FigureGenerator 0.0.1

Making screenshots for presentations and manuscripts.

Screenshot Maker

This project helps create screenshots for medical images for use in presentations and/or manuscripts.

Installation

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

OR directly via Pip:

pip install FigureGenerator

Usage

python ./figure_generator -h
usage: FigureGenerator [-h] -images IMAGES [-masks MASKS]
                       [-mask_opacity MASK_OPACITY] [-colormap COLORMAP]
                       -output OUTPUT [-axisrow AXISROW] [-bounded BOUNDED]
                       [-borderpc BORDERPC] [-v]

Constructing screenshots from medical images.

Contact: [e-mail]

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
  -mask_opacity MASK_OPACITY
                        Mask opacity between 0-1
  -output OUTPUT        Output screenshot file
  -axisrow AXISROW      Put all axes views across each column and stack images and blends in rows, defaults to False
  -bounded BOUNDED      Construct bounding box around binarized ground truth
  -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

1. Vertical screenshot of multiple images:

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:

2. Horizontal screenshot of multiple images:

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: