canns 0.14.2__py3-none-any.whl → 0.15.0__py3-none-any.whl

canns/analyzer/visualization/theta_sweep_plots.py

@@ -760,6 +760,148 @@ def plot_grid_cell_manifold(
         raise e
 
 
+def plot_internal_position_trajectory(
+    internal_position: np.ndarray,
+    position: np.ndarray,
+    max_activity: np.ndarray | None = None,
+    env_size: float | tuple[float, float] | tuple[float, float, float, float] | None = None,
+    config: PlotConfig | None = None,
+    ax: plt.Axes | None = None,
+    # Backward compatibility parameters
+    title: str = "Internal Position (GC bump) vs. Real Trajectory",
+    figsize: tuple[int, int] = (6, 4),
+    cmap: str = "cool",
+    show: bool = True,
+    save_path: str | None = None,
+    **kwargs,
+) -> tuple[plt.Figure, plt.Axes]:
+    """Plot internal position (GC bump) against the real trajectory.
+
+    Args:
+        internal_position: Internal decoded positions ``(T, 2)``.
+        position: Real positions ``(T, 2)``.
+        max_activity: Optional per-time max activity to color the internal position.
+        env_size: Environment size. If float, uses ``[0, env_size]`` for both axes.
+            If a tuple of 2, treats as ``(width, height)``. If a tuple of 4, treats as
+            ``(xmin, xmax, ymin, ymax)``.
+        config: PlotConfig object for unified configuration.
+        ax: Optional axis to draw on instead of creating a new figure.
+        **kwargs: Additional parameters for backward compatibility.
+
+    Returns:
+        tuple: ``(figure, axis)`` objects.
+    """
+    if internal_position.ndim != 2 or internal_position.shape[1] != 2:
+        raise ValueError(
+            f"internal_position must be (T, 2), got shape {internal_position.shape}"
+        )
+    if position.ndim != 2 or position.shape[1] != 2:
+        raise ValueError(f"position must be (T, 2), got shape {position.shape}")
+    if internal_position.shape[0] != position.shape[0]:
+        raise ValueError(
+            "internal_position and position must have the same length: "
+            f"{internal_position.shape[0]} != {position.shape[0]}"
+        )
+    if max_activity is not None and max_activity.shape[0] != internal_position.shape[0]:
+        raise ValueError(
+            "max_activity must have same length as internal_position: "
+            f"{max_activity.shape[0]} != {internal_position.shape[0]}"
+        )
+
+    if config is None:
+        config = PlotConfig(
+            title=title,
+            figsize=figsize,
+            show=show,
+            save_path=save_path,
+            kwargs={"cmap": cmap, **kwargs},
+        )
+
+    plot_kwargs = config.to_matplotlib_kwargs()
+    trajectory_color = plot_kwargs.pop("trajectory_color", "black")
+    trajectory_linewidth = plot_kwargs.pop("trajectory_linewidth", 1.0)
+    scatter_size = plot_kwargs.pop("scatter_size", 4)
+    scatter_alpha = plot_kwargs.pop("scatter_alpha", 0.9)
+    add_colorbar = bool(plot_kwargs.pop("add_colorbar", True))
+    colorbar_options = plot_kwargs.pop("colorbar", {}) if add_colorbar else {}
+    if "cmap" not in plot_kwargs:
+        plot_kwargs["cmap"] = "cool"
+
+    if max_activity is None:
+        add_colorbar = False
+
+    axis_provided = ax is not None
+    if not axis_provided:
+        fig, ax = plt.subplots(figsize=config.figsize)
+    else:
+        fig = ax.figure
+
+    try:
+        scatter = ax.scatter(
+            internal_position[:, 0],
+            internal_position[:, 1],
+            c=max_activity,
+            s=scatter_size,
+            alpha=scatter_alpha,
+            **plot_kwargs,
+        )
+        ax.plot(position[:, 0], position[:, 1], color=trajectory_color, lw=trajectory_linewidth)
+
+        ax.set_aspect("equal", adjustable="box")
+        if config.title:
+            ax.set_title(config.title, fontsize=14, fontweight="bold")
+
+        if env_size is not None:
+            if isinstance(env_size, (tuple, list, np.ndarray)):
+                if len(env_size) == 2:
+                    ax.set_xlim(0, env_size[0])
+                    ax.set_ylim(0, env_size[1])
+                elif len(env_size) == 4:
+                    ax.set_xlim(env_size[0], env_size[1])
+                    ax.set_ylim(env_size[2], env_size[3])
+                else:
+                    raise ValueError("env_size tuple must be length 2 or 4.")
+            else:
+                ax.set_xlim(0, env_size)
+                ax.set_ylim(0, env_size)
+
+        sns.despine(ax=ax)
+
+        if add_colorbar:
+            default_cbar_opts = {"pad": 0.15, "size": "5%", "label": "Max GC activity"}
+            if isinstance(colorbar_options, dict):
+                extra_cbar_kwargs = colorbar_options.get("kwargs", {})
+                for key in ("pad", "size", "label"):
+                    if key in colorbar_options:
+                        default_cbar_opts[key] = colorbar_options[key]
+            else:
+                extra_cbar_kwargs = {}
+
+            divider = make_axes_locatable(ax)
+            cax = divider.append_axes(
+                "right", size=default_cbar_opts["size"], pad=default_cbar_opts["pad"]
+            )
+            cbar = fig.colorbar(scatter, cax=cax, **extra_cbar_kwargs)
+            if default_cbar_opts["label"]:
+                cbar.set_label(default_cbar_opts["label"], fontsize=12)
+
+        if not axis_provided:
+            fig.tight_layout()
+
+        show_flag = config.show and not axis_provided
+        finalize_figure(
+            fig,
+            replace(config, show=show_flag),
+            rasterize_artists=[scatter] if config.rasterized else None,
+            always_close=not show_flag,
+        )
+        return fig, ax
+
+    except Exception as e:
+        plt.close(fig)
+        raise e
+
+
 @dataclass(slots=True)
 class _PlaceCellAnimationData:
     """Immutable container for place cell animation arrays."""

canns/pipeline/asa/runner.py

@@ -628,7 +628,7 @@ class PipelineRunner:
         self, asa_data: dict[str, Any], state: WorkflowState, log_callback
     ) -> dict[str, Path]:
         """Run CohoMap analysis (TDA + decode + plotting)."""
-        from canns.analyzer.data.asa import plot_cohomap_multi
+        from canns.analyzer.data.asa import plot_cohomap_scatter_multi
         from canns.analyzer.visualization import PlotConfigs
 
         tda_dir = self._results_dir(state) / "TDA"
@@ -661,7 +661,7 @@ class PipelineRunner:
         log_callback("Generating cohomology map...")
         pos = self._aligned_pos if self._aligned_pos is not None else asa_data
         config = PlotConfigs.cohomap(show=False, save_path=str(cohomap_path))
-        plot_cohomap_multi(
+        plot_cohomap_scatter_multi(
             decoding_result=decode_result,
             position_data={"x": pos["x"], "y": pos["y"]},
             config=config,
@@ -838,16 +838,16 @@ class PipelineRunner:
     ) -> dict[str, Path]:
         """Run cohomology space visualization."""
         from canns.analyzer.data.asa import (
-            plot_cohospace_neuron_1d,
-            plot_cohospace_neuron_2d,
-            plot_cohospace_population_1d,
-            plot_cohospace_population_2d,
-            plot_cohospace_trajectory_1d,
-            plot_cohospace_trajectory_2d,
+            plot_cohospace_scatter_neuron_1d,
+            plot_cohospace_scatter_neuron_2d,
+            plot_cohospace_scatter_population_1d,
+            plot_cohospace_scatter_population_2d,
+            plot_cohospace_scatter_trajectory_1d,
+            plot_cohospace_scatter_trajectory_2d,
         )
-        from canns.analyzer.data.asa.cohospace import (
-            plot_cohospace_neuron_skewed,
-            plot_cohospace_population_skewed,
+        from canns.analyzer.data.asa.cohospace_scatter import (
+            plot_cohospace_scatter_neuron_skewed,
+            plot_cohospace_scatter_population_skewed,
         )
         from canns.analyzer.visualization import PlotConfigs
 
@@ -937,7 +937,7 @@ class PipelineRunner:
         traj_path = out_dir / "cohospace_trajectory.png"
         if dim_mode == "1d":
             traj_cfg = PlotConfigs.cohospace_trajectory_1d(show=False, save_path=str(traj_path))
-            plot_cohospace_trajectory_1d(
+            plot_cohospace_scatter_trajectory_1d(
                 coords=coords2,
                 times=None,
                 subsample=subsample,
@@ -945,7 +945,7 @@ class PipelineRunner:
             )
         else:
             traj_cfg = PlotConfigs.cohospace_trajectory_2d(show=False, save_path=str(traj_path))
-            plot_cohospace_trajectory_2d(
+            plot_cohospace_scatter_trajectory_2d(
                 coords=coords2,
                 times=None,
                 subsample=subsample,
@@ -958,7 +958,7 @@ class PipelineRunner:
             log_callback(f"Plotting neuron {neuron_id}...")
             neuron_path = out_dir / f"cohospace_neuron_{neuron_id}.png"
             if unfold == "skew" and dim_mode != "1d":
-                plot_cohospace_neuron_skewed(
+                plot_cohospace_scatter_neuron_skewed(
                     coords=coordsbox2,
                     activity=activity,
                     neuron_id=int(neuron_id),
@@ -974,7 +974,7 @@ class PipelineRunner:
                     neuron_cfg = PlotConfigs.cohospace_neuron_1d(
                         show=False, save_path=str(neuron_path)
                     )
-                    plot_cohospace_neuron_1d(
+                    plot_cohospace_scatter_neuron_1d(
                         coords=coordsbox2,
                         activity=activity,
                         neuron_id=int(neuron_id),
@@ -986,7 +986,7 @@ class PipelineRunner:
                     neuron_cfg = PlotConfigs.cohospace_neuron_2d(
                         show=False, save_path=str(neuron_path)
                     )
-                    plot_cohospace_neuron_2d(
+                    plot_cohospace_scatter_neuron_2d(
                         coords=coordsbox2,
                         activity=activity,
                         neuron_id=int(neuron_id),
@@ -1001,7 +1001,7 @@ class PipelineRunner:
             pop_path = out_dir / "cohospace_population.png"
             neuron_ids = list(range(activity.shape[1]))
             if unfold == "skew" and dim_mode != "1d":
-                plot_cohospace_population_skewed(
+                plot_cohospace_scatter_population_skewed(
                     coords=coords2,
                     activity=activity,
                     neuron_ids=neuron_ids,
@@ -1017,7 +1017,7 @@ class PipelineRunner:
                     pop_cfg = PlotConfigs.cohospace_population_1d(
                         show=False, save_path=str(pop_path)
                     )
-                    plot_cohospace_population_1d(
+                    plot_cohospace_scatter_population_1d(
                         coords=coords2,
                         activity=activity,
                         neuron_ids=neuron_ids,
@@ -1029,7 +1029,7 @@ class PipelineRunner:
                     pop_cfg = PlotConfigs.cohospace_population_2d(
                         show=False, save_path=str(pop_path)
                     )
-                    plot_cohospace_population_2d(
+                    plot_cohospace_scatter_population_2d(
                         coords=coords2,
                         activity=activity,
                         neuron_ids=neuron_ids,

canns/pipeline/asa_gui/__init__.py

@@ -2,9 +2,9 @@
 
 from __future__ import annotations
 
-import sys
-import os
 import importlib.util
+import os
+import sys
 
 __all__ = ["main", "ASAGuiApp"]
 
@@ -14,7 +14,9 @@ if _pyside6_missing:
         try:  # pragma: no cover - only used in CI/test runs
             import pytest
 
-            pytest.skip("PySide6 is not installed; skipping asa_gui module.", allow_module_level=True)
+            pytest.skip(
+                "PySide6 is not installed; skipping asa_gui module.", allow_module_level=True
+            )
         except Exception:
             pass
 

canns/pipeline/asa_gui/analysis_modes/pathcompare_mode.py

@@ -10,6 +10,7 @@ from PySide6.QtWidgets import (
     QHBoxLayout,
     QLabel,
     QLineEdit,
+    QPushButton,
     QSpinBox,
     QWidget,
 )
@@ -49,7 +50,7 @@ class PathCompareMode(AbstractAnalysisMode):
         self.dim2.setValue(2)
 
         self.use_box = QCheckBox("Use coordsbox / times_box")
-        self.use_box.setChecked(False)
+        self.use_box.setChecked(True)
 
         self.interp_full = QCheckBox("Interpolate to full trajectory")
         self.interp_full.setChecked(True)
@@ -57,8 +58,13 @@ class PathCompareMode(AbstractAnalysisMode):
 
         self.coords_key = QLineEdit()
         self.coords_key.setPlaceholderText("coords / coordsbox (optional)")
+        self.btn_coordsbox = QPushButton("coordsbox")
+        self.btn_coordsbox.clicked.connect(lambda: self.coords_key.setText("coordsbox"))
+
         self.times_key = QLineEdit()
         self.times_key.setPlaceholderText("times_box (optional)")
+        self.btn_times_box = QPushButton("times_box")
+        self.btn_times_box.clicked.connect(lambda: self.times_key.setText("times_box"))
 
         self.slice_mode = PopupComboBox()
         self.slice_mode.addItem("Time (tmin/tmax)", userData="time")
@@ -125,8 +131,20 @@ class PathCompareMode(AbstractAnalysisMode):
         form.addRow(self._dims2d_label, dims_2d)
         form.addRow(self.use_box)
         form.addRow(self.interp_full)
-        form.addRow("coords key", self.coords_key)
-        form.addRow("times key", self.times_key)
+        coords_row = QWidget()
+        coords_layout = QHBoxLayout(coords_row)
+        coords_layout.setContentsMargins(0, 0, 0, 0)
+        coords_layout.addWidget(self.coords_key, 1)
+        coords_layout.addWidget(self.btn_coordsbox)
+
+        times_row = QWidget()
+        times_layout = QHBoxLayout(times_row)
+        times_layout.setContentsMargins(0, 0, 0, 0)
+        times_layout.addWidget(self.times_key, 1)
+        times_layout.addWidget(self.btn_times_box)
+
+        form.addRow("coords key", coords_row)
+        form.addRow("times key", times_row)
         form.addRow("Slice mode", self.slice_mode)
         form.addRow("tmin (sec, -1=auto)", self.tmin)
         form.addRow("tmax (sec, -1=auto)", self.tmax)
@@ -150,6 +168,10 @@ class PathCompareMode(AbstractAnalysisMode):
         def _refresh_enabled() -> None:
             use_box = bool(self.use_box.isChecked())
             self.interp_full.setEnabled(use_box)
+            self.coords_key.setEnabled(use_box)
+            self.times_key.setEnabled(use_box)
+            self.btn_coordsbox.setEnabled(use_box)
+            self.btn_times_box.setEnabled(use_box)
 
         def _refresh_slice_mode() -> None:
             is_time = self.slice_mode.currentData() == "time"
@@ -210,6 +232,8 @@ class PathCompareMode(AbstractAnalysisMode):
             self.interp_full.setToolTip("插值回完整轨迹。")
             self.coords_key.setToolTip("可选：解码坐标键（默认 coords/coordsbox）。")
             self.times_key.setToolTip("可选：times_box 键名。")
+            self.btn_coordsbox.setToolTip("填入 coordsbox。")
+            self.btn_times_box.setToolTip("填入 times_box。")
             self.slice_mode.setToolTip("按时间或索引裁剪。")
             self.tmin.setToolTip("起始时间（秒），-1 自动。")
             self.tmax.setToolTip("结束时间（秒），-1 自动。")
@@ -226,10 +250,14 @@ class PathCompareMode(AbstractAnalysisMode):
             self.dim.setToolTip("1D decoded dimension index.")
             self.dim1.setToolTip("2D decoded dimension 1.")
             self.dim2.setToolTip("2D decoded dimension 2.")
-            self.use_box.setToolTip("Use coordsbox/times_box alignment (recommended with speed_filter).")
+            self.use_box.setToolTip(
+                "Use coordsbox/times_box alignment (recommended with speed_filter)."
+            )
             self.interp_full.setToolTip("Interpolate back to full trajectory.")
             self.coords_key.setToolTip("Optional decode coords key (default coords/coordsbox).")
             self.times_key.setToolTip("Optional times_box key.")
+            self.btn_coordsbox.setToolTip("Fill coordsbox.")
+            self.btn_times_box.setToolTip("Fill times_box.")
             self.slice_mode.setToolTip("Slice by time or index.")
             self.tmin.setToolTip("Start time (sec), -1 = auto.")
             self.tmax.setToolTip("End time (sec), -1 = auto.")

canns/pipeline/asa_gui/core/runner.py

@@ -651,7 +651,7 @@ class PipelineRunner:
     def _run_cohomap(
         self, asa_data: dict[str, Any], state: WorkflowState, log_callback
     ) -> dict[str, Path]:
-        from canns.analyzer.data.asa import plot_cohomap_multi
+        from canns.analyzer.data.asa import plot_cohomap_scatter_multi
         from canns.analyzer.visualization import PlotConfigs
 
         tda_dir = self._results_dir(state) / "TDA"
@@ -684,7 +684,7 @@ class PipelineRunner:
         log_callback("Generating cohomology map...")
         pos = self._aligned_pos if self._aligned_pos is not None else asa_data
         config = PlotConfigs.cohomap(show=False, save_path=str(cohomap_path))
-        plot_cohomap_multi(
+        plot_cohomap_scatter_multi(
             decoding_result=decode_result,
             position_data={"x": pos["x"], "y": pos["y"]},
             config=config,
@@ -1175,18 +1175,18 @@ class PipelineRunner:
         self, asa_data: dict[str, Any], state: WorkflowState, log_callback
     ) -> dict[str, Path]:
         from canns.analyzer.data.asa import (
-            plot_cohospace_neuron_1d,
-            plot_cohospace_neuron_2d,
-            plot_cohospace_population_1d,
-            plot_cohospace_population_2d,
-            plot_cohospace_trajectory_1d,
-            plot_cohospace_trajectory_2d,
+            plot_cohospace_scatter_neuron_1d,
+            plot_cohospace_scatter_neuron_2d,
+            plot_cohospace_scatter_population_1d,
+            plot_cohospace_scatter_population_2d,
+            plot_cohospace_scatter_trajectory_1d,
+            plot_cohospace_scatter_trajectory_2d,
         )
-        from canns.analyzer.data.asa.cohospace import (
-            compute_cohoscore_1d,
-            compute_cohoscore_2d,
-            plot_cohospace_neuron_skewed,
-            plot_cohospace_population_skewed,
+        from canns.analyzer.data.asa.cohospace_scatter import (
+            compute_cohoscore_scatter_1d,
+            compute_cohoscore_scatter_2d,
+            plot_cohospace_scatter_neuron_skewed,
+            plot_cohospace_scatter_population_skewed,
         )
         from canns.analyzer.visualization import PlotConfigs
 
@@ -1254,11 +1254,11 @@ class PipelineRunner:
         if enable_score:
             try:
                 if dim_mode == "1d":
-                    scores = compute_cohoscore_1d(
+                    scores = compute_cohoscore_scatter_1d(
                         coords2, activity, top_percent=top_percent, times=times
                     )
                 else:
-                    scores = compute_cohoscore_2d(
+                    scores = compute_cohoscore_scatter_2d(
                         coords2, activity, top_percent=top_percent, times=times
                     )
                 cohoscore_path = out_dir / "cohoscore.npy"
@@ -1314,7 +1314,7 @@ class PipelineRunner:
         traj_path = out_dir / "cohospace_trajectory.png"
         if dim_mode == "1d":
             traj_cfg = PlotConfigs.cohospace_trajectory_1d(show=False, save_path=str(traj_path))
-            plot_cohospace_trajectory_1d(
+            plot_cohospace_scatter_trajectory_1d(
                 coords=coords2,
                 times=None,
                 subsample=subsample,
@@ -1322,7 +1322,7 @@ class PipelineRunner:
             )
         else:
             traj_cfg = PlotConfigs.cohospace_trajectory_2d(show=False, save_path=str(traj_path))
-            plot_cohospace_trajectory_2d(
+            plot_cohospace_scatter_trajectory_2d(
                 coords=coords2,
                 times=None,
                 subsample=subsample,
@@ -1334,7 +1334,7 @@ class PipelineRunner:
             log_callback(f"Plotting neuron {neuron_id}...")
             neuron_path = out_dir / f"cohospace_neuron_{neuron_id}.png"
             if unfold == "skew" and dim_mode != "1d":
-                plot_cohospace_neuron_skewed(
+                plot_cohospace_scatter_neuron_skewed(
                     coords=coordsbox2,
                     activity=activity,
                     neuron_id=int(neuron_id),
@@ -1351,7 +1351,7 @@ class PipelineRunner:
                     neuron_cfg = PlotConfigs.cohospace_neuron_1d(
                         show=False, save_path=str(neuron_path)
                     )
-                    plot_cohospace_neuron_1d(
+                    plot_cohospace_scatter_neuron_1d(
                         coords=coordsbox2,
                         activity=activity,
                         neuron_id=int(neuron_id),
@@ -1364,7 +1364,7 @@ class PipelineRunner:
                     neuron_cfg = PlotConfigs.cohospace_neuron_2d(
                         show=False, save_path=str(neuron_path)
                     )
-                    plot_cohospace_neuron_2d(
+                    plot_cohospace_scatter_neuron_2d(
                         coords=coordsbox2,
                         activity=activity,
                         neuron_id=int(neuron_id),
@@ -1384,7 +1384,7 @@ class PipelineRunner:
             else:
                 neuron_ids = list(range(activity.shape[1]))
             if unfold == "skew" and dim_mode != "1d":
-                plot_cohospace_population_skewed(
+                plot_cohospace_scatter_population_skewed(
                     coords=coords2,
                     activity=activity,
                     neuron_ids=neuron_ids,
@@ -1401,7 +1401,7 @@ class PipelineRunner:
                     pop_cfg = PlotConfigs.cohospace_population_1d(
                         show=False, save_path=str(pop_path)
                     )
-                    plot_cohospace_population_1d(
+                    plot_cohospace_scatter_population_1d(
                         coords=coords2,
                         activity=activity,
                         neuron_ids=neuron_ids,
@@ -1414,7 +1414,7 @@ class PipelineRunner:
                     pop_cfg = PlotConfigs.cohospace_population_2d(
                         show=False, save_path=str(pop_path)
                     )
-                    plot_cohospace_population_2d(
+                    plot_cohospace_scatter_population_2d(
                         coords=coords2,
                         activity=activity,
                         neuron_ids=neuron_ids,