optimouse 0.1.2__tar.gz → 0.1.4__tar.gz

{optimouse-0.1.2 → optimouse-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimouse
-Version: 0.1.2
+Version: 0.1.4
 Summary: 2-photon calcium imaging data processing pipeline with CaImAn / Suite2P
 Author-email: Vincent Prevosto <prevosto@mit.edu>, Manuel Levy <levym@mit.edu>
 License-Expression: MIT
@@ -47,9 +47,11 @@ Dynamic: license-file
 
 # 2P-proc (optimouse)
 
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
-[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![Suite2p Version](https://img.shields.io/badge/Suite2p-0.14.0-orange)](https://github.com/MouseLand/suite2p/releases/tag/v0.14.0)  
+
 [![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
 <!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
@@ -57,7 +59,7 @@ Dynamic: license-file
 **2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid or non-rigid)
 - **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
 - **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
@@ -237,6 +239,12 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 }
 ```
 
+Notes:
+- `params_extraction.main` accepts generic Suite2p ops overrides (passed through at ops creation).
+- See notes on parameters, and setting up a local Suite2p environment for testing: `suite2p/readme.md`.
+- `decay_time` is mapped to Suite2p `tau`. Use `decay_time` or `tau` interchangeably.
+
+
 ### 2. Run the pipeline
 
 **On a local machine:**

{optimouse-0.1.2 → optimouse-0.1.4}/README.md

@@ -1,8 +1,10 @@
 # 2P-proc (optimouse)
 
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
-[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![Suite2p Version](https://img.shields.io/badge/Suite2p-0.14.0-orange)](https://github.com/MouseLand/suite2p/releases/tag/v0.14.0)  
+
 [![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
 <!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
@@ -10,7 +12,7 @@
 **2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid or non-rigid)
 - **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
 - **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
@@ -190,6 +192,12 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 }
 ```
 
+Notes:
+- `params_extraction.main` accepts generic Suite2p ops overrides (passed through at ops creation).
+- See notes on parameters, and setting up a local Suite2p environment for testing: `suite2p/readme.md`.
+- `decay_time` is mapped to Suite2p `tau`. Use `decay_time` or `tau` interchangeably.
+
+
 ### 2. Run the pipeline
 
 **On a local machine:**

{optimouse-0.1.2 → optimouse-0.1.4}/optimouse.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimouse
-Version: 0.1.2
+Version: 0.1.4
 Summary: 2-photon calcium imaging data processing pipeline with CaImAn / Suite2P
 Author-email: Vincent Prevosto <prevosto@mit.edu>, Manuel Levy <levym@mit.edu>
 License-Expression: MIT
@@ -47,9 +47,11 @@ Dynamic: license-file
 
 # 2P-proc (optimouse)
 
+[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
 [![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
 [![CaImAn Version](https://img.shields.io/badge/CaImAn-1.12.2+-green)](https://github.com/flatironinstitute/CaImAn)
-[![PyPI Version](https://img.shields.io/pypi/v/optimouse)](https://pypi.org/project/optimouse/)
+[![Suite2p Version](https://img.shields.io/badge/Suite2p-0.14.0-orange)](https://github.com/MouseLand/suite2p/releases/tag/v0.14.0)  
+
 [![DOI](https://zenodo.org/badge/1141473002.svg)](https://doi.org/10.5281/zenodo.18371949)
 <!-- [![Build Status](https://img.shields.io/github/actions/workflow/status/vncntprvst/2P-proc/ci.yml)](https://github.com/vncntprvst/2P-proc/actions) -->
 ![License](https://img.shields.io/badge/license-MIT-red)
@@ -57,7 +59,7 @@ Dynamic: license-file
 **2P-proc (optimouse)** is a 2-photon calcium imaging data processing pipeline built on [CaImAn](https://github.com/flatironinstitute/CaImAn/), [Mesmerize](https://github.com/nel-lab/mesmerize-core/) and [Suite2p](https://github.com/MouseLand/suite2p).
 
 This package provides:
-- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid/non-rigid)
+- **Motion correction**: Rigid and non-rigid motion correction with optional z-drift correction (rigid or non-rigid)
 - **ROI extraction**: CNMF-based or Suite2p-based cell detection and segmentation
 - **Spike deconvolution**: Temporal activity inference from calcium signals
 - **Parameter optimization**: Notebooks for systematic parameter exploration (CaImAn NoRMCorre and CNMF)
@@ -237,6 +239,12 @@ Create a configuration JSON based on `pipeline/configs/config_template_cnmf.json
 }
 ```
 
+Notes:
+- `params_extraction.main` accepts generic Suite2p ops overrides (passed through at ops creation).
+- See notes on parameters, and setting up a local Suite2p environment for testing: `suite2p/readme.md`.
+- `decay_time` is mapped to Suite2p `tau`. Use `decay_time` or `tau` interchangeably.
+
+
 ### 2. Run the pipeline
 
 **On a local machine:**

{optimouse-0.1.2 → optimouse-0.1.4}/optimouse.egg-info/SOURCES.txt

@@ -18,6 +18,9 @@ pipeline/pipeline_cnmf.py
 pipeline/pipeline_mcorr.py
 pipeline/roi_zcorr.py
 pipeline/configs/config_C57_O1M2_10022023_run1run2.json
+pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p.json
+pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p_extractonly_localtest.json
+pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p_og.json
 pipeline/configs/config_C57_O1M2_10022023_run1run2run3run4.json
 pipeline/configs/config_template_cnmf.json
 pipeline/configs/config_template_suite2p.json

optimouse-0.1.4/pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p.json

@@ -0,0 +1,121 @@
+{
+    "experimenter": "Manuel Levy",
+    "subject": {
+        "name": "C57_O1M2",
+        "genotype": "C57/Bl6",
+        "sex": "F",
+        "DOB": "14-Feb-2023",
+        "virus": "PHP.eB.syn.RiboL1.GCaMP8m",
+        "reporter": "GCaMP8m",
+        "injection_date": "01-Aug-2023",
+        "area": "BC_R"
+    },
+    "imaging": {
+        "date": "10022023",
+        "objective": 16,
+        "numerical_zoom": 1,
+        "wavelength": 920,
+        "power": 530,
+        "depth": 160,
+        "fr": 20,
+        "Npixel_x": 765,
+        "Npixel_y": 765,
+        "microns_per_pixel": 1.4542483660130718
+    },
+    "paths": {
+        "concatenation_groups": [
+            1,
+            1
+        ],
+        "data_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-001",
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-002"
+        ],
+        "export_paths": [
+            "/home/wanglab/data/2P/Analysis_2P/C57_O1M2/10022023/run1run2/run1run2_tiff_suite2p"
+        ],
+        "__comment_zstack_paths": "Point to the raw z-stack directory. One per concatenation group (one per data folder works too). If not used, can be removed entirely or left empty.",
+        "zstack_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/ZSeries-10022023-1300-004"
+        ]
+    },
+    "params_mcorr": {
+        "__comment": "Motion correction parameters. Only 'caiman' is supported as method. Delete 'z_motion_correction' block entirely to skip z-motion correction.",
+        "method": "caiman",
+        "main": {
+            "strides": [
+                36,
+                36
+            ],
+            "overlaps": [
+                24,
+                24
+            ],
+            "max_shifts": [
+                12,
+                12
+            ],
+            "max_deviation_rigid": 40,
+            "border_nan": "copy",
+            "pw_rigid": true,
+            "gSig_filt": null
+        },
+        "__comment_save_mcorr_movie": "Accepted: 'tiff' (recommended); 'h5' and 'bin' exist but may not work in all workflows.",
+        "save_mcorr_movie": "tiff",
+        "z_motion_correction": {
+            "zstack_shift": {
+                "Ch": 2,
+                "alpha": 22,
+                "beta": 8,
+                "step": 1,
+                "Nz": 41
+            },
+            "__comment": "Set 'non_rigid' to true to compute f-anat non-rigid. If false, will only compute a rigid z-position.",
+            "non_rigid": false
+        }
+    },
+    "params_extraction": {
+        "__comment": "ROI extraction method choices after motion correction.",
+        "__method_options": [
+            "suite2p",
+            "cnmf",
+            "aind",
+            "none"
+        ],
+        "method": "suite2p",
+        "__suite2p_parameter_options": {
+            "__comment": "Add any Suite2p ops key under 'main' to override Suite2p defaults at ops creation. Keep 'decay_time' (or 'tau') as the minimum required field.",
+            "decay_time_or_tau": "Calcium decay time in seconds (mapped to Suite2p 'tau').",
+            "threshold_scaling": "Detection threshold multiplier; lower finds more ROIs.",
+            "max_overlap": "Maximum allowed ROI overlap before rejection.",
+            "diameter": "Expected ROI diameter in pixels.",
+            "inner_neuropil_radius": "Pixels excluded around ROI for neuropil estimate.",
+            "snr_thresh": "Nonrigid registration SNR threshold.",
+            "do_registration": "1/0 or true/false to enable/disable registration in Suite2p step.",
+            "nonrigid": "true/false for nonrigid registration.",
+            "maxregshift": "Maximum rigid registration shift (fraction of frame size).",
+            "sparse_mode": "true/false sparse ROI detection mode.",
+            "pre_smooth": "Registration pre-smoothing level.",
+            "max_iterations": "Maximum ROI detection refinement iterations."
+        },
+        "main": {
+            "decay_time": 0.3,
+            "threshold_scaling": 0.85,
+            "max_overlap": 0.6,
+            "diameter": 14,
+            "inner_neuropil_radius": 3,
+            "snr_thresh": 1.0,
+            "max_iterations": 35,
+            "sparse_mode": true,
+            "pre_smooth": 1
+        }
+    },
+    "params_extra": {
+        "cleanup": true
+    },
+    "logging": {
+        "__comment": "Where pipeline log files are stored (defaults to export parent).",
+        "log_path": "/home/wanglab/data/2P/Analysis_2P/C57_O1M2",
+        "log_level": "INFO"
+    }
+}

optimouse-0.1.4/pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p_extractonly_localtest.json

@@ -0,0 +1,121 @@
+{
+    "paths": {
+        "export_paths": [
+            "/home/wanglab/data/2P/Analysis_2P/C57_O1M2/10022023/run1run2/run1run2_tiff_suite2p"
+        ],
+        "zstack_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/ZSeries-10022023-1300-004"
+        ],
+        "concatenation_groups": [
+            1,
+            1
+        ],
+        "__comment_zstack_paths": "Point to the raw z-stack directory. One per concatenation group (one per data folder works too). If not used, can be removed entirely or left empty.",
+        "data_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-001",
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-002"
+        ]
+    },
+    "logging": {
+        "__comment": "Where pipeline log files are stored (defaults to export parent).",
+        "log_path": "/home/wanglab/data/2P/Analysis_2P/C57_O1M2",
+        "log_level": "INFO"
+    },
+    "params_extra": {
+        "cleanup": true
+    },
+    "experimenter": "Manuel Levy",
+    "imaging": {
+        "Npixel_y": 765,
+        "fr": 20,
+        "power": 530,
+        "microns_per_pixel": 1.4542483660130718,
+        "depth": 160,
+        "objective": 16,
+        "numerical_zoom": 1,
+        "Npixel_x": 765,
+        "date": "10022023",
+        "wavelength": 920
+    },
+    "params_extraction": {
+        "__comment": "ROI extraction method choices after motion correction.",
+        "main": {
+            "diameter": 14,
+            "inner_neuropil_radius": 3,
+            "max_overlap": 0.6,
+            "pre_smooth": 1,
+            "threshold_scaling": 0.85,
+            "sparse_mode": true,
+            "snr_thresh": 1.0,
+            "decay_time": 0.3,
+            "max_iterations": 35
+        },
+        "__suite2p_parameter_options": {
+            "__comment": "Add any Suite2p ops key under 'main' to override Suite2p defaults at ops creation. Keep 'decay_time' (or 'tau') as the minimum required field.",
+            "diameter": "Expected ROI diameter in pixels.",
+            "inner_neuropil_radius": "Pixels excluded around ROI for neuropil estimate.",
+            "max_overlap": "Maximum allowed ROI overlap before rejection.",
+            "pre_smooth": "Registration pre-smoothing level.",
+            "threshold_scaling": "Detection threshold multiplier; lower finds more ROIs.",
+            "maxregshift": "Maximum rigid registration shift (fraction of frame size).",
+            "do_registration": "1/0 or true/false to enable/disable registration in Suite2p step.",
+            "sparse_mode": "true/false sparse ROI detection mode.",
+            "snr_thresh": "Nonrigid registration SNR threshold.",
+            "decay_time_or_tau": "Calcium decay time in seconds (mapped to Suite2p 'tau').",
+            "nonrigid": "true/false for nonrigid registration.",
+            "max_iterations": "Maximum ROI detection refinement iterations."
+        },
+        "method": "suite2p",
+        "__method_options": [
+            "suite2p",
+            "cnmf",
+            "aind",
+            "none"
+        ]
+    },
+    "params_mcorr": {
+        "__comment": "Motion correction parameters. Only 'caiman' is supported as method. Delete 'z_motion_correction' block entirely to skip z-motion correction.",
+        "__comment_save_mcorr_movie": "Accepted: 'tiff' (recommended); 'h5' and 'bin' exist but may not work in all workflows.",
+        "save_mcorr_movie": "tiff",
+        "z_motion_correction": {
+            "__comment": "Set 'non_rigid' to true to compute f-anat non-rigid. If false, will only compute a rigid z-position.",
+            "non_rigid": false,
+            "zstack_shift": {
+                "alpha": 22,
+                "beta": 8,
+                "Ch": 2,
+                "step": 1,
+                "Nz": 41
+            }
+        },
+        "main": {
+            "overlaps": [
+                24,
+                24
+            ],
+            "border_nan": "copy",
+            "max_shifts": [
+                12,
+                12
+            ],
+            "strides": [
+                36,
+                36
+            ],
+            "pw_rigid": true,
+            "gSig_filt": null,
+            "max_deviation_rigid": 40
+        },
+        "method": "none"
+    },
+    "subject": {
+        "name": "C57_O1M2",
+        "reporter": "GCaMP8m",
+        "DOB": "14-Feb-2023",
+        "area": "BC_R",
+        "sex": "F",
+        "virus": "PHP.eB.syn.RiboL1.GCaMP8m",
+        "injection_date": "01-Aug-2023",
+        "genotype": "C57/Bl6"
+    }
+}

optimouse-0.1.4/pipeline/configs/config_C57_O1M2_10022023_run1run2_tiff_suite2p_og.json

@@ -0,0 +1,113 @@
+{
+    "experimenter": "Manuel Levy",
+    "subject": {
+        "name": "C57_O1M2",
+        "genotype": "C57/Bl6",
+        "sex": "F",
+        "DOB": "14-Feb-2023",
+        "virus": "PHP.eB.syn.RiboL1.GCaMP8m",
+        "reporter": "GCaMP8m",
+        "injection_date": "01-Aug-2023",
+        "area": "BC_R"
+    },
+    "imaging": {
+        "date": "10022023",
+        "objective": 16,
+        "numerical_zoom": 1,
+        "wavelength": 920,
+        "power": 530,
+        "depth": 160,
+        "fr": 20,
+        "Npixel_x": 765,
+        "Npixel_y": 765,
+        "microns_per_pixel": 1.4542483660130718
+    },
+    "paths": {
+        "concatenation_groups": [
+            1,
+            1
+        ],
+        "data_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-001",
+            "/home/wanglab/data/2P/C57_O1M2/10022023/TSeries-10022023-1300-002"
+        ],
+        "export_paths": [
+            "/home/wanglab/data/2P/Analysis_2P/C57_O1M2/10022023/run1run2/run1run2_tiff_suite2p"
+        ],
+        "__comment_zstack_paths": "Point to the raw z-stack directory. One per concatenation group (one per data folder works too). If not used, can be removed entirely or left empty.",
+        "zstack_paths": [
+            "/home/wanglab/data/2P/C57_O1M2/10022023/ZSeries-10022023-1300-004"
+        ]
+    },
+    "params_mcorr": {
+        "__comment": "Motion correction parameters. Only 'caiman' is supported as method. Delete 'z_motion_correction' block entirely to skip z-motion correction.",
+        "method": "caiman",
+        "main": {
+            "strides": [
+                36,
+                36
+            ],
+            "overlaps": [
+                24,
+                24
+            ],
+            "max_shifts": [
+                12,
+                12
+            ],
+            "max_deviation_rigid": 40,
+            "border_nan": "copy",
+            "pw_rigid": true,
+            "gSig_filt": null
+        },
+        "__comment_save_mcorr_movie": "Accepted: 'tiff' (recommended); 'h5' and 'bin' exist but may not work in all workflows.",
+        "save_mcorr_movie": "tiff",
+        "z_motion_correction": {
+            "zstack_shift": {
+                "Ch": 2,
+                "alpha": 22,
+                "beta": 8,
+                "step": 1,
+                "Nz": 41
+            },
+            "__comment": "Set 'non_rigid' to true to compute f-anat non-rigid. If false, will only compute a rigid z-position.",
+            "non_rigid": false
+        }
+    },
+    "params_extraction": {
+        "__comment": "ROI extraction method choices after motion correction.",
+        "__method_options": [
+            "suite2p",
+            "cnmf",
+            "aind",
+            "none"
+        ],
+        "method": "suite2p",
+        "__suite2p_parameter_options": {
+            "__comment": "Add any Suite2p ops key under 'main' to override Suite2p defaults at ops creation. Keep 'decay_time' (or 'tau') as the minimum required field.",
+            "decay_time_or_tau": "Calcium decay time in seconds (mapped to Suite2p 'tau').",
+            "threshold_scaling": "Detection threshold multiplier; lower finds more ROIs.",
+            "max_overlap": "Maximum allowed ROI overlap before rejection.",
+            "diameter": "Expected ROI diameter in pixels.",
+            "inner_neuropil_radius": "Pixels excluded around ROI for neuropil estimate.",
+            "snr_thresh": "Nonrigid registration SNR threshold.",
+            "do_registration": "1/0 or true/false to enable/disable registration in Suite2p step.",
+            "nonrigid": "true/false for nonrigid registration.",
+            "maxregshift": "Maximum rigid registration shift (fraction of frame size).",
+            "sparse_mode": "true/false sparse ROI detection mode.",
+            "pre_smooth": "Registration pre-smoothing level.",
+            "max_iterations": "Maximum ROI detection refinement iterations."
+        },
+        "main": {
+            "decay_time": 0.3
+        }
+    },
+    "params_extra": {
+        "cleanup": true
+    },
+    "logging": {
+        "__comment": "Where pipeline log files are stored (defaults to export parent).",
+        "log_path": "/home/wanglab/data/2P/Analysis_2P/C57_O1M2",
+        "log_level": "INFO"
+    }
+}

{optimouse-0.1.2 → optimouse-0.1.4}/pipeline/configs/config_template_suite2p.json

@@ -87,6 +87,21 @@
             "none"
         ],
         "method": "suite2p",
+        "__suite2p_parameter_options": {
+            "__comment": "Add any Suite2p ops key under 'main' to override Suite2p defaults at ops creation. Keep 'decay_time' (or 'tau') as the minimum required field.",
+            "decay_time_or_tau": "Calcium decay time in seconds (mapped to Suite2p 'tau').",
+            "threshold_scaling": "Detection threshold multiplier; lower finds more ROIs.",
+            "max_overlap": "Maximum allowed ROI overlap before rejection.",
+            "diameter": "Expected ROI diameter in pixels.",
+            "inner_neuropil_radius": "Pixels excluded around ROI for neuropil estimate.",
+            "snr_thresh": "Nonrigid registration SNR threshold.",
+            "do_registration": "1/0 or true/false to enable/disable registration in Suite2p step.",
+            "nonrigid": "true/false for nonrigid registration.",
+            "maxregshift": "Maximum rigid registration shift (fraction of frame size).",
+            "sparse_mode": "true/false sparse ROI detection mode.",
+            "pre_smooth": "Registration pre-smoothing level.",
+            "max_iterations": "Maximum ROI detection refinement iterations."
+        },
         "main": {
             "decay_time": 0.3
         }

{optimouse-0.1.2 → optimouse-0.1.4}/pipeline/utils/pipeline_utils.py

@@ -188,14 +188,24 @@ def cleanup_files(batch_path, export_path, preserve_batch=False):
                 batch_runfile.unlink()
             batch_dir = Path(export_path) / batch_id
             if batch_dir.exists():
-                for attempt in range(3):
+                max_attempts = 6
+                for attempt in range(max_attempts):
                     time.sleep(1 + attempt)
                     try:
                         shutil.rmtree(batch_dir)
                         break
                     except Exception as e:
-                        if attempt == 2:
-                            log_and_print(f"Could not delete {batch_dir}: {e}")
+                        if attempt == max_attempts - 1:
+                            nfs_files = list(batch_dir.glob(".nfs*"))
+                            if nfs_files:
+                                log_and_print(
+                                    f"Could not delete {batch_dir}: {e}. "
+                                    f"Detected NFS temp files: {[p.name for p in nfs_files]}. "
+                                    "A process likely still holds an open handle; retry later.",
+                                    level="warning",
+                                )
+                            else:
+                                log_and_print(f"Could not delete {batch_dir}: {e}")
         for pickle_file in Path(export_path).glob("batch_*.pickle"):
             pickle_file.unlink()
 

{optimouse-0.1.2 → optimouse-0.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "optimouse"
-version = "0.1.2"
+version = "0.1.4"
 description = "2-photon calcium imaging data processing pipeline with CaImAn / Suite2P"
 readme = "README.md"
 requires-python = ">=3.10"