Install

1. create a conda environment

2. Create the environment with the right packages:

conda create -n cms-generator -c soft-matter pims python=3.5 numpy matplotlib h5py scipy ipython lxml pillow

conda activate cms-generator

3. install SciAnalysis:

   pip install git+https://www.github.com/CFN-Softbio/SciAnalysis

4. Clone this repo somewhere:

   git clone https://www.github.com/CFN-Softbio/cms_generators

   cd cms_generators/cms_generators

5. Edit the simulation.py code:

   • the mask directory:
     • mask_dir ="/home/lhermitte/research/projects/code-profiling/masks"
   • place where to save data
     • root_dir ="/home/lhermitte/research/projects/code-profiling/data"
   • sample metadata filename
     • meta_filename = "sample_meta.yml"

   You'll probably just need to modify the middle line

6. Run the simulator: python simulation.py

   This will create data in your root dir. The data is an hdf5 file: - img: the image - attribures : the metadata attributes

   The image will be an image with the same dimensions as the Pilatus 2M detector