simple-napari-cci-annotator 0.0.2__tar.gz

simple_napari_cci_annotator-0.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 LECLERC Simon
+
+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.

simple_napari_cci_annotator-0.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: simple-napari-cci-annotator
+Version: 0.0.2
+Summary: Plugin to easly test a yolo model and retrain it
+Author: Simon Leclerc
+Author-email: simon.leclerc@gu.se
+License: MIT License
+        
+        Copyright (c) 2026 LECLERC Simon
+        
+        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.
+        
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: qtpy
+Requires-Dist: ultralytics
+Requires-Dist: pillow
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: pyqt5; extra == "testing"
+Dynamic: license-file
+
+
+[![License MIT](https://img.shields.io/badge/license-MIT-green)](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/blob/main/LICENSE)
+[![Python 3.10–3.12](https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12-blue)](https://python.org)
+[![tests](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/workflows/tests/badge.svg)](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/actions)
+
+# Simple napari annotator
+
+Minimal napari plugin for YOLO bbox detection + quick correction + retraining.
+
+No dataset browser, no extra workflow logic. User provides the image in napari.
+
+## UI flow
+
+1. Path to model (`.pt`) or model folder
+2. `Load model`
+3. `Predict`
+4. Optional destination folder for retrained model (browse or type)
+5. Edit boxes in napari shapes layer (`yolo_bboxes`)
+6. `Add correction`
+7. `Retrain`
+
+![UI](assets/Plugin_UI.png)
+
+## Starting from scratch
+
+The model input supports either:
+
+- A `.pt` model file, or
+- A folder path.
+
+Folder behavior on `Load model`:
+
+- If the folder already contains one or more `.pt` files, the first one is loaded.
+- If the folder contains no `.pt` file, the plugin copies the bundled `yolov8n.pt` into that folder and loads it.
+- Empty model input is invalid and will show an error.
+
+If you do not have a model yet, start from a pretrained YOLOv8 nano checkpoint and use it as your initial file:
+
+- Direct download: <https://github.com/ultralytics/assets/releases/latest/download/yolov8n.pt>
+- Model overview: <https://docs.ultralytics.com/models/yolov8/>
+
+After downloading, select that `yolov8n.pt` file in the Model field and continue with the correction/retrain loop.
+
+![Loading a model](assets/Loading_model.png)
+
+## Assumptions
+
+- Input image is already RGB 8-bit (or compatible with clipping/conversion).
+- Single class (`0: LABEL`) for now.
+- Exactly one image layer should be present when using `Add correction`.
+
+![Predicting label](assets/Predicting_label.png)
+
+## Folder behavior
+
+Given a model path like:
+
+`.../my_model/best.pt`
+
+The plugin uses `.../my_model` as root.
+
+### Add correction
+
+Each click saves:
+
+- Image to `my_model/corrections/<image_name>_<timestamp>.png`
+- Labels to `my_model/corrections/<image_name>_<timestamp>.txt`
+- Training config to `my_model/corrections/training_config.json` (created/updated)
+
+Image layer behavior:
+
+- If no image layer exists, `Add correction` shows an error.
+- If more than one image layer exists, `Add correction` shows an error.
+- If exactly one image layer exists, that image layer is used for saving correction image data.
+
+`training_config.json` defaults:
+
+- `image_size`: prefilled from the current image size using `max(height, width)`
+- `batch`: `8`
+- `epochs`: `100`
+- `patience`: `30`
+
+You can edit this file before clicking `Retrain`.
+
+Label format is YOLO detection:
+
+`class x_center y_center width height`
+
+normalized to `[0, 1]`.
+
+### Retrain
+
+Each click creates:
+
+- `<retrain_root>/dataset/`
+  - `images/train`, `images/val`
+  - `labels/train`, `labels/val`
+  - `dataset.yaml`
+- Trains YOLO from those corrections
+- Copies best model to:
+  - `<retrain_root>/best.pt`
+- Deletes training traces folder after extracting `best.pt`
+
+`<retrain_root>` resolution:
+
+- If destination field is set, retraining outputs there.
+- Otherwise it defaults to `my_model/retrained_<timestamp>`.
+
+So the retrained folder keeps a clean dataset + final model, without run artifacts.
+
+Warning: Data labeled will be equally divided between traning and validation (50%).

simple_napari_cci_annotator-0.0.2/README.md

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+
+[![License MIT](https://img.shields.io/badge/license-MIT-green)](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/blob/main/LICENSE)
+[![Python 3.10–3.12](https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12-blue)](https://python.org)
+[![tests](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/workflows/tests/badge.svg)](https://github.com/CCI-GU-Sweden/simple-napari-cci-annotator/actions)
+
+# Simple napari annotator
+
+Minimal napari plugin for YOLO bbox detection + quick correction + retraining.
+
+No dataset browser, no extra workflow logic. User provides the image in napari.
+
+## UI flow
+
+1. Path to model (`.pt`) or model folder
+2. `Load model`
+3. `Predict`
+4. Optional destination folder for retrained model (browse or type)
+5. Edit boxes in napari shapes layer (`yolo_bboxes`)
+6. `Add correction`
+7. `Retrain`
+
+![UI](assets/Plugin_UI.png)
+
+## Starting from scratch
+
+The model input supports either:
+
+- A `.pt` model file, or
+- A folder path.
+
+Folder behavior on `Load model`:
+
+- If the folder already contains one or more `.pt` files, the first one is loaded.
+- If the folder contains no `.pt` file, the plugin copies the bundled `yolov8n.pt` into that folder and loads it.
+- Empty model input is invalid and will show an error.
+
+If you do not have a model yet, start from a pretrained YOLOv8 nano checkpoint and use it as your initial file:
+
+- Direct download: <https://github.com/ultralytics/assets/releases/latest/download/yolov8n.pt>
+- Model overview: <https://docs.ultralytics.com/models/yolov8/>
+
+After downloading, select that `yolov8n.pt` file in the Model field and continue with the correction/retrain loop.
+
+![Loading a model](assets/Loading_model.png)
+
+## Assumptions
+
+- Input image is already RGB 8-bit (or compatible with clipping/conversion).
+- Single class (`0: LABEL`) for now.
+- Exactly one image layer should be present when using `Add correction`.
+
+![Predicting label](assets/Predicting_label.png)
+
+## Folder behavior
+
+Given a model path like:
+
+`.../my_model/best.pt`
+
+The plugin uses `.../my_model` as root.
+
+### Add correction
+
+Each click saves:
+
+- Image to `my_model/corrections/<image_name>_<timestamp>.png`
+- Labels to `my_model/corrections/<image_name>_<timestamp>.txt`
+- Training config to `my_model/corrections/training_config.json` (created/updated)
+
+Image layer behavior:
+
+- If no image layer exists, `Add correction` shows an error.
+- If more than one image layer exists, `Add correction` shows an error.
+- If exactly one image layer exists, that image layer is used for saving correction image data.
+
+`training_config.json` defaults:
+
+- `image_size`: prefilled from the current image size using `max(height, width)`
+- `batch`: `8`
+- `epochs`: `100`
+- `patience`: `30`
+
+You can edit this file before clicking `Retrain`.
+
+Label format is YOLO detection:
+
+`class x_center y_center width height`
+
+normalized to `[0, 1]`.
+
+### Retrain
+
+Each click creates:
+
+- `<retrain_root>/dataset/`
+  - `images/train`, `images/val`
+  - `labels/train`, `labels/val`
+  - `dataset.yaml`
+- Trains YOLO from those corrections
+- Copies best model to:
+  - `<retrain_root>/best.pt`
+- Deletes training traces folder after extracting `best.pt`
+
+`<retrain_root>` resolution:
+
+- If destination field is set, retraining outputs there.
+- Otherwise it defaults to `my_model/retrained_<timestamp>`.
+
+So the retrained folder keeps a clean dataset + final model, without run artifacts.
+
+Warning: Data labeled will be equally divided between traning and validation (50%).

simple_napari_cci_annotator-0.0.2/pyproject.toml

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+[project]
+name = "simple-napari-cci-annotator"
+dynamic = ["version"]
+description = "Plugin to easly test a yolo model and retrain it"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+  {name = "Simon Leclerc"},
+  {email = "simon.leclerc@gu.se"},
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Framework :: napari",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy",
+    "qtpy",
+    "ultralytics",
+    "pillow",
+]
+
+[project.optional-dependencies]
+all = ["napari[all]"]
+
+testing = [
+    "tox",
+    "pytest",  # https://docs.pytest.org/en/latest/contents.html
+    "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
+    "pytest-qt",  # https://pytest-qt.readthedocs.io/en/latest/
+    "napari",
+    "pyqt5",
+]
+
+[project.entry-points."napari.manifest"]
+simple-napari-cci-annotator = "simple_napari_cci_annotator:napari.yaml"
+
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
+
+[tool.setuptools.dynamic]
+version = {attr = "simple_napari_cci_annotator.__init__.__version__"}
+
+[tool.black]
+line-length = 79
+target-version = ['py310', 'py311', 'py312']
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+lint.ignore = [
+    "E501", # line too long. let black handle this
+    "SIM117",
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py312"
+fix = true

simple_napari_cci_annotator-0.0.2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

simple_napari_cci_annotator-0.0.2/src/simple_napari_cci_annotator/__init__.py

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+from ._widget import SimpleCciAnnotatorQWidget
+
+__version__ = "0.0.2"
+
+__all__ = [
+    "SimpleCciAnnotatorQWidget",
+]