Installation

RadQy can be installed via pip or conda.

Using pip

pip install radqy

Using conda

conda create -n radqy python=3.10
  conda activate radqy
  pip install radqy

Running

Display the help message:

radqy --help

Expected Output:

usage: radqy [-h] [--ui-download] [--ui-run] [-s S] [-b B] [-u U] [-t {MRI,CT}]
               output_folder_name inputdir [inputdir ...]
  
  positional arguments:
    output_folder_name    The subfolder name in the '...\UserInterface\Data\output_folder_name' directory.
    inputdir              Input folder(s) containing *.dcm, *.mha, *.nii, or *.mat files.
                          Example: 'E:\Data\Rectal\input_data_folder'
  
  optional arguments:
    -h, --help            Show this help message and exit
    --ui-download         Download the UserInterface.zip file
    --ui-run              Run the User Interface
    -s S                  Save foreground masks (default: False)
    -b B                  Number of samples (default: 1)
    -u U                  Percent of middle images to process (default: 100)
    -t {MRI,CT}           Type of scan (MRI or CT) (default: MRI)

Running the Quality Control Script

Run the radqy command using the following syntax:

radqy output_folder_name "input_directory" [options]

Example:

radqy output_results "E:\Data\Rectal\input_data_folder" -s True -b 5 -u 50 -t CT

Arguments:

output_folder_name (required): The subfolder name in the ...\UserInterface\Data\output_folder_name directory.
input_directory (required): Path to the input directory containing image files.

Options:

-s: Save foreground masks (True or False). Default is False.
-b: Number of samples. Default is 1.
-u: Percent of middle images to process. Default is 100.
-t (required): Type of scan (MRI or CT). Default is MRI.

Notes:

There is no need to manually create a subfolder in the Data directory; specifying its name in the command is sufficient.
All actions will be printed in the output console for transparency.
Thumbnail images in .png format will be saved in ...\UserInterface\Data\output_folder_name, with each original filename as a subfolder name.

Running the User Interface

Download the User Interface

To download the User Interface, run the following command:

radqy --ui-download

This command will download and unzip the User Interface into the appropriate directory.

Run the User Interface

To run the User Interface, execute:

radqy --ui-run

If the User Interface is not already downloaded, this command will download it automatically before launching.

Accessing the Front-End Interface Manually

If you prefer to access the User Interface without using the --ui-run command:

Open the Interface:
Navigate to the UserInterface directory (e.g., C:\Users\YourUserName\.radqy\UserInterface).

Double-click on index.html to open the front-end user interface.
Load Results:
In the interface, select the appropriate results.tsv file from the ...\UserInterface\Data\output_folder_name directory.

RadQy

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