XRF-Slicer

XRF-Slicer converts x-ray fluorescence excel data specified in the same format as onion-control.xlsx into .tiff image slices. The first two columns in the excel data represent the x and y image coordinates. The third column represents the physical size of the images in the z-plane. The remaining columns each represent a single image in the z-plane and record pixel intensity for each x-y-coordinate pair of the output image.

The program has both command-line and GUI functionality.

The command line can be run from slicer.py and takes two arguments:

--input: Input path to .xlsx, .xls or .ods file
--output: Output path to store /sli directory containing .tiff images

The GUI can be run from slicer_gui.py. Simply select or enter the paths to input file and output directory and click 'Run Slicer'.

Created for Jarvis Stobbs (Plant Imaging Lead) - [email protected]

Installation

1. Make sure you have Python3 installed

2. Install virtualenv using either of:

    pip install virtualenv
   
    python -m pip install virtualenv
   

3. Create a new virtual environment somewhere in the filesystem:

    virtualenv my_venv
   

4. Activate the environment:

   1. Windows:

       my_venv\Scripts\activate
      

   2. Linux:

       source my_venv/bin/activate
      

5. Install the required modules:

    pip install -r requirements.txt
   

6. Run the program:

   1. Command Line:

       python slicer.py --input path/to/infile.xls --output path/to/outdir
      

   2. Graphical interface

       python slicer_gui.py
      

These links may be useful if you run into trouble:

https://aaronstannard.com/how-to-setup-a-proper-python-environment-on-windows/

https://uoa-eresearch.github.io/eresearch-cookbook/recipe/2014/11/26/python-virtual-env/