itasc 0.2.0.dev0__py3-none-any.whl

itasc/napari/nucleus_tracking_inputs_widget.py

@@ -0,0 +1,248 @@
+"""Ultrack tracking and database-generation parameter section for the nucleus workflow widget."""
+from __future__ import annotations
+
+import os
+
+from qtpy.QtWidgets import (
+    QComboBox,
+    QLabel,
+    QWidget,
+)
+
+from itasc.napari._widget_helpers import (
+    dslider as _dslider,
+    heading as _heading,
+    islider as _islider,
+)
+from itasc.napari.ui_style import (
+    add_section_header,
+    add_section_pair_row,
+    section_grid,
+)
+from itasc.napari.widgets import CollapsibleSection
+from itasc.tracking_ultrack.config import TrackingConfig as _UltrackConfig
+
+
+class NucleusTrackingInputsWidget(QWidget):
+    """Qt controls for Ultrack tracking and database-generation parameters."""
+
+    def __init__(self, parent: QWidget | None = None) -> None:
+        super().__init__(parent)
+
+        db_inner = QWidget(self)
+        db_grid = section_grid()
+        db_grid.setContentsMargins(0, 0, 0, 0)
+        db_inner.setLayout(db_grid)
+
+        solve_inner = QWidget(self)
+        solve_grid = section_grid()
+        solve_grid.setContentsMargins(0, 0, 0, 0)
+        solve_inner.setLayout(solve_grid)
+
+        # ─── DB Generation — Atom-Union Candidates ──────────────────
+        self.db_gen_min_area_spin = _islider(
+            0, 1_000_000, 100, tooltip="Minimum single-atom candidate area in pixels.")
+        self.atom_union_max_area_spin = _islider(
+            0, 100_000, 8000, tooltip="Maximum total pixel area of a candidate union.")
+        self.atom_overlap_budget_spin = _islider(
+            0, 5_000_000, 300_000, step=10_000,
+            tooltip="Per-frame overlap-pair budget — the single branching knob. "
+                    "0 = nested hierarchy, larger = richer non-nested alternatives.")
+
+        # ─── Retained for backward compat (not surfaced in UI) ──────
+        self.db_gen_min_frontier_spin = _dslider(0, 1, 0.0, 0.01, 2, "")
+        self.db_gen_ws_hierarchy_combo = QComboBox()
+        self.db_gen_ws_hierarchy_combo.addItems(["area", "dynamics", "volume"])
+        self.db_gen_n_workers_spin = _islider(1, max(1, os.cpu_count() or 1), 1, tooltip="")
+        self.db_gen_max_area_spin = _islider(0, 10_000_000, 100_000, tooltip="")
+
+        # ─── DB Generation — Linking ────────────────────────────────
+        self.db_gen_max_dist_spin = _dslider(0, 500, 15.0, 1.0, 1)
+        self.db_gen_max_neighbors_spin = _islider(1, 50, 5)
+        self.db_gen_linking_mode_combo = QComboBox()
+        self.db_gen_linking_mode_combo.addItems(["default", "shape"])
+        self.db_gen_area_weight_spin = _dslider(0, 10, 1.0, 0.1, 2)
+        self.db_gen_area_weight_spin.setEnabled(False)
+        self.db_gen_iou_weight_spin = _dslider(0, 10, 1.0, 0.1, 2)
+        self.db_gen_iou_weight_spin.setEnabled(False)
+        self.db_gen_distance_weight_spin = _dslider(0, 10, 0.05, 0.01, 2)
+        self.db_gen_distance_weight_spin.setEnabled(False)
+
+        # ─── DB Generation — Node Scoring ───────────────────────────
+        self.db_gen_quality_weight_spin = _dslider(
+            0, 10, 1.0, 0.05, 2,
+            "Weight applied to signal-based segmentation quality.",
+        )
+        self.db_gen_quality_exp_spin = _dslider(
+            0.1, 50, 8.0, 0.5, 2,
+            "Raises the combined quality and circularity score before storing as node_prob.",
+        )
+        self.db_gen_circularity_weight_spin = _dslider(
+            0, 10, 0.25, 0.05, 2,
+            "Weight applied to shape circularity.",
+        )
+
+        # ─── Ultrack — Track Scope ──────────────────────────────────
+        self.ultrack_max_partitions_spin = _islider(
+            0, 1000, 30, tooltip="0 = use all partitions.")
+        self.ultrack_n_frames_spin = _islider(
+            0, 10000, 0, tooltip="0 = process all frames.")
+
+        # ─── Ultrack — Event Penalties ──────────────────────────────
+        self.ultrack_appear_spin = _dslider(
+            -10, 0, -0.1, 0.05, 2,
+            "ILP penalty for cells appearing. More negative = fewer appearances.",
+        )
+        self.ultrack_disappear_spin = _dslider(
+            -10, 0, -0.1, 0.05, 2,
+            "ILP penalty for cells disappearing. More negative = fewer disappearances.",
+        )
+        self.ultrack_division_spin = _dslider(
+            -10, 0, -0.01, 0.05, 2,
+            "ILP penalty for divisions. More negative = fewer divisions.",
+        )
+
+        # ─── Ultrack — Solver ───────────────────────────────────────
+        self.ultrack_power_spin = _islider(
+            1, 20, 4,
+            tooltip="Solver transform for node_prob and link weights (link_function=power).",
+        )
+        self.ultrack_bias_spin = _dslider(
+            -10, 10, 0.0, 0.05, 2,
+            "Constant offset applied by Ultrack tracking_config.bias.",
+        )
+        self.ultrack_solver_lbl = QLabel("—")
+
+        # ─── Pack DB Generation controls ────────────────────────────
+        row = 0
+
+        add_section_header(db_grid, row, _heading("Candidates")); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Min area:", self.db_gen_min_area_spin,
+            "Max union area:", self.atom_union_max_area_spin,
+        ); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Overlap budget:", self.atom_overlap_budget_spin,
+        ); row += 1
+
+        add_section_header(db_grid, row, _heading("Linking")); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Max distance:", self.db_gen_max_dist_spin,
+            "Max neighbors:", self.db_gen_max_neighbors_spin,
+        ); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Linking mode:", self.db_gen_linking_mode_combo,
+            "Area weight:", self.db_gen_area_weight_spin,
+        ); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "IoU weight:", self.db_gen_iou_weight_spin,
+            "Distance weight:", self.db_gen_distance_weight_spin,
+        ); row += 1
+
+        add_section_header(db_grid, row, _heading("Node Scoring")); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Quality weight:", self.db_gen_quality_weight_spin,
+            "Circularity weight:", self.db_gen_circularity_weight_spin,
+        ); row += 1
+        add_section_pair_row(
+            db_grid, row,
+            "Scoring exponent:", self.db_gen_quality_exp_spin,
+        ); row += 1
+
+        # ─── Pack Ultrack solver controls ───────────────────────────
+        row = 0
+
+        add_section_header(solve_grid, row, _heading("Track Scope")); row += 1
+        add_section_pair_row(
+            solve_grid, row,
+            "Max partitions:", self.ultrack_max_partitions_spin,
+            "N frames:", self.ultrack_n_frames_spin,
+        ); row += 1
+
+        add_section_header(solve_grid, row, _heading("Event Penalties")); row += 1
+        add_section_pair_row(
+            solve_grid, row,
+            "Appear:", self.ultrack_appear_spin,
+            "Disappear:", self.ultrack_disappear_spin,
+        ); row += 1
+        add_section_pair_row(solve_grid, row, "Division:", self.ultrack_division_spin); row += 1
+
+        add_section_header(solve_grid, row, _heading("Solver")); row += 1
+        add_section_pair_row(
+            solve_grid, row,
+            "Power:", self.ultrack_power_spin,
+            "Bias:", self.ultrack_bias_spin,
+        ); row += 1
+        add_section_pair_row(solve_grid, row, "Solver:", self.ultrack_solver_lbl); row += 1
+
+        self.db_section = CollapsibleSection(
+            "Database Generation Parameters",
+            db_inner,
+            expanded=False,
+        )
+        self.solve_section = CollapsibleSection(
+            "Ultrack Solver Parameters",
+            solve_inner,
+            expanded=False,
+        )
+
+        self.db_gen_linking_mode_combo.currentTextChanged.connect(
+            self._on_db_gen_mode_changed
+        )
+
+    def _on_db_gen_mode_changed(self, mode: str) -> None:
+        enabled = mode == "shape"
+        self.db_gen_area_weight_spin.setEnabled(enabled)
+        self.db_gen_iou_weight_spin.setEnabled(enabled)
+        self.db_gen_distance_weight_spin.setEnabled(enabled)
+
+    def db_gen_config(self) -> _UltrackConfig:
+        """Build a TrackingConfig from the current DB-generation controls."""
+        return _UltrackConfig(
+            min_area=self.db_gen_min_area_spin.value(),
+            seg_min_area=self.db_gen_min_area_spin.value(),
+            seg_foreground_threshold=0.0,
+            atom_union_max_area=self.atom_union_max_area_spin.value(),
+            atom_overlap_budget=self.atom_overlap_budget_spin.value(),
+            max_distance=self.db_gen_max_dist_spin.value(),
+            max_neighbors=self.db_gen_max_neighbors_spin.value(),
+            linking_mode=self.db_gen_linking_mode_combo.currentText(),
+            area_weight=self.db_gen_area_weight_spin.value(),
+            iou_weight=self.db_gen_iou_weight_spin.value(),
+            distance_weight=self.db_gen_distance_weight_spin.value(),
+            quality_weight=self.db_gen_quality_weight_spin.value(),
+            quality_exponent=self.db_gen_quality_exp_spin.value(),
+            circularity_weight=self.db_gen_circularity_weight_spin.value(),
+            link_n_workers=self.db_gen_n_workers_spin.value(),
+        )
+
+    def ultrack_config(self) -> _UltrackConfig:
+        """Build a TrackingConfig from all tracking controls (DB-gen + Ultrack solver)."""
+        return _UltrackConfig(
+            seg_min_area=self.db_gen_min_area_spin.value(),
+            seg_max_area=self.db_gen_max_area_spin.value(),
+            seg_foreground_threshold=0.0,
+            seg_min_frontier=self.db_gen_min_frontier_spin.value(),
+            seg_ws_hierarchy=self.db_gen_ws_hierarchy_combo.currentText(),
+            seg_n_workers=self.db_gen_n_workers_spin.value(),
+            max_distance=self.db_gen_max_dist_spin.value(),
+            max_neighbors=self.db_gen_max_neighbors_spin.value(),
+            linking_mode=self.db_gen_linking_mode_combo.currentText(),
+            area_weight=self.db_gen_area_weight_spin.value(),
+            iou_weight=self.db_gen_iou_weight_spin.value(),
+            distance_weight=self.db_gen_distance_weight_spin.value(),
+            quality_weight=self.db_gen_quality_weight_spin.value(),
+            quality_exponent=self.db_gen_quality_exp_spin.value(),
+            circularity_weight=self.db_gen_circularity_weight_spin.value(),
+            power=self.ultrack_power_spin.value(),
+            bias=self.ultrack_bias_spin.value(),
+            appear_weight=self.ultrack_appear_spin.value(),
+            disappear_weight=self.ultrack_disappear_spin.value(),
+            division_weight=self.ultrack_division_spin.value(),
+        )