lbm_suite2p_python 1.0.4__tar.gz → 2.0.0__tar.gz

lbm_suite2p_python-2.0.0/LICENSE.md

@@ -0,0 +1,17 @@
+This software license is the 3-clause BSD license plus a fourth clause that prohibits redistribution for commercial purposes without further permission.
+
+BSD 3-Clause License
+
+Copyright (c) 2024, Miller Brain Observatory.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+Redistributions for commercial purposes are not permitted without the written permission of all code authors. For purposes of this license, commercial purposes is the incorporation of LBM-Suite2p-Python into anything for which you will charge fees or other compensation. Contact mbo@rockefeller.edu for more information.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{lbm_suite2p_python-1.0.4/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 1.0.4
+Version: 2.0.0
 Summary: Light Beads Microscopy Pipeline using Suite2p
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
@@ -8,25 +8,28 @@ Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: <3.13,>=3.11
+Requires-Python: <3.12.10,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: tifffile>=2025.3.30
-Requires-Dist: zarr>=2.18.3
-Requires-Dist: dask>=2025.3.0
-Requires-Dist: mkl-fft>=1.3.13
-Requires-Dist: imageio[ffmpeg]
-Requires-Dist: matplotlib>=3.10.1
-Requires-Dist: h5py
+Requires-Dist: mkl_fft
+Requires-Dist: mbo_utilities[gui,suite3d]>=1.0.7
+Requires-Dist: suite2p_mbo
 Requires-Dist: tqdm
-Requires-Dist: mbo_utilities[all]
-Requires-Dist: suite2p_mbo==1.0.4
-Requires-Dist: pynwb>=3.0.0
-Requires-Dist: icecream>=2.1.4
-Provides-Extra: napari
-Requires-Dist: napari; extra == "napari"
-Provides-Extra: all
-Requires-Dist: napari; extra == "all"
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: dask>=2025.9.1
+Requires-Dist: zarr==3.1.3
+Requires-Dist: seaborn>=0.13.2
+Provides-Extra: cpsam
+Requires-Dist: cellpose==4.0.6; extra == "cpsam"
+Requires-Dist: pytorch; extra == "cpsam"
+Requires-Dist: torchaudio; extra == "cpsam"
+Provides-Extra: cpu
+Requires-Dist: torch>=2.7.0; extra == "cpu"
+Requires-Dist: torchvision>=0.22.0; extra == "cpu"
+Provides-Extra: cu126
+Requires-Dist: torch>=2.7.0; extra == "cu126"
+Requires-Dist: torchvision>=0.22.0; extra == "cu126"
 Dynamic: license-file
 
 # Light Beads Microscopy (LBM) Pipeline: Suite2p
@@ -71,6 +74,9 @@ cd LBM-Suite2p-Python
 pip install ".[all]"  # optional, contains ".[gui, notebook]"
 ```
 
+## Issues
+Widgets may throw "Invalid Rect" errors. This can be safely ignored until it is [resolved](https://github.com/pygfx/wgpu-py/issues/716#issuecomment-2880853089).
+
 ---
 
 ## Acknowledgements

{lbm_suite2p_python-1.0.4 → lbm_suite2p_python-2.0.0}/README.md

@@ -40,6 +40,9 @@ cd LBM-Suite2p-Python
 pip install ".[all]"  # optional, contains ".[gui, notebook]"
 ```
 
+## Issues
+Widgets may throw "Invalid Rect" errors. This can be safely ignored until it is [resolved](https://github.com/pygfx/wgpu-py/issues/716#issuecomment-2880853089).
+
 ---
 
 ## Acknowledgements

lbm_suite2p_python-2.0.0/lbm_suite2p_python/VERSION

@@ -0,0 +1 @@
+2.0.0

lbm_suite2p_python-2.0.0/lbm_suite2p_python/__init__.py

@@ -0,0 +1,36 @@
+from pathlib import Path
+# from lbm_suite2p_python.utils import *
+# from lbm_suite2p_python.volume import *
+# from lbm_suite2p_python.run_lsp import *
+# from lbm_suite2p_python.zplane import *
+# from lbm_suite2p_python.default_ops import default_ops
+
+# try:
+#     import suite3d
+# except ImportError:
+#     HAS_S3D = False
+# else:
+#     HAS_S3D = True
+
+__version__ = (Path(__file__).parent / "VERSION").read_text().strip()
+
+__all__ = [
+    # "run_volume",
+    # "run_plane",
+    # "plot_traces",
+    # "plot_volume_signal",
+    # "plot_projection",
+    # "plot_execution_time",
+    # "plot_noise_distribution",
+    # "animate_traces",
+    # "save_images_to_movie",
+    # "get_common_path",
+    # "update_ops_paths",
+    # "dff_rolling_percentile",
+    # "dff_maxmin",
+    # "dff_shot_noise",
+    # "combine_tiffs",
+    # "load_ops",
+    # "load_planar_results",
+    "default_ops",
+]

lbm_suite2p_python-2.0.0/lbm_suite2p_python/_benchmarking.py

@@ -0,0 +1,29 @@
+import psutil
+import subprocess
+
+
+def get_cpu_percent():
+    return psutil.cpu_percent(interval=None)
+
+
+def get_ram_used():
+    return psutil.virtual_memory().used // (1024 * 1024)
+
+
+def get_gpu_stats():
+    """Return (gpu_util%, mem_used_MiB) for GPU 0 (or zeros if unavailable)."""
+    try:
+        result = subprocess.run(
+            [
+                "nvidia-smi",
+                "--query-gpu=utilization.gpu,memory.used",
+                "--format=csv,noheader,nounits",
+            ],
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        util, mem = result.stdout.strip().split("\n")[0].split(", ")
+        return int(util), int(mem)
+    except Exception:
+        return 0, 0