Metadata-Version: 2.1
Name: FigureGenerator
Version: 0.0.2
Summary: Making screenshots for presentations and manuscripts.
Home-page: UNKNOWN
Author: Sarthak Pati
Author-email: software@cbica.upenn.edu
License: BSD-3-Clause License
Description: # Figure Generator
        
        [![PyPi](https://img.shields.io/pypi/v/FigureGenerator)](https://pypi.org/project/FigureGenerator/)
        [![Build & Tests](https://github.com/CBICA/FigureGenerator/actions/workflows/python-package.yml/badge.svg)](https://github.com/CBICA/FigureGenerator/actions/workflows/python-package.yml)
        [![Codacy Badge](https://app.codacy.com/project/badge/Grade/608de602c1bd4bec810efb0d08f269e6)](https://www.codacy.com/gh/CBICA/FigureGenerator/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=CBICA/FigureGenerator&amp;utm_campaign=Badge_Grade)
        [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/608de602c1bd4bec810efb0d08f269e6)](https://www.codacy.com/gh/CBICA/FigureGenerator/dashboard?utm_source=github.com&utm_medium=referral&utm_content=CBICA/FigureGenerator&utm_campaign=Badge_Coverage)
        [![Code style](https://img.shields.io/badge/Code%20Style-black-000000.svg)](https://github.com/psf/black)
        
        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]
                               [-boundimg BOUNDIMG] [-boundmask BOUNDMASK]
                               [-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
          -boundimg BOUNDIMG    Construct bounding box around non-zero pixels of input images
          -boundmask BOUNDMASK  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
        
        ### **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:
        
        <p align="center">
          <img width="450" src="images/fig_axisrowfalse.png">
        </p>
        <!-- full-size image
        [<img src="images/fig_axisrowfalse.png" width="450"/>](axisrow_false)
        ![axisrow_false](images/fig_axisrowfalse.png)
         -->
        
        ### **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:
        
        [<img src="images/fig_axisrowtrue.png" width="900"/>](axisrow_true)
        <!-- full-size image
        ![axisrow_true](images/fig_axisrowtrue.png)
         -->
        
        ### 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 \
        -bounded True \
        -output C:/input/fig.png 
        ```
        Gives the following output:
        
        [<img src="images/fig_axisrowtrue_boundedimage.png" width="900"/>](axistrue_boundedimage)
        <!-- full-size image
        ![axisrow_true](images/fig_axisrowtrue_boundedimage.png)
         -->
        
        **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 \
        -boundmask True \
        -borderpc 0.001 \
        -output C:/input/fig.png 
        ```
        Gives the following output:
        
        [<img src="images/fig_axisrowtrue_boundedmask.png" width="900"/>](axistrue_boundedmask)
        <!-- full-size image
        ![axisrow_true](images/fig_axisrowtrue_boundedmask.png)
         -->
        
        **Note**: This can be used with vertical orientation as well, by passing `-axisrow False` to the command.
        
        ## Feedback
        
        Please post on GitHub [Discussions](https://github.com/CBICA/FigureGenerator/discussions) or post an [issue](https://github.com/CBICA/FigureGenerator/issues/new/choose).
        
Keywords: medical-imaging,screenshot,figure-generator,publication
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
