Figure Generator

This project helps create high quality figures for medical images for use in presentations and/or manuscripts.

Installation

powershell git clone https://github.com/CBICA/FigureGenerator.git cd screenshot_maker conda create -n venv_screenshot python=3.7 -y conda activate venv_screenshot pip install -e .

OR directly via Pip:

powershell pip install FigureGenerator

Usage

``` python ./figure_generator -h usage: FigureGenerator [-h] -images IMAGES [-masks MASKS] [-opacity OPACITY] [-ylabels YLABELS] -output OUTPUT [-axisrow AXISROW] [-boundtype BOUNDTYPE] [-fontsize FONTSIZE] [-borderpc BORDERPC] [-v]

Constructing screenshots from medical images.

Contact: software@cbica.upenn.edu

This program is NOT FDA/CE approved and NOT intended for clinical use. Copyright (c) 2021 University of Pennsylvania. All rights reserved.

optional arguments: -h, --help show this help message and exit -images IMAGES Input image files (comma-separated without any spaces in path and co-registered) -masks MASKS Mask files (comma-separated without any spaces in path and co-registered with images); if multiple files are passed, first is ground truth -opacity OPACITY Mask opacity between 0-1 -ylabels YLABELS The comma-separated ylabels that will be displayed on the subplots' y-axis -output OUTPUT Output screenshot file -axisrow AXISROW Put all axes views across each column and stack images and blends in rows, defaults to False -boundtype BOUNDTYPE Construct bounding box around specified region; can be 'none, image or mask' -fontsize FONTSIZE Font size for all text on the figure -borderpc BORDERPC Percentage of size to use as border around bounding box (used only when mask and bounded are defined) -v, --version Show program's version number and exit. ```

Examples

Vertical screenshot of multiple images without bounding:

powershell python ./figure_generator \ -images C:/input/subject_001_flair.nii.gz,C:/input/subject_001_t1ce.nii.gz,C:/input/subject_001_t1.nii.gz,C:/input/subject_001_t2.nii.gz \ -masks C:/input/subject_001_seg.nii.gz \ -axisrow False \ -output C:/input/fig.png Gives the following output:

Horizontal screenshot of multiple images without bounding:

powershell python ./figure_generator \ -images C:/input/subject_001_flair.nii.gz,C:/input/subject_001_t1ce.nii.gz,C:/input/subject_001_t1.nii.gz,C:/input/subject_001_t2.nii.gz \ -masks C:/input/subject_001_seg.nii.gz \ -axisrow True \ -output C:/input/fig.png Gives the following output:

<!-- full-size image -->

Horizontal screenshot of multiple images with image-based bounding:

powershell python ./figure_generator \ -images C:/input/subject_001_flair.nii.gz,C:/input/subject_001_t1ce.nii.gz,C:/input/subject_001_t1.nii.gz,C:/input/subject_001_t2.nii.gz \ -masks C:/input/subject_001_seg.nii.gz \ -axisrow True \ -boundtype image \ -output C:/input/fig.png Gives the following output:

<!-- full-size image -->

Note: This can be used with vertical orientation as well, by passing -axisrow False to the command.

Horizontal screenshot of multiple images with mask-based bounding:

powershell python ./figure_generator \ -images C:/input/subject_001_flair.nii.gz,C:/input/subject_001_t1ce.nii.gz,C:/input/subject_001_t1.nii.gz,C:/input/subject_001_t2.nii.gz \ -masks C:/input/subject_001_seg.nii.gz \ -axisrow True \ -boundtype mask \ -borderpc 0.001 \ -output C:/input/fig.png Gives the following output:

<!-- full-size image -->

Note: This can be used with vertical orientation as well, by passing -axisrow False to the command.

Feedback

Please post on GitHub Discussions or post an issue.