napari/settings: replace single checkbox with per-output retention group + presets (Slice 3 of #245)

nellie_napari/nellie_settings.py

@@ -14,9 +14,17 @@
     QDoubleSpinBox,
     QComboBox,
     QScrollArea,
+    QButtonGroup,
+    QRadioButton,
 )
 
 from nellie.feature_extraction.hierarchical import HierarchyConfig
+from nellie.im_info.verifier import (
+    CSVS_ONLY_PRESET,
+    DROPPABLE_KEYS,
+    KEEP_EVERYTHING_PRESET,
+    MASKS_AND_CSVS_PRESET,
+)
 from nellie.segmentation.filtering import FrangiConfig
 from nellie.segmentation.labelling import LabelConfig
 from nellie.segmentation.mocap_marking import MarkersConfig
@@ -25,13 +33,197 @@
 from nellie.tracking.voxel_reassignment import VoxelReassignerConfig
 
 
+# Per-key presentation metadata for the IntermediateRetentionGroup widget.
+# Stage groupings, friendly labels, and tooltips. Order within each stage
+# controls UI display order. See [[wiki/decisions/0014-intermediates-policy-frozenset]].
+_RETENTION_STAGE_GROUPS: list[tuple[str, list[tuple[str, str, str]]]] = [
+    ('Filter', [
+        ('im_preprocessed', 'Frangi vesselness',
+         'Generated by: Filter (Frangi vesselness). Required to re-run Label.'),
+    ]),
+    ('Label', [
+        ('im_instance_label', 'Instance segmentation labels',
+         'Generated by: Label. Required by Network, Markers, Hu, Voxel reassignment, Hierarchy.'),
+    ]),
+    ('Network', [
+        ('im_skel', 'Skeleton',
+         'Generated by: Network. Required by Markers and Hierarchy.'),
+        ('im_skel_relabelled', 'Branch-relabelled skeleton',
+         'Generated by: Network. Required by Hierarchy.'),
+        ('im_pixel_class', 'Pixel classification',
+         'Generated by: Network. Required by Hierarchy.'),
+    ]),
+    ('Markers', [
+        ('im_marker', 'Motion-anchor markers',
+         'Generated by: Markers. Required by Hu tracking.'),
+        ('im_distance', 'Distance transform',
+         'Generated by: Markers. Required by Hierarchy.'),
+        ('im_border', 'Border map',
+         'Generated by: Markers (internal).'),
+    ]),
+    ('Tracking', [
+        ('flow_vector_array', 'Flow vectors',
+         'Generated by: Hu tracking. Required by Voxel reassignment and Hierarchy.'),
+        ('voxel_matches', 'Voxel matches',
+         'Generated by: Hu tracking. Required by Voxel reassignment.'),
+    ]),
+    ('Voxel reassignment', [
+        ('im_branch_label_reassigned', 'Tracked branch labels',
+         'Generated by: Voxel reassignment. Required by Hierarchy.'),
+        ('im_obj_label_reassigned', 'Tracked object labels',
+         'Generated by: Voxel reassignment. Required by Hierarchy.'),
+    ]),
+    ('Hierarchy', [
+        ('adjacency_maps', 'Node-edge adjacency maps',
+         'Generated by: Hierarchy (only when skip_nodes=False). '
+         'Read by the napari analyzer post-pipeline.'),
+    ]),
+    ('Pipeline input', [
+        ('im_path', 'Canonical OME-TIFF (regenerable from source)',
+         'Generated by: ImInfo on first load. Read by every pipeline stage. '
+         'Regenerable from the original microscopy file (expensive).'),
+    ]),
+]
+
+
+_PRESET_NAME_TO_DROP_SET: dict[str, frozenset[str]] = {
+    'Keep everything': KEEP_EVERYTHING_PRESET,
+    'Masks + CSVs only': MASKS_AND_CSVS_PRESET,
+    'CSVs only': CSVS_ONLY_PRESET,
+}
+_PRESET_DROP_SET_TO_NAME: dict[frozenset[str], str] = {
+    v: k for k, v in _PRESET_NAME_TO_DROP_SET.items()
+}
+_CUSTOM_PRESET_NAME = 'Custom'
+
+
+class IntermediateRetentionGroup(QGroupBox):
+    """Per-output intermediate retention controls.
+
+    Composition: a preset radio row at top + stage-grouped checkboxes
+    (one per key in :data:`DROPPABLE_KEYS`). Checkbox semantics:
+    **checked = drop**, unchecked = keep. Selecting a named preset
+    (Keep everything / Masks + CSVs only / CSVs only) sets the
+    checkboxes; toggling any checkbox flips the preset radio to
+    "Custom" automatically.
+
+    The "Custom" radio is set programmatically and is not user-clickable;
+    it is purely informational ("your selection diverges from any named
+    preset").
+
+    Read the current drop set via :meth:`drop_keys`; set it via
+    :meth:`set_drop_keys`.
+    """
+
+    def __init__(self, parent: Optional[QWidget] = None) -> None:
+        super().__init__("Intermediate file retention", parent)
+
+        self._key_checkboxes: dict[str, QCheckBox] = {}
+        self._preset_buttons: dict[str, QRadioButton] = {}
+        self._suppress_signals = False
+
+        outer = QVBoxLayout()
+
+        # Preset radio row.
+        preset_row = QHBoxLayout()
+        preset_row.addWidget(QLabel("Preset:"))
+        self._preset_button_group = QButtonGroup(self)
+        for name in (*_PRESET_NAME_TO_DROP_SET.keys(), _CUSTOM_PRESET_NAME):
+            btn = QRadioButton(name)
+            self._preset_button_group.addButton(btn)
+            self._preset_buttons[name] = btn
+            preset_row.addWidget(btn)
+        # Default selection.
+        self._preset_buttons['Keep everything'].setChecked(True)
+        # "Custom" is informational; user selects it indirectly via toggling
+        # any individual checkbox. Disable direct clicks but keep it visible.
+        self._preset_buttons[_CUSTOM_PRESET_NAME].setEnabled(False)
+        # Wire user-clickable presets to apply the matching drop set.
+        for name in _PRESET_NAME_TO_DROP_SET:
+            self._preset_buttons[name].toggled.connect(
+                lambda checked, n=name: self._on_preset_clicked(n, checked)
+            )
+        outer.addLayout(preset_row)
+
+        # Per-stage checkbox subgroups.
+        for stage_name, entries in _RETENTION_STAGE_GROUPS:
+            stage_box = QGroupBox(stage_name)
+            stage_layout = QVBoxLayout()
+            for key, friendly, tooltip in entries:
+                cb = QCheckBox(f"{friendly} (`{key}`)")
+                cb.setToolTip(tooltip)
+                cb.toggled.connect(self._on_checkbox_toggled)
+                self._key_checkboxes[key] = cb
+                stage_layout.addWidget(cb)
+            stage_box.setLayout(stage_layout)
+            outer.addWidget(stage_box)
+
+        self.setLayout(outer)
+
+    # ------------------------------------------------------------------
+    # Public API
+    # ------------------------------------------------------------------
+
+    def drop_keys(self) -> frozenset[str]:
+        """Return the current drop set (keys whose checkbox is checked)."""
+        return frozenset(
+            key for key, cb in self._key_checkboxes.items() if cb.isChecked()
+        )
+
+    def set_drop_keys(self, drop_keys: frozenset[str]) -> None:
+        """Apply a drop set to the checkboxes; sync the preset radio.
+
+        Validates that ``drop_keys`` is a subset of ``DROPPABLE_KEYS``.
+        Selects the matching named preset radio (or "Custom" if no
+        named preset matches).
+        """
+        unknown = set(drop_keys) - DROPPABLE_KEYS
+        assert not unknown, f"set_drop_keys: unknown keys {sorted(unknown)}"
+        self._suppress_signals = True
+        try:
+            for key, cb in self._key_checkboxes.items():
+                cb.setChecked(key in drop_keys)
+            self._sync_preset_radio_to_drop_set(drop_keys)
+        finally:
+            self._suppress_signals = False
+
+    # ------------------------------------------------------------------
+    # Internals
+    # ------------------------------------------------------------------
+
+    def _on_preset_clicked(self, name: str, checked: bool) -> None:
+        if not checked or self._suppress_signals:
+            return
+        target = _PRESET_NAME_TO_DROP_SET[name]
+        self._suppress_signals = True
+        try:
+            for key, cb in self._key_checkboxes.items():
+                cb.setChecked(key in target)
+        finally:
+            self._suppress_signals = False
+
+    def _on_checkbox_toggled(self, _checked: bool) -> None:
+        if self._suppress_signals:
+            return
+        self._sync_preset_radio_to_drop_set(self.drop_keys())
+
+    def _sync_preset_radio_to_drop_set(self, drop_keys: frozenset[str]) -> None:
+        name = _PRESET_DROP_SET_TO_NAME.get(drop_keys, _CUSTOM_PRESET_NAME)
+        # Temporarily allow Custom to be programmatically selected.
+        was_enabled = self._preset_buttons[_CUSTOM_PRESET_NAME].isEnabled()
+        self._preset_buttons[_CUSTOM_PRESET_NAME].setEnabled(True)
+        # exclusive=True (default) ensures only one is checked.
+        self._preset_buttons[name].setChecked(True)
+        self._preset_buttons[_CUSTOM_PRESET_NAME].setEnabled(was_enabled)
+
+
 @dataclass
 class SettingsConfig:
     """
     Structured representation of the Settings UI state.
     """
     remove_edges: bool
-    remove_intermediates: bool
+    cleanup_drop_keys: frozenset[str]
     voxel_reassign: bool
     analyze_node_level: bool
     track_all_frames: bool
@@ -140,13 +332,7 @@ def __init__(self, napari_viewer: "napari.viewer.Viewer", nellie, parent=None):
             "weird image edge artifacts."
         )
 
-        self.remove_intermediates_checkbox = QCheckBox("Remove intermediate files")
-        self.remove_intermediates_checkbox.setChecked(False)
-        self.remove_intermediates_checkbox.setEnabled(True)
-        self.remove_intermediates_checkbox.setToolTip(
-            "Remove intermediate files after processing. This means only CSV files "
-            "will be saved and intermediate data cannot be recovered."
-        )
+        self.intermediate_retention_group = IntermediateRetentionGroup()
 
         self.voxel_reassign = QCheckBox("Auto-run voxel reassignment")
         self.voxel_reassign.setChecked(True)
@@ -435,15 +621,16 @@ def set_ui(self):
         processor_layout = QVBoxLayout()
 
         subprocessor_layout1 = QHBoxLayout()
-        subprocessor_layout1.addWidget(self.remove_intermediates_checkbox)
         subprocessor_layout1.addWidget(self.remove_edges_checkbox)
+        subprocessor_layout1.addStretch(1)
 
         subprocessor_layout2 = QHBoxLayout()
         subprocessor_layout2.addWidget(self.analyze_node_level)
         subprocessor_layout2.addWidget(self.voxel_reassign)
 
         processor_layout.addLayout(subprocessor_layout1)
         processor_layout.addLayout(subprocessor_layout2)
+        processor_layout.addWidget(self.intermediate_retention_group)
         processor_group.setLayout(processor_layout)
 
         # Tracking settings group
@@ -642,7 +829,7 @@ def to_config(self) -> SettingsConfig:
         """
         return SettingsConfig(
             remove_edges=self.remove_edges_checkbox.isChecked(),
-            remove_intermediates=self.remove_intermediates_checkbox.isChecked(),
+            cleanup_drop_keys=self.intermediate_retention_group.drop_keys(),
             voxel_reassign=self.voxel_reassign.isChecked(),
             analyze_node_level=self.analyze_node_level.isChecked(),
             track_all_frames=self.track_all_frames.isChecked(),
@@ -743,7 +930,7 @@ def apply_config(self, config: SettingsConfig):
             Configuration to apply to the UI.
         """
         self.remove_edges_checkbox.setChecked(config.remove_edges)
-        self.remove_intermediates_checkbox.setChecked(config.remove_intermediates)
+        self.intermediate_retention_group.set_drop_keys(config.cleanup_drop_keys)
         self.voxel_reassign.setChecked(config.voxel_reassign)
         self.analyze_node_level.setChecked(config.analyze_node_level)
         self.track_all_frames.setChecked(config.track_all_frames)