Merge pull request #28 from Xu-Justin/initial_release

Initial release (0.1.0)

.coveragerc

@@ -0,0 +1,9 @@
+[run]
+omit =
+    */site-packages/*
+    */dist-packages/*
+    */distutils/*
+    tests/*
+    patchmentation/dataset.py
+
+disable_warnings = couldnt-parse

.github/workflows/docker-ci.yml

@@ -0,0 +1,32 @@
+name: docker ci
+
+on:
+  push:
+    branches:
+      - '**docker**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v3
+        with:
+          push: true
+          tags: jstnxu/patchmentation:env

.github/workflows/python-app.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        requirements=requirements/requirements-main.txt
+        if [ -f $requirements ]; then pip install -r $requirements; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Run test
+      run: |
+        pytest -v

.gitignore

@@ -0,0 +1,14 @@
+*__pycache__*
+.pytest_cache/*
+
+.coverage
+htmlcov/*
+
+# development tools
+dev.ipynb
+.ipynb_checkpoints
+
+# deployment
+build/*
+dist/*
+*.egg-info/

Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.10.8-slim-bullseye
+
+RUN apt-get update -qq && \
+    apt-get install -y zip unzip htop screen libgl1-mesa-glx libglib2.0-0 libsm6 libxrender1 libxext6 && \
+    rm -rf /var/cache/apk/*
+
+COPY requirements/* /requirements/
+RUN pip --no-cache-dir install -r /requirements/requirements-main.txt
+RUN pip --no-cache-dir install -r /requirements/requirements-test.txt
+RUN pip --no-cache-dir install -r /requirements/requirements-dev.txt
+RUN pip --no-cache-dir install -r /requirements/requirements-streamlit.txt
+
+WORKDIR /workspace
+CMD ["bash"]

README.md

@@ -1 +1,11 @@
-# patchmentation
+# patchmentation
+
+A python library to perform patch augmentation.
+
+## Installation
+
+```bash
+pip install patchmentation
+```
+
+THIS README will be updated soon.

Streamlit/__init__.py

@@ -0,0 +1,2 @@
+from . import section
+from . import page

Streamlit/app.py

@@ -0,0 +1,30 @@
+import os, sys
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+
+import page
+
+import streamlit as st
+from streamlit_option_menu import option_menu
+
+def main():
+    MENU_DATASET = 'Dataset'
+    MENU_PATCHMENTATION = 'Patchmentation'
+
+    with st.sidebar:
+        menu = option_menu(
+            'Main Menu',
+            [
+                MENU_DATASET,
+                MENU_PATCHMENTATION
+            ],
+            default_index=0
+        )
+
+    if menu == MENU_DATASET:
+        page.dataset()
+
+    if menu == MENU_PATCHMENTATION:
+        page.patchmentation()
+
+if __name__ == '__main__':
+    main()

Streamlit/page.py

@@ -0,0 +1,36 @@
+import os, sys
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+
+import section
+from patchmentation import patch_augmentation
+
+import streamlit as st
+import random
+
+def dataset(key: str = 'page-dataset'):
+    dataset = section.dataset(key=f'{key}-dataset')
+    section.display_dataset(dataset, key=f'{key}-display_dataset')
+
+def patchmentation(key: str = 'page-patchmentation'):
+    dataset = section.dataset(key=f'{key}-dataset')
+    shuffle = section.input_shuffle(key=f'{key}-shuffle')
+    negative_patches = section.negative_patch(dataset, key=f'{key}-negative-patches')
+    background_image = section.background_image(key=f'{key}-background_image')
+    actions = section.input_actions(key=f'{key}-input_actions')
+    conf = section.patchmentation_configuration(key=f'{key}-patchmentation_conf')
+
+    if dataset is None:
+        st.error(f'ERROR: Invalid dataset')
+        return
+
+    patches = negative_patches
+    for image_patch in dataset.image_patches:
+        for patch in image_patch.patches:
+            patches.append(patch)
+
+    if shuffle:
+        random.shuffle(patches)
+
+    result_image_patch = patch_augmentation(patches, background_image, conf.get('visibility_threshold', 0.5), actions, max_n_patches=conf.get('max_n_patches', 100))
+    section.display_image_patch(result_image_patch, key=f'{key}-display_result_image_patch')
+    section.refresh_button(key=f'{key}-refresh')