lbm_suite2p_python 3.1.1__tar.gz → 3.2.0__tar.gz

{lbm_suite2p_python-3.1.1/lbm_suite2p_python.egg-info → lbm_suite2p_python-3.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.1.1
+Version: 3.2.0
 Summary: Calcium Imaging Pipeline built with Suite2p, Cellpose and Rastermap
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0}/lbm_suite2p_python/cellpose.py

@@ -390,7 +390,7 @@ def cellpose(
     # cellpose eval parameters
     diameter: float = None,
     flow_threshold: float = 0.0,
-    cellprob_threshold: float = -6.0,
+    cellprob_threshold: float = -4.0,
     min_size: int = 2,
     max_size: int = None,
     max_size_fraction: float = None,
@@ -445,9 +445,9 @@ def cellpose(
         Use GPU if available.
     diameter : float, optional
         Expected cell diameter in pixels. If None, Cellpose auto-estimates.
-    flow_threshold : float, default 0.4
-        Maximum allowed error of flows for each mask.
-    cellprob_threshold : float, default 0.0
+    flow_threshold : float, default 0.0
+        Maximum allowed error of flows for each mask (0 = flow check off).
+    cellprob_threshold : float, default -4.0
         Probability threshold for cell detection. Lower = more cells.
     min_size : int, default 2
         Minimum number of pixels per mask.
@@ -932,8 +932,8 @@ def save_gui_results(
     flows: tuple = None,
     styles: np.ndarray = None,
     diameter: float = None,
-    cellprob_threshold: float = 0.0,
-    flow_threshold: float = 0.4,
+    cellprob_threshold: float = -4.0,
+    flow_threshold: float = 0.0,
     name: str = None,
 ) -> Path:
     """

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0}/lbm_suite2p_python/conversion.py

@@ -622,8 +622,8 @@ def export_for_gui(suite2p_dir, output_path=None, name=None):
         "filename": str(proj_path),
         "flows": None,
         "est_diam": ops.get("diameter"),
-        "cellprob_threshold": ops.get("cellprob_threshold", 0.0),
-        "flow_threshold": ops.get("flow_threshold", 0.4),
+        "cellprob_threshold": ops.get("cellprob_threshold", -4.0),
+        "flow_threshold": ops.get("flow_threshold", 0.0),
     }
 
     seg_file = output_dir / f"{name}_seg.npy"

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0}/lbm_suite2p_python/default_ops.py

@@ -1,84 +1,96 @@
-"""Default ops for the LBM pipeline.
-
-Historically this module hard-coded a flat ops dict whose values
-diverged from suite2p's own defaults in a handful of fields
-(`batch_size=500`, `chan2_thres=0.65`, `tau=1.3`, `diameter=4`, etc.).
-That divergence made the round-trip through `settings.npy` confusing —
-on-disk values that matched the lsp default were flagged as "modified"
-against suite2p's schema, and vice versa.
-
-This module now exposes exactly suite2p's defaults (the values from
-`suite2p.default_settings()` + `suite2p.default_db()`), flattened to the
-fork's flat-ops shape via the same `db_settings_to_ops` translation
-that the rest of lsp uses. There is now ONE source of truth for "what
-default means": suite2p's parameter schema. Any LBM-specific tweaks
-(diameter, tau, etc.) belong in user code, not in the default.
-"""
-
-from mbo_utilities.metadata import get_param, get_voxel_size
-
-
-def s2p_ops() -> dict:
-    """Suite2p's default ops in flat (fork-style) form.
-
-    Composed from `suite2p.default_settings()` + `suite2p.default_db()`
-    via `db_settings_to_ops`, so the rename map and per-section
-    flat-key disambiguation (e.g. extraction.batch_size →
-    extract_batch_size) are applied consistently.
-    """
-    from suite2p import default_settings, default_db
-    from lbm_suite2p_python.db_settings import db_settings_to_ops
-
-    return db_settings_to_ops(default_db(), default_settings())
-
-
-def default_ops(metadata: dict | None = None, ops: dict | None = None) -> dict:
-    """Return default ops for the LBM Suite2p pipeline.
-
-    Parameters
-    ----------
-    metadata : dict, optional
-        Source-data metadata. When provided, `fs` and the (`dx`, `dy`)
-        voxel-size pair are pulled in from the metadata and overlaid
-        onto the suite2p defaults.
-    ops : dict, optional
-        A user-supplied ops dict to start from. When None, starts from
-        `s2p_ops()` (suite2p's defaults).
-
-    Returns
-    -------
-    dict
-        Flat ops dict ready to be passed to `pipeline()` / `run_plane()`.
-
-    Notes
-    -----
-    `nplanes=1` and `nchannels=1` are forced at the end. The lsp
-    pipeline always processes one plane at a time, so these stay fixed
-    regardless of caller input.
-
-    Examples
-    --------
-    >>> import lbm_suite2p_python as lsp
-    >>> ops = lsp.default_ops()
-    >>> lsp.run_plane(
-    ...     ops=ops,
-    ...     input_tiff="D:/demo/raw_data/raw_file_00001.tif",
-    ...     save_path="D:/demo/results",
-    ...     save_folder="v1",
-    ... )
-    """
-    if ops is None:
-        ops = s2p_ops()
-
-    if metadata is not None:
-        fs = get_param(metadata, "fs")
-        if fs is not None:
-            ops["fs"] = fs
-        voxel = get_voxel_size(metadata)
-        if voxel.dx != 1.0 or voxel.dy != 1.0:
-            ops["dx"] = voxel.dx
-            ops["dy"] = voxel.dy
-
-    ops["nplanes"] = 1
-    ops["nchannels"] = 1
-    return ops
+"""Default ops for the LBM pipeline.
+
+Historically this module hard-coded a flat ops dict whose values
+diverged from suite2p's own defaults in a handful of fields
+(`batch_size=500`, `chan2_thres=0.65`, `tau=1.3`, `diameter=4`, etc.).
+That divergence made the round-trip through `settings.npy` confusing —
+on-disk values that matched the lsp default were flagged as "modified"
+against suite2p's schema, and vice versa.
+
+`s2p_ops()` exposes exactly suite2p's defaults (the values from
+`suite2p.default_settings()` + `suite2p.default_db()`), flattened to the
+fork's flat-ops shape via the same `db_settings_to_ops` translation
+that the rest of lsp uses. `default_ops()` then applies a small set of
+LBM detection defaults (`_LBM_DETECTION_DEFAULTS`) on top, so a notebook,
+a bare `pipeline()` / `run_plane()` call, and the GUI all start from the
+same place. An explicit caller-supplied `ops=` is respected, not overlaid.
+"""
+
+from mbo_utilities.metadata import get_param, get_voxel_size
+
+
+# LBM detection defaults that intentionally differ from suite2p's schema.
+# default_ops() applies these on top of the suite2p mirror so notebook,
+# function-call, and GUI runs share one set of defaults.
+_LBM_DETECTION_DEFAULTS = {
+    "do_regmetrics": False,      # PC reg-quality metrics: ~40s/plane on >=1500 frames
+    "cellprob_threshold": -4.0,  # more permissive than suite2p's 0.0 for LBM data
+    "flow_threshold": 0.0,       # flow check disabled
+}
+
+
+def s2p_ops() -> dict:
+    """Suite2p's default ops in flat (fork-style) form.
+
+    Composed from `suite2p.default_settings()` + `suite2p.default_db()`
+    via `db_settings_to_ops`, so the rename map and per-section
+    flat-key disambiguation (e.g. extraction.batch_size →
+    extract_batch_size) are applied consistently.
+    """
+    from suite2p import default_settings, default_db
+    from lbm_suite2p_python.db_settings import db_settings_to_ops
+
+    return db_settings_to_ops(default_db(), default_settings())
+
+
+def default_ops(metadata: dict | None = None, ops: dict | None = None) -> dict:
+    """Return default ops for the LBM Suite2p pipeline.
+
+    Parameters
+    ----------
+    metadata : dict, optional
+        Source-data metadata. When provided, `fs` and the (`dx`, `dy`)
+        voxel-size pair are pulled in from the metadata and overlaid
+        onto the suite2p defaults.
+    ops : dict, optional
+        A user-supplied ops dict to start from. When None, starts from
+        `s2p_ops()` (suite2p's defaults).
+
+    Returns
+    -------
+    dict
+        Flat ops dict ready to be passed to `pipeline()` / `run_plane()`.
+
+    Notes
+    -----
+    `nplanes=1` and `nchannels=1` are forced at the end. The lsp
+    pipeline always processes one plane at a time, so these stay fixed
+    regardless of caller input.
+
+    Examples
+    --------
+    >>> import lbm_suite2p_python as lsp
+    >>> ops = lsp.default_ops()
+    >>> lsp.run_plane(
+    ...     ops=ops,
+    ...     input_tiff="D:/demo/raw_data/raw_file_00001.tif",
+    ...     save_path="D:/demo/results",
+    ...     save_folder="v1",
+    ... )
+    """
+    if ops is None:
+        ops = s2p_ops()
+        ops.update(_LBM_DETECTION_DEFAULTS)
+
+    if metadata is not None:
+        fs = get_param(metadata, "fs")
+        if fs is not None:
+            ops["fs"] = fs
+        voxel = get_voxel_size(metadata)
+        if voxel.dx != 1.0 or voxel.dy != 1.0:
+            ops["dx"] = voxel.dx
+            ops["dy"] = voxel.dy
+
+    ops["nplanes"] = 1
+    ops["nchannels"] = 1
+    return ops

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0}/lbm_suite2p_python/run_lsp.py

@@ -792,6 +792,7 @@ def pipeline(
     keep_raw: bool = False,
     force_reg: bool = False,
     force_detect: bool = False,
+    replot: bool = True,
     num_timepoints: int = None,
     frame_indices: list | None = None,
     dff_window_size: int = None,
@@ -854,6 +855,10 @@ def pipeline(
         Force re-registration even if already complete.
     force_detect : bool, default False
         Force ROI detection even if stat.npy exists.
+    replot : bool, default True
+        Regenerate per-plane figures. Set False to skip per-plane figure
+        regeneration (e.g. the volumetric aggregate over already-plotted
+        planes); suite2p and the volumetric plots are unaffected.
     num_timepoints : int, optional
         Limit processing to first N frames (truncation only). For an
         explicit set of frames or a strided selection, use
@@ -1028,6 +1033,7 @@ def pipeline(
             keep_raw=keep_raw,
             force_reg=force_reg,
             force_detect=force_detect,
+            replot=replot,
             frame_indices=frame_indices,
             dff_window_size=dff_window_size,
             dff_percentile=dff_percentile,
@@ -1067,6 +1073,7 @@ def pipeline(
             keep_raw=keep_raw,
             force_reg=force_reg,
             force_detect=force_detect,
+            replot=replot,
             frame_indices=frame_indices,
             dff_window_size=dff_window_size,
             dff_percentile=dff_percentile,
@@ -1238,6 +1245,7 @@ def run_volume(
     keep_raw: bool = False,
     force_reg: bool = False,
     force_detect: bool = False,
+    replot: bool = True,
     frame_indices: list | None = None,
     dff_window_size: int = None,
     dff_percentile: int = 20,
@@ -1281,6 +1289,9 @@ def run_volume(
         Force re-registration.
     force_detect : bool, default False
         Force detection.
+    replot : bool, default True
+        Regenerate per-plane figures (passed to run_plane). Set False to skip
+        per-plane figure regeneration during a volumetric aggregate.
     frame_indices : list, default None
         List of frame indices to process.
     dff_window_size, dff_percentile, dff_smooth_window : optional
@@ -1418,6 +1429,7 @@ def run_volume(
         keep_raw=keep_raw,
         force_reg=force_reg,
         force_detect=force_detect,
+        replot=replot,
         frame_indices=frame_indices,
         dff_window_size=dff_window_size,
         dff_percentile=dff_percentile,
@@ -2270,6 +2282,7 @@ def run_plane(
     keep_reg: bool = True,
     force_reg: bool = False,
     force_detect: bool = False,
+    replot: bool = True,
     frame_indices: list | None = None,
     dff_window_size: int = None,
     dff_percentile: int = 20,
@@ -2314,6 +2327,9 @@ def run_plane(
         If True, force a new registration.
     force_detect : bool, default False
         If True, force ROI detection.
+    replot : bool, default True
+        Generate per-plane figures. Set False to skip figure generation
+        (keeps ROI stats; only the figures are skipped).
     dff_window_size : int, optional
         Frames for rolling percentile baseline. Default: auto-calculated (~10*tau*fs).
     dff_percentile : int, default 20
@@ -3143,7 +3159,7 @@ def run_plane(
         except Exception as _e:
             print(f"  Warning: persisting post-processing kwargs failed: {_e}")
 
-    # 3b. ROI statistics
+    # 3b. ROI statistics (cheap; feeds the volumetric aggregate, so always run).
     try:
         from lbm_suite2p_python.postprocessing import compute_roi_stats
 
@@ -3152,20 +3168,35 @@ def run_plane(
     except Exception as e:
         print(f"  Warning: ROI stats computation failed: {e}")
 
-    # 4. Plots and Cleanup
-    try:
-        plot_zplane_figures(
-            plane_dir,
-            dff_percentile=dff_percentile,
-            dff_window_size=dff_window_size,
-            dff_smooth_window=dff_smooth_window,
-            norm_method=norm_method,
-            correct_neuropil=correct_neuropil,
-            run_rastermap=rastermap_kwargs is not None,
-            rastermap_kwargs=rastermap_kwargs,
-        )
-    except Exception as e:
-        print(f"  Warning: Plot generation failed: {e}")
+    # 4. Per-plane figures. Timed as the "plots" step (recorded in
+    # processing_history). Skipped when replot=False — e.g. the volumetric
+    # aggregate re-running already-plotted planes, where regenerating the
+    # per-plane figures is the dominant redundant cost.
+    if replot:
+        plot_start = time.time()
+        try:
+            plot_zplane_figures(
+                plane_dir,
+                dff_percentile=dff_percentile,
+                dff_window_size=dff_window_size,
+                dff_smooth_window=dff_smooth_window,
+                norm_method=norm_method,
+                correct_neuropil=correct_neuropil,
+                run_rastermap=rastermap_kwargs is not None,
+                rastermap_kwargs=rastermap_kwargs,
+            )
+        except Exception as e:
+            print(f"  Warning: Plot generation failed: {e}")
+
+        if ops_file.exists():
+            try:
+                _t_ops = load_ops(ops_file)
+                _add_processing_step(_t_ops, "plots", duration_seconds=time.time() - plot_start)
+                save_ops_db_settings(ops_file, _t_ops)
+            except Exception as _e:
+                print(f"  Warning: recording plot timing failed: {_e}")
+    else:
+        print("  replot=False: keeping existing per-plane figures")
 
     if save_json:
         ops_to_json(ops_file)

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0/lbm_suite2p_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.1.1
+Version: 3.2.0
 Summary: Calcium Imaging Pipeline built with Suite2p, Cellpose and Rastermap
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python

{lbm_suite2p_python-3.1.1 → lbm_suite2p_python-3.2.0}/pyproject.toml

@@ -1,106 +1,106 @@
-[build-system]
-requires = ["setuptools>=61", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "lbm_suite2p_python"
-version = "3.1.1"
-description = "Calcium Imaging Pipeline built with Suite2p, Cellpose and Rastermap"
-readme = "README.md"
-license = "BSD-3-Clause"
-requires-python = ">=3.12.7,<3.14"
-keywords = ["Pipeline", "Numpy", "Microscopy", "ScanImage", "Suite2p", "tiff"]
-urls = {homepage = "https://github.com/MillerBrainObservatory/LBM-Suite2p-Python"}
-classifiers=[
-	"Development Status :: 3 - Alpha",
-	"Intended Audience :: Science/Research",
-	"Programming Language :: Python :: 3 :: Only",
-]
-
-dependencies = [
-	"mbo_utilities>=3.2.1",
-	"suite2p>=1.0.0.1",
-	"setuptools<81",
-]
-
-[project.scripts]
-lsp = "lbm_suite2p_python.__main__:main"
-cellpose-gui = "lbm_suite2p_python.gui:main"
-
-[project.optional-dependencies]
-rastermap = [
-	"rastermap",
-]
-# Cellpose for anatomical cell detection (requires PyTorch)
-cellpose = [
-	"cellpose>=4.0.6",
-]
-# All optional dependencies
-all = [
-	"lbm_suite2p_python[rastermap,cellpose]",
-]
-
-[dependency-groups]
-dev = [
-	"pytest>=8.0.0",
-]
-docs = [
-	"docutils>=0.21.2",
-	"myst-nb>=1.2.0",
-	"sphinx>=8.1.3",
-	"roman-numerals-py>=2.0.0,<3.0.0",  # 3.x is broken
-	"sphinx-autodoc2>=0.5.0",
-	"sphinx-copybutton>=0.5.2",
-	"sphinx_togglebutton",
-	"sphinx-design>=0.6.1",
-	"sphinxcontrib-bibtex",
-	"sphinx-tippy",
-	"sphinx_book_theme",
-	"numpydoc",
-	"ipykernel",
-	"sphinxcontrib-images",
-	"sphinxcontrib-video",
-	"jupytext",
-	"scikit-image",
-	"scipy",
-	"pandas",
-	"suite2p",
-]
-
-# https://github.com/charliermarsh/ruff
-[tool.ruff]
-line-length = 88
-src = ["lbm_suite2p_python"]
-exclude = ["docs", "exclude", "demos", "scripts", "dev"]
-
-[tool.ruff.lint]
-pydocstyle = { convention = "numpy" }
-select = ["ALL"]
-ignore = [
-	"D401",   # First line should be in imperative mood (remove to opt in)
-	"COM812", # Missing trailing comma (conflicts with ruff format)
-	"ISC001", # Import sorting (conflicts with ruff format)
-	"FIX002", # Fixable issue
-	"DOC201", # TODO enable in follow-up PR; no doc for return type.
-	"FBT",    # TODO: enable in follow-up PR; require bool options to be keyword-only.
-]
-
-[tool.ruff.lint.per-file-ignores]
-"docs/*.py" = ["D"]
-
-[tool.setuptools.exclude-package-data]
-"*" = ["data/*"]
-
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["lbm_suite2p_python*"]
-
-[tool.coverage.report]
-exclude_lines = [
-	"pragma: no cover",
-	"if TYPE_CHECKING:",
-	"@overload",
-	"except ImportError",
-	"\\.\\.\\.",
-	"raise NotImplementedError()"
-]
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "lbm_suite2p_python"
+version = "3.2.0"
+description = "Calcium Imaging Pipeline built with Suite2p, Cellpose and Rastermap"
+readme = "README.md"
+license = "BSD-3-Clause"
+requires-python = ">=3.12.7,<3.14"
+keywords = ["Pipeline", "Numpy", "Microscopy", "ScanImage", "Suite2p", "tiff"]
+urls = {homepage = "https://github.com/MillerBrainObservatory/LBM-Suite2p-Python"}
+classifiers=[
+	"Development Status :: 3 - Alpha",
+	"Intended Audience :: Science/Research",
+	"Programming Language :: Python :: 3 :: Only",
+]
+
+dependencies = [
+	"mbo_utilities>=3.2.1",
+	"suite2p>=1.0.0.1",
+	"setuptools<81",
+]
+
+[project.scripts]
+lsp = "lbm_suite2p_python.__main__:main"
+cellpose-gui = "lbm_suite2p_python.gui:main"
+
+[project.optional-dependencies]
+rastermap = [
+	"rastermap",
+]
+# Cellpose for anatomical cell detection (requires PyTorch)
+cellpose = [
+	"cellpose>=4.0.6",
+]
+# All optional dependencies
+all = [
+	"lbm_suite2p_python[rastermap,cellpose]",
+]
+
+[dependency-groups]
+dev = [
+	"pytest>=8.0.0",
+]
+docs = [
+	"docutils>=0.21.2",
+	"myst-nb>=1.2.0",
+	"sphinx>=8.1.3",
+	"roman-numerals-py>=2.0.0,<3.0.0",  # 3.x is broken
+	"sphinx-autodoc2>=0.5.0",
+	"sphinx-copybutton>=0.5.2",
+	"sphinx_togglebutton",
+	"sphinx-design>=0.6.1",
+	"sphinxcontrib-bibtex",
+	"sphinx-tippy",
+	"sphinx_book_theme",
+	"numpydoc",
+	"ipykernel",
+	"sphinxcontrib-images",
+	"sphinxcontrib-video",
+	"jupytext",
+	"scikit-image",
+	"scipy",
+	"pandas",
+	"suite2p",
+]
+
+# https://github.com/charliermarsh/ruff
+[tool.ruff]
+line-length = 88
+src = ["lbm_suite2p_python"]
+exclude = ["docs", "exclude", "demos", "scripts", "dev"]
+
+[tool.ruff.lint]
+pydocstyle = { convention = "numpy" }
+select = ["ALL"]
+ignore = [
+	"D401",   # First line should be in imperative mood (remove to opt in)
+	"COM812", # Missing trailing comma (conflicts with ruff format)
+	"ISC001", # Import sorting (conflicts with ruff format)
+	"FIX002", # Fixable issue
+	"DOC201", # TODO enable in follow-up PR; no doc for return type.
+	"FBT",    # TODO: enable in follow-up PR; require bool options to be keyword-only.
+]
+
+[tool.ruff.lint.per-file-ignores]
+"docs/*.py" = ["D"]
+
+[tool.setuptools.exclude-package-data]
+"*" = ["data/*"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["lbm_suite2p_python*"]
+
+[tool.coverage.report]
+exclude_lines = [
+	"pragma: no cover",
+	"if TYPE_CHECKING:",
+	"@overload",
+	"except ImportError",
+	"\\.\\.\\.",
+	"raise NotImplementedError()"
+]