Support Inference with YOLOv8 Models

.github/workflows/release-workflow.yml

@@ -33,11 +33,11 @@ jobs:
         shell: bash
         run: |
           if [ ${{ steps.extract_platform.outputs.platform }} = "windows" ]; then
-          echo "##[set-output name=name;]$(echo Portal Setup ${{ steps.extract_version.outputs.version }}.exe)"
+            echo "##[set-output name=name;]$(echo Portal Setup ${{ steps.extract_version.outputs.version }}.exe)"
           elif [ ${{ steps.extract_platform.outputs.platform }} = "ubuntu" ]; then
-          echo "##[set-output name=name;]$(echo Portal-${{ steps.extract_version.outputs.version }}.AppImage)"
+            echo "##[set-output name=name;]$(echo Portal-${{ steps.extract_version.outputs.version }}.AppImage)"
           else
-          echo "##[set-output name=name;]$(echo Portal-${{ steps.extract_version.outputs.version }}.dmg)"
+            echo "##[set-output name=name;]$(echo Portal-${{ steps.extract_version.outputs.version }}.dmg)"
           fi
         id: extract_executable_name
 
@@ -56,10 +56,10 @@ jobs:
         working-directory: ./src/engine
         shell: bash
         run: |
-          pyinstaller -F run.py --hidden-import pydicom.encoders.gdcm --hidden-import pydicom.encoders.pylibjpeg --hidden-import engineio.async_drivers.threading  --distpath ../../portal_build/dist
+          pyinstaller --collect-data ultralytics --hidden-import pydicom.encoders.gdcm --hidden-import pydicom.encoders.pylibjpeg --hidden-import engineio.async_drivers.threading -F run.py --distpath ../../portal_build/dist
           if [ -f ../../portal_build/dist/run ]; then
-          chmod u+x ../../portal_build/dist/run
-          mv ../../portal_build/dist/run ../../portal_build/dist/run.exe
+            chmod u+x ../../portal_build/dist/run
+            mv ../../portal_build/dist/run ../../portal_build/dist/run.exe
           fi
           chmod u+x ../../portal_build/dist/run.exe
 

.pylintrc

@@ -52,7 +52,7 @@ confidence=
 # --disable=W"
 # TODO: remove R1710 (inconsistent-return-statements)
 # TODO: remove C0111 (missing-docstring)
-disable=similarities,fixme,I0011,E1102,R1710,C0111,C0330
+disable=similarities,fixme,I0011,E1102,R1710,C0111
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
@@ -424,4 +424,4 @@ known-third-party=enchant
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=builtins.Exception

Pipfile

@@ -22,8 +22,10 @@ scandir = "==1.10.0"
 scantree = "==0.0.1"
 shapely = "==2.0.1"
 tensorflow = "==2.10.0"
+tensorflow-macos = {version = "==2.10.0", sys_platform = "== 'darwin'", platform_machine = "== 'arm64'"}
 torch = "==1.12.1"
 torchvision = "==0.13.1"
+ultralytics = "==8.0.133"
 werkzeug = "==2.0.0"
 
 [dev-packages]

build-electron.sh

@@ -10,9 +10,9 @@ trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
 trap 'echo "Exiting shell: \"${last_command}\" command failed with exit code $?."' EXIT
 
 echo "Running build-electron bash job!"
-chmod +x setup-virtualenv.sh build-python.sh 
+chmod +x setup-virtualenv.sh build-python.sh
 echo "Calling setup-virtualenv.sh to setup environment in portal_build"
-. setup-virtualenv.sh 
+. setup-virtualenv.sh
 echo "Calling build-python.sh to build backend executable"
 . build-python.sh
 

build-python.sh

@@ -11,27 +11,40 @@ echo "Running build-python bash job!"
 cd ./portal_build
 echo "$OSTYPE"
 if [[ "$OSTYPE" == "msys" ]]; then
-echo "Activating .venv/Scripts/activate"
-. .venv/Scripts/activate
+    echo "Activating .venv/Scripts/activate"
+    . .venv/Scripts/activate
 else
-echo "Activating .venv/bin/activate"
-. .venv/bin/activate
+    echo "Activating .venv/bin/activate"
+    . .venv/bin/activate
 fi
 echo "Installing Pyinstaller..."
 pip install --upgrade pyinstaller
 
 
 echo "Creating flask executable..."
 if [[ "$OSTYPE" == "msys" ]]; then
-pyinstaller -F run.py --hidden-import pydicom.encoders.gdcm --hidden-import pydicom.encoders.pylibjpeg --hidden-import engineio.async_drivers.threading  --distpath ./dist
-chmod u+x ./dist/run.exe
+    pyinstaller \
+        --collect-data ultralytics \
+        --hidden-import pydicom.encoders.gdcm \
+        --hidden-import pydicom.encoders.pylibjpeg \
+        --hidden-import engineio.async_drivers.threading \
+        -F run.py \
+        --distpath ./dist
+    chmod u+x ./dist/run.exe
 else
-DYLD_LIBRARY_PATH=".venv/bin" pyinstaller -F run.py --hidden-import datature-hub --hidden-import engineio.async_drivers.threading  --distpath ./dist
-chmod u+x ./dist/run
-if [ -f ./dist/run ]; then
-echo "Renaming file"
-mv ./dist/run ./dist/run.exe
-fi
+    DYLD_LIBRARY_PATH=".venv/bin"
+    pyinstaller \
+        --collect-data ultralytics \
+        --hidden-import pydicom.encoders.gdcm \
+        --hidden-import pydicom.encoders.pylibjpeg \
+        --hidden-import engineio.async_drivers.threading \
+        -F run.py \
+        --distpath ./dist
+    chmod u+x ./dist/run
+    if [ -f ./dist/run ]; then
+        echo "Renaming file"
+        mv ./dist/run ./dist/run.exe
+    fi
 fi
 
 echo "Removing extra files - run.spec and build"

build-windows.sh

@@ -0,0 +1,25 @@
+#! /bin/bash
+
+chmod u+x setup-virtualenv.sh
+./setup-virtualenv.sh
+
+. ./portal_build/.venv/Scripts/activate
+
+cd src/app/
+nvm install 16 && nvm use 16
+npm install --legacy-peer-deps
+npm run build:static
+
+cd ../engine/
+pyinstaller \
+    --collect-data ultralytics \
+    --hidden-import pydicom.encoders.gdcm \
+    --hidden-import pydicom.encoders.pylibjpeg \
+    --hidden-import engineio.async_drivers.threading \
+    -F run.py \
+    --distpath ../../portal_build/dist
+
+chmod u+x ../../portal_build/dist/run.exe
+
+cd ../..
+npm run dist

docs/contribution.md

@@ -8,19 +8,75 @@ This file serves as a guide for you to contribute your ideas onto the Portal pla
 
 [What are the Components of Portal?](#components)
 
+[How do I Set Up Portal for Development?](#setting-up)
+
 [How do I Get Started on Contributing?](#contributing)
 
 [How do I Handle Errors while Contributing?](#errors)
 
+[I'm Facing an Issue!](./issues.md)
+
 ## What are the Components of Portal? <a name="components"></a>
 
 The two main components of portal is the **App** and the **Engine**.
 
 The **App** serves as a graphical user interface for users to interact with.
-Events triggerred in **App** may update **App** itself and/or trigger API calls to the **Engine**.
+Events triggered in **App** may update **App** itself and/or trigger API calls to the **Engine**.
 
 The **Engine** performs the more complicated computations. The **Engine** receives a specific API call from the **App**, and performs the function corresponding to the API call, before responding to **App**.
 
+## How do I Set Up Portal for Development? <a name="setting-up"></a>
+
+### <ins>Web Application</ins>
+
+#### Prerequisites
+
+- **Node v16**. You may use [nvm](https://github.com/nvm-sh/nvm) to manage your Node versions.
+- **Python 3.7**. You may run the following commands to install a virtual environment with all the necessary dependencies.
+
+```bash
+chmod u+x setup-virtualenv.sh
+./setup-virtualenv.sh
+source ./portal_build/.venv/Scripts/activate
+```
+
+Alternatively, you can consider other virtual environment managers such as [virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/) or [conda](https://docs.conda.io/en/latest/miniconda.html), follow the installation and environment creation instructions, and then run the following command to install the dependencies.
+
+```bash
+pip install -r requirements.txt
+```
+
+#### Initializing Portal
+
+Open two terminals. In the first terminal, navigate to `src/app` from the root directory of the repository and run the following commands:
+
+```bash
+nvm install 16 && nvm use 16
+npm install --legacy-peer-deps
+npm run build:static
+
+npm run dev
+```
+
+In the second terminal, navigate to `src/engine` from the root directory of the repository and run the following commands:
+
+```bash
+python run.py
+```
+
+Lastly, open your browser and navigate to `localhost:3000` to access Portal. You should be able to see Portal's interface.
+
+### <ins>Windows Build</ins>
+
+We have conveniently provided a bash script to build the Windows executable for testing.
+
+```bash
+chmod u+x build-windows.sh
+./build-windows.sh
+```
+
+To install the executable locally, navigate to `application` from the root directory of the repository and double click on `Portal Setup x.x.x.exe` to install Portal. Follow the instructions on the installer to complete the installation, then check the `Run Portal` box to launch Portal after installation. You should be able to see Portal's interface.
+
 ## How do I Get Started on Contributing? <a name="contributing"></a>
 
 To begin contributing to Portal, first fork the repository, make your changes, then submit a pull request into the Portal's `develop` branch.

docs/issues.md

@@ -1 +1,35 @@
+# Common Issues
 
+## General
+
+- **Portal directory not found**: Build/cache files are stored in the following directories based on your operating system:
+
+  - **Windows EXE**:
+    - Absolute path: `C:\Users\$USER\AppData\Local\Programs\Portal\resources\server`
+    - Relative path: `resources\server`
+  - **Linux Build (localhost)**:
+    - Absolute path: `PATH/TO/portal/portal_build/server`
+    - Relative path: `portal_build/server`
+  - **Development Build**:
+    - Absolute path: `PATH/TO/portal/server`
+    - Relative path: `server`
+
+## Windows Executable
+
+- **No module named `{package}`**: You need to install the module. You can do this by running `pip install {package}` in the command line. If you are using a virtual environment, make sure you are in the correct environment. If you have already installed the module, make sure that you add this module as a `hidden-import` when you are building the executable using PyInstaller. You can do this by adding the `--hidden-import {package}` flag in `build-windows.sh`.
+
+```bash
+pyinstaller \
+    -F run.py \
+    --hidden-import {package} \
+    --distpath ../../portal_build/dist
+```
+
+- **Invalid path/File not found error (`C:\Users\$USER\AppData\Local\Temp\_MEIXXXXX\{package}\{subpackage}\{file}`)**: You need to add the package as a `datas` parameter for PyInstaller. You can do this by adding the `--collect-data` flag in `build-windows.sh`.
+
+```bash
+pyinstaller \
+    -F run.py \
+    --collect-data {package} \
+    --distpath ../../portal_build/dist
+```

lint.sh

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-PYTHONPATH=$(readlink -f src/) pylint --rcfile=.pylintrc src/engine/*.py
+PYTHONPATH=$(readlink -f src/) pylint --rcfile=.pylintrc src/engine/*.py

package.json

@@ -1,6 +1,6 @@
 {
   "name": "portal",
-  "version": "0.5.6",
+  "version": "0.5.8",
   "author": "Datature",
   "private": true,
   "main": "./src/app/main.js",

portal.py

@@ -8,7 +8,7 @@
 
 @File    :   portal.py
 @Author  :   Beatrice Leong
-@Version :   0.5.6
+@Version :   0.5.8
 @Contact :   hello@datature.io
 @License :   Apache License 2.0
 @Desc    :   Script to run portal from the command line.
@@ -43,18 +43,18 @@
 
     if "--gpu" in arguments:
         os.environ["IS_GPU"] = "0"
-        with open(use_gpu_dir, "w+") as gpu_flag:
+        with open(use_gpu_dir, "w+", encoding="utf-8") as gpu_flag:
             gpu_flag.write("0")
     else:
-        with open(use_gpu_dir, "w+") as gpu_flag:
+        with open(use_gpu_dir, "w+", encoding="utf-8") as gpu_flag:
             gpu_flag.write("-1")
 
     use_cache = "0"
     if os.path.isfile(use_cache_dir):
-        with open(use_cache_dir, "r") as cache_flag:
+        with open(use_cache_dir, "r", encoding="utf-8") as cache_flag:
             use_cache = cache_flag.read()
     else:
-        with open(use_cache_dir, "w") as cache_flag:
+        with open(use_cache_dir, "w", encoding="utf-8") as cache_flag:
             cache_flag.write(use_cache)
 
     if os.getenv("IS_ELECTRON"):

requirements.txt

@@ -19,4 +19,5 @@ torchvision==0.13.1
 onnx==1.12.0
 onnx2torch==1.5.6
 onnxruntime==1.14.1
+ultralytics==8.0.133
 werkzeug==2.0.0

setup-virtualenv.sh

@@ -11,21 +11,21 @@ declare -a FILES_NEEDED=(./src/engine/run.py ./Pipfile ./Pipfile.lock)
 missing_files="false"
 
 check_if_file_exists() {
-if ! test -f $1; then
-  missing_files="true"
-  echo "$1 does not exist."
-fi
+    if ! test -f $1; then
+        missing_files="true"
+        echo "$1 does not exist."
+    fi
 }
 
 echo "Running setup bash job!"
 
 for file in "${FILES_NEEDED[@]}"
 do
-check_if_file_exists $file
+    check_if_file_exists $file
 done
-if [[ "$missing_files" == "true" ]]; then 
-echo "Quitting bash job due to missing files. Ensure you have the required files before continuing."
-exit 0
+if [[ "$missing_files" == "true" ]]; then
+    echo "Quitting bash job due to missing files. Ensure you have the required files before continuing."
+    exit 0
 fi
 
 echo "Copying related engine files to portal_build..."
@@ -38,11 +38,11 @@ cd ./portal_build
 echo "Installing Python Environment in portal_build..."
 echo "$OSTYPE"
 if [[ "$OSTYPE" == "msys" ]]; then
-python -m pip install --upgrade pip
-python -m pip install pipenv
+    python -m pip install --upgrade pip
+    python -m pip install pipenv
 else
-python3 -m pip install --upgrade pip
-python3 -m pip install pipenv
+    python3 -m pip install --upgrade pip
+    python3 -m pip install pipenv
 fi
 PIPENV_VENV_IN_PROJECT=1 PIPENV_DEFAULT_PYTHON_VERSION=3.7 pipenv sync -d