        cmd = mock_run.call_args[0][0]
+        assert chosen_dir in cmd
+
+
+def test_plate_overview_cancelled_dialog_does_nothing(widget_with_viewer,
+                                                     monkeypatch):
+    """If the user cancels the directory dialog, nothing is generated."""
+    widget, _ = widget_with_viewer
+    widget.reader = Mock()
+    widget.path_input.setText("/some/experiment")
+
+    monkeypatch.setattr(
+        'pyphenix._widget.QFileDialog.getExistingDirectory',
+        lambda *a, **kw: ""  # user cancelled
+    )
+
+    with patch('pyphenix._widget.generate_plate_overview') as mock_gen, \
+         patch('pyphenix._widget.subprocess.run') as mock_run:
+        widget._generate_plate_overview()
+        mock_gen.assert_not_called()
+        mock_run.assert_not_called()