lbm_suite2p_python 3.0.2__py3-none-any.whl → 3.0.4__py3-none-any.whl

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/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
@@ -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
         )
 
@@ -2052,7 +2052,12 @@ def run_plane(
             nframes_hint = existing_ops.get("nframes_chan1") or existing_ops.get(
                 "nframes"
             )
-            subdir_name = generate_plane_dirname(plane=naming_plane, nframes=nframes_hint)
+            subdir_name = generate_plane_dirname(
+                plane=naming_plane,
+                nframes=nframes_hint,
+                frame_start=(int(min(frame_indices)) + 1) if frame_indices else 1,
+                frame_stop=(int(max(frame_indices)) + 1) if frame_indices else None,
+            )
 
         plane_dir = save_path / subdir_name
         plane_dir.mkdir(exist_ok=True)
@@ -2122,6 +2127,8 @@ def run_plane(
             subdir_name = generate_plane_dirname(
                 plane=naming_plane,
                 nframes=nframes_hint,
+                frame_start=(int(min(frame_indices)) + 1) if frame_indices else 1,
+                frame_stop=(int(max(frame_indices)) + 1) if frame_indices else None,
             )
 
         plane_dir = save_path / subdir_name
@@ -2562,17 +2569,6 @@ 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",
@@ -2581,6 +2577,34 @@ 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-3.0.2.dist-info → lbm_suite2p_python-3.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.0.2
+Version: 3.0.4
 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>=3.0.1
+Requires-Dist: mbo_utilities>=3.0.3
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
 Provides-Extra: rastermap

{lbm_suite2p_python-3.0.2.dist-info → lbm_suite2p_python-3.0.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lbm_suite2p_python/__init__.py,sha256=bIU_X9eDd-P2uZ88v2OWEI0uOeiK6ZvWFs3HNtmhd1Q,3683
+lbm_suite2p_python/__init__.py,sha256=Co20SS9KpWui19s06FUhjXFYXOYkfJ3V6nzqSVZQMGQ,3751
 lbm_suite2p_python/__main__.py,sha256=lMnZnMkCbv8OTh5i5uZlG1sF33PEs42zITw8aG8YKwI,131
 lbm_suite2p_python/_benchmarking.py,sha256=oi7q5VDShYa-YqEiZluJEmOeq-_X2jzz-bjxIalhLZ4,172
 lbm_suite2p_python/cellpose.py,sha256=RVlTfjJXqOSpJMtwXay6rTlR-55hm6Gl1niluuV8hXQ,63223
@@ -10,13 +10,13 @@ lbm_suite2p_python/grid_search.py,sha256=4Sgl2Nx95jHrpm4S9yj0z4R6tR8CrslPRAM8xiD
 lbm_suite2p_python/gui.py,sha256=jA8dg1yEM0ikMNJ0UrE_6joQkuqsmDj9I_pIb-E0YpA,10594
 lbm_suite2p_python/merging.py,sha256=qcQmAnaJPPniSMDDVeu_uZTcstXMYNfvWUBU4zVKLEI,13928
 lbm_suite2p_python/postprocessing.py,sha256=4n5c2qXZsBC65zxBWJC1UBy69N-OA9OFXdzDUUQXRQg,56821
-lbm_suite2p_python/run_lsp.py,sha256=3ODbBG0N6gW5CWKFx-P1kWTfDMuvRaBYzjugDXStyoU,104544
+lbm_suite2p_python/run_lsp.py,sha256=nS4VhqjUKcNnhPvB7eqc_DDVchmt1AQRasIepH5jjKQ,105946
 lbm_suite2p_python/utils.py,sha256=ECqCiwaKy78YFG-qxkiUZbdSW92zHjGjqWWpnIFHy-M,3514
 lbm_suite2p_python/volume.py,sha256=Q6Jc6_qLp6rnk4aHjazuTwsR3QJNRqb-RNdqR-IFTSA,80260
 lbm_suite2p_python/zplane.py,sha256=z9l8ijMCIQsesIU1xWojf7GYp9AW9kTPEc2xlK8O_eA,181600
-lbm_suite2p_python-3.0.2.dist-info/licenses/LICENSE.md,sha256=iZa6bLG-5EfV2LXTfQQ7wdDwslaIc9SrOfyKRtzvCoQ,1981
-lbm_suite2p_python-3.0.2.dist-info/METADATA,sha256=zpbgDRibHMVf_nyassufyEBBFUmyQwXTpTNb-2yBtjA,8830
-lbm_suite2p_python-3.0.2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-lbm_suite2p_python-3.0.2.dist-info/entry_points.txt,sha256=Ow6TsVyBZI0viAeQP6Ty7GJAmoXD7RmMhIxongAWAVM,100
-lbm_suite2p_python-3.0.2.dist-info/top_level.txt,sha256=WhCsVG68YLKWeTNJVwueG_4H3uuiI22I_TERsF-5mGk,19
-lbm_suite2p_python-3.0.2.dist-info/RECORD,,
+lbm_suite2p_python-3.0.4.dist-info/licenses/LICENSE.md,sha256=iZa6bLG-5EfV2LXTfQQ7wdDwslaIc9SrOfyKRtzvCoQ,1981
+lbm_suite2p_python-3.0.4.dist-info/METADATA,sha256=qk1UzFJy3ygtzTOgrgGOPpJtZ7dL8llbknapoSpUG80,8830
+lbm_suite2p_python-3.0.4.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+lbm_suite2p_python-3.0.4.dist-info/entry_points.txt,sha256=Ow6TsVyBZI0viAeQP6Ty7GJAmoXD7RmMhIxongAWAVM,100
+lbm_suite2p_python-3.0.4.dist-info/top_level.txt,sha256=WhCsVG68YLKWeTNJVwueG_4H3uuiI22I_TERsF-5mGk,19
+lbm_suite2p_python-3.0.4.dist-info/RECORD,,