careamics 0.1.0rc1__tar.gz → 0.1.0rc3__tar.gz

{careamics-0.1.0rc1 → careamics-0.1.0rc3}/.github/ISSUE_TEMPLATE/bug_report.md

@@ -25,6 +25,7 @@ If applicable, add screenshots to help explain your problem.
 **Desktop (please complete the following information):**
  - OS: [e.g. iOS]
  - Version [e.g. 22]
+- microscopy-portfolio version [e.g. 0.0.5]
 
 **Environment:**
 Please add here the content of your conda environment with versions.

careamics-0.1.0rc3/.github/workflows/ci.yml

@@ -0,0 +1,108 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+        platform: [ubuntu-latest, macos-13, windows-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -m "not gpu"
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    name: Release
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+
+      - name: Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

{careamics-0.1.0rc1 → careamics-0.1.0rc3}/.gitignore

@@ -3,3 +3,6 @@
 .pytest*
 *.DS_Store*
 **/.ipynb_checkpoints
+.coverage
+coverage.xml
+lightning_logs

careamics-0.1.0rc3/.pre-commit-config.yaml

@@ -0,0 +1,56 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.14
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
+    hooks:
+      - id: ruff
+        args: [--fix, --target-version, py38]
+
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        additional_dependencies:
+          - numpy
+          - types-PyYAML
+          - types-setuptools
+
+  # check docstrings
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.6.0
+    hooks:
+      - id: numpydoc-validation
+
+  # jupyter linting and formatting
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-ruff
+        args: [--fix]
+      - id: nbqa-black
+      #- id: nbqa-mypy
+
+  # strip out jupyter notebooks
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout

careamics-0.1.0rc3/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.3
+Name: careamics
+Version: 0.1.0rc3
+Summary: Toolbox for running N2V and friends.
+Project-URL: homepage, https://careamics.github.io/
+Project-URL: repository, https://github.com/CAREamics/careamics
+Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Requires-Dist: albumentations
+Requires-Dist: bioimageio-core>=0.6.0
+Requires-Dist: psutil
+Requires-Dist: pydantic>=2.5
+Requires-Dist: pytorch-lightning>=2.2.0
+Requires-Dist: pyyaml
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: torch>=2.0.0
+Requires-Dist: zarr
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: sybil; extra == 'dev'
+Provides-Extra: examples
+Requires-Dist: careamics-portfolio; extra == 'examples'
+Requires-Dist: jupyter; extra == 'examples'
+Requires-Dist: matplotlib; extra == 'examples'
+Provides-Extra: tensorboard
+Requires-Dist: protobuf==3.20.3; extra == 'tensorboard'
+Requires-Dist: tensorboard; extra == 'tensorboard'
+Provides-Extra: wandb
+Requires-Dist: wandb; extra == 'wandb'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics Restoration
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+## Installation
+
+``` bash
+pip install careamics
+```
+For more details on the options please follow the installation [guide](https://careamics.github.io/careamics/).
+
+## Usage
+
+CAREamics uses the Engine object to construct the pipeline for both training and prediction. First we import the Engine.
+```python
+from careamics_restoration.engine import Engine
+```
+The Engine could be initialized in 2 ways:
+1. Using the [yaml config](examples/n2v_2D_reference.yml) file
+
+Specify the mandatory parameters in the config file
+```yaml
+experiment_name: Name of the experiment
+working_directory: Path to the working directory, where all the outputs will be stored
+
+algorithm: 
+    loss: type of loss function, e.g. n2v for Noise2Void
+    model: model architecture, e.g. UNet
+    is_3D: True if 3D data, False if 2D data
+
+training:
+  num_epochs: Number of training epochs
+  patch_size: Size of the patches, List of 2 or 3 elements
+  batch_size: Batch size for training
+
+extraction_strategy: Controls how the patches are extracted from the data
+
+data:
+    data_format: File extension, e.g. tif
+    axes: Defines the shape of the input data
+```
+Full description of the configuration parameters is in the [documentation](https://careamics.github.io/careamics/).
+
+
+```python
+engine = Engine(config_path="config.yml")
+
+```
+2. Using the path to the pretrained model
+It's also possible to initialize the Engine using the model checkpoint, saved during the training or downloaded from the [BioImage Model Zoo](https://bioimage.io/#/).
+Checkpoint must contain model_state_dict.
+Read more abount saving and loading models in the [documentation](https://careamics.github.io/careamics/).
+
+Once Engine is initialized, we can start training, providing the relative paths to train and validation data
+
+```python
+engine.train(train_path=train_path, val_path=val_path)
+```
+Training will run for the specified number of epochs and save the model checkpoint in the working directory.
+
+Prediction could be done directly after the training or by loading the pretrained model checkpoint.
+
+```python
+predictions = engine.predict(pred_path=predict_path)
+```
+
+For more examples please take a look at the [notebooks](examples).
+

careamics-0.1.0rc3/README.md

@@ -0,0 +1,78 @@
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics Restoration
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+## Installation
+
+``` bash
+pip install careamics
+```
+For more details on the options please follow the installation [guide](https://careamics.github.io/careamics/).
+
+## Usage
+
+CAREamics uses the Engine object to construct the pipeline for both training and prediction. First we import the Engine.
+```python
+from careamics_restoration.engine import Engine
+```
+The Engine could be initialized in 2 ways:
+1. Using the [yaml config](examples/n2v_2D_reference.yml) file
+
+Specify the mandatory parameters in the config file
+```yaml
+experiment_name: Name of the experiment
+working_directory: Path to the working directory, where all the outputs will be stored
+
+algorithm: 
+    loss: type of loss function, e.g. n2v for Noise2Void
+    model: model architecture, e.g. UNet
+    is_3D: True if 3D data, False if 2D data
+
+training:
+  num_epochs: Number of training epochs
+  patch_size: Size of the patches, List of 2 or 3 elements
+  batch_size: Batch size for training
+
+extraction_strategy: Controls how the patches are extracted from the data
+
+data:
+    data_format: File extension, e.g. tif
+    axes: Defines the shape of the input data
+```
+Full description of the configuration parameters is in the [documentation](https://careamics.github.io/careamics/).
+
+
+```python
+engine = Engine(config_path="config.yml")
+
+```
+2. Using the path to the pretrained model
+It's also possible to initialize the Engine using the model checkpoint, saved during the training or downloaded from the [BioImage Model Zoo](https://bioimage.io/#/).
+Checkpoint must contain model_state_dict.
+Read more abount saving and loading models in the [documentation](https://careamics.github.io/careamics/).
+
+Once Engine is initialized, we can start training, providing the relative paths to train and validation data
+
+```python
+engine.train(train_path=train_path, val_path=val_path)
+```
+Training will run for the specified number of epochs and save the model checkpoint in the working directory.
+
+Prediction could be done directly after the training or by loading the pretrained model checkpoint.
+
+```python
+predictions = engine.predict(pred_path=predict_path)
+```
+
+For more examples please take a look at the [notebooks](examples).
+

careamics-0.1.0rc3/examples/2D/n2n/example_SEM_careamist.ipynb

@@ -0,0 +1,239 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import shutil\n",
+    "from pathlib import Path\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import tifffile\n",
+    "from careamics_portfolio import PortfolioManager\n",
+    "\n",
+    "from careamics import CAREamist"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Import Dataset Portfolio"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Explore portfolio\n",
+    "portfolio = PortfolioManager()\n",
+    "print(portfolio.denoising)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download files\n",
+    "root_path = Path(\"./data\")\n",
+    "files = portfolio.denoising.N2N_SEM.download(root_path)\n",
+    "print(f\"List of downloaded files: {files}\")"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Visualize training data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load images\n",
+    "train_image = tifffile.imread(files[0])\n",
+    "print(f\"Train image shape: {train_image.shape}\")\n",
+    "\n",
+    "# Display images\n",
+    "side = int(np.ceil(np.sqrt(train_image.shape[0])))\n",
+    "fig, ax = plt.subplots(side, side, figsize=(15, 15))\n",
+    "\n",
+    "for i in range(train_image.shape[0]):\n",
+    "    ax.flat[i].imshow(train_image[i], cmap=\"gray\")\n",
+    "    ax.flat[i].axis(\"off\")"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Visualize validation data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "val_image = tifffile.imread(files[2])\n",
+    "print(f\"Validation image shape: {val_image.shape}\")\n",
+    "\n",
+    "# Display images\n",
+    "side = int(np.ceil(np.sqrt(val_image.shape[0])))\n",
+    "fig, ax = plt.subplots(side, side, figsize=(15, 15))\n",
+    "for i in range(val_image.shape[0]):\n",
+    "    ax.flat[i].imshow(val_image[i], cmap=\"gray\")\n",
+    "    ax.flat[i].axis(\"off\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Set paths\n",
+    "\n",
+    "data_path = Path(root_path / \"n2n_sem\")\n",
+    "train_path = data_path / \"train\"\n",
+    "test_path = data_path / \"val\"\n",
+    "\n",
+    "train_path.mkdir(parents=True, exist_ok=True)\n",
+    "test_path.mkdir(parents=True, exist_ok=True)\n",
+    "\n",
+    "shutil.copy(root_path / files[0], train_path / \"train_image.tif\")\n",
+    "shutil.copy(root_path / files[1], test_path / \"test_image.tif\")"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Initialize the Model\n",
+    "\n",
+    "Create a Pytorch Lightning module\n",
+    "\n",
+    "Please take as look at the [documentation](https://careamics.github.io) to see the full list of parameters and configuration options"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "engine = CAREamist(source=\"n2n_2D_SEM.yml\")"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Part 3. Run training \n",
+    "\n",
+    "We need to specify the paths to training and validation data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "engine.train(\n",
+    "    train_source=train_image[0],\n",
+    "    val_source=train_image[1],\n",
+    "    train_target=train_image[2],\n",
+    "    val_target=train_image[3],\n",
+    ")"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Run prediction\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "preds = engine.predict(source=val_image[0], tile_size=(256, 256))"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Visualize the prediction"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fi, ax = plt.subplots(1, 2, figsize=(15, 15))\n",
+    "ax[0].imshow(preds[0].squeeze(), cmap=\"gray\")\n",
+    "ax[0].set_title(\"Prediction\")\n",
+    "ax[1].imshow(val_image[0].squeeze(), cmap=\"gray\")\n",
+    "ax[1].set_title(\"Ground Truth\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.13 ('HDNn')",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "faf8b084d52efbff00ddf863c4fb0ca7a3b023f9f18590a5b65c31dc02d793e2"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

careamics-0.1.0rc3/examples/2D/n2n/n2n_2D_SEM.yml

@@ -0,0 +1,60 @@
+# Name, composed of letters, numbers, spaces, dashes and underscores
+experiment_name: N2V_SEM_N2N
+
+algorithm:
+  algorithm: n2n
+  loss: mae
+  model:
+    architecture: UNet
+    n2v2: False
+  optimizer_parameters:
+    lr: 1e-3
+  lr_scheduler_parameters:
+   factor: 0.5
+   patience: 10
+
+training:
+  # Number of epochs, greater or equal than 1
+  num_epochs: 1
+
+  # Batch size, greater or equal than 1
+  batch_size: 128
+
+  # Optional, use WandB (True or False), must be installed in your conda environment
+  use_wandb: False
+
+  callbacks:
+    # Optional, any parameter for Pytorch lightning callbacks
+
+    # Optional, any parameter for Pytorch lightning ModelCheckpoint
+    checkpoint:
+      # Optional, monitor the validation loss (val_loss) or the validation accuracy (val_acc)
+      # parameters:
+      # dirpath: 'checkpoints'
+      # monitor : val_loss
+      save_last: True
+      save_top_k: 3
+      # TODO should it be here or in predict ?
+      # Optional, path to the checkpoint to load the model
+      # load_path: ''
+
+  # Optional, automatic mixed precision
+  amp:
+    # Use (True or False)
+    use: True
+
+data:
+  # Extension of the data
+  data_type: array
+
+  patch_size: [64, 64]
+  
+  # Axes, among STCZYX with constraints on order
+  axes: YX
+
+  tta_transforms: True
+
+  batch_size: 128
+
+  # Optional, number of workers for data loading, greater or equal than 0
+  num_workers: 0