GaitVision

How to Run the PCA Analysis Tool

This guide will help you get the PCA Analysis Tool up and running on your computer, even if you have no programming experience. Please follow these steps carefully.

Step 1: Install Python

Python is the programming language this application is built with. You need to install it first. If you think python may be already installed, skip ahead to step 3 and try to verify the installation.

The docs here use python for Python related commands. On MacOS/Linux devices you’d typically use python3 instead of python for all python related commands.

1. Download Python:
   • Go to the official Python website: https://www.python.org/downloads/
   • Download the latest stable version of Python 3 (e.g., Python 3.10.x or newer).
2. Install Python:
   • Windows: Run the downloaded .exe file. IMPORTANT: Check the box that says “Add Python to PATH” during installation, and then click “Install Now”.
   • macOS: Run the downloaded .pkg file and follow the on-screen instructions.
3. Verify Installation:
   • Open your computer’s “Terminal” (on macOS) or “Command Prompt” (on Windows).
   • Type python --version and press Enter. You should see a version number like Python 3.10.12.

Step 2: Open the Terminal and Navigate to the Project Folder

1. Open Terminal/Command Prompt:
   • Windows: Search for “Command Prompt” or “PowerShell” in your Start Menu.
   • macOS: Search for “Terminal” in Spotlight (Cmd + Space).
2. Navigate to the PCA Folder:
   • This is a crucial step. All of the following commands must be run from inside the correct project folder.
   • It should look something like this (your path will be different):

     cd "/path/to/your/GaitVision-main/PCA"
     

     Note for Windows users: Your path will look different, e.g., cd "C:\Users\YourUser\Desktop\GaitVision-main\PCA".

💡 Pro Tip: How to Copy a File Path

• On macOS: Right-click on a file or folder, hold down the Option key, and select “Copy [item name] as Pathname”.
• On Windows: Hold down the Shift key and right-click on a file or folder, then select “Copy as path”.

You can then paste this path directly into the terminal after typing cd .

Step 3: Create and Activate a Virtual Environment

This creates a self-contained environment for the application’s dependencies.

1. Create the Virtual Environment:
   • In the Terminal, make sure you are in the “PCA” folder.
   • Type the following command and press Enter:

     python -m venv venv
     

2. Activate the Virtual Environment:

   Now, activate the environment based on your operating system.

   On macOS / Linux

   In your terminal, run:

   source venv/bin/activate
   

   On Windows

   For simplicity, we recommend using Command Prompt for the following steps.

   • In Command Prompt:

     .\venv\Scripts\activate
     

   • In PowerShell:

     .\venv\Scripts\Activate.ps1
     

     Note: If you get an error using PowerShell, you may need to run it as an Administrator and execute the command Set-ExecutionPolicy RemoteSigned. Using Command Prompt is often easier.

   • You’ll know it’s activated when you see (venv) at the beginning of your Terminal prompt.

Step 4: Install Project Dependencies

Now, install the specific libraries the application needs.

1. Install Dependencies:
   • With the virtual environment activated, type the following command and press Enter:

     pip install -r requirements.txt
     

   • This may take a few moments.

Step 5: Run the Application

1. Start the Application:
   • In the same Terminal window, type:

     python pca_pipeline.py
     

   • Press Enter.

Step 6: Use the Application

1. Select a File:
   • A file selection window will pop up. Use this to navigate to and select the CSV file you want to analyse.
2. Analysis and Report:
   • The application will run the analysis. This may take a few moments.
   • Once complete, a PDF report with the analysis results will be automatically generated and opened for you to view.
   • All results, including logs and plots, are saved in a folder named PCA_Analysis inside your computer’s “Documents” folder.

When You’re Done

The application will close automatically after the report is generated. You can then close the Terminal window. To use it again, just follow Step 5 and Step 6.

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Having trouble?

• command not found (e.g., python): This usually means Python was not added to your system’s PATH. When installing, make sure to check the box that says “Add Python to PATH”.

• pip install fails:
  • This can be a network issue. Make sure you are connected to the internet.
  • On Windows, if the installation fails with an error mentioning “C++” or “Microsoft Visual C++”, you may need to install Microsoft’s C++ Build Tools. This is an advanced step, but you can find the tools by searching for “Visual Studio Build Tools”.
• Script fails to run: For any errors, try to read the message in the terminal carefully. It will often give you a clue as to what went wrong (e.g., a file could not be found).

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