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cadtDash

cadtDash is a Python library that visualizes clinical data via a web interface.

First Time Installation

This tool is deveoped using Python 3.9.4. A requirement.txt is provided to set up a virtual environment for this tool.

If this is your first time, you will need to set up a virtual environment. If you are updating the software to the latest version, you may re-use the previous environment unless new packages are included in the requirements.txt (see Update Repo below)

Cloning

There are two ways: one through the GitHub repo interface, and the other via terminal. The following steps assume a Windows operating system but can be easily converted to Unix or Linux systems.

Via the GitHub repo interface

  1. Click the above green “Code” button, then click “Download Zip”. A cadtDash-main.zip file will be downloaded.

  2. Save the zip file to your Downloads/ folder. Open a File Explorer, navigate to the Downloads/ folder and extract the cadtDash-main.zip. You may change the destination where files will be extracted. This destination will be our working folder \you\path\to\cadtDash-main\.

  3. In the working folder, there is a sub-folder called cadtDash-main: \you\path\to\cadtDash-main\cadtDash-main\. This is where all the codes are located.

Via terminal (Windows PowerShell)

  1. Click the magnifying glass in the Windows menu to search for "Windows PowerShell". A terminal will pop up.

  2. Do the following command.

## 1. Proceed to your Downloads/ folder
cd .\Downloads\

## 2. Create a sub-folder to be our working folder
mkdir cadtDash-main

## 3. Proceed to your Downloads/cadtDash-main/ folder
cd .\cadtDash-main\

## 2. Clone the cadtDash repo and rename it as cadtDash-main
git clone https://github.com/elim723/cadtDash.git cadtDash-main

All the codes are located in the folder \you\path\to\cadtDash-main\cadtDash-main\.

Create virtual environment

There are two ways: one through Anaconda in Anaconda prompt, and the other using pip in Windows PowerShell.

Via Anaconda

  1. Click the magnifying glass in the Windows menu to search for "Anaconda prompt". A terminal will pop up.

  2. Do the following commands.

## 1. Proceed to the working folder
cd  \you\path\to\cadtDash-main\

## 2. Create a new virtual environment
#  A new folder "\you\path\to\cadtDash-main\venv" will appear.
python3 -m venv .

## 3. Source the environment
.\venv\Scripts\activate # if Windows
# source bin/activate # if Linux/bash

## 4. Install all required packages
pip install -r cadtDash-main/requirements.txt

The last step may take awhile. If the installation hangs, you may have to press the enter key.

Via Pip

  1. If you haven't had a terminal opened, click the magnifying glass in the Windows menu to search for "Windows PowerShell". A terminal will pop up.

  2. Do the following commands.

## 1. Proceed to the working folder
cd  \you\path\to\cadtDash-main\

## 2. Install virtualenv package
pip install virtualenv

## 2. Create a new virtual environment
#  A new folder "\you\path\to\cadtDash-main\venv" will appear.
#  If "virtualenv not found", it fails to recognize the path to your python executable.
#  Make sure you know where virtualenv.exe is located.
virtualenv venv

## 3. Source the environment
.\venv\Scripts\activate # if Windows
# source venv/bin/activate # if Linux/bash

## 4. Install all required packages
pip install -r cadtDash-main/requirements.txt

The last step may take awhile. If the installation hangs, you may have to press the enter key.

Update Repo

To update a cloned repo, simply pull the latest version via terminal.

## 1. Proceed to the sub-folder
cd  \you\path\to\cadtDash-main\cadtDash-main\

## 2. Pull the latest version
git pull

Note the print out from command. If requirements.txt is changed, you may need to install some new packages for this updates. See First Time Installation secion on how to use requirements.txt.

Usage

  1. Put your "ExampleData.xlsx" in the the working folder \you\path\to\cadtDash-main\. This Excel file must have three sheets (with the exact names) in the following orders:
  • 'CT PE Studies' from PACS
  • 'Aidoc Studies' from AIDoc
  • 'mPower' from mPower
  1. Open a terminal (either Anaconda Prompt or Windows PowerShell) and activate the virtual environment.
## 1. Proceed to the working folder
cd  \you\path\to\cadtDash-main\

## 2. Source the environment
.\venv\Scripts\activate # if Windows
# source venv/bin/activate # if Linux/bash
  1. Run the python script extractFromMPowerData.py
## 1. Proceed to the sub-folder
cd  \you\path\to\cadtDash-main\cadtDash-main\

## 2. Run the python script
python .\extractFromMPowerData.py

A message will pop up.

Dash is running on http://127.0.0.1:8050/

 * Serving Flask app 'extractFromMPowerData' (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: on
  1. Open a web browser (preferably Edge or Chrome) and enter the URL in the message. For example, the above message says the URL is "http://127.0.0.1:8050/". The dashboard will show up.

Exit

To exit, simply close the web browser and the terminal.