unitrefine 0.2.0__tar.gz

unitrefine-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Anoushka Jain
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

unitrefine-0.2.0/MANIFEST.in

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+# What the source package (sdist) on PyPI contains besides src/unitrefine: the tests with their helpers, so they
+# can be run from it, but not the paper's notebooks, datasets and tutorials in UnitRefine/ (they are on GitHub)
+recursive-include tests *.py
+prune UnitRefine
+prune UnitRefine.egg-info

unitrefine-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: unitrefine
+Version: 0.2.0
+Summary: UnitRefine is a machine-learning toolbox that simplifies spike sorting curation by reducing manual curation.
+Author-email: Anoushka Jain <jain.anoushka3@gmail.com>, Chris Halcrow <chrishalcrow@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/anoushkajain/UnitRefine
+Project-URL: Documentation, https://github.com/anoushkajain/UnitRefine#readme
+Project-URL: Issues, https://github.com/anoushkajain/UnitRefine/issues
+Project-URL: Preprint, https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2
+Project-URL: Models, https://huggingface.co/AnoushkaJain3
+Keywords: spike sorting,curation,electrophysiology,machine learning,neuropixels,spikeinterface
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numcodecs==0.15.1
+Requires-Dist: numba>=0.61.0
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: spikeinterface>=0.105.0
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: scikit-learn==1.7
+Requires-Dist: skops>=0.11.0
+Requires-Dist: huggingface-hub>=0.35.0
+Requires-Dist: s3fs>=2025.10.0
+Requires-Dist: mtscomp>=1.0.2
+Provides-Extra: gui
+Requires-Dist: spikeinterface-gui>=0.14.0; extra == "gui"
+Requires-Dist: pyqtgraph>=0.13.7; extra == "gui"
+Requires-Dist: pyqt5>=5.15.11; extra == "gui"
+Requires-Dist: pyqt5-qt5<5.15.18; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "gui"
+Requires-Dist: pyqt5-qt5>=5.15.0; sys_platform == "darwin" and extra == "gui"
+Requires-Dist: pyqt5-qt5>=5.15.0; sys_platform == "linux" and extra == "gui"
+Requires-Dist: matplotlib>=3.8; extra == "gui"
+Requires-Dist: shap>=0.49.1; extra == "gui"
+Dynamic: license-file
+
+# UnitRefine: a community toolbox for automated spike sorting curation
+
+[![Tests](https://github.com/anoushkajain/UnitRefine/actions/workflows/tests.yml/badge.svg)](https://github.com/anoushkajain/UnitRefine/actions/workflows/tests.yml)
+[![License](https://img.shields.io/badge/license-MIT-blue)](https://github.com/anoushkajain/UnitRefine/blob/main/LICENSE)
+
+**UnitRefine** labels spike sorted units as **single units (SUA)**, **multi-units (MUA)** or **noise** with machine
+learning classifiers trained on human curation, so you don't have to curate every unit by hand. It works with any
+probe, species, brain region and spike sorter, and is part of [SpikeInterface](https://github.com/SpikeInterface/spikeinterface).
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/anoushkajain/UnitRefine/main/src/unitrefine/resources/unit_types_example.jpg" width="500"/>
+</p>
+
+With UnitRefine you can:
+
+- label your units with [pretrained models](#pretrained-models)
+- train your own model on your labels, and improve it with active learning, in the [GUI](#the-gui)
+- apply models to many recordings on a [computing cluster](https://github.com/anoushkajain/UnitRefine/blob/main/docs/hpc.md)
+- share models on the [Hugging Face Hub](https://huggingface.co/AnoushkaJain3)
+
+## Preprint
+
+UnitRefine and its validation on mouse, naked mole rat, monkey and human recordings are described in our
+[preprint](https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2).
+
+## The GUI
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/anoushkajain/UnitRefine/main/docs/images/gui_window.png" width="700"/>
+</p>
+
+```bash
+unitrefine --project_folder my_project
+```
+
+A new project comes with the pretrained models. Add your spike sorted data in section 3.3 (a Sorting Analyzer, or a
+Kilosort output folder curated in Phy) and UnitRefine model labels
+its units. To train your own model, label units in the
+[SpikeInterface-GUI](https://github.com/SpikeInterface/spikeinterface-gui/) or import labels you already have.
+
+See the **[GUI tutorial](https://github.com/anoushkajain/UnitRefine/blob/main/src/unitrefine/README.md)** for all steps.
+
+## Pretrained models
+
+A new project downloads these three models from the Hugging Face Hub:
+
+| Model | Labels |
+|-------|--------|
+| [noise vs neural](https://huggingface.co/SpikeInterface/UnitRefine_noise_neural_classifier) + [SUA vs MUA](https://huggingface.co/SpikeInterface/UnitRefine_sua_mua_classifier), used together as a cascade | good (SUA), MUA, noise |
+| [generalized SUA classifier](https://huggingface.co/AnoushkaJain3/UnitRefine-generalized-sua-classifier) | SUA, not SUA |
+
+UnitRefine was trained and tested on these datasets ([more models](https://huggingface.co/AnoushkaJain3)):
+
+| Dataset | Species | Probe | Spike sorter |
+|---------|---------|-------|--------------|
+| UnitRefine base dataset | Mouse | Neuropixels 1.0 | Kilosort 2.5 |
+| International Brain Laboratory | Mouse | Neuropixels 1.0 | IBL sorter (PyKilosort 2.5) |
+| Allen Institute | Mouse | Neuropixels 2.0 | Kilosort 4 |
+| [Shirdhankar et al., 2025](https://doi.org/10.64898/2025.12.15.693140) | Naked mole rat | Neuropixels 2.0 | Kilosort 4 |
+| [Chen et al., 2022](https://www.nature.com/articles/s41597-022-01180-1) | Rhesus macaque | Utah array | Kilosort 4 |
+| [Gerken et al., 2025](https://elifesciences.org/reviewed-preprints/106758) | Human | Behnke–Fried electrodes | Combinato |
+The curated datasets are on [figshare](https://figshare.com/articles/dataset/Curated_dataset/28282799).
+
+## Installation
+
+```bash
+conda create -n unitrefine python=3.13
+conda activate unitrefine
+pip install uv
+uv pip install "unitrefine[gui]"
+```
+
+Without the GUI, e.g. on a computing cluster: `uv pip install unitrefine`. To install from the repository, with
+conda only, or if installing fails, see [Installation](https://github.com/anoushkajain/UnitRefine/blob/main/docs/installation.md).
+
+## Documentation
+
+- [GUI tutorial](https://github.com/anoushkajain/UnitRefine/blob/main/src/unitrefine/README.md)
+- [Tutorial notebooks](https://github.com/anoushkajain/UnitRefine/blob/main/docs/tutorials.md): apply and train models in Python, use a `.csv` of metrics, SHAP plots
+- [Applying models on a computing cluster](https://github.com/anoushkajain/UnitRefine/blob/main/docs/hpc.md)
+- [Installation](https://github.com/anoushkajain/UnitRefine/blob/main/docs/installation.md)
+- [Automated curation in SpikeInterface](https://spikeinterface.readthedocs.io/en/latest/tutorials_custom_index.html#automated-curation-tutorials)
+
+## Citation
+
+If you find UnitRefine useful in your research, please cite:
+
+```bibtex
+@article{jain2025unitrefine,
+  title={UnitRefine: A Community Toolbox for Automated Spike Sorting Curation},
+  author={Jain, Anoushka and Greene, Robyn and Halcrow, Chris and Swann, Jake A and Kleinjohann, Alexander and Spurio, Federico and Graff, Severin and Pan-Vazquez, Alejandro and Kampa, Bj{\"o}rn and Gall, Juergen and Gr{\"u}n, Sonja and Winter, Olivier and Buccino, Alessio and Hennig, Matthias H and Musall, Simon},
+  journal={bioRxiv},
+  year={2025},
+  doi={10.1101/2025.03.30.645770}
+}
+```
+
+## Acknowledgements
+
+UnitRefine builds on [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) and
+[SpikeInterface-GUI](https://github.com/SpikeInterface/spikeinterface-gui/). Many thanks to Alessio, Sam, Zack and Joe
+for their help and feedback, and to the whole SpikeInterface team.
+
+- **Code refactoring and integration in SpikeInterface:** Chris Halcrow, Jake Swann, Robyn Greene, Sangeetha Nandakumar (IBOTS)
+- **Model curators:** Nilufar Lahiji, Sacha Abou Rachid, Severin Graff, Luca Koenig, Natalia Babushkina, Simon Musall
+- **Advisors and collaborators:** Alessio Buccino, Olivier Winter, Sonja Grün, Matthias Hennig, Simon Musall
+
+Feedback and contributions are welcome: please [open an issue](https://github.com/anoushkajain/UnitRefine/issues) or a
+pull request. UnitRefine is released under the MIT license.

unitrefine-0.2.0/README.md

@@ -0,0 +1,109 @@
+# UnitRefine: a community toolbox for automated spike sorting curation
+
+[![Tests](https://github.com/anoushkajain/UnitRefine/actions/workflows/tests.yml/badge.svg)](https://github.com/anoushkajain/UnitRefine/actions/workflows/tests.yml)
+[![License](https://img.shields.io/badge/license-MIT-blue)](https://github.com/anoushkajain/UnitRefine/blob/main/LICENSE)
+
+**UnitRefine** labels spike sorted units as **single units (SUA)**, **multi-units (MUA)** or **noise** with machine
+learning classifiers trained on human curation, so you don't have to curate every unit by hand. It works with any
+probe, species, brain region and spike sorter, and is part of [SpikeInterface](https://github.com/SpikeInterface/spikeinterface).
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/anoushkajain/UnitRefine/main/src/unitrefine/resources/unit_types_example.jpg" width="500"/>
+</p>
+
+With UnitRefine you can:
+
+- label your units with [pretrained models](#pretrained-models)
+- train your own model on your labels, and improve it with active learning, in the [GUI](#the-gui)
+- apply models to many recordings on a [computing cluster](https://github.com/anoushkajain/UnitRefine/blob/main/docs/hpc.md)
+- share models on the [Hugging Face Hub](https://huggingface.co/AnoushkaJain3)
+
+## Preprint
+
+UnitRefine and its validation on mouse, naked mole rat, monkey and human recordings are described in our
+[preprint](https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2).
+
+## The GUI
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/anoushkajain/UnitRefine/main/docs/images/gui_window.png" width="700"/>
+</p>
+
+```bash
+unitrefine --project_folder my_project
+```
+
+A new project comes with the pretrained models. Add your spike sorted data in section 3.3 (a Sorting Analyzer, or a
+Kilosort output folder curated in Phy) and UnitRefine model labels
+its units. To train your own model, label units in the
+[SpikeInterface-GUI](https://github.com/SpikeInterface/spikeinterface-gui/) or import labels you already have.
+
+See the **[GUI tutorial](https://github.com/anoushkajain/UnitRefine/blob/main/src/unitrefine/README.md)** for all steps.
+
+## Pretrained models
+
+A new project downloads these three models from the Hugging Face Hub:
+
+| Model | Labels |
+|-------|--------|
+| [noise vs neural](https://huggingface.co/SpikeInterface/UnitRefine_noise_neural_classifier) + [SUA vs MUA](https://huggingface.co/SpikeInterface/UnitRefine_sua_mua_classifier), used together as a cascade | good (SUA), MUA, noise |
+| [generalized SUA classifier](https://huggingface.co/AnoushkaJain3/UnitRefine-generalized-sua-classifier) | SUA, not SUA |
+
+UnitRefine was trained and tested on these datasets ([more models](https://huggingface.co/AnoushkaJain3)):
+
+| Dataset | Species | Probe | Spike sorter |
+|---------|---------|-------|--------------|
+| UnitRefine base dataset | Mouse | Neuropixels 1.0 | Kilosort 2.5 |
+| International Brain Laboratory | Mouse | Neuropixels 1.0 | IBL sorter (PyKilosort 2.5) |
+| Allen Institute | Mouse | Neuropixels 2.0 | Kilosort 4 |
+| [Shirdhankar et al., 2025](https://doi.org/10.64898/2025.12.15.693140) | Naked mole rat | Neuropixels 2.0 | Kilosort 4 |
+| [Chen et al., 2022](https://www.nature.com/articles/s41597-022-01180-1) | Rhesus macaque | Utah array | Kilosort 4 |
+| [Gerken et al., 2025](https://elifesciences.org/reviewed-preprints/106758) | Human | Behnke–Fried electrodes | Combinato |
+The curated datasets are on [figshare](https://figshare.com/articles/dataset/Curated_dataset/28282799).
+
+## Installation
+
+```bash
+conda create -n unitrefine python=3.13
+conda activate unitrefine
+pip install uv
+uv pip install "unitrefine[gui]"
+```
+
+Without the GUI, e.g. on a computing cluster: `uv pip install unitrefine`. To install from the repository, with
+conda only, or if installing fails, see [Installation](https://github.com/anoushkajain/UnitRefine/blob/main/docs/installation.md).
+
+## Documentation
+
+- [GUI tutorial](https://github.com/anoushkajain/UnitRefine/blob/main/src/unitrefine/README.md)
+- [Tutorial notebooks](https://github.com/anoushkajain/UnitRefine/blob/main/docs/tutorials.md): apply and train models in Python, use a `.csv` of metrics, SHAP plots
+- [Applying models on a computing cluster](https://github.com/anoushkajain/UnitRefine/blob/main/docs/hpc.md)
+- [Installation](https://github.com/anoushkajain/UnitRefine/blob/main/docs/installation.md)
+- [Automated curation in SpikeInterface](https://spikeinterface.readthedocs.io/en/latest/tutorials_custom_index.html#automated-curation-tutorials)
+
+## Citation
+
+If you find UnitRefine useful in your research, please cite:
+
+```bibtex
+@article{jain2025unitrefine,
+  title={UnitRefine: A Community Toolbox for Automated Spike Sorting Curation},
+  author={Jain, Anoushka and Greene, Robyn and Halcrow, Chris and Swann, Jake A and Kleinjohann, Alexander and Spurio, Federico and Graff, Severin and Pan-Vazquez, Alejandro and Kampa, Bj{\"o}rn and Gall, Juergen and Gr{\"u}n, Sonja and Winter, Olivier and Buccino, Alessio and Hennig, Matthias H and Musall, Simon},
+  journal={bioRxiv},
+  year={2025},
+  doi={10.1101/2025.03.30.645770}
+}
+```
+
+## Acknowledgements
+
+UnitRefine builds on [SpikeInterface](https://github.com/SpikeInterface/spikeinterface) and
+[SpikeInterface-GUI](https://github.com/SpikeInterface/spikeinterface-gui/). Many thanks to Alessio, Sam, Zack and Joe
+for their help and feedback, and to the whole SpikeInterface team.
+
+- **Code refactoring and integration in SpikeInterface:** Chris Halcrow, Jake Swann, Robyn Greene, Sangeetha Nandakumar (IBOTS)
+- **Model curators:** Nilufar Lahiji, Sacha Abou Rachid, Severin Graff, Luca Koenig, Natalia Babushkina, Simon Musall
+- **Advisors and collaborators:** Alessio Buccino, Olivier Winter, Sonja Grün, Matthias Hennig, Simon Musall
+
+Feedback and contributions are welcome: please [open an issue](https://github.com/anoushkajain/UnitRefine/issues) or a
+pull request. UnitRefine is released under the MIT license.

unitrefine-0.2.0/pyproject.toml

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+[project]
+name = "unitrefine"
+version = "0.2.0"
+description = "UnitRefine is a machine-learning toolbox that simplifies spike sorting curation by reducing manual curation."
+authors = [
+    { name = "Anoushka Jain", email = "jain.anoushka3@gmail.com" },
+    { name = "Chris Halcrow", email = "chrishalcrow@gmail.com" },
+]
+readme = "README.md"
+requires-python = ">=3.11,<3.14"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = ["spike sorting", "curation", "electrophysiology", "machine learning", "neuropixels", "spikeinterface"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+# what applying models needs, also without a screen, e.g. on a computing cluster (unitrefine-apply, see docs/hpc.md)
+dependencies = [
+    "numcodecs==0.15.1",
+    "numba>=0.61.0",
+    "pandas>=2.2.3",
+    "spikeinterface>=0.105.0",
+    "pyyaml>=6.0.2",
+    "scikit-learn==1.7",
+    "skops>=0.11.0",
+    "huggingface-hub>=0.35.0",
+    "s3fs>=2025.10.0",
+    # reading compressed IBL recordings (.cbin), e.g. for + Phy output
+    "mtscomp>=1.0.2",
+]
+
+[project.optional-dependencies]
+# the GUI: pip install "unitrefine[gui]". `uv sync` installs it too (see default-groups below)
+gui = [
+    "spikeinterface-gui>=0.14.0",
+    "pyqtgraph>=0.13.7",
+    "pyqt5>=5.15.11",
+    "pyqt5-qt5<5.15.18; sys_platform == 'win32' and platform_machine == 'AMD64'",
+    "pyqt5-qt5>=5.15.0; sys_platform == 'darwin'",
+    "pyqt5-qt5>=5.15.0; sys_platform == 'linux'",
+    "matplotlib>=3.8",
+    "shap>=0.49.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/anoushkajain/UnitRefine"
+Documentation = "https://github.com/anoushkajain/UnitRefine#readme"
+Issues = "https://github.com/anoushkajain/UnitRefine/issues"
+Preprint = "https://www.biorxiv.org/content/10.1101/2025.03.30.645770v2"
+Models = "https://huggingface.co/AnoushkaJain3"
+
+[build-system]
+# 77: the license as `license = "MIT"`
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+# resources holds the images and fonts used by the GUI
+packages = ["unitrefine", "unitrefine.resources", "unitrefine.resources.fonts"]
+package-dir = {"unitrefine" = "src/unitrefine"}
+
+[tool.setuptools.package-data]
+"unitrefine.resources" = ["*"]
+"unitrefine.resources.fonts" = ["*"]
+
+[project.scripts]
+unitrefine = "unitrefine.launcher:main"
+# without the GUI, e.g. on a computing cluster (see src/unitrefine/cli.py)
+unitrefine-apply = "unitrefine.cli:apply_main"
+unitrefine-download-models = "unitrefine.cli:download_main"
+
+[dependency-groups]
+# for running the tests: uv run pytest
+dev = ["pytest>=8"]
+# so `uv sync` installs the GUI, as it always has. Without it: uv sync --no-group gui
+gui = ["unitrefine[gui]"]
+
+[tool.uv]
+default-groups = ["dev", "gui"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+filterwarnings = [
+    # from the small synthetic recordings the tests make
+    "ignore::UserWarning:spikeinterface.*",
+    "ignore::DeprecationWarning",
+]
+
+

unitrefine-0.2.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

unitrefine-0.2.0/src/unitrefine/__init__.py

@@ -0,0 +1,75 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    # the version in pyproject.toml, e.g. to say which version a problem was found with
+    __version__ = version("unitrefine")
+except PackageNotFoundError:
+    # run from the source folder without installing it
+    __version__ = "unknown"
+
+# The SpikeInterface-GUI scripts run in their own process. They print these markers so the main
+# window can show which step they are on while they open, and when their window is shown.
+SIGUI_SHOWN_MARKER = "UNITREFINE_SIGUI_WINDOW_SHOWN"
+SIGUI_STEP_MARKER = "UNITREFINE_SIGUI_STEP:"
+# printed when labels could not be saved where they belong and were saved to a backup file instead
+LABELS_BACKUP_MARKER = "UNITREFINE_LABELS_BACKUP:"
+
+
+# The labels are passed to the SpikeInterface-GUI in curation format 2, which spikeinterface-gui handles
+# correctly (also for units shown without a label) from this version on
+MINIMUM_SIGUI_VERSION = "0.14.0"
+
+
+def check_sigui_version():
+    """
+    Stops the SpikeInterface-GUI script with a clear message if spikeinterface-gui is too old: older versions
+    would not save the labels set with the n/g/m keys correctly.
+    """
+    import sys
+    from packaging.version import parse
+    import spikeinterface_gui
+
+    installed = getattr(spikeinterface_gui, "__version__", "0")
+    if parse(installed) < parse(MINIMUM_SIGUI_VERSION):
+        print(f"UnitRefine needs spikeinterface-gui {MINIMUM_SIGUI_VERSION} or newer, but {installed} is installed, "
+              f"which would not save your labels correctly. Please upgrade it, e.g. with "
+              f"'pip install --upgrade spikeinterface-gui' or 'uv sync'.", flush=True)
+        sys.exit(1)
+
+
+def unwritable_file_message(path, error):
+    """What to tell the user when a file can't be written, e.g. because it is read-only."""
+    advice = ("The file is read-only or open in another program. In File Explorer, right-click it, choose "
+              "Properties and untick 'Read-only' (or close the other program), then try again.")
+    return f"UnitRefine could not save {path}:\n{error}\n\n{advice}"
+
+
+def save_labels_or_backup(labels, path, write=None, **to_csv_kwargs):
+    """
+    Saves the labels set in the SpikeInterface-GUI to `path` (with `write(labels, path)` if given). If that
+    fails, e.g. because the file is read-only, the labels are saved to a backup file in the home folder, so
+    they are not lost, and the main window is told where (LABELS_BACKUP_MARKER). Returns where they were saved.
+    """
+    import time
+    from pathlib import Path
+
+    path = Path(path)
+    try:
+        if write is not None:
+            write(labels, path)
+        else:
+            labels.to_csv(path, **to_csv_kwargs)
+        return path
+    except OSError as error:
+        backup = Path.home() / f"UnitRefine_unsaved_{time.strftime('%Y%m%d_%H%M%S')}_{path.name}"
+        labels.to_csv(backup, **to_csv_kwargs)
+        print(unwritable_file_message(path, error), flush=True)
+        print(f"Your labels were saved to {backup} instead. Once {path.name} can be written, copy that file over it.",
+              flush=True)
+        print(f"{LABELS_BACKUP_MARKER}{backup}|{path}", flush=True)
+        return backup
+
+
+def report_sigui_step(step_name):
+    """Called by the SpikeInterface-GUI scripts when they start a step, e.g. 'loading'."""
+    print(f"{SIGUI_STEP_MARKER}{step_name}", flush=True)

unitrefine-0.2.0/src/unitrefine/apply_models.py

@@ -0,0 +1,111 @@
+from pathlib import Path
+
+import PyQt5.QtWidgets as QtWidgets
+from spikeinterface_gui.main import check_folder_is_analyzer
+
+from unitrefine.predictions import find_analyzers
+
+
+class ApplyModelsDialog(QtWidgets.QDialog):
+    """Pick the analyzers to apply the selected models to, and the folder to save the predictions in."""
+
+    def __init__(self, selection_text, default_output_folder, parent=None):
+
+        super().__init__(parent)
+
+        self.setWindowTitle("UNITREFINE: Apply models to analyzers")
+        self.setMinimumWidth(650)
+
+        layout = QtWidgets.QVBoxLayout(self)
+
+        selection_label = QtWidgets.QLabel(f"Models: {selection_text}")
+        selection_label.setWordWrap(True)
+        layout.addWidget(selection_label)
+
+        analyzers_label = QtWidgets.QLabel("Analyzers the models will be applied to:")
+        analyzers_label.setStyleSheet("font-weight: bold;")
+        layout.addWidget(analyzers_label)
+
+        self.analyzer_list = QtWidgets.QListWidget()
+        self.analyzer_list.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
+        layout.addWidget(self.analyzer_list)
+
+        buttons_layout = QtWidgets.QHBoxLayout()
+        add_button = QtWidgets.QPushButton("+ Add analyzer folder")
+        add_button.clicked.connect(self.add_analyzer_folder)
+        add_all_button = QtWidgets.QPushButton("+ Add all analyzers inside a folder")
+        add_all_button.setToolTip("Searches up to 3 folder levels down for Sorting Analyzer folders")
+        add_all_button.clicked.connect(self.add_analyzers_inside_folder)
+        remove_button = QtWidgets.QPushButton("Remove selected")
+        remove_button.clicked.connect(self.remove_selected)
+        buttons_layout.addWidget(add_button)
+        buttons_layout.addWidget(add_all_button)
+        buttons_layout.addWidget(remove_button)
+        layout.addLayout(buttons_layout)
+
+        output_label = QtWidgets.QLabel("Save the predictions (one csv per analyzer) in:")
+        output_label.setStyleSheet("font-weight: bold;")
+        layout.addWidget(output_label)
+
+        output_layout = QtWidgets.QHBoxLayout()
+        self.output_folder_form = QtWidgets.QLineEdit(str(default_output_folder))
+        browse_button = QtWidgets.QPushButton("Browse")
+        browse_button.clicked.connect(self.choose_output_folder)
+        output_layout.addWidget(self.output_folder_form)
+        output_layout.addWidget(browse_button)
+        layout.addLayout(output_layout)
+
+        button_box = QtWidgets.QDialogButtonBox()
+        self.apply_button = button_box.addButton("Apply", QtWidgets.QDialogButtonBox.AcceptRole)
+        button_box.addButton(QtWidgets.QDialogButtonBox.StandardButton.Cancel)
+        button_box.accepted.connect(self.accept_if_ready)
+        button_box.rejected.connect(self.reject)
+        layout.addWidget(button_box)
+
+    def add_paths(self, paths):
+        existing = set(self.analyzer_paths())
+        for path in paths:
+            if str(path) not in existing:
+                self.analyzer_list.addItem(str(path))
+                existing.add(str(path))
+
+    def add_analyzer_folder(self):
+        folder = QtWidgets.QFileDialog.getExistingDirectory(self, "Select a Sorting Analyzer folder")
+        if folder == "":
+            return
+        if check_folder_is_analyzer(folder):
+            self.add_paths([Path(folder)])
+        else:
+            print(f"Selected directory {folder} is not a SortingAnalyzer.")
+
+    def add_analyzers_inside_folder(self):
+        folder = QtWidgets.QFileDialog.getExistingDirectory(self, "Select a folder containing Sorting Analyzers")
+        if folder == "":
+            return
+        analyzers = find_analyzers(folder)
+        print(f"Found {len(analyzers)} Sorting Analyzers in {folder}.")
+        self.add_paths(analyzers)
+
+    def remove_selected(self):
+        for item in self.analyzer_list.selectedItems():
+            self.analyzer_list.takeItem(self.analyzer_list.row(item))
+
+    def choose_output_folder(self):
+        folder = QtWidgets.QFileDialog.getExistingDirectory(self, "Select the folder to save the predictions in")
+        if folder != "":
+            self.output_folder_form.setText(folder)
+
+    def analyzer_paths(self):
+        return [self.analyzer_list.item(row).text() for row in range(self.analyzer_list.count())]
+
+    def output_folder(self):
+        return self.output_folder_form.text().strip()
+
+    def accept_if_ready(self):
+        if len(self.analyzer_paths()) == 0:
+            QtWidgets.QMessageBox.warning(self, "No analyzers", "Add at least one analyzer to apply the models to.")
+            return
+        if self.output_folder() == "":
+            QtWidgets.QMessageBox.warning(self, "No output folder", "Choose a folder to save the predictions in.")
+            return
+        self.accept()