lbm_suite2p_python 3.0.6__tar.gz → 3.0.8__tar.gz

{lbm_suite2p_python-3.0.6/lbm_suite2p_python.egg-info → lbm_suite2p_python-3.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 3.0.6
+Version: 3.0.8
 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>=3.0.3
+Requires-Dist: mbo_utilities>=3.0.7
 Requires-Dist: suite2p>=1.0.0.1
 Requires-Dist: setuptools<81
 Provides-Extra: rastermap

{lbm_suite2p_python-3.0.6 → lbm_suite2p_python-3.0.8}/lbm_suite2p_python/__init__.py

@@ -70,6 +70,8 @@ from lbm_suite2p_python.postprocessing import (
     load_ops,
     load_planar_results,
     dff_rolling_percentile,
+    zscore_trace,
+    baseline_percentile_dff,
     dff_shot_noise,
     compute_roi_stats,
 )
@@ -131,6 +133,8 @@ __all__ = [
     "load_ops",
     "load_planar_results",
     "dff_rolling_percentile",
+    "zscore_trace",
+    "baseline_percentile_dff",
     "dff_shot_noise",
     "compute_roi_stats",
 

{lbm_suite2p_python-3.0.6 → lbm_suite2p_python-3.0.8}/lbm_suite2p_python/cli.py

@@ -207,6 +207,11 @@ Examples:
         "--dff-smooth", type=int, dest="dff_smooth_window",
         help="smoothing window for dF/F"
     )
+    dff.add_argument(
+        "--norm-method", choices=["dff", "zscore"], default="dff",
+        dest="norm_method",
+        help="normalization for norm_traces.npy (default: dff)"
+    )
     dff.add_argument(
         "--correct-neuropil", dest="correct_neuropil",
         action=argparse.BooleanOptionalAction, default=True,
@@ -570,6 +575,7 @@ def main():
             dff_window_size=args.dff_window_size,
             dff_percentile=args.dff_percentile,
             dff_smooth_window=args.dff_smooth_window,
+            norm_method=args.norm_method,
             correct_neuropil=args.correct_neuropil,
             cell_filters=cell_filters,
             accept_all_cells=args.accept_all_cells,

{lbm_suite2p_python-3.0.6 → lbm_suite2p_python-3.0.8}/lbm_suite2p_python/conversion.py

@@ -871,7 +871,7 @@ def get_results(path, include_traces=True):
         "F": None,
         "Fneu": None,
         "spks": None,
-        "dff": None,
+        "norm_traces": None,
         "ops": None,
         "seg_file": None,
     }
@@ -902,7 +902,7 @@ def get_results(path, include_traces=True):
 
         # Load traces if requested
         if include_traces and fmt == "suite2p":
-            for name in ["F", "Fneu", "spks", "dff"]:
+            for name in ["F", "Fneu", "spks", "norm_traces"]:
                 trace_file = path / f"{name}.npy"
                 if trace_file.exists():
                     result[name] = np.load(trace_file)