lbm_suite2p_python 3.2.1__tar.gz → 3.2.2__tar.gz

{lbm_suite2p_python-3.2.1/lbm_suite2p_python.egg-info → lbm_suite2p_python-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.2.1
+Version: 3.2.2
 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
@@ -11,9 +11,11 @@ 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>=3.2.1
+Requires-Dist: mbo_utilities>=3.2.7
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
+Requires-Dist: torch
+Requires-Dist: torchvision
 Provides-Extra: rastermap
 Requires-Dist: rastermap; extra == "rastermap"
 Provides-Extra: cellpose

{lbm_suite2p_python-3.2.1 → lbm_suite2p_python-3.2.2}/lbm_suite2p_python/cli.py

@@ -23,6 +23,7 @@ Examples:
 """
 
 import argparse
+import json
 import sys
 from pathlib import Path
 from typing import Any
@@ -67,6 +68,7 @@ def _get_ops_help() -> dict[str, str]:
         "cellprob_threshold": "cellpose cell probability threshold (lower = more cells)",
         "flow_threshold": "cellpose flow error threshold",
         "anatomical_only": "cellpose detection mode: 0=off, 1=max_proj, 2=mean, 3=enhanced, 4=max",
+        "algorithm": "detection algorithm: sparsery, sourcery, or cellpose",
         "pretrained_model": "cellpose model name (e.g., cpsam, cyto2, nuclei)",
         "do_registration": "whether to run motion correction",
         "nonrigid": "use nonrigid (piecewise) registration",
@@ -103,6 +105,10 @@ Examples:
   lsp data/ output/ --planes 1 2 3            # specific planes (1-indexed)
   lsp data/ output/ --num-timepoints 500      # quick test with 500 frames
   lsp data/ output/ --diameter 8              # custom cell diameter
+  lsp data/ output/ --tau 1.3 --algorithm cellpose         # decay + detection algorithm
+  lsp data/ output/ --fix-phase --phasecorr-method median  # reader phase correction
+  lsp data/ output/ --reader-kwargs '{"roi": 2}'           # arbitrary imread kwargs
+  lsp data/ output/ --ops-file my_ops.json    # load saved ops (CLI flags override)
   lsp --list-ops                              # show all suite2p parameters
         """,
     )
@@ -245,15 +251,57 @@ Examples:
         help="maximum cell diameter in pixels"
     )
 
-    # reader options (for raw data)
+    # reader options (forwarded to mbo_utilities.imread)
     reader = parser.add_argument_group("reader options (raw scanimage data)")
     reader.add_argument(
-        "--fix-phase", action="store_true",
-        help="apply bidirectional phase correction"
+        "--fix-phase", action=argparse.BooleanOptionalAction, default=None,
+        help="bidirectional phase correction (reader default: on)"
     )
     reader.add_argument(
-        "--use-fft", action="store_true",
-        help="use FFT for subpixel phase correction"
+        "--use-fft", action=argparse.BooleanOptionalAction, default=None,
+        help="FFT-based subpixel phase correction"
+    )
+    reader.add_argument(
+        "--phasecorr-method", choices=["mean", "median", "max"], default=None,
+        help="phase-correction reduction method (default: mean)"
+    )
+    reader.add_argument(
+        "--channel", type=int, default=None,
+        help="zero-based color channel to read (multi-channel sources)"
+    )
+    reader.add_argument(
+        "--reader-kwargs", type=str, default=None, metavar="JSON",
+        help='extra imread kwargs as JSON, e.g. \'{"roi": 2}\''
+    )
+
+    # writer options (forwarded to the binary/zarr writer)
+    writer = parser.add_argument_group("writer options")
+    writer.add_argument(
+        "--writer-kwargs", type=str, default=None, metavar="JSON",
+        help='extra writer kwargs as JSON, e.g. \'{"target_chunk_mb": 200}\''
+    )
+
+    # rastermap options
+    rmap = parser.add_argument_group("rastermap options")
+    rmap.add_argument(
+        "--rastermap", action="store_true",
+        help="enable rastermap (planar + volumetric) with default settings"
+    )
+    rmap.add_argument(
+        "--rastermap-kwargs", type=str, default=None, metavar="JSON",
+        help='rastermap config JSON with "planar"/"volumetric" keys, '
+             'e.g. \'{"planar": {"n_clusters": 50}}\''
+    )
+
+    # advanced
+    advanced = parser.add_argument_group("advanced")
+    advanced.add_argument(
+        "--ops-file", type=str, default=None,
+        help="base ops from a .npy/.json file or suite2p dir; CLI flags override"
+    )
+    advanced.add_argument(
+        "--replot", action=argparse.BooleanOptionalAction, default=True,
+        help="regenerate per-plane figures (default: on)"
     )
 
     # dynamically add all ops parameters
@@ -324,8 +372,9 @@ def list_ops():
         "Main Settings": ["nplanes", "nchannels", "fs", "tau", "frames_include"],
         "Registration": ["do_registration", "nonrigid", "batch_size", "maxregshift",
                         "smooth_sigma", "nimg_init", "subpixel"],
-        "Cell Detection": ["roidetect", "sparse_mode", "spatial_scale", "threshold_scaling",
-                          "max_overlap", "connected", "nbinned", "max_iterations"],
+        "Cell Detection": ["roidetect", "algorithm", "sparse_mode", "spatial_scale",
+                          "threshold_scaling", "max_overlap", "connected", "nbinned",
+                          "max_iterations"],
         "Cellpose": ["anatomical_only", "diameter", "cellprob_threshold", "flow_threshold",
                     "pretrained_model", "spatial_hp_cp"],
         "Signal Extraction": ["neuropil_extract", "neucoeff", "spikedetect",
@@ -405,6 +454,65 @@ def build_cell_filters(args) -> list | None:
     return filters if filters else None
 
 
+def _parse_json_arg(flag: str, value: str) -> dict:
+    """parse a JSON object from a CLI flag value; exit cleanly on error."""
+    try:
+        parsed = json.loads(value)
+    except json.JSONDecodeError as e:
+        raise SystemExit(f"Error: {flag} is not valid JSON: {e}")
+    if not isinstance(parsed, dict):
+        raise SystemExit(f"Error: {flag} must be a JSON object")
+    return parsed
+
+
+def _load_ops_file(path: str) -> dict:
+    """load a base ops dict from a .json/.npy file or a suite2p directory."""
+    from lbm_suite2p_python import load_ops
+
+    p = Path(path).expanduser()
+    if p.suffix.lower() == ".json":
+        if not p.exists():
+            raise SystemExit(f"Error: --ops-file not found: {p}")
+        with open(p, "r", encoding="utf-8") as fh:
+            data = json.load(fh)
+        if not isinstance(data, dict):
+            raise SystemExit("Error: --ops-file JSON must be an object")
+        return data
+    return load_ops(p)
+
+
+def build_reader_kwargs(args) -> dict | None:
+    """build imread kwargs from CLI reader args (None if empty)."""
+    kw = {}
+    if args.fix_phase is not None:
+        kw["fix_phase"] = args.fix_phase
+    if args.use_fft is not None:
+        kw["use_fft"] = args.use_fft
+    if args.phasecorr_method is not None:
+        kw["phasecorr_method"] = args.phasecorr_method
+    if args.channel is not None:
+        kw["channel"] = args.channel
+    if args.reader_kwargs:
+        kw.update(_parse_json_arg("--reader-kwargs", args.reader_kwargs))
+    return kw or None
+
+
+def build_writer_kwargs(args) -> dict | None:
+    """build writer kwargs from CLI writer args (None if empty)."""
+    if args.writer_kwargs:
+        return _parse_json_arg("--writer-kwargs", args.writer_kwargs)
+    return None
+
+
+def build_rastermap_kwargs(args) -> dict | None:
+    """build rastermap_kwargs from CLI args (None if disabled)."""
+    if args.rastermap_kwargs:
+        return _parse_json_arg("--rastermap-kwargs", args.rastermap_kwargs)
+    if args.rastermap:
+        return {"planar": {}, "volumetric": {}}
+    return None
+
+
 def build_ops(args, base_ops: dict) -> dict:
     """build ops dict from CLI args, overriding base_ops."""
     from lbm_suite2p_python.default_ops import s2p_ops
@@ -512,6 +620,13 @@ def main():
 
     output_path.mkdir(parents=True, exist_ok=True)
 
+    # parse config/advanced args up front so invalid JSON or a missing ops
+    # file fails before any logging or processing work begins
+    base_extra_ops = _load_ops_file(args.ops_file) if args.ops_file else None
+    reader_kwargs = build_reader_kwargs(args)
+    writer_kwargs = build_writer_kwargs(args)
+    rastermap_kwargs = build_rastermap_kwargs(args)
+
     log_path = output_path / "log.txt"
     log_file = open(log_path, "w", encoding="utf-8", buffering=1)
     _orig_stdout, _orig_stderr = sys.stdout, sys.stderr
@@ -538,17 +653,10 @@ def main():
     print(f"Input:  {input_path}")
     print(f"Output: {output_path}")
 
-    # build ops
-    base_ops = lsp.default_ops()
+    # build ops (optionally starting from a user-supplied ops file)
+    base_ops = lsp.default_ops(ops=base_extra_ops) if base_extra_ops else lsp.default_ops()
     ops = build_ops(args, base_ops)
 
-    # build reader kwargs
-    reader_kwargs = {}
-    if args.fix_phase:
-        reader_kwargs["fix_phase"] = True
-    if args.use_fft:
-        reader_kwargs["use_fft"] = True
-
     # build cell filters
     cell_filters = build_cell_filters(args)
 
@@ -562,6 +670,10 @@ def main():
     print(f"  Cellpose model: {ops.get('pretrained_model', 'cpsam')}")
     if cell_filters:
         print(f"  Cell filters: {cell_filters}")
+    if reader_kwargs:
+        print(f"  Reader: {reader_kwargs}")
+    if rastermap_kwargs:
+        print(f"  Rastermap: {sorted(rastermap_kwargs)}")
 
     print(f"\n{'='*60}\n")
 
@@ -590,7 +702,10 @@ def main():
             cell_filters=cell_filters,
             accept_all_cells=args.accept_all_cells,
             save_json=args.save_json,
-            reader_kwargs=reader_kwargs if reader_kwargs else None,
+            reader_kwargs=reader_kwargs,
+            writer_kwargs=writer_kwargs,
+            rastermap_kwargs=rastermap_kwargs,
+            replot=args.replot,
             workers=args.workers,
             skip_volumetric=args.skip_volumetric,
             threads_per_worker=args.threads_per_worker,

{lbm_suite2p_python-3.2.1 → lbm_suite2p_python-3.2.2/lbm_suite2p_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.2.1
+Version: 3.2.2
 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
@@ -11,9 +11,11 @@ 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>=3.2.1
+Requires-Dist: mbo_utilities>=3.2.7
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
+Requires-Dist: torch
+Requires-Dist: torchvision
 Provides-Extra: rastermap
 Requires-Dist: rastermap; extra == "rastermap"
 Provides-Extra: cellpose

{lbm_suite2p_python-3.2.1 → lbm_suite2p_python-3.2.2}/lbm_suite2p_python.egg-info/requires.txt

@@ -1,6 +1,8 @@
-mbo_utilities>=3.2.1
+mbo_utilities>=3.2.7
 suite2p>=1.0.0.1
 setuptools<81
+torch
+torchvision
 
 [all]
 lbm_suite2p_python[cellpose,rastermap]

{lbm_suite2p_python-3.2.1 → lbm_suite2p_python-3.2.2}/pyproject.toml

@@ -1,106 +1,117 @@
-[build-system]
-requires = ["setuptools>=61", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "lbm_suite2p_python"
-version = "3.2.1"
-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 = "3.2.2"
+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>=3.2.7",
+	"suite2p>=1.0.0.1",
+	"setuptools<81",
+	"torch",
+	"torchvision",
+]
+
+[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",
+]
+
+[tool.uv.sources]
+torch = [{ index = "pytorch-cu126" }]
+torchvision = [{ index = "pytorch-cu126" }]
+
+[[tool.uv.index]]
+name = "pytorch-cu126"
+url = "https://download.pytorch.org/whl/cu126"
+explicit = true
+
+# 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()"
+]