lbm_suite2p_python 3.0.3__tar.gz → 3.0.5__tar.gz

{lbm_suite2p_python-3.0.3/lbm_suite2p_python.egg-info → lbm_suite2p_python-3.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.0.3
+Version: 3.0.5
 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
@@ -11,7 +11,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: <3.14,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: mbo_utilities>=3.0.2
+Requires-Dist: mbo_utilities>=3.0.3
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
 Provides-Extra: rastermap

{lbm_suite2p_python-3.0.3 → lbm_suite2p_python-3.0.5}/lbm_suite2p_python/__init__.py

@@ -7,6 +7,7 @@ from lbm_suite2p_python.run_lsp import (
     run_plane,
     add_processing_step,
     generate_plane_dirname,
+    compute_enhanced_mean_image
 )
 
 from lbm_suite2p_python.cellpose import (
@@ -95,6 +96,7 @@ __all__ = [
     "default_ops",
     "add_processing_step",
     "generate_plane_dirname",
+    "compute_enhanced_mean_image"
 
     # Cellpose / HITL Workflow
     "train_cellpose",

{lbm_suite2p_python-3.0.3 → lbm_suite2p_python-3.0.5}/lbm_suite2p_python/run_lsp.py

@@ -101,7 +101,7 @@ def _call_upstream_pipeline(ops, f_reg, f_raw, f_reg_chan2, f_raw_chan2,
     return ops
 
 
-def _compute_enhanced_mean_image(img, ops):
+def compute_enhanced_mean_image(img, ops):
     """Compat shim for upstream's removal of `compute_enhanced_mean_image`.
 
     Upstream suite2p replaced `compute_enhanced_mean_image(img, ops)` with
@@ -237,7 +237,6 @@ def _copy_if_needed(src: Path, dst: Path, *, overwrite_empty: bool = True) -> bo
     if dst.exists():
         if not (overwrite_empty and dst.stat().st_size == 0):
             return False
-    print(f"  Copying {src.name} from {src.parent} -> {dst.parent}")
     shutil.copy2(src, dst)
     return True
 
@@ -263,6 +262,7 @@ def _stage_source_into_plane_dir(
     plane_dir = Path(plane_dir)
     plane_dir.mkdir(parents=True, exist_ok=True)
 
+    print(f"  Staging plane outputs: {src_dir.name} -> {plane_dir.name}")
     _copy_if_needed(src_dir / "ops.npy", plane_dir / "ops.npy")
     for fname in _DETECTION_OUTPUT_FILES:
         _copy_if_needed(src_dir / fname, plane_dir / fname)
@@ -1729,7 +1729,7 @@ def run_plane_bin(ops) -> bool:
                 print("  Computed meanImg from binary")
 
         if "meanImgE" not in ops and "meanImg" in ops:
-            ops["meanImgE"] = _compute_enhanced_mean_image(
+            ops["meanImgE"] = compute_enhanced_mean_image(
                 ops["meanImg"].astype(np.float32), ops
             )
             print("  Computed meanImgE from meanImg")
@@ -1791,7 +1791,7 @@ def run_plane_bin(ops) -> bool:
 
     # ensure meanImgE is always present in final ops (safety net)
     if "meanImgE" not in ops and "meanImg" in ops:
-        ops["meanImgE"] = _compute_enhanced_mean_image(
+        ops["meanImgE"] = compute_enhanced_mean_image(
             ops["meanImg"].astype(np.float32), ops
         )
 
@@ -2026,6 +2026,10 @@ def run_plane(
         )
 
         existing_ops = np.load(src_dir / "ops.npy", allow_pickle=True).item()
+        # remember the original acquisition source before the merge below
+        # overwrites data_path with the staged binary path. needed by
+        # force_reg path when the source has no data_raw.bin.
+        original_data_path = existing_ops.get("data_path")
         metadata = {
             k: v
             for k, v in existing_ops.items()
@@ -2073,20 +2077,71 @@ def run_plane(
             "data_path": str(input_path.resolve()),
         }
 
-        # registration would need to write to data.bin, but data.bin
-        # lives at the source dir — running it would clobber the user's
-        # source binary. force detection-only; user can re-register from
-        # the original tiff/zarr if they want fresh registration.
-        if ops_user.get("do_registration", 1):
-            logger.warning(
-                "do_registration=1 ignored when staging from an existing "
-                "registered binary into a different save_path — running "
-                "registration would clobber the source data.bin. Forcing "
-                "do_registration=0 (detection-only)."
-            )
-            ops["do_registration"] = 0
+        if not force_reg:
+            # registration would need to write to data.bin, but data.bin
+            # lives at the source dir — running it would clobber the user's
+            # source binary. force detection-only; user can re-register
+            # from the original tiff/zarr by passing force_reg=True (Force
+            # in the GUI), which routes writes into the new plane_dir.
+            if ops_user.get("do_registration", 1):
+                logger.warning(
+                    "do_registration ignored when staging into a different "
+                    "save_path — running registration would clobber the "
+                    "source data.bin. Forcing do_registration=0 "
+                    "(detection-only). Pass force_reg=True (Force in the "
+                    "GUI) to re-register into the new save_path."
+                )
+                ops["do_registration"] = 0
 
         _stage_source_into_plane_dir(src_dir, plane_dir, ops)
+
+        if force_reg:
+            # writes go to plane_dir/data.bin — discard the source pointer
+            # that _stage_source_into_plane_dir set.
+            ops.pop("reg_file", None)
+            # existing_ops carries a `raw_file` path from the original
+            # run; if keep_raw=False removed the file, the string is
+            # still present but stale. existence-check, don't trust the
+            # string alone.
+            _raw = ops.get("raw_file")
+            if not _raw or not Path(_raw).exists():
+                import shutil
+                target_raw = plane_dir / "data_raw.bin"
+                # prefer the original acquisition (tiff/zarr) when it's
+                # still on disk — avoids re-registering already-
+                # registered data. Skip when it points at the same .bin
+                # the user just loaded (no improvement, and imread of a
+                # stale data_path could be wrong).
+                use_original = (
+                    bool(original_data_path)
+                    and Path(original_data_path).exists()
+                    and Path(original_data_path).resolve() != input_path.resolve()
+                )
+                if use_original:
+                    print(
+                        f"  Force registration: rewriting data_raw.bin from "
+                        f"{Path(original_data_path).name}"
+                    )
+                    file = imread(Path(original_data_path), **reader_kwargs)
+                    if hasattr(file, "metadata"):
+                        metadata = dict(file.metadata)
+                    else:
+                        metadata = get_metadata(Path(original_data_path))
+                    skip_imwrite = False
+                else:
+                    # original acquisition is gone (or IS the input).
+                    # seed data_raw.bin from the staged data.bin so
+                    # registration has frames to work with. Re-registers
+                    # already-registered data (near-zero shifts) — fine
+                    # for detection / bad-frame re-runs.
+                    print(
+                        f"  Force registration: original acquisition "
+                        f"unavailable; seeding data_raw.bin from "
+                        f"{input_path.name} (re-registering already-"
+                        f"registered data)"
+                    )
+                    shutil.copy2(input_path, target_raw)
+                    ops["raw_file"] = str(target_raw)
     else:
         skip_imwrite = False
 
@@ -2569,17 +2624,6 @@ def run_plane(
         )
         np.save(plane_dir / "dff.npy", dff)
 
-        # Record the dF/F params that actually drew the dff.npy +
-        # figures. These live as top-level ops keys (NOT in the suite2p
-        # settings schema), so save_ops_db_settings writes them to
-        # ops.npy but leaves settings.npy / db.npy untouched. That keeps
-        # settings.npy as a record of suite2p stages and lets ops.npy
-        # carry the post-processing knobs separately.
-        current_ops["dff_window_size"] = dff_window_size
-        current_ops["dff_percentile"] = dff_percentile
-        current_ops["dff_smooth_window"] = dff_smooth_window
-        current_ops["correct_neuropil"] = bool(correct_neuropil)
-
         _add_processing_step(
             current_ops,
             "dff_calculation",
@@ -2588,6 +2632,34 @@ def run_plane(
         )
         save_ops_db_settings(ops_file, current_ops)
 
+    # 3b. Persist post-processing kwargs to ops.npy unconditionally.
+    # These live as top-level ops keys (NOT in the suite2p settings
+    # schema), so settings.npy / db.npy stay a record of the suite2p
+    # stages only — ops.npy carries the lsp / GUI-tunable knobs. Done
+    # outside the F.npy/Fneu.npy gate above so detection-skipped runs
+    # still leave a record of which knobs the caller passed in. Callers
+    # like mbo_utilities / mbo studio diff these against their dataclass
+    # defaults to flag "modified" parameters in the GUI.
+    if ops_file.exists():
+        try:
+            _post_ops = load_ops(ops_file)
+            _post_ops["dff_window_size"] = dff_window_size
+            _post_ops["dff_percentile"] = dff_percentile
+            _post_ops["dff_smooth_window"] = dff_smooth_window
+            _post_ops["correct_neuropil"] = bool(correct_neuropil)
+            _post_ops["accept_all_cells"] = bool(accept_all_cells)
+            _post_ops["save_json"] = bool(save_json)
+            # cell_filters: list[dict] (or None). Stored as-is so a reload
+            # can reconstruct each criterion's enabled/value pair.
+            _post_ops["cell_filters"] = cell_filters
+            # rastermap_kwargs: nested dict {"planar": {...}, "volumetric":
+            # {...}} or None. Presence of a key is the per-mode enable
+            # signal; sub-dict contents override Rastermap() defaults.
+            _post_ops["rastermap_kwargs"] = rastermap_kwargs
+            save_ops_db_settings(ops_file, _post_ops)
+        except Exception as _e:
+            print(f"  Warning: persisting post-processing kwargs failed: {_e}")
+
     # 3b. ROI statistics
     try:
         from lbm_suite2p_python.postprocessing import compute_roi_stats

{lbm_suite2p_python-3.0.3 → lbm_suite2p_python-3.0.5/lbm_suite2p_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.0.3
+Version: 3.0.5
 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
@@ -11,7 +11,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: <3.14,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: mbo_utilities>=3.0.2
+Requires-Dist: mbo_utilities>=3.0.3
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
 Provides-Extra: rastermap

{lbm_suite2p_python-3.0.3 → lbm_suite2p_python-3.0.5}/lbm_suite2p_python.egg-info/requires.txt

@@ -1,4 +1,4 @@
-mbo_utilities>=3.0.2
+mbo_utilities>=3.0.3
 suite2p>=1.0.0.1
 setuptools<81
 

{lbm_suite2p_python-3.0.3 → lbm_suite2p_python-3.0.5}/pyproject.toml

@@ -1,106 +1,106 @@
-[build-system]
-requires = ["setuptools>=61", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "lbm_suite2p_python"
-version = "3.0.3"
-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>=3.0.2",
-	"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 = "3.0.5"
+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>=3.0.3",
+	"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()"
+]