canns 0.13.0__py3-none-any.whl → 0.13.1__py3-none-any.whl

canns/analyzer/data/asa/__init__.py

@@ -18,6 +18,12 @@ from .config import (
 )
 from .decode import decode_circular_coordinates, decode_circular_coordinates_multi
 from .embedding import embed_spike_trains
+from .fly_roi import (
+    BumpFitsConfig,
+    CANN1DPlotConfig,
+    create_1d_bump_animation,
+    roi_bump_fits,
+)
 from .fr import (
     FRMResult,
     compute_fr_heatmap_matrix,
@@ -60,6 +66,10 @@ __all__ = [
     "plot_cohomap_multi",
     "plot_3d_bump_on_torus",
     "plot_2d_bump_on_manifold",
+    "BumpFitsConfig",
+    "CANN1DPlotConfig",
+    "create_1d_bump_animation",
+    "roi_bump_fits",
     "compute_fr_heatmap_matrix",
     "save_fr_heatmap_png",
     "FRMResult",

canns/analyzer/data/asa/decode.py

@@ -33,7 +33,7 @@ def decode_circular_coordinates(
     real_of : bool
         Whether the experiment is open-field (controls box coordinate handling).
     save_path : str, optional
-        Path to save decoding results. Defaults to ``Results/spikes_decoding.npz``.
+        Path to save decoding results. If ``None``, results are not saved.
 
     Returns
     -------
@@ -174,13 +174,12 @@ def decode_circular_coordinates(
         "centsinall": centsinall,
     }
 
-    # Save results
-    if save_path is None:
-        os.makedirs("Results", exist_ok=True)
-        save_path = "Results/spikes_decoding.npz"
-
-    os.makedirs(os.path.dirname(save_path), exist_ok=True)
-    np.savez_compressed(save_path, **results)
+    # Save results (only when requested)
+    if save_path is not None:
+        save_dir = os.path.dirname(save_path)
+        if save_dir:
+            os.makedirs(save_dir, exist_ok=True)
+        np.savez_compressed(save_path, **results)
 
     return results
 
@@ -264,13 +263,12 @@ def decode_circular_coordinates1(
         "centsinall": centsinall,
     }
 
-    # Save results
-    if save_path is None:
-        os.makedirs("Results", exist_ok=True)
-        save_path = "Results/spikes_decoding.npz"
-
-    os.makedirs(os.path.dirname(save_path), exist_ok=True)
-    np.savez_compressed(save_path, **results)
+    # Save results (only when requested)
+    if save_path is not None:
+        save_dir = os.path.dirname(save_path)
+        if save_dir:
+            os.makedirs(save_dir, exist_ok=True)
+        np.savez_compressed(save_path, **results)
 
     return results
 
@@ -291,7 +289,7 @@ def decode_circular_coordinates_multi(
     spike_data : dict
         Spike data dictionary containing ``'spike'``, ``'t'`` and optionally ``'x'``/``'y'``.
     save_path : str, optional
-        Path to save decoding results. Defaults to ``Results/spikes_decoding.npz``.
+        Path to save decoding results. If ``None``, results are not saved.
     num_circ : int
         Number of H1 cocycles/circular coordinates to decode.
 
@@ -383,11 +381,10 @@ def decode_circular_coordinates_multi(
         "centsinall": centsinall,
     }
 
-    if save_path is None:
-        os.makedirs("Results", exist_ok=True)
-        save_path = "Results/spikes_decoding.npz"
-
-        os.makedirs(os.path.dirname(save_path), exist_ok=True)
+    if save_path is not None:
+        save_dir = os.path.dirname(save_path)
+        if save_dir:
+            os.makedirs(save_dir, exist_ok=True)
         np.savez_compressed(save_path, **results)
     return results
 

canns/analyzer/data/{legacy/cann1d.py → asa/fly_roi.py}

@@ -4,7 +4,7 @@ from dataclasses import dataclass
 
 import numpy as np
 from matplotlib import pyplot as plt
-from matplotlib.animation import FuncAnimation, PillowWriter
+from matplotlib.animation import FuncAnimation
 from scipy.optimize import linear_sum_assignment
 from scipy.special import i0
 from tqdm import tqdm
@@ -66,22 +66,6 @@ class BumpFitsConfig:
     random_seed: int | None = None
 
 
-@dataclass
-class AnimationConfig:
-    """Configuration for 1D CANN bump animation."""
-
-    show: bool = False
-    max_height_value: float = 0.5
-    max_width_range: int = 40
-    npoints: int = 300
-    nframes: int | None = None
-    fps: int = 5
-    bump_selection: str = "strongest"
-    show_progress_bar: bool = True
-    repeat: bool = False
-    title: str = "1D CANN Bump Animation"
-
-
 @dataclass
 class CANN1DPlotConfig(PlotConfig):
     """Specialized PlotConfig for CANN1D visualizations."""
@@ -141,9 +125,9 @@ class AnimationError(CANN1DError):
     pass
 
 
-def bump_fits(data, config: BumpFitsConfig | None = None, save_path=None, **kwargs):
+def roi_bump_fits(data, config: BumpFitsConfig | None = None, save_path=None, **kwargs):
     """
-    Fit CANN1D bumps to data using MCMC optimization.
+    Fit CANN1D bumps to ROI data using MCMC optimization.
 
     Parameters:
         data : numpy.ndarray
@@ -318,10 +302,10 @@ def create_1d_bump_animation(
     Parameters:
         fits_data : numpy.ndarray
             Shape (n_fits, 4) array with columns [time, position, amplitude, kappa]
-        config : AnimationConfig, optional
+        config : CANN1DPlotConfig, optional
             Configuration object with all animation parameters
         save_path : str, optional
-            Output path for the generated GIF
+            Output path for the generated animation (e.g. .gif or .mp4)
         **kwargs : backward compatibility parameters
 
     Returns:
@@ -336,6 +320,8 @@ def create_1d_bump_animation(
     for key, value in kwargs.items():
         if hasattr(config, key):
             setattr(config, key, value)
+    if save_path is not None:
+        config.save_path = save_path
 
     try:
         # ==== Smoothing functions ====
@@ -520,7 +506,10 @@ def create_1d_bump_animation(
             fig, update, frames=nframes, init_func=init, blit=use_blitting, repeat=config.repeat
         )
 
-        # Save animation with progress tracking
+        ani = None
+        progress_bar_enabled = getattr(config, "show_progress_bar", True)
+
+        # Save animation with unified backend selection
         if config.save_path:
             # Warn if both saving and showing (causes double rendering)
             if config.show and nframes > 50:
@@ -528,31 +517,95 @@ def create_1d_bump_animation(
 
                 warn_double_rendering(nframes, config.save_path, stacklevel=2)
 
-            if config.show_progress_bar:
-                pbar = tqdm(total=nframes, desc=f"Saving animation to {config.save_path}")
+            from ...visualization.core import (
+                emit_backend_warnings,
+                get_imageio_writer_kwargs,
+                get_matplotlib_writer,
+                select_animation_backend,
+            )
 
-                def progress_callback(current_frame, total_frames):
-                    pbar.update(1)
+            backend_selection = select_animation_backend(
+                save_path=config.save_path,
+                requested_backend=getattr(config, "render_backend", None),
+                check_imageio_plugins=True,
+            )
+            emit_backend_warnings(backend_selection.warnings, stacklevel=2)
+            backend = backend_selection.backend
 
+            if backend == "imageio":
                 try:
-                    ani.save(
-                        config.save_path,
-                        writer=PillowWriter(fps=config.fps),
-                        progress_callback=progress_callback,
-                    )
-                    pbar.close()
-                    print(f"\nAnimation successfully saved to: {config.save_path}")
-                except Exception as e:
-                    pbar.close()
-                    print(f"\nError saving animation: {e}")
-                    raise
-            else:
-                try:
-                    ani.save(config.save_path, writer=PillowWriter(fps=config.fps))
+                    import imageio
+
+                    writer_kwargs, mode = get_imageio_writer_kwargs(config.save_path, config.fps)
+                    with imageio.get_writer(config.save_path, mode=mode, **writer_kwargs) as writer:
+                        frames_iter = range(nframes)
+                        if progress_bar_enabled:
+                            frames_iter = tqdm(
+                                frames_iter,
+                                desc=f"Rendering {config.save_path}",
+                            )
+
+                        init()
+                        for frame_idx in frames_iter:
+                            update(frame_idx)
+                            fig.canvas.draw()
+                            frame = np.asarray(fig.canvas.buffer_rgba())
+                            if frame.shape[-1] == 4:
+                                frame = frame[:, :, :3]
+                            writer.append_data(frame)
+
                     print(f"Animation saved to: {config.save_path}")
                 except Exception as e:
-                    print(f"Error saving animation: {e}")
-                    raise
+                    import warnings
+
+                    warnings.warn(
+                        f"imageio rendering failed: {e}. Falling back to matplotlib.",
+                        RuntimeWarning,
+                        stacklevel=2,
+                    )
+                    backend = "matplotlib"
+
+            if backend == "matplotlib":
+                ani = FuncAnimation(
+                    fig,
+                    update,
+                    frames=nframes,
+                    init_func=init,
+                    blit=use_blitting,
+                    repeat=config.repeat,
+                )
+
+                writer = get_matplotlib_writer(config.save_path, fps=config.fps)
+
+                if progress_bar_enabled:
+                    pbar = tqdm(total=nframes, desc=f"Saving to {config.save_path}")
+
+                    def progress_callback(current_frame, total_frames):
+                        pbar.update(1)
+
+                    try:
+                        ani.save(
+                            config.save_path,
+                            writer=writer,
+                            progress_callback=progress_callback,
+                        )
+                        print(f"Animation saved to: {config.save_path}")
+                    finally:
+                        pbar.close()
+                else:
+                    ani.save(config.save_path, writer=writer)
+                    print(f"Animation saved to: {config.save_path}")
+
+        # Create animation object for showing (if not already created)
+        if config.show and ani is None:
+            ani = FuncAnimation(
+                fig,
+                update,
+                frames=nframes,
+                init_func=init,
+                blit=use_blitting,
+                repeat=config.repeat,
+            )
 
         if config.show:
             # Automatically detect Jupyter and display as HTML/JS
@@ -1043,7 +1096,7 @@ def _mcmc(
 
 if __name__ == "__main__":
     data = load_roi_data()
-    bumps, fits, nbump, centrbump = bump_fits(
+    bumps, fits, nbump, centrbump = roi_bump_fits(
         data, n_steps=5000, n_roi=16, save_path=os.path.join(os.getcwd(), "test.npz")
     )
 

canns/analyzer/data/asa/fr.py

@@ -135,7 +135,8 @@ def save_fr_heatmap_png(
         Plot configuration. Use ``config.save_path`` to specify output file.
     **kwargs : Any
         Additional ``imshow`` keyword arguments. ``save_path`` may be provided here
-        as a fallback if not set in ``config``.
+        as a fallback if not set in ``config``. If ``save_path`` is omitted, the
+        figure is only displayed when ``show=True``.
 
     Notes
     -----
@@ -172,11 +173,6 @@ def save_fr_heatmap_png(
         if not config.ylabel:
             config.ylabel = ylabel
 
-    if config.save_path is None:
-        raise ValueError(
-            "save_path must be provided via config.save_path or as a keyword argument."
-        )
-
     config.save_dpi = dpi
 
     M = np.asarray(M)
@@ -391,7 +387,8 @@ def plot_frm(
         Plot configuration. Use ``config.save_path`` to specify output file.
     **kwargs : Any
         Additional ``imshow`` keyword arguments. ``save_path`` may be provided here
-        as a fallback if not set in ``config``.
+        as a fallback if not set in ``config``. If ``save_path`` is omitted, the
+        figure is only displayed when ``show=True``.
 
     Examples
     --------
@@ -423,11 +420,6 @@ def plot_frm(
         if not config.ylabel:
             config.ylabel = "Y bin"
 
-    if config.save_path is None:
-        raise ValueError(
-            "save_path must be provided via config.save_path or as a keyword argument."
-        )
-
     config.save_dpi = dpi
 
     frm = np.asarray(frm)

canns/analyzer/data/asa/plotting.py

@@ -295,8 +295,19 @@ def plot_path_compare(
     ax0 = axes[0]
     ax0.set_title("Physical path (x,y)")
     ax0.set_aspect("equal", "box")
-    ax0.axis("off")
     ax0.plot(x, y, lw=0.9, alpha=0.8)
+    # Keep a visible frame while hiding ticks for a clean path outline.
+    ax0.set_xticks([])
+    ax0.set_yticks([])
+    for spine in ax0.spines.values():
+        spine.set_visible(True)
+    # Add a small padding so the frame doesn't touch the path.
+    x_min, x_max = np.min(x), np.max(x)
+    y_min, y_max = np.min(y), np.max(y)
+    pad_x = (x_max - x_min) * 0.03 if x_max > x_min else 1.0
+    pad_y = (y_max - y_min) * 0.03 if y_max > y_min else 1.0
+    ax0.set_xlim(x_min - pad_x, x_max + pad_x)
+    ax0.set_ylim(y_min - pad_y, y_max + pad_y)
 
     ax1 = axes[1]
     ax1.set_title("Decoded coho path")

canns/pipeline/asa/widgets.py

@@ -3,10 +3,10 @@
 This module provides reusable UI components for the ASA analysis interface.
 """
 
-from pathlib import Path
 import os
 import subprocess
 import sys
+from pathlib import Path
 
 from rich.ansi import AnsiDecoder
 from rich.text import Text

{canns-0.13.0.dist-info → canns-0.13.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: canns
-Version: 0.13.0
+Version: 0.13.1
 Summary: A Python Library for Continuous Attractor Neural Networks
 Project-URL: Repository, https://github.com/routhleck/canns
 Author-email: Sichao He <sichaohe@outlook.com>

{canns-0.13.0.dist-info → canns-0.13.1.dist-info}/RECORD

@@ -3,19 +3,17 @@ canns/_version.py,sha256=zIvJPOGBFvo4VV6f586rlO_bvhuFp1fsxjf6xhsqkJY,1547
 canns/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 canns/analyzer/__init__.py,sha256=EQ02fYHkpMADp-ojpVCVtapuSPkl6j5WVfdPy0mOTs4,506
 canns/analyzer/data/__init__.py,sha256=5LJ8Q4SyDpi6CAzyW3lSpra3I0BgG20kmQMceONw7A4,158
-canns/analyzer/data/asa/__init__.py,sha256=MNsWjFFWFbnDbYPgvF43Kj4Tv8pPpqmdJnlNbK2_fbI,1670
+canns/analyzer/data/asa/__init__.py,sha256=vfZCggZ_FvXwlYXLKErc_eltN6nOQiHWIivGYqpt8NM,1885
 canns/analyzer/data/asa/cohospace.py,sha256=n6DfPWUH_k67KrPbNMt1EUdxMuRFFmXCaqh4gcuXngM,27847
 canns/analyzer/data/asa/config.py,sha256=zVs-snLkD93hGc97GEX9CkcjTtUqORvMCs3khHhqd64,6288
-canns/analyzer/data/asa/decode.py,sha256=5haC6WclPIDQgPtnDfjKoWFbDwJVyaBzTEiRbdPnbyU,16579
+canns/analyzer/data/asa/decode.py,sha256=NG8vVx2cPG7uSJDovnC2vzk0dsqU8oR4jaNPxxrvCc0,16501
 canns/analyzer/data/asa/embedding.py,sha256=rT3hOHk6BzHF1X5YznIFxE_dDveklbT0fx9GtA2w3z0,9550
 canns/analyzer/data/asa/filters.py,sha256=D-1mDVn4hBEAphKUgx1gQEUfgbghKcNQhZmr4xEExQA,7146
-canns/analyzer/data/asa/fr.py,sha256=VRvruZl5NBfK7QEsRLsqHSftelHFXghzJfBU1nov-YQ,13593
+canns/analyzer/data/asa/fly_roi.py,sha256=_scBOd-4t9yv_1tHk7wbXJwPieU-L-QtFJY6fhHpxDI,38031
+canns/analyzer/data/asa/fr.py,sha256=jt99H50e1RRAQgMIdkfK0rBbembZJEr9SMrxK-ZI_LA,13449
 canns/analyzer/data/asa/path.py,sha256=p3r8EGcJi8NewNFutr3kdO-ekdU_5Icpy6nAoELzSq4,12233
-canns/analyzer/data/asa/plotting.py,sha256=7EfVSUERju6lggXyZ8U_BkJznaoTgwY2w3aVfyoy5rs,40325
+canns/analyzer/data/asa/plotting.py,sha256=xuKRuq12pITK0BOC4Bj3ZfJs-07DA2OUHCpJmtJLOnw,40852
 canns/analyzer/data/asa/tda.py,sha256=Hn110SBN4wKgHmcwPRkxHdbQ5DFW2xLdSv26J37_Zxc,30342
-canns/analyzer/data/legacy/__init__.py,sha256=JNFKxWBlT2p4Nf70Ddby67-4UYNaVS7lQFAy5wXEE-8,92
-canns/analyzer/data/legacy/cann1d.py,sha256=QN4vbYXrfcxAVbPhaYiXGoP5QzTc6hWJJGo5ETP_RSU,35793
-canns/analyzer/data/legacy/cann2d.py,sha256=RaibP0byPKK9qGefQme0-uZLwqTKOFGBL3VfmbRZOjk,86659
 canns/analyzer/metrics/__init__.py,sha256=WaTCJE2WhqPtZXYTtMilF_f0LZUfz2h9a25HzwmCwP8,132
 canns/analyzer/metrics/spatial_metrics.py,sha256=ZdS7tGH3lMgNlSYoHlH8IPsCw4XL0KtEnGALg_WHRX8,8965
 canns/analyzer/metrics/systematic_ratemap.py,sha256=MzXfa6_fGgrxD5xEd4hfrZR_fyUmhXQCxnPE3hUonE8,14004
@@ -65,7 +63,7 @@ canns/pipeline/asa/runner.py,sha256=PfHXlI-m3m-IYVFcFRhSODfPoRlCrloDOqEftvAfasg,
 canns/pipeline/asa/screens.py,sha256=DbqidxmoKe4KzSLuxuriVv1PIVFn5Z-PfScVfjrIiEA,5954
 canns/pipeline/asa/state.py,sha256=XukidfcFIOmm9ttT226FOTYR5hv2VAY8_DZt7V1Ml2g,6955
 canns/pipeline/asa/styles.tcss,sha256=eaXI3rQeWdBYmWdLJMMiSO6acHtreLRVKKoIHb2-dBk,3349
-canns/pipeline/asa/widgets.py,sha256=9pO6fJ13sQUm4vxETdSpYDXDA7z0mi3yFZO_RDakxpY,8087
+canns/pipeline/asa/widgets.py,sha256=3vPGGQWP9V5FwuwqykCVp7dzAHdpcFkDqib0DtIw-lQ,8087
 canns/pipeline/gallery/__init__.py,sha256=PPOvxmTRzEnj33jHlsFlaWuEfhrcNe39pMPQkTisjlo,187
 canns/task/__init__.py,sha256=sfo8TBBVAqkx73Nu5lVv77UCwZjKqjt042ezW4Wv2Ec,350
 canns/task/_base.py,sha256=rdRy4mr6x53z4aJv04UJcpqCyv78AxB1k1DhxnriLpg,4401
@@ -84,8 +82,8 @@ canns/trainer/utils.py,sha256=ZdoLiRqFLfKXsWi0KX3wGUp0OqFikwiou8dPf3xvFhE,2847
 canns/typing/__init__.py,sha256=mXySdfmD8fA56WqZTb1Nj-ZovcejwLzNjuk6PRfTwmA,156
 canns/utils/__init__.py,sha256=OMyZ5jqZAIUS2Jr0qcnvvrx6YM-BZ1EJy5uZYeA3HC0,366
 canns/utils/benchmark.py,sha256=oJ7nvbvnQMh4_MZh7z160NPLp-197X0rEnmnLHYlev4,1361
-canns-0.13.0.dist-info/METADATA,sha256=E-6ivcs7Yrp4Hffey9nfIQttDe6dzWwAbg-sT09auAg,8827
-canns-0.13.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-canns-0.13.0.dist-info/entry_points.txt,sha256=HDzYp0e9E1wfKYRkYtnUgVKK_u33_7eIn9exgm7t-wg,75
-canns-0.13.0.dist-info/licenses/LICENSE,sha256=u6NJ1N-QSnf5yTwSk5UvFAdU2yKD0jxG0Xa91n1cPO4,11306
-canns-0.13.0.dist-info/RECORD,,
+canns-0.13.1.dist-info/METADATA,sha256=4HIOm94szk2GaS6A9Kbp9nZHXfoqVvNj_rOBdrExZWE,8827
+canns-0.13.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+canns-0.13.1.dist-info/entry_points.txt,sha256=HDzYp0e9E1wfKYRkYtnUgVKK_u33_7eIn9exgm7t-wg,75
+canns-0.13.1.dist-info/licenses/LICENSE,sha256=u6NJ1N-QSnf5yTwSk5UvFAdU2yKD0jxG0Xa91n1cPO4,11306
+canns-0.13.1.dist-info/RECORD,,

canns/analyzer/data/legacy/__init__.py

@@ -1,6 +0,0 @@
-"""Legacy data-analysis modules (deprecated)."""
-
-__all__ = [
-    "cann1d",
-    "cann2d",
-]