Simpleware Scripts

This repository contains modules and scripts intended to be implemented within Synopsys Simpleware's scripting environment. Presently, these scripts are not intended to be executed outside the Simpleware scripting environment or directly within alternative IDEs.

Table of Contents

• Installation & Use
• Quality Checks
  • List of Scripts
• Segmentation

Installation & Use

Installation is intended to be relatively straight forward and easy.

• Download the repository to your device and add it to your folder within the shared drive.
• Once downloaded, load the script you would like to utlize into Simpleware's scripting environment
• Review the comments/readme section of the script for specific usage instructions
• As long as you are mounted to the P-drive, you should be able to implement the scripts with minor/no modifications
• Template scripts are pre-loaded with the code below so as to import this module and its functions into the scripting enviroment.

import sys
module_path = "P:\\WoodsLab\\ACT-head_models\\FEM\\Sam\\Scripts\\Python\\Simpleware\\quality_checking\\"
sys.path.append(module_path)
import quality_check_functions as qc

• This adds a master version of the module to the system path for importing to the environment
• If you are having issues, ensure that the module exists at the specied module_path location and that the module is up-to-date
• Please only edit the shared-drive version of the module if absolutely necessary and with extreme caution
• Note that Simpleware will not re-import modules within the same session; if edits are made to the module, exit the Simpleware window, re-open, and re-import the updated module. Otherwise, Simpleware will continue using the originally imported version of the module

Quality Checks

This folder contains templated scripts and the module for the segmentation quality checking process. quality_check_functions.py is the module hosting all functions; the file itself should not be executed withing Simpleware. Instead, users should implement one of the templated scripts included in the repository.

Please implement edits to a localized version or direct concerns to the author. When implementing scripts, refer to the comments to ensure proper execution. Some do not require user input and will execute on command. Templated scripts may require the user to specify the participant's ID number, sublist categorization, target tissue masks, etc. Please see each script's comments for more information regarding user input.

List of Scripts

• finalize_sip_file.py: Finalize the quality checking process at stage 1 or stage 2
• generate_base_file.py: Generate the initial visual check/base.sip file for later quality checks
• import_masks.py: Import individual tissue mask into the current project file
• remove_overlap.py: Remove the intersecting overlap between tissue masks based on priority levels
• set_colors_order.py: Assign colors and mask order according to pre-determined palette and priority
• start_stop_visual_checks.py: Save and finalize current participant's base visual checking file before generating and saving the next participant's base visual checking file

Segmentation

This section is a work in progress. This folder will house scripts and functions utilized during the tissue segmentation T1 weighted MRI scans using Synopsys Simpleware. This folder will mirror the Quality Checking folder by establishing a module of functions that are then called through user-friendly templated scripts.

• skin.py: Automate the segmentation of the skin mask.
• csf.py: Automate (re)generation of cerebrospinal fluid mask.